MADMAN BIOLOGY

LIFE THROUGH THE EYES OF A LUNATIC

VOLUME I: THE BASICS

A THOMAS TROTTER Production

COPYRIGHT 2012 by Thomas Trotter. All rights are reserved and enforced by God. If you dont believe in God then I suppose youre off the hook

FOR PERSONAL USE ONLY. All writings, images and graphs are property of their respective owners. This book is not for sale, nor should it be. All information contained herein may be factually incorrect or misleading. This book is not intended to replace any real or imagined textbook, nor should it be used for any college-related curriculum. Youve been warned.

WHATS INSIDE
Otherwise known as the Table of Contents

Foreword 1 Biology is the Scientific Study of Life

Characteristics of Life Levels of Organization Evolution: The Overarching Theme in Biology Ecosystems Dynamics Energy Conservation Three Domains of Life Feedback Mechanisms Common Biology Definitions

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1 1 3 4 4 7 8 8

2 The Chemical Context of Life

Structure of an Atom Molecules & Chemical Bonds Reactions Molecular Shape and Function

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11 13 15 15

3 Water
Specific Heat Ionization of Water Hydrogen Ions pH Acids, Bases & Buffers

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18 18 19 19 20

4 Carbon and the Molecular Diversity of Life

Functional Groups Isomers

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5 Large Biological Molecules

Carbohydrates: Sugars & Energy Rich Molecules Lipids: Fats, Steroids & Energy Rich Molecules Proteins: Big Mother Fuckers Nucleic Acids: Those Things that make DNA

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26 27 30 34

6 Cell Structure
Microscopes, Microscopy, Fractionation Eukaryotic vs. Prokaryotic Cells The Nucleus Ribosomes: Protein Synthesis Endomembrane System (Eukaryotic) Cytoskeleton Cellular Junctions

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37 38 40 41 41 44 46

7 Membranes
Major Components of a Membrane Structure Membrane Proteins Synthesis of Membranes Permeability of Lipid Membrane Diffusion Tonicity Facilitated Diffusion Membrane Potential and Ion Pumps Bulk Transport (Endo- and Exocytosis)

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49 49 50 51 52 52 53 53 54 56

8 Introduction to Metabolism
Energy Thermodynamics Chemical Reactions and Energy Enzymes Regulating Enzyme Activity

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59 60 60 63 65

9 Cellular Respiration
ATP Catabolic Pathways Cellular Aerobic Respiration Regulating Aerobic Respiration Fermentation

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67 70 72 79 80

10 Photosynthesis
Chloroplasts Light Reactions Calvin Cycle Photorespiration

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84 85 89 90

11 Cell Communication
Signal Transduction: Essential Components Local Communication: Direct Contact Local Signaling: Paracrine & Synaptic Long Distance Signaling: Endocrine Signaling Molecules Ligand Response Protein Phosphorylation Receptors Phosphorylation Cascade nd 2 Messengers Apoptosis Complexity

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91 92 92 93 94 94 94 95 97 97 98 98

12 Cell Division & The Cell Cycle

Genetic Material Cell Cycle

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99 100

Interphase Mitotic Phase Binary Fission Molecular Control of the Cell Cancer Cells

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13 Meiosis and Genetics

Asexual vs. Sexual Reproduction Sexual Reproduction Requires Meiosis Meiosis Recombining Genes Differences Between Meiosis and Mitosis Genetic Variability Humans

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109 110 112 114 116 116 116

14 Mendel and the Gene Concept

Mendel Mendels Monohybrid Cross Mendels First Law: Segregation Essential Genetic Terms F2 Generation Mendels Second Law: Independent Assortment Incomplete Dominance Codominance Polygenic Inheritance Epistasis Environmental Effects Mendelian Inheritance in Man

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119 119 120 121 122 122 123 123 124 124 125 125

15 Chromosomal Basis of Inheritance

Where are Genes Located? Sex Linked Genes: Morgans White Eyed Flies Sex Determination Chromosome Inactivation Linked Genes Genetic Disorders Alteration in Chromosome Structure

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127 127 128 128 129 129 131

16 Molecular Basis for Inheritance

Models of DNA Replication DNA Replication Telomeres

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135 136 141

17 Gene to Protein
An Overview Transcription: A General View RNA Polymerase Review RNA Processing: A General View Translation: A General View

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143 144 148 148 150

Mutation

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18 Regulation of Gene Expression

Bacterial Operons Eukaryote Gene Regulation Regulation by Non-Coding RNA Cancer

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157 158 160 161

19 Viruses, A Brief Survey

Viruses Bacteriophage Animal Viruses HIV Virus Evolution Viroids & Prions

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165 167 166 167 167 168

20 Biotechnology
Recombinant DNA DNA Cloning DNA Technology Uses Electrophoresis

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173 173 176 177

21 Genomes and Genome Evolution

Genomes

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22 Descent with Modification

The Historical Context for Evolutionary History The Darwinian Evolution The Evidence of Evolution

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181 182 184

23 The Evolution of Populations

Genetic Variation, The Substrate for Natural Selection Mutations and Sexual Recombination The Hardy-Weinberg Principle Natural Selection, Genetic Drift and Gene Flow

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189 190 192 193

24 The Origin of Species

What is a Species Modes of Speciation Hybrid Zones

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197 199 202

25 The History of Life on Earth

The Origin of Life Major Events in the History of Life on Earth Continental Drift, Mass Extinction and Adaptive Radiation The Evolution of Complex Structures

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205 206 212 214

26 Phylogeny and the Tree of Life The Papers

Phylogenies Show Evolutionary Relationships The Construction of Phylogenetic Trees Introduction to Summary Statistics and Graphs Techniques in Microscopy & Cellular Structure Reflects Function Using Quantitative Techniques and Statistics Determining the Properties of an Enzyme Determining How Materials Enter Cells Measuring Cellular Respiration Simulating Genes in Populations (Genetic Drift)

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215 217 223 231 235 239 245 249 253

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The Exams
Exam 1 Exam 2 Exam 3 Practice Exam 1 Practice Exam 2 Practice Exam 3

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259 265 271 279 287 299 317 323 329 337 343

Biology Today

Glossary References

An Introduction to Life on Earth Energy Flow in the Life of a Cell The Study Guide Terraforming Mars Boiling Water

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347 429

F O R E W O R D

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FOREWORD
What the fuck is this? How has it come to this, and so soon? Things werent meant to move this fast. I was supposed to have more time, more space to maneuver, and more spark to drive this fucking bat shit insane train. And yet, here I am, proposing yet another tomb of bombastic horseplaya 400 some odd page manifesto for the starved, crazed, and obsessed biology student; a blueprint for demise. I am not the author of this book. Sure, I typed each and every word located within these pages, but I cannot claim the ideas or structure behind them. In essence, I am a human Xerox machine, deployed at random, fed with cigarettes and sleepless nights, and ravaged by the horrors of college-level science. I stole the bulk of this book. The scant few pages that I can claim as my own are overshadowed by the pirated grayscale artwork littered throughout the first 26 chapters. Those are cool, and I am not. Those not familiar with my style of study will no doubt be shocked by the crudeness of the writing. These are notes; often times ripped directly from a PowerPoint presentation. This is not a cohesive collective of biological terms and theories; it is a windowless room filled with midgets, whom all shout random things about photosynthesis and DNA replication. Its a fucking horror show. That may be a bit too harsh. In reality, there is some sound factual information to be gleaned from these cheap, standard-grade pages. It certainly wont replace any formal textbook, but it will provide you with just enough information so that you wont look like a complete tool on test day. I can almost certainly guarantee this. More on tests: yes, I have included three of the four tests I took during this hellish semester (the final was omitted). However, these tests should not be used for cheat sheets, as they are specific to the class I was in. I have included them as yet another means of study. The practice exams are another beastthey were lazily crafted by the selfacclaimed meritorious drunkards that lead Cleveland States SLA (Student Lecture Association), and are rarely helpful. I have included them as a snarky aside to all those righteous assholes who run that dimwitted association. With that said, you may get some value out of them, as Im sure your class is structured quite differently than mine.

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In regards to the formatting of this book, I have done my best. There just wasnt much I could do with the material. In particular, the papers located near the end of this book look like utter horse shit. I make no apologies for this, so fuck off. Theres not much more to say about this book. Not a lot of time was spent crafting it. In reality, it is to serve as a remindera palpable conjuration of the time I spent learning this shit. It is meant to be carried in a nondescript bag, shrouded by books with actual merit, talked about my no one, read by the same, burned in back alley drums for heat, and scoffed at by real students. If youre into this type of stuff, you can look forward to future volumes of Madman Biology, though I certainly wouldnt blame you if you werent. Hell, Im not even sure if Im into it, and Im paying through the fucking dick for these classes. For the interested, you can check out Madman Ethics and read about my zany adventures through moral philosophy. Or try Madman Chemistry, and read about all the boring shit you can do with household chemicals (tip: drink them). Or, you can take this book, chuck it in the nearest garbage can, and fuck off. I dont care, nor do I want to. Thank you, and enjoy. -Thomas Trotter

MADMAN BIOLOGY
there is but one man to guide our rise; and he will look upon us as his enemy.

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BIOLOGY IS THE SCIENTIFIC STUDY OF LIFE

CHARACTERISTICS OF LIFE

There are several characteristics we can use to identify whether or not something is alive. There are, however, some problems with this method. For instance, virsues meet a lot of the definitions, but are not made up of cells and are therefore not living. Anyway, here they are, in no particular order. Reproduction Energy Metabolism Cells all living things are composed of cells (viruses are not, therefore not living). Response to environment Order- to have and maintain Regulation, or homeostasisthe steady state of physiological condition of the body (temp, pH, fluid, etc) Evolutionary adaptation.

LEVELS OF ORGANIZATION

We can organize all living things on earth, as well as earth itself, into several categories. We start with the largest (the biosphere) and work our way down to the smallest (atoms). You should know this material like the back of your hand, and questions concerning this hierarchy will appear elsewhere in the course (read: the final). Here you go. 1. The Biosphere: the parts of Earth that support life. 2. Ecosystems: all living things and the characteristics of a particular area of the biosphere. 3. Communities: all living things in an ecosystem. 4. Populations: all of the organisms of a particular species within a community.

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5. Organisms: single organisms within a population (example: one human, one tree, etc). 6. Organs and organ systems. 7. Tissues 8. Cells 9. Organelles 10. Molecules 11. Atoms

EMERGENT PROPERTIES

What were talking about here are emergent properties. We can view and study life at many different levels. Some are macro levels, such as studying the biosphere, while other are micro, such as studying the organelles of a cell. The point is, if we start by studying the atoms and molecules of a living organism and work our way outwards towards the macro end of life, new properties relating to that organism will emerge. Just as a box of bicycle parts has different properties as an assembled bicycle, so too do new properties of life emerge as we broaden our scope of study.

What the fuck is reductionism, and how do we kill it? These are the questions that plague the curious biologist. Reductionism is the process of reduction a complex system to simpler components that are more manageable to study, and it is a powerful strategy in biology. For instance, it is very difficult to study the inner-workings of c ell it is still alive and part of a living organism. Therefore, biologists will take cell samples (effectively dead cells) and study those. This gives greater control to the biologist. However, limitations rear their child-molesting heads when we take reductionism out for a spin. Consider this: how the fuck do we study the functions of a cell when it is not functioning? If its dead, then its not doing anythingits just laying about like some homeless bum.

REDUCTIONISM

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Listen, evolution is the main theme of biology. We can look at all the different species on earth and see how diverse they are. You have horses, sea horses, and Charlie horses. You have humans, and monkeys, and black people. You have bacteria, amoebas, and fat black people. But we thrown into the blender that is evolution we can also see how unified we are. We can trace our heritage back so some single-celled organism that crawled forth from the murky oceans of early Earth. All life on earth has this heritage. In other words: we all have a common ancestorand no, its not God or Jesus or Buddha or Mohammed, or Shiva. Its probably your mom, or something. Darwin (1809 1882, pictured below) led the charge in Evolution. In particular, it was his theory of natural selection that contributed to the overall theory of evolution. Organisms living on Earth are modified descendants of common ancestors. This is called decent with modification, and theres a whole chapter on it later. Populations change over time. Unity in diversity: all living things use the same rules (genes, cells, etc.)

EVOLUTION: THE OVERARCHING THEME IN BIOLOGY

SYSTEMS BIOLOGY

When speaking in biological terms, a system can be anything from a cell to a biosphere. As you can imagine, it is much more difficult to study the biosphere and all life contained within it then it is to study a single

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cell. It is for this reason that scientists are developing new strategies for studying whole systems. The goal of systems biology is to construct models of the dynamic behavior of whole biological systems. I guess that makes sense. If we can construct a computer model that can accurately predict how a change in one or more variables will affect other components of a system, then we would be the greatest Systems Biologists in the fucking universe.

ORGANISMS INTERACT WITH THEIR ENVIRONMENTS, EXCHANGING MATTER AND ENERGY

Imagine a tree in a forest. Think about all the ways a tree interacts with its environment and how it exchanges matter and energy. The roots of a tree will absorb water and minerals from the soil. The leaves of the tree will soak up carbon dioxide and sunlight to drive photosynthesis, converting the water and CO2 into sugar and oxygen. Perhaps this tree has some fruit that will be eaten by a passing animal. The point is, both the tree and environment are affected by the interactions between them.

ECOSYSTEM DYNAMICS

There are two major processes involved in any ecosystem. One process is the cycling of nutrients. For example, the minerals absorbed by a tree will eventually be returned to the soil by organisms that decompose leaf litter, dead roots, and other organic debris. Another example, you die and I chuck you body in a ditch. While you rot away maggots eat your brain and body and you become one with the earth. The second process is the one way flow of energy from sunlight to producers to consumers. Producers are such things as plants and other photosynthetic organisms, which use light to make sugar. Consumers are those organisms that feed on producers.

ENERGY CONVERSION

So it takes energy to eat, fuck, sleep, and rape choir boys. Where do we get all this energy? Well, we get it from a complex exchange between the sun and producers of energy. As described above, plants absorb energy from the sun and convert it to sugar. We eat the plants and use the sugar as fuel for our muscles. That energy is converted into kinetic energy. And we mustnt forget that with each exchange of energy some is lost as heat (thermal energy).

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STRUCTURE AND FUNCTION ARE CORRELATED AT ALL LEVELS OF BIOLOGICAL ORGANIZATION

What we need to take away from this theme is that form fits function. In other words, the form or anatomy of an organism is suited to its function. A leaf is broad and flat so it can maximize the amount of sunlight it absorbs. A bird has hollow bones so that it can fly. A WOW nerd has excess fat so he/she can survive marathon LAN parties. Its that simple, folks.

CELLS ARE THE ORGANISMS BASIC UNITS OF STRUCTURE AND FUNCTION

The activities of organisms are all based on the activities of cells. Humans have many different cells which are responsible for all the functions we are capable of. The cells in our eyes are responsible for movement, while the cells in our asses are responsible for shutting the sphincter whenever a broomstick nears. Cells share certain characteristics. For example, all cells and encased in a membrane that regulates the passage of materials between the cell and its surroundings. Also, all cells use DNA. However, we can distinguish between two main forms of cells, as described below:

Eukaryotic Cells: a cell that is subdivided by internal membranes into various membrane-enclosed organelles. You are made of eukaryotic cells. Typically, the largest organelle is the nucleus (which contains the DNA), with others floating

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about in the cytoplasm, or the area between the outer membrane and the nucleus. Prokaryotic Cells: These are much simpler and smaller than eukaryotic cells. The DNA is not separated from the rest of the cell. They also lack other membrane-enclosed organelles found in eukaryotic cells.

THE CONTINUITY OF LIFE IS BASED ON HERITABLE INFORMATION IN THE FORM OF DNA

So cells have these things call chromosomes, which contain almost all the cells genetic material, or its DNA. DNA is the substance of genes, the units of inheritance that transmit information from parents to offspring. For instance, your abnormally large testicles are a result of certain genes being passed from your deadbeat dad to you.

Each chromosome has one very long DNA molecule, which has hundreds or thousands of genes arranged along its length. The DNA molecule is made up of two long chains arranged in a double helix. Each chain link is one of four kinds of chemical building blocks called nucleotides (which well learn about later, so dont concern yourself too much with this). Specific sequential arrangements of these four chemical letters encode the precise information in genes, which are typically hundreds or thousands of nucleotides long. More generally, genes program the cells production of large molecules called proteins. Proteins serve as the tools that actually build and maintain the cell and carry out its activities. The book then gets into RNA, which is a molecule that controls the production of proteins. The sequence of nucleotides along a gene is transcribed into RNA, which is then translated into a specific protein with a unique A short segment of DNA shape and function. There are many different types of proteins, and humans have about 750,000 different ones. The entire library of genetic instructions that an organism inherits is called its genome.

DNA STRUCTURE AND FUNCTION

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Depending on the book youre reading, this list can change significantly. Over the years biologists have been trying to shorten and whittle away these domainsso that what was once seven domains became three. Adjust accordingly. 1. Bacteria: prokaryotes, or single celled organisms (no nucleus) 2. Archaea: prokaryotes, or single celled organisms. 3. Eucarya: eukaryotes, or single and multi-cellular organisms. Cells have nucleus, organelles, etc. More on this in chapter six.

THREE DOMAINS OF LIFE

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FEEDBACK MECHANISMS REGULATE SYSTEMS

There are two types of feedback systems, and both of them are fucking awesome to the max! Lets fucking do it! Negative feedback: This is more common. An example would be when you are cold you start shivering. The shivering warms you body. When you are warm you stop shivering. These types of mechanisms will be explained in greater detail later in the book, so hold your fucking horses until then. Positive feedback: relatively rare, and not really regulation. An example would be when a baby is ready to be born it pushes on the cervix, therefore sending a signal to the brain which then sends oxtorin in the blood which causes the cervix to contract which stimulates the sensory ends of the cervix which starts the whole process over. It is like a never ending loop. Another example is blood clotting.

DEFINITIONS

Here are some common words youll encounter as we continue through this chapter and book. Be familiar with them, as they pop up all over the fucking place. In particular, be familiar with the scientific definition of a theory and be able to distinguish it from a hypothesis, or the colloquial definition of a theory.

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Data: recorded observations or items of information Qualitative: descriptions Quantitative: recorded measurements. Inductive Reasoning: draws conclusions through the logical process of induction. Deductive Reasoning: uses general premises to make predictions. Controlled Experiments: compare results of control and experimental groups. Ideally, the only variable that differs between the control group and the experimental group is the one of interest (the one you are studying). A controlled experiment means that control groups are used to cancel out the effects of Theory: a theory is broader in scope than a hypothesis. It is general and can lead to new testable hypothesis. A theory has withstood many tests over time (such as cell theory and evolution). All in all, a theory is really just a best guess. We can never truly understand nature.

*The Scientific Method

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SCIENTISTS USE TWO MAIN FORMS OF INQUIRY IN THEIR STUDY OF NATURE.

Discovery science describes natural science and processes. They analyze data. On the other hand, hypothesis based science provides a tentative answer to a fell framed question. A scientific hypothesis leads to predictions that can be tested by observation or experimentation. You can never prove a hypothesis; you can just fail to falsify it. A hypothesis must also be testable and within the realm of reality.

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THE CHEMICAL CONTEXT OF LIFE

All living things conform to the basic principles of chemistry, physics, including thermodynamics. All living things are composed of matter in form of atoms, molecules and macromolecules. Matter is defined as anything made of atoms, has mass, and takes up space. An element is a substance that cannot be broken down by ordinary chemical means. An atom is made up of protons (+), neutrons (no charge) and electrons (-). Protons and neutrons reside in the nucleus, while the electrons orbit in shells around the nucleus. Below is a brief description of each (please note that further information on atoms, molecules, and atomic structure is located within the tombs of Madmen Chemistry). Proton: the number of protons defines the element. They contribute mass and have a positive charge. The atomic number = the number of protons. Electrons: moves around nucleus in a cloud (or shell). Does not contribute mass. Neutron: Contributes mass and may decay. The number of neutrons may vary with element (called isotopes).

STRUCTURE OF AN ATOM

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Atomic mass is equal to protons + neutrons and is measured in Daltons (6.024 x 1023 daltons/gram). Atoms with the same atomic number but different atomic mass are called isotopes. Isotopes have the same chemical properties, though some are radioactive. Neutrons decay at a constant rate into proton and electron. Carbon-14 is radioactive. It is used in medical imagery, biological traces, and to determine the age of artifacts, fossils, and other applications.

ATOMIC MASS

ELECTRONS

Below you will find some interesting and useful facts about electrons. These massless little pieces of shit sure have a history with chemistry and biology, and they play an important role later in this book when we discuss cellular respiration and photosynthesis (chemiosmosis). Enjoy. The number of electrons determines the chemical properties of atoms. This is categorically different than physical properties, which is determined by the number of protons, or the atomic number. The number of protons determines what element it is. They are held in orbit by the attraction to the positively charged nucleus. The nucleus is held together by strong nuclear forces, which arent really understood that well (or at least I dont understand it very well, which isnt saying a lot). Ions are atoms that have gained or lost electrons (can also be applied to molecules such as cyanide). A cation has lost an electron to become positive, while an anion has gained an electron to become negative. Electrons go into shells, which are energy levels. The energy is proportional to the distance the electron is from the nucleus. In Biology we are only concerned with the first 3 shells (some elements have many more). The 3rd shell is the highest, the 2nd is the middle, and the 1st is the lowest. See the illustration on the next page for a more detailed look into energy levels/shells.

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Valence electrons = the number of electrons in the outermost shell(s). They determine the chemical reactivity of an element. Atoms with a full outer shell are inert (noble gases). Atoms will transfer or share electrons to fill an incomplete shell. Chemical bonds=interactions between atoms to complete valence shell. Can be ionic bonding or molecular bonding.

MOLECULES & CHEMICAL BONDS

A molecule is a group of atoms held together by chemical bonds. There are several types of bonds that we are concerned with at this point. Covalent: The strongest type, involves the sharing of electrons. Ionic: Electrons that are either gained or lost. Hydrogen: The weakest, though important for water, proteins and DNA. Hydrophobic/Hydrophilic: Molecules that either fear or are attracted to water. These are particularly important when dealing with lipids and membranes. Van der Waals Attraction: interaction between something Theres really no need to concern yourself with this type of interaction, as they dont come into play until way later in this book. Just be aware that they exist..

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COVALENT BONDS

Covalent bonds are created by the sharing of one or more valence electrons. There are two types of covalent bonds: polar and nonpolar. Polar bonds occur when one atom has a different electronegativity. For instance, oxygen has a high electronegativity and when it combines with hydrogen (to form H2O) the electrons from the hydrogen atoms spend more time near the oxygen atom. This gives the oxygen atom a slight negative charge and the hydrogen atom a slight positive charge. Electrons spend more time near the atom with the greater electronegativity. Molecules have regions with slightly positive and negative regions.

HYDROGEN BONDING

This is a type of polar interaction when hydrogens slightly positive charge attracts the negative charge of another molecule. This has to do with dipole moments, and is discussed further in chemistry (so read that shit if you want some brain pain). This is essential for life (water, proteins, DNA, etc). The hydrogen bond is represented as a . While a covalent bond is represented as ____. 1. Hydrogen bonding between water molecules.

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Reactions can go both ways. You start with your reactants and end up with your products. There is equilibrium with reactions (when reactions happening in both directions cancel each other out). There are four basic types of reactions, including oxidative, combustion, precipitation, and nuclear. Read more of Madman Chemistry for further information.

REACTIONS

MOLECULAR SHAPE AND FUNCTION

Function of a molecule depends on its shape. The shape of a molecule depends on its arrangements of atoms and bonds. We will talk more about this in later chapters. In particular, proteins and enzymes work because of their specific shape.

The intricate shape of this molecule determines its function

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WATER
Were going to keep this chapter nice and simple. Water is an interesting substance for various reasons (least of which is the fact that it keeps your dumbass alive and kicking), and well explore several of these in this chapter and in chapters to come. Dont concern yourself too much with the details. So first, lets get a few basic definitions out of the way. Cohesion: Hydrogen bonds between H2O molecules. Adhesion: Attraction of water to other polar molecules (like a cell wall). Helps water move up a tree to the leaves. Surface tension: How hard it is to break the surface of a liquid.

Water is a solvent and it dissolves polar molecules, as it too is polar. This is the like dissolves like fact. Nonpolar molecules will not dissolve or disassociate in water. Solvent: water, or substance that is the dissolving agent Solute: Substance dissolved in solvent. Solution: homogenous mixture of 2 or more substances (solvent and at least one solute)

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Water organizes molecules. Nonpolar molecules exclude water because they dont form hydrogen bonds. This is called hydrophobic. Polar molecules associate with water. This is called hydrophilic. Liquid water is denser than ice. This is why ice floats on water. Water has a high heat of vaporization.

The hydrophilic heads of the phospholipid bilayer allows it to exist in a watery envinronment while the hydrophobic tails prevent water and other polar substances from crossing into the cell.

The specific heat of water (or any substance) is the amount of heat that must be absorbed or lost to change the temperature of 1 gram of water by 1 degree Celsius. This is expressed in the form c/g/C, as it is typically measured in Calories or kilocalories. Specific heat can also be measured in joules. The specific heat of water is 1c/g/C. Water can be ionized into hydrogen ions (H+) and hydroxide ions (OH-). At 25 degrees Celsius, 1 liter of pure water contains 10-7 moles of hydrogen and hydroxide ions. (this is about 1 in 550 million).

SPECIFIC HEAT

IONIZATION OF WATER

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These are hydrogen atoms that have lost an electron. They are essentially protons. Sometimes it is written as H 3 O+,, or the hydronium atom pictured on the previous page (it exists in nature this way). The amount of hydrogen ions determines the pH of cytoplasm, and is essential for photosynthesis and cellular respiration (the electrons gained from hydrogen atoms are used to power cellular machiner, such as ATP synthase, which is discussed more in chapter 7), and is pretty much important for all of life.

HYDROGEN IONS

PH

This is a scale used to indicate the H+ ions in a solution. pH = -log[H+] What is in the brackets is the concentration measured in moles. A pH less than 7 is acid, while a pH greater than 7 is basic. 7 is neutral (water is neutral). What this means is that a high concentration of H+ ions results in an acidic solution, whereas a solution low in H+ ions results in it being basic (or alkaline).

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ACIDS, BASES AND BUFFERS

Just some terms below. Acid: a substance that increases H+ concentration in solution. Base: substance that increases OH- (or decreases H+) concentration in a solution Buffer: substance that acts to balance pH. A buffer can accept H+ from a solution or donate H+ to a solution (depending on whether the solution is basic or acidic). Living things have complex buffering systems that maintain pH within a narrow range.

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CARBON AND THE MOLECULAR DIVERSITY OF LIFE

FUNCTIONAL GROUPS
You need to know all of these functional groups. Hydroxyl: -OH compounds end in ol, as in alcohol. Carbonyl: =O Called Ketones when the carbonyl group is located within the carbon skeleton. Called an Aldehyde when the carbonyl group is at the end (or head) of the carbon skeleton. Carboxyl: carbon bonded to OH and double bonded to O (is acidic) Amino: NH 2 (is basic) Sulfhydryl: -SH Phosphate: phosphate atom bonded to 3 O atoms and doubled bonded to one O Methyl: C bonded to three H atoms.

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ISOMERS

Isomers are two monomers/polymers/molecules wherein all components are the same but the shape or structure is different. Enzymes distinguish between isomers based on molecular shape. Below is a list of isomers. KNOW THESE Structural Isomers: Same number of atoms but a different arrangement. Stereoisomers: Functional group is switched on the carbon atom (one functional group is mirrored on one carbon atom). Geometric Isomers: There are two types of geometric isomers. Cis isomers are where the two Xs are on the same side (see slide). Trans isomers are where the two Xs are on opposite sides.

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ENANTIOMERS

Mirrored isomers, like your hands, or like the picture found below.

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LARGE BIOLOGICAL MOLECULES

THERE ARE FOUR MAIN TYPES OF BIOLOGICAL MOLECULES
And they are: lipids, carbohydrates, proteins and nucleic acids. Lets explore each one in great depth. Know this shit like the back of your mother fucking hand. But first we need to do a little review of polymers, monomers, and all the shit that goes along with it. Monomer: A building block for a polymer. All four of the biological molecules we will be discussing are created using unique monomers (with the exception of lipids). Polymer: A long chain of monomers. The chains of monomers are created by a dehydration reaction, which is when a hydrogen atom from one monomer forms a covalent bond with the hydroxyl group of another. The H and OH combine to form H 2 O, which releases into the ether. This is also called a condensation reaction or dehydration synthesis. On the other hand, polymers can be broken down into monomers by hydrolysis, which is when a molecule of water breaks apart a polymer, dissociating into H and OH.

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The monomer of a carbohydrate is called a monosaccharide. Glucose is a monosaccharide. Monosaccharides contain a carbonyl and hydroxyl group (usually) and usually form ring structures. They also typically appear in a 1:2:1 ration of C,H,O. Simple sugars, such as glucose, are composed of 3-7 carbon atoms. Aldoses: the carbonyl group is located on the terminal end of the monomer (monosaccharide). Ketoses: the carbonyl group is located internally. Alpha & Beta Glucose: The human body can break down alpha glucose, while the beta glucose goes right through the body (the digestive tract).

CARBOHYDRATES: SUGARS, ENERGY RICH MOLECULES

Disaccharides consist of 2 sugars. Their main use is for transported energy and some energy storage (though ineffective). As ane example, two glucose monomers combine by dehydration synthesis (called a glycosidic linkage, as described below) to create Maltose. Glycosidic Linkage: Also called a Glycosidic bond, this is responsible for linking together two or more monosaccharides. It is sometimes called a 1-4 linkage because the hydrogen atom located on carbon atom #1 in a monomer links together with the hydroxyl group on carbon atom #4 on another monomer. This is just another name for a dehydration bond.

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The polymer of a carbohydrate is called a polysaccharide. Many monosaccharides strung together by 1-4 Glycosidic bonds. They have many uses. Lets look at some of them: 1. Structural (for plants): cellulose is a good example of a structural carbohydrate. Many beta glucose monomers string together to create a cellulose molecule, which string together to create microfibrills, which creates the structures for many plant cell walls. Please note that most animals are not able to break down the 1-4 Glycosidic bonds. 2. Structural (fungi, algae, arthropods): chitin is the second most abundant organic compound on earth. It forms the exoskeletons of arthropods, the cell walls of fungi and algae, and can be sued to make surgical thread, such as sutures

LIPIDS: FATS, STERIODS & ENERGY RICH MOLECULES

Lipids are the most diverse in chemical structure. Most of them are hydrophobic, meaning they are not soluble in water. They store energy very efficiently and have many different uses. There are three main types of lipids, which are discussed below.

FATS (TRIGLYCERIDES)

The structure of fat molecules is different than that of a protein or carbohydrate. As far as monomer and polymers go, there really arent any. Fat functions as energy storage, insulation, and protection (it can protect vital organs). A fat molecule is made up of two parts.

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Glycerol head: The head or backbone of a fat molecule is comprised of a glycerol molecule. Each glycerol molecule has three hydroxyl groups (Hence the tri in triglyceride). Carboxylic Acid Tail (hydrocarbon). A carboxylic acid is comprised of a carboxyl group (which give up H+ protons, hence the acid name) attached to a long hydrocarbon tail (a tail made up entirely of C and H atoms). The carboxyl group attaches to the hydroxyl group on the glycerol head by dehydration synthesis (called an ESTER BOND). A completed fat molecule has one glycerol head attached to three carboxylic acid tails.

A saturated triglceride molecule

Saturated Fats: A saturated fat is one wherein the carboxylic acid tail is completely saturated with hydrogen atoms. Every carbon atom is single bonded to either a hydrogen atom or another carbon atom. There are no double bonds present. They are solid at room temperature and usually come from animals. Unsaturated Fats: An unsaturated fat is one wherein the carboxylic acid tail is kinked, or where a carbon atom is double bonded to a hydrogen atom. There can by many double bonds in an unsaturated fat. These are liquid at room temperature and usually come from plants and fish (in the form of oils).

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PHOSPHOLIPIDS

Primarily used to create membranes in cells. A phospholipid is amphipathic, which means that it is both hydrophobic and hydrophilic. As discussed above, the hydrocarbon tail of a fat molecule is nonpolar, as is the glycerol molecule it is attached to. However, a phospholipid contains a phosphate group (hence the name) and a choline molecule attached to the glycerol molecule. This makes the head polar, or hydrophilic. Thats really all you need to know.

STEROIDS

Cholesterol and some hormones are examples of steroids within our bodies. A steroid is comprised of 4 fused rings (they are not bonded like traditional polymers). Two examples would be Estradiol and testosterone (female and male hormones). The different functional groups determine the hormones function (estradiol has a hydroxyl group while testosterone has a carbonyl and methyl group.

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PROTEINS: BIG MOTHER FUCKERS

Proteins are extremely diverse and are responsible for movement and transport (within the blood, across cell membranes) cell signaling (hormones), cell structure (the shape of the cell) and defense (against viruses, etc.). First, lets get some basic vocabulary out of the way. Monomer: Amino Acids are the monomers of proteins. There is a general structure for all amino acids, which is as follows: a carbon atom bonded to a hydrogen atom, an amino group (NH 2 ), a carboxyl group and a variable group (sometimes called a side chain). Refer to illustrations. There are 21 common amino acids that we need to be familiar with. Peptide: A short chain of amino acids (10 or less) is called a peptide. Polypeptide: A longer chain of amino acids. This would be the polymer for Proteins. There may be thousands of amino acids in one polypeptide, many polypeptides in one protein, and may be produced from more than one gene. Peptide Bond: amino acids join together through dehydrations synthesis, called a peptide bond.

FORM

The backbone of a polypeptide is made up of the general structure, while the side chain is made up of all the individual variable groups. The carboxyl group end is sometimes called c terminus, while the amino group end is sometimes called n terminus. The 3 dimensional shape of a protein determines its function (called conformation).

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Above are 21 amino acids. These monomers make up every protein in your body. Know these like the back of your greasy, malformed hand. Dont fuck around with this shit. Its probably a good idea to memorize their shape, their polarity, and their 3 letter abbreviated name as well. Trust me, this shit will come in handy.

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PROTEIN STRUCTURE

For more information see the illustration on page 31. 1. Primary Structure: The sequence of amino acids. 2. Secondary Structure: The hydrogen bonds between backbone amino acids determine the shape of the chain. Can be an alpha helix or a beta pleated sheet. 3. Tertiary Structure: The different bonds between the different variable groups (the interaction of R groups) determine the tertiary structure of a protein. These can include ionic bonds, hydrophobic and van der Waals interactions, hydrogen bonds or disulfide bridges (a bridge between 2 sulfur atoms). 4. Quaternary Structure: More than one subunit (protein), or conformation. For example, collagen is made up of many strands of proteins (each strand called a subunit). The quaternary structure is the fiber of collagen, the tertiary structure is the protein strand, the secondary structure is the polypeptide shape, and the primary structure is the sequence of amino acids that create the protein.

PROTEIN FOLDING

Chaperone proteins aid in proper folding and isolate proteins from other proteins. The entire process is summed up in the illustration located within the PowerPoint notes (or you can view the one below, though it is slightly different).

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PROTEIN DENATURATION

Protein Denaturation happens when a protein loses its normal shape. This can be caused by heat, pH levels, or solvents (acetone, etc). A denaturated protein does not function properly. However, a denaturated protein can be renaturated if the right conditions are met.

THE SEQUENCE OF AMINO ACIDS IN A PROTEIN IS DETERMINED BY DNA

The code in DNA is transcribed into mRNA. The mRNA leaves the nucleus of the cell and is read by a ribosome, which builds the proteins. The sequence of nucleotides in mRNA is encoded by DNA, which is the next section. More on transcription and translation later.

NUCLEIC ACIDS: THOSE THINGS THAT MAKE DNA NUCLEOTIDES

The monomer for nucleic acids. There are many important nucleotides, including ATP (the energy currency of cells), cAMP and cGMP (cellular communication) and NAD and FAD (energy metabolism). A nucleoside similar to a nucleotide, but missing the phosphate group. The structure of a nucleotide is as follows. Nitrogen Base. 5 Carbon Sugar (deoxyribose in DNA and ribose in RNA) Phosphate group

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There are five different nitrogen bases that work to create the nucleotides found in DNA and RNA. They fall into two categories, listed below: 1. Pyrimidines: Bases that contain only 1 ring. Included in this group are: Cytosine, Thymine (DNA only), and uracil (RNA only) 2. Purines: Bases that contain 2 rings. Included in this group are Adenine and Guanine.

NITROGEN BASE

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NUCLEIC ACIDS

The polymer is sometimes called a polynucleotide. Nucleotides are joined by phosphodiester bonds. The backbone of a nucleic acid is formed from the sugar-phosphate groups. This strand of nucleotides also has directionality, which is goes from 5 to 3 (these are the numbers associated with the carbon atoms in the sugar group). 5 connects to the phosphate group, while 3 is the hydroxyl group. In a strand of DNA the 3 is left free while the 5 is always connected to a phosphate group.

DNA is arranged in a double helix, and the two strands run antiparallel to one another. Also comprised of complimentary nitrogen base pairs. T and A always pair up and G and C always pair up. DNA is held together by hydrogen bonds between the complimentary nitrogen bases. To clear this up, nucleic acids are formed from nucleotides, using phosphodiester bonds, while DNA is formed from nucleic acids, using hydrogen bonds. Well talk more about this in a later chapter.

DNA

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CELL STRUCTURE
MICROSCOPES, MICROSCOPY, FRACTIONATION
Light Microscope (LM): Visible light is passed through the specimen and then through glass lenses. These are the standard types of microscopes we will be using in labs. Can magnify things to about 1000 times their size, and can resolve details finer than about .2 micrometers (um) or 200 nanometers (nm).

Electron Microscope: Focuses a bean of electrons through the specimen or onto its surface. There are two types of electron microscopes. Scanning Electron Microscope: Specimen is coated in a thin layer of gold and then scanned by the electron beam. The beam excites electrons on the surface of the gold and are then detected and transmitted to a video screen. Good topography and depth of field. Transmission Electron Microscope: Used to study the internal structure of cells.

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Cell Fractionation: This is the process of taking apart and separating the major organelles of a cell. This is typically done with a centrifuge, and is accomplished via the different weights/masses of the cells organelles.

EUKARYOTIC VS PROKARYOTIC CELLS

We all know (hopefully) that there are two types of cells, prokaryotic and eukaryotic. The domains of Bacteria and Archaea consist of prokaryotic cells, while protists, fungi, animals and plants all consist of eukaryotic cells (the domain eukarya). But what is different about them, and what do they share in common? SAME: all cells are encased in a plasma membrane. All cells contain cytosol, the fluid encased by the plasma membrane. All cells have chromosomes, DNA, and ribosomes. DIFFERENT: Location of the DNA (in the nucleus for eukaryotic and in the nucleoid of prokaryoticthe nucleoid is not encased by a membrane). Eukaryotic cells are much larger. More on this in later chapters, so dont concern yourself too much with this.

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CELL THEORY
All living things are composed of one or more cells. Cells are the smallest living things. Cells arise from the division of previous cells.

ORDER OF MAGNITUDE
Eukaryotic cells = 10-100um (microns) 1-10um = nucleus, most bacteria, mitochondrion 100nm (nanometer)= smallest bacteria and viruses 10-100nm = ribosomes, viruses 1-10nm = proteins, lipids .01-1nm = atoms and small molecules

COMMON FEATURES OF ALL CELLS

Here are some more common characteristics of all cells. Plasma membrane consisting of a phospholipid bilayer that acts as a barrier between external and internal environment of a cell. Genetic material or chromosomes with DNA. In eukaryotic cells, this is found in the nucleus. In prokaryotic cells, this is found in the nucleoid. Cytosol, or the aqueous solution inside a cell. Ribosomes, or the molecular machines that make/synthesize proteins.

PROKARYOTIC CELLS

Here are some common features of prokaryotic cells. Nucleoid houses single stranded DNA. Ribosomes, or the organelles that synthesize proteins. Cell walls that provides support and structure. Capsule, provides

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protection. Plasma Membrane, provides a barrier (see above). Flagella, assists in movement. Fimbriae, assists the cell in adhering to things

THE DIFFERENCES BETWEEN ANIMAL AND PLANT CELLS

There are several key differences. An animal cell can have microvili or flagellum for transport (some plant cells have flagella and cilia) and communication, whereas plant cells have a cell wall that keeps the cell in place. Animal cells have centrioles (which well discuss soon) and lysosomes. Plant cells have a central vacuole, chloroplasts and plasmodesmata. Both animal and plant cells contain mitochondria.

THE NUCLEUS

Most cells have a nucleus (some, like blood cells, do not). The nucleus contains a substance called chromatin, which is made of DNA and histones, which are proteins that DNA will wrap around. Nucleolus, which is responsible for ribosomal RNA (rRNA) synthesis).

THE NUCLEAR ENVELOPE (MEMBRANE)

This is a double membrane (a phospholipid bilayer) that acts as a barrier between the nucleus and the cytoplasm. Substances that enter or exit the nucleus move through pores in the nuclear envelope. The outer membrane is continuous with the Endoplasmic Reticulum, which is discussed below.

CHROMATIN

Chromatin is composed of DNA and histones, which are proteins. DNA will coil around a histone to create a nucleosome.

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RIBOSOMES: PROTEIN SYNTHESIS

Ribosomes are found in both eukaryotic and prokaryotic cells. Free ribosomes float around in the cytoplasm and produce cytosolic proteins. Bound ribosomes are attached to the rough ER and produce proteins for export, hormones, or modify existing proteins. A ribosome consists of two parts, the large subunit and small subunit. Theses subunits associate only during protein synthesis (i.e. they are separate until protein synthesis begins). A ribosome (and its subunits) are composed of proteins and rRNA (ribosomal RNA). Ribosomes do not have a membrane.

ENDOMEMBRANE SYSTEM (ONLY IN EUKARYOTIC CELLS)

The endomembrane system is responsible for protein modification, protein trafficking, and certain metabolic functions. Vesicles, or membranous sacs, move substances in a cell. Transport vesicles move stuff, while secretory vesicles release substances from the cell (also called exocytosis). Each part of the endomembrane system is discussed below.

ENDOPLAMIC RETICULUM (ER)

SMOOTH ER: The smooth ER is free of ribosomes and is responsible for lipid synthesis (such as steroids), carbohydrate synthesis, detoxification (drugs and poison), and regulation of internal Calcium ions. ROUGH ER: The rough ER has ribosomes attached to it, and is therefore responsible for protein synthesis, protein modification (sometimes called post-translation), and membrane synthesis.

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GOLGI APPARATUS

The Golgi Apparatus consists of a cis face (or the receiving side of the apparatus, the cisternae, and the trans face (the shipping side of the apparatus). A transport vesicle fuses with the cis face and secretory vesicles leave via the trans face. The Golgi Apparatus is responsible for chemical modifications (such as glycolipids, or adding a carbohydrate to a lipid), sorting proteins to particular cellular locations, and some carbohydrate synthesis.

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Lysosomes are membrane bound. Lyse means to break apart. Lysosomes are responsible for breaking down or recycling cellular materials. They contain digestive enzymes (proteins). They are created in and bud off from the Golgi apparatus. In phagocytosis, lysosomes will fuse with a food vacuole and digest the food inside. In endocytosis, receptor proteins are recycled from the cell surface. In Autophagy, old or unneeded organelles, or microbes that have invaded the cytoplasm are delivered to the lysosomes.

LYSOSOME

VACUOLES

These are membrane bound and have diverse functions. Found in plant cells. Vacuoles are large membrane-bound structures. They can store toxic materials or water, are responsible for growth of a cell, and take up much of the space of a cell. Contractile vacuoles pump H 2 O out of a cell. Food vacuoles are formed via phagocytosis.

ENERGY ORGANELLES

There are two types of energy organelles: mitochondria and chloroplasts. Chloroplasts are only found in plant cells. Both have: DNA, ribosomes, double membrane. Both are responsible for energy

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metabolism, and both divide (or reproduce by binary fusion. Lets discuss each. Mitochondria: produce ATP (energy) by cellular respiration. Found in both plant and animal cells. Chloroplasts: synthesize organic molecules using energy from the sun. This is called photosynthesis, which well talk more about in another chapter.

Peroxisomes can also be considered a metabolic compartment. Peroxisomes contain oxidative enzymes that transfer H atoms to O atoms. They produce H 2 O 2 as a byproduct (hydrogen peroxide), which is highly reactive and potentially toxic to the cell. Therefore, peroxisomes have enzymes that covert H 2 O 2 to water. Keep an eye out for these buggers in lab.

PEROXISOMES

CYTOSKELETON

The cytoskeleton is made of proteins. They are a complex network of protein fibers, which are polymers of protein subunits (amino acids). Polymerization = fibers grow. Depolymerization = fibers shrink. The cytoskeleton is made up of microtubules (largest), microfilaments (smallest) and intermediate filaments (intermediate). They have three general functions. Cell shape and structure. Anchor organelles and proteins. Movement (movement of vesicles, organelles and cytoplasm within the cell and movement of the cell itself, such as a muscle contracting).

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CENTROSOMES

A centrosome consists of centrioles and the area surrounding them. A centriole is comprised of 9 sets of 3 microtubules arranged in a ring. They are only found in animal cells and some protists (just a single pair). They are important in animal and cell division.

A variety of cell types use cilia and flagella. They arise from the basal body and consist of 9 pair of microtubules that surround a central pair. Cilia are shorter than flagella. Motor proteins, called dyneins, move cilia and flagella by utilizing ATP. Not much of this stuff will be on the test. Molecular motor proteins (called kinesins) carry vesicles on microtubule tracks. These also require ATP, and the direction of transport is determined by the particular motor proteins in uses.

MOVEMENT: CILIA AND FLAGELLA

MICROFILAMENTS (ACTIN)

Microfilaments have a variety of functions, including structural support, cell movement (motility, such as muscle contraction and amoeboid movement) and cytoplasmic streaming (in plants only).

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EXTRACELLULAR MATRIX (ANIMAL CELLS ONLY)

The extracellular matrix is a complex assortment of proteins with diverse functions that are secreted by the cell into extracellular fluid.

CELLULAR JUNCTIONS

Tight Junctions: the plasma membranes of neighboring cells are very tightly pressed against each other and bound together by specific proteins. This junction is intended to prevent leakage and keep bad things from entering the extracellular matrix. Desmosomes: responsible for cell adhesion, binding cells together, and anchoring the cytoskeleton. Uses intermediate filaments to anchor desmosomes in the cytoplasm. Gap Junctions: responsible for cell communication (pores in the cell that allow ions and other material to enter or exit the cell). Plasmodesmata: responsible for joining plant cells. It is similar to a gap junction, though more sophisticated. See page 48.

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MEMBRANES
MAJOR COMPONENTS OF A MEMBRANE
Phospholipid bilayer: consisting of a hydrophilic head (phosphate group and choline) and a hydrophobic take (glycerol and two hydrocarbon tail bonded by an ester bond). This is known as amphipathic. Integral Membrane Proteins: these are proteins that span across the entire membrane. Peripheral Proteins: these proteins do NOT span across the membrane. Carbohydrates and Glycolipids attach to the membrane as well. Cholesterol within the lipid bilayer (just a little, and is used to maintain membrane fluidity).

STRUCTURE

The structure of a membrane is STABLE but NOT STATIC. It conforms to the fluid mosaic model and does not break apart (unless you rip it or something). Components of the membrane may move within the bilayer and vary over time (and in different cells). Amount of

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cholesterol, number and type of proteins, changes in locations of proteins, and types of fatty acids attached to phosophlipids all have the ability to change. Individual phospholipids flip LATERALLY quite often. The flip-flop, or flip vertically about once a month. This is due to the amphipathic nature of the phospholipid. The composition of the hydrocarbon tail can change over time, known as membrane fluidity. They can change from saturated to unsaturated, which either increases or decreases fluidity. Cholesterol acts to maintain fluidity. In a classic experiment, proteins from a mouse were tagged and placed together with tagged proteins from a human. After an hour the membranes of each cell fused together and the proteins mixed.

The fluid mosaic model of the lipid bilayer

The side of the water contains polar or charged amino acids. The part within the bilayer would be nonpolar, or hydrophobic. The functions of membrane proteins are vast. Listed below are some of the more common ones: Transport proteins: requires ATP, moves stuff through the bilayer into the cell. Enzymes embedded in the membrane. Cellular Communication: responsible for signaling. The receptor is embedded in the membrane. Cell recognition: made of glycoproteins. Junctions: discussed in last chapter. Attached to extracellular matrix and cytoskeleton (discussed in last chapter as well).

MEMBRANE PROTEINS

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SYNTHESIS OF MEMBRANES
Follow these steps 1. Start in the ER, where synthesis of membrane proteins and lipids happens. Carbohydrates are added to the proteins, making them glycoproteins. 2. Golgi apparatus. The glycoproteins undergo further carbohydrate modification and lipids acquire carbohydrates, making glycolipids. 3. The proteins, glycolipids, and secretory proteins are transported in vesicles to the plasma membrane. 4. The vesicles fuse with the membrane, releasing secretory proteins from the cell. Vesicle fusion positions the carbohydrates of membrane glycolipids and glycoproteins on the outside of the plasma membrane.

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PERMEABILITY OF LIPID MEMBRANE

The membrane allows select things to enter and exit the cell. High Permeability: gases (O 2 , N 2 , CO 2 ), or very small, uncharged, nonpolar molecules. Low: Small, polar organic molecules (glucose). Very Low: large macromolecules and charged ions need assistance. Water needs an aqua pore to enter; as it is polar (it cannot easily cross the hydrophobic hydrocarbon tail).

Diffusion is defined as the movement of a solute from a region of high concentration to a region of low concentration. Equilibrium is reached with when both sides of the membrane have equal concentrations. Naturally, this is called the concentration gradient (going from high to low). When diffusion happens across the membrane we call it passive transport because no energy is needed. Refer to the permeability of lipid membranes for a list of substances that can cross the membrane by using passive transport (those with HIGH permeability). Osmosis is the diffusion of water. In this case, water is the solution while any dissolved substances are the solute. Water will move through a selectively permeable membrane in order to balance out the regions of concentration.

DIFFUSION

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TONICITY

Tonicity is defined as the ability of the solution to cause a cell to gain or lose water. There are three types of solutions. 1. Isotonic: same solute concentrations as cell, therefore there is no water movement. (Plant cells are flaccid in an isotonic solution). 2. Hypertonic: solute concentration is higher than the cells; therefore water moves out of the cell. This will cause the cell to shrink, possibly killing it. (Plant cells will also deflate, which is called plasmolyzed). 3. Hypotonic: solute concentration is less than the cell; therefore water will move in to the cell. This will cause the cell to expand. When a cell pops, it has been lysed. (Plant cells are turgid in a hypotonic solution. This is a normal state for them).

FACILITATED DIFFUSION

Facilitaded diffusion is the diffusion of solutes through membrane proteins. There are several ways this is accomplished. Passive Transport: Solutes move according to their concentration gradient. Specific proteins allow particular solutes to cross. This type of diffusion does NOT require ATP, or energy. The speed of passive transport has a maximum, and can become saturated, which is the rate at which transport can go no higher. Proteins can consist of channels (ion channels, etc.) or carriers. Refer to slides for illustrations. Active Transport: This is when a solute is transported AGAINST its concentration gradient. This means that solutes move from low to high concentration (the opposite of passive transport).

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This is essential to life, and the cell maintains the concentration gradient different from its surroundings. The sodium-potassium pump is probably the best known active transport system. Na cations are pumped OUT of the cell, while K cations are pumped INTO the cell. The pump is electrogenic, meaning that it generates a membrane potential, allowing it to transport solutes against their concentration gradient. Membrane potential is discussed in the next bullet point.

MEMBRANE POTENTIAL AND ION PUMPS

Membrane potential is the voltage difference across a membrane, and is created by differences in the distribution of cations and anions inside and outside the cell. The membrane is more POSITIVE on the extracellular side and more NEGATIVE on the cytoplasm side. Electrogenic pumps (ion pumps) generate the voltage across the membrane. There are two forces that can drive ions across the membrane (electrochemical gradient). Chemical Force: such as concentration gradient or diffusion. Electrical Force: such as voltage gradient, membrane potential, and the idea that opposites attract.

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The sodium-potassium pump in action.

These exist in plant, fungi and bacteria cells. In a proton pump energy from ATP creates a proton gradient, which can be used to do work (or pump H+ protons out of the cell). A proton gradient only represents potential energy. This involves the active transport of one solute driving the transport of another. Okay, so lets use the example in the book. When a proton pump ejects protons into the extracellular fluid, some of them will return to the cytoplasm by way of a cotransporter, such as Sucrose-H+ cotransporter. This protein actively transports both sucrose polymers and hydrogen protons across the membrane. This cotransporter increases the concentration of protons inside the cells, and the proton pumps more out. One drives the other.

PROTON PUMPS

COTRANSPORTER

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BULK TRANSPORT (THE BIG STUFF)

There are several types of bulk transport, including endocytosis and exocytosis. Bulk transport requires a lot of energy, and involves membrane vesicles to either bring things into the cell, or secrete things from the cell.

ENDOCYTOSIS

There are three types of endocytosis we are concerned with. Endo means inside, and therefore endocytosis is the process of transporting large things INTO the cell. Phagocytosis: material from the extracellular space is engulfed and brought into the cell. Large particles are surrounded by the membrane, which then fuses to create a food vacuole or some other type of vesicle. This is how while blood cells kill bacteria. They engulf the shit and eat it up! Pinocytosis: material from the extracellular space is engulfed and brought into the cell. The difference between pinocytosis and phagocytosis lies in the size of the object being brought in. In pinocytosis the materials are very small solutes. In phagocytosis the materials are larger, such as food or other types of particles. So, SIZE IS THE FACTOR. Receptor-Mediated Endocytosis: In this type of endocytosis, ligands (specific substances in the extracellular matrix) bind to protein receptors on the outside of the cell membrane. These

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ligands stimulate the formation of a vesicle that brings the ligand into the cell. This is a way to bring SPECIFIC molecules into the cell.

1.

2.

3.

1. Phagocytosis. 2. Pinocytosis. 3. Receptor mediated endocytosis

EXOCYTOSIS

In exocytosis, secretory vesicles filled with stuff (hormones, etc.) fuse with the plasma membrane and release materials into the extracellular space.

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INTRODUCTION TO METABOLISM
METABOLISM
Metabolism is defined as all of an organisms chemical reactions. There are two main types of chemical reactions related to metabolism Catabolic: these reactions RELEASE energy and BREAK DOWN molecules (hydrolysis). Anabolic: these reactions REQUIRE energy and SYNTHESIZE molecules (dehydration reactions)

ENERGY

Energy is defined as the capacity to cause change. There are three types of energy we are concerned with. Kinetic: energy associated with motion. If you are moving at 100 mph, you have a lot of energy. You could smash through a wall, or something. Heat (Thermal): energy associated with the random movement of atoms/molecules.

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Potential: energy of matter because of, or based on its location or structure. If you are standing atop a cliff you have a lot of potential energy. Chemical Potential energy is energy released in catabolic reactions. Ionic and molecular bonds contain this chemical potential energy.

THERMODYNAMICS

Thermodynamics is the study of energy and its transformation. There are two laws of thermodynamics that we are concerned with. 1st LAW OF THERMODYNAMICS: Total energy in the universe is CONSTANT. Energy CAN be transferred and/or transformed, but it CANNOT be created or destroyed. As an example, cells DO NOT create energy; they convert energy into a form that can be used. That energy comes from the food we eat, or from the sun (with plants). Well talk more about this in a bit. 2nd LAW OF THERMODYNAMICS: Transformation of energy increases entropy (S) of the universe. Entropy is defined as disorder or randomness. As observed, spontaneous processes occur without the input of energy and increase entropy. As well, during energy transformation some energy is converted into UNUSABLE energy (usually heat) that increases energy.

CHEMICAL REACTIONS AND ENERGY

Biochemists want to know which reactions occur spontaneously (i.e. without the input of energy). In order to do this they must determine energy changes in reactions. Please not that a spontaneous reaction is NOT the same as an instantaneous reaction. Some spontaneous reactions take years to complete.

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In order to determine the changes in energy during a chemical reaction we need to define a few parameters. First, enthalpy is the TOTAL energy and is denoted by an H. Second, Entropy, as already defined, is the UNUSABLE energy, or energy that increases disorder in the universe (usually heat) and is denoted by an S. Finally, free energy is USABLE energy, and is denoted by a G. In order to calculate the free, or usable energy, we need an equation, as seen below. =

This equation states: The change in free energy is equal to the change in enthalpy minus the change in entropy times the temperature (in degrees Kelvin). So now that we have an equation to determine the change in USABLE, or free energy, we can determine which reactions are spontaneous. Reactions, or processes with a NEGATIVE G are SPONTANEOUS. Reactions, or processes with a POSITIVE G require energy. Another way to think about G is to consider the products and reactants of a chemical reaction. Look at the equation below: =

Now, the products of a reaction represent the free energy left after the reaction has occurred. On the other hand, the reactants of G represent the free energy present at the beginning of the reaction. When G is very high, the energy is less stable (it wants to move towards disorder) but has a greater work capacity. On the other hand, when G is low there is less free energy, making it more stable but lessening its work capacity. IMPORTANT: In a spontaneous change, the free energy of a system (any system) decreases. This means that G has been lowered, making it more stable. The released free energy can be harnessed to do work.

ENDERGONIC REACTIONS

Endo literally means inwards. In an endergonic reaction the net G is POSITIVE. This means that there is more free energy in the products than in the reactants. These are also anabolic reactions, as they require energy. An example would be small molecules (reactants) forming a large macromolecule (product). A macromolecule has more free energy than individual molecules (and is therefore less stable). In order to create a macromolecule energy is required (to form bonds, etc.).

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EXERGONIC REACTIONS

Exer means outward. In an exergonic reaction the net G is NEGATIVE. This means that there is less free energy in the products than there are in the reactants. Spontaneous reactions are exergonic. These reactions are also CATABOLIC, as they release energy. An example would be the breakdown of a macromolecule (via hydrolysis) into its component molecules. Component molecules have less free energy (and are therefore more stable) than a macromolecule.

ACTIVATION ENERGY (E A )

This is the energy needed to start a reaction. Reactants need to get into a transition state in order for a reaction to occur, and the activation energy is the amount of energy needed to get the reactants there. Refer to slides for further illustration of this point.

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Enzymes are proteins (usually) that catalyze reactions (both exergonic and endergonic). Most enzymes are proteins, though some RNA molecules have catalytic activity and are called ribozymes. They do this by lowering the activation energy needed for the reaction to occur. Note that the G in not affected by enzymes. In order to lower the E A , enzymes have several tricks up their sleeves, as listed below. Orient the substrates (reactants) Strain the bonds. Create a favorable micro-environment (for instance, by changing the pH). Covalently bonding with the substrates, holding them in place. This is called transient covalent bonding.

ENZYMES

ACTIVE SITE

Enzymes have active sites, or sites where the substrate is able to bind to the enzyme. This slightly changes the shape of the enzyme. The process is called induced fit.

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ENZYMES ARE SPECIFIC

enzymes are specific for particular substrates. A substrate will come along, bind to the active site via induced fit creating the enzyme substrate complex, which changes its shape slightly. A reaction will then occur and the products are released. The enzyme will then return to its original shape, allowing more substrates to enter, starting the process over again. Please note that this is a basic description and does not take into account negative or positive feedback loops (discussed in chapter one, and discussed further in chapter 9 and 10).

ENVIRNOMENTAL FACTORS

Certain environmental factors can influence the function of an enzyme. Temperature and pH are two examples. For instance, the enzymes in your stomach operate normally in a low pH environment (your stomach is very acidic). If those enzymes were in your intestines they wouldnt function as well, as the pH is much higher (basic).

ENZYME HELPERS

Please note that the following terms apply generally. You will find exceptions. COFACTOR: a nonprotein enzyme helper that is usually inorganic (metal. COENZYME: nonprotein, organic molecules (often carrier or transport molecules), such as vitamins or things derived from vitamins.

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REGULATING ENZYME ACTIVITY COMPETITIVE INHIBITION

Below are several ways that the activity of enzymes is regulated. This is a method of regulating enzyme activity. An inhibitor binds to the active site of an enzyme and prevents the substrate from binding. Inhibitors and substrates then compete for the active site. Inhibitors can be toxins or natural substances.

ALLOSTERIC REGULATION

This is a method of regulating enzyme activity. Some enzymes have allosteric sites (different than active sites), where a regulatory molecules (an inhibitor or activator) can bind. This will change the shape of the active site, a process known as active inhibit.

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ALLOSTERIC ACTIVATION

This is where an activator/inhibitor changes the shape of the active site so a substrate can bind. This is a type of allosteric regulation. Binding of substrate to one active site stabilizes conformation (the shape) of other subunits, and makes binding of substrates more likely. This is different than allosteric activation in that there are many subunits within the enzyme. In a biological pathway, a negative feedback loop in one in which the end product inhibits an earlier step in the pathway. A biological pathway is comprised of many different enzymes. Enzyme A produces a product that bind to Enzyme B, which produces a product that binds to Enzyme C, and so on and so forth. In a negative feedback loop, the last enzyme in the chain produces a product that inhibits the first enzyme in the chain, effectively shutting down the pathway. Look back to chapter 1 for more information on feedback loops (including positive).

COOPERATIVITY

NEGATIVE FEEDBACK

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CELLULAR RESPIRATION
ATP
ATP or Adenosine triphosphate is the energy that powers cellular work. There are approximately 4000 to 5000 gene codes for proteins that use ATP (there are 25,000 genes in the human genome, give or take a few). ATP is similar to a nucleotide of RNA. It is comprised of a Ribose sugar, and Adenine nitrogen base, and three phosphate groups (only 1 phosphate group in RNA). The bonds between the phosphate groups are very unstable and are broken by hydrolysis, which as we know is an exergonic reaction (-G). When one phosphate group breaks off ATP becomes ADP, or adenosine diphosphate. There are two ways in which ATP is made, as listed below: Substrate Level Phosphorylation: one phosphate group is transferred from an organic molecule to ADP. Think about it this way: an enzyme carries a substrate and an ADP molecule. The substrate has an extra phosphate group attached to it. The enzyme lowers the activation energy (E A ) and a reaction occurs. This reaction creates a dehydration reaction between the ADP molecule and the phosphate group from the substrate. You now have ATP. Not much ATP is produced from this method.

Oxidative Phosphorylation: This way of making ATP is quite complex. A protein called ATP Synthase takes a free phosphate group and a molecule of ADP and combines them together to make ATP.

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This may get a little confusing, so try and follow me here. ATP is created from exergonic reactions, and drives endergonic reactions. Lets start with the first part: ATP is created from exergonic reactions. First, the reaction that actually forms ATP is endergonicthat is, when one molecule of ADP and one phosphate group react to from ATP you have more free energy (though less stability). But in order for you to get ADP and P 1 you need to have an exergonic reaction. Now, ATP works by losing its P 1 , which is an exergonic reaction. However, that P 1 binds to anther molecule (hence, giving it energy). This is an endergonic reaction. There is a nice illustration on page 151 if you are still confused. Here are some examples:

ATP DRIVES ENDERGONIC REACTIONS

ATP Phosphorylates gultamic acid, making the amino acid less stable. So, here we have one amino acid, gultamic acid, floating around. ATP comes along and phosphorylates it (gives it P 1 ). The products of this reaction are gultamic acid with a phosphate group attached (has more free energy and is less stable) and ADP (ATP lost P 1 ). Ammonia comes along and displaces the phosphate group from the gultamic acid. The products of this reaction are Glu-NH 2 and P 1 . So, the phosphate group is now free to rebind with an ADP molecule. The whole reaction ends up being an exergonic reaction, as the net G is negative. Transport and Motor Proteins: Some membrane proteins transport solutes against their concentration gradient (or help solutes pass through the hydrophobic part of the plasma membrane). These proteins require ATP to work. This transport work happens when ATP phosphorylates a transport protein. When the work is completed, the protein releases the phosphate groupwhich can then bind to ADP to create another molecule of ATP. The same holds true for mechanical proteins. Motor proteins, like those that walk along the cytoskeletal track require ATP for each step they take. ATP bind noncovalently to motor proteins, and then is hydrolyzed. The ADP and P 1 molecule are then able to form ATP.

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CATABOLIC PATHWAYS
This is a common and efficient way to make lots of ATP. In eukaryotes this happens in the mitochondria, and in some prokaryotes it happens all in the cytosol. There are many pathways that feed into aerobic respiration, but for now we will stick with the oxidation of glucose.

AEROBIC RESPIRATION

COMPLETE OXIDATION OF GLUCOSE

Remember this formula (for real!). There are many steps in this reaction, and well be going through each of them later on.

C 6 H 12 O 6 + 6 O 2 6 CO 2 + 6 H 2 O + ATP
This is known as the complete oxidation of glucosewhen a molecule of glucose reacts with 6 molecules of oxygen to form 6 molecules of carbon dioxide, 6 molecules of water, and ATP. This is also known as an oxidation-reduction reaction. Energy is held in the carbon-hydrogen bonds, and when a reaction occurs some that energy is either lost or gained. In glycolysis, glucose has been oxidized to carbon dioxide, as it has lost electrons, and oxygen has become reduced to water, as it has gained electrons. You see, energy is captured from individual steps when electrons are transferred to intermediates (often associated with a H+ atomcalled dehydrogenation). The amount of energy transferred defines whether or not a molecule or element has been oxidized or reduced.

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First, an oxidation-reduction reaction is also referred to as a redox reaction. These reactions always occur togetherthat is, one is oxidized and one is reduced. You will never find a reaction where both are reduced, or both are oxidized. As stated, the energy comes from the transferring of electrons (e-), and are often associated with H+ atoms (protons). The loss of an electron = oxidation, whereas the gain of an electron = reduction.

ENERGY TRANSFER IN REDOX REACTIONS

Electron Donor: An electron donor simply means that a compound/molecule donates its electrons in a reaction. Lets say that compound A is an electron donor. This means that in a chemical reaction A will be oxidized, as it has lost electrons. This may be confusing, but it can also be referred to as a reducing agent, as it gives its electrons to another compound/molecule (causing it to become reduced). Electron Acceptor: This compound/molecule will accept electrons in a chemical reaction. Lets say that compound B is an electron acceptor. This means that in a chemical reaction B will be reduced, as it has gained electrons. This is also called a oxidizing agent, as it accepts electrons from another molecule/compound that is being oxidized. NAD+: this is a coenzyme that carries electrons. It stands for Nicotinamide Adenine Dinucleotide. This is because it is composed of two nucleotides, one with an adenine nitrogen base and one with a nicotinamide nitrogen base. In its oxidized form it is NAD+, as it is able to accept electrons (it has a positive charge). When it accepts electrons (and protons) it becomes reduced NADH. This process is

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called dehydrogense. Each molecule of NAD can accept 2 electrons and 1 proton (with the other proton donated to solution). NAD is reduced in glycolysis and the citric acid cycle. This means that it is not reduced in the electron transport chain. NADH is energy rich. NADH carries electrons to the Electron Transport Chain, where it is then oxidized, able to go and get more electrons to continue the cycle.

CELLULAR AEROBIC RESPIRATION

There are four main steps of cellular respiration (all of which will be discussed in detail). This process takes place in the cytoplasm and mitochondria (in both the inner and outer membrane, the intermembrane space, and in the mitochondrial matrix. This is aerobic. Lets get to it.

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Occurs in the CYTOSOL. Glycolysis starts with one molecule of glucose. This molecule is primedmeaning that two molecules of ATP are reduced to that the glucose becomes fructose 1,6 bisphosphate. This initial energy investment (of 2 ATP) will be recouped later. Lets go through this step by step.

GLYCOLYSIS

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Setp One - Energy Investment: First, glucose becomes Glucocse-6phospate from the addition of one phosphate group from one ATP molecule. The enzyme that catalyzes this reaction is called hexokinase. Step Two - Energy Investment: Glucose-6-Phospate then becomes its isomer Fructose-6-phospate. The enzyme that catalyzes this reaction is called phosphoglucoisomerase. For testing purposes, this enzyme has the word isomer in it. Step Three - Energy Investment: This new fructose-6-phosphate then becomes fructose-1, 6-bisphospate after ATP comes along and donates another phosphate group. The 1 and 6 refer to the two phosphate groups and the corresponding carbon atom they are attached to. The enzyme that catalyzes this reaction (and its an important one) is called PHOSPHOFRUCTOKINASE. This enzyme is a major regulatory point, and well find out why later. Step Four The Split: Once fructose-1, 6-bisphospate is made, the enzyme aldolase comes along and splits it into two G3P molecules (that is, two 3-carbon sugar molecules). Dont bother with the names, as they dont hang around for all that long. We now have 2 molecules going into the system, so all values will be doubled. Step Five Energy Payoff: So, now we have these two sugars. 2 molecules of NAD+ come along (one for each sugar) and take a total of 2 electrons and 2 hydrogen ions from each sugar. At the same time a free P 1 group comes along and binds with each sugar. NAD then becomes NADH and moves on towards the electron transport chain. Step Six Energy Payoff: so now we have two sugars, each with 2 phosphate groups attached. Two molecules of ADP then come along and take one phosphate group from each sugar, making ATP. This is catalyzed by the help of an enzyme, called phosphoglycerokinase. For those interested, any enzyme that has kinase in it simply means that it is an enzyme that transfers phosphate groups. Step Seven Rearrangement: We are not too concerned with this step, but atoms are rearranged in the two sugars. Two molecules of The resulting molecules are called H 2 O are removed. phosphoenolpyruvate. Step Eight Energy Payoff Again: These new molecules are then synthesized into pyruvate. Two molecules of ADP come along (one for phosphoenolpyruvate) and remove a phosphate group, forming

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2 ATP. The enzyme that catalyzes this reaction is called Pyruvate Kinase. REMEMBER THAT ONE. Summary: So, glycolysis is the process by which one molecule of glucose is transformed into two molecules of pyruvate. This process happens in the cytosol outside of the mitochondrion. During this process, 2 ATP are initially used to get the process going (called priming). In the end, 4 ATP and 2 NADH are produced. This gives us a net gain of 2 ATP and 2 NADH. Now, lets follow pyruvate.

Once we have pyruvate, it is transported into the mitochondria where it is oxidized into Acetyl CoA by aerobic respiration (so long as oxygen is present). If no oxygen is present it goes through the process of fermentation, which is discussed towards the end of this chapter. This process occurs in the mitochondrial matrix of eukaryotes (the outer or inner membrane) and in the cytosol of some prokaryotes. Lets work through this shit!

PYRUVATE OXIDATION

Pyruvate comes from the cytosol to the mitochondrial matrix by way of a transport protein. Once inside it is decarboxylated, meaning that a molecule CO 2 of removed from each molecule of pyruvate (remember, there are two). NAD comes along and steals electrons and hydrogen ions from each molecule, reducing it to NADH Coenzyme A comes along and bonds to the decarboxylated molecule, making Acetyl CoA (CoA represents the Coenzyme A). SUMMARY: Pyruvate oxidation produces 2 molecules of NADH, 2 molecules of CO 2 , and becomes acetyl CoA.

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ACETYL CoA TO THE CITRIC ACID CYCLE (KREBS)

The citric acid cycle (sometimes called the Krebs cycle) mitochondrial matrix. Acetyl CoA moves into the citric acid cycle and goes through 8 steps, all discussed below.

Step One: CoA is removed, leaving just the acetyl group, which then enters the Krebs/citric acid cycle. Step Two: Acetyl group joined with oxaloacetate to form citrate. Atoms are rearranged to form an isomer of citrate, called isocitrate. Step Three: NAD comes along, taking electrons and hydrogen ions. At the same time CO 2 is released from the molecule. Step Four: NAD comes along again, taking electrons and hydrogen ions. At the same time, another molecule of CO 2 is released. As well, the CoA comes back into play, attaching itself to the new molecule (each molecule in this process has a different name, but we are not too concerned with that shit). Step Five: A phosphate group, P 1 , comes along and blasts off the CoA. This phosphate group creates something called GTP, which is released. ADP then comes along, takes the phosphate group from GTP, and creates 1 ATP. The GTP then becomes GDP (since it lost one of its phosphate groups), and returns to the molecule.

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Step Six: FAD, another coenzyme that carries electrons, comes along and takes some electrons and hydrogen ions, reducing it to FADH 2 Step Seven: H 2 O is added to the molecule, turning furmarate into malate. Step Eight: Another molecule of NAD comes along and takes more electrons and hydrogen ions. The resulting molecule is oxaloacetate, allowing the process to begin again. Its the circle of mother fucking life! Summary: So, acetyl CoA comes into the citric acid cycle, loses its CoA and binds to oxaloacetate to become citrate, goes through a series of reactions which end up regenerating oxaloacetate (so the process can continue), and produces the following (values are for both molecules of acetyl CoA that enter the citric acid cycle): 4 molecules of CO 2 6 NADH, 2 ATP, and 2 FADH 2

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Oxidative phosphorylation occurs in this final step, which consists of two parts. This part of cellular respiration takes place in the mitochondrial matrix. The proteins involved in this process are attached to the inner-mitochondrial membrane. Lets take a look at each part of this process:

ELECTRON TRANSPORT & CHEMIOSMOSIS

Electron Transport Chain: The electron transport chain is a series of protein complexes that carry and accept electrons from all the NADH and FADH 2 we acquired in the first three steps. There are 4 different proteins, each with its own name. At each step along this chain of proteins electrons are dropped off by either NADH or FADH 2 . This oxidizes the molecules back to NAD and FAD so they can go back and get more electrons. The electrons enter the proteins and pump protons (H+) against their concentration gradientfrom the mitochondrial matrix to the intermembrane space. Oxygen is said to be the final electron acceptor, as it produces water in the final (4th) protein in the chain. They hydrogen protons that are pumped into intermembrane space are used in the second part of this process: Chemiosmosis: The enzyme at work here is ATP Synthase, a rotary machine that makes ATP from ADP and P 1 . The protons that are in the intermembrane space move down their concentration gradient via diffusion. They pass through ATP Synthase and are funneled into the rotor mechanism, which turns and causes conformational changes in the enzyme. These changes produce ATP (in a way that

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can only be described as MAGIC). This makes between 32 and 34 ATP (variation comes from different species). So, all the electrons that we gathered through the steps were used to pump protons against their concentration gradient. This allowed those protons to diffuse back into the mitochondrial matrix, driving ATP Synthase, and creating a shit load of ATP.
ATP SYNTHASE

So, in the end we produce 36 or 38 ATP, 6 CO 2 , 10 NADH and 2 FADH 2 . All you have to do is remember where each part of this reaction occurs, and how much of those molecules are produced.

SUMMARY

REGULATING AEROBIC RESPIRATION

Cells can regulate aerobic respiration by using the classic negative feedback loop. In step three of glycolysis we talked about phosphofructokinase, an enzyme that catalyzes the formation of fructose-1, 6-bisphosphate. This enzyme is allosteric, meaning that it

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has activator and inhibitor binding sites. When phosphofructokinase is active, AMP stimulates it. When it is inhibited, ATP from glycolysis, the citric acid cycle or oxidative phosphorylation binds to the inhibitor site. Also, citrate from the citric acid cycle can inhibit phosphofructokinase, stopping the reaction from occurring.

FERMENTATION

When oxygen is not present to oxidize pyruvate, fermentation can occur. Fermentation results in ethanol or lactate being produced. Well discuss each one in detail. Alcohol Fermentation As stated, fermentation happens when pyruvate cannot be oxidized. When this happens, pyruvate is reduced to acetaldehyde (by the removal of a CO 2 moleculewhich give alcohol its fizz), which is then further reduced by NADH (from glycolysis) to form Ethanol. Remember, in this cycle we start with 2 molecules of pyruvate, so in the end we have two molecules of ethanol. This process produces 2 ATP. Lactic Acid Fermentation This is similar to alcohol fermentation, except that the two molecules of pyruvate are reduced to two molecules of Lactate from the 2 NADH from glycolysis.

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CATABOLIC PATHWAYS AND ATP FORMATION RECAP

So, we three catabolic pathways: fermentation, anaerobic respiration and aerobic respiration. We did not discuss anaerobic respiration, so here are some different kinds: Obilgate Anaerobes: cannot survive in the presence of O 2 , use only fermentation and/or respiration. Facultative Anaerobe: can use either fermentation or aerobic respiration depending on O 2 availability.

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PHOTOSYNTHESIS
PHOTOSYNTHESIS
Photosynthesis is the process by which plants take in water and carbon dioxide to make glucose, oxygen and water. It is the opposite (almost) reaction that was discussed in the previous chapter, metabolism and cellular respiration. It takes inorganic molecules and turns them into organic molecules, and that shit is amazing. It is the most important endergonic process known to man, as without plants we would all be sucking dirt. Photosynthesis is the source for all atmospheric oxygen, and provided the environment for aerobic respiration and eukaryotes to evolve. Most of the worlds biomass can do photosynthesis, including plants, algae and protists. Plants also supply the world with food. The simplified equation for photosynthesis looks like this:

10

6 H 2 O + 6 CO 2 + photons C 6 H 12 O 6 + 6 O 2

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Photosynthesis consists of two separate processes, light reactions and dark reactions (called the Calvin cycle). Well talk about each one in a moment. First, a few definitions. Autotrophs: or producers of organic molecules from CO 2 and other inorganic materials (this would be plants. Heterotrophs: or consumers that live on organic matter produced by other organisms. That would be me! I eat the shit out of other organisms.

CHLOROPLASTS

These little photosynthetic organelles evolved from cyanobacteria and contain light absorbing pigments. They have two membranes, and outer and an inner, with an intermembrane space between them. The parts of the chloroplasts are listed below: Thylakoid: contain light absorbing photopigments. These are suborganelles and are the site of photosynthesis. Consists of a membrane and an inner thylakoid space. Granum: A stack of thylakoids Stroma: Aqueous fluid within the chloroplast.

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LIGHT REACTIONS

First of all, visible light is part of the electromagnetic spectrum radiated by the sun. Photons behave like a particle that can be absorbed by the photopigments inside the thylakoid. These pigments absorb light of a particular wavelength (they dont absorb green, hence why most plants are that color). The photopigments are located in a protein complex photosystems. There are three main types of pigments: Chlorophyll A: is the primary pigment that converts light energy to chemical energy. Chlorophyll B and Carotenoids: accessory pigments.

LINEAR ELECTRON FLOW

These protein complexes are located in the thylakoid membrane, and require light and water. Light enters the photosystem and hits the photopigments. This starts a chain reaction, where one photopigment bumps into another. This transfer of energy eventually excites a special pair of chlorophyll A molecules, which donate electrons to the primary electron acceptor. This is a redox reaction, and the only step that depends of light is that of photons striking the photopigments. There are two separate photosystems, discussed below:

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PHOTOSYSTEM II

Contrary to its name, this is the first system in the pathway. Light enters and excites the photopigments. This reaction then excites the special pair of chlorophyll A molecules, which donate electrons (taken from one molecule of water, leaving O and two H+ ions in the thylakoid space) to the primary acceptor. This primary electron acceptor then transports the electrons (via an electron transport chain) to the: This protein is also embedded in the thylakoid membrane, and as electrons pass through it they pump protons into the thylakoid space, creating a high concentration of H+ protons, which will later be used in chemiosmosis. Electrons from the cytochrome complex are then transferred via an electron acceptor to Photosystem I.

CYTOCHROME COMPLEX

Light excites photopigments which in turn excite a special pair of chlorophyll A molecules. These molecules donate electrons to the primary electron acceptor. Also, electrons from the cytochrome complex end up here. These electrons pass through a series of redox reactions and are transported down a second electron transport chain via a protein called ferrodoxin (however, this electron transport chain does not pump protons as it did with photosystem II and cytochrome complex). These electrons then end up in NADP Reductase.

PHOTOSYSTEM I

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NADP+ REDUCTASE

This enzyme catalyzes the transfer of electrons from ferrodoxin to NADP+ to form NADPH. These molecules then go off to the Calvin Cycle.

ATP SYNTHASE

The proton gradient created in the thylakoid space by the electron transport chain of photosystem II and the cytochrome complex allows the hydrogen ions to pass through ATP Synthase, driving the creation the ATP. The protons move down their concentration gradient, back towards the stroma. The ATP is used to power the Calvin Cycle, or dark reactions if you prefer.

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This cycle reduces CO 2 using energy from ATP and NADPH (obtained in the linear electron flow) and occurs in the STROMA. There are three phases you need to know. Carbon Fixation: This phase requires 3 molecules of CO 2 , which enter one at a time. Each CO 2 molecule combines with a molecule of ribulose bisphosphate (RuBP) via the enzyme rubisco. This produces a six carbon molecule, which is short lived as it splits into two molecules of 3PG (3-phosphoglycerate). Reduction: Each molecule of 3PG is reduced to 3bisphosphoglycerate via ATP. This new molecule is further reduced to G3P (glyceraldehydes-3-phosphate) via NADPH. Six G3P are made for every three carbon molecules that enter the Calvin cycle. One G3P goes off to form glucose while the other five make their way to phase 3. Regeneration OF Rubp: The molecules of G3P are reduced via ATP to produce RuBP, which allows the cycle to start over again. Summary: The Calvin cycle uses 9 ATP, 6 NADPH and 3 CO 2 for each cycle. It produces on G3P each cycle (two G3P glucose). If you remember back to chapter nine, the process of glycolysis created two molecules of G3P from one molecule of glucose, which were then reduced to two molecules of pyruvate. Here we have the opposite, 2 molecules of G3P (from two cycles) create one molecule of glucose.

CALVIN CYCLE

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Under hot, arid conditions, leaves lose water by evaporation through openings in the leaves called stromata. In order to conserve their water, plants will close their stromata. This limits the amount of CO 2 available and allows O 2 to accumulate (carbon dioxide cannot enter and oxygen cannot escapelike breathing in and out). Since CO 2 is unavailable, Rubisco will combine with O 2 instead. This causes phase one of the Calvin cycle (carbon fixation) to stop. Obviously, this is a major fuck up for the plant. However, there are some adaptations that minimize photorespirationand these adaptations occur in C4 plants (such as sugarcane, corn, and some grasses). Lets talk about them: C4 Pathway: CO 2 is fixed to oxaloacetate (a 4C molecule) in a mesophyll cell. The 4C molecule is then reduced, and one molecule of CO 2 is transported to a bundle sheath cell, where the Calvin cycle takes place. This costs the cell more ATP. Cam Plants: even though the Calvin cycle is a dark reaction, it still requires light from the linear electron flow of the photosystems to operate (since the photosystems create ATP and NADPH). So, in order to compensate for this, some plants (succulents like cacti and pineapples) incorporate CO 2 into a four-carbon organic acid at night. This keeps CO 2 fixed during the night. Then, during the day CO 2 is released and the Calvin cycle can continue on.

PHOTORESPIRATION

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CELL COMMUNICATION
SIGNAL TRANSDUCTION: ESSENTIAL COMPONENTS
There are three parts to signal transduction, each listed below with a short description.

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Reception: A signal molecule, or a ligand, binds to a receptor protein. This receptor protein/enzyme can be embedded in the plasma membrane or be free floating in the cytoplasm. The receptor molecule changes shape once ligand binding has occurred (if embedded in a membrane, the protein will change shape on both sides of it). Ligand bind is only temporary. Transduction: One or more relay molecules carry the signal along the transduction pathway. This occurs in the cytoplasm. Response: The signal transduction pathway ends with a cellular response. These are very diverse, and include such functions as: contracting muscles, division, death of the cell, activation or inactivation of a particular enzyme, or transcription of DNA.

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LOCAL COMMUNICATION: DIRECT CONTACT

Cells communicate in a variety of ways. Local communication is one wherein the cells are in close contact with one another. In previous chapters we have discussed gap junctions (animal cells) and plasmodesmata (plant cells). These junctions are when cells are virtually connected to one another. Cell-to-cell recognition happens when one protein from the plasma membrane of one cell interacts with the protein in the plasma membrane of another cell. Here we have signals being secreted, a form of exocytosis. Lets discuss each one separate. Paracrine Signaling: This occurs when one secreting cell releases ligands via exocytosis, or secretory vesicles. These ligands diffuse through the extracellular fluid, towards the target cells, where they bind and a response is activated. Synaptic Signaling: Here we have a nerve cell and a target cell. An electrical signal travels along the nerve cell and triggers the release of neurotransmitters. These neurotransmitters diffuse across the synapse (synaptic gap) towards the target cell, where they bind and a response is initiated.

LOCAL SIGNALING: PARACRINE & SYNAPTIC

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LONG DISTANCE SIGNALING: ENDOCRINE

Here we have an endocrine cell and a target cell. An endocrine cell will secrete signaling molecules, or hormones, into the blood stream via exocytosis and diffusion. These hormones will travel through the blood stream towards the target cell. The target cells have the appropriate receptorsones needed to be affected by the ligands.

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SIGNALING MOLECULES

As already stated, signaling molecules are also called ligands. There are many types of ligands, some of which are discussed below: Proteins: many hormones and growth factors. Steroids: such as gonadal steroids, cortisol, testosterone, estrogen (derived from cholesterol, meaning they are hydrophobic and can pass through the plasma membrane) and others. Lipid soluble. Small Molecules: There are many small molecules that function as ligands. Organic: amino acids, nucleotides. Inorganic: NO, CO 2 , and some metal ions. Inorganic ligands are important for drugs.

Small inorganic molecules NO and CO 2 are common ligands

LIGAND RESPONSE

The response to a ligand may be different in different cells. For instance, acetylcholine, a ligand, decreases the rat and force of contraction when bound to a cell in heart muscles. However, it also causes saliva secretion when bound to salivary gland cells. Furthermore, it causes contraction when bound to skeletal muscles. What this means is this: there can be different receptors for one ligand, resulting in different effects. This is also known as molecular switching. First of all, we must recall what a phosphate group is. Its molecular formula is PO 4 , however we often write it as P 1 to indicate one phosphate group. Now, phosphorylation is when a P 1 is added to or taken away from a molecule. This is accomplished via helper proteins that either add or remove a P 1 . Whether the P 1 activates or deactivates depends on the particular protein/molecule it is attached to (i.e. removing a P 1 can activate a molecule, as can adding one). There are two different types of proteins: Kinases: these proteins add a P 1 group from a molecule. As a side note, 2% of our genes may code for kinases. Kinases can also be transmembrane receptors. Phophatases: These proteins remove a P 1 group from a molecule.

PROTEIN PHOSPHORYLATION

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There are four major types of receptors that we should be familiar with for testing purposes. Dont concern yourself too much with the details, as those are best left to higher level Biology classes. Just do you best and try to not fuck it up.

RECEPTORS

G PROTEIN-COUPLED RECEPTOR

Here we have a G Protein-couple receptor spanning the plasma membrane. A ligand comes along and binds to the receptor, causing the receptor to change shape. This causes a G Protein, also in the membrane, to change shape via GTP (the inactive G protein has a molecule of GDP attached to it). This moves the G Protein to move within the membrane to an enzyme. This enzyme is the activated, and it too changes shape. The enzyme then induces a cellular response. Meanwhile, GTP is hydrolyzed (releases its P 1 group) and goes inactive. About 4% of the human genome encodes for these types of receptors.

LIGAND-GATED ION CHANNEL

Here we have an ion channel embedded in a membrane. A ligand comes along and binds with the receptor. This causes the ion channel to open, and allows ions to diffuse through into the cell. These ions then induce a cellular response. Simple.

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RECEPTOR TYROSINE KINASES (RKSs)

This is an odd one. Here we have two identical enzymes embedded in a membrane. Each enzyme has three tyrosine amino acids attached to them (remember, these are polar amino acids), making a total of six between the two. As well, each enzyme has a ligand-binding site. Now, when each binding site has a ligand attached to it, the enzyme will come together into one. This enzyme is then called a dimer (because there are two enzymes in one). Next, six ATP come along and autophosphorylate the six tyrosine kinase regions, donating one P 1 group to each. This fully activated receptor tyrosine kinase can then bind to and activate relay proteins, which cause cellular responses. Since there are six tyrosine binding sites, a total of six cellular responses can happen. These receptors are located within in the cell (i.e. not embedded in a membrane). The ligands that bind to these receptors are hydrophobic. An example is this: a hormone located in the extracellular fluid diffuses through the plasma membrane of a cell. Once inside, it binds to a receptor protein, which activates a hormone-receptor complex (this is a transcription factoror a protein that binds to DNA and regulates transcription). This hormone-receptor complex moves into the nucleus of the cell and binds to DNA. The DNA then sends mRNA out into the cytoplasm, carrying instructions for new proteins to be manufactured in ribosomes. This is an alteration in gene expressionor a new way of making proteins.

INTRACELLULAR RECEPTOR

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PHOSPHORYLATION CASCADE

These cascading phosphorylations amplify signal transduction. A ligand comes along and binds to a receptor. This receptor then activates a rely molecule, which in turn activates a protein kinase. This protein kinase is then phosphorylated via ATP, which h activates another protein kinase. The original protein kinase is dephosphorylated via a protein phosphatase, stripping it of its P 1 group. This process continues until response proteins are activated, leading to a cellular response. If this is in anyway confusing, refer to the illustration in the classroom slides. There are several different types of 2nd messengers, including cAMP, DAG, IP 3 and Ca++. These 2nd messengers can be utilized by G protein-couple receptors and RTKs. They are considered 2nd messengers because of their secondary use in signal transduction. A first messenger will trigger the release of a 2nd messenger, and so on.

2nd MESSENGERS

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APOPTOSIS

This the cell death! This was first discovered in C. elegans (a worm). A death ligand comes along and binds to a receptor, which signals self-destruction (or suicide) to the cell.

COMPLEXITY

What we have been studying are simple examples of signal transduction. In reality, this process is much more complicated, often involving more than one ligand and several different receptor proteins. The cancer pathway is just one example (provided in the classroom slides, for those interested). Thats it for chapter 11.

An example of a complex pathway. Holy mother of shit!

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CELL DIVISION & THE CELL CYCLE

CELL DIVISION OVERVIEW
Cell division is a property of life, and is responsible for reproduction (binary fission) development (plant, animal embryos), growth (from fetus to adult), normal replacement of old cells (intestinal epithelium or skin cells), and repair (wounds and such).

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CHALLENGES

Cellular division has some challenges, conveniently listed below: Cellular component duplication: or the doubling of all organelles, cytoplasm, nucleus, etc. DNA (chromosome) replication: errors may occur when DNA is replicated. DNA distribution to the daughter cells. Regulation and Integration: cycling time or the amount of time from one division to the next needs to be highly regulated. Cancer is the exception to regulate processes.

GENETIC MATERIAL

Here are some basic definitions for this chapter. Genome: The genetic material of an organism or virus; the complete complement or an organisms genes along with its noncoding nucleic acid sequences. In eukaryotes, genetic material is found in the nucleus, mitochondria and chloroplasts (note that plants have both mitochondria and chloroplasts, whereas animals only have mitochondria). Chromosomes: In eukaryotic cells, chromosomes are linear strands of chromatin, or DNA wrapped around histones (refer to chapter six). These strand are anywhere from 2-6 cm in length. Humans have somatic cells , which have 46 chromosomes (23 inherited from each parent). However, gametes, or human sperm and eggs, have

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23 chromosomes. This would make sense as a sperm and egg come together to make 46 chromosomes. NOTE: Chromosomes must be duplicated and properly distributed to daughter cells during cell division.

CELL CYCLE

The cell cycle lasts from one division to another and is a dynamic process. During the cell cycle all material within the cell doubles, cells growth and change shape, and major changes happen within the nucleus. There are TWO phases within the cell cycle, so lets talk about each one:

INTERPHASE

This is the time for active growth, chromosome replication and DNA synthesis. There are three parts to the interphase, as seen below:

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Or Gap 1, this is a phase of growth for the cell. It occurs after the previous cell cycle had completed. It lasts anywhere from 8-10 hours, and is generally the longest part of the entire cell cycle (though in humans the S phase may be the longest).

G 1 PHASE

S PHASE

This phase is characterized by DNA synthesis, or chromosome replication, and the duplication of all other organelles contained within the cell. This phase lasts anywhere from 4-8 hours. Of course, times vary depending on the type of cell, development, temperature, nutrition, etc. Lets talk a little more about chromosome replication, as it can get quite complicated. Chromosome Replication: As already stated, chromosomes are comprised of linear strands of chromatin, or DNA wrapped tightly around proteins (histones). Lets start by talking about one chromosome, and how it replicates. One chromosome contains 1 strand of DNA. During chromosome replication (another name for DNA synthesis), you gets something called sister chromatids, or 1 chromosome and 2 DNA molecules. A sister chromatid is a singular object held together by centromeres, or specialized regions of the chromosome (comprised of cohesion proteins) where two sister chromatids are most closely attached. As stated, a sister chromatid is comprised of 1 chromosome; however, in reality a sister chromatid consists of homologous chromosomes, or chromosomes that contain the same genes, have the same length, and have the same centromere position. We call these homologous chromosomes a singular object simply by virtue. When the sister chromatids separate, you get a 1 chromosome and 1 DNA molecule for each of the 2 daughter cells. Another way to think about this: a sister chromatid becomes 2 chromosomes and 2 DNA molecules when mitosis is complete. This is an issue of definition.

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G 2 PHASE

Or Gap 2, this phase is another waiting period characterized by the growth of the cell. It lasts anywhere from 4-6 hours.

MITOTIC PHASE

This phase occurs after the G 2 phase and consists of mitosis (nuclear division) and cytokinesis (cytoplasmic division). Lets talk about each one in more detail.

MITOSIS

Mitosis is the process by which cells divide their nucleus into two. There are 5 stages of mitosis, each one discussed below. Prophase During the prophase, chromatin will condense to form chromatids. In a human cell, this means there will be 46 chromatids (or 92 chromosomes held together at the centromere). Also, during prophase the nuclear envelope disappears. This stage leads to Prometaphase In this stage you have spindle fibers attaching to kinetochores or sister chromatids. We will talk more about kinetochores and the mitotic spindle in a bit. Metaphase Here we see that microtubules that are connected to kinetochores cause the chromatids to line up along the metaphase

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plate (an imaginary structure located at the center of the mitotic spindle). A signal is given, leading to: Anaphase Microtubules drag sister chromatids by their centromeres to opposite poles of the mitotic spindle. This means that the there are 46 chromosome at each pole of the spindle. This leads to: Telophase Chromosomes uncoil, the nuclear envelope reform (around each set of 46 chromosomes), and cytokinesis can occur. However, before we get into cytokinesis, lets talk some more about the mitotic spindle.

MITOTIC SPINDLE

The mitotic spindle is a structure comprised of microtubules that control chromosome alignment, segregation and separation of sister chromatids. There are some important features of the mitotic spindle that you should be aware of:

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Aster: Fibers that anchor the mitotic spindle to the plasma membrane, or cell wall. Centrosomes: We discussed centrosomes in chapter six. These structures (comprised of 9 sets of 3 microtubules arranged in a ring) are located at both poles of the mitotic spindle. Kinetochores: These are special protein structures located at the centromeres of chromosomes and sister chromatids that attached to microtubules during prometaphase/metaphase. Kinetochore Microtubules: these are microtubules that connect to the kinetochores and align chromosomes along the metaphase plate (discussed above). Overlapping Non-Kinetochore/Polar Microtubules: these are microtubules that are responsible for cytokinesis, which is described in detail later.

As already stated, the mitotic spindle is responsible for aligning sister chromatids and then pulling them to opposite poles, or centrosomes. The act of pulling them requires ATP, as a motor protein located within on the kinetochores will literally pull the chromosome towards the pole (destroying the kinetochores microtubule in the processreducing them to tubulin subunits). Thats it for the mitotic

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spindle. Just be familiar with how this process works and the associated vocabulary.

CYTOKINESIS

Cytokinesis is the division of the cytoplasm. Obviously, plant and animal cells have different methods of dividing into two cells, so lets talk about each one separately. Animal Cells: In animal cells, actin and myosin fibers (microfilaments) form a ring around the plasma membrane and contract, or pinch (creating a cleavage furrow) the cell into two daughter cells. Were not going into great detail here. Plant Cells: In plant cells, vesicles from the Golgi apparatus form a cell plate down the middle of the parent cell. When the cell plate is complete it is then called a cell wall, and two daughter cells are born.

BINARY FISSION

Binary fission is the process of cellular reproduction where NO mitosis occurs. Prokaryotes reproduce this was, as do some single-cellular eukaryotes. Prokaryotes have a single circular chromosome comprised of double-stranded DNA. Replication of the DNA starts at the origin of replication (ori). It form two loops, the cell elongates, and is then split in two (at a point called the septum). Not much on this one.

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So, they did this experiment where they took one cell in the S phase and put it next to another cell in the G 1 phase. Guess what happened? Well, the cell in G 1 phase immediately went into the S phase, signifying that some molecular control was happening. The same thing happened when they took a cell in mitosis and put it next to a cell in G 1 phase. The cell immediately went into mitosis, completely skipping the S phase, where its DNA and organelles are duplicated. Anyway, molecular control of the cell cycle involves checkpoints, where the cell will examine itself and decide whether or not to continue with the cycle. There are three, each discussed briefly below: G 1 Checkpoint: At this point, located in the G 1 phase of Interphase, division of the cell is halted unless a go ahead signal is received. When a cell is stopped, it enters the G 0 phase and exits the cell cycle. Most of our cells are in the G 0 phaseotherwise we would continue to grow and grow. It if receives the go ahead signal, the cell will typically proceed with the entire cellular cycle (S phase, mitosis, cytokinesis).

MOLECULAR CONTROL OF THE CELL CYCLE

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G 2 Checkpoint: At this point, located at the end of the G 2 phase (just before mitosis) the cell will examine itself for any damaged DNA or cellular components. If it finds any, the cellular cycle will likely stop. M Checkpoint: At this point, just at the end of mitosis (in the mitotic phase), the cell will check itself again to determine if everything went according to plan. If so, it will continue on to cytokinesis and split in two. If things fucked up, it will likely undergo apoptosis, or programmed cell death.

These molecules, such as Cdk/cyclin complexes regulate the cellular cycle. Lets talk about them some more. Cyclin Dependent Kinases (Cdks): these molecules phosphorylate a variety of target proteins related to cellular division. If you remember back to chapter 11, kinases are proteins that add P 1 groups. Cyclins: these enzymes bind to Cdks and regulate their ability to phosphorylate. So, cyclins regulate Cdks, and Cdks regulate cellular division.

REGULATORY MOLECULES

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MPF & THE G 2 CHECKPOINT

To begin, each checkpoint uses different cyclins and Cdks to regulate passage. However, in the G 2 checkpoint we find a complex of cyclinCdks called MPF (maturation promoting factor). This complex controls passage through the G 2 checkpoint. As the cyclin concentration rises MPF activity rises as well. During the mitotic phase, these levels drop back down, meaning that cyclin and MPF levels cycle over the cell cycle. MPF will then trigger the breakdown of cyclin. NOTE: while cycling and MPF levels fluctuate, Cdk levels do NOT. Cell signaling pathways can trigger the cell cycle, such as growth factors or tissue injury. As an example, a growth factor may travel from an endocrine cell to a target cell, bind with a Receptor Tyrosine Kinase protein embedded within the plasma membrane, trigger a signal transduction (refer to chapter 11), leading to a cellular response (in this case, the synthesis of cyclins to get those checkpoints going).

CELL CYCLE EXTERNAL CONTROL

CANCER CELLS

Cancer cells have abnormal control pathways, including pathways normally activated by growth factors. They are characterized by their loss of contact inhibition and anchorage dependency. In a normal cell, cell surface protein interactions and the subsequent signal transduction will inhibit cell division. In cancer cells this is not true; they will continue to grow and grow.

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MEIOSIS AND GENETICS

WHAT IS INHERITED
Lets start with some basic vocabulary. First, a gene is a sequence of nucleotides, or part of DNA. Each chromosome has hundred of genes in it (with the exception of the human Y chromosome). A gene is also a hereditary unit. Humans have around 25 thousand genes.

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ASEXUAL VS. SEXUAL REPRODUCTION

To begin, sexual reproduction is defined as having offspring produced from the union of gametes (fusion of two genomes), is restricted to eukaryotic cells, and requires meiosis, which well discuss in a bit. Asexual reproduction, on the other hand, describes offspring that are produced from a single parent (via mitosis). Organisms that do this usually produce genetically identical offspring.

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SEXUAL REPRODUCTION REQUIRES MEIOSIS

While asexual reproduction only requires mitosis, sexual reproduction (the best kind of reproduction) requires meiosis. First of all, the life cycles of sexual reproduction involves the union of 2 gametes (or the fusion of two genomes). Gametes are haploid cells. The life cycle is a mechanism to maintain chromosome numbers within a species. This means that humans will always have 23 pairs of chromosomes (a total of 46 chromosomes). Typically, all sexually reproducing species have characteristic diploid and haploid number of chromosomes. As stated, humans have 23 pairs, while other species have different numbers. This number is constant within a species (unless mutation fucks shit up). Meiosis must occur at some point during the life cycle of sexual reproduction, and involves two rounds of cell division with a reduction in chromosomes (2n to n). There are three types of life cycles in respect to sexual reproduction, as discussed below: Gametic Meiosis (Animals): This life cycle is characterized by fertilization of two gametes (two haploid cells) resulting in a diploid zygote (which undergoes mitosis). Gametes are the only haploid cells in this life cycle, and there is NO mitosis in the haploid stage. Meiosis can only occur in germ cells, or cells associated with the development of gametes (testes and ovaries).

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Zygotic Meiosis (Most Fungi & Some Protists): In this life cycle, the haploid stage dominates, there is NO mitosis in the diploid stage, and the zygote is the only diploid cell. The zygote (or the diploid cell) will undergo meiosis while the gametes (or haploid cells) undergo mitosis.

Alternation Of Generations (Sporic Meiosis): In this life cycle, meiosis can only occur with diploid cells. However, both diploid and haploid cells undergo mitosis, producing both diploid and haploid individuals. As a clarification: meiosis PRODUCES haploid individuals and gametes FORM BY mitosis.

Summary: So, a zygote is always diploid (2n), and gametes are always haploid (n). Individuals can be diploid or haploid, zygotes can divide by mitosis OR meiosis, but only diploid cells can undergo meiosis, as the process results in the reduction of chromosome.

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MEIOSIS

So, meiosis has two stages, meiosis I and meiosis II. Both stages contain a prophase, metaphase, anaphase and telophase. DNA is still replicated in the S phase, but there is NO DNA replication between meiosis I and meiosis II. The result of meiosis is four haploid daughter cells, each containing half as many chromosomes as the parent diploid cell. Before we begin going through each of the two stages we need to get some basic vocabulary out of the way. Lets get to it: Sister Chromatids: These are the same as in mitosis. When DNA synthesis occurs in the S phase you get one chromosome consisting of two chromatids, or sister chromatids. These chromatids are held together at the centromere (1 centromere for every sister chromatid). Homologous Crhomosomes: Two chromosomes (each consisting of two chromatids) that carry the same genetic code (not exactly the same, but chromosomes that code for the same thing). In humans, one chromosome comes from the mother and the other from the father. Synapsis: The independent alignment of homologous chromosomes during meiosis I. These homologous chromosomes physically join together by proteins along their entire length, creating a synaptonemal complex. A tetrad or bivalent is a word used to describe two joined homologous chromosomes (for a total of 4 chromatids). Synapsis occurs during prophase 1. Crossing Over (Chiasma Formation): This happens with NONSISTER chromatids turning meiosis I. Crossing over occurs in prophase 1 (during synapsis) through anaphase I, as they are separated via microtubules connected to kinetochores. Segregation Of Homologs: This is another name for reduction division, which occurs in meiosis I during anaphase I. It is considered a reduction division because a diploid cell become two haploid cells in meiosis 1.

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MEIOSIS I

As stated directly above, meiosis I is the process by which a diploid cell (2n) because 2 haploid cells (n). Lets briefly go through the stages of meiosis I:

Prophase I: Homologous chromosomes undergo synapsis, fusing together length wise. The start of crossing over (Chaismata) occurs. The nuclear envelope fragments and the spindle begins to form. At this point in a human cell there are 23 homologous chromosomes, 46 sister chromatids (92 chromatids), and 46 centrioles. Metaphase I: Homologous chromosomes line up along the metaphase plate and microtubules attach to the kinetochores.

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Anaphase I: Homologous chromosomes separate (the sister chromatids are still together). Telophase I & Cytokinesis: Nuclear envelope reforms around the two new nuclei, a cleavage furrow forms and the cell divides in two. A this point in human cell each has 23 pairs of sister chromatids (they are haploid, as the father cell had 46).

This is essentially mitosis but with haploid cells. Instead of homologous chromosomes separating during anaphase, you get sister chromatids separating during anaphase II, resulting in four haploid cells (each with 23 chromosomesfor a human). There is no synapsis or crossing over during meiosis II, as there are no homologous chromosomes.

MEIOSIS II

RECOMBINING GENES

There are two ways to recombine genes, one of which we already discussed. Lets go through them again: Crossing Over: This occurs at prophase I. Homologous chromosomes go through synapsis where they bind to one another along their entire length. Nonsister chromatids then exchange pieces of DNA (called genetic recombination). This makes them no longer identical, and one chromatid will have both maternal and paternal genes.

Independent Alignment: This occurs during metaphase I and involves the arrangement of chromosomes along the metaphase plate. The order in which they arrange determines the assortment of chromosomes that end up in the haploid cells. Refer to slide illustrations if you are still not clear on this.

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DIFFERENCES BETWEEN MEIOSIS AND MITOSIS

Here are some key differences between mitosis and meiosis:

Meiosis involves two rounds of cell division, as well as reduction division, and produces four haploid cells. Mitosis involves only one round of cell division and produces two diploid cells. Meiosis involves synapsis, or the pairing of homologous chromosomes. Mitosis does not. Meiosis involves crossing over of genetic information (i.e. pieces of the chromosome are exchanged between nonsister chromatids). Meiosis produces genetically diverse cells due to crossing over and independent assortment. Mitosis produces genetically identical cells.

GENETIC VARIABLITY

The ultimate source of genetic variability is mutation. Other sources include recombination of existing variations (independent assortment and crossing over), random fertilization, evolutionary change and natural selection.

HUMANS

As already stated elsewhere in this guide, humans have a diploid number of 46. We have 22 pairs of autosomes and 1 pair of sex chromosomes (X and Y). A male will produce millions of gametes in his

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lifetime (thats a lot of sperm). A woman, however, will only produce around 500 gametes, or eggs, during her lifetime. In fact, all of a womans eggs are present when she is born. A meiocyte is any cell that undergoes meiosis.

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MENDEL & THE GENE CONCEPT

Mendel is considered the father of modern genetics. He was an Austrian monk and is known for his experiments and studies on true-breeding traits of flowering pea plants. He did cross-pollination (hybridization) experiments in which he removed the stamens (pollen) from a target plant, transferred pollen from a donor plant with different traits to the target plant, allowed the pod to develop, planted the seeds, and examined the offspring. What he discovered was amazing, and well be discussing this as this chapter progresses.

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MENDEL

Mendel was a sexy beast!

Mendel took two different true breeding plants (plants that produced the same results regardless of character), called the P generation, and bread them together. The first generation of offspring he called the F 1 generation. He found that the F 1 generation only produced one of the character traits associated with the P generation. He called this trait dominant and he called the trait that did not appear recessive. The leading theory up until that point was that of blending, or two character traits blending into a new one. When he bred a purple flower with a white flower he found that all the offspring had purple pedalsthere was no blending, or light purple pedals. He found that the color purple was a dominant trait, and white as a recessive trait. Next, he allowed the F 1 generation to breed, creating an F 2 generation. In this generation he found that recessive traits suddenly reappeared! He counted the offspring and found that the ratio of dominant to recessive traits was 3:1.

MENDELS MONOHYBRID CROSS

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MENDELS FIRST LAW: SEGREGATION

As already stated, Mendel found that no blending occurred when he bred his true breeding plants. He also found that recessive traits did NOT disappear from the F 1 generation; they were simply latent, waiting to reappear in the F 2 and subsequent generations. Parents, he found, provide discrete factors, which we now called genes. Individuals receive two genes, one from each parent, and they segregate during gamete formation. The separation of genes occurs because homologous chromosomes segregate during meiosis I, as well as independent assortment.

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ESSENTIAL GENETIC TERMS

Here are some essential genetic terms used in this chapter. Gene: Or sometimes called Mendels factor, a gene is a basic unit of heredity. It is a segment of DNA located at a particular site (locus) on a chromosome that contains code for a particular protein (or functional RNA). Allele: an allele is an alternate for of a gene. Individual inherit 2 allelesone from each parent. So you may two genes that encode for eye colorone for brown and one for blue. These genes are called alleles, because they code for the same thing (eye color) but are alternative forms (one for blue, one for brown).

Homozygous: This is an individual that has 2 copies of the same allele. So, both alleles would code for the same color eyes (PP) Heterozygous: This is an individual that has 2 different alleles, such as one for blue eyes and one for brown eyes (Pp) Dominant Allele: This allele will determine the appearance in a heterozygote. The symbol for a dominant allele is an uppercase letter (P) Recessive Allele: This allele will have no effect on appearance in a heterozygote. The symbol for a recessive allele is a lower case letter (p). Genotype: All of the alleles present in an individual. Phenotype: Physical, visible manifestations of the genotype (such as eye color, hair color, skin color, size, etc.).

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F2 GENERATION

The F 2 generation will display a phenotype ration of 3:1 and a genotype ration of 1:2:1. For the genotype, that means one will be true-breeding homozygous dominant, two will be non true-breeding heterozygous, and one will be truebreeding homozygous recessive. An illustration can be seen below of this:

MENDELS SECOND LAW: INDEPENDENT ASSORTMENT

Essentially, this law states that pairs of alleles will segregate independently of each other pair of alleles. So, if you have a green pea plant with round peas and mate it with a yellow pea plant with wrinkled peas, each allele (color and whether or not it is wrinkled) will segregate independently, with each giving you a 3:1 phenotypic ratio.

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INCOMPLETE DOMINANCE

In this case we find that the heterozygote is intermediate between homozygous dominant and homozygous recessive. This is not blending. An example would be a white flower mating with a red flower (both are homozygous) giving rise to a pink flower. The F 2 phenotype is 1:2:1.

PLEIOTROPY

Here we have a single gene affecting more than one trait, as is the case for sickle cell anemia.

CODOMINANCE

Here we have two dominant alleles being expressed. We also see the concept of multiple alleles in a population (an individual still only has two), as is the case for blood type. There are three alleles for blood type, and depending on the combination you receive you will be one of four possible blood groups. The alleles actually affect the appearance of red blood cellsmore specifically, their associated carbohydrates. Blood type is also a good example of a recessive trait (blood type O) being the most common. Blood type O is also the universal donor, as it lacks carbohydrate groups. See illustration for a better understanding.

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POLYGENIC INHERITANCE

Here we find that multiple pairs of genes contribute to the phenotype. These are quantitative (can be count) characteristics, such as height and human skin color. This is due to independent assortment, crossing over, and the additive effects of polygenic inheritance.

EPISTASIS

Here we have the gene product at one locus altering phenotypic expression of a gene at another locus. One gene will mask the appearance of another gene and produces a modified 9:3:3:1 phenotypic ratio. The example used in class looks at fur color of mice. When one gene is epistatic to another it produces a 9:3:4 phenotypic ratio.

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ENVIRONMENTAL EFFECTS

Gene expression can be modified by environmental conditions. For example, the pH of soil can affect the color of certain flowers. Furthermore, temperature can affect the enzymatic activity, which can affect the amount of pigment produced in the fur of certain cats.

MENDELIAN INHERITANCE IN MAN

To finish off this chapter we will briefly discuss some recessive and dominant disorders. Albinism is a disorder that affects pigment production. People who are carriers for this disorder are always heterozygous. When two heterozygous people mate, one of their

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offspring will be homozygous recessive, or an albino. Cystic fibrosis and sickle-cell anemia are other recessive disorders. Achondroplasia (dwarfism) and Huntingtons disease are examples of rare dominant disorders, and illustrate how recessive alleles can be more common than dominant ones.

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CHROMOSOMAL BASIS OF INHERITANCE

First of all, Mendel didnt know about DNA or chromosomes, and it wasnt until the late 1800s when mitosis and meiosis were discovered. He had no idea that genes were the factors controlling his experiments. In fact, his work went mostly unnoticed until the early 1900s, when his paper was rediscovered. Scientists of time postulated that genes are parts of chromosomes, and it was Morgans white-eyed flies experiment that proved it. Morgan was infatuated with mating flies, or more specifically, mating Drosophila. These flies, like humans, have XY sex chromosomes, with the gene for eye color being on the X chromosome. What he did was take a wild type (normal red eyed) female and mate it with a mutant (white eyed) male. What he found was that only males had white eyes. The illustration below shows both the F 1 and F 2 generations.

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WHERE ARE GENES LOCATED

SEX LINKED GENES: MORGANS WHITE EYED FLIES

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The sex of an organism (or at least, some organisms) is determined by chromosomal makeup. In mammals, the gene on the Y chromosome determines sex. It initiates development of male gonads (gonads develop as female by default). Just in case you dont know, males are XY while females are XX. Genes located on the X chromosome are considered sex-linked genes, however, many genes found on X are not related to sex. Furthermore, Individuals without an X chromosome will NOT survive. Females must be homozygous and males must be hemizygous (i.e. they have only one X chromosome).

SEX DETERMINATION

CHROMOSOME INACTIVATION

This can happen in mammals, or more specifically, in female mammals. One X chromosome becomes highly condensed and is nonfunctional. The inactive X chromosome shrinks into what is called a Barr body.

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Linked genes are genes on the same chromosome (autosome). Refer to the slides for a better understanding of this concept. When conducting a dihybrid cross (a cross with two alleles), linked genes DO NOT display Mendelian phenotypic ratios. This is due to crossing-over of homologous chromosomes in prophase I of meiosis. Also, depending on the distance of each gene, parental types are more frequent and recombinant types are the rarest.

LINKED GENES

GENETIC DISORDERS

There are several genetic disorders we need to talk about before moving on to the next chapter (yes, this is a short one!). Lets discuss each: Non-Disjunction: This is when homologous chromosomes fail to separate during meiosis I, or sister chromatids fail to separate during meiosis II. This will obviously affect the number of chromosomes in each daughter cell (can be + or -). In mammals, autosomal non disjunction is almost always lethal. A monosomy refers to a cell that only has 1 copy of the chromosome (ALL are lethal), while a trisomy refers to a cell that has 3 copies of a chromosome (almost all are lethal). Non-disjunction of sex chromosomes results in all sorts of wacky disorders. For instance, a

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female with three X chromosomes is pretty normal and fertile. However, a female with only one X chromosome (Turner Syndrome, the only known viable monosomy) is sterile. Males with an extra Y, or Jacobss syndrome, are viable and fertile. Klinefelter syndrome, or XXY, results in a sterile male. Non-disjunction can also occur in mitosis.

Aneuploidies: As discussed above, non-disjunction results in an abnormal number of chromosome, and that autosomal nondisjunction are almost always embryonic lethal. However, Down syndrome, or trisomy-21 is an autosomal aneuploidy that is viable. This happens during meiosis I in females, and has to do with arrested development of egg cells. An embryo will receive an extra chromosome (number 21), making them n=47, and resulting in severe mental retardation.

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ALTERATION IN CHROMOSOME STRUCTURE

These are fuck up that can happen in either mitosis or meiosis. Deletion: can be harmful, but not necessarily so. Duplication: source of new genetic material, and important for evolution. Inversion: can interfere with crossing over and may be important for evolution. Reciprocal Translocation: this creates new linkage groups that can be fused together, and is often associated with the origin of new species. Very important for evolution.

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MOLECULAR BASIS FOR INHERITANCE

DNA was discovered by Miescher in 1869. He studied puss from the wounds of soldiers. He did not know if genetic material is DNA or protein, he simply found it. Later experiments, which well talk about soon, found that DNA is genetic material. Then, in 1928 Griffith discovers transformation in his famous experiment. He found that dead S cells (which would kill mice when injected) would transform healthy R cells into S cells.

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Then, in 1944 Avery discovers that the transforming substance from Griffiths experiment is DNA. He found that the molecule that carries the heritable information can only be DNA, even though most scientists of the time told him to fuck off and die. In 1952 it was known that viruses were made up of DNA and protein. It was also known that viruses use host cells to manufacture copies of itself. However, it still wasnt clear if it was DNA or protein. This brings us to the big one: In 1952 Hershey and Chase demonstrate that DNA is viral genetic material transferred from viruses to host cells. They did this by using

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radioactive elements and a blender to test both proteins and DNA molecules.

Then, in 1950 came Chargaffs rule stating that DNA bases vary across species, but within a species A and T always match and C and G always match. They are then said to be equimolar. Rosalind Franklin and Maurice Wilkins used x-ray diffraction of DNA crystals to determine that DNA is a helix, running antiparallel with a sugar phosphate backbone and nitrogenous bases in the interior. This provided crucial structural information to Watson and Crick, who were also working on a model for DNA. Watson (an asshole) and Crick used the experimental results of other (Franklin and Chargaff) to build their DNA model. Their first model was constructed out of cardboard cutouts. Their famous work on the double helix structure of DNA was published in 1953. They deduced the base-pairing rules stating that a purine and pyrimidine must be the answer for nitrogenous base pairing, as their width was consistent with x-ray data.

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Finally, in 1958 Meselson and Stahl demonstrate that semiconservative replication is the process by which DNA replicates. They used isotopes of nitrogen and density centrifugation. You can read all about it if youre a dumb shit or something.

MODELS OF DNA REPLICATION

At the time when Watson and Crick were fucking around with DNA, there were already some models in place for the replication of DNA, described below:

Conservative: this model has a new DNA molecule being built from scratch. The old molecule is conserved, or untouched. Semiconservative: This model was put forth by Watson and Crick, explaining that each molecule of DNA was comprised of one old strand and one new strand. This model is what we study today. Dispersive: This model suggests that each strand of DNA is comprised of old and new material. As we now know, this is bat shit insane.

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Now were really going to get into the meat of this chapter. As you now know, humans have 46 chromosomal DNA molecules, numerous mitochondrial DNA molecules, and over 6 billion base pairs. DNA replication occurs during the S phase of mitosis or meiosis, and takes about 2-8 hours. There arent many errors (about 1 in 10 billion nucleotides). Each strand of DNA runs from the 5 end to the 3 end, with a free OH group at the 3 end. The two molecules run antiparallel. The sugar phosphate backbone is held together by phosphodiester bonds, while hydrogen bonds hold together the complimentary base pairs. Lets fucking do this shit.

DNA REPLICATION

INITIATION OF DNA REPLICATION PROKARYOTES

First of all, prokaryotes have a double-stranded DNA molecule that is arranged in a loop. There is an origin of replication (1 ori, as it is called). When the DNA molecule begins to replicate, a replication bubble is formed, followed shortly by a replication fork, or a place where each strand forks off to become replicated. In the end, you have two daughter strands of DNA, each arranged in a circle.

Unlike prokaryotes, eukaryotes have multiple origins of replication, replication bubbles and replication forks. The actual process of replicating DNA is complicated, so look at the slides if you get confused. There are many enzymes and proteins associated with DNA replication. This anabolic reaction (adding nucleotides together to form DNA) requires lots of energy from the cell, and the replication apparatus itself (replisome) is so complex that if might blow your head clean off your dumb body. Here are some helpful facts: DNA replication always happens from 5 to 3. Deoxynucleoside triphosphates are always added to the growing 3 end. When DNA forks off, you get one strand that is arranged from 5 to 3 and one that is arranged from 3 to 5. The leading strand is said to be continuous, as elongation occurs in the 5 to 3 direction. The

INITIATION OF DNA REPLICATION EUKARYOTES

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lagging strand is said to be discontinuous, as it cannot replicate in the same fashion. Well talk more about this later. Topoisomerase: is an enzyme that prevents twisting ahead of the replication fork. This means that it runs along the original DNA molecule, untwisting it before it forks off and is replicated.

Helicase: is an enzyme that unwinds and separates the two parental strands of DNA. Single-Strand Binding Proteins: are proteins that keep the strands separate from one another. Primase: is an enzyme that begins the replication process by providing a RNA primera short bit of code that allows new nucleotides to bind. Well talk more about this soon. Polymerases: are enzymes that add nucleotides at the growing 3 end of the new DNA strand. Eukaryotes have at least 12 to 15 different polymerases. Do not confuse this process with primase, as a polymerase cannot initiate the replication process. It can only add new nucleotides

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LEADING STRAND SYNTHESIS

This strand is replicated continuously from 5 to 3. An RNA primer is added to the origin of replication allowing elongation to begin. Afterwards DNA polymerase III comes along and begins adding new nucleotides. This process continues as the parental DNA molecule is unwound by helicase.

LAGGING STRAND SYNTHESIS

This strand is replicated discontinuously. Short segments, called Okazaki fragments are added to the parental strand. Furthermore, multiple primers are needed to synthesize the lagging strange, and the primers must also be removed once synthesis has begun (usually done

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by DNA polymerase I). The Okazaki fragments must also be joined together to complete the molecule of DNA, a process that is helped along by the enzyme ligase.

REPLICATION ERRORS

Sometimes your body fucks up and makes a mistake. Luckily, there are some measures in place that allow the process to self correct. For instance, DNA polymerase proofreads as it elongates the new strand, checking for errors. If it finds one, part of the strand is cut out (by even more enzymes) and polymerase will fill in the gap. However, these errors also present mutations, a component of evolution.

DNA EXCISION REPAIR OF DAMAGED DNA

Sometimes a thymine dimer (two adjacent T bases covalently bond together, causing a kink) occurs do to damage from UV light. In these cases, the enzyme nuclease comes along and cuts out the damaged segment. Then, polymerase comes along and fills in the missing nucleotides. Finally, ligase attaches the new segment to the original,

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undamaged DNA strand, completing the repair process. This is a simplified view of DNA repair. In reality, there are +30 proteins and enzymes involved with the process. Take a genetics class if you want to learn more.

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TELOMERES

Telomeres are the ends of linear chromosomes, and they contain 100 to 1000 copies of noncoding DNA sequence. Since chromosomes shorten after each round of cell division, telomeres keep the coding sequences of DNA intact. Every time a chromosome shortens, only the noncoding telomere sequence is cut off.

TELOMERASE

This is an enzyme that is associated withyou guessed ittelomeres. The enzyme itself has a built in RNA template. The enzyme will bind with the end of a leading DNA strand and extend it with the telomere sequence of nucleotides. As a side note, this enzyme may have an important implication for cancer and aging, as cancerous cells have active telomerases (they are usually off).

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GENE TO PROTEIN
AN OVERVIEW
This chapter will probably ramble on and on endlessly, so be prepared for a lot of information. We all know that DNA codes for proteins, or polypeptides, which consist of a sequence of amino acids. In order for a protein to be made, the code contained within the DNA must make its way to the ribosomes in the cytoplasm. To fuck shit up even more, DNA cannot leave the nucleus of the cell. However, in comes RNAor more specifically, mRNA (messenger RNA)to save the mother fucking day. mRNA is transcribed from the DNA molecule, and is then transported to ribosomes, where it is translated into a protein or polypeptide (these terms are interchangeable). Transcription involves the DNA template, RNA polymerase (see chapter 16 for a definition on polymerases), and mRNA. Translation involves ribosomes, tRNA and genetic codes.

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DNA

Nucleotide sequences contain information (or at least most of them do). This information could be a sequence of amino acids (to make a protein), blueprints for cellular structures (such as telomeres and centromeres), and can help regulate our body and cellular activity. As we learned way back in the exam 1 review, there are about 22 known amino acids. We also know that there are only four different nitrogen bases associated with DNA. Now, if DNA codes for amino acids, how do it specify which amino acid? Simple, with groups of three nucleotides. This allows for 64 different codons, or genetic codes to be made (4 x 4 x 4 = 64). Now, since there are 64 different codons and only 22 different amino acids, some amino acids have multiple codons. Check out the codon dictionary for reference (theres no need to memorize this as it will be provided on teststhat is, if your teacher isnt a complete dick). Condons are read from 5 to 3, and only 61 of

GENETIC CODE

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them code for amino acids. The other three are called stop codons, and provide an end point to the reading frame (consecutive groups of three nucleotides).

EVOLUTION OF GENETIC CODE

The genetic code is universal, indicating that all living organisms on earth have a common ancestor. There are some minor exceptions, such as mitochondria, some ciliates and other organisms (there are a total of 15 different genetic code dictionaries), but we arent too concerned about those. Furthermore, there is some evidence that this code is still evolving, but again, we wont get into that.

TRANSCRIPTION A GENERAL VIEW

There are three main parts to transcription: initiation (containing a promoter region), elongation (from 5 to 3, with the 3 end being the growing end and requiring NTP energy) and termination. In eukaryotes, the completed transcript must be processed before it is functional (and well talk more about this later). Lets look at each part individually:

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The initiation phase of transcription involves what are called promoters. One of these promoters is called the TATA Box, which is a segment of DNA where the base pairs are TATAAAA. This is essential in the assembly of the initiation complex. Transcription factors also play a major role in initiation, as several of them must bind to the DNA before RNA polymerase II can do so. When RNA polymerase finally binds (along with more transcription factors) the initiation complex is complete, and the process of transcription can begin.

INITIATION

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ELONGATION

Elongation is also known as the the transcription bubble. First of all, RNA polymerase II has a helicase-like activity, in that it can unwind the DNA strand, revealing the template strand (the strand that will code for the mRNA strand). The other strand of DNA, referred to as the nontemplate strand, is identical to RNA (accept Thymine is replaced with Uracil). Again, RNA nucleotides are added to the growing 3 end, which is referred to as downstream. These nucleotides can be added as quickly as 40 a second, and multiple RNA polymerases are present. This makes multiple copies of the mRNA, and the number depends on the strength of the promoter (well talk more about this in chapter 18).

TERMINATION

We dont really get into the specifics of termination, as it is beyond the scope of this class. Suffice to say, specific termination is rare. Other processing signals intervene to terminate the transcription process. However, in bacteria, transcription of terminator sequence causes RNA polymerase to detach, ending the process.

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RNA POLYMERASE REVIEW

In bacteria there is one single RNA polymerase molecule. In eukaryotes there are 3 (none of which require a primer), as listed below: RNA Polymerase I: is used for pre-rRNA, a ribosome component. RNA Polymerase II: is used for pre-mRNA, or messenger RNA that is processed into mRNA and sent off for translation. RNA Polymerase III: is used for pre-tRNA, or transfer RNA, which is used in to build the polypeptide chain inside the ribosomes.

So, DNA codes for pre-mRNA, and pre-mRNA is processed into mRNA inside the nucleus. This involves adding a 5 cap to the code snippet (comprised of modified guanine nucleotidewhich is recognized by ribosomes as being translatable), intron removal (or the splicing of exons), and adding a 3 poly-A tail at AAUAA signal. This AAUAA signal cuts the pre-mRNA molecule and adds up to 250 AAA codons. This stabilizes the messages, as the longer the tail is the longer the mRNA molecule will survive. We wont talk anymore about the 5 cap or the 3 poly-A tail, but we will discuss intron removal:

RNA PROCESSING A GENERAL VIEW

INTRON REMOVAL

A pre-mRNA molecule is comprised of introns and exons. An intron is a non-coding sequence of bases, and an exon is a coding sequence that is retained in mRNA. Introns are removed by splicesomes, which are RNA protein complexes. The length of an intron sequence can be anywhere from 22 to 10,000, and there is no known function for them. The process itself is highly precise, as the intron is removed as a lariat or lasso-like segment and destroyed. The catalysis of intron removal involves snRNA, or small nuclear RNA and other proteins (such as ribozymes, discussed below). The catalytic activity comes from the RNA.

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RIBOZYMES

As mentioned above, ribozymes are catalytic RNA, first discovered by Tom Cech and Sid Altman. They have a potential for antiviral and anticancer research, and are significant towards evolution. They were discovered in self-splicing rRNa in tetrhymena, a small organism that gets way too much attention (elephants are much cooler!). Thats all.

EXONS

Exons are the coding segments of pre-mRNA that are retained in mature mRNA. Exons often code for functional domains of proteins. The open reading frame of a mature mRNA consists of the spliced together exons. However, exons also include UTRs, or untranslated regions of code, which are not included in the reading frame. Exons are sometimes shared among genes, and alternative splicing promotes evolutionary shuffling of exons, leading to new proteins (and introns probably help too, as sometimes splicing can go wrong and an intron is left in).

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SECONDARY STRUCTURE

The structure of eukaryotic mRNA is linear and circular, due to intramolecular hydrogen bonding, forming a secondary structure. On the other hand, prokaryotic mRNA has no processing, as translation begins before message is completed (theres no pre-mRNA).

TRANSLATION A GENERAL VIEW

Translation occurs in ribosomes, polypeptides and tRNA, which has amino acids attached to it. tRNA also has anti-codons, which consist of three base pairs that are complimentary to the mRNA strand. The start codon is AUG and there are 3 different stop codons (refer to the genetic dictionary). Well start by talking more about tRNA:

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This is considered an adapter molecule, and there are about 45 of them. As mentioned, they contain an anitcodon that is complimentary to the mRNA strand, and have a cloverleaf secondary structure (due to hydrogen bonds between some of the base pairs. Amino acids are attached to the 3 end. tRNA must be charged for correct translation to occur, and this is accomplished by the enzyme aminoacyl-tRNA Synthase. ATP helps attach the correct amino acid to the correct tRNA before it enters a ribosome.

tRNA

RIBOSOMES

Ribosomes consist of two subunits, the large and the small. The ribonucleoprotein complex consists of rRNA, ribozymes and the two subunits. There are 1000s of ribosomes per cell, and each ribosome has three sites for the tRNA, the E, P, and A (just think EPA for testing purposes). There is an orderly biochemical process for building polypeptides, and a short summation of it can be found below:

mRNA binds to the small subunit of the ribosome at the mRNA binding site (mRNA is read from 5 to 3 in the ribosome). An initiator tRNA comes along and binds to the start codon (AUG). The large subunit of the ribosome comes down and covers the initiator tRNA, positioning it in the middle P site. This creates the translation initiation complex. GTP is required for this step. Initiation occurs at the N-terminus of the polypeptide (the amino end). A tRNA comes along and enters the A site, or the aminoacyl-tRNA binding site.

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LSU ribozymes catalyzed peptide bond formation between the initiator amino acid and the amino acid in the A site. GTP moves the initiator tRNA to the E site, or the exit site, where it is removed from the ribosome. It also moves the tRNA from the A site to the P site. The process repeats as many times as necessary to build the correct polypeptide, which is referred to as elongation. Eventually a stop codon is reached, and the ribosome pauses. A release factor enters the ribosome and kicks out the now free polypeptide (this also requires GTP). This end of the polypeptide is referred to as the C-terminus. The subunits of the ribosome separate.

POLYRIBOSOME

A polyribosome, or a polysome, is a complex of many ribosomes. A mRNA molecule can be translated many times over. As the mRNA leaves one ribosome it enters another and is translated again, producing another polypeptide.

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PROTEIN PROCESSING

We have to remember that proteins are 3-dimensional structures, and have secondary and tertiary features. As a polypeptide is made many things can happen to it. Chaperonin, in some cases, comes along, scoops up the polypeptides, and guides the folding process (or can delay the folding process). There are many more post-translational modifications, such as sulfation (adding sulfate groups), lipoylation (adding lipids), amino acid modification (adding amino groups), and protease cleavage (for 2 or more polypeptides). You should also remember the quaternary structure, where several polypeptides interact with one another.

TARGETING OF POLYPEPTIDES

Ribosomes are located in two places: the cytoplasm and the rough ER (RER). If you recall, the RER is responsible for processing membrane and secreted proteins. Now, in some cases, ribosomes are directed to the RER by signal peptides, and then dock on the RER via a signal recognition particle (a protein). In these cases, the polypeptide is

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deposited, or secreted into the ER lumen (inside the ER). You can get a better picture of this by looking at the class slides (42).

MUTATION

A mutation is an alteration of the DNA sequence, as is raw material for evolution. A single base pair change is called a point mutation. A bit of vocabulary for this section: wildtype refers to a normal gene, while mutant refers to an individual with mutated genes, or new alleles. Sickle Cell disease is the most common genetic disease among black people, and occurs when an individual is homozygous for it. It is a single base pair mutation, and it completely fucks shit up. There are several different types of mutations, each discussed below: Silent: or synonymous mutation involves a single base pair change that has no effect on the amino acid sequence. Missense: is a mutation that involves a single base pair change that does alter the amino acid sequence. The sequence no longer matches the wildtype, and this could be harmful (or advantageous, in some cases). Nonsense: is a mutation that involves a single base pair change that creates a stop codon, prematurely ending the amino acid sequence. This mutation is very often harmful.

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Frameshift: is a mutation that involves the addition or subtraction of one or two base pairs. These alter the reading frame, and can cause either a missense or a nonsense mutation. Frameshift mutations are often very bad, as the entire reading frame is altered, resulting in a polypeptide that is nothing like the wildtype. Every amino acid could be wrong. 3bp Indel: or a 3 base pair insertion or deletion is a mutation that involves just thatthe insertion or deletion of 3 base pairs. This is no frameshift, not one amino acid is either mission or added. This is often not a problem for the protein.

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REGULATION OF GENE EXPRESSION

First of all, not all genes are expressed in a cell. Second of all, there are multiple ways to regulate genes or gene activity, including transcriptional, post-transcriptional, and post-translational methods. Weve already talked about a few ways gene expression is controlled, including feedback inhibition, which is a metabolic modulation of enzyme activity. Weve also talked about transcriptional regulation of gene expression (see chapter 17). The first part of this chapter looks at how bacterial operons regulate gene expression in bacteria.

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GENE REGULATION AN OVERVIEW

BACTERIAL OPERONS

First off, an operon is a cluster of genes that are tightly linked (continuous) and transcribed as a single mRNA. The actual details of this are beyond the scope of this class, but know that operons are regulated by a product of regulatory genes. A regulatory protein binds to the operator region of DNA near gene. Negative gene regulation involves a repressor binding to the DNA, inhibiting transcription. Positive regulation involves an activator molecule binding to DNA for transcription. There are two types of NEGATIVE REGULATION, discussed below:

LAC OPERON

As mentioned, the lac operon is a negative regulation technique that is normally turned OFF, meaning that a repressor molecule is bound to the DNA. This repressor stops transcription of mRNA, or stops the production of Beta-galactosidase enzymes, which breaks down lactose into glucose and galactose. However, when lactose is

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present inside the cell, it binds allosterically to the active receptor, changing its shape and making it inactive. This means that mRNA is then able to transcribe the mRNA, which makes beta-galactosidase, which then breaks down the lactose present in the cell.

TRP OPERON

This is similar to the lac operon, though involves tryptophan. When tryptophan accumulates inside the cell, excess molecules will bind to one of the enzymes that catalyze the formation of it. This binding will change the shape of the enzyme and stop production of tryptophan. This is a classic example of a negative feedback loop, or negative inhibition.

As expected, gene regulation in eukaryotic cells is much more complex, and is multi-level. Our main focus is one transcription initiation and processes involving RNA. Most gene regulation is positive control. Lets get to it.

EUKARYOTE GENE REGULATION

CHROMATIN

We all know what chromatin is, right? It is DNA that is tightly wrapped around histones. When DNA is in this configuration it cannot be transcribed as it is too tight for proteins to reach. This chromatin is said to be heterochromatin. Now, in order for DNA to be transcribed, some sort of histone modification needs to be done. This is where acetylation comes into play. You see, acetylation of histone tails promotes loose chromatin structures that permits transcription. This loose form of chromatin is called euchromatin.

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TRANSCRIPTION FACTORS

Weve already met TBP, or the TATA binding protein, which is an essential factor in DNA transcription. This is one of hundreds of transcriptional factors that promote gene expression. They bind to promoters and enhancers, such as steroid hormone receptors and Hox genes (control animal development). Some transcription factors recruit RNA polymerase, and others play a major role in cell differentiation, cell development, and the onset or development of cancer.

POST-TRANSCRIPTIONAL

So, after DNA has been transcribed we have a pre-mRNA molecule. Here, we can have all sorts of fun little events that control or alter gene expression, including alternative splicing of introns and exons (that could give rise to new proteins), alternative promoters, or mRNA editing (enzymatic base changes, insertions of base pairs, or deletions of base pairs). Or, you could have all elements together.

POST-TRANSLATIONAL

So, once mRNA is translated to a polypeptide, there are still ways to control the expression of genes, including protease cleavage, which is the cutting of a protein. Other chemical modifications include: phosphorylation, methylation, hydroxylation, glycosylation,

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farnesylation, and many others. Some allosteric interactions also play a role, such as those talked about above. Proteins also have a half-life, and by a process called ubiquitination a protein can be broken down into its component peptides/amino acids.

REGULATION BY NON-CODING RNA

This is currently a very hot topic in biology, as it is hugely important in development and evolution. We will be discussing two types of noncoding RNA, as seen below. This is micro-RNA, and it is mother-fucking single stranded. Strands of micro-RNA are about 17-24 nucleotides in length, and they target many mRNAs. They effectively interfere with translation by binding to mRNA through base pairing. They may also affect chromatin structure (that is, if it is acetylated).

miRNA

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siRNA

This is small interfering RNA, and is double stranded. It binds to mRNA and cleaves it. We are not too concerned with this, and it will not be on the test.

CANCER

The study of cancer is important for a variety of reasons, including medically, economically and socially. In general, cancer is an uncontrolled cell proliferation caused by their failure to under normal apoptosis, their reactivation of telomerase, their loss of contact inhibition, their reversion to a more embryonic phenotype (now thats fucked up) and their mutations in genes that control the cell cycle checkpoints. It is thought that most cancers are the result of error in a single progenitor cellor what I like to call it, RAMBO CELL. You see, gene regulation is a highly integrated activity in cells, and controls cell signaling, feedback loops, environment, and genetic background. In cancer cells, this integration is disturbed. There are two types of genes associated with cancer, as discussed below:

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First of all, a proto-oncogene is a normal cellular gene that is responsible for normal cell growth and division. If this cell mutates into an oncogene, it can cause cancer. Familiarize yourself with the slide illustrations, as they provide clear examples of this mutation. EXAMPLE: mutations in the ras proto-oncogene can lead to the production of a hyperactive Ras protein and increased cell division.

ONCOGENES & PROTO-ONCOGENES

First of all, tumor-suppressor genes do exactly what their name suggeststhey suppress tumors, or inhibit cell proliferation. Furthermore, tumor-suppressor proteins made from these genes repair damaged DNA, control cell adhesion, and inhibit the cell cycle in the cell-signaling pathway. However, they too can mutate, creating either an inactive gene product or a decreased amount of gene product. As you can guess, this can seriously fuck shit up. EXAMPLE: mutations in the p53 tumor-suppressor gene can lead to continued rounds of cell division and loss of apoptosis. Note: Multiple mutations are generally needed for full-fledged cancer: thus the incidence increases with age. At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several tumor-suppressor genes.

TUMOR-SUPPRESSOR GENES

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VIRUSES, A BRIEF SURVEY

VIRUSES: AN OVERVIEW
Viruses are nonliving genetic entities that can infect most forms of life. They consist of a protein coat and a nucleic acid core (some have a lipid bilayer). They can only reproduce inside cells. They likely coevolved win many forms of life. They use transduction, or the horizontal transfer of genes between hosts. They are highly mutable, and likely evolved from transposable genetic elements such as retrotransposons and retroviruses (which well discuss shortly).

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IMPORTANCE OF VIRUSES

Here are some reasons why viruses are important: They are useful experimental models for evolution and selfassembly. They are trandsductivethe viral mediated transfer of genes between organisms and sometimes across species. This is an important evolutionary force in moving genes, particularly in prokaryotes. Ecological: viruses are found in nearly every environment. Disease: studying viruses can help us better agriculture and human health.

Viruses have a nucleic acid core (either RNA or DNA), have a proteins sheath capsid (often icosahedral), and some even have a lipid envelope (which is very fragile and associated with RNA viruses such as influenza and other retroviruses). They range in size from 17 to 1000 nanometers and are best seen with an electron microscope. As mentioned, they only replicate in cells. They can also be crystallized for better study.

VIRUS COMPOSITION

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VIRAL GENOMES

Viruses rely on the host cells transcription and translation machinery to replicate themselves. As mentioned, they contain either RNA or DNA (which can be single or double stranded, though single stranded DNA is RARE). The genome of the virus encodes for viral proteins, such as those that make up the capsid or envelope. RNA viruses may encode for replicase or reverse transcriptase, and DNA viruses may encode for DNA polymerase. There may be as many as 100 genes within a viral genome.

GENERAL LIFE CYCLE

The general life cycle of a virus consists of entry to the cell, transcription and translation of the viral genome, replication of viral proteins, self assembly, and finally exiting the cell. Often times this will destroy the cell.

BACTERIOPHAGE

A bacteriophage or a phage is a virus that infects bacteria. There are thousands of known phages, and most of them are species specific, such as E. coli. Phages consist of a head, a tail, and tail fibers that act as anchors. The phage will inject its DNA/RNA into a host cell via its tail, which acts as a syringe. Bacteriophages have two distinct life cycles, the lytic and lysogenic. Lets briefly talk about each:

LYTIC CYCLE

In this cycle, the phage injects is viral genome into the host cell, the host cell then replicates viral proteins, the proteins self assemble, and the host cell lyses, liberating the replicated phages. Obviously, this kills the cell. This cycle is closely associated with the T series of bacteriophages (a specific order of phages).

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LYSOGENIC CYCLE

In this cycle, the phage injects its viral genome into the host cell and is incorporated into the bacterial chromosomes, becoming a prophage. Upon activation (such as stress or environmental factors) the viral genome becomes active, initiating the lytic cycle. Since the advent of genome sequencing, it has been found that many bacteria contain prophages. There is a chance of vertical transmission of viral genome to cell offspring. The viral genome will replicate during mitosis and both daughter cells will have the prophage. In order for thevirus to resume the lytic cycle, the viral genome must first exit the hosts chromosome. During this process, the viral genome may pick up one or more of the hosts genes, which can then be transduced to the next infected cell. This is a major means of genetic exchange among bacteria and Archaea in natural populations.

ANIMAL VIRUSES

Animal viruses can contain either RNA or DNA, and some have lipid envelopes (most RNA viruses do, fewer DNA). The lipid envelope is made in the Golgi (and can go through the ER), where glycoproteins are added. Often times, assembly is NOT lethal to the host cell. There are numerous life cycles for animal viruses, and we wont be discussing any of them, so stick that in your ass and smoke it.

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This is an example of a retrovirus, which is related to retrotransposons. It contains RNA that encodes for reverse transcriptase, which is able to make complimentary DNA from an RNA molecule. It is among the simplest of RNA viruses. It leads to AIDS, or acquired immunodeficiency syndrome, which is the depletion of T4 helper cells in the immune system. It is an STD and there is no vaccine or permanent cure. It originated in chimpanzees and is thought to be transmitted to humans via the bush-meat trade (not hot sex with apes, as your sick mind would have you believe). Hiv Structure: HIV consists of a lipid bilayer with and internal capsid. Inside the capsid are 2 RNA molecules and 2 reverse transcriptase molecules. All of the proteins that make up this structure are encoded by the HIV genome contained in the RNA. The capsid proteins are gag and pol, while the envelope protein is env (these are just abbreviations for the actual names of the genes that control protein production). Hiv Life Cycle: Once the virus has fused with a host cell, the capsid within the lipid bilayer will dissolve, allowing the viral RNA and reverse transcriptase to roam free within the cytoplasm. Here, reverse transcriptase will do its job and make DNA from its viral RNA. This DNA will then be incorporated into the hosts chromosomal DNA, a structure that is referred to as a provirus. Here, the provirus will be transcribed by mRNA and translated by ribosomes to make more capsid proteins and viral RNA for the next generation. The new generation will self assemble and leave the cell (intact), going off to infect more cells.

HIV

VIRUS EVOLUTION

There is much speculation on this topic as viruses do not fit the definition of living organisms. Since viruses can reproduce only within cell, they probably evolved as bits of cellular nucleic acid. Candidates for the source of viral genomes are plasmids, circular DNA in bacteria

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and yeasts, and transposons, which are small mobile DNA segments. Plasmids, transposons and viruses are all mobile genetic elements. NOTE: some think that life may have evolved from viruses. As well, DNA may have evolved from viral RNA.

VIROIDS

Well, viroids are infectious, naked RNA molecules that are circular and single-stranded (meaning they are resistant to nucleases) that are about 250 to 400 nucleotides long. They are common in plants and transported via the phloem. They DO NOT encode proteins. They replicate in the nucleus via dsRNA intermediates (not important). They may cause disease by interfering with intron removal, as they appear to be derived from spliceosome RNA.

PRIONS

These are highly controversial for one reason: they are infectious protein particles. Prions can cause mad cow disease, Kuru, and Creutzfeldt disease. Essentially, a prion is a large, misfolded protein. Contact between misfolded and normal protein causes normal protein to misfold. The example in the notes shows a normal protein contain alpha helices. When contact by a prion, the normal protein misfolds into beta pleaded sheets. Prions are also resistant to digestion (protease digestion). Normal prion proteins have no known function,

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though research suggests a role in long-term memory (since they are located in the brain), blood cell formation and cell adhesion.

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BIOTECHNOLOGY
BIOTECHNOLOGY
Biotechnology is characterized by the ability to isolate and manipulate genes in vitro, to determine nucleotide sequence of genes or a genome, to improve crop plants and food animals, to improve human health, and to lead to a greater and deeper understanding of evolution. It was in the 1960s that discoveries were made that lead to the ability to manipulate DNA in a test tube. Gene cloning was applied to the genetics of bacterial plasmids, the restriction of endonucleases, and DNA ligases. Ultimately, this led to genetic engineering, or gene and genome sequencing. This has applications in personalized genetics and gene replacement therapy, and has unprecedented evolutionary insights.

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RECOMBINANT DNA

DNA CLONING

A clone is descended from a single individual (DNA from a plant or animal cell). DNA cloning results in billions of exact copies for biochemical analysis, including sequencing. It can be done by cloning DNA in bacterium (or yeasts) or via PCR in a machine (well discuss this later).

RESTRICTION ENZYMES

These are enzymes that cut DNA into many restriction fragments, and are thought to be of bacterial origin. Restriction endocucleases break phosphodiester bonds and target specific nucleotide sequences, called restriction sites (often palindromes). The ends of these restriction fragments are said to be sticky, as they have a single strand overhang. They can also be blunt and non-sticky. Restriction ends are made by the same enzyme, regardless of source of DNA. Complementary sticky ends can be joined by DNA ligase (which reseals phosphodiester bonds), resulting in recombinant DNA molecules. Essentially, a strand of DNA is cut into pieces, and those

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pieces are rearranged and reassembled into a new code. The restriction ends allow this to happen by providing overhangs.

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CLONING VECTOR

A cloning vector has several properties, including origin of replication, suitable restriction sites, selectable markers, and other engineered enhancements. Cloning vectors can be bacterial plasmids, viruses, cosmids, or artificial chromosomes. The major purpose of a cloning vector is to replicate DNA inserted into it. In order to clone into a cloning vector, several steps must be followed: Digest DNA of interest with restriction enzyme. This cuts apart the DNA. Digest vector with same enzyme. This cuts the vector apart. Mix the vector and the DNA together and mix. Transform competent bacterial cells. Grow bacteria in antibiotics. Screen library of cells for cell(s) with gene of interest. A library is a collection of clones (plasmids, viruses, etc.). The genomic library consists of the entire DNA of an organism. cDNA, or copy DNA is derived from mRNA. Because of this, cDNA is missing all the introns that were originally cut out of the pre-mRNA. Study cloned insert.

PCR stands for polymerase chain reaction. This is a non-biological way to amplify DNA (no living cell is required for this). This was a revolution in molecular biology techniques. PCR uses a machine called a thermocycler and an enzyme called taq polymerase, which is thermostable. The reaction mixture consists of: template DNA, dNTPs, Mg++, DNA polymerase, a buffer, and primers. Essentially, DNA is added to this machine and heated up, causing them to become denaturated. The primers then come along and bind to the strands of DNA. Finally, DNA polymerase comes along and extends the primer to complete a molecule of DNA. This process is exponential. You start with one and end with two, then you get 4, 16, 32, 64, and so on. Here are some uses of PCR: Research: numerous routine applications. Forensics: amplification of DNA from a tiny sample. Anthropology: recovery of genes from human remains. Evolution: to study the ancient DNA of organisms, such as the mammoths.

PCR

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DNA TECHNOLOGY USES

There are several uses for DNA technology. To study sequence, expression and function of a specific gene, regulatory and non-regulatory regions. To sequence complete genomes. DNA cloning allows researchers to compare genes and alleles between individuals, to locate gene expression in tissues/organs and in the developmental stage, and to determine the role of a gene in an organism.

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Is the separation of nucleic acids and proteins in an electrical field depending on their mass and/or charge. And thats it for this fucking study guide. Theres one more to be had, so stick around for that piece of shit.

ELECTROPHORESIS

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GENOMES AND GENOME EVOLUTION

GENOMES

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DESCENT WITH MODIFICATION

THE HISTORICAL CONTEXT FOR EVOLUTIONARY THEORY
Explain the mechanism for evolutionary change proposed by Charles Darwin in On the Origin of Species. During Darwins voyage he studied many adaptations, or characteristics of organisms that enhance their survival and reproduction in specific environments. He proposed that these adaptations arise from a mechanism called natural selection, or a process in which individuals with certain inherited traits leave more offspring than individuals with other traits. Define Evolution and Adaptation. a. Evolution: a change in the genetic composition of a population from generation to generation. Or, simply, descent with modification.

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b. Adaptation: characteristics of organisms that enhance their survival and reproduction in specific environments. Describe the theories of catastrophism, gradualism and uniformitarianism. a. Catastrophism: states that events in the past occurred suddenly and were caused by mechanisms different from those operating in the present. A meteor strike is a catastrophic mechanism, such as the one that killed most dinosaurs.

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b. Gradualism: states that profound changes take place through cumulative effect of slow but continuous processes. Earths geologic features are explained via gradualism, as they are still occurring today. c. Uniformitarianism: states that the mechanisms of change are constant over time. Natural selection is one such mechanism, though is associated with evolution. Explain the mechanism for evolutionary change proposed by Jean Baptiste Lamarck. Explain why modern biology has rejected Lamarcks theories. Lamarck proposed that parts of the body that are used the most get bigger over time, and those parts that are not used deteriorate. Another principle, that of inheritance of acquired characteristics stated that an organism could pass these modifications to its offspring. Modern genetics refutes this mechanism as there is no way to pass on acquired characteristics, or even develop them through use and disuse.

THE DARWINIAN REVOLUTION

Describe how Darwins observations on the voyage of the HMS Beagle led him to formulate and support his theory of evolution. Darwin observed many species on his trip to the Galapagos Islands, but it was the birds he collected that led him to natural selection. He noted many adaptations in these birdsadaptations that were not found anywhere else in the worldand began to perceive that new species could arise from an ancestral form by the gradual accumulation of adaptations to different environments. In particular, it was the finches and their varying beaks that led him to this discovery. Explain what Darwin meant by descent with modification. Darwin thought that there was unity in lifethat all organisms descended from an ancestor that lived in the distant past. These descendants lived in various habitats over millions of years, and had accumulated diverse modifications, or adaptations, that fit them to specific ways of life. The mechanism by which this works is natural selection.

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Explain what evidence convinced Darwin that species change over time. I believe that the species he discovered on the Galapagos Islands were what led him to this conviction. Particularly the birdswhich he hypothesized had been colonized by organisms that had strayed from South America and then diversified, giving rise to new species on various islands.

Describe observations and two inferences that led Darwin to propose natural selection as a mechanism for evolutionary change. Darwin discussed selective breeding of domesticated plants and animals. Humans have modified other species (think dogs) over many generations by selective breedinga process called artificial selection. There are a total of four observations and two inferences made by Darwin, as listed below: a. Observation 1: Members of a population often vary greatly in their traits. b. Observation 2: Traits are inherited from parents to offspring. c. Observation 3: All species are capable of producing more offspring than their environment can support. d. Observation 4: Owing to lack of food or other resources, many of these offspring do not survive.

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e. Inference 1: Individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than other individuals. f. Inference 2: This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations. Explain how an essay by the Rev. Thomas Malthus influenced Charles Darwin. Darwin realized that the capacity to over reproduce was characteristic of all species after reading this essay. The essay was about human sufferingdisease, famine and warand how it was an inescapable consequence of the human populations potential to increase faster than food supplies and other resources. Explain why an individual organism cannot evolve. Natural selection occurs through interactions between individual organisms and their environment. However, individuals do not evolveit is the population that evolves over time. This has to do with heritable traits being passed on to offspring, as discussed below. Explain why natural selection can act only on heritable traits. There is little evidence that acquired traitsor those traits that an individual acquires over their lifetimecan be inherited by their offspring. Rather, it is the heritable traits that are either amplified or diminished via natural selectionor those traits that can be passed on to offspring. This has everything to do with the mountains of evidence that support natural selection and evolution. Describe the experiments that supported Endlers hypothesis that differences in color patterns in male guppies are due to selective pressure based on predation. So, these guppies use exotic color patterns to attract females for matting purposes. However, their bright colors also attract predators. So, Endler went out and studied these fish. He found that in ponds where predation was high, guppies with drab colors were more frequent. He found that in ponds where predation was low, bright colors were more frequent. Therefore, he hypothesized that intense predation caused natural selection in male guppies, favoring either drab or bright colors depending on the intensity of predation.

THE EVIDENCE OF EVOLUTION

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Describe how natural selection favors the evolution of drugresistant pathogens. So, when we take drugs to kill a virus, there may be a few drugresistant viruses floating around. What happens is that these drugresistant one are able to reproducein fact, they are the only ones able to reproducethus lowering the effect (or completely negating the effect) of the drug in question. HIV is a good example of this, as the viruses that survive the early doses reproduce, passing on the alleles that enable them to resist the drug. In this way, the frequency of resistant viruses increases rapidly in the population. Explain how the fossil record may be used to test our current understanding of evolutionary patterns. So, the fossil record is a great tool into understanding evolutionary changes that have occurred over time in various groups of organisms. This record can be used to test hypotheses arising from other kinds of evidence (such as the hypothesis that early land vertebrates evolved from a group of fishes and that early amphibians evolved from descendants of early land vertebrates), by using radioactive dating techniques to determine the age of the fossils. Based on these dates, we can tell which species came first. Explain how the existence of homologous and vestigial structures can be explained by Darwins theory of natural selection. First of all, homology is similarity in characteristics among related species resulting from common ancestry. Variations on a structural

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themesuch as arms, forelegs, flippers and wings of different animalsthat were present in a common ancestor are homologous structures. Furthermore, vestigial structures are remnants of features that served important functions in the organisms ancestors. When we compare the stages of development in different animal species we can see even more anatomical homologies, which even further support the idea that these differences arose via natural selection. Then we come to convergent evolution, which is the independent evolution of similar features in different lineages.

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Explain how evidence from biogeography supports the theory of evolution by natural selection. Islands generally have species of plants and animals that are endemic, which means they are found nowhere else in the world. However, most of the island species are closely related to mainland species, suggesting that islands are colonized by species from the nearest mainland.

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Explain the problem with the statement that Darwinism is just a theory. Distinguish between the scientific and colloquial use of the word theory. The colloquial use of the word theory is more closely associated with a hypothesis. A scientific theory is more comprehensive, and accounts for many observations and explains and integrates a wide variety of phenomenon.

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THE EVOLUTION OF POPULATIONS

GENETIC VARIATION, THE SUBSTRATE FOR NATURAL SELECTION
Explain the statement It is the population, not the individual that evolves. This can be seen in the finches that Darwin studied. A finchs beak does not change over the course of its lifethat is, it does not get bigger or smaller depending on its environmentrather, it is the population over time that changes. Explain how Mendels particulate hypothesis of inheritance provided necessary support for Darwins theory of evolution by natural selection. Mendel proposed a particulate model of inheritance, which stated that organisms transmit discrete heritable unites (now called genes) to their offspring. Darwin did not know about genes, but it was this paper that set the stage for understanding genetic differences on which evolution is based. Explain how quantitative and discrete characters contribute to variation within a population. First of all, discrete characters are those that are mainly determined by a single gene locus wither different alleles that produced distinct phenotypes (such as the color of a flower). Quantitative characters usually result from the influence of two or more genes on a single phenotypic character. These characters can be measured at both the whole-gene level and molecular level. Distinguish between average heterozygosity and nucleotide variability. Explain why average heterozygosity tends to be greater than nucleotide variability. Well, average heterozygosity is the average percent of loci that are heterozygous, and is often estimated by surveying the protein products of genes using gel electrophoresis. Nucleotide variability is measured by comparing the DNA sequence of two individuals in a population and then averaging the data from many such comparisons.

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Define a cline. A cline is a type of geographic variationwhich accounts for the differences in genetic composition of separate populations. A cline is a graded change in character along a geographic axisthat is, one population of fish up north (in cold water) will be different than a population of the same fish down south (in warm water).

A bloodtype cline of Europe.

MUTATION AND SEXUAL RECOMBINATION

Explain why the majority of point mutations (in total DNA) are harmless. First of all, a point mutation is the change of as little as one base in a gene, and they are relatively harmless (most of the time). This is because most of the DNA in eukaryotic genomes does NOT code for protein products. Also, there is redundancy in the genetic code, and even a point mutation in a gene that encodes a protein will have no effect on the proteins function if the amino acid composition is not changed. Moreover, even if there is a change in an amino acid, this may not affect the proteins shape and function. Explain why mutation has little quantitative effect on allele frequencies in a large population.

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This is because it is sexual reproduction that produces most of the genetic variation in a population from the unique combination of alleles that each individual receives. There are three mechanisms for this, crossing over, independent assortment of chromosomes, and fertilization. Even though an individuals genome is the accumulation of past mutations, it is these three mechanisms that affect allele frequency in a large population. Also, mutation rates tend to be low in plants and animals, averaging about one mutation in every 100,000 genes per generation, and they are often even lower in prokaryotes. Describe the significance of transposons in the generation of genetic variability. Transposable elements are an important source of variation. Transposons are mobile segments of DNA usually associated with viruses. It is thought that viruses evolved from transposons. The activity of these transposons results in genetic variability (theres not much in the chapter on this, so do you best!). Note: horizontal gene transfer is a process that works via transposons. This would inevitably mix genetic codes, producing greater variability. Explain how sexual recombination generates genetic variability. As mentioned above, it is crossing over, independent assortment of chromosomes, and fertilization that generates genetic variability in respects to sexual recombination. During meiosis, homologous chromosomes, one inherited from each parent, trade some of their alleles by crossing over. These homologous chromosomes and the alleles they carry are then distributed at random into gametes. Then, because myriad possible mating combinations exist in a population, fertilization brings together gametes of individuals that are likely to have different genetic backgrounds.

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THE HARDY-WEINBERG PRINCIPLE

Define the terms population, species, and gene pool. a. Population: a group of individuals of the same species that live in the same area and interbreed, producing fertile offspring. b. Species: a population or group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, but do not produce viable, fertile offspring with members of other such groups. c. Gene Pool: all of the alleles for all the loci in a all individuals of a population. If only one allele exists for a particular locus in a population, that allele is said to be fixed and all individuals are homozygous. If there are two or more, then individuals can either be heterozygous or homozygous. Explain why meiosis and random fertilization alone will not alter the frequency of alleles or genotypes in a population. Well, you also need natural selection and evolution for the frequency to change. This is known as the Hardy-Weinberg principle, as is described below. List the five conditions that must be met for a population to remain in Hardy-Weinberg equilibrium. First of all, the Hardy-Weinberg principle states that frequencies of alleles and genotypes in a population will remain constant from generation to generation, provided that only Mendelian segregation and recombination of alleles are at work. Such a gene pool is said to be in Hardy-Weinberg equilibrium. There are five conditions that must be met for this to occur, as listed below: 1. No mutations. As weve already discussed, mutations can modify the gene pool by altering, deleting, or duplicating entire genes. 2. Random mating. If everyone mated with their family, random mixing of gametes would not occur. 3. No natural selection. 4. Extremely large population size. 5. No gene flow. Write the Hardy-Weinberg equation. Use the equation to calculate allele frequencies when the frequency of homozygous recessive individuals in a population is 25%. Below is the equation to use when calculating allele frequencies (the Hardy-Weinberg equation): 2 + 2 + 2 = 1

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Where p2 is the expected frequency of homozygous dominant, 2pq is the expected frequency of heterozygous, and q2 is the expected frequency of homozygous recessive. In order to calculate when homozygous recessive is at 25%, we need to do a bit of math! Since we know what q2 is, we now need to know what p is. = 1 Now that we have an equation for p we can plug in the numbers and get the answer. First we calculate what q is from q2. 2 = 0.25 = 0.25 = 0.5 = 1 0.5 = 0.5 2 = 2 0.5 0.5 = 0.5

NATURAL SELECTION, GENETIC DRIFT AND GENE FLOW

Explain the following statement: Only natural selection leads to the adaptation of organisms to their environment. This is because selection results in alleles being passed to the next generation in proportions different from their proportions in the present generation. Also, those with traits that are better suited to their environment tend to produce more offspring that those with traits that are less well suited. Explain the role of population size in genetic drift. The smaller the size the more likely it is that chance alone will cause a deviation from the predicted results. Genetic drift is the process by which allele frequencies fluctuate unpredictably from one generation to the next, and when you have a small population the effects are amplified.

Genetic Drift (Combined Allele Frequency Data)

Allele Frequency (p) 1 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Generations (t) Allele 1 Allele 2 Allele 3 Allele 4 Allele 5 Allele 6

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Distinguish between the bottleneck effect and the founder effect. Well, the founder effect is when few individuals become isolated from a larger population, then establish a new population whose gene pool differs from the source population. The bottleneck effect occurs when there is a sudden change in the environment, such as a fire or flood that drastically reduces the size of a population. This causes certain alleles to either be overrepresented or underrepresented, and can have substantial effects on the gene pool until the population becomes large enough that chance events have less effect.

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Describe how gene flow can act to reduce genetic differences between adjacent populations. Well, gene flow is the transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes. An example would be insects carrying pollen from one population of plants to another population. Because alleles are exchanged among populations, gene flow tends to reduce the genetic differences between populations. If it is extensive enough, gene flow can result in neighboring populations combining into a single population. Define relative fitness. This is the contribution an individual makes to the gene pool of the next generations, relative to the contributions of other individuals. Distinguish among directional, disruptive, and stabilizing selection. Give an example of each mode of selection. a. Directional Selection: this occurs when conditions favor individuals exhibiting one extreme of a phenotypic range, thereby shifting the frequency curve for the phenotypic character in one direction or another. Example: black bears in Europe became bigger during each frigid glacial period, and then shrunk during the warmer inter-glacial periods. b. Disruptive Selection: this occurs when conditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes. Example: the blackbellied seedcracker finches in Cameroon. They either have very large beaks (for hard seeds) or very small seeds (for soft seeds), and not many in-between. c. Stabalizing Selection: occurs when conditions favor the intermediate phenotype and acts against either extreme. Example: human birth weight. Babies that are either too small or too large suffer higher rates of mortality.

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Explain how diploidy can protect a rare recessive allele from elimination by natural selection. A considerable amount of genetic variations is hidden from selection in the form of recessive alleles. These alleles can persist by propagation in heterozygous individuals, and is exposed to natural selection only when both parents carry the same recessive allele and two copies end up in the same zygote (this happens rarely). Describe how heterozygote advantage and frequency dependent selection promote balanced polymorphism. Balanced polymorphism or balanced selection occurs when natural selection maintains two or more forms in a population. Heterozygote advantage occurs if individuals who are heterozygous at a particular locus have greater fitness than do both kinds of homozygotes. In frequency-dependent selection, the fitness of a phenotype declines if it becomes too common in the population. Define neutral variations. Explain why natural selection does not act on these alleles. In humans, many of the nucleotide differences in noncoding sequences appear to confer no selective advantage or disadvantage and therefore are considered neutral variation. Natural selection does not act on these alleles because they have little to no effect on reproductive success. List and explain at least four reasons why natural selection cannot produce perfect organisms. 1. Selection can act only on existing variations. Natural selection favors only the fittest phenotypes among those currently in the population, which may not be the ideal traits. 2. Evolution is limited by historical constraints. Each species has a legacy of descent with modification from ancestral forms. It does not scrap the ancestral anatomy and build from scratch. 3. Adaptations are often compromises. Since organisms do many things, evolution must make compromises. For instance, a seal spends a lot of time on land. It could move around better to escape predators if it had legs, but then it wouldnt be able to swim as well. 4. Chance, natural selection, and the environment interact. You get the point.

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THE ORIGIN OF SPECIES

WHAT IS A SPECIES?
Define Ernst Mayrs biological species concept. This is the primary definition of species used in the textbook, and states: a species is a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspringbut do not produce viable, fertile offspring with members of other such groups. Reproductive compatibility unites members of a biological species. Distinguish between prezygotic and postzygotic reproductive barriers. To begin, both are forms of reproductive isolationthe existence of biological factors that impede members of two species from producing viable, fertile offspring. Prezygotic barriers block fertilization from occurring. This is accomplished in one of three ways: by impeding members of different species from attempting to mate, by preventing an attempted mating from being completed successfully, or by hindering fertilization if mating is completed successfully. Postzygoic barriers contribute to reproductive isolation after fertilization has occurred. Developmental errors may reduce survival among hybrid embryos, or problems after birth may cause hybrids to be infertile or may decrease their chance of surviving long enough to reproduce. Describe several prezygotic reproductive barriers and give an example of each. There are five such examples listed in the book, so here you go: 1. Habitat Isolation: two species occupy different habitats within the same area may not encounter each other. Example: a mountain may be in the way. 2. Temporal Isolation: species that breed during the different times of the day, different seasons, or different years cannot mix their gametes.

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3. Behavioral Isolation: courtship rituals that attract mates and other behaviors unique to a species are effect reproductive barriers, even between closely related species. 4. Mechanical Isolation: mating is attempted, but morphological differences prevent its successful completion. 5. Gametic Isolation: sperm of one species may not be able to fertilize the eggs of another species.

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Explain a possible cause for hybrid breakdown. First of all, hybrid breakdown is a postzygotic reproductive barrier in which some first generation hybrids are viable and fertile, but when they mate with one another or with either parent species, offspring of the next generation are feeble or sterile. One possible cause could be the amount of recessive alleles present in the next generation. Explain how hybrid breakdown maintains separate species even if fertilization occurs. Youre on your own for this one. It may have something to do with the next generation of offspring being feeble or sterile, but not a lot is said in the book about this. Describe some limitations of the biological species concept. (1)There is no way to evaluate the reproductive isolation of fossils. (2)The concept does NOT apply to organisms that reproduce asexually. (3)Gene flow occurs between many pairs of species that are morphologically and ecologically distinct, despite the definition claiming that a species is designated by the absence of gene flow. Define and distinguish among the following: ecological species concept, phylogenetic species concept, and morphological species concept. These are alternate definitions for what a species is (and, of course, there are problems with all of them). Okay, lets get to it! a. Morphological Species Concept: this characterizes a species by body shape and other structural features. b. Ecological Species Concept: this views a species in terms of its ecological niches, the sum of how members of the species interact with the nonliving parts of the environment. For example, two species of frogs differ in the foods they eat or the climate they can tolerate. c. Phylogenetic Species Concept: this defines a species as the smallest group of individuals that share a common ancestor, forming one branch on the tree of life. The phylogenetic history of a species is traced by comparing its characteristics, such as morphology and molecular sequences, with those of other organisms.

MODES OF SPECIATION

Distinguish between allopatric and sympatric speciation. In allopatric speciation, gene flow is interrupted when a population is divided into geographically isolated subpopulations. For example, a mountain range or lake divides a population. In contrast, sympatric

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speciation occurs in populations that live in the same geographic area, and gene flow is reduced by such factors as polyploidy, habitat differentiation, and sexual selection. Sympatric speciation is much less common than allopatric speciation.

Define allopatric speciation. Describe the mechanisms that may lead to genetic divergence of isolated gene pools. As mentioned above, geographic isolation causes an interruption in gene flow. Once the population has become isolated, mutations, natural selection and genetic drift alter allele frequency. There are numerous examples in the book of this happening, including the monkey flower Mimulus guttatus, which evolved to be more copper tolerant in populations near copper mines. Explain how reproductive barriers evolve. Describe an example of the evolution of a prezygotic barrier and the evolution of a postzygotic barrier. Reproductive barriers evolve in many diverse ways. The bottleneck effect, the founder effect, polyploidy (defined below) and allopatric/sympatric speciation all contribute to the evolution of reproductive barriers. A prezygotic barrier may evolve from any of the isolating factors described above (habitat, temporal, behavior, etc). A post zygotic barrier may evolve from reduced hybrid viability, reduced hybrid fertility or hybrid breakdown.

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Define sympatric speciation and explain how polyploidy can cause reproductive isolation. First of all, polyploidy is a condition in which a species may originate from an accident during cell division, resulting in extra sets of chromosomes. There are two types of polyploidy (discussed below), and both are more common in plants.

Distinguish between autopolyploid and an allopolyploid speciation and describe examples of each. a. Autopolyploid: is an individual that has more than two chromosome sets that are derived from a single species. This results from a failure in cell division (going from diploid to tetraploid). This causes the tetraploid to be reproductively isolated from the diploid (they can only produce viable, fertile offspring with other tetraploidsor triploids, though with reduced fertility).

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b. Allopolyploid: is when two different species interbreed and

produce a hybrid offspring. Most hybrid species are sterile because the set of chromosomes from one species cannot pair during meiosis with the set of chromosomes from the other species. However, in subsequent generations, various mechanisms can change a sterile hybrid into a fertile polyploidy, called an allopolyploid. Allopolyploids are fertile only when mating with each otherthey cannot breed with either parent species.

Explain how habitat differentiation has led to sympatric speciation in North American maggot flies. This type of sympatric speciation occurs when genetic factors enable a subpopulation to exploit a habitat or resource not used by the parent population. The N.A. maggot flys original habitat was the native hawthorn tree, but about 200 years ago, some populations colonized apple trees that had been introduced by European settlers. As apples mature more quickly than hawthorn fruit, natural selection has favored apple-feeding flies with rapid development. These apple-feeding populations now show temporal isolation from the hawthorn-feeding, providing a prezygotic restriction to gene flow between the two populations.

HYBRID ZONES

Define the term hybrid zone. Describe the three outcomes for hybrid zones over time. A hybrid zone is a region in which members of different species meet and mate, producing at least some offspring of mixed ancestry. This can occur when allopatric populations come back into contact with one another. There are three outcomes for hybrid zones over time, listed below: a. Reinforcement: or the strengthening of reproductive barriers. This is due to the hybrid species being less fit and therefore natural selection strengthens prezygotic barriers to reproduction.

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b. Fusion: or the weakening of reproductive barriers. This occurs when two species contact one another in a hybrid zone, but the barriers to reproduction are not strong. This allows so much gene flow to occur that reproductive barriers weaken further and the gene pools of the two species become increasingly alike. This can cause two hybridizing species to fuse into a single species. c. Stability: or the continued formation of hybrid individuals. Nothing dramatic happens, and the world is at peace.

Describe examples that illustrate rapid and gradual speciation events. In a punctuated, or rapid, pattern, new species change most as they branch from a parent species and then change little for the rest of their existence. The wild sunflower is an example of this. In gradual speciation, other species diverge from one another much more gradually over time. You are an example of this. Explain how a small number of genetic changes may lead to speciation in plants and animals. The example in the book goes back to the monkey flower. There are two closely related species of this flower and the reproductive barrier particularly the barrier of pollinator choicebetween them is influenced by a relatively small number of genes. This barrier is affected by at least two loci in the flower which influences flower color, thus attracting different pollinators.

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THE HISTORY OF LIFE ON EARTH

THE ORIGIN OF LIFE
Describe evidence that suggests that RNA was the first genetic material. Explain the significance of the discovery of ribozymes. RNA is thought to be the first genetic material due to its ability to carry out enzyme-like catalytic functions, called ribozymes. These ribozymes are capable of self-replication (thanks to natural selection) due to the fact that single-stranded RNA molecules are more stable and replicate faster with fewer errors than other sequences. This means that an RNA molecule will leave more descendant molecules, provided it exists in the right environment.

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Describe how natural selection may have worked in an early RNA world. See the above question. As an elaboration, in certain environments, RNA molecules will assume a variety of specific three-dimensional shapes. Now, due to replication errors, the descendants of an RNA molecule are not always exact. These errors can sometimes cause the descendant RNA molecule to assume a different, more stable shape, making that molecule more adept at self-replication than the ancestral sequence.

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Describe how natural selection may have favored the proliferation of stable protobionts with self-replicating, catalytic RNA. These protobionts with catalytic RNA in them would be different from those that carried RNA without such capabilitiesmainly that they could exploit their environment and resources better. Now, if the protobiont could grow, split, and pass its catalytic RNA molecules to its daughters, those daughters could also exploit their resources better. This would cause the population of protobionts with catalytic RNA to increase.

MAJOR EVENTS IN THE HISTORY OF LIFE ON EARTH

Explain why the fossil record provides an incomplete chronicle of evolutionary change. Many of Earths organisms probably did not die in the right place at the right time to be preserved as fossils. Of those fossils formed, many were destroyed by later geologic processes, and only a fraction of the others have been discovered. As a result, the known fossil record is biased in favor of species that existed for a long time, were abundant and widespread in certain kinds of environments, and had hard shells, skeletons, or other parts that facilitated their fossilization. Explain how radiometric dating can be used to determine the absolute age of rock strata. Explain how magnetism can be used to date rock strata. Radiometric dating is based on the decay of radioactive isotopes. Radioactive isotopes decay to daughter isotopes at a constant rate, expressed by the half-life, or the time required for 50% of the parent isotope to decay. Each radioactive isotope has a characteristic halflifeone that is NOT affected by temperature, pressure, or other such environmental variables. Carbon-14/Carbon-12 ratio is used to

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determine the age of fossils up to about 75,000 years old. Dating the rocks around the fossils works for those that are older than 75,000 years old (most organisms do not use radioisotopes that have long half-lives, such as uranium-238, to build their bones or shells). Now, the magnetism of rocks can also provide dating information. During the formation of rocks, ion particles align themselves with Earths magnetic field. When the rock hardens, the ions are frozen in time. We know that Earths magnetic field has reversed repeatedly in the past, so to the reversals in one location can be matched with corresponding patters elsewhere.

Describe the major events in Earth's history from its origin until 2 billion years ago. In particular, note when Earth first formed, when life first evolved, and what forms of life existed in each eon. Archaean Eon 4.6 billion years ago: Earth forms. 3.5 billion years ago: oldest fossils of prokaryotic cells appear. Proterozoic Eon 2.1 billion years ago: oldest fossils of eukaryotic cells appear. 635 million years ago: diverse algae and soft-bodied invertebrate animals appear. Phanerozoic Eon (we live in this eon)

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Consists of the Paleozoic, Mesozoic and Cenozoic eras. Started 542 million years ago. Encompasses multicellular eukaryotic life. 251 million years ago: dinosaurs evolve. 65.5 million years ago: major radiation of mammals, birds and pollinating insects. 1.8 million years ago: humans appear. Study the images from the textbook and notes.

Name the reactions that have produced O 2 on Earth. Describe the accumulation of atmospheric O 2 over time and the effects of this accumulation on living things. Most atmospheric oxygen is of biological origin, produced during the water-splitting step of photosynthesis. Oxygen probably dissolved in the surrounding water when it was first produced. When it reached a high enough level it began to react with dissolved iron, precipitating iron oxide, which accumulated as sediment. Once all the dissolved iron precipitated, additional oxygen dissolved in the water until the seas and lakes became saturated. After this, oxygen began to gas out of the water and enter the atmosphere. O 2 increased gradually from about 2.7 to 2.2 billion years ago, but then shot up relatively rapidly to more than 10% of its present level. This is when most prokaryotic group probably died, and when cellular respiration evolved. Explain the endosymbiotic theory for the evolution of the eukaryotic cell. Describe the evidence that supports this theory. Endosymbiosis is a model which posits that mitochondria and plastids (chloroplasts and related organelles) were formerly small prokaryotes that began living within larger cells. The term endosymbiont refers to a cell that lives within another cell, call the host cell. Evidence: the inner membranes of both organelles (mitochondria and plastids) have enzymes and transport systems that are homologous to those found in the plasma membrane of living prokaryotes. They replicate by a splitting process that is similar to that of certain prokaryotes. They have a single, circular DNA molecule that, like the chromosomes of bacteria, is not associated with histones or large amounts of other proteins. They have ribosomes (which are more similar to prokaryotic ribosomesin terms of size, nucleotide sequence, and sensitivity to certain antibiotics) and other cellular machinery needed to transcribe and translate their DNA into proteins.

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Endosymbiotic Theory

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State the evidence that suggests that the common ancestor of multicellular eukaryotes lived 1.5 billion years ago. It is a rough agreement with the fossil record. The oldest known fossils of multicellular eukaryotes are of relatively small algae that lived about 1.2 billion years ago. Larger and more diverse multicellular eukaryotes do not appear in the fossil record until about 565 million years ago. Explain the possible significance of Snowball Earth in the history of life on Earth. The Snowball Earth hypothesis suggests that, during severe ice ages, most life would have been confined to areas near deep-sea vents and hot springs or to equatorial regions of the ocean that lacked ice cover. The fossil record of the first major diversification of multicellular eukaryotes corresponds roughly to the time when snowball Earth thawed. Life could spread and diversify with all that ice gone.

Briefly describe the Cambrian explosion This is the sudden appearance of many phyla of living animals. It happened during the Cambrian period (535-525 million years ago). Prior to the Cambrian explosion, all large animals were soft-bodied. Afterwards, animals developed new defensive adaptations such as heavy body armor and sharp spines. Describe the key evolutionary adaptations that arose as life colonized land. The gradual evolutionary venture out of aquatic environments was associated with adaptations that made it possible to reproduce on land and that helped prevent dehydration. Plants developed roots and leaves that aid in the absorption of minerals from the soil.

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CONTINENTAL DRIFT, MASS EXTINCTION, AND ADAPTIVE RADIATION

Describe the mass extinctions that ended the Permian and Cretaceous periods. Permian Period: this extinction (251 million years ago) claimed about 96% of marine animal species and drastically altered life in the ocean. Terrestrial life was also affected. It occurred at the same time of enormous volcanic eruptions in what is now Siberia. These eruptions spewed enough lava, ash and CO 2 to warm the global climate by an estimated 6C. The temperature differences between the equator and the poles would have slowed the mixing of ocean water, which in turn would have reduced the amount of oxygen available to marine organisms. Cretaceous Period: this extinction (65 million years ago) claimed about 50% of all marine species and eliminated many families of terrestrial plans and animals, including most of the dinosaurs. It is thought that a giant asteroid or comet collided with Earth, blotting out the sunlight with its huge cloud of debris. This would have severely disturbed the global climate. Evidence for this comes from a thin layer of clay enriched in iridium (a

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element that is rare on Earth) that separates sediments from the Mesozoic and Cenozoic eras, and from a giant crater off the Yucatan cost of Mexico. A sixth mass extinction may be currently underway. Explain this statement. Not much to explain. People smarter than you or I think we are causing a mass extinction via habitat destruction and modification to the global environment. Define adaptive radiation. Describe, with suitable examples, three circumstances under which adaptive radiation may occur. Adaptive radiation is a period of evolutionary change in which groups of organisms form many new species whose adaptations allow them to fill different ecological roles, or niches, in their communities. Adaptive radiation can be a direct consequence of colonization of an isolated region, evolutionary innovation, vacant ecological niches, and an adaptive radiation in a group of organisms (such as plants) that another group uses as food. Large scale adaptive radiation occurred after each of the big five mass extinction events. After dinosaurs disappeared, mammals expanded greatly in both diversity and size, filling the ecological roles once occupied by terrestrial dinosaurs. Regional adaptive radiations occur over a more limited geographic area. Such radiations can be initiated when a few organisms make their way to a new, often distant location in which they face relatively little competition from other organisms. The Hawaiian archipelago is a great showcase for thisas are the finches from the Galapagos Islands.

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THE EVOLUTION OF COMPLEX STRUCTURES

Explain why evolutionary change is not goal-directed. An evolutionary trend does not imply that there is some intrinsic drive toward a particular phenotype. Evolution is the result of the interactions between organisms and their current environments; if environmental conditions change, an evolutionary trend may cease or even reverse itself. The cumulative effect of these ongoing interactions between organisms and their environments is enormous: it is through them that the staggering diversity of life has arisen. The classic example of this is the modern horse. Its evolutionary history is filled with evolutionary dead ends.

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PHYLOGENY AND THE TREE OF LIFE

Distinguish between phylogeny and systematics. Systematics is the reconstruction and study of phylogenies. A phylogeny is the evolutionary history of a species or group of species. In contrast, systematics is a discipline focused on classifying organisms and determining their evolutionary relationships. Data like fossils and molecules and genes are used to infer evolutionary relationships. Taxonomy is the process by which organisms are named and classified. Explain the following characteristics of the Linnaean system of classification: Binomial nomenclature: The first part of the binomial is the name of the genus to which the species belongs. In our case it is Homo. The second part, called the specific epithet, is unique for each species within a genus. In our case it is sapiens.

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PHYLOGENIES SHOW EVOLUTIONARY RELATIONSHIPS

Hierarchical classification: species are grouped into a hierarchy of increasingly inclusive categories, as seen below:

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Domain Kingdom Phylum Class Order Family Genus Species

Explain the justification for the proposal to replace Linnaean classification with phylocode designations for monophyletic taxa. The categories of the Linnaean classification system provide little information about phylogenythat is, the evolutionary relationships between similar species. Such difficulties have led some sytematists to propose that classification be based entirely on evolutionary relationships. PhyloCode is an approach that only names groups that include a common ancestor and all of its descendants. Explain the statement: A phylogenetic tree represents a hypothesis about evolutionary relationships. A phylogenetic tree depicts the evolutionary relationships among species as a series of dichotomies, or two way branch points. Each branch point represents the divergence of two evolutionary lineages from a common ancestor.

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Explain why it is crucial to distinguish between homology and analogy before selecting characters to use in the reconstruction of phylogeny. Describe how homology and analogy can be distinguished from each other. Homologies are similarities (can be structural, such as arms, legs, wings etc) in species due to a shared ancestry. Analogies (or homoplasies) are similarities due to convergent evolution rather than shared ancestry. In order to classify a species correctly, one must first distinguish between the two, or the phylogenetic tree will be incorrect. As an example: a bat has wingsa structural trait it shares with birds due to convergent evolutionand is therefore not grouped with birds. However, bird wings and bat wings are homologous in respect to vertebrate forelimbs. This is because birds and bats have a common ancestor that had forelimbs.

THE CONSTRUCTION OF PHYLOGENETIC TREES

Define a clade. Distinguish between a monophyletic clade and paraphyletic and polyphyletic groupings of species. Clade: In the approach to systematics called cladistics, common ancestry is the primary criterion used to classify organisms. Using this methodology, biologists place species into groups called clades,

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each of which includes an ancestral species and all of its descendants. If these conditions are met, you have a monophyletic clade. Paraphyletic Grouping: This group consists of an ancestral species and some, but not all, of its descendants. Polyphyletic Grouping: This group includes taxa with different ancestorsor a set of species that does not include the most recent common ancestor of the set.

Distinguish between shared ancestral characters and shared derived characters. Synapomorphies and symplesiomorphies. A shared ancestral character is a character that originated in an ancestor of a taxon. In contrast, a shared derived character is a character shared by all species of a taxon but not found in an ancestor. Our backbone is an ancestral character (all mammals have a backbone, as did our ancestor), and our hair is a derived character (all mammals have hair, but our shared ancestor did not). Synapomorphies are shared, derived character states. Symplesiomorphies are share, ancestral character states.

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Explain why shared derived characters are useful in establishing a phylogeny, while shared ancestral characters are not. Shared derived characters are unique to particular clades. Because all features of organisms arose at some point in history of life, it should be possible to determine the clade in which each shared derived character first appeared and use that information to infer evolutionary relationships. Describe the evidence that suggests there is a universal tree of life. The reconstruction of the tree of life is based largely on sequence comparisons of rRNA genes, which code for the RNA parts of ribosomes. Because ribosomes are fundamental to the workings of the cell, rRNA genes have evolved so slowly that homologies between distantly related organisms can still be detectedmaking these genes very useful for determining evolutionary relationships among deep branches in the history of life. Also, horizontal gene transfer, as seen in the next section:

Explain why the occurrence of horizontal gene transfer has led to the suggestion that the history of life should be represented by a ring rather than a tree. Some biologists hypothesize that the first eukaryote may have arisen through a fusion between an ancestral bacterium and an ancestral Archaean. Because phylogenetic trees are based on the assumption

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that genes are passed vertically from one generation to the next, the occurrence of such horizontal transfer events helps to explain why universal trees built using different genes can give inconsistent results (and also explains why the tree is ring-like).

THE PAPERS
Labwork associated with Bio 201 at CSU

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INTRODUCTION TO SUMMARY STATISTICS AND GRAPHS

INTRODUCTION
The following information was obtained from the Mensural Data Stats & Graphs Lab spreadsheet for Lab Section 52 (included as last page). Listed below are the sample size, mean, median, variance, standard deviation and Interquartile range for three variables: height, right cubit and left cubit.
Height Left Cubit Right Cubit

Sample Size Mean/Average Median Variance Standard Deviation Interquartile Range

24 169.1 169.4 100.4 10.0 10.5

24 44.4 43.8 11.2 3.3 2.85

24 44.4 44.0 12.0 3.5 3.63

From this data we can see that, while both the right and left cubit averages are the same, the median in respects to the right cubit is slightly larger (+0.2 cm). This slight difference can also be seen in both the variance and the standard deviation. Furthermore, with a variance of 100.44, we can see that height varies considerably more than either the right or left cubit, as seen graphically in the histograms below:

Left Cubit
9 8 7 6 5 4 3 2 1 0 35.0-39.9 40.0-41.9 42.0-43.9 44.0-45.9 46.0-47.9 48.0-49.9 50.0-51.9 Frequency Frequency

Right Cubit
8 7 6 5 4 3 2 1 0 35.0-39.9 40.0-41.9 42.0-43.9 44.0-45.9 46.0-47.9 48.0-49.9 50.0-51.9

Left Cubit (in cm)

Right Cubit (in cm)

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These histograms illustrate a clear central tendency in respects of all three variables, with height being the clearest indication of a normal curve. Furthermore, with a median of 44.0, we can also see that the right cubit skews slightly to the right when compared with the left cubit. This indicates that, on average, people have a slightly longer right cubit.
52 50 48 Right Cubit 46 44 42 40 38 36 34 139 149 159 169 Height 179 189

Height vs. Right Cubit

The above scatter plot graph indicates a positive linear relationship between height and right cubitthat as height increases the right cubit increases as well. This is also true in respects to height and left cubit.

Left Cubit vs. Right Cubit

51 49 47 Right Cubit 45 43 41 39 37 35 35 37 39 41 43 45 Left Cubit 47 49 51

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The above scatter plot graph indicates a positive linear relationship between the right cubit and the left cubit: that as one increases, the other increases equally. This means that most students have a right and left cubit of relatively equal length. Relationship Between Height and Left Cubits for a Sample of CSU Students y = -0.2388x + 88.542
55.0
Left Cubit (cm)

50.0 45.0 40.0 35.0 150.0

160.0

170.0 Height (cm)

180.0

190.0

200.0

The above graph represents a relationship between height and left cubit of a hypothetical group of students. These results indicate that as height increases, the left cubit decreases. This is odd; as actual data supports that the left cubit would increase along with height. Those students on either end of the spectrum (in relation to height) would look quite bizarre, with taller students having shorter cubits and shorter students having longer cubits.
Relationship Between Height and Left Cubits for a Sample of CSU Students y = 0.2464x + 3.5089
55.0 50.0 45.0 40.0 35.0 150.0

Left Cubit (cm)

160.0

170.0 Height (cm)

180.0

190.0

200.0

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The above graph illustrates the relationship between height and left cubit for another hypothetical group of students. The results indicate that as height increases, the left cubit increases as well. The data represented within the graph is typical of real world results, such as those found in scatter plot graph for this class. Students would look quite normal. Relationship Between Height and Left Cubits for a Sample of CSU Students y = 0.0x + 46.3
55.0 Left Cubit (cm) 50.0 45.0 40.0 35.0 150.0

160.0

170.0 Height (cm)

180.0

190.0

200.0

This final graph represents another hypothetical relationship between height and left cubit. In this instance we see that the left cubit has no predicable patter when compared with height. As height increases we see that the left cubit can vary significantly. If this were representative of real life, we would have a quite a diverse group of students. Two students of equal height could have wildly different left cubit lengths. These two graphs (located on the next page) represent the female and male heights for all sections of Bio 201 Lab. From this data we can determine that males are generally taller than females, with an average height of 178.5 cm (for men) versus 163.1 cm (for women). We also see that male height varies more than female height, with a variance of 65.88 for men and 54.63 for women. Overlapping does occur between 160.0 cm and 179.9 cm. However, there are no females with a height exceeding 179.9 cm, nor are there males with a height below 160.0 cm, as illustrated in the histogram located on page 229:

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Female Height for All Sections

35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0

Number of Female Students

Height (in cm)

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Male Height for All Sections

35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0

Number of Male Students

Height (in cm)

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Male & Female Height for All Sections

35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0

Number of Students

Male Female

Height (in cm)

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TECHNIQUES IN MICROSCOPY & CELLULAR STRUCTURE REFLECTS FUNCTION

The following table was reproduced from pg. 21 of Biological Investigations 8th edition by Warren D. Dolphin. It describes four properties relating to each of the three objectives used in class, and illustrates that, as magnification and resolving power increase, the field of view and brightness of field decrease. Image Properties Magnification Field of View Brightness of Field Resolving Power Scanning Least Greatest Greatest Least Objectives Low Intermediate Intermediate Intermediate Intermediate

High Greatest Least Least Greatest

In order to observe the tube feet of a sea star one would most likely use a light microscope. A sea stars tube feet are visible without a microscope, but for greater detail a light microscope would certainly come in handy. A light microscope would also be useful in determining the sex of a fruit fly, as the differences between male and female fruit flies are phenotypic. However, if one wanted to view the chromosomes of a fruit fly he/she would need a much more powerful microscope most likely a scanning electron microscopeand even though some light microscopes are capable of producing images of a fruit flys threadlike chromosomes, a SEM would undoubtedly yield a more defined image. There were a total of six slides/organisms viewed in this lab, all of which are illustrated (poorly) on the last page of this report. On the following page is a summary of each slide along with its corresponding letter code. Bacteria Types W.M 29-3952 (BAC20) Features: small, squiggly pink lines. Most are bunched together in a large mass, with a few stragglers jutting out across the field of view. Magnification: 400x

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A. Anabaena 29-4924 Features: Small, segmented lines. Each segment of the line appears to be spherical. Some are pink while others are blue. Magnification: 400x B. Paramecium Caudatum W.M. Features: Pink, oval shaped cell. A nucleus is visible. Small dark dots (vacuoles?) are littered about the cytoplasm. Magnification: 400x C. Dicot (?) Leaf Epidermis Sedum 30-3650 Features: Tightly compacted, angular cells. Looks like a puzzle. The cells have a blue-green tint to them. Some areas are darker than others. Magnification: 400x D. Mammal Cerebellum Sec. 31-3666 Features: A brown blotch with dark/black circles spread throughout it. These spots could be organelles, though it is hard to distinguish. Magnification: 400x E. Frog Skin Pigment 92 W3644 Features: Dark brown, highly irregular shape. Due to the color it is hard to make out any defining organelles. Looks almost like an ink blot. Magnification: 400x The differences between prokaryotic and eukaryotic cells are numerous, and certain structures (or lack thereof) of prokaryotic cells support the conclusion that the first living cells on earth were prokaryotes. For instance, it is theorized that mitochondria and chloroplasts present in eukaryotes were originally prokaryotic organisms. These organelles were once bacteria, and at some point in time were incorporated into the larger, more complex eukaryotes. Most prokaryotes also possess a cell wall, which would have helped protect them from the harsh conditions of early Earth. Prokaryotic cells also possess flagellum and cilia, which help them move and cling to surfaces, a structural aspect that many eukaryotic cells lack and one that assists prokaryotes in surviving the elements. Support for this position all comes in the form of fossil records, which show prokaryotes existing nearly half-a-billion years before eukaryotes (Gogarten, 1999).

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Works Cited
Gogarten, J Peter. 1999 When did eukaryotic cells (cells with nuclei and other internal organelles) first evolve? What do we know about how they evolved from earlier life-forms? URL: http://www.scientificamerican.com/article.cfm?id=whendid-eukaryotic-cells

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USING QUANTITATIVE TECHNIQUES AND STATISTICS

The first part of this exercise involved pipetting various volumes of water into a beaker and recording the weight. Theoretically, the various volumes of water should have added up to 40 mL, and would therefore have a combined weight of 40 grams (1 mL H 2 0 = 1 gram). In practice, however, pipetting techniques rarely achieve such accuracy. The histogram located below illustrates the results of this exercise.

Water Weight
41 40 39 38 37 36 35 34 33 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 Determination Weight (in grams)

A total of 40 determinations were made by the students in lab section 52. From this data we can calculateusing spreadsheet softwarethe following summary statistics (values rounded to the nearest 0.00): Mean 38.62 Median 38.74 Variance 1.39 Standard Dev. 1.18 IQ Range 1.71

With a mean of 38.62, we can calculate the percent error in this exercise by using the following formula:

% =

38.62 40.00 100 = 3.45% 40.00

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The percent error for this exercise is -3.45%, indicating that most errors resulted in an actual value that was less than the theoretical value of 40.00 grams. This is further reinforced by the histogram, as it illustrates that only four of the forty determinations (or 10%) yielded a value equal to or greater than 40.00 grams. Reasons for this negative percent error could include improper pipetting, lax data recording, and improperly calibrated scales. Calculating percent error is an important part of this and all data-driven experiments as it evaluates the accuracy of the instruments and techniques employed. Furthermore, it serves as a mediating function that helps refine the way researchers perform experiments and collect data. The second portion of this lab involved measuring the absorbance of an unknown solution of bromophenol blue in water (solution A). To do this, an absorbance curve for a 0.02mg/ml solution of bromophenol blue in water was determined, resulting in the following:

Absorbance Curve
2.5 2 1.5 1 0.5 0 400 450 500 550 600 650 Wavelenght (nm) Absorbance

Wavelength (nm) 425 450 475 500 525 550 575 600 625

The table and absorbance curve above illustrate that the greatest absorbance (of 1.933) was achieved 0.055 at a wavelength of 600 nm. This 0.081 complementary wavelength of light 0.152 was subsequently used to determine 0.304 the unknown concentration of 0.587 Solution A. In order to accurately 1.036 determine unknown solution A, 1.756 eight different dye dilutions 1.933 (consisting of bromophenol blue and 0.292 water) were created. Furthermore, one blank tube of water was used to calibrate the spectrophotometer, Absorbance

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giving us a total of 10 tubes. The concentration and absorbance for each dye dilution (including the blank) was determined, giving rise to the following information (located on next page): Tube 1 2 3 4 5 6 7 8 9 10 ml of Dye 0.00 0.50 1.00 1.50 2.00 2.50 3.00 3.50 4.00 UNKNOWN ml of H 2 O 4.00 3.50 3.00 2.50 2.00 1.50 1.00 0.50 0.00 0.00 Concentration 0.00 mg/ml 0.0025 mg/ml 0.005 mg/ml 0.0075 mg/ml 0.01 mg/ml 0.0125 mg/ml 0.015 mg/ml 0.0175 mg/ml 0.02 mg/ml 0.0125 mg/ml Absorbance 0.000 0.227 0.362 0.673 0.767 1.111 1.399 1.619 1.785 1.075

From this information we can see that our unknown solution A had an absorbance of 1.075 at a wavelength of 600 nm. Therefore, we can assume that the dye concentration of this solution is 0.0125 mg/ml, as it corresponds with the data collected for tube six, which measured an absorbance of 1.111. Furthermore, we can now create a standard curve of absorbance versus concentration to support this conclusion, as seen below:

Absorbance Vs. Concentration 2 1.8 1.6 Absorbance 1.4 1.2 1 0.8 0.6 0.4 0.2 0 0 0.0025 0.005 0.0075 0.01 0.0125 0.015 0.0175 0.02 0.0225 Concentration (mg/ml)

Standard Curve

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DETERMINING THE PROPERTIES OF AN ENZYME

This experiment aims to determine the properties of peroxidase--an enzyme that converts hydrogen peroxide, or H 2 O 2 , to water and O 2 by varying the conditions and environments in which it functions, reacting the solution with guaiacola dye that physically alters the color of active O 2 and then measuring its absorbance via a spectrophotometer. Four different experiments were done, measuring the effects that temperature, pH, the inhibitor hydroxylamine, and boiling of the extract has on the activity of peroxidase. For each experiment, a null and alternate hypothesis is statedwith one being rejected upon conclusion of the experiment. The first of these experiments involved measuring the effects of temperature on peroxidase activity. Four samples were prepared, each with 2.0 mL of H 2 O 2 , 1.0 mL of turnip extract (containing peroxidase), 4.0 mL of buffer (with a pH of 5), and 1.0 mL of guaiacol dye. The null hypothesis for this experiment states: temperature will have a measurable effect on peroxidase activity. The alternate hypothesis states: temperature will have no effect on peroxidase activity. The results are shown in the scatter plot below:

Temperature Effects on Peroxidase Activity

2.000 Absorbance Units 1.500 1.000 0.500 0.000 0 50 100 150 Time (seconds) 4C 19C (room temp) 32C 48C

This data illustrates that temperature does has an effect on peroxidase activitymainly that the optimum temperature for this

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reaction is 32C. This can be further illustrated by graphing the change in absorbance per second versus temperature, as seen below:

Absorbance/sec Vs. Temperature

0.009 0.008 0.007 Absorbance/sec 0.006 0.005 0.004 0.003 0.002 0.001 0 0 10 20 30 40 50 60 Temperature (C)

The following graph illustrates the relationship between temperature and the change in absorbance per second. Here we see that an optimum temperature of 32 C produced the greatest change in absorbancethat of 0.0085 units per second. Furthermore, temperatures that exceed 32C cause the absorbance per second rate to decreaselikely indicating that peroxidase becomes denatured and ineffective as temperature increases. This data supports the null hypothesis, and the alternate hypothesis can be rejected. The second part of this experiment involved measuring the effects of pH on peroxidase activity. As with temperature, enzymes have an optimal pH level. At this optimal level, peroxidase will react more rapidly with hydrogen peroxide, producing a greater change in guaiacol dye activity that can be measured via the spectrophotometer (1). Solutions containing a buffer with a pH that is either too high or too low can cause enzymes to become denatured, effectively limiting its activity (2). For this experiment, four different buffers (pH 3, pH 5, pH 7, and pH 9) were tested and measured for absorbance. The null hypothesis states: pH will affect the activity of peroxidase. The

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alternate hypothesis states: ph will not affect the activity of peroxidase. Results for this experiment are found on the following page:

Effects of pH on Peroxidase Activity

1.000 Absorbance Units 0.800 0.600 0.400 0.200 0.000 0 50 100 150 Time (seconds) pH3 pH5 pH7 pH9

From this data we can see that pH has a clear effect on peroxidase activity. The optimal pH was found to be 5, which yielded an absorbance of 0.828 at 120 seconds. Furthermore, a pH level of 9 produced the least change in absorbance, from 0.077 to 0.198, indicating that peroxidase activity is negatively affected by a higher pH. This relationship can be further illustrated by graphing the change in absorbance/second versus pH, as seen below:

Absorbance/sec Vs. pH
0.006 Absorbance/sec 0.005 0.004 0.003 0.002 0.001 0 0 2 4 pH 6 8 10

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The relationship between absorbance/second and pH can now be seen more clearly. As pH increases to 5, peroxidase activity increases as well. A pH over 5 will create a decrease in peroxidase activity. This indicates that the optimal pH for peroxidase is 5, and that any value higher or lower than 5 will cause a decrease in peroxidase activity. Therefore, the null hypothesis can be accepted, and the alternate hypothesis rejected. The third part of this experiment tested the effects of an inhibitor (2% hydroxylamine) on peroxidase activity. Hydroxylamine has a structure similar to hydrogen peroxide, and is therefore able to bind with the active site of peroxidase (1). For this experiment, the hydroxylamine was mixed with the extract and allowed to react for 10 minutes before being mixed with a solution containing H 2 O 2 , guaiacol and a buffer (with a pH of 5) and measured via the spectrophotometer. Naturally, the null hypothesis for this experiment states: hydroxylamine will inhibit peroxidases ability to actively bind to hydrogen peroxide. The alternate hypothesis states: hydroxylamine will not cause a change in peroxidase activity. Results for this experiment are found below:

Effects of Inhibitor on Peroxidase Activity

1.400 1.200 Absorbtion Units 1.000 0.800 0.600 0.400 0.200 0.000 0 50 100 150 Time (seconds) Normal Extract Inhibitor

We can clearly see that the inhibitor hydroxylamine has an effect on peroxidase activity. In fact, the solution containing the inhibitor displayed no measurable change in absorbance during the 120 seconds it was in the spectrophotometer, staying at a constant 0.006

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absorbance. The null hypothesis is accepted, and the alternate hypothesis can be rejected. The fourth and final experiment tested the effects of boiling the extract on peroxidase activity. Enzymes can become denatured when exposed to high levels of heat, inhospitable pH levels and certain solvents (such as acetone), which alters their shape and their ability to function effectively (2). The experiments performed above show that peroxidase functions well at a pH of 5 and at a temperature of 32C. Any change in either of those two factors will cause a decrease in peroxidase activity. Therefore, the null hypothesis for this experiment states: boiling the extract prior to measuring absorbance will cause the enzyme peroxidase to become denatured, negatively affecting its ability to bind with hydrogen peroxide. The alternate hypothesis states: boiling the extract will have no effect on peroxidase activity. Results for this experiment are found below:

Effects of Boiled Extract

1.4 Absorbance Units 1.2 1 0.8 0.6 0.4 0.2 0 0 50 100 Time (sec) 150 Boiled Extract Normal Extract

The data above shows that boiling the extract has a dramatic effect on peroxidase activity. In fact, peroxidase nearly ceases to function when exposed to high levels of heat, supported by the fact that absorbance remained at a constant 0.009 during the 120 seconds it was inside the spectrophotometer. Therefore, we can accept the null hypothesis and reject the alternate hypothesis.

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References 1. Dolphin, Warren D. 2008. Biological Investigations: Form, Function, Diversity & Process. McGraw Hill Higher Education, Eighth Edition. 2. Modney, Barbara K. 2011. PowerPoint Presentation Notes for Biology 201. Cleveland State University.

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DETERMINING HOW MATERIALS ENTER CELLS

The first part of this experiment, the Simultaneous Osmosis and Diffusion, involved placing a dialysis membrane half-filled with 2% albumin dissolved in 3% NaCl within a solution of 0.25% starch dissolved in 1% Na 2 SO 4 . The membrane was allowed to sit within the solution for 30 minutes. Both solution were tested before and after and experiment to determine which molecules were able to diffuse through the membrane. The following table details the results from the Simultaneous Osmosis and Diffusion experiment: Table 4.1 Results of Osmosis/Diffusion Experiment with Dialysis Tubing Outside Bag Inside Bag Start Start End End + + + + + + + + + + Not needed for outside 16.82 g 18.02 g

NaCl Na 2 SO 4 Protein Starch Weight

From this table we see that while sodium chloride and sodium sulfate were able to move through the dialysis membrane, protein and starch were not. This likely has to do with molecular weight. The dialysis membrane allows only small molecules to pass throughthat is, molecules with a molecular weight less than 1000 amu. Therefore, sodium chloride (58.5 amu) and sodium sulfate (142 amu) were able to pass through the membrane, while the protein and starchwhose molecular weight exceeds 30,000were unable to (1). Both NaCl and Na 2 SO 4 moved along their concentration gradient (from high to low), with NaCl moving from inside the bag to outside, and Na 2 SO 4 moving from outside the bad to inside. Furthermore, water within the solution was able to pass through the dialysis membrane as it too has a low molecular weightevidenced by the fact that the bag gained significant weight (+1.20 grams) by the end of the experiment.

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The second part of this experiment involved measuring the fluid height in an osmometer. The combined data for seven successive lab sections can be seen in the following scatter plot (on the following page):

Osmometer Data
900 800 Fluid Height (mm) 700 600 500 400 300 200 100 0 0 50 100 150 200 250 Time (min)

Here we see that water movement slows down over time. The osmometer is constructed in such a way that the sugar molecules within it are unable to pass through the membrane, meaning that water will continue to move across the membrane until the pressure differences reach equilibrium, at which point no water movement will be observed (1). The third part of this experiment involved observing osmosis in living cells. Two slides were prepared, one containing a portion of Elodea leaf in water, and the other containing Elodea leaf in a concentrated solution of 35% sucrose(illustrations for this experiment are included on a separate sheet of paper). When placed in the sucrose solution water from within the Elodea leaf cells diffused across the plasma membrane, causing the visible portions of the cell (chloroplasts and cytoplasm) to amass near the center, leaving the central vacuole mostly empty. Hypothetically, these cells could be returned to their normal, turgid state if placed within plain water. Since the cells are in a flaccid state, water would move back into the cell via osmosis, filling the central vacuole, and redistributing the organelles.

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Critical Thinking Question #5 A fish in a freshwater environment, or a hypo-osmotic medium, would have different osmotic regulatory challenges than a fish in a saltwater environment due to the lower number of osmotically active particles in fresh water. This means the freshwater fish would be constantly taking in water via osmosis (water would be leaving a fish in a saltwater, or hyper-osmotic environment). This presents an osmotic regulatory challenge, one which fish are obviously adapted for. Organs, such as skin and kidneys, work to regulate osmosis in animals such as fish (1).

1. Dolphin, Warren D. 2008. Biological Investigations: Form, Function, Diversity & Process. McGraw Hill Higher Education, Eighth Edition.

References

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MEASURING CELLULAR RESPIRATION

The first part of this experiment involved measuring the aerobic cellular respiration via the rate of oxygen consumption for three experimental setups: normal germinating peas, glass beads, and freeze dried peas mixed with the glass beads. Three respirometer tubes were prepared, each with an equal amount of peas and/or glass beads, and each with four to five drops of potassium hydroxide (KOH) present between layers of absorbent and nonabsorbent cotton. Each tube was capped with a rubber stopper attached to a pipette and placed in a bin of water. The tubes were allowed five minutes to equilibrate before being submerged in the water. The raw rate of oxygen consumption was measured every three minutes over the span of 15 minutes, giving rise to the following information: Raw Oxygen Consumption (mL)
Tube 1 2 3 Contents Normal Peas Freeze Dried Peas & Glass Beads Glass Beads 0 0.10 0 0

Reading Time (minutes)

3 0.22 0 0 6 0.33 0 0 9 0.37 0 0 12 0.38 0 0.13 15 0.51 0 0.14

Raw Oxygen Consumption

0.6 Raw Oxygen Consumption (in mL) 0.5 0.4 0.3 0.2 0.1 0 -0.1 0 3 6 9 Time (minutes) y = 0.0104x - 0.0329 y=0 12 15 Freeze Dried Peas & Glass Beads Glass Beads y = 0.0245x + 0.1348 Normal Peas

This data illustrates that, during the 15 minute period, the respirometer containing the normal germinating peas showed the

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greatest amount of oxygen consumption (approximately 0.0245 mL a minute). This change in O 2 consumption is attributed to the active cellular respiration happening in the live tissue of the peas, a process not present in either the freeze-dried peas or the glass beads. Interestingly, the respirometer containing only glass beads, which acted solely as a control, did show a slight uptick in oxygen consumption around the 9 minute mark; a capricious phenomenon that is likely attributed to my heedless fondling of the respirometers pipette (I get excited). Luckily, the fact that it is a control affords my brutish hands some leeway, as any errors that occurred during this experiment can be parsed simply by comparing data sets and adjusting oxygen consumption values accordingly (ignoring negative values), as seen table 8.3 below:
Corrected Oxygen Consumption (mL) Tube Contents 1 Normal Peas 2 Freeze Dried Peas & Glass Beads 0 0.0 0 Reading Time (minutes) 3 6 9 12 0.05 0.11 0.16 0.19 0 0 0 0 15 0.22 0

Furthermore, the mixture of freeze-dried peas and glass beads displayed no measurable change in oxygen consumption, presumably because the H 2 O needed for cellular respiration to occur is not present in either subject. We can compare the rate of oxygen consumption between normal peas and freeze dried peas by examining the specific rate of O 2 consumption per gram of tissue. To do this, we divide the slope values obtained from the scatter plot by the mass of the peas: ( ) = = 2.93 103 // = 0.0 // 0.245 / 8.36

( ) =

0.0 / 1.87

It should now be exceptionally evident that normal germinating peas exhibit a greater rate of oxygen consumption when compared to freeze-dried peas. The second part of this lab exercise involved testing various mixtures for the presence of ethanol, one of the two final products of anaerobic respiration, by using a simple iodoform procedure. Six tubes were prepared, each containing 1.5 mL of Lugols iodine and 1.5 mL of sodium hydroxide (NaOH). Each tube then received one of six mixtures

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listed in table 8.1 below. If ethanol was present in a mixture it would react with Lugols iodine and NaOH to form a yellow precipitate, or iodoform (indicated by a +). Table 8.1 Iodoform Test Tube 1 2 3 4 5 6 Sample Water Ethanol & Water Anaerobic Distillate Control Corn Syrup Distillate Aerobic Distillate Wine Distillate Iodoform Test Results N/A + + N/A N/A +

As expected, the anaerobic distillate tested positive for the presence of ethanol, as did the mixture of ethanol and water, and the wine distillate. Water and the corn syrup distillate did not react with the iodine and served as controls for the ethanol/water and anaerobic distillate mixtures, respectively. Testing water and the corn syrup distillate was necessary in order to rule out the chance that iodine and water (or iodine and corn syrup) react to form a similar yellow precipitate. As well, the aerobic distillate did not react with iodine, and as such contained no ethanol. This is to be expected, as ethanol is only produced during anaerobic respiration. Testing the aerobic distillate ensured that a greater level of confidence when confirming the presence of ethanol in the anaerobic, ethanol/water and wine distillates. Many organisms are able to breakdown glucose in the absence of oxygen via anaerobic respiration. The cells of such organisms take in glucose and, via glycolysis, break each molecule down into two molecules of pyruvic acid, which are then converted into lactic acid or ethanol by the oxidation of NADH 2 (obtained from glycolysis). The lactic acid or ethanol is then excreted from the cell, completing the process of fermentation. Furthermore, organisms that survive in anaerobic conditions gain considerably less energy from glucose than organisms that undergo aerobic respiration (1). The Gulf of Mexico dead zone is an area of water that, due to a low concentration of oxygen, is unable to support most animal life. Such dead zones are caused by nitrogen and phosphorous enrichment,

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which allow algae blooms to develop (unlimited algae growth), consequentially depleting oxygen from the surrounding environment. Sewage, animal wastes, and fertilizers used in farming are several of the primary sources that can lead to nitrogen and phosphorous enrichment. Such dead zones can be found across the world, and affect everything from biodiversity to the commercial fishing industry (2). References 1. Dolphin, Warren D. 2008. Biological Investigations: Form, Function, Diversity & Process. McGraw Hill Higher Education, Eighth Edition. 2. Bruckner, Monica. 2011. The Gulf of Mexico Dead Zone. Montana State University http://serc.carleton.edu/microbelife/topics/deadzone/

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SIMULATING GENES IN POPULATIONS (GENETIC DRIFT)

In the first part of this lab genetic drift was simulated (physically) using yellow and red colored beads, which represented two alleles in a haploid organism. Out of a sample of 1000, the first generation represented an equal 50/50 distribution of red and yellow alleles. Subsequent generations consisted of unequal distributions, primarily due to the random nature of pulling beads out of the container considered here as genetic driftand to the allele frequency conditions set forth by the containers/populations. This exercise was conducted twice and each lasted until the frequency of either the red or yellow allele went to 0% (or until 17 generations had passed), as illustrated in the scatter plots below and to the left:

Allele Frequency (Trial 1)

1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0 0 1 2 3 Generations (t) 4 5 6 Allele Frequency (p)

Trial one shows that the red allele vanished after only five generations (the yellow allele went to 100%), indicating that this particular population of haploid organisms will no longer carry the red allele in their collective genotype. The fact that this happened so quickly is due to the small sample size. Theoretically, the allele frequency for a larger sample size would take considerably longer to reach 0 or 100%, if at all.

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Allele Frequency (p)

Allele Frequency (Trial 2)

0.5

0 0 1 2 3 Generations (t) 4 5

Trial two shows that the red alleles frequency went to 100% after only four generations, indicating that the yellow allele was no longer present in the populations genotype. From the scatter plot we see a gradual rise in red allele frequency, which is to be expected from a population that contains greater than 50% red allele frequency. Again, the speed at which this occurred is likely attributed to the diminutive sample size. Furthermore, this experiment was conducted across several different classes, and the combined data for each was compiled into the following scatter plot:

Genetic Drift (Combined Allele Frequency Data)

1 0.9 Allele Frequency (p) 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 Generations (t) Allele 1 Allele 2 Allele 3 Allele 4 Allele 5 Allele 6 Allele 7 Allele 8

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Here we see a wide range of allele frequency behavior. Some classes show sharp declines in allele frequency, while others show a wobbling path with no significant change. However, in all cases the change in allele frequency is attributed to the randomness of genetic drift. In the second part of this lab, genetic drift was simulated using computer software. Three different populations sizes were tested (50, 250 and 500) using ten autosomal loci, each containing two alleles, for a length of 1000 generations. Initially, the null hypothesis for this model states: population size has no effect on genetic drift. The following table (reproduced from the handout) details the results of this exercise:
Table 1.1

Run 1 2 3 4 5 6 7 8 9 10 Loci Fixed % Loci Fixed

# of fixed loci after 1000 generations N=50 N=250 N=500 10 7 7 10 9 8 10 8 5 10 9 1 10 9 7 10 8 6 10 9 2 10 6 4 10 3 4 10 7 5 100 75 49 100 75 49

From this table we can reject the null hypothesis and state the alternate hypothesis: population size does have an effect on genetic driftor more specifically, larger populations exhibit less intense genetic drift than small populations. When n=50, all loci become fixed after 1000 generations. Since each locus has only 2 alleles, the genetic variation in this population is nonexistent, as each organism has identical alleles. When n= 250, the number of fixed loci is lowered to 75, and is even further reduced (to 49) when n=500. Since genetic drift is less intense as a population increases, the genetic diversity within a population is strengthened as it increases.

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THE EXAMS
For the Cheater in All of US

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PRACTICE EXAM 1
1. A localized group of organisms that belong to the same species is called a A. biosystem B. community C. population D. family E. ecosystem 2. The hereditary material of all livingthings and most viruses is: a. Complexcarbohydrate b. DNA c. Polypeptide d. RNA e. Triacylglycerides 3. Which of the following is NOT a characteristic of science? A. Observability/detectability B. Science makes predictions C. Scientific predictions can be tested D. Scientific hypotheses do not rely on the supernatural E. Scientific theories are proven true 4. Which of the following is NOT a characteristic of all living organisms? A. adaptation to their environment B. reproduction C. response to stimuli D. multicellularity 5. The maintenance of a relatively constant internal environment that typically is different from the external environment defines ____ A. reproduction B. development C. adaptation D. ordered complexity E. homeostasis 6. Each element has a distinct number of ______ A. Atoms B. Neutrons C. Protons D. Electrons E. Molecules 7. Atoms with the same ______ but different ______ are called isotopes. A. atomic number atomic mass B. atomic mass atomic number C. number of electrons number of neutrons D. number of neutrons number of electrons E. number of electrons number of protons 8. Which property of water is responsible for the cooling effect of perspiration? A. cohesion B. high specific heat C. high heat of vaporization D. lower density of ice E. solubility

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14. A polar molecule is a molecule with __________. a. the ability to resists changes in temperature b. an unequal distribution of 10. In the reaction C6H12O6 + 6O2 charges 6H2O + 6CO2 c. no kinetic energy d.random movement A. Only C6H12O6 is a reactant B. Both CO2 and H2O are reactants C. O2 is one of two products D. 6O2 and 6CO2 are reactants E. None of the above are true 11. A pH of 4 is ____________ times more ____________ than a pH of 7. A. 3; basic B. 3; acidic C. 1000; neutral D. 1000; basic E. 1000; acidic 12. A substance which helps maintain constant pH of a solution is called a/n: a. anion b. buffer c. chaperone d. reactant e. ribozyme 13. The concentrationo f H- ions in asolution with a pH of 9 is - that of a solution with a pH of 6. A. 3X B. 1/3X 15. Compounds that have different three-dimensional structures but identical chemical formulas are called __________. a. enzymes b. carbohydrates c. isomers d. acids 16. Substances such as lemon and tomato, with a pH __________, are considered acidic. a. equal to 0 b. equal to 14 c. above 7 d. below 7 17. In a group of water molecules, hydrogen bonds form between _____. A two hydrogen atoms in different water molecules B the oxygen atoms in different water molecules C the oxygen atom in one water molecule and a hydrogen atom in another water molecule

9. The chemical behavior of an atom is determined most directly by the: A. atomic number. B. atomic weight. C. number of energy levels. D. number of valence electrons.

C. 1/10th D. 1/100th E. 1/1000th

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2. In Figure 1G, the functional group at the arrow is: 18. The tendency of water a. carbonyl molecules to stay close to each b. carboxyl other as a result of hydrogen c. hydroxyl bonding _____. d. keto A provides the surface tension that allows leaves to float on water e. methyl B is called cohesion C keeps water moving through the 3. In Figure 1, which of the following is glucose? vessels in a tree trunk a. B D acts to moderate temperature b. D E all of the above c. E d. F 19. Sweating has a cooling effect e. H because of water's high _____. A Buffering capacity 4. In Figure 1, which of the B surface tension following is a disaccharide? C heat of vaporization a. A D specific heat b. C E density c. H d. I 20. Nonpolar molecules that cluster away from water molecules e. K are called _____ molecules.) 5. In Figure 1C, the circled portion A ionic is a: B hydrophilic a. monosaccharide C hydrophobic b. nucleotide D saponified c. peptide E none of the above d. purine e. triglyceride Ch. 4+5 1. In Figure 1 (see end of exam), which of the following associations 6. The C-C bond as in Figure 1G is: a. covalent is INCORRECT? b. glycosidic a. A :: polysaccharide c. hydrogen b. B :: aromatic amino acid d. ionic c. D :: polyalcohol d. H :: steroid

D the hydrogen atoms in a single water molecule E none of the above

e. J :: unsaturated fatty acid

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7. The growing end of a polypeptide is the __ end. a. alpha b. amino c. carboxyl d. omega e. R group 8. What part of an amino acid confers its unique properties? a. amino group b. carboxyl group c. R group d. none of these 9. The major lipid component of biological membranes is: a. glycoprotein b. polypeptide c. phospholipid d. steroid e. none of these

d. Unsaturated fatty acids are straight and unbent 12. Which of the following is NOT a biological function of proteins? a. enzyme catalysis b. defense c. transport d. motion e. store and transfer genetic information 13. In proteins, is a common example of (a) __________. a. primary structure b. quaternary structure c. tertiary structure d. secondary structure e. domain

14. Glucose: a. is made anabolically in photosynthesis 10. Which part of a phospholipid forms hydrogen bonds with water? b. is a structural isomer of fructose c. forms rings when dissolved in a. The phosphate-containing water head d. is a hexose b. The glycerol component e. all of the above c. The unsaturated fatty acid d. Both of the two fatty acids 15. Cellulose is undigestible by e. None of the above most mammals because: a. it is composed of the beta form 11. Which of the following is of glucose. FALSE? b. it is related to chitin, the cell a. Cholesterol is found in animal, wall component of fungal cell walls but not plant, membranes c. it contains peptide bonds b. Oils are composed primarily of fats high in unsaturated fatty acids d. a and c e. a and b c. Typically, fatty acids contain even numbers of Acarbon atoms

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16. The primary (1) structure of a protein: a. refers to the sequence of amino acids encoded by its gene b. determines the higher orders of protein structure c. determines the function of the protein d. all of the above e. none of the above 17. Which of the following is FALSE? a. 22 different types of amino acids are found in polypeptides b. alanine and valine have hydrophobic R groups c. glutamate and glutamic acid are different names for the same amino acid d. prostaglandin is a type of terpene e. serine contains a hydroxyl group that may be used to attach a phosphate

of the statement is false, the statement is false. 19. Isotopes have the same atomic number but different atomic mass 20. Cysteine stabilizes 2 and 3 structure through disulfide linkages 21. The amino acid aspartate has a charged R group. 22. Ionic bonds are formed by the sharing of electrons 23. Triacylglycerides have three fatty acids covalently bonded to glycerol.

Ch. 6 + 7 1. All living things are composed of__________ with_____________. a. cellsordered complexity b. cellscell walls c. tissuesdifferent 18. The structural building material cell types of arthropods d. cellsnuclei and many fungi is ___, which is a modified 2. An average eukaryotic cell form of ___. is about _________ in a. cellulose ... sucrose diameter. b. chitin ... cellulose a. .2 micrometer c. keratin ... fructose b. 2 micrometer d. starch ... glucose c. 20 micrometer e. ribose ... RNA d. 2 mm True/False: answer each of the 3. A cell has the following following True or False. If any part components: Enzymes,

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DNA, ribosomes, a phospholipid bilayer as a membrane, and mitochondria. You reason it could be a cell from_______. a. A bacterium b. An animal but not a plant c. A plant but not an animal d. A plant or animal 4. A bacterial toxin effectively destroys cellular ribosomes. Which activity would logically stop first? a. Cellular movement b. Protein synthesis c. Energy production d. Active transport 5. Proteins are often modified in this organelle: a. Nucleus b. Mitochondria c. Lysosomes d. Golgi Apparatus 6. Which of the following are not found in ALL living things? a. Ribosomes b. Plasma membrane c. DNA d. Mitochondria 7. Which of the following is not membrane bound? a. Endoplasmic reticulum

b. c. d. e.

Peroxisome Golgi apparatus Nucleus Nucleoid

8. Which of the following contain DNA? a. Ribosomes b. Chloroplasts c. Mitochondria d. B and c e. A,b, and c 9. Plant cells often contain a ______________that is used for storing water and other substances a. Nucleus b. Chloroplast c. Golgi apparatus d. Centriole e. Central vacuole

10. Intelligent, friendly aliens have donated cells to cell biologists to study. The scientists discover that the cells contain a nucleus with DNA, ribosomes, centrioles and mitochondria. The alien cells are most similar to which cell types found on earth? a. Bacterial cell b. Plant cell c. Animal cell d. Prokaryotic cell e. B and c

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11. Which of the following is improperly matched? a. Cytoskeleton: vesicular transport b. Nucleus: DNA c. Cell membrane: lipid bilayer d. Membrane protein: active transport e. Vesicle: energy production 12. Cells in the pituitary gland synthesize the protein growth hormone. Which of the following organelles would be very abundant in these cells relative to a cell that synthesized steroid hormones: a. Lysosomes b. Mitochondria c. Peroxisomes d. Rough Endoplasmic Reticulum e. Smooth Endoplasmic Reticulum 13. Which of the following requires ATP? a. Simple diffusion b. Facilitated diffusion c. Active transport d. Osmosis e. B and c 14. Isotonic solutions: a. Will exhibit a net movement of

b. c. d. e.

solute from one solution to the other Have equal concentrations of solute and water Have unequal concentration of solute and water None of the above All of the above

15. A single cell is transferred to a hypertonic salt solution. Which of the following is going to happen? a. The cell bursts b. The cell shrinks c. Salt is pumped out of the cell d. All of these 16. A cell of the immune system cell can engulf a bacteria by: a. Exocytosis b. Phagocytosis c. Pinocytosis d. Sodium potassium pump 17. True/False: A prokaryotic cell is simpler than a eukaryotic cell 18. T/F Liver cells function as a major detoxifying system in vertebrate animals; therefore the smooth ER

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would be particularly abundant in these cells. 19. T/F Cell walls are considered part of the cytoskeleton

20. T/F Biological membranes are active, dynamic structures

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PRACTICE EXAM 2
Questions on this practice test come from a combination of sources, including last years exam and quiz questions, SLA quiz questions, and questions written by Leaders. The answer key will be available for you to look at in SLA next week, not for you to keep. Bring specific questions to SLA Leaders.

1. The energy from ADP + Pi comes from ___________ cellular reactions. The energy then released when ATP is hydrolyzed to ADP+ Pi, is used for _________ cellular reactions. a. exergonicendergonic b. endergonicexergonic c. exergonicexergonic d. endergonicendergonic e. aerobicanaerobic 2. Molecules A+B react such that A donates an electron to B, which we here represent as forming A+ and B-. We can then say that a. A and B were oxidized b. A and B were reduced c. A was oxidized and B reduced d. A was reduced and B oxidized e. Both were fermented 3. In cellular respiration, when the final electron acceptor is oxygen, resulting in the formation of water, the process is called: a. Fermentation b. Aerobic respiration c. Anaerobic respiration d. Substrate level phosphorylation e. Heterotrophy f. A and B g. All of the above h. None of the above 4. In aerobic respiration, which reactant is oxidized? a. Sugar

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b. c. d. e. f.

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Oxygen Carbon Dioxide Water A+B C+D

5. Select the true statement concerning oxygen and cellular respiration a. It is incorporated into CO2 b. It is incorporated into the terminal phosphate of ATP c. It is incorporated into water d. It is the final electron acceptor in the electron transport chain e. C and D 6. During fermentation, ATP is produced by ____________ a. Substrate level phosphorylation b. Oxidative phosphorylation c. A and B d. The Krebs Cycle e. None of the above 7. The electron accepting form of nicotinamide adenine dinucleotide is a. Oxygen b. Adenine c. NAD+ d. NADH e. FAD+ f. NADP+ 8. Substrate level phosphorylation of ADP a. Occurs during glycolysis, the Krebs Cycle, and the electron transport chain b. Produces less ATP than oxidative phosphorylation c. Requires oxygen d. Produces CO2 e. Requires NAD+ and FAD 9. Beginning with one molecule of glucose, the output of glycolysis is ___________, in addition to ATP and NADH. a. 2 molecules of glucose b. 2 molecules of phosphofructokinase

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c. d. e. f.

1 molecule of oxaloacetate 2 molecules of pyruvate None of the above All of the above

10. An important regulatory point in glycolysis is the enzyme phosphofructokinase, which is: a. Inhibited by high levels of ATP b. Inhibited by low levels of ATP c. Inhibited by high levels of AMP d. Activated by the presence of oxygen e. Activated by the presence of glucose 11. The electron transport chain is located in a. The mitochondrial matrix b. Cytoplasm c. Extracellular space d. Inner mitochondrial membrane 12. What is chemiosmosis? a. The production of NADH and FADH2 in cellular respiration b. The movement of electrons through the electron transport chain c. The breakdown of oxygen as it enters the mitochondria d. The synthesis of ATP by ATP synthase, using a proton gradient e. None of the above 13. which of the following is true of enzymes: a. They are usually carbohydrates b. They raise the activation energy for exergonic reactions c. They are used up in their reactions d. They increase the speed of reactions by lowering the activation energy 14. Catalysts: a. Include proteins and ribozymes in biological systems b. Raise the electricity in a reaction c. Lower the potential energy in a reaction d. All of the above

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e. None of the above 15. The capacity to do work of cause change is the books definition of a. Kinesis b. Active transport c. Energy d. Entropy e. Gibsons Free Lunch 16. In competitive inhibition the inhibitor binds to the _________site of an enzyme a. Transdomain b. Active c. Allosteric d. A and C 17. Which term most precisely describes the general process of breaking down large molecules into smaller ones? a. Catabolism b. Anabolism c. Condensation reactions d. Energy 18. Anabolic pathways a. Release energy as they degrade polymers to monomers b. Consume energy to build polymers from monomers c. Do not depend on enzymes d. Lead to the synthesis of catabolic pathways 19. Where in a plant cell can you find the thylakoid membrane? a. Chloroplast b. Mitochondria c. Nucleus d. Celll wall e. All of the above f. None of the above 20. Which products of the Light reactions are used in the Calving Cycle? a. FADH2 and NADH

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b. ATP and ADP c. FADH2 and NADPH d. ATP and NADPH 21. When rubisco steals a carbon atom from CO2 and attaches it to RuBP, the process is known as. a. Carbon reductin b. Carbon fixation c. Carbon oxidation d. Sugar synthesis e. Carbon synthesis 22. Which of the following occur in Photosystem II a. ATP is produced b. NADP is reduced c. Splitting of water d. A and B e. B and C f. All of the above 23. Which of the following is NOT true of plasma membrane signal receptor proteins: a. They span the plasma membrane b. They may initiate a signal transduction cascade in the cytoplasm c. They bind the signal molecule forever d. Their ligands are typically hydrophilic molecules e. They undergo conformational change upon binding with the ligand 24. Which of the following does NOT span the plasma membrane? a. G-protein coupled receptor b. Tyrosine kinase receptor c. Ion Channel d. Intracellular receptor 25. Protein phosphatases can a. Remove phosphates b. Inactivate proteins c. Add phosphates d. A and B e. A, B, and C

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26. Kinases could a. Add a phosphate b. Remove a tyrosine c. Add a tyrosine d. Remove a phosphate e. All of the above 27. Receptors are located on the ___________cell and bind___________. a. Target cellenzymes b. Signaling cellsecond messengers c. Target cellligand d. Ligandhormones e. Signaling cellDNA 28. Testosterone and cortisol are examples of ________ signal. a. Amino acid derivatives b. Inorganic c. Peptide d. Steroid e. Protein 29. ______________ signaling occurs by diffusion of signal molecule to surrounding cells. a. Autocrine b. Endocrine c. Paracrine d. Synaptic e. Transcriptional 30. The overall process in which information carried by a signal molecule is translated into changes that occur inside the cell is called a. Signal translation b. Signal induction c. Signal interaction d. Signal transduction 31. A duplicated chromosome has __________ chromatid(s) a. One

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b. Two c. Three d. Six 32. A somatic cell having two of each type of chromosome has a(n) _________ chromosome number. a. Diploid b. Haploid c. Tetraploid d. Abnormal 33. After Mitosis, the chromosome number of a daughter cell is __________ the parents cell. a. the same as b. one half c. rearranged compared to d. doubled compared to 34. The chromosomes in this picture are in which phase of mitosis? a. Prophase b. Anaphase c. Metaphase d. Telophase e. Cytokinesis 35. T/F During metaphase all chromosomes are aligned at the spindle equator 36. T/F During telophase daughter nuclei form 37. T/F During anaphase chromosomes start to condense 38. T/F During anaphase sister chromatids move apart 39. Meiosis and cytoplasmic division function in a. Asexual reproduction of single-celled eukaryotes b. Growth and tissue repair c. Sexual reproduction d. B and C 40. Sexual reproduction requires: a. Meiosis

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b. c. d. e.

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Fertilization Spore formation A and b None of the above are correct

41. Generally, a pair of homologous chromosomes a. Carry the same genes b. Interact at meiosis c. Are the same length and shape d. All of the above e. None of the above 42. Meiosis ________________ the parental chromosome number a. Doubles b. Halves c. Maintains d. Mixes up 43. Meiosis ends with the formation of __________________ a. Two cells b. Two nuclei c. Eight cells d. Four nuclei 44. T/F The chromosome number includes all chromosomes in a given type of cell 45. T/F Different forms of a gene are called alleles 46. T/F Mitosis produces 4 genetically different daughter cells 47. T/F Meiosis produces 4 genetically different daughter cells 48. An organisms ____________is determined by its___________. a. genotype, phenotype b. phenotype, genotype c. alleles, phenotype d. F1 generation, alleles

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49. Referring to Mendels experiment, what was the phenotypic ratio of the F1 generation after crossing purple (PP) and white (pp) flower pea plants? a. All the F1 plants had white flowers b. All the F1 plants had a blended appearance, like light purple c. All the F1 plants had had purple flowers d. of the F1 flowers were purple, and white 50. The observable traits of an organism are its a. Phenotype b. Genotype c. Pedigree d. Sociobiology 51. Molecules activated by a signal transduction pathway that control gene expression are called___________. a. Ligands b. Receptors c. 2nd messengers d. Transcription factors e. Kinases 52. Allosteric sites of enzymes: a. Are enzymes where substrates bind b. Regulate enzyme activity through binding of small molecules c. Bind competitive inhibitors d. A and C e. None of the above 53. Which of the following is NOT involved in the first step of the Calvin Cycle? a. CO2 b. Glyceraldehyde 3 Phosphate c. Rubisco d. Ribulose bisphosphate e. C and D 54. Excited electrons from photosystem II are used to a. Reduce NADP+

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b. Oxidize water c. Reduce cytochromes in the electron transport chain d. Produce ATP e. None of the above 55. In the Calvin Cycle, 3-PGA is reduced by _____________. a. ATP b. CO2 c. NADP+ d. NADPH e. ADP 56. Which of the following is NOT a product or reactant of the light reactions of photosynthesis? a. ATP b. O2 c. NADP+ d. NADPH e. CO2 57. In the making of ATP by substrate level phosphorylation: a. ADP receives a phosphate from an organic molecule b. ATP Synthase is used c. NADH is utilized d. A and B e. A and C f. B and C g. A, B, and C 58. Where is the energy located in the glucose molecule? a. Carbonyl group b. C-C bonds c. C-H bonds d. Hydroxyl groups 59. In a redox reaction a. Both oxidation and reduction occur b. The molecule which accepts an electron is considered oxidized c. Electron transfers are associated with transfer of protons d. A and B

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e. A and C f. B and C g. A, B, and C 60. Which of the following does NOT occur in glycolysis in the presence of oxygen? a. ATP is produced by substrate level phosphorylation b. ATP is used to make fructose-1,6-bisphosphate c. FAD is reduced d. One glucose yields 2 pyruvates e. All of the above occur

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PRACTICE EXAM 3
1. Who showed that the substance responsible for transformation in Griffith's experiments is DNA? a. Avery, McLeod, McCarty b. Beadle and Tatum c. Chargaff d. Franklin e. Hammerling f. Hershey and Chase g. Watson and Crick 2. In 1910, Morgan crossed a male fruit fly with a new mutant trait, white eyes, with a wild type, red-eyed, female. In the F2 offspring that were subsequently produced, of the individuals had white eyes, but all were males. This demonstrated the phenomenon of: a. pleiotropy b. recessiveness c. crossing over d. X linkage e. epistasis 3. A genetic defect in humans results in the absence of sweat glands in the skin. Some men have this defect all over their bodies, but in women it is usually expressed in a peculiar way: A woman with this defect typically has small patches of skin with sweat glands and other patches without sweat glands. In women, the pattern of sweat-gland distribution can best be explained by _____. A a mutation B X chromosome inactivation C RNA splicing D an operon E a homeobox 4. Which of the following associations is INCORRECT? a. DNAPolymeraseIII :: removal of Okazaki fragments b. helicase :: unwinding of DNA c. ligase :: close 5'-3' phosphodiester bonds d. SSB :: maintain single strand state e. topoisomerase :: relieve stress

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5. Which of the following is CORRECT in reference to Figure 2? (see end of test) a. The leading strand is synthesized using f as a template b. A 3' phosphate is present at a c. A 5' phosphate is present at b d. Strand a is an Okazaki fragment e. All of the above are correct. 6. Which of the following is NOT true about DNA Polymerase a. It utilizes dNTP sustrates b. It requires a primer with a free 5' -OH group c. It requires a template d. It exists in multiple forms in bacterial and eukaryotic cells e. It can have proofreading activity 7. Which substance shown here, binds to the site where messenger RNA will be synthesized?

a. RNA polymerase b. template DNA strand c. nucleotide d. adenine 8.DNA ____ contain deoxyribose, phosphate, and nitrogenous bases. A) B) C) D) carbon cells ribose cells nucleotides purines

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9. DNA strands separate and produce both parental DNA and new DNA during ____. A) semiconservative replication B) conservative replication C) RNA binding D) Okazaki binding 10. Polymerase synthesizes small segments of the DNA strand, which are called ____. A) polymerase fragments B) Okazaki fragments C) helix fragments D) strand pieces 11.The synthesis of messenger RNA from template DNA is called ____. A) transcription B) intron processing C) helix transfer D) ribosomal transfer 12. What eukaryotic gene regulation is shown here?

a. RNA interference b. lac operon c. trp operon d. d. mutation

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13. This shows Griffith's transformation experiment. What did the experiment demonstrate? A) mice are immune to bacteria B) strains of bacteria do not change form C) bacteria cannot be killed by heating D) strains of bacteria could change form

14. Hershey and Chase used a ____ to infect bacteria in their experiments. A) yeast toxin B) water molecule C) non-viral molecule D) bacteriophage 15. What three types of RNA are found in living cells? A) fragmented, helix, protein B) messenger, ribosomal, transfer C) protein, Okazaki, transfer D) ribosomal, helix, radioactive 16. The ability to control which genes are expressed is called ____. A) messenger control B) helix response C) external gene selection D) gene regulation

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17. A permanent change in a cell's DNA is called a (an) ____. A) operon B) mutation C) RNA interface D) homeobox gene 18.The chromosomal abnormality in which a fragment of a chromosome breaks off and then reattaches to the original chromosome in the same place but in the reverse direction is called _____. A inversion B translocation C transduction D transformation E duplication 19.What appears to be the mechanism for genomic imprinting? A DNA methylation that silences particular genes B crossing over C DNA methylation that activates particular genes D non-disjunction E both a and c 20. Genetic information of eukaryotic cells is transferred from the nucleus to the cytoplasm in the form of _____. A proteins B lipids C RNA D carbohydrates E DNA 21. What mRNA codon would be made from the DNA triplet CGT? A. ATU B GCA C TCU D CTA E UCG 22.The codons AAA, CCC, GGG, and UUU specify the amino acids lysine, proline, glycine, and phenylalanine, respectively. What peptide sequence would be encoded by the sequence 5'-CCCAAATTTGGG-3', if present in the coding strand of the DNA?

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A B C D E

lys-pro-gly-phe pro-lys-phe-gly gly-phe-lys-pro phe-gly-pro-lys gly-phe-pro-lys

23. In transcription, _____. A the promoter region acts as an initial binding site for RNA polymerase B only one of the DNA strands is used as the template C the RNA nucleotides used are produced by the cell D all of the above E none of the above 24. Gene A is normally found on chromosome number 15 in humans. If amniocentesis reveals fetal cells containing gene A on chromosome 17, but not on 15, the best explanation would be that _____. A crossing over occurred during synapsis of meiosis I in one parent's gametes B base substitution occurred either during gametogenesis or in the mitotic divisions following fertilization C an inversion of gene A occurred on chromosome 15 D translocation occurred E at least one parent probably had a genetic syndrome 25. In eukaryotes, which of the following mechanisms of gene regulation operates after transcription, but before translation of mRNA into protein? A RNA splicing B DNA packaging into nucleosomes C action of repressors and activators D protein degradation E all of the above 26. Which statement about feedback inhibition is true? A) It is typically found in anabolic pathways. B) It allows a cell to adapt quickly to fluctuations in the availability of important substances. C) The end product of the metabolic pathway controls the activity of the first enzyme in the pathway.

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D) If the end product accumulates in the cell, the whole pathway is shut down. E) all of the above 27. In prokaryotic genomes groups of functionally related genes along with their promoters and operators are found together in __________ A) a repressor B) an operon C) a regulatory gene D) an enhancer E) a transcription factor 28. In general, operons that encode the enzymes of a biosynthetic (anabolic) pathway (such as the trp operon) are _____, and those encoding the enzymes of a catabolic pathway (such as the lac operon) are _____. A) repressible; inducible B) inducible; repressible C) permanently on; permanently off D) permanently off; permanently on E) easily mutated; resistant to mutations 29. In an inducible operon, the inducer is often the _____ in the pathway being regulated; the inducer binds to the _____, thus rendering it _____. A)end product; corepressor; inactive B)end product; repressor; inactive C)substrate; corepressor; inactive D)substrate; repressor; active E)substrate; repressor; inactive 30. Post-transcriptional controls _____. A) can include translational controls B) can affect mRNA stability C) may regulate the rate at which a molecule is translated D) can regulate mRNA splicing E) all of the above 31. A cancer cell _____. A) is typically more than 10 times larger than a normal cell B) usually does not contain a nucleus

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C) does not respond to the chemical signals that control cell division D) requires less nutrients than a normal cell E) all of the above 32)Why are phages useful in treating bacterial infections in humans? A Because of their host specificity, they only attack bacteria. They do not affect eukaryotic cells. B Because of their specificity, a phage can be used that will only infect the pathogenic bacteria, leaving helpful bacteria alone. C Because phages are free to evolve, bacteria are less likely to develop a lasting resistance to them. D They are not useful, and the practice has been banned in all countries. E The first three answers are correct. 33) Emerging viruses can originate from which of the following sources? A animal viruses B the mutation of existing human viruses C viruses previously confined to small, isolated populations that can now spread due to technological or social changes such as the development of affordable international travel D all of the above E none of the above 34) What is the function of hemagglutinin in the influenza virus? A Hemagglutinin is the name of the reverse transcriptase enzyme in the influenza virus. B Hemagglutinin helps release new viruses from infected cells. C Hemagglutinin is part of the protein capsid of the influenza virus. D Hemagglutinin is the protein that helps the influenza virus attach to host cells. E Hemagglutinin is involved in assembling the membrane envelope that the virus uses as a cloak when it leaves an infected cell. 35. Transgenic organisms can be scientifically or commercially useful only if _____. A) the inserted ("foreign") gene is drawn from the human genome B) the inserted ("foreign") gene is expressed in the host organism C) the host organism is a microorganism

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D) the vector is a plasmid E) all of the above 36. The technique invented by Mullis to amplify DNA without cloning is called: a. cDNA b. PCR c. RFLP d. Sanger sequencing 37. An enzyme that cuts DNA at a symmetrical sequence of bases is called a _____. A) reverse transcriptase B) restriction enzyme C) cDNA D) palindrome E) ligase 38. In genetic engineering, "sticky end" refers to _____. A) a technique for finding a gene of interest within a nucleus without destroying the cell B) the ability of plasmids to stick to a bacterial cell wall and thus be taken up into the bacterium C) short bits of single-stranded DNA left at the end of DNA molecules cut by restriction enzymes D) the site on mRNA that sticks to the DNA during transcription E) none of the above 39. What two enzymes are needed to produce recombinant DNA? A) a restriction enzyme and a topoisomerase B) a restriction enzyme and a ligase C) a restriction enzyme and a polymerase D) a polymerase and a ligase E) a polymerase and a topoisomerase 40. Which arrangement of the following four enzymes represents the order in which they would be used in a typical gene-cloning experiment resulting in the insertion of a cDNA into a bacterial plasmid? Begin with the gene's mRNA transcript.

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A) restriction enzyme, reverse transcriptase, DNA polymerase, DNA ligase B) restriction enzyme, DNA ligase, reverse transcriptase, DNA polymerase C) reverse transcriptase, DNA polymerase, restriction enzyme, DNA ligase D) reverse transcriptase, DNA ligase, DNA polymerase, restriction enzyme E) reverse transcriptase, restriction enzyme, DNA polymerase, DNA ligase 41. During meiosis, homologous chromosomes sometimes "stick together" and do not separate properly. This phenomenon is known as _____. A cellular sterility B meiotic failure C gametic infertility D nondisjunction E sticky chiasmata 42. Bacteria use restriction enzymes to _____. A synthesize DNA B synthesize RNA C synthesize protein D destroy foreign protein E destroy foreign DNA 43. An enzyme that cuts DNA at a symmetrical sequence of bases is called a _____. A reverse transcriptase B restriction enzyme C cDNA D palindrome E ligase 44.In genetic engineering, "sticky end" refers to _____. A a technique for finding a gene of interest within a nucleus without destroying the cell B the ability of plasmids to stick to a bacterial cell wall and thus be taken up into the bacterium

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C short bits of single-stranded DNA left at the end of DNA molecules cut by restriction enzymes D the site on mRNA that sticks to the DNA during transcription E none of the above 45.Which one of the following enzymes could seal a nick in one strand of a double-stranded DNA molecule by creating a sugar-phosphate bond between the adjacent, unjoined nucleotides? A DNA ligase B reverse transcriptase C restriction enzyme D terminator enzyme E DNA polymerase 46. What is the origin of the phospholipid membrane that envelops many animal viruses? A It is produced by viral enzymes and contains only viral proteins and phospholipids. B It is assembled from free phospholipids floating in the cell's cytoplasm. C It is "stolen" from the host cell and contains only host cell proteins and phospholipids. D It is assembled in the ER based on signals sent out by the viral genome. E It is "stolen" from the host cell, but it contains some proteins encoded by the viral genome. 47.Prions are _____ that are thought to cause disease by _____. A abnormally shaped proteins; inducing similar but normally shaped proteins in the brain to adopt the abnormal form B RNA molecules; encoding toxic proteins C mutant DNA molecules; encoding toxic proteins D an abnormal type of capsid; dramatically enhancing the rate of viral infection E DNA molecules; jumping around the genome and mutating genes 48) In a particular species of mammal, black hair (B) is dominant to green hair (b), and red eyes (R) are dominant to white eyes (r). When a BbRr individual is mated with a bbrr individual, offspring are produced

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in a ratio of 5 black hair and red eyes:5 green hair and white eyes:1 black hair and white eyes:1 green hair and red eyes. Which of these explanations accounts for this ratio? A Green-haired individuals have a higher prenatal mortality than blackhaired individuals. B The genes for hair color and the genes for eye color are carried on different chromosomes. C The expected results did not take genetic recombination into account. D The genes for both of these traits are carried on the autosomes. E The genes for hair color and eye color are linked. 49) In Klinefelter syndrome, individuals are phenotypically male, but they have reduced sperm production and may have some breast development in adolescence. The cells of Klinefelter individuals have two X chromosomes and one Y (they are XXY instead of XY). This occurs because of what meotic error? ( Concept 15.4) A translocation B polyploidy C aneuploidy D duplication E monosomy 50. Which of the following is false? a) bacterial cells typically have a single RNA b) RNA polymerase has helicase activity c) RNA polymerase II synthesizes pre-mRNA in eukaryotes d) RNA polymerase does not require a primer e) RNA polymerase synthesizes RNA that is complementary to the coding strand of DNA 51. At one point as a cell carried out its day-to-day activities, the nucleotides GAT were paired with the nucleotides CUA. This pairing occurred _____. A) in a double-stranded DNA molecule B) during translation C) during transcription D) when an mRNA codon paired with a tRNA anticodon E) It is impossible to say, given this information.

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52. Which one of the following catalyzes the linkage between ribonucleotides to form RNA during gene expression? A) RNA polymerase B) RNA ligase C) ribozyme D) reverse transcriptase E) tRNA 53. In eukaryotic cells, a terminator in mRNA synthesis is _____. A) an enzyme whose specific function is to stop synthesis B) a molecule of tRNA that recognizes a stop codon C) a specific nucleotide sequence in DNA that signals the RNA polymerase to stop D) a specific nucleotide sequence in mRNA that signals the RNA polymerase to stop and to release from the DNA E) none of the above 54. In a eukaryotic cell, transcription takes place _____. A) on the cell membrane B) in the rough endoplasmic reticulum C) in the cytoplasm D) on free ribosomes E) in the nucleus 55. Which of the following summaries of protein synthesis is correct? A) DNA transposons leave the nucleus, are transported to a ribosome, and catalyze the polymerization of amino acids in a protein. B) DNA exchanges its thymine units with uracil in polymerase. This activates polymerase, and it starts joining amino acids together. C) Transfer RNAs line up on a ribosome, and amino acids bind to them with hydrogen bonds. D) Messenger RNA is made on a DNA template, and then amino-acidbearing transfer RNAs bind to it through codon-anticodon pairing. E) DNA strands separate in the nucleus to form mRNA. mRNA leaves the nucleus and is transcribed into tRNA on ribosomes. 56. The Philadelphia chromosome present in individuals with chronic myelogenous leukemia forms as the result of: a) chromosomal deletion b) chromosomal duplication c) a mutation in a tumor suppressor gene

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d) a chromosomal reciprocal translocation e) a single mutation in a proto-oncogene 57) If the codon CAG is mutated to UAG it is a(n): a) frameshift mutation b) missense mutation c) nonsense mutation d) indel e) point mutation f) a and e g) b and e h) c and e I) d and e 58) RAS is an example of a: a) growth hormone b) operon repressor c) proto-oncogene d) transcription factor e) tumor-suppressor gene 59) Which of the following describes viruses: a) the are living entities b) they evolved from cells c) The have capsids containing both RNA and DNA in the same virus d) The reproduce only inside cells e) They typically have hundreds of genes in their genomes f) They use genetic dictionaries different from prokaryotes and eukaryotes g) a, b, c, and d only 60) HIV: a) is a DNA containing virus b) is an enveloped virus c) has two reverse transcriptase molecules in its capsid d) a and b e) a and c f) b and c g) a, b, and c

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BIOLOGY TODAY
Even more bullshit from bygone days.

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AN INTRODUCTION TO LIFE ON EARTH

(Before I begin taking notes I should warn all readers that this is my first hard science class. By hard, I meanbased on facts. Its also my first natural science course. So, I may not know what Im talking about the entire timeand things will definitely get confusing, so I seriously recommend reading the book and taking your own notes. That is all. Oh, and there are hundreds of definitions to rememberso be warned.)

WHAT ARE THE CHARACTERISTICS OF LIVING THINGS?:

The first question they offer up is, What are the characteristics of living things? While they admit that describing such a complex thing is difficult, they do make a list of some characteristicsso, Ill do the same. First of all, living things have a complex structure made almost entirely of organic, carbon based molecules. Living things acquire and use energy from their environment and convert them into different forms. Living things engage in homeostasis (which we should know about from psychology). Living things grow. Living things can evolve. Living things respond to stimuli from their environment. Living things reproduce using a molecular blueprint called DNA. Thats all. Life on Earth is composed of a hierarchy of structures, with each level of hierarchy based on the one below it and providing the foundation for the one above it. Living things are also complex. Table salt, as the book points out, is rather simplewhile the ocean is rather unorganized, and a flea is highly organized, with many different elements that link together to form its whole existence. All of life is built on a chemical foundation based on elements. As we should know, atoms are the smallest particles of and element that retains properties. When atoms come together they form molecules. For example, when two hydrogen atoms and one oxygen atom come together they form one water molecule (H2O). The molecules of life (which are carbon-based) are called organic molecules. As we should also know, a cell is the smallest unit of life. The cell contains many parts that will be discussed in a later chapter. It goes on to talk about all the other hierarchies of life, though I wont get into them because you can look at the nice graph on page 3.

LIVING THINGS ARE BOTH COMPLEX AND ORGANIZED

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Living things need energy to do anything and everything (reproduce, work, and so on). The atoms and molecules of which all living organisms are composed of are called nutrients, and can be extracted from the air, water, or soilor even from other living things. The sum total of all the chemical reactions needed to sustain life is called metabolism. They go on to define energy as the ability to do work. We should all know that plants obtain energy from photosynthesis, while humans and other animals obtain it from plants and other animals. Ultimately, however, all the energy that sustains life comes from the sun. Its the circle of life, man.

LIVING THINGS MUST ACQUIRE & USE MATERIALS & ENERGY

HOMEOSTASIS MAINTAINS CONSTANT INTERNAL CONDITIONS

To stay alive and function effectively, organisms must keep the conditions within their bodies fairly constant, a process called homeostasis. The human body, as an example, has many different ways to maintain homeostasis (such as sweating, metabolizing more food in cold weather, and so on). Well, theres not much more here.

GROWTH IS A PROPERTY OF ALL ORGANISMS

Yes, growth is a property of all living things. This is true, and nothing else should be mentioned (seeing that nothing else is mentioned in the book). Ah ha!

LIVING THINGS RESPOND TO STIMULI

Okay, so living things respond to stimulithis is true. Animals and humans have developed very complex ways of responding to stimuli. When you are hungry, there are reactions going on in your stomach to tell you. You can see light, hear noises, and so on. Most animals have better developed senses than humans, but who caresright?

LIVING THINGS REPRODUCE THEMSELVES

This section and the next one are pretty self explanatory, so I wont comment on them.

LIVING THINGS HAVE THE CAPACITY TO EVOLVE

Evolution is, perhaps, the most interesting concept that will be discussed in Biology (in my opinion, anyway). I wont get into it now, since this is just an introduction, and we will be getting into it in detail later.

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All organisms can be grouped into three different categories called domains. They are, Bacteria, Archaea, and Eukarya. Members of the Bacteria and Archaea domains are mostly comprised of simple, singlecell organisms. As for the Eukarya domain, it can be further divided into four kingdomsthat of Protista, Fungi, Animalia, and Plantae. The factors used to classify each organism vary, but three common ones are used. They are: cell type, number of cells, and mode of nutrition (how they acquire their energy).

CATEGORIZING THE DIVERSITY OF LIFE

BACTERIA, ARCHAEA, AND EUKARYA

There are two different types of cells. They are known as prokaryotic and eukaryotic. Eukaryotic cells are much more complex than prokaryotic. They have a nucleus, they have many different organelles, and they are larger. This is pretty much all you need to know, so lets leave it at that. Okay, there is some more we must contend with. Bacteria, Archaea and members of the Protista kingdom are primarily unicellular, while members of the other kingdoms are multicellular. Okay, how about I introduce a few more terms and definitions? Sounds good, right? Well, as you should know, organisms differ in the way they obtain energy. Living things that capture energy from the sunlight are called autotrophs. Living things that obtain their energy from other living things are called heterotrophs. I am a heterotroph. You are a heterotroph, and the plants outside your window are autotrophs. Thats it.

MEMBERS OF DIFFERENT KINGDOMS AND ENERGY ACQUISITION

WHAT DOES THE SCIENCE OF BIOLOGY ENCOMPASS?: SCIENTIFIC PRINCIPLES UNDERLIE ALL SCIENTIFIC INQUIRY
The scientific inquiry is based on a small set of assumptions. These are called principles, and they are: the principles of natural causality, uniformity in space and time, and common perception. Natural Causality: Okay, this principle is rather easy to understand. While some people believe that events throughout time are the result of some super natural being, scientists (particularly biologists) believe in the idea of natural causalitystating that things happened naturally. There is no High God in the skyit is simply nature.

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The Natural Laws: There are laws in our existence that are constantthat will never be changed or broken. Such laws include: gravity, the speed of light, and the interaction of atoms. These laws have never changed, and never will. They will remain the same no matter where you areeven if your on Pluto. There is mention of the term creationism, which is a philosophical belief that God created everything a long time ago. While no one can disprove this theory, scientists dont pay much attention to it. Perception of Events and the Scientific Inquiry: Okay, so people tend to perceive events in a similar fashion. While we dont perceive aesthetic things the same way, we do perceive colors, and other things the same. This allows scientists to rely on the information about the natural world. Isnt that just great. Okay, so have any of you out there head of the scientific method? I would surely hope so. If you havent, then I recommend dropping this class and going back to first grade where you can spend quality time showing your power ranger toys. Anyway, there are four basic steps in the scientific method. 1, observation, 2 hypothesis, 3 experiment, and, 4 conclusion. The book goes ahead and defines these four steps, though I wont because you should know them. However, I will get into some other aspectswell, no I wont.

THE SCIENTIFIC METHOD IS THE BASIS FOR SCIENTIFIC INQUIRY

SCIENCE IS A HUMAN ENDEAVOR

Okay, so they just say that scientists are human beings, driven by the same urges as any other person, and they are prone to make mistakes. Mistakes should be embracedfor without mistakes some things may never have been discovered, as we will learn in just one moment. A Good Scientist is Prepared to Take Advantage of Chance Events: If you dont know who the founder of penicillin is, take especial note here. Alexander Fleming found penicillin on a chanceactually by mistake. One of his culture dishes had been left outwhich most scientists would of thrown outand when he inspected it he found that no bacteria was growing around the mold. So, the moral of the story is, embrace mistakesbecause they might just turn out to be something that can make you famous and rich.

SCIENTIFIC THEORIES HAVE BEEN THOROUGHLY TESTED

Okay, so the word theory means something different in biology than it does in, say, psychology. A theory in biology is an explanation of a

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natural phenomenon, developed through extensive and reproducible observations. It is more like a principle, or a natural law. The theory of gravitation is an example. It says that evolution is probably the foremost scientific theorywhich well talk about in just a moment.

EVOLUTION THREE NATURAL PROCESSES UNDERLIE EVOLUTION

Darwin and Wallace formulated the theory of evolution back in the mid 1800s. Evolution arises as a consequences of three natural processes: (1) genetic variation among members of a population; (2) inheritance of those variations by offspring of parents who carry the variation; and (3) natural selection, the survival and enhanced reproduction of organisms with favorable variations. Well get into these in more description in future chapters. Much of the Variability Among Organisms is Inherited: what this section is saying is this: we are all different because of genetic mutations in the strings of DNA. Along the line of time such mutations occurred (either hurting or helping the offspring) and created different looking, sounding, and so on people and animals. No two people are the sameand this is the reason why. Environmental influences have some to do with it, but its mostly genetic. Natural Selection Tends to Preserve Genes: And what is there to know about Natural Selection? Well, how about survival of the fittest. Over time good genetic mutations prevailed in human society, and the weak were left to die off. This is called natural selection. I dont want to get too far into it because the section is rather short, and I know there are several chapters devoted to the theory of evolutionso Ill just skip ahead to the last section.

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ENERGY FLOW IN THE LIFE OF A CELL

I dont know why, but Biology presents a problem for methat of not knowing what the hell anyone is talking about. Ive never been good at natural sciences, but I didnt think Id have this much trouble. Maybe its just all this chemistry stuffbecause I never took it in high schoolI opted for Physics. Anyway, lets get on with the notes. These are rather short, so youll have a break. Enjoy.

So, what the hell is energy? Well, the simple definition is the capacity to do work. Work can be anything from photosynthesis to moving around. There are two types of energy. Kinetic Energy and Potential Energy. Kinetic energy is the energy of movementincluding light, electricity, and movement of large objects. Potential energy is basically stored energy that has potential to become kinetic energy. Potential energy includes chemical energy stored in bonds that hold atoms together in molecules, and electrical energy stored in a battery. Kinetic energy can be converted into potential energy and vice-versa. The book says that if you want to understand the flow of energy you need to know two things. (1) the quantity of available energy and (2), the usefulness of the energy. Lets get on to thermodynamics.

WHAT IS ENERGY?

THERMODYNAMICS AND BASIC PROPERTIES OF ENERGY

Thermodynamics define the basic properties and behavior of energy. There are several laws of thermodynamics. The first law sates that, assuming there is no change in quantity of energy; the amount of energy remains constant. This law is known as the law of conservation of energy. Energy cannot be created or destroyed, but it can change from one form to another (this goes along with the first law). The second law of thermodynamics states that when energy is converted from one form to another the amount of useful energy decreases. This law also tells us about the organization of matter. Regions of concentrated energy tend to be regions of great orderliness. So, if energy does not enter a system that system will move towards a more random disordered state. This tendency toward loss of orderliness and high-level of energy and an increase in randomness, disorder, and lowlevel energy is called entropy. Become very familiar with this term.

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So, if energy is drawn to disorder and randomness, why are humans so organized and complex. Well, we are because we have high concentrations of energy. However, our whole life system includes the sunbecause the sun gives us our energy. Because the sun is constantly pumping out extremely high levels of energythat is, random, disordered energyit outweighs the amount of orderliness we have here on earth. The whole system is more disordered than ordered. Do you understand? Okay. Read the book then. First I need to define a few terms. A chemical reaction converts substances known as reactants into another set of substances called the products. There are two, and only two, types of chemical reactions exergonic and endergonic. The reaction is exergonic if the reactants have more energy than the products. This reaction releases energy. And the reaction is endergonic if the products have more energy than the reactants. This reaction requires an influx of energy from some outside source. All right, moving on. . .

SUNLIGHT AND ENTROPYWHY HUMANS HAVENT BLOWN THEMSELVES UP

HOW DOES ENERGY FLOW IN CHEMICAL REACTIONS?

EXERGONIC REACTIONS

Since you already know what an exergonic reaction is, we will move on to other terms. First, all chemical reactions require an initial input of energy called the activation energy. They need this energy to get started. The usual source of activation energy comes from kinetic energy of movement. They give an example that when a runner runs, he or she is burning sugar inside his or her body. The energy in one molecule of sugar is greater than the carbon dioxide and water produced when sugar is burned.

ENDERGONIC REACTIONS

Okay, knowing that in endergonic reactions the products have more energy than the reactants, and that the reaction requires an influx of energy from some outside source to get started, we can conclude that endergonic reactions are uphillgoing from low energy to high energy. The example is: when plants photosynthesizeusing carbon dioxide and watertheir product (sugar) has more energy than do the initial molecules. The influx of energy to get the reaction started comes from the sunas we should already know. Great.

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COUPLED REACTIONS

Not all endergonic reactions get their energy from the sun. Some obtain this energy from exergonic, or energy-releasing, reactions. In coupled reactions, an exergonic reaction provides the energy needed to drive an endergonic reaction. All living things constantly use energy given off by exergonic reactions to drive essential endergonic reactions. But you see, exergonic reactions typically occur away from the endergonic reactionsso there must be a way that the energy is transferred, right? Well, energy-carrier molecules normally transfer energy from place to placethe most common energy-carrier molecule being ATP (which well learn more about later).

CHEMICAL REACTIONS ARE REVERSIBLE

Okay, so most chemical reactions are reversible. They can go in either wayproducts to reactants, or reactants to products. The book gives a fine example, and explains it better than I canso look at it. What are metabolic reactions? What the hell is metabolism? Well, metabolism of a cell is the sum of all its chemical reactions. Many of these chemical reactions are linked in sequences called metabolic pathways. Different metabolic pathways may utilize the same molecules; as a result, all the reactions and all the molecules of a cell are interconnected in a single, enormously complicated metabolic pathway. The same laws of thermodynamics govern chemical reactions in cellsbut how do metabolic pathways arise? The biochemistry of cells is finely tuned in three ways. (1) Cells regulate chemical reactions through the use of proteins called enzymes. (2) Cells couple reactions together, driving endergonic reactions with the energy released from exergonic reactions. And (3) Cells synthesize energy-carrier molecules (such as ATP) to carry energy from exergonic reactions to endergonic reactions. Enoughlets move on.

HOW DO CELLS CONTROL THEIR METABOLIC REACTIONS?

BODY TEMPERATURE AND SPONTANEOUS REACTIONS

In general, how fast a reaction occurs is determined by its activation energy. So, reactions that require a low level of activation energy can proceed swiftly at body temperatures, while reactions that require a high level of activation energy move more slowlyor are nonexistent at body temperature. Raising the temperature, thereby increasing the speed of molecules, can accelerate most reactions.

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Catalysts reduce activation energythis is a fact. Catalysts are molecules that speed up the rate of reaction without themselves being used up or permanently altered. Catalysts speed up reaction by reducing the activation energy. There are three important principles about all catalysts: (1) Catalysts speed up reactions. (2) Catalysts can speed up only those reactions that would occur spontaneously anyways, but at a much slower rate. And (3) catalysts are not consumed in the reactions they promote. No matter how many reactions they accelerate, the catalysts are not permanently changed. All right! So, Enzymes are biological catalysts, normally proteins, synthesized by living organisms. Enzymes are like the catalysts that we just looked at, but they have two important aspects that separate them from inorganic ones. (1) Enzymes are normally very specific, catalyzing at most only a few types of chemical reactions. In most cases, an enzyme catalyzes a single reaction that involves one or two specific molecules but leaves even quite similar molecules untouched. And (2) Enzyme activity is regulatedthat is enhanced or suppressedin many cases by the very molecules whose reaction they catalyze. Enzymes are proteins with complex thee-dimensional shapes. Each enzyme has a dimpleor a groovecalled the active site, into which reactant molecules, called substrates, can enter. The enzyme only allows certain substrates to enter its active sitemuch like a lock and key. Enzymes speed up chemical reactions because the interactions between the substrate and the enzyme are like a series of minireactions, each with a very low activation energy. These many reactions build up and allow the overall reaction to surmount and proceed at body temperature. Enzymes, and their complex three-dimensional shapes, are very sensitive to the environment. Each enzyme has evolved to operate at a specific pH, temperature, and salt concentration. Most enzymes operate at a pH between 6 and 8. Some enzymes also require the help of coenzymeswhich are organic molecules that bind to the enzyme and interact with the substrate molecule. Coenzymes help weaken the

CATALYSTS

WHAT ARE ENZYMES?

THE STRUCTURE OF ENZYMES

THE ACTIVITY OF ENZYMES AND THEIR ENVIRONMENT

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bonds of the substrate, allowing it to react with the enzyme. How wonderful! Cells regulate the amount and activity of their enzymes, thus precisely regulating their metabolic reactions. To be useful, metabolic reactions within cells must be carefully controlledthey must occur at the proper rate and with the proper timing. I wont say anything furtherread this section on your own. Weve already talked about his concept. Energy-carrier molecules work something like rechargeable batteries, picking up an energy charge at an exergonic reaction and taking it to an endergonic reaction. Moving on.

CELLS, ENZYMES AND METABOLIC REACTIONS

HOW IS CELLULAR ENERGY CARRIED BETWEEN REACTIONS?

ATP

The most common energy-carrier molecule in cells is adenosine triphosphate, or ATP. The life span of an ATP molecule is very short, because this energy carrier is continuously being formed, broken apart to ADP, and resynthesized. ATP is not a long-term energy storage moleculeit is a short-term carrier. Not all energy is carried by ATPin fact, some energy is transferred to electrons. Electron carriers capture these energetic electrons. Loaded electron carriers then donate the electrons, along with their energy, to other molecules. We will learn more about these in later chapters.

ELECTRON CARRIERS

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THE STUDY GUIDE

CHAPTER ONE WHAT ARE THE KEY CHARACTERISTICS THAT MAKE SOMETHING LIVING?

Well, the first is that living things have a complex structure made almost entirely of organic, carbon based molecules. Living things acquire and use energy from their environment and convert it into different forms. Living things engage in homeostasis (the balancing of needsin a sense). Living things grow. Living things can evolve. Living things respond to stimuli from their environment. And, living things reproduce using a molecular blueprint known as DNA.

The basic steps of the scientific method are as follows: Observation Hypothesis Experiment Conclusion [It is important to have controls in any experiment so that that the experimenter can isolate what it is he is testing. For instance, look back to the short paper on the water boiling experiment and find why controls are always good to have. If one didnt have controls, any experiment one would conduct would be invalid.]

WHAT ARE THE BASIC STEPS OF THE SCIENTIFIC METHOD AND WHY ARE CONTROLS SO IMPORTANT?

CHAPTER TWO:
Questions from the Online Atom Assignment What are the three main particles of an atom? Answer: Proton, neutron, electron Protons and neutrons move around in the nucleus of an atom: True What is an ion? Answer: An ion is an atom or molecule that has a net charge. This is because there are either more or less electrons than normal. Elements with the same chemical properties are grouped in rows or columns in the periodic table? Answer: all elements in the same

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column of the Periodic Table share the same number of Valence Electrons. Elements combine to form what? Answer: Molecules Elements are more stable when what happens to their energy shells? Answer: When they become filled with their specified limits (usually 8 electrons) Why is hydrogen gas more stable than hydrogen atoms? Answer: hydrogen gas is two hydrogen atoms bonded together in a covalent bond. The two atoms share each others electrons, thus they feel as if they have two electrons and subsequently feel as if their orbital is full (remember, it is the lowest energy shell).

WHAT IS A CHEMICAL BOND COMPOSED OF?

Well, basically, the losing or gaining of electrons would constitute a chemical bond. Also, chemical reactions are behind the making and breaking of chemical bonds.

CHAPTER THREE WHAT ARE THE TWO LAWS OF THERMODYNAMICS?

Well, the first law says that, assuming there is no change in quantity of energy, the amount of energy remains constant. Also, energy cannot be created or destroyed, but it can change from one for to another (this law is called, law of conservation of energy). The second law states that when energy is converted from one form to another the amount of useful energy decreases. This law also tells us about the organization of matter. Regions of concentrated energy tend to be regions of great orderliness. So, if energy does not enter a system, that system will move towards more disorderwhich is known as entropy.

WHAT IS ACTIVATION ENERGY? ALSO, WHY IS ENERGY IMPORTANT TO ENDOTHERMIC AND EXOTHERMIC REACTIONS?

Well, well well. All chemical reactions require an initial input of energy, called activation energy, to get them started. As for the second part,

WHAT ARE ENZYMES? WHAT DO THEY DO? WHY ARE THEY IMPORTANT TO LIVING BEINGS?
Okay, to begin with, enzymes are biological catalysts (they reduce the amount of activation energy needed and speed up the rate of reaction without themselves being used up), normally proteins, synthesized by

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living organisms. Enzymes are very specific, catalyzing only a few specific chemical reactions. I think this is good enough.

CHAPTER FOUR

Okay, I know about the cell membranes and all that mumbo-jumbo. However, there are a few terms I must brush up on. Diffusion can happen from low areas of concentration to high areas of concentration or vice-versa. Osmosis is the diffusion of water across cell membranes. Simple diffusion is when things easily go through cell membranes (such as water, though it is called something different because biologists are name-crazy sum-a-bitches). Facilitated diffusion is when things go through the membrane with help from channel proteins and carrier proteins. Well, passive transport is when things move across, or through, the cell membrane with ease and without help. However, during active transport, things must utilize energy from other sources to get through the membrane. Transfer proteins, and carrier proteins are the helpers during active transport. The three types of active transport are: Active transport: movement of individual small molecules or ions through membrane-spanning proteins, using cellular energy, normally ATP. Endocytosis: Movement of large particles, including large molecules or entire microorganisms, into a cell by engulfing extracellular material, as the plasma membrane forms membranebound sacs that enter the cytoplasm. Exocytosis: movement of materials out of a cell by enclosing the material in a membranous sac that moves to the cell surface, fuses with the plasma membrane, and opens to the outside, allowing its contents to diffuse away.

WHAT ARE THE DIFFERENT TYPES OF DIFFUSION?

WHAT IS ACTIVE TRANSPORT AND PASSIVE TRANSPORT?

TERMS TO KNOW

Isotonic: The extracellular fluid has the same concentration on the outside as on the inside. Animal cells are usually like this. Hypertonic: Solution that have a higher concentration of dissolved particles than does a cells cytoplasm, and thus cause water to leave the cell by osmosis.

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Hypotonic: Solutions that have a lower concentration of dissolved particles than a cells cytoplasm does, and thus cause water to enter the cell by osmosis.

CHAPTER FIVE

For study question for chapter five, look towards Homework assignment 3. What are the similarities and differences between animal and plant cells (both eukaryotic)? Again, look at the Homework Assignment 3.

CHAPTER SIX WHAT ARE CHLOROPLASTS AND WHAT IS THE ROLE OF CHLOROPHYLL?

Chloroplasts are specialized organelles, surrounded by a double membrane, that are the sites of photosynthesis in the eukaryotic cells of plants and of photosynthetic protists. Chlorophyll is a green pigment that captures energy (sun light) during photosynthesis and transfers it to other molecules in the thylakoid membranes.

The two stages that occur in photosynthesis are the light dependent and the light independent reactions. In the light-dependent reaction, chlorophyll and other molecules in the membranes of the thy6lakoids capture sunlight energy and convert some of it into the chemical energy of energy-carrier molecules (ATP and NADPH). In the light-independent reaction, enzymes in the stroma use the chemical energy of the carrier molecules to drive the synthesis of glucose or other organic molecules. Light dependent reactions occur in the membranes of the thylakoid. The light-independent reactions occur in the stroma. I know that I mentioned it above, but it doesnt hurt to repeat, repeat, repeat.

WHAT ARE THE TWO STAGES OF PHOTOSYNTHESIS AND WHAT ULTIMA TELY OCCURS IN EACH?

WHERE DOES EACH STAGE HAPPEN (IN THE CELL)?

WHAT IS USED AND PRODUCED IN THE LIGHT REACTION (LIGHT DEPENDENT)?

Well, sunlight is used and ATP and NADPH is produced.

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In the process of chemiosmosis, hydrogen ions move down their concentration gradient from the intermembrane compartment to the matrix by means of these ATP-synthesizing enzymes. The flow of hydrogen ions provides the energy to synthesize 32 to 34 molecules of ATP from ADP.

WHAT IS CHEMIOSMOSIS?

WHY IS SURFACE AREA IMPORTANT?

Mitochondria and chloroplasts maximize their surface area so that they are able to produce the maximum amount of energy (in the mitochondria) and to photosynthesize the maximum amount of energy (in chloroplasts).

WHAT IS ATP USED FOR?

ATP is an energy carrier molecule used in many cellular function.

WHAT IS USED AND PRODUCED IN THE LIGHT INDEPENDENT REACTION AND WHAT NAME IS GIVEN TO THE CYCLE IN THIS STAGE?

Well, the energy carrier molecules from the light-dependent reaction (ATP and NADPH) are used to produce glucose and other organic molecules. The Calvin-Benson-Cycle (or the C3 cycle) occurs in the lightindependent reaction.

WHAT DOES IT PRODUCE (THE CYCLE)? WHAT DOES NADPH DO?

The C3 cycle produces (though a complex series of reactions) glucose. NADPH is much like ATP, in that it is used as an energy-carrier molecule.

WHAT IS PHOTORESPIRATION AND WHY CAN THIS BE A PROBLEM WHEN WATER IS SCARCE IN THE LEAVES OF PLANTS?

When O2 combines with RuBP (rather than CO2) it is called photorespiration (rather than carbon fixation). Basically the plant cant breath. When the plant is living in a hot, dry climate, CO2 from the air cant get in, and the O2 generated by the photosynthesis cant get out. With CO2 levels low and O2 levels high, photorespiration dominates. Plants, especially seedlings, may die during hot, dry weather because they are unable to capture enough energy in glucose to meet their metabolic needs.

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HOW DO C4 PLANTS DEAL WITH THIS PROBLEM?

C4 plants have evolved in a way to reduce photorespiration and boost photosynthesis during dry weather. Basically they have developed more chloroplasts in different cells, called bundle-sheath cells. Also the chemical reactions that occur in a C4 plant are different and allow for the plant to survive during the hot seasons.

CHAPTER SEVEN WHAT HAPPENS IN GLYCOLYSIS AND WHERE IN THE CELL DOES THIS HAPPEN?

The initial reactions that break down glucose without the use of oxygen are collectively called glycolysis. Glycolysis occurs in the fluid portion of the cytoplasm and results in a molecule of glucose being cleaved into two molecules of pyruvate.

WHAT IS USED AND WHAT IS PRODUCED? WHERE DOES THE PYRUVATE GO (AND DOES MY ANSWER DEPEND ON THE PRESENCE OF SOMETHING)?

During glycolysis only two molecules of ATP and two molecules of NADPH is produced (it also produces pyruvate). Glucose is the reactant used in this chemical reaction. The pyruvate goes on to cellular respiration where it is further broken down and its energy is harvested as ATP. However, some cells ferment pyruvate to form lactate. There is too much oxygen.

STRUCTURES OF MITOCHONDRIA

The mitochondria consists of a double membrane which houses cristae (the folds of the inner membrane), the matrix (the space inside the inner membrane),and the intermembrane compartment (which is basically what it says) The Krebs cycle happens in the matrix of the mitochondria. A pair of pyruvate from glycolysis migrates (diffusion) into mitochondria inner matrix. It binds with Co-enzyme A, releasing 2 CO2 and 2 NADPH (per one pyruvate). Acetyl CoA (co-enzyme A) then enters the Krebs cycle. The Krebs cycle finishes breaking down carbon molecules into CO2 and produces ATP and several electron carrier molecules: (1 FADH2 and 3

KREBS CYCLE AND ITS PURPOSE:

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NADH per acetyl CoA). CO2 then diffuses out of the mitochondria and cell. Carrier molecules enter the electron transport system.

WHAT DOES NADH AND FADH FUNCTION AS (ELECTRON CARRIERS?)

yes, they function as electron carriers during the Krebs cycle.

In the inner-membrane of the mitochondria, energy carrier molecules dump their electrons in the electron transport system. This transport system pumps hydrogen ions out of the matrix to create H+ gradient. H+ drives production of ATP ions. The majority of ATP is produced in the electron transport system (somewhere from 32-34 ATP). At the end, electrons bind with oxygen (from the air you breath) and H+ to produce water. The products of this are: 32-34 ATP molecules, and H2O (any amount would do).

WHAT HAPPENS IN THE ELECTRON TRANSPORT SYSTEM?

WHAT IS ATP USED FOR?

ATP is an energy carrier molecule, and you should all know that.

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TERRAFORMING MARS
PROJECT OVERVIEW: VERY BRIEF
A History of & What is Terraforming: The term first appeared in a science fiction novel by Carl Sagan (who also wrote Contact). Very simple definition: Making a previously inhabitable environment habitable by the use of planetary engineering and by utilizing technological innovations. This is rather unimportant when viewing the entire schemethough students should be informed what were talking about. Possible Planets to Terraform: (Why Mars is our best chance). As of now, Mars is really our only chance. Others have proposed setting up colonies in space, on the Moon, on Mercury, on one of Jupiters satellites, and so on. Then theres always the possibility of other planets revolving around stars in other galaxies (or in our own). However, with current technology Mars is our best chance. Colonizing the farthest reaches of space is still left to the Science Fiction writers. Why would we Terraform Mars: (Good question) is the end of Earth rapidly approaching? Must we really move to Mars because weve hacked Earth to pieces through the years? Is Earth in trouble? As was discussed in Chapter 27 of our Biology book, Earth is rapidly reaching its maximum capacity point. Soon there wont be enough physical space for humans to move aboutunless we follow Chinas rather drastic measures of decreasing population. Or course there is always the idea that soon enough we will run out of natural resources. However, most articles and chapters Ive read on terraforming have ignored this question. It appears as if many are simply intrigued with knowing whether or not such a feat is possible. Reasons for why would have to be inferred or intuited. How would we Terraform Mars: (Both technological and social elements must be considered). Most of the research points towards the technology that must be used (or perhaps created) in order to get Mars to the point where humans may walk freely on its surface. Many of the ideas include a living biosphere that would support human (and other) life while working to transform Mars landscape into a completely habitable environment. Many of the methods are comparably similar in design, though few still seem like Science

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Fiction (the whole rocketing Mars into another orbital pattern, and so on). They seemingly ignore the social and moral principles that come along with taming a foreign planet. Specifics can get a bit hairy. Some basic principles that might be discussed are: raising the temperature of Mars (which may be accomplished by one of many theories) in order to melt the polar caps, importing primitive plants to saturate the atmosphere with breathable gases, setting up large biospheres that would be capable of supporting a few thousand people, and building large factories that would produces chlorofluorocarbons in order to create a green house effect. One must also consider the possibility of who would go to Mars. Would it be like Noahs Ark, only Noahs spaceship? In order for plants to thrive on Mars, social elements must not be considered, but for humans, one would need to consider the sociological institutions that humans have relied on for thousands of years. Would children be taught the history of Earth, or the history of Mars? Would there be a school system, a criminal systemwould new laws need to be written for Martians? This could possibly open up a whole host of questionssome of which could lead into the next section, should we terraform Mars. Should we Terraform Mars: (From an ethical standpointit appears that some of the methods may destroy, or render Mars inhabitable to any form of life for many years). For instance, one method described involves hurling several hundred thermo-nuclear bombs at Mars in order to increase the temperature. This would certainly raise the temp, but in the process it would fill Mars with radiation, and humans wouldnt be able to live on it for thousands (if not millions) of years. As some have stated, in order to terraform Mars, some destructive forces must be exercised. If we did terraform and inhabit Mars, what would prevent humans from destroying it (as we have the Earth), using up all its natural resources, and reproducing until its maximum capacity is reached? Other theories involve sending large meteors at Mars (which has a lot in common with the whole thermo-nuclear idea). What if we find that life does exist on Marsperhaps frozen in the polar caps, or thriving below the surface? Mars Direct Mission: (From the book, Islands in the Sky: Bold New Ideas for Colonizing Space). This is a formal mission proposed by Robert M. Zubrin and David A. Baker. Very in depth. Still debating whether or not to bring this aspect into the project. They have schematics of the ships required to transport materials and people,

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calculations of nearly every aspect, and so on. This could possibly substitute the section above entitled How would we terraform Mars. Plausibility of Mars Direct Mission and others like it: (Is it possible right now to terraform Mars?). Most of it still seems like science fiction. However, many have claimed that the technology needed to perform such a large and daunting task is right at our fingertips its just the time we need to invest and the resources (not to mention a collective global effort) needed that has pushed many into believing such a process is fundamentally impossible. Some have proposed that in a mere few decades Mars could be well on its way to being capable of supporting primitive plant life, and even allowing humans to walk around freely, without the aid of a space suit (or course humans wouldnt be able to breathe the air). However, others still claim that such ideas should be left to the minds of fiction writers.

NOTES FOR PRESENTATION SLIDE ONE: TITLE SLIDE. SLIDE TWO: SECONDARY TITLE SLIDE. SLIDE THREE: WHAT IS TERRAFORMING?

There are several definitions, one from Oxford English dictionary and another from a well-known scientist, Martin (M.J.) Fogg. The picture near the bottom depicts an artists interpretation of just three stages of terraforming. One can see the transformation from a barren, inhabitable environment to a lush, colorful earth-like landscape. The word terraforming was first used in science fiction novels, though was later adapted by the scientific community and included in dictionaries worldwide. Terraforming as a science is a relatively new phenomenonand with each new discovery about space and other planets, the science of terraforming is furthered.

SLIDE FOUR: WHY WOULD WE NEED TERRAFORMING?

This slide offers several general explanation of why humans would possibly want to seek out a new world to explore and inhabit. The doomsday comet, which has recently become quite popular with the media, is perhaps the most extravagant threat to life on Earth. If we were to discover an asteroid on a collision course with Earth, and we had no conventional means to stop it, having a planet close by where humans (and all forms of life for that matter) could easily travel to and live would be invaluable. The second explanation of why humans

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would possibly need to terraform other planets has to do with the rapidly increasing populace. In birth rates continue as they have, soon enough there wont be enough physical space to support us. Having another planet to explore and conquer, so to speak, would provide breathing room for mother Earth. The third explanation has to do with the rapidly depleting natural resources. In the near future, it may be necessary to terraform another planet just so we can extract its resources, or take advantage of its environment. This is, after all, what humans are great at.

SLIDE FIVE: NO TITLE

Martin Fogg offers up another explanation. Simply, he states that it has always been the goal of space exploration to find new worlds to inhabit and settle. This explanation has more to do with just simply finding out whether such a feat is impossiblepushing the envelope, and so on.

SLIDE SIX: POSSIBLE PLANETS TO TERRAFORM

There have been speculations about terraforming Mercury, or even setting up biospheres on the moon, though are only real chance seems to be Mars. Mercury and the Moon would require constant input of the elements needed to sustain life (oxygen, nitrogen, food, water, and so on)whereas Mars could be theoretically terraformed into a planet capable of supporting life on its own, without the need for a biosphere or a constant replenishing of chemicals and supplies. And of course there is always the possibility that in the future other planets in other galaxies will be discovered, some of which might have an environment resembling Earths, or near to it. As technology continues to advance at a rapid pace, these finds may not be too far off. Mars is our best chance for several reasons. First off, Mars is relatively close to eartha trip from Earth to Mars takes a little over six months. In the future, this time may be dramatically reduced. Secondly, Mars distance from the sun, its tilt, rotation, and gravity are all similar to Earths. Third, Mars has large amounts of water stored in its polar caps, large amounts of CO2 in its soil, and all the other chemicals needed to sustain life (most of which are also trapped in the soilas speculated). Fourth, Mars terrain is often compared with that of a vast, expansive desert. Its terrain is suitable for life to live on (its not covered in lava, or ice, and so on).

SLIDE SEVEN: WHY IS MARS OUR BEST CHANCE?

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SLIDE EIGHT: HOW WOULD WE TERRAFORM MARS?

This slide offers up five key modifications that must be made to Mars in order to get the process of terraforming in motion. Perhaps the most important steps involve the presence of liquid water (accomplished through the warming of the planet., and the increasing of O2 and N2 in the atmosphere. These steps alone would produce an environment suitable for some species of primitive plants to survive. The mass of the atmosphere must be increased in order for humans to survive without protective wear.

This slide offers the more destructive methods proposed to warm Mars. Thermo-nuclear bombs could be detonated below the surface of Mars. This destructive force would then cause CO2 to escape from the Martian soil and into the atmosphere. While it may seem like a good way to get the terraforming process started, but the radiation left over from such an explosion (not just one bomb would be used, but hundreds) would render Mars surface inhabitable to man for many years. It somewhat self-defeating. The second destructive method proposed is the manipulation of an asteroid so that it crashes into the surface of Mars. Such a catastrophe would have the same results as detonating a few hundred thermo-nuclear bombs, though without the radiation. However, the plausibility of manipulating and directing an asteroid towards Mars seems to be still in the realm of science fiction. NASA has developed such devices though (which could possibly be used to direct a comet away from its collision course with Earth). Both of these techniques would warm the planet to a high enough degree where the polar caps would begin melting and filling the Martian landscape with water. Both of these techniques would increase the mass of the atmosphere, which would then in turn block out more UV rays.

SLIDE NINE: SURFACE TEMPERATURE (1)

SLIDE TEN: SURFACE TEMPERATURE (2)

Here are two more techniques that could possibly be used to warm the surface temperature of Mars. The first is rather extravagant. If we could build a huge mirror in space, and position it behind Mars, it would reflect the suns rays directly onto the polar caps, thus melting them. It is also believed that a thin layer of CO2 is covering the polar caps, and this layer as were would evaporate into the atmosphere (therefore adding to its mass). Such a mirror, however, would require about 200,000 tons of aluminum. Such a large amount of aluminum could not

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be transported to Mars (well, it could, but it would be damn expensive) so other means of aluminum harvesting would need to be created (for instance, taking it from an asteroid, or meteor, or even from Mars). The second technique described involves an artificial greenhouse effect. If we could set up large plants on the surface of Mars that only produced large amount of CFCs, we could create a greenhouse effect that would warm the planet. Such gases, however, only last so long, so an insane amount of them would need to be produced and distributed. This technique is the longer of the two. By using CFCs to create an artificial greenhouse, the terraforming of Mars would be delayed considerably while the planet warmed up.

SLIDE ELEVEN: INTERLINKING MODIFICATIONS

This slide is pretty self-explanatory.

SLIDE TWELVE: PLAUSIBILITY OF TERRAFORMING MARS

Here we come into contact with the question, Can We Terraform Mars? and Should we Terraform Mars? The Can We question is rather hard to answerseeing that much of the technology needed to terraform is not present. The Should We question is more of a philosophical look on it. What if we find life on Mars? By terraforming Mars we could be killing an alien species. All in all, we need to explore and study Mars more closely before we even consider terraforming it. This also raised the question of, if we have treated Earth so badly that we need to go and find another planet to live on, what will stop us from treated that planet just as bad? Should we really be traveling around the universe, sucking all the resources out of a planet before moving on to another? These questions could go on indefinably. (Movie of Mars rotating). This slide gives the logical approach to the terraforming of Mars. First we will set up a small team of scientists on its surface so they can perform all the experiments and tests they want. When we have a better understanding of Mars, then we can think about the big steps in terraforming.

SLIDE THIRTEEN: POSSIBILITIES

SLIDE FOURTEEN: THE FUTURE

Just a conclusion slide. Throw in a bit of science fiction.

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BOILING WATER
INITIAL THOUGHTS: HYPOTHESIS
Taking my line of thought backwardsbefore I entertained any idea about boiling waterI would have said that regular old water boils faster than salt water. I would have explained it (to a friend of lesser education) in terms of magicthat the salt, possessing some sort of magic power, will somehow slow the boiling process. Of course Id be killing him with bull feathers, but thats how one wins and argument pertaining to a subject that neither arguer knows a shred of information about. The world of atoms, molecules, hydrogen and covalent bonds was a jumbled mess to me. However, after being introduced to these topics I have obtained a small amount of clarity, and, perhaps, am better able to predict an outcome. Therefore, and with the understanding that when salt is added to water the amount of hydrogen bounds diminishes (explained by the hydrogen atoms being attracted to the negative chlorine atoms, and the oxygen atoms being attracted to the positive sodium atoms), I will predict that salt water will boil faster.

METHOD

To design an experiment requires, firstly, knowledge about the subject. Having made macaroni and cheese many times, Im familiar with boiling water. I will secondly need to formulate a method of experimentation where elimination of as many confounding variables is possible. This may prove to be difficult, seeing that overlooking even one variable (and I assume there are many) will offset the entire experiment. I suppose one should start with two identical pots. The pots should be left out overnight so their temperatures are the same. Second, an equal amount of water and salt water should be placed in each pot. The water, as well, should be left to sit overnight (to ensure the water in each pot has identical temperatures). Next, one will need to test the burner to see what the highest temperature it will reach (one should use the same burner, as well). Seeing that the burner may take an unequal time to heat to its maximum temperature, the pots should be set upon the burner when it has already reached its peak temperature. I imagine there is some sort of device to test the temperature of the burner, and I recommend one use it. In each scenario one should make sure the burner is heated to its maximum

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temperature before placing the pot on. The moment the pot is placed upon the burner a time watch should be started (the same time watch should be used for each pot). The experimenter should then record when the water first begins to boil and again when a rolling boil is achieved. A thermometer should be placed in each pot (the same thermometer), and the experimenter should record when the temperature of the water reaches its boiling point. Before each pot is placed on the burner the experimenter should check the room temperature to make sure it remains constant. After the water in the first pot has been boiled, a chunk of time should be allowed for the stove itself to cool off (perhaps one should even check the temperature of the stove before each experiment begins). After the stove is cool, the experimenter should then repeat, exactly, the steps done for the first pot.

CONCLUSION

It all goes well; it should be found that salt water boils faster than spring water. The hypothesis above explains why this should be. In my case I was unable to get materials needed for testing temperatures of both the burner and the stove, though the results did prove my hypothesis correctthe salt water boiled faster.

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accommodation The automatic adjustment of an eye to focus on near objects. acetylcholine (asset-ill-coal-een) One of the most common neurotransmitters; functions by binding to receptors and altering the permeability of the postsynaptic membrane to specific ions, either depolarizing or hyperpolarizing the abdomen membrane. In vertebrates, the portion of the trunk acetyl CoA containing visceral organs other than heart The entry compound for the Krebs cycle in and lungs; in arthropods, the posterior cellular respiration; formed from a portion of the body, made up of similar fragment of pyruvate attached to a segments and containing the reproductive coenzyme. organs and part of the digestive tract. acid abiotic [L. acidus, sour] [Gk. a, not, without + bios, life] A substance that increases the hydrogen ion Nonliving; specifically, the nonliving concentration in a solution. components of an ecosystem, such as acid precipitation temperature, humidity, the mineral content Rain, snow, or fog that is more acidic than of the soil, etc. pH 5.6. abscisic acid (ABA) acoelomate (ab-sis-ik) [L. ab, away, off + scissio, (a-seel-oh-mate) dividing] A solid-bodied animal lacking a cavity A plant hormone that generally acts to between the gut and outer body wall. inhibit growth, promote dormancy, and acrosome help the plant tolerate stressful conditions. (ak-ruh-some) abscission An organelle at the tip of a sperm cell that [L. ab, away, off + scissio, dividing] helps the sperm penetrate the egg. In plants, the dropping of leaves, flowers, ACTH fruits, or stems at the end of a growing Abbreviation of adrenocorticotropic season, as the result of formation of a twohormone. layered zone of specialized cells (the actin abscission zone) and the action of a [Gk. aktis, a ray] hormone (ethylene). A globular protein that links into chains, absorption two of which twist helically about each [L. absorbere, to swallow down] other, forming microfilaments in muscle The movement of water and dissolved and other contractile elements in cells. substances into a cell, tissue, or organism. action potential absorption spectrum A rapid change in the membrane potential The range of a pigment's ability to absorb of an excitable cell, caused by stimulusvarious wavelengths of light. triggered, selective opening and closing of abyssal zone voltage-sensitive gates in sodium and (uh-bis-ul) potassium ion channels. The portion of the ocean floor where light activation energy does not penetrate and where The energy that must be possessed by temperatures are cold and pressures atoms or molecules in order to react. intense. active site acclimatization The specific portion of an enzyme that (uh-kly-mih-ty-zay-shun) attaches to the substrate by means of weak Physiological adjustment to a change in an chemical bonds. environmental factor.

GLOSSARY A

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active transport The movement of a substance across a biological membrane against its concentration or electrochemical gradient, with the help of energy input and specific transport proteins. adaptation [L. adaptare, to fit] (1) The evolution of features that make a group of organisms better suited to live and reproduce in their environment. (2) A peculiarity of structure, physiology, or behavior that aids the organism in its environment. adaptive peak An equilibrium state in a population when the gene pool has allele frequencies that maximize the average fitness of a population's members. adaptive radiation The emergence of numerous species from a common ancestor introduced into an environment, presenting a diversity of new opportunities and problems. adenosine diphosphate (ADP) A nucleotide consisting of adenine, ribose, and two phosphate groups; formed by the removal of one phosphate from an ATP molecule. adenosine monophosphate (AMP) A nucleotide consisting of adenine, ribose, and one phosphate group; can be formed by the removal of two phosphates from an ATP molecule; in its cyclic form, functions as a "second messenger" for a number of vertebrate hormones and neurotransmitters. adenosine triphosphate (ATP) An adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed. This energy is used to drive endergonic reactions in cells. adenylyl cyclase An enzyme that converts ATP to cyclic AMP in response to a chemical signal. ADH Abbreviation of antidiuretic hormone. adhesion [L. adhaerere, to stick to] The tendency of different kinds of molecules to stick together.

ADP Abbreviation of adenosine diphosphate. adrenal gland (uh-dree-nul) [L. ad, near + renes, kidney] An endocrine gland located adjacent to the kidney in mammals; composed of two glandular portions: an outer cortex, which responds to endocrine signals in reacting to stress and effecting salt and water balance, and a central medulla, which responds to nervous inputs resulting from stress. adrenaline A hormone, produced by the medulla of the adrenal gland, that increases the concentration of glucose in the blood, raises blood pressure and heartbeat rate, and increases muscular power and resistance to fatigue; also a neurotransmitter across synaptic junctions. Also called epinephrine. See Epinephrine. adrenocorticotropic hormone (ACTH) A hormone, produced by the anterior lobe of the pituitary gland, that stimulates the production of cortisol by the adrenal cortex. adventitious [L. adventicius, not properly belonging to] Referring to a structure arising from an unusual place, such as roots growing from stems or leaves. aerobic (air-oh-bik) [Gk. aer, air + bios, life] Containing oxygen; referring to an organism, environment, or cellular process that requires oxygen. afferent [L. ad, near + ferre, to carry] Bringing inward to a central part, applied to nerves and blood vessels. agar A gelatinous material prepared from certain red algae that is used to solidify nutrient media for growing microorganisms. age structure The relative number of individuals of each age in a population. agnathan (ag-naa-thun) A member of a jawless class of vertebrates represented today by the lampreys and hagfishes. agonistic behavior (ag-on-is-tik) A type of behavior involving a contest of

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some kind that determines which competitor gains access to some resource, such as food or mates. AIDS (acquired immunodeficiency syndrome) The name of the late stages of HIV infection; defined by a specified reduction of T cells and the appearance of characteristic secondary infections. aldehyde (al-duh-hyde) An organic molecule with a carbonyl group located at the end of the carbon skeleton. aldosterone (al-dah-stair-own) [Gk. aldaino, to nourish + stereo, solid] An adrenal hormone that acts on the distal tubules of the kidney to stimulate the + reabsorption of sodium (Na ) and the passive flow of water from the filtrate. aleurone layer [Gk. aleuron, flour] The outermost cell layer of the endosperm of the grains (seeds) of wheat and other grasses; when acted upon by gibberellin, the aleurone layer releases enzymes that digest the stored food of the endosperm into small nutrient molecules that can be taken up by the embryo. alga pl. algae (al-gah, al-jee) A photosynthetic, plantlike protist. alkaline Pertaining to substances that increase the relative number of hydroxide ions (OH ) in a solution; having a pH greater than 7; basic; opposite of acidic. all-or-none event An action that occurs either completely or not at all, such as the generation of an action potential by a neuron. allantois (al-an-toh-iss) [Gk. allant, sausage] One of four extraembryonic membranes; serves as a repository for the embryo's nitrogenous waste. allele (al-eel) [Gk. allelon, of one another] An alternative form of a gene. allele frequency The proportion of a particular allele in a population.

allergic reaction An inflammatory response triggered by a weak antigen (an allergen) to which most individuals do not react; involves the release of large amounts of histamine from mast cells. allometric growth (al-oh-met-rik) The variation in the relative rates of growth of various parts of the body, which helps shape the organism. allopatric speciation (al-oh-pat-rik) [Gk. allos, other + patra, fatherland, country] A mode of speciation induced when the ancestral population becomes segregated by a geographical barrier. allopolyploid (al-oh-pol-ee-ploid) A common type of polyploid species resulting from two different species interbreeding and combining their chromosomes. allosteric site (al-oh-steer-ik) A specific receptor site on an enzyme molecule remote from the active site. Molecules bind to the allosteric site and change the shape of the active site, making it either more or less receptive to the substrate. allozymes Slightly different versions of the same enzyme, distinguishable via gel electrophoresis. alpha helix A spiral shape constituting one form of the secondary structure of proteins, arising from a specific hydrogen-bonding structure. alternation of generations A life cycle in which there is both a multicellular diploid form, the sporophyte, and a multicellular haploid form, the gametophyte; characteristic of plants. alternative splicing In alternative splicing, the same pre-mRNA molecule, which consists of introns and exons, is spliced in different ways to produce mature mRNAs of different lengths and different functionality.

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altruistic behavior (al-troo-is-tik) The aiding of another individual at one's own risk or expense. alveolus pl. alveoli (al-vee-oh-lus) [L. dim. of alveus, cavity, hollow] (1) One of the deadend, multilobed air sacs that constitute the gas exchange surface of the lungs. (2) One of the milk-secreting sacs of epithelial tissue in the mammary glands. amino acid (am-ee-no) [Gk. Ammon, referring to the Egyptian sun god, near whose temple ammonium salts were first prepared from camel dung] An organic molecule possessing both carboxyl and amino groups. Amino acids serve as the monomers of proteins. amino group A functional group that consists of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of +1. aminoacyltRNA synthetases A family of enzymes, at least one for each amino acid, that catalyze the attachment of an amino acid to its specific tRNA molecule. ammonification The process by which decomposers break down proteins and amino acids, releasing the excess nitrogen in the form of ammonia + (NH 3 ) or ammonium ion (NH 4 ). amniocentesis (am-nee-oh-sen-tee-sis) A technique for determining genetic abnormalities in a fetus by the presence of certain chemicals or defective fetal cells in the amniotic fluid, obtained by aspiration from a needle inserted into the uterus. amnion (am-nee-on) [Gk. dim. of amnos, lamb] The innermost of four extraembryonic membranes; encloses a fluid-filled sac in which the embryo is suspended. amniote A vertebrate possessing an amnion surrounding the embryo; reptiles, birds, and mammals are amniotes.

amniotic egg A shelled, water-retaining egg that enables reptiles, birds, and egg-laying mammals to complete their life cycles on dry land. amoeboid [Gk. amoibe, change] Moving or feeding by means of pseudopodia (temporary cytoplasmic protrusions from the cell body). AMP Abbreviation of adenosine monophosphate. Amphibia The vertebrate class of amphibians, represented by frogs, salamanders, and caecilians. amphipathic molecule A molecule that has both a hydrophilic region and a hydrophobic region. anabolic steroids Synthetic chemical variants of the male sex hormone testosterone; they produce increased muscle mass but also suppress testosterone production, leading to shrinkage of the testes, growth of the breasts, and premature baldness; long-term use increases the risk of kidney and liver damage and of liver cancer. anabolism [Gk. ana, up + -bolism (as in metabolism)] Within a cell or organism, the sum of all biosynthetic reactions (that is, chemical reactions in which larger molecules are formed from smaller ones). anaerobic an-air-oh-bik) [Gk. an, without + aer, air + bios, life] Lacking oxygen; referring to an organism, environment, or cellular process that lacks oxygen and may be poisoned by it. anagenesis (an-uh-jen-eh-sis) A pattern of evolutionary change involving the transformation of an entire population, sometimes to a state different enough from the ancestral population to justify renaming it as a separate species; also called phyletic evolution. analogy The similarity of structure between two species that are not closely related; attributable to convergent evolution.

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analogous [Gk. analogos, proportionate] Applied to structures similar in function but different in evolutionary origin, such as the wing of a bird and the wing of an insect. anaphase (anna-phase) [Gk. ana, up + phasis, form] The third stage of mitosis, beginning when the centromeres of duplicated chromosomes divide and sister chromotids separate from each other, and ending when a complete set of daughter chromosomes are located at each of the two poles of the cell. androgen (an-droh-jens) [Gk. andros, man + genos, origin, descent] The principal male steroid hormones, such as testosterone, which stimulate the development and maintenance of the male reproductive system and secondary sex characteristics. aneuploidy (an-yoo-ploy-dee) A chromosomal aberration in which certain chromosomes are present in extra copies or are deficient in number. angiosperm (an-jee-o-sperms) [Gk. angeion, vessel + sperma, seed] A flowering plant, which forms seeds inside a protective chamber called an ovary. anion (an-eye-on) A negatively charged ion. annual [L. annus, year] A plant that completes its entire life cycle in a single year or growing season. antennae Long, paired sensory appendages on the head of many arthropods. anterior [L. ante, before, toward, in front of] Referring to the head end of a bilaterally symmetrical animal. anther [Gk. anthos, flower] The terminal pollen sac of a stamen, inside which pollen grains with male gametes form in the flower of an angiosperm.

antheridium pl. antheridia In plants, the male gametangium, a moist chamber in which gametes develop. anthocyanin Natural water-soluble pigments of blue, purple or red which are dissolved in the cell-sap vacuole of plant cells. anthropoid [Gk. anthropos, man, human] A higher primate; includes monkeys, apes, and humans. antibiotic [Gk. anti, against + bios, life] A chemical that kills bacteria or inhibits their growth. antibody [Gk. anti, against] An antigen-binding immunoglobulin, produced by B cells, that functions as the effector in an immune response. anticodon A specialized base triplet on one end of a tRNA molecule that recognizes a particular complementary codon on an mRNA molecule. antidiuretic hormone (ADH) [Gk. anti, against + diurgos, thoroughly wet + hormaein, to excite] A hormone important in osmoregulation. antigen (an-teh-jen) [Gk. anti, against + genos, origin, descent] A foreign macromolecule that does not belong to the host organism and that elicits an immune response. aorta (a-ore-ta) [Gk. aeirein, to lift, heave] The major artery in blood-circulating systems; the aorta sends blood to the other body tissues. aphotic zone (ay-foe-tik) [Gk. aeirein, to lift, heave] The part of the ocean beneath the photic zone, where light does not penetrate sufficiently for photosynthesis to occur. apical dominance (ay-pik-ul) [L. apex, top] Concentration of growth at the tip of a plant shoot, where a terminal bud partially inhibits axillary bud growth. apical meristem (ay-pik-ul mare-eh-stem) [L. apex, top + Gk. meristos, divided]

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Embryonic plant tissue in the tips of roots and in the buds of shoots that supplies cells for the plant to grow in length. apomorphic character (ap-oh-more-fik) A derived phenotypic character, or homology, that evolved after a branch diverged from a phylogenetic tree. apoplast (ap-oh-plast) In plants, the nonliving continuum formed by the extracellular pathway provided by the continuous matrix of cell walls. apoptosis Programmed cell death brought about by signals that trigger the activation of a cascade of "suicide" proteins in the cells destined to die. aposematic coloration (ap-oh-so-mat-ik) The bright coloration of animals with effective physical or chemical defenses that acts as a warning to predators. aquaporin A transport protein in the plasma membranes of a plant or animal cell that specifically facilitates the diffusion of water across the membrane (osmosis). aqueous solution (ay-kwee-us) A solution in which water is the solvent. arboreal [L. arbor, tree] Tree-dwelling. Archaea One of two prokaryotic domains, the other being the Bacteria. archegonium pl. archegonia (ar-kih-go-nee-um) [Gk. archegonos, first of a race] In plants, the female gametangium, a moist chamber in which gametes develop. archenteron (ark-en-ter-on) [Gk. arch, first, or main + enteron, gut] The endoderm-lined cavity, formed during the gastrulation process, that develops into the digestive tract of an animal. Archezoa Primitive eukaryotic group that includes diplomonads, such as Giardia; some systematists assign kingdom status to archezoans.

arteriole A very small artery. See also artery. artery A vessel that carries blood away from the heart to organs throughout the body. arteriosclerosis A cardiovascular disease caused by the formation of hard plaques within the arteries. artificial selection The selective breeding of domesticated plants and animals to encourage the occurrence of desirable traits. ascus pl. asci A saclike spore capsule located at the tip of the ascocarp in dikaryotic hyphae; defining feature of the Ascomycota division of fungi. asexual reproduction A type of reproduction involving only one parent that produces genetically identical offspring by budding or by the division of a single cell or the entire organism into two or more parts. assimilation The energy-requiring process by which plant cells convert nitrate ions (NO 3 ) taken up by the roots of plants into ammonium + ions (NH 4 ), which can then be used in the synthesis of amino acids and other nitrogenous compounds. associative learning The acquired ability to associate one stimulus with another; also called classical conditioning. assortative mating A type of nonrandom mating in which mating partners resemble each other in certain phenotypic characters. asymmetric carbon A carbon atom covalently bonded to four different atoms or groups of atoms. atmospheric pressure [Gk. atmos, vapor + sphaira, globe] The weight of the Earth's atmosphere over a unit area of the Earth's surface. atom [Gk. atomos, indivisible] The smallest unit of matter that retains the properties of an element. atomic number The number of protons in the nucleus of an atom, unique for each element and

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designated by a subscript to the left of the elemental symbol. atomic weight The total atomic mass, which is the mass in grams of one mole of the atom. ATP Abbreviation of adenosine triphosphate, the principal energy-carrying compound of the cell. ATP synthase A cluster of several membrane proteins found in the mitochondrial cristae (and bacterial plasma membrane) that function in chemiosmosis with adjacent electron transport chains, using the energy of a hydrogen-ion concentration gradient to make ATP. ATP synthases provide a port through which hydrogen ions diffuse into the matrix of a mitrochondrion. atrioventricular node [L. atrium, yard, court, hall + ventriculus, the stomach + nodus, knot] A group of slow-conducting fibers in the atrium of the vertebrate heart that are stimulated by impulses originating in the sinoatrial node (the pacemaker) and that conduct impulses to the bundle of His, a group of fibers that stimulate contraction of the ventricles. atrioventricular valve A valve in the heart between each atrium and ventricle that prevents a backflow of blood when the ventricles contract. atrium pl. atria (a-tree-um) [L. yard, court, hall] A chamber that receives blood returning to the vertebrate heart. autogenesis model According to this model, eukaryotic cells evolved by the specialization of internal membranes originally derived from prokaryotic plasma membranes. autoimmune disease An immunological disorder in which the immune system turns against itself. autonomic nervous system (awt-uh-nahm-ik) [Gk. autos, self + nomos, usage, law] A subdivision of the motor nervous system of vertebrates that regulates the internal environment; consists of the sympathetic and parasympathetic divisions.

autopolyploid (aw-toe-pol-ee-ploid) A type of polyploid species resulting from one species doubling its chromosome number to become tetraploid, which may self-fertilize or mate with other tetraploids. autosome (awtuh-some) [Gk. autos, self + soma, body] A chromosome that is not directly involved in determining sex, as opposed to the sex chromosomes. autotroph (aw-toh-trohf) [Gk. autos, self + trophos, feeder] An organism that obtains organic food molecules without eating other organisms. Autotrophs use energy from the sun or from the oxidation of inorganic substances to make organic molecules from inorganic ones. auxin (awk-sins) [Gk. auxein, to increase + in, of, or belonging to] A class of plant hormones, including indoleacetic acid (IAA), having a variety of effects, such as phototropic response through the stimulation of cell elongation, stimulation of secondary growth, and the development of leaf traces and fruit. auxotroph (awk-soh-trohf) A nutritional mutant that is unable to synthesize and that cannot grow on media lacking certain essential molecules normally synthesized by wild-type strains of the same species. Aves The vertebrate class of birds, characterized by feathers and other flight adaptations. axillary bud [Gk. axilla, armpit] An embryonic shoot present in the angle formed by a leaf and stem. axis An imaginary line passing through a body or organ around which parts are symmetrically aligned. axon (aks-on) [Gk. axon, axle] A typically long extension, or process, from a neuron that carries nerve impulses away from the cell body toward target cells.

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complementary DNA strand by another pair of nucleotides. base-pairing principle B cell In the formation of nucleic acids, the A type of lymphocyte that develops in the requirement that adenine must always pair bone marrow and later produces with thymine (or uracil) and guanine with antibodies, which mediate humoral cytosine. immunity. basidium pl. basidia Bacteria A reproductive appendage that produces One of two prokaryotic domains, the other sexual spores on the gills of mushrooms. being the Archaea. The fungal division Basidiomycota is named bacteriophage for this structure. [L. bacterium + Gk. phagein, to eat] Batesian mimicry A virus that parasitizes a bacterial cell. (baytz-ee-un mim-ih-kree) bacterium pl. bacteria A type of mimicry in which a harmless A prokaryotic microorganism in Domain species looks like a different species that is Bacteria. poisonous or otherwise harmful to balanced polymorphism predators. A type of polymorphism in which the behavior frequencies of the coexisting forms do not All of the acts an organism performs, as in, change noticeably over many generations. for example, seeking a suitable habitat, bark obtaining food, avoiding predators, and All tissues external to the vascular cambium seeking a mate and reproducing. in a plant growing in thickness, consisting of behavioral ecology phloem, phelloderm, cork cambium, and A heuristic approach based on the cork. expectation that Darwinian fitness Barr body (reproductive success) is improved by A dense object lying along the inside of the optimal behavior. nuclear envelope in female mammalian benthic zone cells, representing an inactivated X The bottom surfaces of aquatic chromosome. environments. basal body biennial [Gk. basis, foundation] (by-en-ee-ul) [L. biennium, a space of two A eukaryotic cell organelle consisting of a 9 years; bi, twice + annus, year] + 0 arrangement of microtubule triplets; A plant that requires two years to complete may organize the microtubule assembly of a its life cycle. cilium or flagellum; structurally identical to bilateral symmetry a centriole. [L. bi, twice, two + lateris, side; Gk. basal metabolic rate (BMR) summetros, symmetry] [Gk. basis, foundation + metabole, change] Characterizing a body form with a central The minimal number of kilocalories a longitudinal plane that divides the body into resting animal requires to fuel itself for a two equal but opposite halves. given time. bilateria base (by-leh-teer-ee-uh) [L. bi, twice, two + A substance that reduces the hydrogen ion lateris, side] concentration in a solution. See Alkaline. Members of the branch of eumetazoans basement membrane possessing bilateral symmetry. The floor of an epithelial membrane on bile which the basal cells rest. A yellow secretion of the vertebrate liver, base-pair substitution temporarily stored in the gallbladder and A point mutation; the replacement of one composed of organic salts that emulsify fats nucleotide and its partner from the in the small intestine.

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binary fission The type of cell division by which prokaryotes reproduce; each dividing daughter cell receives a copy of the single parental chromosome. binomial [L. bi, twice, two + Gk. nomos, usage, law] The two-part Latinized name of a species, consisting of genus and specific epithet. biochemical pathway [Gk. bios, life + chemeia, alchemy] An ordered series of chemical reactions in a living cell, in which each step is catalyzed by a specific enzyme; different biochemical pathways serve different functions in the life of the cell. biodiversity hotspot A relatively small area with an exceptional concentration of species. bioenergetics The study of how organisms manage their energy resources. biogeochemical cycles [Gk. bios, life + geo, earth + chemeia, alchemy; kyklos, circle, wheel] The various nutrient circuits, which involve both biotic and abiotic components of ecosystems. biogeography The study of the past and present distribution of species. biological clock [Gk. bios, life + logos, discourse] Proposed internal factor(s) in organisms that governs functions that occur rhythmically in the absence of external stimuli. biological magnification A trophic process in which retained substances become more concentrated with each link in the food chain. biological species A population or group of populations whose members have the potential to interbreed. biomass [Gk. bios, life] The dry weight of organic matter comprising a group of organisms in a particular habitat. biome (by-ome) One of the world's major communities, classified according to the predominant

vegetation and characterized by adaptations of organisms to that particular environment. biosphere (by-oh-sfeer) [Gk. bios, life + sphaira, globe] The entire portion of Earth that is inhabited by life; the sum of all the planet's communities and ecosystems. biosynthesis [Gk. bios, life + synthesis, a putting together] Formation by living organisms of organic compounds from elements or simple compounds. biotechnology The industrial use of living organisms or their components to improve human health and food production. biotic (by-ot-ik) [Gk. bios, life] Pertaining to the living organisms in the environment. bipedal [L. bi, twice, two + pes, foot] Walking upright on two feet. blade (1) The broad, expanded part of a leaf. (2) The broad, expanded photosynthetic part of the thallus of a multicellular alga or a simple plant. blastocoel (blas-toh-seel) [Gk. blastos, sprout + koilos, a hollow] The fluid-filled cavity that forms in the center of the blastula embryo. blastocyst [Gk. blastos, sprout + kystis, sac] An embryonic stage in mammals; a hollow ball of cells produced one week after fertilization in humans. blastodisc [Gk. blastos, sprout + discos, a round plate] Disklike area on the surface of a large, yolky egg that undergoes cleavage and gives rise to the embryo. blastopore (blas-toh-por) [Gk. blastos, sprout + poros, a way, means, path] The opening of the archenteron in the gastrula that develops into the mouth in protostomes and the anus in deuterostomes.

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blastula (blas-tyoo-la) [Gk. blastos, sprout] The hollow ball of cells marking the end stage of cleavage during early embryonic development. blood A type of connective tissue with a fluid matrix called plasma in which blood cells are suspended. blood-brain barrier A specialized capillary arrangement in the brain that restricts the passage of most substances into the brain, thereby preventing dramatic fluctuations in the brain's environment. blood pressure The hydrostatic force that blood exerts against the wall of a vessel. bond energy The quantity of energy that must be absorbed to break a particular kind of chemical bond; equal to the quantity of energy the bond releases when it forms. bond strength The strength with which a chemical bond holds two atoms together; conventionally measured in terms of the amount of energy, in kilocalories per mole, required to break the bond. book lungs Organs of gas exchange in spiders, consisting of stacked plates contained in an internal chamber. botany [Gk. botanikos, of herbs] The study of plants. bottleneck effect Genetic drift resulting from the reduction of a population, typically by a natural disaster, such that the surviving population is no longer genetically representative of the original population. Bowman's capsule A cup-shaped receptacle in the vertebrate kidney that is the initial, expanded segment of the nephron where filtrate enters from the blood. box A small portion of a gene or protein that appears in many genes or proteins that are related in structure; the box usually has some specific function, sometimes called a

"motif", like binding DNA or interacting with specific proteins or other molecules. brain The master control center in an animal; in vertebrates, the brain and spinal cord make up the central nervous system. brainstem The hindbrain and midbrain of the vertebrate central nervous system. In humans, it forms a cap on the anterior end of the spinal cord, extending to about the middle of the brain. bryophyte (bry-oh-fites) The mosses, liverworts, and hornworts; a group of nonvascular plants that inhabit the land but lack many of the terrestrial adaptations of vascular plants. bronchus pl. bronchi (bronk-us, bronk- eye) [Gk. bronchos, windpipe] One of a pair of respiratory tubes branching into either lung at the lower end of the trachea; it subdivides into progressively finer passageways, the bronchioles, culminating in the alveoli. bud (1) In plants, an embryonic shoot, including rudimentary leaves, often protected by special bud scales. (2) In animals, an asexually produced outgrowth that develops into a new individual. budding An asexual means of propagation in which outgrowths from the parent form and pinch off to live independently or else remain attached to eventually form extensive colonies. buffer A substance that consists of acid and base forms in solution and that minimizes changes in pH when extraneous acids or bases are added to the solution. bulb A modified bud with thickened leaves adapted for underground food storage. bulbourethral gland (bul-bo-you-ree-thral) One of a pair of glands near the base of the penis in the human male that secrete fluid that lubricates and neutralizes acids in the urethra during sexual arousal.

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Calvin cycle The second of two major stages in photosynthesis (following the light reactions), involving atmospheric CO 2 fixation and reduction of the fixed carbon into carbohydrate. calyx [Gk. kalyx, a husk, cup] Collectively, the sepals of a flower. CAM photosynthesis See Crassulacean acid metabolism. CAM plant A plant that uses crassulacean acid C 3 pathway metabolism, an adaptation for See Calvin cycle. photosynthesis in arid conditions, first C 3 plant discovered in the family Crassulaceae. A plant that uses the Calvin cycle for the Carbon dioxide entering open stomata initial steps that incorporate CO 2 into during the night is converted into organic organic material, forming a three-carbon acids, which release CO 2 for the Calvin cycle compound as the first stable intermediate. during the day, when stomata are closed. C 4 pathway Cambrian explosion The set of reactions by which some plants A burst of evolutionary origins when most initially fix carbon in the four-carbon of the major body plans of animals compound oxaloacetic acid; the carbon appeared in a relatively brief time in dioxide is later released in the interior of geological history; recorded in the fossil the leaf and enters the Calvin cycle. record about 545 to 525 million years ago. C 4 plant capillary A plant that prefaces the Calvin cycle with (kap-ill-air-ee) [L. capillaris, relating to hair] reactions that incorporate CO 2 into fourA microscopic blood vessel that penetrates carbon compounds, the end-product of the tissues and consists of a single layer of which supplies CO 2 for the Calvin cycle. endothelial cells that allows exchange calcitonin between the blood and interstitial fluid. (kal-sih-toh-nin) capillary action A mammalian thyroid hormone that lowers The movement of water or any liquid along blood calcium levels. a surface; results from the combined effect callus of cohesion and adhesion. [L. callos, hard skin] capsid In plants, undifferentiated tissue; a term The protein shell that encloses the viral used in tissue culture, grafting, and wound genome; rod-shaped, polyhedral, or more healing. completely shaped. calmodulin capsule (kal-mod-yoo-lin) (kap-sul) [L. capsula, a little chest] An intracellular protein to which calcium (1) A slimy layer around the cells of certain binds in its function as a second messenger bacteria. (2) The sporangium of a in hormone action. bryophyte. calorie (cal) carbohydrate [L. calor, heat] [L. carbo, charcoal + hydro, water] The amount of heat energy required to A sugar (monosaccharide) or one of its raise the temperature of 1 g of water 1C; dimers (disaccharides) or polymers the amount of heat energy that 1 g of water (polysaccharides). releases when it cools by 1C. The Calorie carbon cycle (with a capital C), usually used to indicate Worldwide circulation and reutilization of the energy content of food, is a kilocalorie. carbon atoms, chiefly due to metabolic

bulk flow The movement of water due to a difference in pressure between two locations. bundle of His In the vertebrate heart, a group of muscle fibers that carry impulses from the atrioventricular node to the walls of the ventricles; the only electrical bridge between the atria and the ventricles.

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processes of living organisms. Inorganic carbon, in the form of carbon dioxide, is incorporated into organic compounds by photosynthetic organisms; when the organic compounds are broken down in respiration, carbon dioxide is released. Large quantities of carbon are "stored" in the seas and the atmosphere, as well as in fossil fuel deposits. carbon fixation The incorporation of carbon from CO 2 into an organic compound by an autotrophic organism (a plant, another photosynthetic organism, or a chemoautotrophic bacterium). carbonyl group (kar-buh-nil) A functional group present in aldehydes and ketones, consisting of a carbon atom double-bonded to an oxygen atom. carboxyl group (kar-box-ul) A functional group present in organic acids, consisting of a single carbon atom doublebonded to an oxygen atom and also bonded to a hydroxyl group. carcinogen (kar-sin-oh-jen) A chemical agent that causes cancer. cardiac muscle (kar-dee-ak) A type of muscle that forms the contractile wall of the heart; its cells are joined by intercalated discs that relay each heartbeat. cardiac output The volume of blood pumped per minute by the left ventricle of the heart. cardiovascular system [Gk. kardio, heart + L. vasculum, a small vessel] A closed circulatory system with a heart and branching network of arteries, capilleries, and veins. carnivore [L. caro, carnis, flesh + voro, to devour] An animal, such as a shark, hawk, or spider, that eats other animals. carotenoids (keh-rot-en-oydz) [L. carota, carrot] Accessory pigments, yellow and orange, in the chloroplasts of plants; by absorbing wavelengths of light that chlorophyll

cannot, they broaden the spectrum of colors that can drive photosynthesis. carpel (kar-pel) [Gk. karpos, fruit] The female reproductive organ of a flower, consisting of the stigma, style, and ovary. carrying capacity The maximum population size that can be supported by the available resources, symbolized as K. cartilage (kar-til-ij) [L. cartilago, gristle] A type of flexible connective tissue with an abundance of collagenous fibers embedded in chondrin. Casparian strip (kas-par-ee-un) (after Robert Caspary, German botanist) A water-impermeable ring of wax around endodermal cells in plants that blocks the passive flow of water and solutes into the stele by way of cell walls. catabolic pathway (kat-uh-bol-ik) A metabolic pathway that releases energy by breaking down complex molecules into simpler compounds. catabolism [Gk. katabole, throwing down] Within a cell or organism, the sum of all chemical reactions in which large molecules are broken down into smaller parts. catabolite activator protein (CAP) (ka-tab-ul-lite) In E. coli, a helper protein that stimulates gene expression by binding within the promoter region of an operon and enhancing the promoter's ability to associate with RNA polymerase. catalyst [Gk. katalysis, dissolution] A substance that lowers the activation energy of a chemical reaction by forming a temporary association with the reacting molecules; as a result, the rate of the reaction is accelerated. Enzymes are catalysts. category [Gk. kategoria, category] In a hierarchical classification system, the level at which a particular group is ranked.

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cation (kat-eye-on) An ion with a positive charge, produced by the loss of one or more electrons. cation exchange A process in which positively charged minerals are made available to a plant when hydrogen ions in the soil displace mineral ions from the clay particles. cell [L. cella, a chamber] A basic unit of living matter separated from its environment by a plasma membrane; the fundamental structural unit of life. cell center A region in the cytoplasm near the nucleus from which microtubules originate and radiate. cell cycle An ordered sequence of events in the life of a dividing eukaryotic cell, composed of the M, G 1 , S, and G 2 phases. cell-cycle control system A cyclically operating set of proteins that triggers and coordinates events in the eukaryotic cell cycle. cell fractionation The disruption of a cell and separation of its organelles by centrifugation. cell-mediated immunity The type of immunity that functions in defense against fungi, protists, bacteria, and viruses inside host cells and against tissue transplants, with highly specialized cells that circulate in the blood and lymphoid tissue. cell membrane The outer membrane of the cell; the plasma membrane. cell plate A double membrane across the midline of a dividing plant cell, between which the new cell wall forms during cytokinesis. cell theory All living things are composed of cells; cells arise only from other cells. No exception has been found to these two principles since they were first proposed well over a century ago. cell wall A protective layer external to the plasma membrane in plant cells, bacteria, fungi, and some protists. In the case of plant cells,

the wall is formed of cellulose fibers embedded in a polysaccharide-protein matrix. The primary cell wall is thin and flexible, whereas the secondary cell wall is stronger and more rigid, and is the primary constituent of wood. cellular differentiation The structural and functional divergence of cells as they become specialized during a multicellular organism's development; dependent on the control of gene expression. cellular respiration The most prevalent and efficient catabolic pathway for the production of ATP, in which oxygen is consumed as a reactant along with the organic fuel. cellulose (sell-yoo-lose) [L. cellula, a little cell] A structural polysaccharide of cell walls, consisting of glucose monomers joined by (1-4) glycosidic linkages. Celsius scale A temperature scale (C) equal to 5/9 (F 32) that measures the freezing point of water at 0C and the boiling point of water at 100C. central nervous system (CNS) In vertebrate animals, the brain and spinal cord. centriole (sen-tree-ole) [Gk. kentron, center] A structure in an animal cell, composed of cylinders of microtubule triplets arranged in a 9 + 0 pattern. An animal cell usually has a pair of centrioles, which are involved in cell division. centromere (sen-tro-mere) [Gk. kentron, center + meros, a part] The centralized region joining two sister chromatids. centrosome Material present in the cytoplasm of all eukaryotic cells and important during cell division; also called microtubule-organizing center. cephalochordate A chordate without a backbone, represented by lancelets, tiny marine animals.

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cerebellum (seh-reh-bell-um) [L. dim. of cerebrum, brain] Part of the vertebrate hindbrain (rhombencephalon) located dorsally; functions in unconscious coordination of movement and balance. cerebral cortex (seh-ree-brul) [L. cerebrum, brain] The surface of the cerebrum; the largest and most complex part of the mammalian brain, containing sensory and motor nerve cell bodies of the cerebrum; the part of the vertebrate brain most changed through evolution. cerebrum (seh-ree-brum) [L. brain] The dorsal portion, composed of right and left hemispheres, of the vertebrate forebrain; the integrating center for memory, learning, emotions, and other highly complex functions of the central nervous system. chaparral (shap-uh-ral) A scrubland biome of dense, spiny evergreen shrubs found at midlatitudes along coasts where cold ocean currents circulate offshore; characterized by mild, rainy winters and long, hot, dry summers. character displacement A phenomenon in which species that live together in the same environment tend to diverge in those characteristics that overlap; exemplified by Darwin's finches. chemical bond An attraction between two atoms resulting from a sharing of outer-shell elctrons or the presence of opposite charges on the atoms; the bonded atoms gain complete outer electron shells. chemical equilibrium In a reversible chemical reaction, the point at which the rate of the forward reaction equals the rate of the reverse reaction. chemical reaction A process leading to chemical changes in matter; involves the making and/or breaking of chemical bonds. chemiosmosis (kee-mee-os-moh-sis) The production of ATP using the energy of hydrogen-ion gradients across membranes

to phosphorylate ADP; powers most ATP synthesis in cells. chemiosmotic coupling The mechanism by which ADP is phosphorylated to ATP in mitochondria and chloroplasts. The energy released as electrons pass down an electron transport chain is used to establish a proton gradient across an inner membrane of the organelle; when protons subsequently flow down this electrochemical gradient, the potential energy released is captured in the terminal phosphate bonds of ATP. chemoautotroph (kee-moh-aw-toh-trohf) An organism that needs only carbon dioxide as a carbon source but that obtains energy by oxidizing inorganic substances. chemoheterotroph (kee-moh-het-er-oh-trohf) An organism that must consume organic molecules for both energy and carbon. chemoreceptor A receptor that transmits information about the total solute concentration in a solution or about individual kinds of molecules. chemosynthetic Applied to autotrophic bacteria that use the energy released by specific inorganic reactions to power their life processes, including the synthesis of organic molecules. chiasma pl. chiasmata (ky-as-muh) The X-shaped, microscopically visible region representing homologous chromatids that have exchanged genetic material through crossing over during meiosis. chitin (ky-tin) [Gk. chiton, a tunic, undergarment] A structural polysaccharide of an amino sugar found in many fungi and in the exoskeletons of all arthropods. chlorophyll [Gk. chloros, green + phyllon, leaf] A green pigment located within the chloroplasts of plants; chlorophyll a can participate directly in the light reactions, which convert solar energy to chemical energy. chloroplast (klor-oh-plast) [Gk. chloros, green + plastos, formed]

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An organelle found only in plants and photosynthetic protists that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water. cholesterol (kol-ess-teh-rol) A steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids. Chondrichthyes The vertebrate class of cartilaginous fishes, represented by sharks and their relatives. chondrin A protein-carbohydrate complex secreted by chondrocytes; chondrin and collagen fibers form cartilage. chordate (kor-date) A member of a diverse phylum of animals that possess a notochord; a dorsal, hollow nerve cord; pharyngeal gill slits; and a postanal tail as embryos. chorion (core-ee-on) [Gk. skin, leather] The outermost of four extraembryonic membranes; contributes to the formation of the mammalian placenta. chorionic villus sampling (CVS) (kor-ee-on-ik vill-us) A technique for diagnosing genetic and congenital defects while the fetus is in the uterus. A small sample of the fetal portion of the placenta is removed and analyzed. chromatid (crow-ma-tid) [Gk. chroma, color] Either of the two strands of a replicated chromosome, which are joined at the centromere. chromatin (kro-muh-tin) [Gk. chroma, color] The complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing, chromatin exists as a mass of very long, thin fibers that are not visible with a light microscope. Chromista In some classification systems, a kingdom consisting of brown algae, golden algae, and diatoms.

chromosome [Gk. chroma, color + soma, body] A threadlike, gene-carrying structure found in the nucleus. Each chromosome consists of one very long DNA molecule and associated proteins. See chromatin. chromosome map A diagram of the linear order of the genes on a chromosome. chytrid Fungus with flagellated stage; possible evolutionary link between fungi and protists. cilium pl. cilia (silly-um) [L. eyelash] A short cellular appendage specialized for locomotion, formed from a core of nine outer doublet microtubules and two inner single microtubules ensheathed in an extension of plasma membrane. circadian rhythms [L. circa, about + dies, day] A physiological cycle of about 24 hours, present in all eukaryotic organisms, that persists even in the absence of external cues. cladistics (kluh-dis-tiks) A taxonomic approach that classifies organisms according to the order in time at which branches arise along a phylogenetic tree, without considering the degree of morphological divergence. cladogenesis (klay-doh-gen-eh-sis) [Gk. clados, branch + genesis, origin] A pattern of evolutionary change that produces biological diversity by budding one or more new species from a parent species that continues to exist; also called branching evolution. cladogram A dichotomous phylogenetic tree that branches repeatedly, suggesting a classification of organisms based on the time sequence in which evolutionary branches arise. class A taxonomic grouping of related, similar orders; category above order and below phylum.

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classical conditioning A type of associative learning; the association of a normally irrelevant stimulus with a fixed behavioral response. cleavage The process of cytokinesis in animal cells, characterized by pinching of the plasma membrane; specifically, the succession of rapid cell divisions without growth during early embryonic development that converts the zygote into a ball of cells. cleavage furrow The first sign of cleavage in an animal cell; a shallow groove in the cell surface near the old metaphase plate. cline [Gk. klinein, to lean] Variation in features of individuals in a population that parallels a gradient in the environment. cloaca (kloh-ay-kuh) A common opening for the digestive, urinary, and reproductive tracts in all vertebrates except most mammals. clonal selection (kloh-nul) The mechanism that determines specificity and accounts for antigen memory in the immune system; occurs because an antigen introduced into the body selectively activates only a tiny fraction of inactive lymphocytes, which proliferate to form a clone of effector cells specific for the stimulating antigen. clone [Gk. klon, twig] (1) A lineage of genetically identical individuals or cells. (2) In popular usage, a single individual organism that is genetically identical to another individual. (3) As a verb, to make one or more genetic replicas of an individual or cell. Also, see gene cloning. cloning vector An agent used to transfer DNA in genetic engineering, such as a plasmid that moves recombinant DNA from a test tube back into a cell, or a virus that transfers recombinant DNA by infection. closed circulatory system A type of internal transport in which blood is confined to vessels.

cnidocyte (ni-do-site) [Gk. knide, nettle + kytos, vessel] A stinging cell containing a nematocyst; characteristic of cnidarians. cochlea (koh-klee-uh) [Gk. kochlias, snail] The complex, coiled organ of hearing that contains the organ of Corti. codominance A phenotypic situation in which both alleles are expressed in the heterozygote. codon (koh-on) A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code. coelom (see-lome) [Gk. koilos, a hollow] A body cavity completely lined with mesoderm. coelomate (see-loh-mate) An animal whose body cavity is completely lined by mesoderm, the layers of which connect dorsally and ventrally to form mesenteries. coenocytic (sen-oh-sit-ik) Referring to a multinucleated condition resulting from the repeated division of nuclei without cytoplasmic division. coenzyme [L. co, together + Gk. en, in + zyme, leaven] An organic molecule serving as a cofactor. Most vitamins function as coenzymes in important metabolic reactions. coevolution [L. co, together + e-, out + volvere, to roll] The mutual influence on the evolution of two different species interacting with each other and reciprocally influencing each other's adaptations. cofactor Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or may bind loosely with the substrate during catalysis.

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cohesion [L. cohaerere, to stick together] The binding together of like molecules, often by hydrogen bonds. cohesion species concept The idea that specific evolutionary adaptations and discrete complexes of genes define species. cohesion-tension theory A theory accounting for the upward movement of water in plants. According to this theory, transpiration of a water molecule results in a negative (below 1 atmosphere) pressure in the leaf cells, inducing the entrance from the vascular tissue of another water molecule, which, because of the cohesive property of water, pulls with it a chain of water molecules extending up from the cells of the root tip. cold aclimation response The process by which plants increase their tolerance to freezing by exposure to low, nonfreezing temperatures. coleoptile (coal-ee-op-tile) [Gk. koleon, sheath + ptilon, feather] The sheath enclosing the apical meristem and leaf primordia of a germinating monocot. collagen [Gk. kolla, glue] A glycoprotein in the extracellular matrix of animal cells that forms strong fibers, found extensively in connective tissue and bone; the most abundant protein in the animal kingdom. collecting duct The location in the kidney where filtrate from renal tubules is collected; the filtrate is now called urine. collenchyma cell (koal-en-keh-muh) [Gk. kolla, glue] A flexible plant cell type that occurs in strands or cylinders that support young parts of the plant without restraining growth. colony A group of organisms of the same species living together in close association. commensalism (kuh-men-sul-iz-um) [L. com, together + mensa, table] A symbiotic relationship in which the

symbiont benefits but the host is neither helped nor harmed. See Symbiosis. community All the organisms that inhabit a particular area; an assemblage of populations of different species living close enough together for potential interaction. companion cell A type of plant cell that is connected to a sieve-tube member by many plasmodesmata and whose nucleus and ribosomes may serve one or more adjacent sieve-tube members. competition Interaction between members of the same population or of two or more populations using the same resource, often present in limited supply. competitive exclusion principle The concept that when the populations of two species compete for the same limited resources, one population will use the resources more efficiently and have a reproductive advantage that will eventually lead to the elimination of the other population. competitive inhibitor A substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics. complement fixation An immune response in which antigenantibody complexes activate complement proteins. complement system A group of at least 20 blood proteins that cooperate with other defense mechanisms; may amplify the inflammatory response, enhance phagocytosis, or directly lyse pathogens; activated by the onset of the immune response or by surface antigens on microorganisms or other foreign cells. complementary DNA (cDNA) A DNA molecule made in vitro using mRNA as a template and the enzyme reverse transcriptase. A cDNA molecule therefore corresponds to a gene, but lacks the introns present in the DNA of the genome. complete digestive tract A digestive tube that runs between a mouth and an anus; also called alimentary canal. An incomplete digestive tract has only one opening.

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complete flower A flower that has sepals, petals, stamens, and carpels. compound [L. componere, to put together] A chemical combination, in a fixed ratio, of two or more elements. compound eye A type of multifaceted eye in insects and crustaceans consisting of up to several thousand light-detecting, focusing ommatidia; especially good at detecting movement. concentration gradient A regular increase of decrease in the intensity or density of a chemical substance. Cells often maintain concentration + gradients of H ions across their membranes. When a gradient exists, the ions or other chemical substances involved tend to move from where they are more concentrated to where they are less concentrated. condensation See Dehydration synthesis. condensation reaction A reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water; also called dehydration reaction. cone cell (1) In plants, the reproductive structure of a conifer. (2) In vertebrates, a type of photoreceptor cell in the retina, concerned with the perception of color and with the most acute discrimination of detail. conidium pl. conidia A naked, asexual spore produced at the ends of hyphae in ascomycetes. conifer A gymnosperm whose reproductive structure is the cone. Conifers include pines, firs, redwoods, and other large trees. conjugation (kon-joo-gay-shun) [L. conjugatio, a joining, connection] In bacteria, the transfer of DNA between two cells that are temporarily joined. connective tissues Animal tissue that functions mainly to bind and support other tissues, having a sparse population of cells scattered through an extracellular matrix.

conservation biology A goal-oriented science that seeks to counter the biodiversity crisis, the current rapid decrease in Earth's variety of life. consumer, in ecological systems A heterotroph that derives its energy from living or freshly killed organisms or parts thereof. Primary consumers are herbivores; higher-level consumers are carnivores. continental drift The gradual movement of the Earth's continents that has occurred over hundreds of millions of years. continuous variation A gradation of small differences in a particular trait, such as height, within a population; occurs in traits that are controlled by a number of genes. contraception The prevention of pregnancy. convection The mass movement of warmed air or liquid to or from the surface of a body or object. convergent evolution [L. convergere, to turn together; evolutio, to unfold] The independent development of similarity between species as a result of their having similar ecological roles and selection pressures. cooperativity (koh-op-ur-uh-tiv-eh-tee) An interaction of the constituent subunits of a protein causing a conformational change in one subunit to be transmitted to all the others. cork [L. cortex, bark] A secondary tissue that is a major constituent of bark in woody and some herbaceous plants; made up of flattened cells, dead at maturity; restricts gas and water exchange and protects the vascular tissues from injury. cork cambium [L. cortex, bark + cambium, exchange] A cylinder of meristematic tissue in plants that produces cork cells to replace the epidermis during secondary growth. corolla (ko-role-a) [L. dim. of corona, wreath, crown]

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Petals, collectively; usually the conspicuously colored flower parts. corpus callosum [L. callous body] In the vertebrate brain, a tightly packed mass of myelinated nerve fibers connecting the two cerebral hemispheres. corpus lutuem [L. yellowish body] A secreting tissue in the ovary that forms from the collapsed follicle after ovulation and produces progesterone. cortex [L. bark] (1) The outer, as opposed to the inner, part of an organ, as in the adrenal gland. (2) In a stem or root, the primary tissue bounded externally by the epidermis and internally by the central cylinder of vascular tissue. cortisol A steroid hormone, produced by the adrenal cortex, that promotes the formation of glucose from protein and fat; also suppresses the inflammatory and immune responses. cotransport The coupling of the "downhill" diffusion of one substance to the "uphill" transport of another against its own concentration gradient. cotyledon (kot-eh-lee-don) [Gk. kotyledon, a cupshaped hollow] The one (monocot) or two (dicot) seed leaves of an angiosperm embryo. countercurrent exchange The opposite flow of adjacent fluids that maximizes transfer rates; for example, blood in the gills flows in the opposite direction in which water passes over the gills, maximizing oxygen uptake and carbon dioxide loss. coupled reactions In cells, the linking of endergonic (energyrequiring) reactions to exergonic (energyreleasing) reactions that provide enough energy to drive the endergonic reactions forward. covalent bond (koh-vay-lent) [L. con, together + valere, to be strong] A chemical bond formed as a result of the sharing of one or more pairs of electrons.

Crassulacean acid metabolism A process by which some species of plants in hot, dry climates take in carbon dioxide during the night, fixing it in organic acids; the carbon dioxide is released during the day and used immediately in the Calvin cycle. crista pl. cristae (kris-tuh) An infolding of the inner membrane of a mitochondrion that houses the electron transport chain and the enzyme catalyzing the synthesis of ATP. cross-fertilization Fusion of gametes formed by different individuals; as opposed to self-fertilization. crossing over The reciprocal exchange of genetic material between nonsister chromatids during synapsis of meiosis I. cryptic coloration (krip-tik) A type of camouflage that makes potential prey difficult to spot against its background. cuticle (kyoo-teh-kul) [L. cuticula, dim. of cutis, the skin] (1) A waxy covering on the surface of stems and leaves that acts as an adaptation to prevent desiccation in terrestrial plants. (2) The exoskeleton of an arthropod, consisting of layers of protein and chitin that are variously modified for different functions. cyanobacteria (sy-an-oh-bak-teer-ee-uh) Photosynthetic, oxygen-producing bacteria (formerly know as blue-green algae). cyclic AMP Cyclic adenosine monophosphate, a ringshaped molecule made from ATP that is a common intracellular signaling molecule (second messenger) in eukaryotic cells, for example, in vertebrate endocrine cells. It is also a regulator of some bacterial operons. cyclic electron flow A route of electron flow during the light reactions of photosynthesis that involves only photosystem I and produces ATP but not NADPH or oxygen. cyclin (sy-klin) A regulatory protein whose concentration fluctuates cyclically.

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cyclin-dependent kinase (Cdk) A protein kinase that is active only when attached to a particular cyclin. cytochrome (sy-toh-krome) [Gk. kytos, vessel + chroma, color] An iron-containing protein, a component of electron transport chains in mitochondria and chloroplasts. cytokines In the vertebrate immune system, protein factors secreted by macrophages and helper T cells as regulators of neighboring cells. cytokinesis (sy-toh-kin-ee-sis) [Gk. kytos, vessel + kinesis, motion] The division of the cytoplasm to form two separate daughter cells immediately after mitosis. cytokinin (sy-toh-ky-nins) [Gk. kytos, vessel + kinesis, motion] A class of related plant hormones that retard aging and act in concert with auxins to stimulate cell division, influence the pathway of differentiation, and control apical dominance. cytoplasm (sy-toh-plaz-um) [Gk. kytos, vessel + plasma, anything molded] The entire contents of the cell, exclusive of the nucleus, and bounded by the plasma membrane. cytoplasmic determinants In animal development, substances deposited by the mother in the eggs she produces that regulate the expression of genes affecting the early development of the embryo. cytoplasmic streaming A circular flow of cytoplasm, involving myosin and actin filaments, that speeds the distribution of materials within cells. cytoskeleton (sy-toh-skel-eh-ton) A network of microtubules, microfilaments, and intermediate filaments that branch throughout the cytoplasm and serve a variety of mechanical and transport functions.

cytosol (sy-toh-sol) The semifluid portion of the cytoplasm. cytotoxic T cell (TC) A type of lymphocyte that kills infected cells and cancer cells.

dalton (dawl-ton) The atomic mass unit; a measure of mass for atoms and subatomic particles. Darwinian fitness A measure of the relative contribution of an individual to the gene pool of the next generation. daughter cell A cell that is the offspring of a cell that has undergone mitosis or meiosis. The term "daughter" does not indicate the sex of the cell. day-neutral plant A plant whose flowering is not affected by photoperiod. deciduous [L. decidere, to fall off] Refers to plants that shed their leaves at a certain season. decomposers Saprotrophic fungi and bacteria that absorb nutrients from nonliving organic material such as corpses, fallen plant material, and the wastes of living organisms, and convert them into inorganic forms. dehydration reaction A chemical reaction in which two molecules covalently bond to one another with the removal of a water molecule. deletion (1) A deficiency in a chromosome resulting from the loss of a fragment through breakage. (2) A mutational loss of a nucleotide from a gene. demography The study of statistics relating to births and deaths in populations. denaturation For proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive. For DNA, the separation of the two strands of

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the double helix. Denaturation occurs under extreme conditions of pH, salt concentration, and temperature. dendrite (den-dryt) [Gk. dendron, tree] One of usually numerous, short, highly branched processes of a neuron that conveys nerve impulses toward the cell body. denitrification The process by which certain bacteria living in poorly aerated soils break down nitrates, using the oxygen for their own respiration and releasing nitrogen back into the atmosphere. density The number of individuals per unit area or volume. density-dependent factor Any factor influencing population regulation that has a greater impact as population density increases. density-dependent inhibition The phenomenon observed in normal animal cells that causes them to stop dividing when they come into contact with one another. density-independent factors Any factor influencing population regulation that acts to reduce population by the same percentage, regardless of size. deoxyribonucleic acid (DNA) (dee-oks-ee- ry-boh-noo-klay-ik) A double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins. deoxyribose The sugar component of DNA, having one less hydroxyl group than ribose, the sugar component of RNA. dependent variable In an experiment, the dependent variable is the factor that responds when another factor is manipulated. depolarization An electrical state in an excitable cell whereby the inside of the cell is made less negative relative to the outside than at the resting membrane potential. A neuron membrane is depolarized if a stimulus decreases its voltage from the resting

potential of 70 mV in the direction of zero voltage. deposit-feeder A heterotroph, such as an earthworm, that eats its way through detritus, salvaging bits and pieces of decaying organic matter. dermal tissue system The protective covering of plants; generally a single layer of tightly packed epidermal cells covering young plant organs formed by primary growth. dermis [Gk. derma, skin] The inner layer of the skin, beneath the epidermis. desmosome (dez-muh-some) [Gk. desmos, bond + soma, body] A type of intercellular junction in animal cells that functions as an anchor. determinate cleavage A type of embryonic development in protostomes that rigidly casts the developmental fate of each embryonic cell very early. determinate growth A type of growth characteristic of animals, in which the organism stops growing after it reaches a certain size. determination The progressive restriction of developmental potential, causing the possible fate of each cell to become more limited as the embryo develops. detritus (deh-try-tis) Dead organic matter. detritivores [L. detritus, worn down, worn away + voro, to devour] Organisms that live on dead and discarded organic matter; include large scavengers, smaller animals such as earthworms and some insects, as well as decomposers (fungi and bacteria). deuterostome (doo-ter-oh-stomes) [Gk. deuteros, second + stoma, mouth] One of two distinct evolutionary lines of coelomates, consisting of the echinoderms and chordates and characterized by radial, indeterminate cleavage, enterocoelous

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formation of the coelom, and development of the anus from the blastopore. development The progressive production of the phenotypic characteristics of a multicellular organism, beginning with the fertilization of an egg. diaphragm [Gk. diaphrassein, to barricade] A sheet of muscle that forms the bottom wall of the thoracic cavity in mammals; active in ventilating the lungs. diastole (dy-ass-toh-lee) The stage of the heart cycle in which the heart muscle is relaxed, allowing the chambers to fill with blood. diastolic pressure The pressure in an artery during the ventricular relaxation phase of the heart cycle. dicot (dy-kot) A subdivision of flowering plants whose members possess two embryonic seed leaves, or cotyledons. dicotyledon (dye-cottle-ee-don) [Gk. di, double, two + kotyledon, a cup-shaped hollow] A member of the class of flowering plants having two seed leaves, or cotyledons, among other distinguishing features; often abbreviated as dicot. differentiation See cellular differentiation. diffusion [L. diffundere, to pour out] The spontaneous tendency of a substance to move down its concentration gradient from a more concentrated to a less concentrated area. digestion [L. digestio, separating out, dividing] The process of breaking down food into molecules small enough for the body to absorb. dihybrid (dy-hy-brid) A hybrid individual that is heterozygous for two genes or two characters. dihybrid cross A breeding experiment in which parental varieties differing in two traits are mated.

dikaryon dy-kah-ree-on) A mycelium of certain septate fungi that possesses two separate haploid nuclei per cell. dioecious (dy-ee-shus) (dye-ee-shus) [Gk. di, two + oikos, house] Referring to a plant species that has staminate and carpellate flowers on separate plants. dimorphism Displaying two separate growth forms. diploid cell (dip-loyd) [Gk. di, double, two + ploion, vessel] A cell containing two sets of chromosomes (2n), one set inherited from each parent. directed molecular evolution A laboratory version of evolution at the molecular level that can produce "designer molecules." A large starting population of molecules (typically nucleic acids) that varies randomly in base sequence and shape is subjected to replication with variation, followed by selection. After several cycles of replication and selection, the population of molecules will evolve toward one containing a high proportion of molecules well adapted to the selection criterion applied. directional selection Natural selection that favors individuals on one end of the phenotypic range. disaccharide (dy-sak-ur-ide) [Gk. di, two + sakcharon, sugar] A double sugar, consisting of two monosaccharides joined by dehydration synthesis. diurnal [L. diurnus, of the day] Applied to organisms that are active during the daylight hours. dispersion The distribution of individuals within geographical population boundaries. diversifying selection [L. diurnus, of the day] Natural selection that favors extreme over intermediate phenotypes.

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division A taxonomic grouping of related, similar classes; a high- level category below kingdom and above class. Division is generally used in the classification of prokaryotes, algae, fungi, and plants, whereas an equivalent category, phylum, is used in the classification of protozoa and animals. DNA Abbreviation of deoxyribonucleic acid. DNA ligase (ly-gaze) width="400" valign="TOP"> A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of a new DNA fragment to the 5' end of a growing chain. DNA methylation The addition of methyl groups (CH 3 ) to bases of DNA after DNA synthesis; may serve as a long-term control of gene expression. DNA polymerase An enzyme that catalyzes the elongation of new DNA at a replication fork by the addition of nucleotides to the existing chain. DNA probe A chemically synthesized, radioactively labeled segment of nucleic acid used to find a gene of interest by hydrogen-bonding to a complementary sequence. domain A taxonomic category above the kingdom level; the three domains are Archaea, Bacteria, and Eukarya. dominance hierarchy A linear "pecking order" of animals, where position dictates characteristic social behaviors. dominant allele In a heterozygote, the allele that is fully expressed in the phenotype. dormancy [L. dormire, to sleep] A period during which growth ceases and metabolic activity is greatly reduced; dormancy is broken when certain requirements, for example, of temperature, moisture, or day length, are met. dorsal

[L. dorsum, the back] Pertaining to or situated near the back; opposite of ventral. double circulation A circulation scheme with separate pulmonary and systemic circuits, which ensures vigorous blood flow to all organs. double fertilization A mechanism of fertilization in angiosperms, in which two sperm cells unite with two cells in the embryo sac to form the zygote and endosperm. double helix The form of native DNA, referring to its two adjacent polynucleotide strands wound into a spiral shape. Down syndrome A human genetic disease resulting from having an extra chromosome 21, characterized by mental retardation and heart and respiratory defects. duodenum (doo-oh-dee-num) [L. duodeni, twelve each - from its length, about 12 fingers' breadth] The first section of the small intestine, where acid chyme from the stomach mixes with digestive juices from the pancreas, liver, gallbladder, and gland cells of the intestinal wall. duplication An aberration in chromosome structure resulting from an error in meiosis or mutagens; duplication of a portion of a chromosome resulting from fusion with a fragment from a homologous chromosome. dynein (dy-nin) A large contractile protein forming the sidearms of microtubule doublets in cilia and flagella.

ecdysone (ek-deh-sone) A steroid hormone that triggers molting in arthropods. ecological efficiency The ratio of net productivity at one trophic level to net productivity at the next lower level.

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ecological niche The sum total of an organism's utilization of the biotic and abiotic resources of its environment. ecological pyramid A graphic representation of the quantitative relationships of numbers of organisms, biomass, or energy flow between the trophic levels of an ecosystem. Because large amounts of energy and biomass are dissipated at every trophic level, these diagrams nearly always take the form of pyramids. ecological species concept The idea that ecological roles (niches) define species. ecological succession Transition in the species composition of a biological community, often following ecological disturbance of the community; the establishment of a biological community in an area virtually barren of life. ecology [Gk. oikos, home + logos, a discourse] The study of how organisms interact with their environments. ecosystem [Gk. oikos, home + systema, that which is put together] A level of ecological study that includes all the organisms in a given area as well as the abiotic factors with which they interact; a community and its physical environment. ecotype Gk. oikos, home + L. typus, image] A locally adapted variant of a species, differing genetically from other ecotypes of the same species. ectoderm [Gk. ecto, outside + derma, skin] The outermost of the three primary germ layers in animal embryos; gives rise to the outer covering and, in some phyla, the nervous system, inner ear, and lens of the eye. ectotherm [Gk. ecto, outside + therme, heat] An animal such as a reptile, fish, or amphibian, that must use environmental energy and behavioral adaptations to regulate its body temperature.

effector cell [L. ex, out of + facere, to make] definition efferent [L. ex, out of + ferre, to bear] Carrying away from a center, applied to nerves and blood vessels. egg A female gamete, which usually contains abundant cytoplasm and yolk; nonmotile and often larger than a male gamete. ejaculatory duct In the male, a duct from each testis that join to form the urethra. electric potential The difference in the amount of electric charge between a region of positive charge and a region of negative charge. The establishment of electric potentials across the plasma membrane and across organelle membranes makes possible a number of phenomena, including the chemiosmotic synthesis of ATP, the conduction of nerve impulses, and muscle contraction. electrochemical gradient The diffusion gradient of an ion, representing a type of potential energy that accounts for both the concentration difference of the ion across a membrane and its tendency to move relative to the membrane potential. electrogenic pump An ion transport protein generating voltage across the membrane. electromagnetic spectrum The entire spectrum of radiation; ranges in wavelength from less than a nanometer to more than a kilometer. electron A particle with a single negative charge; one or more electrons orbit the nucleus of the atom. electron acceptor Substance that accepts or receives electrons in an oxidation-reduction reaction, becoming reduced in the process. electron carrier A molecule that conveys electrons; one of several membrane proteins in electron transport chains in cells. Electron carriers shuttle electrons during the redox reactions that release energy used to make ATP.

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electron donor Substance that donates or gives up electrons in an oxidation-reduction reaction, becoming oxidized in the process. electron microscope (EM) A microscope that focuses an electron beam through a specimen, resulting in resolving power a thousandfold greater than that of a light microscope. A transmission electron microscope (TEM) is used to study the internal structure of thin sections of cells. A scanning electron microscope (SEM) is used to study the fine details of cell surfaces. electron shell An energy level at which an electron orbits the nucleus of an atom. electron transport chain A sequence of electron-carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP. electronegativity The tendency for an atom to pull electrons toward itself. element Any substance that cannot be broken down to any other substance. embryo (em-bree-oh) [Gk. en, in + bryein, to swell] A developing stage of multicellular organisms; in humans, the stage in the development of offspring from the first division of the zygote until body structures begin to appear; about the ninth week of gestation. See Fetus. embryo sac The female gametophyte of angiosperms, formed from the growth and division of the megaspore into a multicellular structure with eight haploid nuclei. enantiomer (eh-nan-she-uh-mer) One of a pair of molecules that are mirrorimage isomers of each other. endangered species A species that is in danger of extinction throughout all or a significant portion of its range. endemic species Species that are confined to a specific, relatively small geographic area. endemic

An organism found only in one particular location. endergonic reaction (en-dur-gon-ik) [Gk. endon, within + ergon, work] A nonspontaneous chemical reaction in which free energy is absorbed from the surroundings. endocrine gland (en-doh-krin) [Gk. endon, within + krinein, to separate] A ductless gland that secretes hormones directly into the bloodstream. endocrine system The internal system of chemical communication involving hormones, the ductless glands that secrete hormones, and the molecular receptors on or in target cells that respond to hormones; functions in concert with the nervous system to effect internal regulation and maintain homeostasis. endocytosis (en-doh-sy-toh-sis) [Gk. endon, within + kytos, vessel] The cellular uptake of macromolecules and particulate substances by localized regions of the plasma membrane that surround the substance and pinch off to form an intracellular vesicle. endoderm (en-doh-durm) [Gk. endon, within + derma, skin] The innermost of the three primary germ layers in animal embryos; lines the archenteron and gives rise to the liver, pancreas, lungs, and the lining of the digestive tract. endodermis (en-doh-dur-mis) [Gk. endon, within + derma, skin] The innermost layer of the cortex in plant roots; a cylinder one cell thick that forms the boundary between the cortex and the stele. endogenous Arising from internal structures or functional causes. endomembrane system The collection of membranes inside and around a eukaryotic cell, related either through direct physical contact or by the transfer of membranous vesicles.

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endometrium (en-doh-mee-tree-um) [Gk. endon, within + metrios, of the womb] The inner lining of the uterus, which is richly supplied with blood vessels. endoplasmic reticulum (en-doh-plaz-mik reh-tik-yoo-lum) [Gk. endon, within + plasma, from cytoplasm; L. reticulum, network] An extensive membranous network in eukaryotic cells, continuous with the outer nuclear membrane and composed of ribosome-studded (rough) and ribosomefree (smooth) regions. endorphin A hormone produced in the brain and anterior pituitary that inhibits pain perception. endoskeleton (en-doh-skel-eh-ton) A hard skeleton buried within the soft tissues of an animal, such as the spicules of sponges, the plates of echinoderms, and the bony skeletons of vertebrates. endosperm (en-doh-spurm) [Gk. endon, within + sperma, seed] A nutrient-rich tissue formed by the union of a sperm cell with two polar nuclei during double fertilization, which provides nourishment to the developing embryo in angiosperm seeds. endospore A thick-coated, resistant cell produced within a bacterial cell exposed to harsh conditions. endosymbiotic theory (en-doh-sim-by-ot-ic) A hypothesis about the origin of the eukaryotic cell, maintaining that the forerunners of eukaryotic cells were symbiotic associations of prokaryotic cells living inside larger prokaryotes. endothelium (en-doh-theel-ee-um) [Gk. endon, + thele, nipple] The innermost, simple squamous layer of cells lining the blood vessels; the only constituent structure of capillaries. endotherm (en-doh-thurm) [Gk. endon, within + therme, heat] An animal that uses metabolic energy to

maintain a constant body temperature, such as a bird or mammal. See also Homeotherm. endotoxin (en-doh-toks-in) A component of the outer membranes of certain gram-negative bacteria responsible for generalized symptoms of fever and ache. energy The capacity to do work by moving matter against an opposing force. energy of activation (E A ) The amount of energy that reactants must absorb before a chemical reaction will start. enhancer A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes. entropy (en-truh-pee) [Gk. en, in + trope, turning] A quantitative measure of disorder or randomness, symbolized by S. environmental grain An ecological term for the effect of spatial variation, or patchiness, relative to the size and behavior of an organism. enzyme [Gk. en, in + zyme, leaven] A class of proteins serving as catalysts, chemical agents that change the rate of a reaction without being consumed by the reaction. epidermis (ep-eh-der-mis) [Gk. epi, on or over + derma, skin] (1) The dermal tissue system in plants. (2) The outer covering of animals. epigenesis (ep-eh-jen-eh-sis) The progressive development of form in an embryo. epididymis (ep-ih-did-eh-mis) A long coiled tube into which sperm pass from the testis and are stored until mature and ejaculated. epigenesis A cartilaginous flap that blocks the top of the windpipe, the glottis, during swallowing, which prevents the entry of food or fluid into the respiratory system.

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epinephrine A hormone produced as a response to stress; also called adrenaline. See Adrenaline. epiphyte (ep-eh-fite) A plant that nourishes itself but grows on the surface of another plant for support, usually on the branches or trunks of tropical trees. episome A plasmid capable of integrating into the bacterial chromosome. epistasis [Gk. a stopping] A phenomenon in which one gene alters the expression of another gene that is independently inherited. epithelial tissue (ep-eh-theel-ee-ul) [Gk. epi, on or over + thele, nipple] Sheets of tightly packed cells that line organs and body cavities. epitope A localized region on the surface of an antigen that is chemically recognized by antibodies; also called antigenic determinant. equilibrium [L. aequus, equal + libra, balance] The state of a system in which no further net change is occurring; result of counterbalancing forward and backward processes. equilibrium species Species characterized by low reproduction rates, long development times, large body size, and long adult life with repeated reproductions. erythrocyte (er-rith-ro-site) [Gk. erythros, red + kytos, vessel] A red blood cell; contains hemoglobin, which functions in transporting oxygen in the circulatory system. esophagus (eh-sof-eh-gus) A channel that conducts food, by peristalsis, from the pharynx to the stomach. essential amino acids The amino acids that an animal cannot synthesize itself and must obtain from food.

Eight amino acids are essential in the human adult. estivation (es-teh-vay-shun) A physiological state characterized by slow metabolism and inactivity, which permits survival during long periods of elevated temperature and diminished water supplies. estrogens [Gk. oistros, frenzy + genos, origin, descent] The primary female steroid sex hormones, which are produced in the ovary by the developing follicle during the first half of the cycle and in smaller quantities by the corpus luteum during the second half. Estrogens stimulate the development and maintenance of the female reproductive system and secondary sex characteristics. estrous cycle (es-trus) A type of reproductive cycle in all female mammals except higher primates, in which the nonpregnant endometrium is reabsorbed rather than shed, and sexual response occurs only during midcycle at estrus. ethology [Gk. ethos, habit, custom + logos, discourse] The comparative study of patterns of animal behavior, with emphasis on their adaptive significance and evolutionary origin. ethylene (eth-ul-een) The only gaseous plant hormone, responsible for fruit ripening, growth inhibition, leaf abscission, and aging. etiolation [Fr. etioler, to blanch] In plants, a condition characterized by stem elongation, poor leaf development, and lack of chlorophyll; occurs in plants growing in the dark or with greatly reduced light. euchromatin (yoo-kroh-muh-tin) The more open, unraveled form of eukaryotic chromatin, which is available for transcription. eukaryotic cell A type of cell with a membrane-enclosed nucleus and membrane-enclosed

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organelles, present in protists, plants, fungi, and animals; also called eukaryote. eukaryote [Gk. eu, good + karyon, nut, kernel] An organism whose cells contain membraine-bound organelles and whose DNA is enclosed in a cell nucleus and is associated with proteins. eumetazoa (yoo-met-uh-zoh-uh) Members of the subkingdom that includes all animals except sponges. eusocial [Gk. eu, good + L. socius, companion] Applied to animal societies, such as those of certain insects, in which sterile individuals work on behalf of reproductive individuals. eutherian mammals Placental mammals; those whose young complete their embryonic development within the uterus, joined to the mother by the placenta. eutrophic lake A highly productive lake, having a high rate of biological productivity supported by a high rate of nutrient cycling. eutrophication A process in which an aquatic environment accumulates high nutrient levels due to factors such as industrial or urban pollution or run-off of fertilizers from nearby agricultural lands. The nutrients lead to dense blooms of algae and aquatic plants that cloud lake water, deplete specific minerals and dissolved gases, and can cause natural plant and animal populations to decline. evaporative cooling The property of a liquid whereby the surface becomes cooler during evaporation, owing to a loss of highly kinetic molecules to the gaseous state. evolution [L. e-, out + volvere, to roll] All the changes that have transformed life on Earth from its earliest beginnings to the diversity that characterizes it today. evolutionary species concept The idea that evolutionary lineages and ecological roles can form the basis of species identification.

exaptation A structure that evolves and functions in one environmental context but that can perform additional functions when placed in some new environment. excitatory postsynaptic potential (EPSP) (post-sin-ap-tik) An electrical change (depolarization) in the membrane of a postsynaptic neuron caused by the binding of an excitatory neurotransmitter from a presynaptic cell to a postsynaptic receptor; makes it more likely for a postsynaptic neuron to generate an action potential. excretion The disposal of nitrogen-containing waste products of metabolism. excretory system The organ system that disposes of nitrogencontaining metabolic wastes. exergonic reaction (eks-ur-gon-ik) [Gk. ex, out of + ergon, work] A spontaneous chemical reaction in which there is a net release of free energy. exocrine glands [Gk. ex, out of + krinein, to separate] Glands, such as sweat glands and digestive glands, that secrete their products into ducts that empty onto surfaces, such as the skin, or into cavities, such as the interior of the stomach. exocytosis (eks-oh-sy-toh-sis) [Gk. ex, out of + kytos, vessel] The cellular secretion of macromolecules by the fusion of vesicles with the plasma membrane. exon The coding region of a eukaryotic gene that is expressed. Exons are separated from each other by introns. exoskeleton A hard encasement on the surface of an animal, such as the shells of mollusks or the cuticles of arthropods, that provides protection and points of attachment for muscles. exotoxin (eks-oh-toks-in) A toxic protein secreted by a bacterial cell that produces specific symptoms even in the absence of the bacterium.

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exponential growth In populations, the increasingly accelerated rate of growth due to the increasing number of individuals being added to the reproductive base. Exponential growth is very seldom approached or sustained in natural populations. expression vector A vector that allows a DNA sequence cloned into it to be transcribed when the vector is introduced into a cell. expressivity In genetics, the degree to which a particular genotype is expressed in the phenotype of individuals with that genotype. extinct [L. exstinctus, to be extinguished] No longer existing. extracellular matrix (ECM) The substance in which animal tissue cells are embedded; consists of protein and polysaccharides. extraembryonic membranes Four membranes (yolk sac, amnion, chorion, allantois) that support the developing embryo in reptiles, birds, and mammals.

switches to fermentation under anaerobic conditions. FAD Abbreviation of flavin adenine dinucleotide, a coenzyme that functions as an electron acceptor in the Krebs cycle. Fallopian tube See Oviduct. family A taxonomic grouping of related, similar genera; the category below order and above genus. fat (triacylglycerol) (tri-ah-sil-glis-er-all) A biological compound consisting of three fatty acids linked to one glycerol molecule. fatty acid A long carbon chain carboxylic acid. Fatty acids vary in length and in the number and location of double bonds; three fatty acids linked to a glycerol molecule form fat. feedback inhibition A method of metabolic control in which the end-product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway. feedback systems Control mechanisms whereby an increase or decrease in the level of a particular factor inhibits or stimulates the production, utilization, or release of that factor; important in the regulation of enzyme and F 1 (first filial generation) The first filial or hybrid offspring in a genetic hormone levels, ion concentrations, temperature, and many other factors. cross-fertilization. fermentation F 2 (second filial generation) A catabolic process that makes a limited Offspring resulting from interbreeding of amount of ATP from glucose without an the hybrid F 1 generation. electron transport chain and that produces F factor A fertility factor in bacteria, a DNA segment a characteristic end-product, such as ethyl alcohol or lactic acid. that confers the ability to form pili for fertilization conjugation and associated functions required for the transfer of DNA from donor The union of haploid gametes to produce a diploid zygote. to recipient. May exist as a plasmid or fetus integrated into the bacterial chromosome. [L. pregnant] facilitated diffusion The spontaneous passage of molecules and An unborn or unhatched vertebrate that has passed through the earliest ions, bound to specific carrier proteins, developmental stages; a developing human across a biological membrane down their from about the second month of gestation concentration gradients. until birth. facultative anaerobe fiber (fak-ul-tay-tiv an-uh-robe) A lignified cell type that reinforces the An organism that makes ATP by aerobic xylem of angiosperms and functions in respiration if oxygen is present but that

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mechanical support; a slender, tapered sclerenchyma cell that usually occurs in bundles. fibril [L. fibra, fiber] Any minute, threadlike structure within a cell. fibrin (fy-brin) The activated form of the blood-clotting protein fibrinogen, which aggregates into threads that form the fabric of the clot. fibroblast (fy-broh-blast) A type of cell in loose connective tissue that secretes the protein ingredients of the extracellular fibers. fibrous protein Insoluble structural protein in which the polypeptide chain is coiled along one dimension. Fibrous proteins constitute the main structural elements of many animal tissues. filament [L. filare, to spin] (1) A chain of cells. (2) In flowers, the stalk of a stamen. filtrate Fluid extracted by the excretory system from the blood or body cavity. The excretory system produces urine from the filtrate after extracting valuable solutes from it and concentrating it. filtration The first stage of kidney function; blood plasma is forced, under pressure, out of the glomerular capillaries into Bowman's capsule, through which it enters the renal tubule. first law of thermodynamics (thur-moh-dy-nam-iks) The principle of conservation of energy. Energy can be transferred and transformed, but it cannot be created or destroyed. fitness The genetic contribution of an individual to succeeding generations relative to the contributions of other individuals in the population. fixed action pattern A highly stereotypical behavior that is innate and must be carried to completion once initiated.

flaccid (flas-id) Limp; walled cells are flaccid in isotonic surroundings, where there is no tendency for water to enter. flagellum pl. flagella (fla-jell-um) [L. flagellum, whip] A long cellular appendage specialized for locomotion, formed from a core of nine outer doublet microtubules and two inner single microtubules, ensheathed in an extension of plasma membrane. flower The reproductive structure of angiosperms; a complete flower includes sepals, petals, stamens (male structures), and carpels (female structures). fluid-feeder An animal that lives by sucking nutrient-rich fluids from another living organism. fluid mosaic model The currently accepted model of cell membrane structure, which envisions the membrane as a mosaic of individually inserted protein molecules drifting laterally in a fluid bilayer of phospholipids. follicle (fol-eh-kul) A microscopic structure in the ovary that contains the developing ovum and secretes estrogens. follicle-stimulating hormone (FSH) A protein hormone secreted by the anterior pituitary that stimulates the production of eggs by the ovaries and sperm by the testes. food chain The pathway along which food is transferred from trophic level to trophic level, beginning with producers. food web The elaborate, interconnected feeding relationships in an ecosystem. fossil [L. fossilis, dug up] The remains of an organism, or direct evidence of its presence (such as tracks). May be an unaltered hard part (tooth or bone), a mold in a rock, petrification (wood or bone), unaltered or partially altered soft parts (a frozen mammoth).

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founder effect A cause of genetic drift attributable to colonization by a limited number of individuals from a parent population. fovea [L. pit] A small area in the center of the retina in which cones are concentrated; the area of sharpest vision. fragile X syndrome A hereditary mental disorder, partially explained by genomic imprinting and the addition of nucleotides to a triplet repeat near the end of an X chromosome. frameshift mutation A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of 3, thus resulting in improper grouping into codons. free energy A quantity of energy that interrelates entropy (S) and the system's total energy (H); symbolized by G. The change in free energy of a system is calculated by the equation G = H T S, where T is absolute temperature. free energy of activation The initial investment of energy necessary to start a chemical reaction; also called activation energy. frequency-dependent selection A decline in the reproductive success of a morph resulting from the morph's phenotype becoming too common in a population; a cause of balanced polymorphism in populations. fruit [L. fructus, fruit] A mature ovary of a flower that protects dormant seeds and aids in their dispersal. function [L. fungor, to busy oneself] Characteristic role or action of a structure or process in the normal metabolism or behavior of an organism. functional group A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.

G protein A GTP-binding protein that relays signals from a plasma-membrane signal receptor, known as a G-protein linked receptor, to other signal-transduction proteins inside the cell. When such a receptor is activated, it in turn activates the G protein, causing it to bind a molecule of GTP in place of GDP. Hydrolysis of the bound GTP to GDP inactivates the G protein. G-protein linked receptor A signal receptor protein in the plasma membrane that responds to the binding of a signal molecule by activating a G protein. G 1 phase The first growth phase of the cell cycle, consisting of the portion of interphase before DNA synthesis begins. G 2 phase The second growth phase of the cell cycle, consisting of the portion of interphase after DNA synthesis occurs. gametangium pl. gametangia (gam-eh-tanj-ee-um) [Gk. gamein, to marry + L. tangere, to touch] The reproductive organ of bryophytes, consisting of the male antheridium and female archegonium; a multichambered jacket of sterile cells in which gametes are formed. gamete (gam-eet) [Gk. wife] A haploid egg or sperm cell; gametes unite during sexual reproduction to produce a diploid zygote. gametophyte (guh-mee-toh-fite) The multicellular haploid form in organisms undergoing alternation of generations, which mitotically produces haploid gametes that unite and grow into the sporophyte generation. ganglion pl. ganglia (gang-lee-un) (gang-lee-ah) [Gk. ganglion, a swelling] A cluster (functional group) of nerve cell bodies in a centralized nervous system.

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gap junction A type of intercellular junction in animal cells that allows the passage of material or current between cells. gap phases In the cell cycle, the phases that precede (G 1 ) and follow (G 2 ) the synthesis (S) phase in which DNA is replicated; in the G 1 phase, the cell doubles in size, and its enzymes, ribosomes, and other cytoplasmic molecules and structures increase in number; in the G 2 phase, the replicated chromosomes begin to condense and the structures required for mitosis or meiosis are assembled. gastric [Gk. gaster, stomach] Pertaining to the stomach. gastrin A digestive hormone, secreted by the stomach, that stimulates the secretion of gastric juice. gastrovascular cavity [Gk. gaster, stomach + L. vasculum, a small vessel] The central digestive compartment, usually with a single opening that functions as both mouth and anus. gastrula (gas-troo-la) [Gk. gaster, stomach] The two-layered, cup-shaped embryonic stage. gastrulation (gas-truh-lay-shun) The formation of a gastrula from a blastula. gated ion channel A specific ion channel that opens and closes to allow the cell to alter its membrane potential. Gause's principle See Competitive exclusion principle. gel electrophoresis (jell eh-lek-troh-for-ee-sis) The separation of nucleic acids or proteins, on the basis of their size and electrical charge, by measuring their rate of movement through an electrical field in a gel. gene [Gk. genos, birth, race; L. genus, birth, race, origin] A discrete unit of hereditary information

consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses). gene amplification The selective synthesis of DNA, which results in multiple copies of a single gene, thereby enhancing expression. gene cloning The production of multiple copies of a gene. gene flow The loss or gain of alleles from a population due to the emigration or immigration of fertile individuals, or the transfer of gametes, between populations. gene pool The total aggregate of genes in a population at any one time. genetic code The system of nucleotide triplets in DNA and RNA that carries genetic information; referred to as a code because it determines the amino acid sequence in the enzymes and other protein molecules synthesized by the organism. genetic drift Changes in the gene pool of a small population due to chance. genetic isolation The absence of genetic exchange between populations or species as a result of geographic separation or of premating or postmating mechanisms (behavioral, anatomical, or physiological) that prevent reproduction. genetic map An ordered list of genetic loci (genes or other genetic markers) along a chromosome. genetic recombination The general term for the production of offspring that combine traits of the two parents. genome (jee-nome) The complete complement of an organism's genes; an organism's genetic material. genomic imprinting The parental effect on gene expression. Identical alleles may have different effects on offspring, depending on whether they arrive in the zygote via the ovum or via the sperm.

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genomic library A set of thousands of DNA segments from a genome, each carried by a plasmid, phage, or other cloning vector. genotype (jee-noh-type) The genetic makeup of an organism. genus pl. genera (jee-nus) [L. genus, race, origin] A taxonomic category above the species level, designated by the first word of a species' binomial Latin name. geographical range The geographic area in which a population lives. geological time scale A time scale established by geologists that reflects a consistent sequence of historical periods, grouped into four eras: Precambrian, Paleozoic, Mesozoic, and Cenozoic. germ cells [L. germinare, to bud] Gametes or the cells that give rise to gametes. germination [L. germinare, to bud] In plants, the resumption of growth or the development from seed or spore. gibberellin (jib-ur-el-in) [Fr. gibberella, genus of fungi] A class of related plant hormones that stimulate growth in the stem and leaves, trigger the germination of seeds and breaking of bud dormancy, and stimulate fruit development with auxin. gill A localized extension of the body surface of many aquatic animals, specialized for gas exchange. gland [L. glans, glandis, acorn] A structure composed of modified epithelial cells specialized to produce one or more secretions that are discharged to the outside of the gland. glial cell (glee-ul) [Gk. glia, glue + L. cella, a chamber] A nonconducting cell of the nervous system that provides support, insulation, and protection for the neurons.

globular protein [L. dim. of globus, a ball] A polypeptide chain folded into a roughly spherical shape. glomerulus (gluh-mare-yoo-lus) [L. glomus, ball] A ball of capillaries surrounded by Bowman's capsule in the nephron and serving as the site of filtration in the vertebrate kidney. glucagon [Gk. glykys, sweet + ago, to lead toward] A peptide hormone secreted by pancreatic endocrine cells that raises blood glucose levels; an antagonistic hormone to insulin. glucocorticoid A corticosteroid hormone secreted by the adrenal cortex that influences glucose metabolism and immune function. glucose [Gk. glykys, sweet] A six-carbon sugar (C 6 H 12 O 6 ); the most common monosaccharide in animals. glycerol A three-carbon molecule with three hydroxyl ( ) groups attached; a glycerol molecule can combine with three fatty acid molecules to form a fat or an oil. glycocalyx (gly-koh-kay-liks) A fuzzy coat on the outside of animal cells, made of sticky oligosaccharides. glycogen (gly-koh-jen) [Gk. glykys, sweet + genos, race or descent] An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch. glycolipids [Gk. glykys, sweet + lipos, fat] Organic molecules similar in structure to fats, but in which a short carbohydrate chain rather than a fatty acid is attached to the third carbon of the glycerol molecule; as a result, the molecule has a hydrophilic "head" and a hydrophobic "tail." Glycolipids are important constituents of the plasma membrane and of organelle membranes. glycolysis (gly-kol-eh-sis) [Gk. glykys, sweet + lysis, loosening] The splitting of glucose into pyruvate.

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Glycolysis is the one metabolic pathway that occurs in all living cells, serving as the starting point for fermentation or aerobic respiration. glycoprotein [Gk. glykys, sweet + proteios, primary] A protein with covalently attached carbohydrate. Golgi apparatus (goal-jee) An organelle in eukaryotic cells consisting of stacks of flat membranous sacs that modify, store, and route products of the endoplasmic reticulum. gonadotropins (goh-nad-oh-troh-pinz) [Gk. gone, seed + trope, a turning] Hormones that stimulate the activities of the testes and ovaries; a collective term for follicle-stimulating and luteinizing hormones. gonads [Gk. gone, seed] The male and female sex organs; the gamete-producing organs in most animals. graded potential A local voltage change in a neuron membrane induced by stimulation of a neuron, with strength proportional to the strength of the stimulus and lasting about a millisecond. gradualism A view of Earth's history that attributes profound change to the cumulative product of slow but continuous processes. Gram stain A staining method that distinguishes between two different kinds of bacterial cell walls. granum pl. grana (gran-um) [L. grain or seed] A stacked portion of the thylakoid membrane in the chloroplast. Grana function in the light reactions of photosynthesis. gravitropism (grav-eh-troh-piz-um) [L. gravis, heavy + Gk. trope, turning] A response of a plant or animal in relation to gravity. greenhouse effect The warming of planet Earth due to the atmospheric accumulation of carbon

dioxide, which absorbs infrared radiation and slows its escape from the irradiated Earth. gross primary productivity (GPP) The total primary productivity of an ecosystem. gross productivity A measure of the rate at which energy is assimilated by the organisms in a trophic level, a community, or an ecosystem. ground meristem [Gk. merizein, to divide] A primary meristem that gives rise to ground tissue in plants. ground tissue system A tissue of mostly parenchyma cells that makes up the bulk of a young plant and fills the space between the dermal and vascular tissue systems. growth factor A protein that must be present in the extracellular environment (culture medium or animal body) for the growth and normal development of certain types of cells. guard cell A specialized epidermal plant cell that forms the boundaries of the stomata. guttation The exudation of water droplets caused by root pressure in certain plants. gymnosperm (jim-noh-spurm) [Gk. gymnos, naked + sperma, seed] A vascular plant that bears naked seeds not enclosed in any specialized chambers.

habitat [L. habitare, to live in] The place in which individuals of a particular species can usually be found. habituation [L. habitus, condition] A simple kind of learning involving a loss of sensitivity to unimportant stimuli, allowing an animal to conserve time and energy.

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half-life The average time required for the disappearance or decay of one-half of any amount of a given substance. haploid cell (hap-loyd) [Gk. haploos, single + ploion, vessel] A cell containing only one set of chromosomes (n). Hardy-Weinberg equilibrium The steady-state relationship between relative frequencies of two or more alleles in an idealized population; both the allele frequencies and the genotype frequencies will remain constant from generation to generation in a population breeding at random in the absence of evolutionary forces. Hardy-Weinberg theorem An axiom maintaining that the sexual shuffling of genes alone cannot alter the overall genetic makeup of a population. haustorium pl. haustoria In parasitic fungi, a nutrient-absorbing hyphal tip that penetrates the tissues of the host but remains outside the host cell membranes. Haversian system (ha-ver-shun) One of many structural units of vertebrate bone, consisting of concentric layers of mineralized bone matrix surrounding lacunae, which contain osteocytes, and a central canal, which contains blood vessels and nerves. heat The total amount of kinetic energy due to molecular motion in a body of matter. Heat is energy in its most random form. heat of vaporization The amount of heat required to change a given amount of a liquid into a gas; 540 calories are required to change 1 gram of liquid water into vapor. heat-shock protein A protein that helps protect other proteins during heat stress, found in plants, animals, and microorganisms. helper T cell (T H ) A type of T cell that is required by some B cells to help them make antibodies or that helps other T cells respond to antigens or secrete lymphokines or interleukins.

heme [Gk. haima, blood] The iron-containing group of heme proteins such as hemoglobin and the cytochromes. hemoglobin (hee-moh-gloh-bin) [Gk. haima, blood + L. globus, a ball] An iron-containing protein in red blood cells that reversibly binds oxygen. hemophilia [Gk. haima, blood + philios, friendly] A group of hereditary disorders characterized by failure of the blood to clot and consequent excessive bleeding from even minor wounds. hemolymph In invertebrates with an open circulatory system, the body fluid that bathes tissues. hepatic [Gk. hepatikos, liver] Pertaining to the liver. hepatic portal vessel A large circulatory channel that conveys nutrient-laden blood from the small intestine to the liver, which regulates the blood's nutrient content. herbaceous (her-bay-shus) [L. herba, grass] In plants, nonwoody. herbivore [L. herba, grass + vorare, to devour] A heterotrophic animal that eats plants. heredity [L. herres, heredis, heir] The transmission of characteristics from parent to offspring. hermaphrodite (her-maf-roh-dite) [Gk. Hermes and Aphrodite] An individual that functions as both male and female in sexual reproduction by producing both sperm and eggs. heterochromatin (het-ur-oh-kroh-muh-tin) Nontranscribed eukaryotic chromatin that is so highly compacted that it is visible with a light microscope during interphase. heterochrony Evolutionary changes in the timing or rate of development. heterocyst (het-ur-oh-sist) A specialized cell that engages in nitrogen

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fixation on some filamentous cyanobacteria. heteromorphic (het-ur-oh-mor-fik) A condition in the life cycle of all modern plants in which the sporophyte and gametophyte generations differ in morphology. heterosporous (het-ur-os-pur-us) Referring to plants in which the sporophyte produces two kinds of spores that develop into unisexual gametophytes, either female or male. heterotroph (het-ur-oh-trohf) [Gk. heteros, other, different + trophos, feeder] An organism that obtains organic food molecules by eating other organisms or their by-products. heterozygote (het-ur-oh-zy-gote) [Gk. heteros, other + zygotos, a pair] A diploid organism that carries two different alleles at one or more genetic loci. heterozygote advantage A mechanism that preserves variation in eukaryotic gene pools by conferring greater reproductive success on heterozygotes over individuals homozygous for any one of the associated alleles. heterozygous (het-ur-oh-zy-gus) Having two different alleles for a given genetic character. hibernation [L. hiberna, winter] A physiological state that allows survival during long periods of cold temperatures and reduced food supplies, in which metabolism decreases, the heart and respiratory system slow down, and body temperature is maintained at a lower level than normal. histamine (hiss-tuh-meen) A substance released by injured cells that causes blood vessels to dilate during an inflammatory response. histone (hiss-tone) A small protein with a high proportion of positively charged amino acids that binds to

the negatively charged DNA and plays a key role in its chromatin structure. HIV Abbreviation of human immunodeficiency virus, the infectious agent that causes AIDS; HIV is an RNA retrovirus. holoblastic cleavage (hoh-loh-blas-tik) A type of cleavage in which there is complete division of the egg, as in eggs having little yolk (sea urchin) or a moderate amount of yolk (frog). homeobox A 180-nucleotide sequence within a homeotic gene encoding the part of the protein that binds to the DNA of the genes regulated by the protein. homeosis Evolutionary alteration in the placement of different body parts. homeostasis (home-ee-oh-stay-sis) [Gk. homos, same or similar + stasis, standing] The steady-state physiological condition of the body. homeotherm [Gk. homos, same or similar + therme, heat] An organism, such as a bird or mammal, capable of maintaining a stable body temperature independent of the environment. homeotic genes (home-ee-ot-ik) Genes that control the overall body plan of animals by controlling the developmental fate of groups of cells. hominid [L. homo, man] Humans and closely related primates; includes modern and fossil forms, such as the australopithecines, but not the apes. hominoid [L. homo, man] Hominids and the apes. homologous chromosomes (home-ol-uh-gus) [Gk. homologia, agreement] Chromosome pairs of the same length, centromere position, and staining pattern that possess genes for the same characters at corresponding loci. One homologous chromosome is inherited from the

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organism's father, the other from the mother. homologous structures Structures in different species that are similar because of common ancestry. homology [Gk. homologia, agreement] Similarity in characteristics resulting from a shared ancestry. homosporous (home-os-pur-us) Referring to plants in which a single type of spore develops into a bisexual gametophyte having both male and female sex organs. homozygote [Gk. homos, same or similar + zygotos, a pair] A diploid organism that carries identical alleles at one or more genetic loci. homozygous (home-oh-zy-gus) Having two identical alleles for a given trait. hormone [Gk. hormaein, to excite] One of many types of circulating chemical signals in all multicellular organisms that are formed in specialized cells, travel in body fluids, and coordinate the various parts of the organism by interacting with target cells. host (1) An organism on or in which a parasite lives. (2) A recipient of grafted tissue. Human Genome Project An international collaborative effort to map and sequence the DNA of the entire human genome. human immunodeficiency virus (HIV) The infectious agent that causes AIDS; HIV is an RNA retrovirus. humoral immunity (hyoo-mur-al) The type of immunity that fights bacteria and viruses in body fluids with antibodies that circulate in blood plasma and lymph, fluids formerly called humors. hybrid [L. hybrida, the offspring of a tame sow and a wild boar] (1) Offspring of two parents that differ in one or more inheritable characteristics. (2) Offspring of two different varieties or of two different species.

hybrid zone A region where two related populations that diverged after becoming geographically isolated make secondary contact and interbreed where their geographical ranges overlap. hydrocarbon [L. hydro, water + carbo, charcoal] An organic molecule consisting only of carbon and hydrogen. hydrogen bond A type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule. hydrolysis (hy-drol-eh-sis) [L. hydro, water + Gk. lysis, loosening] A chemical process that lyses or splits molecules by the addition of water; an essential process in digestion. hydrogen ion A single proton with a charge of +1. The dissociation of a water molecule (H 2 O) leads to the generation of a hydroxide ion + (OH ) and a hydrogen ion (H ). hydrophilic (hy-droh-fil-ik) [L. hydro, water + Gk. philios, friendly] Having an affinity for water. hydrophobic (hy-droh-foh-bik) [L. hydro, water + Gk. phobos, fearing] Having an aversion to water; tending to coalesce and form droplets in water. hydrostatic skeleton (hy-droh-stat-ik) A skeletal system composed of fluid held under pressure in a closed body compartment; the main skeleton of most cnidarians, flatworms, nematodes, and annelids. hydroxyl group (hy-droks-ul) A functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols. hyperpolarization An electrical state whereby the inside of the cell is made more negative relative to the

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outside than at the resting membrane potential. A neuron membrane is hyperpolarized if a stimulus increases its voltage from the resting potential of 70 mV, reducing the chance that the neuron will transmit a nerve impulse. hypertonic solution [Gk. hyper, above + tonos, tension] A solution with a greater solute concentration than another, a hypotonic solution. hypha (hy-fa) [Gk. hyphe, web] A filament that collectively makes up the body of a fungus. hypothalamus (hy-poh-thal-uh-mus) [Gk. hypo, under + thalamos, inner room] The ventral part of the vertebrate forebrain; functions in maintaining homeostasis, especially in coordinating the endocrine and nervous systems; secretes hormones of the posterior pituitary and releasing factors, which regulate the anterior pituitary. hypothesis [Gk. hypo, under + tithenai, to put] A temporary working explanation or supposition based on accumulated facts and suggesting some general principle or relation of cause and effect; a postulated solution to a scientific problem that must be tested and if not validated, discarded. hypotonic solution [Gk. hypo, under + tonos, tension] A solution with a lesser solute concentration than another, a hypertonic solution.

ichthyologist Biologists who specialize in the study of fish behavior, anatomy, physiology, and evolution. imaginal disk (i-maj-in-ul) An island of undifferentiated cells in an insect larva, which are committed (determined) to form a particular organ during metamorphosis to the adult.

imbibition [L. imbibere, to drink in] The capillary movement of water into germinating seeds and into substances such as wood and gelatin, which swell as a result. immune response A highly specific defensive reaction of the body to invasion by a foreign substance or organism; consists of a primary response in which the invader is recognized as foreign, or "not-self," and eliminated and a secondary response to subsequent attacks by the same invader. Mediated by two types of lymphocytes B cells, which mature in the bone marrow and are responsible for antibody production, and T cells, which mature in the thymus and are responsible for cell-mediated immunity. immunoglobulin (Ig) (im-myoo-noh-glob-yoo-lin) One of the class of proteins comprising the antibodies. imprinting A type of learned behavior with a significant innate component, acquired during a limited critical period. inbreeding The mating of individuals that are closely related genetically. inclusive fitness The relative number of an individual's alleles that are passed on from generation to generation, either as a result of his or her own reproductive success, or that of related individuals. incomplete dominance A type of inheritance in which F 1 hybrids have an appearance that is intermediate between the phenotypes of the parental varieties. incomplete flower A flower lacking sepals, petals, stamens, or carpels. incomplete metamorphosis (met-uh-mor-foh-sis) A type of development in certain insects, such as grasshoppers, in which the larvae resemble adults but are smaller and have different body proportions. The animal goes through a series of molts, each time looking more like an adult, until it reaches full size. independent assortment See Mendel's second law.

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independent variable In an experiment, when one factor is manipulated, a second factor responds. The independent variable is the factor that is manipulated. indeterminate cleavage A type of embryonic development in deuterostomes, in which each cell produced by early cleavage divisions retains the capacity to develop into a complete embryo. indeterminate growth A type of growth characteristic of plants, in which the organism continues to grow as long as it lives. induced fit The change in shape of the active site of an enzyme so that it binds more snugly to the substrate, induced by entry of the substrate. induction [L. inducere, to induce] (1) The ability of one group of embryonic cells to influence the development of another. (2) In genetics, the phenomenon in which the presence of a substrate (the inducer) initiates transcription and translation of the genes coding for the enzymes required for its metabolism. inflammatory response A line of defense triggered by penetration of the skin or mucous membranes, in which small blood vessels in the vicinity of an injury dilate and become leakier, enhancing the infiltration of leukocytes; may also be widespread in the body. ingestion A heterotrophic mode of nutrition in which other organisms or detritus are eaten whole or in pieces. inhibitory postsynaptic potential (IPSP) (post-sin-ap-tik) An electrical charge (hyperpolarization) in the membrane of a postsynaptic neuron caused by the binding of an inhibitory neurotransmitter from a presynaptic cell to a postsynaptic receptor; makes it more difficult for a postsynaptic neuron to generate an action potential. innate releasing mechanism In ethology, a circuit within an animal's brain that is hypothesized to respond to a specific stimulus, setting in motion, or

"releasing," the sequence of movements that constitute a fixed action pattern. inner cell mass A cluster of cells in a mammalian blastocyst that protrudes into one end of the cavity and subsequently develops into the embryo proper and some of the extraembryonic membranes. inositol trisphosphate (IP 3 ) (in-nos-i-tahl) The second messenger, which functions as an intermediate between certain nonsteroid hormones and the third 2+ messenger, a rise in cytoplasmic Ca concentration. insertion A mutation involving the addition of one or more nucleotide pairs to a gene. insertion sequence The simplest kind of a transposon, consisting of inserted repeats of DNA flanking a gene for transposase, the enzyme that catalyzes transposition. insight learning The ability of an animal to perform a correct or appropriate behavior on the first attempt in a situation with which it has had no prior experience. instar The stage of an arthropod's life cycle between molts (shedding of the exoskeleton). As an example, the third instar is the stage of the life cycle between the second and third molting cycles. Some arthropods molt throughout their entire life and may have as many as 30 instars. Insects tend to have a set number of instars, the number varying by species. The instars succeed one another until the final mature instar, when the organism stops molting. insulin A vertebrate hormone that lowers blood glucose levels by promoting the uptake of glucose by most body cells and the synthesis and storage of glycogen in the liver; also stimulates protein and fat synthesis; secreted by endocrine cells of the pancreas called islets of Langerhans. interferon A chemical messenger of the immune system, produced by virus-infected cells and capable of helping other cells resist the virus.

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interleukin Interleukin-1, a chemical regulator (cytokin) secreted by macrophages that have ingested a pathogen or foreign molecule and have bound with a helper T cell; stimulates T cells to grow and divide and elevates body temperature. Interleukin-2, secreted by activated T cells, stimulates helper T cells to proliferate more rapidly. intermediate filament A component of the cytoskeleton that includes all filaments intermediate in size between microtubules and microfilaments. interneuron An association neuron; a nerve cell within the central nervous system that forms synapses with sensory and motor neurons and integrates sensory input and motor output. internode The segment of a plant stem between the points where leaves are attached. interphase The period in the cell cycle when the cell is not dividing. During interphase, cellular metabolic activity is high, chromosomes and organelles are duplicated, and cell size may increase. Interphase accounts for 90% of the time of each cell cycle. interstitial cells (in-tur-stish-ul) Cells scattered among the seminiferous tubules of the vertebrate testis that secrete testosterone and other androgens, the male sex hormones. interstitial fluid The internal environment of vertebrates, consisting of the fluid filling the spaces between cells. intertidal zone The shallow zone of the ocean where land meets water. intrinsic rate of increase The difference between the number of births and the number of deaths, symbolized as r max ; the maximum population growth rate. introgression (in-troh-gres-shun) The transplantation of genes between species resulting from fertile hybrids mating successfully with one of the parent species.

intron A noncoding, intervening sequence within a eukaryotic gene. invagination [L. in, in + vagina, sheath] The local infolding of a layer of tissue, especially in animal embryos, so as to form a depression or pocket opening to the outside. inversion An aberration in chromosome structure resulting from an error in meiosis or from mutagens; reattachment in a reverse orientation of a chromosomal fragment to the chromosome from which the fragment originated. invertebrate An animal without a backbone; invertebrates make up 95% of animal species. in vitro fertilization (vee-troh) Fertilization of ova in laboratory containers followed by artificial implantation of the early embryo in the mother's uterus. ion (eye-on) An atom that has gained or lost electrons, thus acquiring a charge. ionic bond A chemical bond resulting from the attraction between oppositely charged ions. isogamy (eye-sog-uh-mee) A condition in which male and female gametes are morphologically indistinguishable. isolating mechanisms Mechanisms that prevent genetic exchange between individuals of different populations or species; they prevent mating or successful reproduction even when mating occurs; may be behavioral, anatomical, or physiological. isomer (eye-sum-ur) One of several organic compounds with the same molecular formula but different structures and therefore different properties. The three types are structural isomers, geometric isomers, and enantiomers.

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isomorphic generations Alternating generations in which the sporophytes and gametophytes look alike, although they differ in chromosome number. isotonic solution [Gk. isos, equal + tonos, tension] Solutions of equal solute concentration. isotope (eye-so-tope) [Gk. isos, equal + topos, place] One of several atomic forms of an element, each containing a different number of neutrons and thus differing in atomic mass.

joule (J) A unit of energy: 1 J = 0.239 cal; 1 cal = 4.184 J. juvenile hormone (JH) A hormone in arthropods, secreted by the corpora allata glands, that promotes the retention of larval characteristics. juxtaglomerular apparatus (JGA) Specialized tissue located near the afferent arteriole that supplies blood to the kidney glomerulus; the JGA raises blood pressure by producing renin, which activates angiotensin.

K-selection The concept that in certain (K-selected) populations, life history is centered around producing relatively few offspring that have a good chance of survival. karyogamy The fusion of nuclei of two cells, as part of syngamy. karyokinesis Division of the nucleus during the cell cycle. karyotype (kar-ee-oh-type) [Gk. kara, the head + typos, stamp or print] A method of organizing the chromosomes of a cell in relation to number, size, and type.

keratin [Gk. karas, horn] One of a group of tough, fibrous proteins formed by certain epidermal tissues and especially abundant in skin, claws, hair, feathers, and hooves. keystone predator A predatory species that helps maintain species richness in a community by reducing the density of populations of the best competitors so that populations of less competitive species are maintained. keystone species A species that is of exceptional importance in maintaining the species diversity of a community; when a keystone species is lost, the diversity of the community decreases and its structure is significantly altered. kidney In vertebrates, the organ that regulates the balance of water and solutes in the blood and the excretion of nitrogenous wastes in the form of urine. kilocalorie (kcal) A thousand calories; the amount of heat energy required to raise the temperature of 1 kg of water 1C. kin selection A phenomenon of inclusive fitness, used to explain altruistic behavior between related individuals. kinesis (kih-nee-sis) A change in activity rate in response to a stimulus. kinetic energy (kih-net-ik) [Gk. kinetikos, putting in motion] The energy of motion, which is directly related to the speed of that motion. Moving matter does work by transferring some of its kinetic energy to other matter. kinetochore (kih-net-oh-kor) [Gk. kinetikos, putting in motion + choros, chorus] A specialized region on the centromere that links each sister chromatid to the mitotic spindle. kingdom A taxonomic category, the second broadest after domain.

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Koch's postulates A set of four criteria for determining whether a specific pathogen is the cause of a disease. Krebs cycle A chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules to carbon dioxide; occurs within the mitochondrion; the second major stage in cellular respiration.

two traits are located on different pairs of homologous chromosomes. law of segregation Mendel's first law, stating that allele pairs separate during gamete formation, and then randomly re-form pairs during the fusion of gametes at fertilization. leaching The dissolving of minerals and other elements in soil or rocks by the downward movement of water. leading strand The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction. lacteal leaf (lak-teel) The main site of photosynthesis in a plant; A tiny lymph vessel extending into the core consists of a flattened blade and a stalk of an intestinal villus and serving as the (petiole) that joins the leaf to the stem. destination for absorbed chylomicrons. learning lagging strand The process that leads to modification in A discontinuously synthesized DNA strand individual behavior as the result of that elongates in a direction away from the experience. replication fork. leukocyte lamella (loo-koh-site) [Gk. leukos, white + kytos, (lah-mell-ah) [L. dim. of lamina, plate or vessel] leaf] A white blood cell; typically functions in Layer, thin sheet. immunity, such as phagocytosis or antibody larva pl. larvae production. (lar-vuh) [L. ghost] leukotriene A free-living, sexually immature form in A type of prostaglandin produced by various some animal life cycles that may differ from white blood cells involved in the the adult in morphology, nutrition, and inflammatory and immune responses and in habitat. allergic reactions. lateral line system lichen A mechanoreceptor system consisting of a (ly-ken) series of pores and receptor units An organism formed by the symbiotic (neuromasts) along the sides of the body of association between a fungus and a fishes and aquatic amphibians; detects photosynthetic alga. water movements made by an animal itself life cycle and by other moving objects. The entire sequence of stages in the life of lateral meristem an organisms, from the adults of one (mare-eh-stem) [L. latus, lateris, side + Gk. generation to the adults of the next. meristos, divided] life-history pattern The vascular and cork cambium, a cylinder A group of traits, such as size and number of dividing cells that runs most of the length of offspring, length of maturation, age at of stems and roots and is responsible for first reproduction, and the number of times secondary growth. reproduction occurs, that affect law of independent assortment reproduction, survival, and the rate of Mendel's second law, stating that each population growth. allele pair segregates independently during life table gamete formation; applies when genes for A table of data summarizing mortality in a population.

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ligament A type of fibrous connective tissue that joins bones together at joints. ligand (lig-und) A molecule that binds specifically to a receptor site of another molecule. ligand-gated ion channel receptor A signal receptor protein in a cell membrane that can act as a channel for the passage of a specific ion across the membrane. When activated by a signal molecule, the receptor either allows or blocks passage of the ion, resulting in a change in ion concentration that usually affects cell functioning. light-dependent reactions The reactions of the first stage of photosynthesis, in which light energy is captured by chlorophyll molecules and converted to chemical energy stored in ATP and NADPH molecules. light-independent reactions The carbon-fixing reactions of the second stage of photosynthesis; energy stored in ATP and NADPH by the light-dependent reactions is used to reduce carbon from carbon dioxide to simple sugars; light is not required for these reactions. light microscope (LM) An optical instrument with lenses that refract (bend) visible light to magnify images of specimens. light reactions The steps in photosynthesis that occur on the thylakoid membranes of the chloroplast and convert solar energy to the chemical energy of ATP and NADPH, evolving oxygen in the process. lignin (lig-nin) A hard material embedded in the cellulose matrix of vascular plant cell walls that functions as an important adaptation for support in terrestrial species. limbic system (lim-bik) [L. limbus, border] A group of nuclei (clusters of nerve cell bodies) in the lower part of the mammalian forebrain that interact with the cerebral cortex in determining emotions; includes the hippocampus and the amygdala.

linkage The tendency for certain alleles to be inherited together because they are located on the same chromosome. linked genes Genes that are located on the same chromosome. linkage group A pair of homologous chromosomes. linkage map A genetic map based on the frequencies of recombination between markers during crossing over of homologous chromosomes. The greater the frequency of recombination between two genetic markers, the farther apart they are assumed to be. lipid (lih-pid) [Gk. lipos, fat] One of a family of compounds, including fats, phospholipids, and steroids, that are insoluble in water. lipoprotein [Gk. lipos, fat + proteios, primary] A protein bonded to a lipid; includes the low-density lipoproteins (LDLs) and highdensity lipoproteins (HDLs) that transport fats and cholesterol in blood. locus pl. loci (loh-kus) [L. place] A particular place along the length of a certain chromosome where a given gene is located. logistic population growth A model describing population growth that levels off as population size approaches carrying capacity. long-day plant A plant that flowers, usually in late spring or early summer, only when the light period is longer than a critical length. loop of Henle (after F. G. J. Henle, German pathologist) The long hairpin turn, with a descending and ascending limb, of the renal tubule in the vertebrate kidney; functions in water and salt reabsorption. lumen [L. light] The cavity of a tubular structure, such as endoplasmic reticulum or a blood vessel. lungs The invaginated respiratory surfaces of terrestrial vertebrates, land snails, and

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spiders that connect to the atmosphere by narrow tubes. luteinizing hormone (LH) (loo-tee-in-eye-zing) A protein hormone secreted by the anterior pituitary that stimulates ovulation in females and androgen production in males. lymph (limf) [L. lympha, water] The colorless fluid, derived from interstitial fluid, in the lymphatic system of vertebrate animals. lymph node [L. lympha, water + nodus, knot] A mass of spongy tissues, separated into compartments; located throughout the lymphatic system, lymph nodes remove dead cells, debris, and foreign particles from the circulation; also are sites at which foreign antigens are displayed to immunologically active cells. lymphatic system (lim-fat-ik) A system of vessels and lymph nodes, separate from the circulatory system, that returns fluid and protein to the blood. lymphocyte [L. lympha, water + Gk. kytos, vessel] A white blood cell. The lymphocytes that complete their development in the bone marrow are called B cells, and those that mature in the thymus are called T cells. lymphokine A chemical, released by an activated cytotoxic T cell, that attracts macrophages and stimulates phagocytosis. lysis [Gk. lysis, a loosening] Disintegration of a cell by rupture of its plasma membrane. lysogenic bacteria (lye-so-jenn-ick) [Gk. lysis, a loosening + genos, race or descent] Bacteria carrying a bacteriophage integrated into the bacterial chromosome. The virus may subsequently set up an active cycle of infection, causing lysis of the bacterial cells. lysogenic cycle A type of phage replication cycle in which the viral genome becomes incorporated into the bacterial host chromosome as a prophage.

lysosome (ly-so-some) [Gk. lysis, loosening + soma, body] A membrane-enclosed bag of hydrolytic enzymes found in the cytoplasm of eukaryotic cells. lysozyme (ly-so-zime) An enzyme in perspiration, tears, and saliva that attacks bacterial cell walls. lytic cycle (lit-ik) A type of viral replication cycle resulting in the release of new phages by death or lysis of the host cell.

M phase The mitotic phase of the cell cycle, which includes mitosis and cytokinesis. macroevolution Evolutionary change on a grand scale, encompassing the origin of novel designs, evolutionary trends, adaptive radiation, and mass extinction. macromolecule [Gk. makros, large + L. dim. of moles, mass] A giant molecule of living matter formed by the joining of smaller molecules, usually by condensation synthesis. Polysaccharides, proteins, and nucleic acids are macromolecules. macronutrient [Gk. makros, large + L. nutrire, to nourish] An inorganic nutrient required in large amounts for plant growth, such as nitrogen, potassium, calcium, phosphorus, magnesium, and sulfur. macrophage (mak-roh-fage) [Gk. makros, large + phagein, to eat] An amoeboid cell that moves through tissue fibers, engulfing bacteria and dead cells by phagocytosis. major histocompatibility complex (MHC) A large set of cell surface antigens encoded by a family of genes. Foreign MHC markers trigger T-cell responses that may lead to the rejection of transplanted tissues and organs.

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Malpighian tubule (mal-pig-ee-un) A unique excretory organ of insects that empties into the digestive tract, removes nitrogenous wastes from the blood, and functions in osmoregulation. Mammalia The vertebrate class of mammals, characterized by body hair and mammary glands that produce milk to nourish the young. mantle A heavy fold of tissue in mollusks that drapes over the visceral mass and may secrete a shell. marine [L. marini(us), from mare, the sea] Living in salt water. marsupial (mar-soop-ee-ul) [Gk. marsypos, pouch, little bag] A mammal, such as a koala, kangaroo, or opossum, whose young complete their embryonic development inside a maternal pouch called the marsupium. mass number The sum of the number of protons and neutrons in an atom's nucleus. mast cell A type of noncirculating white blood cell, found in connective tissue, that is the major protagonist in allergic reactions; when an allergen binds to complementary antibodies on the surface of a mast cell, large amounts of histamine are released from the cell. matrix The nonliving component of connective tissue, consisting of a web of fibers embedded in homogeneous ground substance that may be liquid, jellylike, or solid. matter Anything that takes up space and has mass. mechanoreceptor A sensory receptor that detects physical deformations in the body's environment associated with pressure, touch, stretch, motion, and sound. medulla (med-dull-a) [L. the innermost part] The inner, as opposed to the outer, part of an organ, as in the adrenal gland.

medulla oblongata (meh-doo-luh obb-long-gah-tuh) The lowest part of the vertebrate brain; a swelling of the hindbrain dorsal to the anterior spinal cord that controls autonomic, homeostatic functions, including breathing, heart and blood vessel activity, swallowing, digestion, and vomiting. medusa The floating, flattened, mouth-down version of the cnidarian body plan. The alternate form is the polyp. megapascal (MPa) (meg-uh-pass-kal) A unit of pressure equivalent to 10 atmospheres of pressure. megaspore [Gk. megas, great, large + spora, a sowing] In plants, a haploid (n) spore that develops into a female gametophyte. meiosis (my-oh-sis) [Gk. meioun, to make smaller] A two-stage type of cell division in sexually reproducing organisms that results in gametes with half the chromosome number of the original cell. membrane potential The charge difference between the cytoplasm and extracellular fluid in all cells, due to the differential distribution of ions. Membrane potential affects the activity of excitable cells and the transmembrane movement of all charged substances. memory cell A clone of long-lived lymphocytes, formed during the primary immune response, that remains in a lymph node until activated by exposure to the same antigen that triggered its formation. Activated memory cells mount the secondary immune response. Mendel's first law See law of segregation. Mendel's second law See law of independent assortment. meniscus The curved top surface of a column of liquid. menstrual cycle (men-stroo-ul) [L. mensis, month] A type of reproductive cycle in higher female primates, in which the nonpregnant

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endometrium is shed as a bloody discharge through the cervix into the vagina. meristem (mare-eh-stem) [Gk. merizein, to divide] Plant tissue that remains embryonic as long as the plant lives, allowing for indeterminate growth. meroblastic cleavage (mare-oh-blas-tik) A type of cleavage in which there is incomplete division of yolk-rich egg, characteristic of avian development. mesentery (mez-en-ter-ee) [Gk. mesos, middle + enteron, gut] A membrane that suspends many of the organs of vertebrates inside fluid-filled body cavities. mesoderm (mez-oh-durm) [Gk. mesos, middle + derma, skin] The middle primary germ layer of an early embryo that develops into the notochord, the lining of the coelom, muscles, skeleton, gonads, kidneys, and most of the circulatory system. mesophyll (mez-oh-fil) [Gk. mesos, middle + phyllon, leaf] The ground tissue of a leaf, sandwiched between the upper and lower epidermis and specialized for photosynthesis. messenger RNA (mRNA) A type of RNA synthesized from DNA in the genetic material that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein. metabolism (meh-tab-oh-liz-um) [Gk. metabole, change] The totality of an organism's chemical processes, consisting of catabolic and anabolic pathways. metamorphosis (met-uh-mor-fuh-sis) [Gk. metamorphoun, to transform] The resurgence of development in an animal larva that transforms it into a sexually mature adult. metanephridium pl. metanephridia (met-uh-neh-frid-ee-um) In annelid worms, a type of excretory tubule with internal openings called

nephrostomes that collect body fluids and external openings called nephridiopores. metaphase [Gk. meta, middle + phasis, form] The second stage of mitosis. During metaphase, all the cell's duplicated chromosomes are lined up at an imaginary plane equidistant between the poles of the mitotic spindle. metapopulation A subdivided population of a single species. metastasis (meh-tas-teh-sis) The spread of cancer cells beyond their original site. MHC Abbreviation of major histocompatibility complex. microbe [Gk. mikros, small + bios, life] A microscopic organism. microevolution A change in the gene pool of a population over a succession of generations. microfilament A solid rod of actin protein in the cytoplasm of almost all eukaryotic cells, making up part of the cytoskeleton and acting alone or with myosin to cause cell contraction. micronutrient [Gk. mikros, small + L. nutrire, to nourish] An inorganic nutrient required in only minute amounts for plant growth, such as iron, chlorine, copper, manganese, zinc, molybdenum, and boron. microspore [Gk. mikros, small + spora, a sowing] In plants, a haploid (n) spore that develops into a male gametophyte; in seed plants, it becomes a pollen grain. microtubule [Gk. mikros, small + L. dim. of tubus, tube] A hollow rod of tubulin protein in the cytoplasm of all eukaryotic cells and in cilia, flagella, and the cytoskeleton. microvillus pl. microvilli One of many fine, fingerlike projections of the epithelial cells in the lumen of the small intestine that increase its surface area. middle lamella A thin layer of adhesive extracellular material, primarily pectins, found between

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the primary walls of adjacent young plant cells. mimicry [Gk. mimos, mime] A phenomenon in which one species benefits by a superficial resemblance to an unrelated species. A predator or species of prey may gain a significant advantage through mimicry. mineral In nutrition, one of many chemical elements, other than carbon, hydrogen, oxygen, and nitrogen, that an organism requires for proper body functioning. mineralocorticoid A corticosteroid hormone secreted by the adrenal cortex that regulates salt and water homeostasis. minimum dynamic area The amount of suitable habitat needed to sustain a viable population. minimum viable population size (MVP) The smallest number of individuals needed to perpetuate a population. missense mutation The most common type of mutation involving a base-pair substitution within a gene that changes a codon, but the new codon makes sense in that it still codes for an amino acid. mitochondrial matrix The compartment of the mitochondrion enclosed by the inner membrane and containing enzymes and substrates for the Krebs cycle. mitochondrion pl. mitochondria (my-toh-kon-dree-un) [Gk. mitos, thread + chondros, cartilage or grain] An organelle in eukaryotic cells that serves as the site of cellular respiration. mitosis (my-toh-sis) [Gk. mitos, thread] A process of nuclear division in eukaryotic cells conventionally divided into five stages: prophase, prometaphase, metaphase, anaphase, and telophase. Mitosis conserves chromosome number by equally allocating replicated chromosomes to each of the daughter nuclei. modern synthesis A comprehensive theory of evolution emphasizing natural selection, gradualism, and populations as the fundamental units of

evolutionary change; also called neoDarwinism. molarity A common measure of solute concentration, referring to the number of moles of solute in 1 L of solution. mold A rapidly growing, asexually reproducing fungus. mole [L. moles, mass] The number of grams of a substance that equals its molecular weight in daltons and contains Avogadro's number of molecules. molecular formula A type of molecular notation indicating only the quantity of the constituent atoms. molecular weight The sum of the atomic weights of the constituent atoms in a molecule. molecule [L. dim. of moles, mass] Two or more atoms held together by covalent bonds. molting A process in arthropods in which the exoskeleton is shed at intervals to allow growth by the secretion of a larger exoskeleton. monoclonal antibody (mon-oh-klone-ul) A defensive protein produced by cells descended from a single cell; an antibody that is secreted by a clone of cells and, consequently, is specific for a single antigenic determinant. monocot (mon-oh-kot) A subdivision of flowering plants whose members possess one embryonic seed leaf, or cotyledon. monocotyledon [Gk. monos, single + kotyledon, a cupshaped hollow] A member of the class of flowering plants having one seed leaf, or cotyledon, among other distinguishing features; often abbreviated as monocot. monoculture Cultivation of large land areas with a single plant variety. monoecious

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(mo-nee-shus) [Gk. monos, single + oikos, house] Referring to a plant species that has both staminate and carpellate flowers on the same individual. monohybrid A hybrid individual that is heterozygous for one gene or a single character. monohybrid cross A breeding experiment that uses parental varieties differing in a single character. monomer [Gk. monos, single + meros, part] The subunit that serves as the building block of a polymer. monophyletic (mon-oh-fy-leh-tik) Pertaining to a taxon derived from a single ancestral species that gave rise to no species in any other taxa. monosaccharide [Gk. monos, single + sakcharon, sugar] A The simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides. Also known as simple sugars, the molecular formulas of monosaccharides are generally some multiple of CH 2 O. monotreme [Gk. monos, single + trema, hole] An egg-laying mammal, represented by the platypus and echidna. morphogen A substance, such as bicoid protein, that provides positional information in the form of a concentration gradient along an embryonic axis. morphogenesis [Gk. morphe, form + genesis, origin] The development of body shape and organization during ontogeny. morphological [Gk. morphe, form + logos, discourse] Pertaining to form and structure, at any level of organization. morphological species concept The idea that species are defined by measurable anatomical criteria. morphology [Gk. morphe, form + logos, discourse] The form and structure of an organism and its parts. morphospecies

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A species defined by its anatomical features. mortality rate [L. mors, death] Death rate. mosaic development A pattern of development, such as that of a mollusk, in which the early blastomeres each give rise to a specific part of the embryo. In some animals, the fate of the blastomeres is established in the zygote. mosaic evolution The evolution of different features of an organism at different rates. motor neuron A nerve cell that transmits signals from the brain or spinal cord to muscles or glands. motor unit A single motor neuron and all the muscle fibers it controls. MPF (M-phase promoting factor) A protein complex required for a cell to progress from late interphase to mitosis; the active form consists of cyclin and cdc2, a protein kinase. muscle fiber Muscle cell; a long, cylindrical, multinucleated cell containing numerous myofibrils, which is capable of contraction when stimulated. mRNA See messenger RNA. Mllerian mimicry (myoo-ler-ee-un) A mutual mimicry by two unpalatable species. multigene family A collection of genes with similar or identical sequences, presumably of common origin. mutagen (myoot-uh-jen) [L. mutare, to change + genus, source or origin] A chemical or physical agent that interacts with DNA and causes a mutation. mutagenesis (myoot-uh-jen-uh-sis) The creation of mutations. mutant [L. mutare, to change] An organism carrying a gene that has undergone a mutation. mutation

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(myoo-tay-shun) [L. mutare, to change] A rare change in the DNA of genes that ultimately creates genetic diversity. mutualism (myoo-choo-ul-iz-um) [L. mutuus, lent, borrowed] A symbiotic relationship in which both the host and the symbiont benefit. See Symbiosis. mycelium (my-seel-ee-um) [Gk. mykes, fungus] The densely branched network of hyphae in a fungus. mycorrhizae (my-koh-ry-zee) [Gk. mykes, fungus + rhiza, root] Mutualistic associations of plant roots and fungi. myelin sheath (my-eh-lin) [Gk. myelinos, full of marrow] In a neuron, an insulating coat of cell membrane from Schwann cells that is interrupted by nodes of Ranvier where saltatory conduction occurs. myofibril (my-oh-fy-bril) [Gk. mys, muscle + L. fibra, fiber] A fibril collectively arranged in longitudinal bundles in muscle cells (fibers); composed of thin filaments of actin and a regulatory protein and thick filaments of myosin. myoglobin (my-uh-glow-bin) [Gk. mys, muscle + L. globus, a ball] An oxygen-storing, pigmented protein in muscle cells. myosin (my-uh-sin) [Gk. mys, muscle] A type of protein filament that interacts with actin filaments to cause cell contraction.

functions as an electron acceptor in the lightdependent reactions of photosynthesis. natural killer cell A nonspecific defensive cell that attacks tumor cells and destroys infected body cells, especially those harboring viruses. natural logarithm The logarithm (log) to base e where e 2.718. The natural logarithm is represented by the symbol ln. natural selection Differential success in the reproduction of different phenotypes resulting from the interaction of organisms with their environment. Evolution occurs when natural selection causes changes in relative frequencies of alleles in the gene pool. nectar [Gk. nektar, the drink of the gods] A sugary fluid that attracts insects to plants. negative feedback A primary mechanism of homeostasis, whereby a change in a physiological variable that is being monitored triggers a response that counteracts the initial fluctuation. nematocyst [Gk. nema, nematos, thread + kyst, bladder] A threadlike stinger, containing a poisonous or paralyzing substance, found in the cnidocyte of cnidarians. nephridium pl. nephridia [Gk. nephros, kidney] A tubular excretory structure found in many invertebrates. nephron (nef-ron) [Gk. nephros, kidney] The tubular excretory unit of the vertebrate kidney. neritic zone (neh-rit-ik) The shallow regions of the ocean overlying the continental shelves. nerve A ropelike bundle of neuron fibers (axons + NAD (nicotinamide adenine dinucleotide) and dendrites) tightly wrapped in Abbreviation of nicotinamide adenine connective tissue. dinucleotide, a coenzyme present in all cells nerve fiber that helps enzymes transfer electrons A filamentous process extending from the during the redox reactions of metabolism. cell body of a neuron and conducting the NADP nerve impulse; an axon. Abbreviation of nicotinamide adenine dinucleotide phosphate, a coenzyme that

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nerve impulse A rapid, transient, self-propagating change in electric potential across the membrane of an axon. nervous system All the nerve cells of an animal; the receptor-conductor-effector system; in humans, the nervous system consists of the central nervous system (brain and spinal cord) and the peripheral nervous system. net primary production In a community or an ecosystem, the increase in the amount of plant or algal material between the beginning and end of a specified time period, such as a growing season. net primary productivity (NPP) The gross primary productivity minus the energy used by the producers for cellular respiration; represents the storage of chemical energy in an ecosystem available to consumers. net productivity In a trophic level, a community, or an ecosystem, the amount of energy (in calories) stored in chemical compounds or the increase in biomass (in grams or metric tons) in a particular period of time; it is the difference between gross productivity and the energy used by the organisms in respiration. neural crest A band of cells along the border where the neural tube pinches off from the ectoderm; the cells migrate to various parts of the embryo and form the pigment cells in the skin, bones of the skull, the teeth, the adrenal glands, and parts of the peripheral nervous system. neural groove Dorsal, longitudinal groove that forms in a vertebrate embryo; bordered by two neural folds; preceded by the neural-plate stage and followed by the neural-tube stage. neural plate Thickened strip of ectoderm in early vertebrate embryos that forms along the dorsal side of the body and gives rise to the central nervous system. neural tube Primitive, hollow, dorsal nervous system of the early vertebrate embryo; formed by

fusion of neural folds around the neural groove. neuromodulator A chemical agent that is released by a neuron and diffuses through a local region of the central nervous system, acting on neurons within that region; generally has the effect of modulating the response to neurotransmitters. neuromuscular junction The junction between an axon terminal of a motor neuron and a muscle fiber innervated by that motor neuron; the axon terminal of a motor neuron is typically branched, forming neuromuscular junctions with a number of different muscle fibers. neuron (noor-on) [Gk. nerve] A nerve cell; the fundamental unit of the nervous system, having structure and properties that allow it to conduct signals by taking advantage of the electrical charge across its cell membrane. neurosecretory cells Hypothalamus cells that receive signals from other nerve cells, but instead of signaling to an adjacent nerve cell or muscle, they release hormones into the bloodstream. neurotransmitter A chemical messenger released from the synaptic terminal of a neuron at a chemical synapse that diffuses across the synaptic cleft and binds to and stimulates the postsynaptic cell. neutral variation Genetic diversity that confers no apparent selective advantage. neutron (new-tron) An electrically neutral particle (a particle having no electrical charge), found in the atom. niche See Ecological niche. nitrification The oxidation of ammonia or ammonium to nitrites and nitrates, as by nitrifying bacteria. nitrogen cycle Worldwide circulation and reutilization of nitrogen atoms, chiefly due to metabolic processes of living organisms; plants take

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up inorganic nitrogen and convert it into organic compounds (chiefly proteins), which are assimilated into the bodies of one or more animals; bacterial and fungal action on nitrogenous waste products and dead organisms return nitrogen atoms to the inorganic state. nitrogen fixation The assimilation of atmospheric nitrogen by certain prokaryotes into nitrogenous compounds that can be directly used by plants. nitrogenase (nih-trah-juh-nayz) An enzyme, unique to certain prokaryotes, that reduces N 2 to NH 3 . nitrogenous base (nigh-tra-jen-us) An organic base that contains the element nitrogen. nocturnal [L. nocturnus, of night] Applied to organisms that are active during the hours of darkness. node [L. nodus, knot] A point along the stem of a plant at which leaves are attached. nodes of Ranvier (ran-veer) The small gaps in the myelin sheath between successive glial cells along the axon of a neuron; also, the site of high concentration of voltage-gated ion channels. nomograph A graph that allows a third variable to be measured when the values of two related variables are known. noncompetitive inhibitor A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing its conformation so that it no longer binds to the substrate. noncyclic electron flow A route of electron flow during the light reactions of photosynthesis that involves both photosystems and produces ATP, NADPH, and oxygen; the net electron flow + is from water to NADP . noncyclic photophosphorylation

(fo-toh-fos-for-eh-lay-shun) The production of ATP by noncyclic electron flow. nondisjunction [L. non, not + disjungere, to separate] An accident of meiosis or mitosis, in which both members of a pair of homologous chromosomes or both sister chromatids fail to move apart properly. nonpolar covalent bond A type of covalent bond in which electrons are shared equally between two atoms of similar electronegativity. nonsense mutation A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein. noradrenaline A hormone, produced by the medulla of the adrenal gland, that increases the concentration of glucose in the blood, raises blood pressure and heartbeat rate, and increases muscular power and resistance to fatigue; also one of the principal neurotransmitters; also called norepinephrine. norepinephrine See noradrenaline. norm of reaction The range of phenotypic possibilities for a single genotype, as influenced by the environment. notochord (no-toh-kord) [Gk. noto, back + L. chorda, cord] A longitudinal, flexible rod formed from dorsal mesoderm and located between the gut and the nerve cord in all chordate embryos. nuclear envelope [L. nucleus, a kernel] The membrane in eukaryotes that encloses the nucleus, separating it from the cytoplasm. nucleic acid (new-clay-ick) A polymer consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular activities. The two types are DNA and RNA.

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nucleic acid probe In DNA technology, a labeled singlestranded nucleic acid molecule used to tag a specific nucleotide sequence in a nucleic acid sample. Molecules of the probe hydrogen-bond to the complementary sequence wherever it occurs; radioactive or other labeling of the probe allows its location to be detected. nucleoid (noo-klee-oid) A dense region of DNA in a prokaryotic cell. nucleoid region The region in a prokaryotic cell consisting of a concentrated mass of DNA. nucleolus (noo-klee-oh-lus) [L. a small kernel] A specialized structure in the nucleus, formed from various chromosomes and active in the synthesis of ribosomes. nucleoside (noo-klee-oh-side) An organic molecule consisting of a nitrogenous base joined to a five-carbon sugar. nucleosome (noo-klee-oh-some) [L. nucleus, a kernel + Gk. soma, body] The basic, beadlike unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound around a protein core composed of two copies of each of four types of histone. nucleotide (noo-klee-oh-tide) [L. nucleus, a kernel] The building block of a nucleic acid, consisting of a five-carbon sugar covently bonded to a nitrogenous base and a phosphate group. nucleus [L. a kernel] (1) An atom's central core, containing protons and neutrons. (2) The chromosome-containing organelle of a eukaryotic cell. (3) A cluster of neurons. null hypothesis In statistical analysis, a hypothesis proposing that there is no statistically significant difference between the observed results of an experiment and the expected results.

obligate aerobe (ob-lig-it air-obe) An organism that requires oxygen for cellular respiration and cannot live without it. obligate anaerobe (an-ur-obe) An organism that cannot use oxygen and is poisoned by it. oceanic zone The region of water lying over deep areas beyond the continental shelf. oligotrophic lake A nutrient-poor, clear, deep lake with minimum phytoplankton. omnivore [L. omnis, all + vorare, to devour] A heterotrophic animal that consumes both meat and plant material. oncogene (on-koh-jeen) [Gk. onkos, tumor + genos, birth, race] A gene found in viruses or as part of the normal genome that is involved in triggering cancerous characteristics. ontogeny (on-toj-en-ee) The embryonic development of an organism. oocyte (o-uh-sight) [Gk. oion, egg + kytos, vessel] A cell that gives rise by meiosis to an ovum. oogamy (oh-og-um-ee) A condition in which male and female gametes differ, such that a small, flagellated sperm fertilizes a large, nonmotile egg. oogenesis (oo-oh-jen-eh-sis) The process in the ovary that results in the production of female gametes. open circulatory system An arrangement of internal transport in which blood bathes the organs directly and there is no distinction between blood and interstitial fluid. operant conditioning A type of associative learning that directly affects behavior in a natural context; also called trial-and-error learning.

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operator A segment of DNA that interacts with a repressor protein to regulate the transcription of the structural genes of an operon. operon (op-ur-on) [L. opus, operis, work] A unit of genetic function common in bacteria and phages, consisting of coordinately regulated clusters of genes with related functions. opportunistic species Species characterized by high reproduction rates, rapid development, early reproduction, small body size, and uncertain adult survival. opsonization An immune response in which the binding of antibodies to the surface of a microbe facilitates phagocytosis of the microbe by a macrophage. orbital [L. orbis, circle, disk] In the current model of atomic structure, the volume of space surrounding the atomic nucleus in which an electron will be found 90 percent of the time. order A taxonomic grouping of related, similar families; the category below class and above family. organ [Gk. organon, tool] A specialized center of body function composed of several different types of tissues. organ-identity gene A plant gene in which a mutation causes a floral organ to develop in the wrong location. organ of Corti The actual hearing organ of the vertebrate ear, located in the floor of the cochlear canal in the inner ear; contains the receptor cells (hair cells) of the ear. organelle (or-guh-nel) [Gk. organon, instrument, tool] One of several formed bodies with a specialized function, suspended in the cytoplasm and found in eukaryotic cells. organic [Gk. organon, instrument, tool] Pertaining to (1) organisms or living things

generally, or (2) compounds formed by living organisms, or (3) the chemistry of compounds containing carbon. organic chemistry The study of carbon compounds (organic compounds). organic compound A chemical comound containing the element carbon and usually synthesized by cells. organism An individual living thing, such as a bacterium, fungus, protist, plant or animal. organogenesis (or-gan-oh-jen-eh-sis) [Gk. organon, instrument, tool + genos, origin, descent] An early period of rapid embryonic development in which the organs take form from the primary germ layers. orgasm Rhythmic, involuntary contractions of certain reproductive structures in both sexes during the human sexual response cycle. origin of replication A specific sequence of bases in a nucleic acid molecule to which the enzymes responsible for replicating the nucleic acid bind to initiate the copying process. osmoconformer An animal that does not actively adjust its internal osmolarity because it is isotonic with its environment. osmolarity (oz-moh-lar-eh-tee) Solute concentration expressed as molarity. osmoregulation Adaptations to control the water balance in organisms living in hypertonic, hypotonic, or terrestrial environments. osmoregulator An animal whose body fluids have a different osmolarity than the environment, and that must either discharge excess water if it lives in a hypotonic environment or take in water if it inhabits a hypertonic environment. osmosis (oz-moh-sis) [Gk. osmos, impulse, thrust] The diffusion of water across a selectively permeable membrane.

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osmotic potential (oz-mot-ik) [Gk. osmos, impulse, thrust] The tendency of water to move across a selectively permeable membrane into a solution; it is determined by measuring the pressure required to stop the osmotic movement of water into the solution. osmotic pressure A measure of the tendency of a solution to take up water when separated from pure water by a selectively permeable membrane. Osteichthyes The vertebrate class of bony fishes, characterized by a skeleton reinforced by calcium phosphate; the most abundant and diverse vertebrates. ostracoderm (os-trak-uh-durm) An extinct agnathan; a fishlike creature encased in an armor of bony plates. outgroup A species or group of species that is closely related to the group of species being studied, but clearly not as closely related as any study-group members are to each other. ovarian cycle (oh-vair-ee-un) The cyclic recurrence of the follicular phase, ovulation, and the luteal phase in the mammalian ovary, regulated by hormones. ovarian follicle [L. ovum, egg + folliculus, small ball] A developing oocyte and the specialized cells surrounding it; located near the surface of the ovary; following ovulation, forms the corpus luteum. ovary (oh-vur-ee) [L. ovum, egg] 1) In flowers, the portion of a carpel in which the egg-containing ovules develop. (2) In animals, the structure that produces female gametes and reproductive hormones. oviduct [L. ovum, egg + ductus, duct] A tube passing from the ovary to the vagina in invertebrates or to the uterus in vertebrates. oviparous (oh-vip-ur-us) Referring to a type of development in which

young hatch from eggs laid outside the mother's body. ovoviviparous (oh-voh-vy-vip-ur-us) Referring to a type of development in which young hatch from eggs that are retained in the mother's uterus. ovulation The release of an egg from ovaries. In humans, an ovarian follicle releases an egg during each menstrual cycle. ovule (ov-yool) [L. dim. of ovum, egg] A structure that develops in the plant ovary and contains the female gametophyte. ovum pl. ova (oh-vum) [L. egg] The female gamete; the haploid, unfertilized egg, which is usually a relatively large, nonmotile cell. oxidation The loss of electrons from a substance involved in a redox reaction. oxidative phosphorylation (fos-for-eh-lay-shun) The production of ATP using energy derived from the redox reactions of an electron transport chain. oxidizing agent The electron acceptor in a redox reaction. oxygen debt In muscle, the cumulative deficit of oxygen that develops during strenuous exercise when the supply of oxygen is inadequate for the demand; ATP is produced anaerobically by glycolysis, and the resulting pyruvic acid is converted to lactic acid, which is subsequently metabolized when adequate oxygen is available.

pacemaker A specialized region of the right atrium of the mammalian heart that sets the rate of contraction; also called the sinoatrial (SA) node. See Sinoatrial node. paedogenesis (pee-doh-jen-eh-sis) The precocious development of sexual maturity in a larva.

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paedomorphosis (pee-doh-mor-foh-sis) The retention in an adult organism of the juvenile features of its evolutionary ancestors. paleontology (pay-lee-un-tol-uh-jee) [Gk. palaios, old + onta, things that exist + logos, discourse] The scientific study of fossils. palisade cells [L. palus, stake + cella, a chamber] In plant leaves, the columnar, chloroplastcontaining parenchyma cells of the mesophyll. pancreas (pang-kree-us) [Gk. pan, all + kreas, meat, flesh] In vertebrates, a small, complex gland located between the stomach and the duodenum, which produces digestive enzymes and the hormones insulin and glucagon. Pangaea (pan-jee-uh) The supercontinent formed near the end of the Paleozoic era when plate movements brought all the land masses of Earth together. paraphyletic (par-uh-fy-leh-tik) Pertaining to a taxon that excludes some members that share a common ancestor with members included in the taxon. parasite (par-uh-site) [Gk. para, beside, akin to + sitos, food] An organism that absorbs nutrients from the body fluids of living hosts. parasitism A symbiotic relationship in which the symbiont (parasite) benefits at the expense of the host by living either within the host (endoparasite) or outside the host (ectoparasite). See Symbiosis. parasympathetic division [Gk. para, beside, akin to] One of two divisions of the autonomic nervous system; generally enhances body activities that gain and conserve energy, such as digestion and reduced heart rate. parathyroid glands [Gk. para, beside, akin to + thyra, a door] Four endocrine glands, embedded in the

surface of the thyroid gland, that secrete parathyroid hormone and raise blood calcium levels. parazoa (par-uh-zoh-uh) Members of the subkingdom of animals consisting of the sponges. parenchyma (pur-en-kim-uh) [Gk. para, beside, akin to + en, in + chein, to pour] A relatively unspecialized plant cell type that carries most of the metabolism, synthesizes and stores organic products, and develops into more differentiated cell types. parental generation In an experimental genetic cross, the parents of the F1 generation; homozygous for the trait(s) being studied. parthenogenesis (par-then-oh-jen-eh-sis) [Gk. parthenon, virgin + genesis, birth] A type of reproduction in which females produce offspring from unfertilized eggs. partial pressures The concentration of gases; a fraction of total pressure. passive transport The diffusion of a substance across a biological membrane. pathogen [Gk. pathos, suffering + genos, origin, descent] An organism or a virus that causes disease. pattern formation The ordering of cells into specific threedimensional structures, an essential part of shaping an organism and its individual parts during development. pedigree A family tree describing the occurrence of heritable characters in parents and offspring across as many generations as possible. pelagic zone (pel-ay-jik) The area of the ocean past the continental shelf, with areas of open water often reaching to very great depths. penetrance In genetics, the proportion of individuals with a particular genotype that show the phenotype ascribed to that genotype.

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peptide bond [Gk. pepto, to soften, digest] The covalent bond between two amino acid units, formed by condensation synthesis. peptidoglycan (pep-tid-oh-gly-kan) A type of polymer in bacterial cell walls consisting of modified sugars cross-linked by short polypeptides. perception The interpretation of sensations by the brain. perennial (pur-en-ee-ul) [L. per, through + annus, year] A plant that lives for many years. pericycle (pair-eh-sy-kul) [Gk. peri, around + kyklos, circle] A layer of cells just inside the endodermis of a root that may become meristematic and begin dividing again. periderm (pair-eh-durm) The protective coat that replaces the epidermis in plants during secondary growth, formed of the cork and cork cambium. peripheral nervous system [Gk. peripherein, to carry around] The sensory and motor neurons that connect to the central nervous system. peristalsis [Gk. peristellein, to wrap around] Rhythmic waves of contraction of smooth muscle that push food along the digestive tract. peritoneum [Gk. peritonos, stretched over] A membrane that lines the body cavity and forms the external covering of the visceral organs. peritubular capillaries [Gk. peri, around + L. tubus, tube] In the vertebrate kidney, the capillaries that surround the renal tubule; water and solutes are reabsorbed into the bloodstream through the peritubular capillaries and some substances are secreted from them into the renal tubule. permeable [L. permeare, to pass through] Penetrable by molecules, ions, or atoms;

usually applied to membranes that let given solutes pass through. peroxisome (per-oks-eh-some) A microbody containing enzymes that transfer hydrogen from various substrates to oxygen, producing and then degrading hydrogen peroxide. petiole (pet-ee-ole) [Fr. from L. petiolus, dim. of pes, pedis, a foot] The stalk of a leaf, which joins the leaf to a node of the stem. pH scale A measure of hydrogen ion concentration + equal to log [H ] and ranging in value from 0 to 14. phage (fage) A virus that infects bacteria; also called a bacteriophage. phagocytosis (fay-goh-sy-toh-sis) [Gk. phagein, to eat + kytos, vessel] A type of endocytosis involving large, particulate substances. pharynx (fah-rinks) An area in the vertebrate throat where air and food passages cross; in flatworms, the muscular tube that protrudes from the ventral side of the worm and ends in the mouth. phenetics (feh-neh-tiks) An approach to taxonomy based entirely on measurable similarities and differences in phenotypic characters, without consideration of homology, analogy, or phylogeny. phenotype [Gk. phainein, to show + typos, stamp, print] The physical and physiological traits of an organism. pheromone (fair-uh-mone) [Gk. phero, to bear, carry] A small, volatile chemical signal that functions in communication between animals and acts much like a hormone in influencing physiology and behavior. phloem

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(floh-um) [Gk. phloos, bark] The portion of the vascular system in plants consisting of living cells arranged into elongated tubes that transport sugar and other organic nutrients throughout the plant. phosphate group A functional group important in energy transfer. phospholipids (fos-fo-lip-ids) Molecules that constitute the inner bilayer of biological membranes, having a polar, hydrophilic head and a nonpolar, hydrophobic tail. phosphorylation Addition of a phosphate group or groups to a molecule. photic zone (foh-tik) The narrow top slice of the ocean, where light permeates sufficiently for photosynthesis to occur. photoautotroph (foh-toh-aw-toh-trohf) An organism that harnesses light energy to drive the synthesis of organic compounds from carbon dioxide. photoheterotroph (foh-toh-het-ur-oh-trohf) An organism that uses light to generate ATP but that must obtain carbon in organic form. photon (foh-tahn) A quantum, or discrete amount, of light energy. photoperiodism [Gk. photos, light] A physiological response to day length, such as flowering in plants. photophosphorylation (foh-toh-fos-for-uh-lay-shun) [Gk. photos, light + phosphoros, bringing light] The process of generating ATP from ADP and phosphate by means of a protonmotive force generated by the thylakoid membrane of the chloroplast during the light reactions of photosynthesis. photoreceptor [Gk. photos, light] A cell or organ capable of detecting light.

photorespiration [Gk. photos, light + L. respirare, to breathe] A metabolic pathway that consumes oxygen, releases carbon dioxide, generates no ATP, and decreases photosynthetic output; generally occurs on hot, dry, bright days, when stomata close and the oxygen concentration in the leaf exceeds that of carbon dioxide. photosynthesis [Gk. photos, light + syn, together + tithenai, to place] The conversion of light energy to chemical energy that is stored in glucose or other organic compounds; occurs in plants, algae, and certain prokaryotes. photosystem [Gk. photos, light + systema, that which is put together] The light-harvesting unit in photosynthesis, located on the thylakoid membrane of the chloroplast and consisting of the antenna complex, the reaction-center chlorophyll a, and the primary electron acceptor. There are two types of photosystems, I and II; they absorb light best at different wavelengths. phototropism [Gk. photos, light + trope, turning] Growth of a plant shoot toward or away from light. phyletic change [Gk. phylon, race, tribe] The changes taking place in a single lineage of organisms over a long period of time; one of the principal patterns of evolutionary change. phylogeny (fy-loj-en-ee) [Gk. phylon, race, tribe] The evolutionary history of a species or group of related species. phylum pl. phyla [Gk. phylon, race, tribe] A taxonomic category; phyla are divided into classes. physiology [Gk. physis, nature + logos, a discourse] The study of function in cells, organs, or entire organisms; the processes of life. phytoalexin (fy-toh-ah-lek-sin) An antibiotic, produced by plants, that

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destroys microorganisms or inhibits their growth. phytochrome (fy-tuh-krome) [Gk. phyton, plant + chroma, color] A pigment involved in many responses of plants to light. phytoplankton [Gk. phyton, plant + planktos, wandering] Aquatic, free-floating, microscopic, photosynthetic organisms. pigment [L. pigmentum, paint] A colored substance that absorbs light over a narrow band of wavelengths. pilus pl. pili (pill-us) A surface appendage in certain bacteria that functions in adherence and the transfer of DNA during conjugation. pineal gland (pin-ee-ul) A small endocrine gland on the dorsal surface of the vertebrate forebrain; secretes the hormone melatonin, which regulates body functions related to seasonal day length. pinocytosis (py-noh-sy-toh-sis) [Gk. pinein, to drink + kytos, vessel] A type of endocytosis in which the cell ingests extracellular fluid and its dissolved solutes. pith The core of the central vascular cylinder of monocot roots, consisting of parenchyma cells, which are ringed by vascular tissue; ground tissue interior to vascular bundles in dicot stems. pituitary gland (pi-too-ih-tair-ee) [L. pituita, phlegm] An endocrine gland at the base of the hypothalamus; consists of a posterior lobe (neurohypophysis), which stores and releases two hormones produced by the hypothalamus, and an anterior lobe (adenohypophysis), which produces and secretes many hormones that regulate diverse body functions. placenta (pluh-sen-tuh) [Gk. plax, a flat object] A structure in the pregnant uterus for nourishing a viviparous fetus with the

mother's blood supply; formed from the uterine lining and embryonic membranes. placental mammal A member of a group of mammals, including humans, whose young complete their embryonic development in the uterus, joined to the mother by a placenta. See Eutherian mammals. placoderm (plak-oh-durm) A member of an extinct class of fishlike vertebrates that had jaws and were enclosed in a tough, outer armor. plankton [Gk. planktos, wandering] Mostly microscopic organisms that drift passively or swim weakly near the surface of oceans, ponds, and lakes. planula [L. dim. of planus, a wanderer] The ciliated, free-swimming type of larva formed by many cnidarians. plasma [Gk. form or mold] The liquid matrix of blood in which the cells are suspended. plasma cell A derivative of B cells that secretes antibodies. plasma membrane [Gk. plasma, form or mold + L. membrana, skin, parchment] The membrane at the boundary of every cell that acts as a selective barrier, thereby regulating the cell's chemical composition. plasmid (plaz-mid) A small ring of DNA that carries accessory genes separate from those of a bacterial chromosome. Also found in some eukaryotes, such as yeast. plasmodesma pl. plasmodesmata (plaz-moh-dez-muh) [Gk. plassein, to mold + desmos, band, bond] An open channel in the cell wall of plants through which strands of cytosol connect from adjacent cells. plasmogamy The fusion of the cytoplasm of cells from two individuals; occurs as one stage of syngamy.

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plasmolysis (plaz-mol-eh-sis) A phenomenon in walled cells in which the cytoplasm shrivels and the plasma membrane pulls away from the cell wall when the cell loses water to a hypertonic environment. plastid [Gk. plastos, formed or molded] One of a family of closely related plant organelles, including chloroplasts, chromoplasts, and amyloplasts (leucoplasts). platelet (plate-let) [Gk. platus, flat] A small enucleated blood cell important in blood clotting; derived from large cells in the bone marrow. pleated sheet One form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds. pleiotropy (ply-o-trop-ee) [Gk. pleios, more + trope, a turning] The ability of a single gene to have multiple effects. plesiomorphic character (pleez-ee-oh-mor-fik) A primitive phenotypic character possessed by a remote ancestor. pluripotent stem cell A cell within bone marrow that is a progenitor for any kind of blood cell. point mutation A change in a gene at a single nucleotide pair. polar [L. polus, end of axis] Having parts or areas with opposed or contrasting properties, such as positive and negative charges, head and tail. polar body Minute, nonfunctioning cell produced during those meiotic divisions that lead to egg cells; contains a nucleus but very little cytoplasm. polar covalent bond A type of covalent bond between atoms that differ in electronegativity. The shared electrons are pulled closer to the more

electronegative atom, making it slightly negative and the other atom slightly positive. polar molecule A molecule (such as water) with opposite charges on opposite sides. polar nuclei In angiosperms, the two nuclei of the central cell of the female gametophyte; they fuse with a sperm nucleus to form the triploid (3n) endosperm nucleus. pollen [L. fine dust] An immature male gametophyte that develops within the anthers of stamens in a flower. pollination (pol-eh-nay-shun) [L. pollen, fine dust] The placement of pollen onto the stigma of a carpel by wind or animal carriers, a prerequisite to fertilization. polyandry (pol-ee-an-dree) A polygamous mating system involving one female and many males. polygenic inheritance (pol-ee-jen-ik) [Gk. polus, many + genos, race, descent] An additive effect of two or more gene loci on a single phenotypic character. polygyny (pol-ij-en-ee) A polygamous mating system involving one male and many females. polymer (pol-eh-mur) [Gk. polus, many + meris, part or portion] A large molecule consisting of many identical or similar monomers linked together. polymerase An enzyme, such as DNA polymerase or RNA polymerase, that catalyzes the synthesis of a polymer from its subunits. polymerase chain reaction (PCR) A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules and nucleotides. polymorphic (pol-ee-mor-fik) Referring to a population in which two or more physical forms are present in readily noticeable frequencies.

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polymorphism (pol-ee-mor-fiz-um) [Gk. polus, many + morphe, form] The coexistence of two or more distinct forms of individuals (polymorphic characters) in the same population. polynucleotide (pol-ee-noo-klee-oh-tide) A polymer made up of many nucleotides covalently bonded together. polyp (pol-ip) [Gk. polus, many + pous, foot] The sessile variant of the cniderian body plan. The alternate form is the medusa. polypeptide (pol-ee-pep-tide) [Gk. polus, many + pepto, to soften, digest] A polymer (chain) of many amino acids linked together by peptide bonds. polyphyletic Pertaining to a taxon whose members were derived from two or more ancestral forms not common to all members. polyploid [Gk. polus, many + ploion, vessel] Cell with more than two complete sets of chromosomes per nucleus. polyploidy (pol-ee-ploid-ee) A chromosomal alteration in which the organism possesses more than two complete chromosome sets. polyribosome (pol-ee-ry-boh-some) An aggregation of several ribosomes attached to one messenger RNA molecule. polysaccharide (pol-ee-sak-ur-ide) [Gk. polus, many + sakcharon, sugar] A polymer of up to over a thousand monosaccharides, formed by condensation synthesis. polysome See Polyribosome. population A group of individuals of one species that live in a particular geographic area. population bottleneck Type of genetic drift that occurs as the result of a population being drastically reduced in numbers by an event having little to do with the usual forces of natural selection.

population density The number of individuals of a population per unit area or volume of living space. population viability analysis (PVA) A method of predicting whether or not a species will persist in a particular environment. positional information Signals, to which genes regulating development respond, indicating a cell's location relative to other cells in an embryonic structure. positive feedback A physiological control mechanism in which a change in some variable triggers mechanisms that amplify the change. posterior Of or pertaining to the rear, or tail, end. postsynaptic membrane (post-sin-ap-tik) The surface of the cell on the opposite side of the synapse from the synaptic terminal of the stimulating neuron that contains receptor proteins and degradative enzymes for the neurotransmitter. postzygotic barrier (post-zy-got-ik) Any of several species-isolating mechanisms that prevent hybrids produced by two different species from developing into viable, fertile adults. potential energy The energy stored by matter as a result of its location or spatial arrangement. predation An interaction between species in which one species, the predator, eats the other, the prey. predator [L. praedari, to prey upon; from prehendere, to grasp, seize] An organism that eats other living organisms. pressure-flow hypothesis A hypothesis accounting for sap flow through the phloem system. According to this hypothesis, the solution containing nutrient sugars moves through the sieve tubes by bulk flow, moving into and out of the sieve tubes by active transport and diffusion.

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prey [L. prehendere, to grasp, seize] An organism eaten by another organism. prezygotic barrier (pree-zy-got-ik) A reproductive barrier that impedes mating between species or hinders fertilization of ova if interspecific mating is attempted. primary consumer An herbivore; an organism in the trophic level of an ecosystem that eats plants or algae. primary germ layers The three layers (ectoderm, mesoderm, endoderm) of the late gastrula, which develop into all parts of an animal. primary growth Growth initiated by the apical meristems of a plant root or shoot. primary immune response The initial immune response to an antigen, which appears after a lag of several days. primary producer An autotroph, which collectively make up the trophic level of an ecosystem that ultimately supports all other levels; usually a photosynthetic organism. primary productivity The rate at which light energy or inorganic chemical energy is converted to the chemical energy of organic compounds by autotrophs in an ecosystem. primary structure The level of protein structure referring to the specific sequence of amino acids. primary succession A type of ecological succession that occurs in an area where there were originally no organisms. primer An already existing short RNA chain bound to template DNA to which DNA nucleotides are added during DNA synthesis. primate A member of the order of mammals that includes anthropoids and prosimians. primitive [L. primus, first] Not specialized; at an early stage of evolution or development. primordium pl. primordia

[L. primus, first + ordiri, to begin to weave] A cell or organ in its earliest stage of differentiation. principle of allocation The concept that each organism has an energy budget, or a limited amount of total energy available for all of its maintenance and reproductive needs. prion An infectious form of protein that may increase in number by converting related proteins to more prions. probe See Nucleic acid probe. procambium (pro-kam-bee-um) [L. pro, before + cambium, exchange] A primary meristem of roots and shoots that forms the vascular tissue. producer, in ecological systems An autotrophic organism, usually a photosynthesizer, that contributes to the net primary productivity of a community. progesterone (pro-jes-teh-roan) [L. progerere, to carry forth or out + steiras, barren] A steroid hormone secreted by the corpus luteum of the ovary; maintains the uterine lining during pregnancy. prokaryotic cell [L. pro, before + Gk. karyon, nut, kernel] A type of cell lacking a membrane-enclosed nucleus and membrane-enclosed organelles; found only in the domains Bacteria and Archaea. prometaphase The phase of mitosis in which the nuclear envelope breaks into fragments. Some of the spindle fibers reach the chromosomes and attach to protein structures at the centromeres, called kinetochores, while others make contact with microtubules coming from the opposite pole. The opposing spindle fibers move the chromosomes toward the metaphase plate, an imaginary plane equidistant from the poles. promoter A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA.

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prophage A phage genome that has been inserted into a specific site on the bacterial chromosome. prophase [Gk. pro, before + phasis, form] The first stage of mitosis, during which duplicated chromosomes condense from chromatin, and the mitotic spindle forms and begins moving the chromosomes toward the center of the cell. prosimian [L. pro, before + simia, ape] A lower primate; includes lemurs, lorises, tarsiers, and bush babies, as well as many fossil forms. prostaglandin (PG) (pros-tuh-glan-din) [Gk. prostas, a porch or vestibule + L. glans, acorn] One of a group of modified fatty acids secreted by virtually all tissues and performing a wide variety of functions as messengers. prostate gland [Gk. prostas, a porch or vestibule + L. glans, acorn] A gland in human males that secretes an acid-neutralizing component of semen. protein (pro-teen) [Gk. proteios, primary] A three-dimensional biological polymer constructed from a set of 20 different monomers called amino acids. protein kinase An enzyme that transfers phosphate groups from ATP to a protein. protein phosphatase An enzyme that removes phosphate groups from proteins, often functioning to reverse the effect of a protein kinase. proteoglycans (pro-tee-oh-gly-kanz) A glycoprotein in the extracellular matrix of animal cells, rich in carbohydrate. proteasome A giant protein complex that recognizes and destroys proteins tagged for elimination by the small protein ubiquitin. protoderm (pro-toh-durm) [Gk. protos, first + derma, skin] The outermost primary meristem, which

gives rise to the epidermis of roots and shoots. proton A subatomic particle with a single positive electrical charge, found in the nucleus of the atom. proton-motive force The potential energy stored in the form of an electrochemical gradient, generated by the pumping of hydrogen ions across biological membranes during chemiosmosis. proton pump An active transport mechanism in cell membranes that consumes ATP to force hydrogen ions out of a cell and, in the process, generates a membrane potential. protonephridium (pro-toh-nef-rid-ee-um) An excretory system, such as the flame-cell system of flatworms, consisting of a network of closed tubules having external openings called nephridiopores and lacking internal openings. proto-oncogene (pro-toh-onk-oh-jeen) A normal cellular gene corresponding to an oncogene; a gene with a potential to cause cancer, but that requires some alteration to become an oncogene. protoplasm [Gk. protos, first + plasma, anything molded] Living matter. protoplast The contents of a plant cell exclusive of the cell wall. protostome (pro-toh-stome) [Gk. protos, first + stoma, mouth] A member of one of two distinct evolutionary lines of coelomates, consisting of the annelids, mollusks, and arthropods, and characterized by spiral, determinate cleavage, schizocoelous formation of the coelom, and development of the mouth from the blastopore. protozoan pl. protozoa A protist that lives primarily by ingesting food, an animal-like mode of nutrition. provirus Viral DNA that inserts into a host genome.

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proximate causation The hypothesis about why natural selection favored a particular animal behavior. pseudocoelom [Gk. pseudes, false + koilos, a hollow] A body cavity consisting of a fluid-filled space between the endoderm and the mesoderm; characteristic of the nematodes. pseudocoelomate (soo-doh-seel-oh-mate) An animal, such as a rotifer or roundworm, whose body cavity is not completely lined by mesoderm. pseudopodium (soo-doh-poh-dee-um) [Gk. pseudes, false + pous, pod-, foot] A cellular extension of amoeboid cells used in moving and feeding. pulmonary [L. pulmonis, lung] Pertaining to the lungs. pulmonary artery [L. pulmonis, lung] In birds and mammals, an artery that carries deoxygenated blood from the right ventricle of the heart to the lungs, where it is oxygenated. pulmonary vein [L. pulmonis, lung] In birds and mammals, a vein that carries oxygenated blood from the lungs to the left atrium of the heart, from which blood is pumped into the left ventricle and from there to the body tissues. pulse A measurement of heart rate; distention of an artery that can be felt each time the heart contracts. punctuated equilibrium A theory of evolution advocating spurts of relatively rapid change followed by long periods of stasis. Punnett square The checkerboard diagram used for analysis of allele segregation. pupa [L. girl, doll] A developmental stage of some insects, in which the organism is nonfeeding, immotile, and sometimes encapsulated or in a cocoon; the pupal stage occurs between the larval and adult phases.

purine [Gk. purinos, fiery, sparkling] A nitrogenous base, such as adenine or guanine, with a characteristic two-ring structure; one of the components of nucleic acids. pyramid, ecological See Ecological pyramid. pyramid of energy A diagram of the energy flow between the trophic levels of an ecosystem; plants or other autotrophs (at the base of the pyramid) represent the greatest amount of energy, herbivores next, then primary carnivores, secondary carnivores, etc. pyrimidine A nitrogenous base, such as cytosine, thymine, or uracil, with a characteristic single-ring structure; one of the components of nucleic acids.

quantitative character A heritable feature in a population that varies continuously as a result of environmental influences and the additive effect of two or more genes (polygenic inheritance). quaternary structure The particular shape of a complex, aggregate protein, defined by the characteristic three-dimensional arrangement of its constituent subunits, each a polypeptide. queen In social insects (ants, termites, and some species of bees and wasps), the fertile, or fully developed, female whose function is to lay eggs. quiescent center A region located within the zone of cell division in plant roots, containing meristematic cells that divide very slowly.

R plasmid A bacterial plasmid carrying genes that confer resistance to certain antibiotics.

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r-selection The concept that in certain (r-selected) populations, a high reproductive rate is the chief determinant of life history. radial cleavage A type of embryonic development in deuterostomes in which the planes of cell division that transform the zygote into a ball of cells are either parallel or perpendicular to the polar axis, thereby aligning tiers of cells one above the other. radial symmetry [L. radius, a spoke of a wheel + Gk. summetros, symmetry] Characterizing a body shaped like a pie or barrel, with many equal parts radiating outward like the spokes of a wheel; present in cnidarians and echinoderms. radiation [L. radius, a spoke of a wheel, hence, a ray] Energy emitted in the form of waves or particles. radiata Members of the radially symmetrical animal phyla, including cnidarians. radicle An embryonic root of a plant. radioactive dating [L. radius, a spoke of a wheel, hence, a ray] A method of determining the age of fossils and rocks using half-lives of radioactive isotopes. radioactive isotope An isotope, an atomic form of a chemical element, that is unstable; the nucleus decays spontaneously, giving off detectable particles and energy. radiometric dating A method paleontologists use for determining the ages of rocks and fossils on a scale of absolute time, based on the halflife of radioactive isotopes. reactant A starting material in a chemical reaction. receptor On or in a cell, a specific protein molecule whose shape fits that of a specific molecular messenger, such as a hormone. receptor-mediated endocytosis (en-doh-sy-toh-sis) The movement of specific molecules into a cell by the inward budding of membranous vesicles containing proteins with receptor

sites specific to the molecules being taken in; enables a cell to acquire bulk quantities of specific substances. receptor potential An initial response of a receptor cell to a stimulus, consisting of a change in voltage across the receptor membrane proportional to the stimulus strength. The intensity of the receptor potential determines the frequency of action potentials traveling to the nervous system. recessive allele [L. recedere, to recede] In a heterozygote, the allele that is completely masked in the phenotype. reciprocal altruism (al-troo-iz-um) Altruistic behavior between unrelated individuals; believed to produce some benefit to the altruistic individual in the future when the current beneficiary reciprocates. recognition sequence A specific sequence of nucleotides at which a restriction enzyme cleaves a DNA molecule. recognition species concept The idea that specific mating adaptations become fixed in a population and form the basis of species identification. recombinant An offspring whose phenotype differs from that of the parents. recombinant DNA A DNA molecule made in vitro with segments from different sources. recombination The formation of new gene combinations; in eukaryotes, may be accomplished by new associations of chromosomes produced during sexual reproduction or crossing over; in prokaryotes, may be accomplished through transformation, conjugation, or transduction. redox reaction (ree-doks) A chemical reaction involving the transfer of one or more electrons from one reactant to another; also called oxidation-reduction reaction. reducing agent The electron donor in a redox reaction.

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reduction [L. reducere, to lead back] The gaining of electrons by a substance involved in a redox reaction. reflex [L. reflectere, to bend back] An automatic reaction to a stimulus, mediated by the spinal cord or lower brain. refractory period (ree-frak-tor-ee) The short time immediately after an action potential in which the neuron cannot respond to another stimulus, owing to an increase in potassium permeability. regulative development A pattern of development, such as that of a mammal, in which the early blastomeres retain the potential to form the entire animal. relative fitness The contribution of one genotype to the next generation compared to that of alternative genotypes for the same locus. relay neuron Neuron that transmits signals between different regions of the central nervous system. releaser A signal stimulus that functions as a communication signal between individuals of the same species. releasing hormone A hormone produced by neurosecretory cells in the hypothalamus of the vertebrate brain that stimulates or inhibits the secretion of hormones by the anterior pituitary. renal [L. renes, kidneys] Pertaining to the kidney. repetitive DNA Nucleotide sequences, usually noncoding, that are present in many copies in a eukaryotic genome. The repeated units may be short and arranged tandemly (in series) or long and dispersed in the genome. replication The process of making a copy of something. replication fork A Y-shaped point on a replicating DNA molecule where new strands are growing.

repressible enzyme An enzyme whose synthesis is inhibited by a specific metabolite. repressor [L. reprimere, to press back, keep back] A protein that suppresses the transcription of a gene. reproductive isolation Two populations of organisms are isolated if their members are unable to interbreed and produce fertile offspring. Various structural, behavioral, and biochemical features can prevent interbreeding and thus reproductively isolate populations as distinct species. Reptilia [L. reprimere, to press back, keep back] The vertebrate class of reptiles, represented by lizards, snakes, turtles, and crocodilians. resolving power [L. resolvere, to loosen, unbind] A measure of the clarity of an image; the minimum distance that two points can be separated and still be distinguished as two separate points. resource partitioning The division of environmental resources by coexisting species populations such that the niche of each species differs by one or more significant factors from the niches of all coexisting species populations. respiration [L. respirare, to breathe] (1) In aerobic organisms, the intake of oxygen and the liberation of carbon dioxide. (2) In cells, the oxygen-requiring stage in the breakdown and release of energy from fuel molecules. resting potential The membrane potential characteristic of a nonconducting, excitable cell, with the inside of the cell more negative than the outside. restriction enzyme A degradative enzyme that recognizes and cuts up DNA (including that of certain phages) that is foreign to a bacterium. restriction fragment length polymorphisms (RFLPs) Differences in DNA sequence on homologous chromosomes that result in different patterns of restriction fragment lengths (DNA segments resulting from

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treatment with restriction enzymes); useful as genetic markers for making linkage maps. restriction site A specific sequence on a DNA strand that is recognized as a "cut site" by a restriction enzyme. reticular formation [L. reticulum, a network] A brain circuit involved with alertness and direction of attention to selected events; consists of a loose network of interneurons running through the brainstem, plus certain neurons in the thalamus that function as an extension of this network. reticulum [L. network] A fine network (e.g., endoplasmic reticulum). retina (reh-tin-uh) [L. dim. of rete, net] The innermost layer of the vertebrate eye, containing photoreceptor cells (rods and cones) and neurons; transmits images formed by the lens to the brain via the optic nerve. retinal The light-absorbing pigment in rods and cones of the vertebrate eye. retrovirus (reh-troh-vy-rus) [L. turning back] An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancercausing viruses. reverse transcriptase (trans-krip-tase) An enzyme encoded by some RNA viruses that uses RNA as a template for DNA synthesis. rhizoid [Gk. rhiza, root] Rootlike anchoring structure in fungi and nonvascular plants. rhizome [Gk. rhizoma, mass of roots] In vascular plants, a horizontal stem growing along or below the surface of the soil; may be enlarged for storage or may function in vegetative reproduction. rhodopsin [Gk. rhizoma, mass of roots] A visual pigment consisting of retinal and

opsin. When rhodopsin absorbs light, the retinal changes shape and dissociates from the opsin, after which it is converted back to its original form. ribonucleic acid (RNA) (ry-boh-noo-klay-ik) A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis and as the genome of some viruses. ribose The sugar component of RNA. ribosomal RNA (rRNA) The most abundant type of RNA. Together with proteins, it forms the structure of ribosomes that coordinate the sequential coupling of tRNA molecules to the series of mRNA codons. ribosome A cell organelle constructed in the nucleolus, functioning as the site of protein synthesis in the cytoplasm. Consists of rRNA and protein molecules, which make up two subunits. ribozyme An enzymatic RNA molecule that catalyzes reactions during RNA splicing. RNA Abbreviation of ribonucleic acid. RNA polymerase (pul-im-ur-ase) An enzyme that links together the growing chain of ribonucleotides during transcription. RNA processing Modification of RNA before it leaves the nucleus, a process unique to eukaryotes. RNA splicing The removal of noncoding portions (introns) of the RNA molecule after initial synthesis. rod cell One of two kinds of photoreceptors in the vertebrate retina; sensitive to black and white and enables night vision. root The descending axis of a plant, normally below ground and serving both to anchor the plant and to take up and conduct water and dissolved minerals.

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root cap A cone of cells at the tip of a plant root that protects the apical meristem. root hair A tiny projection growing just behind the root tips of plants, increasing surface area for the absorption of water and minerals. root pressure The upward push of water within the stele of vascular plants, caused by active pumping of minerals into the xylem by root cells. rough ER That portion of the endoplasmic reticulum studded with ribosomes. rubisco Ribulose carboxylase, the enzyme that catalyzes the first step (the addition of CO 2 to RuBP, or ribulose bisphosphate) of the Calvin cycle. ruminant An animal, such as a cow or a sheep, with an elaborate, multicompartmentalized stomach specialized for an herbivorous diet.

surrounding a muscle cell (muscle fiber); capable of propagating action potentials. sarcomere [Gk. sarx, the flesh + meris, part of, portion] The fundamental, repeating unit of striated muscle, delimited by the Z lines. sarcoplasmic reticulum (sar-koh-plaz-mik reh-tik-yoo-lum) [Gk. sarx, the flesh + plasma, from cytoplasm + L. reticulum, network] A modified form of endoplasmic reticulum in striated muscle cells that stores calcium used to trigger contraction during stimulation. saturated fatty acid A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton. savanna (suh-van-uh) A tropical grassland biome with scattered individual trees, large herbivores, and three distinct seasons based primarily on rainfall, maintained by occasional fires and drought. Schwann cells A chain of supporting cells enclosing the S phase axons of many neurons and forming an The synthesis phase of the cell cycle, insulating layer called the myelin sheath. constituting the portion of interphase sclereid during which DNA is replicated. (skler-ee-id) SA (sinoatrial) node A short, irregular sclerenchyma cell in The pacemaker of the heart, located in the nutshells and seed coats and scattered wall of the right atrium. At the base of the through the parenchyma of some plants. wall separating the two atria is another sclerenchyma cell patch of nodal tissue called the [Gk. skleros, hard] atrioventricular node (AV). A rigid, supportive plant cell type usually saltatory conduction lacking protoplasts and possessing thick (sahl-tuh-tor-ee) secondary walls strengthened by lignin at Rapid transmission of a nerve impulse along maturity. an axon resulting from the action potential second law of thermodynamics jumping from one node of Ranvier to The principle whereby every energy another, skipping the myelin-sheathed transfer or transformation increases the regions of membrane. entropy of the universe. Ordered forms of saprobe energy are at least partly converted to heat, [Gk. sapros, rotten, putrid + bios, life] and in spontaneous reactions, the free An organism that acts as a decomposer by energy of the system also decreases. absorbing nutrients from dead organic second messenger matter. A small, nonprotein, water-soluble sarcolemma molecule or ion, such as calcium ion or [Gk. sarx, the flesh + lemma, husk] cyclic AMP, that relays a signal to a cell's The specialized plasma membrane

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interior in response to a signal received by a signal receptor protein. secondary compound A chemical compound synthesized through the diversion of products of major metabolic pathways for use in defense by prey species. secondary consumer A member of the trophic level of an ecosystem consisting of carnivores that eat herbivores. secondary growth The increase in girth of the stems and roots of many plants, especially woody, perennial dicots. secondary immune response The immune response elicited when an animal encounters the same antigen at some later time. The secondary immune response is more rapid, of greater magnitude, and of longer duration than the primary immune response. secondary productivity he rate at which all the heterotrophs in an ecosystem incorporate organic material into new biomass, which can be equated to chemical energy. secondary sex characteristics Characteristics of animals that distinguish between the two sexes but that do not produce or convey gametes; includes facial hair of the human male and enlarged hips and breasts of the female. secondary structure The localized, repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bond formation between peptide linkages. secondary succession A type of succession that occurs where an existing community has been severely cleared by some disturbance. secretion [L. secermere, to sever, separate] (1) The discharge of molecules synthesized by the cell. (2) In the vertebrate kidney, the discharge of wastes from the blood into the filtrate from the nephron tubules. sedimentary rock (sed-eh-men-tar-ee) Rock formed from sand and mud that once settled in layers on the bottom of seas,

lakes, and marshes. Sedimentary rocks are often rich in fossils. seed An adaptation for terrestrial plants consisting of an embryo packaged along with a store of food within a resistant coat. segregation See Mendel's first law. selection The process by which the forms of organisms in a population that are better adapted to the environmental conditions increase in frequency relative to less welladapted forms over a number of generations. selection coefficient The difference between two fitness values, representing a relative measure of selection against an inferior genotype. selective permeability [L. seligere, to gather apart + permeare, to go through] A property of biological membranes that allows some substances to cross more easily than others. selective pressure An environmental factor that favors the survival and reproduction of those genetic variants within a population that are better adapted to the environment. self-incompatibility The capability of certain flowers to block fertilization by pollen from the same or a closely related plant. self-fertilization The union of egg and sperm produced by a single hermaphroditic organism. self-pollination The transfer of pollen from anther to stigma in the same flower or to another flower of the same plant, leading to self-fertilization. semen (see-men) [L. seed] The fluid that is ejaculated by the male during orgasm; contains sperm and secretions from several glands of the male reproductive tract. semicircular canals A three-part chamber of the inner ear that functions in maintaining equilibrium. semilunar valve A valve located at the two exits of the heart, where the aorta leaves the left ventricle

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and the pulmonary artery leaves the right ventricle. seminal vesicle [L. semen, seed + vesicula, a little bladder] A gland in males that secretes a fluid (a component of semen) that lubricates and nourishes sperm. seminiferous tubules [L. semen, seed + ferre, to bear or carry + dim. of tubus, tube] Highly coiled tubes in the testes in which sperm are produced. sensation An impulse sent to the brain from activated receptors and sensory neurons. sensory neuron A nerve cell that receives information from the internal and external environments and transmits the signals to the central nervous system. sensory receptor A specialized structure that responds to specific stimuli from an animal's external or internal environment; transmits the information of an environmental stimulus to the animal's nervous system by converting stimulus energy to the electrochemical energy of action potentials. sepal (see-pul) A whorl of modified leaves in angiosperms that encloses and protects the flower bud before it opens. septum [L. fence] A partition, or cross wall, that divides a structure, such as a fungal hypha, into compartments. sessile [L. sedere, to sit] Attached; not free to move about. sex chromosomes The pair of chromosomes responsible for determining the sex of an individual. sex-linked genes Genes located on one sex chromosome but not the other. sex-linked trait An inherited trait, such as color discrimination, determined by a gene located on a sex chromosome and that therefore shows a different pattern of inheritance in males and females.

sexual dimorphism (dy-mor-fiz-um) A special case of polymorphism based on the distinction between the secondary sex characteristics of males and females. sexual reproduction A type of reproduction in which two parents give rise to offspring that have unique combinations of genes inherited from the gametes of the two parents. sexual selection Selection based on variation in secondary sex characteristics, leading to the enhancement of sexual dimorphism. shoot system The aerial portion of a plant body, consisting of stems, leaves, and flowers. short-day plant A plant that flowers, usually in late summer, fall, or winter, only when the light period is shorter than a critical length. sieve tube member A chain of living cells that form sieve tubes in phloem. sign stimulus An external sensory stimulus that triggers a fixed action pattern. signal peptide A stretch of amino acids on polypeptides that targets proteins to specific destinations in eukaryotic cells. signal-transduction pathway A mechanism linking a mechanical or chemical stimulus to a cellular response. sink habitat A habitat where mortality exceeds reproduction. sinoatrial node [L. sinus, fold, hollow + atrium, yard, court, hall + nodus, knot] Area of the vertebrate heart that initiates the heartbeat; located where the superior vena cava enters the right atrium; the pacemaker. sister chromatids (kroh-muh-tidz) Replicated forms of a chromosome joined together by the centromere and eventually separated during mitosis or meiosis II. skeletal muscle Striated muscle generally responsible for the voluntary movements of the body.

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sliding-filament model The theory explaining how muscle contracts, based on change within a sarcomere, the basic unit of muscle organization, stating that thin (actin) filaments slide across thick (myosin) filaments, shortening the sarcomere; the shortening of all sarcomeres in a myofibril shortens the entire myofibril. small nuclear ribonucleoprotein (snRNP) (ry-boh-noo-klee-oh-pro-teen) One of a variety of small particles in the cell nucleus, composed of RNA and protein molecules; functions are not fully understood, but some form parts of spliceosomes, active in RNA splicing. smooth ER That portion of the endoplasmic reticulum that is free of ribosomes. smooth muscle A type of muscle lacking the striations of skeletal and cardiac muscle because of the uniform distribution of myosin filaments in the cell. social dominance A hierarchical pattern of social organization involving domination of some members of a group by other members in a relatively orderly and long-lasting pattern. society [L. socius, companion] An organization of individuals of the same species in which there are divisions of resources, divisions of labor, and mutual dependence; a society is held together by stimuli exchanged among members of the group. sociobiology The study of social behavior based on evolutionary theory. sodium-potassium pump A special transport protein in the plasma membrane of animal cells that transports sodium out of and potassium into the cell against their concentration gradients. solute (sol-yoot) A substance that is dissolved in a solution. solution A homogeneous, liquid mixture of two or more substances.solvent The dissolving agent of a solution. Water is the most versatile solvent known.

somatic cell [Gk. soma, body] Any cell in a multicellular organism except a sperm or egg cell. somatic nervous system [Gk. soma, body] The branch of the motor division of the vertebrate peripheral nervous system composed of motor neurons that carry signals to skeletal muscles in response to external stimuli. somatotropin [Gk. soma, body + trope, a turning] A hormone, produced by the pituitary gland, that stimulates protein synthesis and promotes the growth of bone; also known as growth hormone. source habitat A habitat where reproduction exceeds mortality and from which excess individuals disperse. Southern blotting A hybridization technique that enables researchers to determine the presence of certain nucleotide sequences in a sample of DNA. specialized (1) Of cells, having particular functions in a multicellular organism. (2) Of organisms, having special adaptations to a particular habitat or mode of life. speciation The origin of new species in evolution. species pl. species [L. kind, sort] A particular kind of organism; members possess similar anatomical characteristics and have the ability to interbreed. species diversity The number and relative abundance of species in a biological community. species richness The number of species in a biological community. species selection A theory maintaining that species living the longest and generating the greatest number of species determine the direction of major evolutionary trends. species-specific Characteristic of (and limited to) a particular species.

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specific Unique; for example, the proteins in a given organism, the enzyme catalyzing a given reaction, or the antibody to a given antigen. specific heat The amount of heat that must be absorbed or lost for 1 g of a substance to change its temperature 1C. spectrophotometer An instrument that measures the proportions of light of different wavelengths absorbed and transmitted by a pigment solution. sperm [Gk. sperma, seed] A male gamete. spermatid [Gk. sperma, seed] Each of four haploid (n) cells resulting from the meiotic divisions of a spermatocyte; each spermatid becomes differentiated into a sperm cell. spermatocytes [Gk. sperma, seed + kytos, vessel] The diploid (2n) cells formed by the enlargement and differentiation of the spermatogonia; they give rise by meiotic division to the spermatids. spermatogonia [Gk. sperma, seed + gonos, a child, the young] The unspecialized diploid (2n) cells on the walls of the seminiferous tubules that, by enlargement, differentiation, and meiotic division, become spermatocytes, then spermatids, then sperm cells. spermatogenesis The continuous and prolific production of mature sperm cells in the testis. sphincter (sfink-ter) [Gk. sphinkter, a band] A ringlike valve, consisting of modified muscles in a muscular tube, such as a digestive tract; closes off the tube like a drawstring. spinal cord Part of the vertebrate central nervous system; consists of a thick, dorsal, longitudinal bundle of nerve fibers extending posteriorly from the brain.

spindle An assemblage of microtubules that orchestrates chromosome movement during eukaryotic cell division. spiracle [L. spirare, to breathe] One of the external openings of the respiratory system in terrestrial arthropods. spiral cleavage A type of embryonic development in protostomes, in which the planes of cell division that transform the zygote into a ball of cells occur obliquely to the polar axis, resulting in cells of each tier sitting in the grooves between cells of adjacent tiers. spliceosome (sply-see-oh-some) A complex assembly that interacts with the ends of an RNA intron in splicing RNA; releases an intron and joins two adjacent exons. splitting evolution See Cladogenesis. spongy parenchyma In plant leaves, a tissue composed of loosely arranged chloroplast-containing parenchyma cells. sporangiophore (spo-ran-ji-o-for) [Gk. spora, seed + phore, from phorein, to bear] A specialized hypha or a branch bearing one or more sporangia. sporangium pl. sporangia [Gk. spora, seed] A capsule in fungi and plants in which meiosis occurs and haploid spores develop. spore [Gk. spora, seed] In the life cycle of a plant or alga undergoing alternation of generations, a meiotically produced haploid cell that divides mitotically, generating a multicellular individual, the gametophyte, without fusing with another cell. sporophyte [Gk. spora, seed + phytos, growing] The multicellular diploid form in organisms undergoing alternation of generations that results from a union of gametes and that meiotically produces haploid spores that grow into the gametophyte generation.

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sporopollenin A secondary product, a polymer synthesized by a side branch of a major metabolic pathway of plants that is resistant to almost all kinds of environmental damage; especially important in the evolutionary move of plants onto land. stablizing selection Natural selection that favors intermediate variants by acting against extreme phenotypes. stamen [L. a thread] The pollen-producing male reproductive organ of a flower, consisting of an anther and filament. starch [M.E. sterchen, to stiffen] A storage polysaccharide in plants consisting entirely of glucose. statocyst [Gk. statos, standing + kystis, sac] A type of mechanoreceptor that functions in equilibrium in invertebrates through the use of statoliths, which stimulate hair cells in relation to gravity. stele The central vascular cylinder in roots where xylem and phloem are located. stem The aboveground part of the axis of vascular plants, as well as anatomically similar portions below ground (such as rhizomes). stem cells The common, self-regenerating cells in the marrow of long bones that give rise, by differentiation and division, to red blood cells and all of the different types of white blood cells. stereoisomer A molecule that is a mirror image of another molecule with the same molecular formula. stereoscopic vision [Gk. stereos, solid + optikos, pertaining to the eye] Ability to perceive a single, threedimensional image from the simultaneous but separate images delivered to the brain by each eye.

steroids A class of lipids characterized by a carbon skeleton consisting of four rings with various functional groups attached. stigma [Gk. stigme, a prick mark, puncture] In plants, the region of a carpel serving as a receptive surface for pollen grains, which germinate on it. stimulus [L. goad, incentive] Any internal or external change or signal that influences the activity of an organism or of part of an organism. stoma pl. stomata [Gk. mouth] A microscopic pore surrounded by guard cells in the epidermis of leaves and stems that allows gas exchange between the environment and the interior of the plant. strategy [Gk. strategein, to maneuver] A group of related traits, evolved under the influence of natural selection, that solve particular problems encountered by living organisms; often includes anatomical, physiological, and behavioral characteristics. striated muscle [L. from striare, to groove] Skeletal voluntary muscle and cardiac muscle. The name derives from the striped appearance, which reflects the arrangement of contractile elements. strict aerobe An organism that can survive only in an atmosphere of oxygen, which is used in aerobic respiration. strict anaerobe An organism that cannot survive in an atmosphere of oxygen. Other substances, such as sulfate or nitrate, are the terminal electron acceptors in the electron transport chains that generate their ATP. stroma [Gk. a bed, from stronnymi, to spread out] The fluid of the chloroplast surrounding the thylakoid membrane; involved in the synthesis of organic molecules from carbon dioxide and water. stromatolite Rock made of banded domes of sediment in which are found the most ancient forms of

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life: prokaryotes dating back as far as 3.5 billion years. structural formula A type of molecular notation in which the constituent atoms are joined by lines representing covalent bonds. structural gene A gene that codes for a polypeptide. style [L. stilus, stake, stalk] In angiosperms, the stalk of a carpel, down which the pollen tube grows. substrate [L. substratus, strewn under] (1) The substance on which an enzyme works. (2) The foundation to which an organism is attached. substrate-level phosphorylation The formation of ATP by directly transferring a phosphate group to ADP from an intermediate substrate in catabolism. succession See Ecological succession. sucrose Cane sugar; a common disaccharide found in many plants; a molecule of glucose linked to a molecule of fructose. sugar Any monosaccharide or disaccharide. summation A phenomenon of neural integration in which the membrane potential of the postsynaptic cell in a chemical synapse is determined by the total activity of all excitatory and inhibitory presynaptic impulses acting on it at any one time. suppressor T cell (T S ) A type of T cell that causes B cells as well as other cells to ignore antigens. surface tension A measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen bonding of surface molecules. survivorship curve A plot of the number of members of a cohort that are still alive at each age; one way to represent age-specific mortality. suspension-feeder An aquatic animal, such as a clam or a baleen whale, that sifts small food particles from the water.

sustainable agriculture Long-term productive farming methods that are environmentally safe. sustainable development The long-term prosperity of human societies and the ecosystems that support them. swim bladder An adaptation, derived from a lung, that enables bony fishes to adjust their density and thereby control their buoyancy. symbiont (sim-by-ont) The smaller participant in a symbiotic relationship, living in or on the host. symbiosis [Gk. syn, together with + bioonai, to live] An ecological relationship between organisms of two different species that live together in direct contact. sympathetic division One of two divisions of the autonomic nervous system of vertebrates; generally increases energy expenditure and prepares the body for action. sympatric speciation [Gk. syn, together with + patra, fatherland, country] A mode of speciation occurring as a result of a radical change in the genome that produces a reproductively isolated subpopulation in the midst of its parent population. symplast In plants, the continuum of cytoplasm connected by plasmodesmata between cells. synapomorphies Shared derived characters; homologies that evolved in an ancestor common to all species on one branch of a fork in a cladogram, but not common to species on the other branch. synapse (sin-aps) [Gk. synapsis, a union] The locus where one neuron communicates with another neuron in a neural pathway; a narrow gap between a synaptic terminal of an axon and a signal-receiving portion (dendrite or cell body) of another neuron or effector cell. Neurotransmitter molecules released by synaptic terminals diffuse

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across the synapse, relaying messages to the dendrite or effector. synapsis The pairing of replicated homologous chromosomes during prophase I of meiosis. synaptic cleft A narrow gap separating the synaptic knob of a transmitting neuron from a receiving neutron to an effector. synaptic knob The relay point at the tip of a transmitting neuron's axon, where signals are sent to another neuron or to an effector. synaptic terminal A bulb at the end of an axon in which neurotransmitter molecules are stored and released. syngamy (sin-gam-ee) The process of cellular union during fertilization. synthesis [Gk. syntheke, a putting together] The formation of a more complex substance from simpler ones. synthesis phase In the cell cycle, the phase in which the DNA of the chromosomes is replicated and DNAassociated proteins, such as histones, are synthesized. systematics The branch of biology that studies the diversity of life; encompasses taxonomy and is involved in reconstructing phylogenetic history. systemic acquired resistance (SAR) A defensive response in infected plants that helps protect healthy tissue from pathogenic invasion. systole (sis-toh-lee) The stage of the heart cycle in which the heart muscle contracts and the chambers pump blood. systolic pressure The pressure in an artery during the ventricular contraction phase of the heart cycle.

T cell A type of lymphocyte responsible for cellmediated immunity that differentiates under the influence of the thymus. taiga (ty-guh) The coniferous or boreal forest biome, characterized by considerable snow, harsh winters, short summers, and evergreen trees. taxis (taks-iss) A movement toward or away from a stimulus. taxon pl. taxa [Gk. taxis, arrange, put in order] The named taxonomic unit at any given level. taxonomy [Gk. taxis, arrange, put in order + nomos, law] The branch of biology concerned with naming and classifying the diverse forms of life. telomerase An enzyme that catalyzes the lengthening of telomeres; the enzyme includes a molecule of RNA that serves as a template for new telomere segments. telomere The protective structure at each end of a eukaryotic chromosome. Specifically, the tandemly repetitive DNA (see Repetitive DNA) at the end of the chromosome's DNA molecule. telophase [Gk. telos, end + phasis, form] The fourth and final stage of mitosis, during which daughter nuclei form at the two poles of a cell. Telophase usually occurs together with cytokinesis. temperate bacteriophage A bacterial virus that may become incorporated into the host-cell chromosome. temperate deciduous forest A biome located throughout midlatitude regions where there is sufficient moisture to support the growth of large, broad-leaf deciduous trees.

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temperate virus A virus that can reproduce without killing the host. temperature A measure of the intensity of heat in degrees, reflecting the average kinetic energy of the molecules. template A pattern or mold guiding the formation of a negative or complementary copy. tendon A type of fibrous connective tissue that attaches muscle to bone. tentacles [L. tentare, to touch] Long, flexible protrusions located about the mouth of many invertebrates; usually prehensile or tactile. terminator A special sequence of nucleotides in DNA that marks the end of a gene; it signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene. territory An area or space occupied and defended by an individual or a group; trespassers are attacked (and usually defeated); may be the site of breeding, nesting, food gathering, or any combination thereof. tertiary consumer A member of a trophic level of an ecosystem consisting of carnivores that eat mainly other carnivores. tertiary structure (tur-shee-air-ee) Irregular contortions of a protein molecule due to interactions of side chains involved in hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges. testcross Breeding of an organism of unknown genotype with a homozygous recessive individual to determine the unknown genotype. The ratio of phenotypes in the offspring determines the unknown genotype. testis pl. testes [Gk. testicle] The male reproductive organ, or gonad, in which sperm and reproductive hormones are produced.

testosterone [Gk. testis, testicle + steiras, barren] The most abundant androgen hormone in the male body. tetanus (tet-un-us) The maximal, sustained contraction of a skeletal muscle, caused by a very fast frequency of action potentials elicited by continual stimulation. tetrad [Gk. tetras, four] In genetics, a pair of homologous chromosomes that have replicated and come together in prophase I of meiosis; consists of four chromatids. tetrapod A vertebrate possessing two pairs of limbs, such as amphibians, reptiles, birds, and mammals. thalamus [Gk. thalamos, chamber] One of two integrating centers of the vertebrate forebrain. Neurons with cell bodies in the thalamus relay neural input to specific areas in the cerebral cortex and regulate what information goes to the cerebral cortex. thallus [Gk. thallos, a young twig] A simple plant or algal body without true roots, leaves, or stems. theory [Gk. theorein, to look at] A generalization based on many observations and experiments; a verified hypothesis. thermodynamics [Gk. therme, heat + dynamis, power] The study of transformations of energy. The first law of thermodynamics states that, in all processes, the total energy of a system plus its surroundings remains constant. The second law states that all natural processes tend to proceed in such a direction that the disorder or randomness of the system increases. thermoregulation The maintenance of internal temperature within a tolerable range.

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thick filament A filament composed of staggered arrays of myosin molecules; a component of myofibrils in muscle fibers. thigmomorphogenesis A response in plants to chronic mechanical stimulation, resulting from increased ethylene production; an example is thickening stems in response to strong winds. thigmotropism (thig-moh-troh-piz-um) The directional growth of a plant in relation to touch. thorax [Gk. breastplate] (1) In vertebrates, that portion of the trunk containing the heart and lungs. (2) In crustaceans and insects, the fused, legbearing segments between head and abdomen. threatened species Species that are likely to become endangered in the foreseeable future throughout all or a significant portion of their range. threshold potential The potential an excitable cell membrane must reach for an action potential to be initiated. thylakoid (thy-luh-koid) [Gk. thylakos, a small bag] A flattened membrane sac inside the chloroplast, used to convert light energy to chemical energy. thymus (thy-mus) An endocrine gland in the neck region of mammals that is active in establishing the immune system; secretes several messengers, including thymosin, that stimulate T cells. thyroid gland [Gk. thyra, a door] An endocrine gland that secretes iodinecontaining hormones (T 3 and T 4 ), which stimulate metabolism and influence development and maturation in vertebrates, and cacitonin, which lowers blood calcium levels in mammals.

thyroid-stimulating hormone (TSH) A hormone produced by the anterior pituitary that regulates the release of thyroid hormones. Ti plasmid A plasmid of a tumor-inducing bacterium that integrates a segment of its DNA into the host chromosome of a plant; frequently used as a carrier for genetic engineering in plants. tight junction A type of intercellular junction in animal cells that prevents the leakage of material between cells. tissue [L. texere, to weave] An integrated group of cells with a common structure and function. tonoplast A membrane that encloses the central vacuole in a plant cell, separating the cytosol from the cell sap. torpor In animals, a physiological state that conserves energy by slowing down the heart and respiratory systems. totipotency The ability of embryonic cells to retain the potential to form all parts of the animal. trace element An element indispensable for life but required in extremely minute amounts. trachea (tray-kee-uh) The windpipe; that portion of the respiratory tube that has C-shaped cartilagenous rings and passes from the larynx to two bronchi. trachea pl. tracheae (trake-ee-a) [Gk. tracheia, rough] Tiny air tubes that branch throughout the insect body for gas exchange. tracheal system A gas exchange system of branched, chitinlined tubes that infiltrate the body and carry oxygen directly to cells in insects. tracheid (tray-key-idd) [Gk. tracheia, rough] A water-conducting and supportive element of xylem composed of long, thin cells with tapered ends and walls hardened with lignin.

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tract A group or bundle of nerve fibers with accompanying connective tissue, located within the central nervous system. transcription [L. trans, across + scribere, to write] The synthesis of RNA on a DNA template. transcription factor A regulatory protein that binds to DNA and stimulates transcription of specific genes. transduction [L. trans, across + ducere, to lead] The transfer of genetic material (DNA) from one cell to another by a virus. transfer RNA (tRNA) [L. trans, across + ferre, to bear or carry] An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA. transformation [L. trans, across + formare, to shape] (1) The conversion of a normal animal cell to a cancerous cell. (2) A phenomenon in which external DNA is assimilated by a cell. transgenic [L. trans, across + formare, to shape] Having artificially altered genetic material. A transgenic organism is one that has had its genotype altered by the introduction of a gene or DNA sequence into its genome by genetic manipulation; the introduced gene or DNA segment is called a transgene. translation [L. trans, across + latus, that which is carried] The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of "language" from nucleotides to amino acids. translocation [L. trans, across + locare, to put or place] (1) An aberration in chromosome structure resulting from an error in meiosis or from mutagens; attachment of a chromosomal fragment to a nonhomologous chromosome. (2) During protein synthesis, the third stage in the elongation cycle when the RNA carrying the growing polypeptide moves from the A site to the P site on the ribosome. (3) The transport via phloem of food in a plant.

transpiration [L. trans, across + spirare, to breathe] The evaporative loss of water from a plant. transposon (trans-poh-son) [L. transponere, to change the position of] A transposable genetic element; a mobile segment of DNA that serves as an agent of genetic change. triplet code A set of three-nucleotide-long words that specify the amino acids for polypeptide chains. triploblastic Possessing three germ layers: the endoderm, mesoderm, and ectoderm. Most eumetazoa are triploblastic. trophic level [Gk. trophos, feeder] The division of species in an ecosystem on the basis of their main nutritional source. The trophic level that ultimately supports all others consists of autotrophs, or primary producers. trophic structure The different feeding relationships in an ecosystem that determine the route of energy flow and the pattern of chemical cycling. trophoblast [Gk. trophos, feeder + blastos, sprout] The outer epithelium of the blastocyst, which forms the fetal part of the placenta. tropic [Gk. trope, a turning] Pertaining to behavior or action brought about by specific stimuli, for example, phototropic ("light-oriented") motion, gonadotropic ("stimulating the gonads") hormone. tropic hormone A hormone that has another endocrine gland as a target. tropical rain forest The most complex of all communities, located near the equator where rainfall is abundant; harbors more species of plants and animals than all other terrestrial biomes combined. tropism A growth response that results in the curvature of whole plant organs toward or

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away from stimuli due to differential rates of cell elongation. tuber [L. tuber, bump, swelling] A much-enlarged, short, fleshy underground stem, such as that of the potato. tumor A mass that forms within otherwise normal tissue, caused by the uncontrolled growth of a transformed cell. tumor suppressor gene A gene whose protein products inhibit cell division, thereby preventing uncontrolled cell growth (cancer). tundra A biome at the extreme limits of plant growth; at the northernmost limits, it is called arctic tundra, and at high altitudes, where plant forms are limited to low shrubby or matlike vegetation, it is called alpine tundra. turgid (tur-jid) Firm; walled cells become turgid as a result of the entry of water from a hypotonic environment. turgor pressure [L. turgere, to swell] The force directed against a cell wall after the influx of water and the swelling of a walled cell due to osmosis. tyrosine kinase An enzyme that catalyzes the transfer of phosphate groups from ATP to the amino acid tyrosine in a substrate protein. tyrosine kinase receptor A receptor protein in the plasma membrane that responds to the binding of a signal molecule by catalyzing the transfer of phosphate groups from ATP to tyrosines on the cytoplasmic side of the receptor. The phosphorylated tyrosines activate other signal-transduction proteins within the cell.

unsaturated fatty acid A fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail. Such bonding reduces the number of hydrogen atoms attached to the carbon skeleton. urea [Gk. ouron, urine] A soluble form of nitrogenous waste excreted by mammals and most adult amphibians. ureter [Gk. from ourein, to urinate] A duct leading from the kidney to the urinary bladder. urethra [Gk. from ourein, to urinate] A tube that releases urine from the body near the vagina in females or through the penis in males; also serves in males as the exit tube for the reproductive system. uric acid [Gk. ouron, urine] An insoluble precipitate of nitrogenous waste excreted by land snails, insects, birds, and some reptiles. urine [Gk. ouron, urine] The liquid waste filtered from the blood by the kidney and stored in the bladder pending elimination through the urethra. urochordate A chordate without a backbone, commonly called a tunicate, a sessile marine animal. uterus [L. womb] A female reproductive organ where eggs are fertilized and/or development of the young occurs.

ultimate causation The hypothetical evolutionary explanation for the existence of a certain pattern of animal behavior.

vaccine A harmless variant or derivative of a pathogen that stimulates a host's immune system to mount defenses against the pathogen. vacuole [L. vacuus, empty] A membrane-enclosed sac taking up most of the interior of a mature plant cell and containing a variety of substances

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important in plant reproduction, growth, and development. vagina Part of the female reproductive system between the uterus and the outside opening; the birth canal in mammals; also accommodates the male's penis and receives sperm during copulation. valence shell The outermost energy shell of an atom, containing the valence electrons involved in the chemical reactions of that atom. Van der Waals interactions Weak attractions between molecules or parts of molecules that are brought about by localized charge fluctuations. vaporization [L. vapor, steam] The change from a liquid to a gas; evaporation. variation Diversity among the members of a population. Variation among individuals can exist at many levels, including genetic, physiologic and behavioral. vas deferens pl. vasa deferentia (vass deff-er-ens) [L. vas, a vessel + deferre, to carry down] The tube in the male reproductive system in which sperm travel from the epididymis to the urethra. vascular [L. vasculum, a small vessel] Containing or concerning vessels that conduct fluid. vascular bundle In plants, a group of longitudinal supporting and conducting tissues (xylem and phloem). vascular cambium [L. vasculum, a small vessel + cambium, exchange] A continuous cylinder of meristematic cells surrounding the xylem and pith that produces secondary xylem and phloem. vascular plants Plants with vascular tissue, consisting of all modern species except the mosses and their relatives. vascular tissue Plant tissue consisting of cells joined into tubes that transport water and nutrients throughout the plant body.

vascular tissue system A system formed by xylem and phloem throughout the plant, serving as a transport system for water and nutrients, respectively. vector [L. carrier] In recombinant DNA, a small, selfreplicating DNA molecule, or a portion thereof, into which a DNA segment can be spliced and introduced into a cell; generally a plasmid or a virus. vegetative reproduction Cloning of plants by asexual means. vein [L. vena, a blood vessel] A vessel that returns blood to the heart. vena cava (vee-na cah-va) [L. blood vessel + hollow] A large vein that brings blood from the tissues to the right atrium of the fourchambered mammalian heart. The superior vena cava collects blood from the forelimbs, head, and anterior or upper trunk; the inferior vena cava collects blood from the posterior body region. ventilation Any method of increasing contact between the respiratory medium and the respiratory surface. ventral [L. venter, belly] Pertaining to the undersurface of an animal that holds its body in a horizontal position; to the front surface of an animal that holds its body erect. ventricle [L. ventriculus, the stomach] A muscular chamber of the heart that receives blood from an atrium and pumps blood out of the heart, either to the lungs or to the body tissues. venule A very small vein. See also Vein. vertebral column [L. vertebra, joint] The backbone; in nearly all vertebrates, it forms the supporting axis of the body and protects the spinal cord. vertebrate A chordate animal with a backbone: the mammals, birds, reptiles, amphibians, and various classes of fishes.

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vesicle [L. vesicula, a little bladder] A small, intracellular membrane-bound sac. vessel element [L. vas, a vessel] A specialized short, wide cell in angiosperms; arranged end to end, they form continuous tubes for water transport. vestigial organ A type of homologous structure that is rudimentary and of marginal or no use to the organism. viable [L. vita, life] Able to live. villus pl. villi [L. a tuft of hair] In vertebrates, one of the minute, fingerlike projections lining the small intestine that serve to increase the absorptive surface area of the intestine. viroid (vy-roid) A plant pathogen composed of molecules of naked RNA only several hundred nucleotides long. virulent Capable of overcoming a host's defense mechanisms and causing a disease sometimes of rapid onset and severe symptoms. virus [L. slimy, liquid, poison] A submicroscopic, noncellular particle composed of a nucleic acid core and a protein coat (capsid); parasitic; reproduces only within a host cell. viscera [L. internal organs] The collective term for the internal organs of an animal. visceral muscle Smooth muscle found in the walls of the digestive tract, bladder, arteries, and other internal organs. visible light That portion of the electromagnetic spectrum detected as various colors by the human eye, ranging in wavelength from about 400 nm to about 700 nm.

vitalism The belief that natural phenomena are governed by a life force outside the realm of physical and chemical laws. vitamin [L. vita, life] An organic molecule required in the diet in very small amounts; vitamins serve primarily as coenzymes or parts of coenzymes. viviparous (vy-vip-er-us) Referring to a type of development in which the young are born alive after having been nourished in the uterus by blood from the placenta. voltage-gated channel Ion channel in a membrane that opens and closes in response to changes in membrane potential (voltage); the sodium and potassium channels of neurons are examples.

water cycle Worldwide circulation of water molecules, powered by the sun. Water evaporates from oceans, lakes, rivers, and, in smaller amounts, soil surfaces and bodies of organisms; water returns to the Earth in the form of rain and snow. Of the water falling on land, some flows into rivers that pour water back into the oceans and some percolates down through the soil until it reaches a zone where all pores and cracks in the rock are filled with water (groundwater); the deep groundwater eventually reaches the oceans, completing the cycle. water potential The physical property predicting the direction in which water will flow, governed by solute concentration and applied pressure. water vascular system A network of hydraulic canals unique to echinoderms that branches into extensions called tube feet, which function in locomotion, feeding, and gas exchange.

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wavelength The distance between crests of waves, such as those of the electromagnetic spectrum. wild type An individual with the normal phenotype. wobble A violation of the base-pairing rules in that third nucleotide (5' end) of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3' end) of a codon. worker A member of the nonreproductive laboring caste of social insects.

zooplankton [Gk. zoe, life + plankton, wanderer] A collective term for the nonphotosynthetic organisms present in plankton. zygote (zi-goat) [Gk. zygon,yolk, pair] The diploid product of the union of haploid gametes in conception; a fertilized egg.

xylem [Gk. xylon, wood] The tube-shaped, nonliving portion of the vascular system in plants that carries water and minerals from the roots to the rest of the plant.

yeast A unicellular fungus that lives in liquid or moist habitats, primarily reproducing asexually by simple cell division or by budding of a parent cell. yolk The stored food in egg cells that nourishes the embryo. yolk sac One of four extraembryonic membranes that supports embryonic development; the first site of blood cells and circulatory system function.

zoned reserve systems Habitat areas that are protected from human alteration and surrounded by lands that are used and more extensively altered by human activity. zoology [Gk. zoe, life + logos, a discourse] The study of animals.

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REFERENCES
Gogarten, J Peter. 1999 When did eukaryotic cells (cells with nuclei and other internal organelles) first evolve? What do we know about how they evolved from earlier life-forms? URL: http://www.scientificamerican.com/article.cfm?id=when-dideukaryotic-cells Dolphin, Warren D. 2008. Biological Investigations: Form, Function, Diversity & Process. McGraw Hill Higher Education, Eighth Edition. Modney, Barbara K. 2011. PowerPoint Presentation Notes for Biology 201. Cleveland State University. Bruckner, Monica. 2011. The Gulf of Mexico Dead Zone. Montana State University URL: http://serc.carleton.edu/microbelife/topics/deadzone/ Campbell & Reece. 2008. Biology. Pearson Benjamin Cummings, Eight Edition Cleveland State University SLA Leaders. 2011. Practice Exams 1, 2, 3. Cleveland State University. Illustrations contained within this book come from various Internet websites. Thomas Trotter is not the creator of these images. If you have any questions, comments or concerns about any content that appears in this book, please contact Thomas Trotter at the following email address: thomastrotter22@hotmail.com This book is not intended for sale or distribution.

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