Week 4

SYCPA Regents Prep - Living Environment

Molecular Biology & Genetics

Week 4 Molecular Biology & Genetics

This packet provides a review of concepts that may be tested in the NYS Living Environment Regents and is based on the NYS Core Curriculum. This course will cover individual topics over 6 weeks as listed below:
Week Week Week Week Week Week 1 2 3 4 5 6 - Scientific Method - Ecology - Human Body Systems Molecular Biology & Genetics - Labs - Evolution & Human Impact

The order of these topics is chosen based on their average weight in past Living Environment Regents. The individual packets will consist of a review for the specific topic followed by past regents questions.

Good Luck! SYCPA Say Yes Collegiate Prep Academy

Week 4 Molecular Biology & Genetics

Molecular Biology Review

Cell Basics Vocabulary: axon, ATP, cell, cell membrane, cell theory, cell wall, chloroplast, circulation, contractile vacuole, coordination, cyton, digestion, dendrite, DNA, dynamic equilibrium, endoplasmic reticulum, enzymes, eukaryotic, excretion, food vacuole, homeostasis, hormones, immunity, life processes, locomotion, mitochondrion, movement, nucleus, neurotransmitter, organ system, organs, organelles, progesterone, prokaryotic, receptor molecules, reproduction, respiration, ribosome, synthesis, system, target cell, target organs, terminal branches, tissue Living VS. Non-Living Complex organisms, such as humans, require many systems for their life processes. Less complex living things may lack the complex systems of more complex organisms, but they still carry on the basic life activities. While non-living things may carry on some of these life processes, they do not carry on all of them, or these activities do not interact in a manner allowing the non-living thing to reproduce itself. Living things carry out almost all the life processes or activities. These life processes include digestion, respiration, circulation, excretion, locomotion, immunity, coordination, and synthesis. Non-living things are incapable of carrying out at least one or more of the life processes. The sum of the energy used in all the life processes represents the metabolism of the organism. Homeostasis The ability to carry on the life processes allow a living thing to maintain dynamic equilibrium or homeostasis with their surroundings. Homeostasis is a state of balance or steady state between a living thing and its environment. Homeostasis in an organism is constantly threatened. Failure to respond effectively to a failure of homeostasis can result in disease or death. The components of living things in humans and other organisms, from organ systems to cell organelles, interact to maintain a balanced internal environment. This balanced internal environment is called dynamic equilibrium or homeostasis. To successfully accomplish this, organisms possess many control mechanisms that detect internal changes and correct them to restore the internal balance of the organism. If an organism fails to maintain homeostasis, this may result in disease or death. Non-living things possess few control mechanisms to maintain homeostasis. Organizational Levels Important levels of organization for structure and function of living things include cells, tissues, organs, organ systems, and whole organisms. The organs and systems of the body help to provide all the cells with their basic needs to carry on the life functions. The cells of the body are of different kinds and are grouped in ways that help their function. All living things are composed of one or more cells, each capable of carrying out the life functions. The organelles present in single-celled organisms often act in the same manner 3

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as the tissues and systems found in many celled organisms. Single-celled organisms perform all of the life processes needed to maintain homeostasis, by using specialized cell organelles. Living things have different levels of organization. The simplest level of organization is that of the cell. A group of cells with a similar function is called a tissue. Groups of tissues working together to perform a common function are called organs. An example of this would include the nervous, muscle, and other tissues which make up the heart. Groups of organs working together to perform a common function are referred to as a system or organ system. The blood vessels, blood, and the heart are organs which work together to form the circulatory system. Many different systems function together to allow a complex organism to function. Cell Structure Cells have particular structures or organelles that perform specific jobs. These structures perform the life activities within the cell. Just as body systems are coordinated and work together in complex organisms, the cells making up those systems must also be coordinated and organized in a cooperative manner so they can function efficiently together. Inside the cell a variety of cell organelles, formed from many different molecules, carry out the transport of materials, energy capture and release, protein building, waste disposal, and information storage. Each cell is covered by a membrane that performs a number of important functions for the cell as well. Cell Theory All organisms contain one or more cells which are capable of carrying on the life activities needed by the organism. This idea is often referred to as the cell theory. Parts of the Cell Theory

The cell is the unit of structure in all living things. The cell is the unit of function in all living things. All cells come from preexisting cells.

A few exceptions to this theory exist. Viruses lack typical cellular structure. There also is some question as to how the the first cell arose. In general, the cell theory holds true for most living things, however. Cell Types There are two distinct types of cells. Prokaryotic cells lack a nucleus and other organelles. Two domains of organisms have this type of cell - Archaebacteria and Eubacteria, the simplist of all organisms. They still perform life functions but all activities must be accomplished in the cytoplasm. Eukarotic cells are found in organisms from the domain Eukarya, which includes all protists (Ameoba and Paramecium are examples), Fungi (yeast and mushrooms are examples), Plants (mosses, ferns, gymnosperm pines and angiosperm 4

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flowering plants are examples), and Animals (humans are examples).

Cell Organelles Cells have particular structures that perform specific jobs. These cell structures are called organelles and perform the actual work of the cell. These organelles are formed from many different molecules. Some functions carried out by organelles include the transport of materials, energy capture and release, protein building, waste disposal, and information storage. Single celled organisms also have organelles similar to those in more advanced organisms to complete their life processes. Many enzymes are needed for the chemical reactions involved in cellular life processes to occur. A Typical Animal Cell

Some Cell Organelles

Week 4 Molecular Biology & Genetics

Cell Organelle

Function control center of the cell

nucleus

contains DNA which directs the synthesis of proteins by the cell carries on the process of cell respiration converting glucose to ATP energy the cell can use transport channels within the cell found on the endoplasmic reticulum and free within the cell responsible for the synthesis of proteins for the cell

mitochondrion endoplasmic reticulum

ribosome

cell membrane food vacuole contractile vacuole

selectively regulates the materials moving to and from the cell stores and digests food found in many single celled aquatic organisms pumps out wastes and excess water from the cell found in plant cells and algae

chloroplast carries on the process of photosynthesis cell wall surrounds and supports plant cells

Life Functions Humans and many other organisms require multiple systems for digestion, respiration, reproduction, circulation, excretion, movement, coordination, and immunity. The systems collectively perform thelife processes. Once nutrients enter a cell, the cell will use those raw materials for energy or as building blocks in the synthesis of compounds necessary for life. The energy we initially obtain must must be changed into a form cells can use. A type of protein called an enzyme allows for these changes to occur within the cell. Humans and other complex organisms require many different organ systems to carry on the activities required for life. These life activities or processes include digestion, respiration, reproduction, circulation, excretion, movement, coordination, and immunity. Life Processes Digestion breakdown of food to simpler molecules which can enter the cells

Week 4 Molecular Biology & Genetics

Circulation Movement (locomotion)

the movement of materials within an organism or its cells change in position by a living thing removal of cellular waste products by an organism (wastes may include carbon dioxide, water, salt, and urea and are released during exhalation, perspiration, and urine formation.) process which converts the energy in food toATP (the form of energy which can be used by the cells) the making of more organisms of one's own kind -- not needed by an individual living thing but is needed by its species the ability of an organism to resist disease causing organisms (pathogens) and foreign invaders the control of the various activities of an organism (mostly involves the nervous system and endocrine glands in complex animals) the production of more complex substances by combining two or more simpler substances

Excretion

Respiration

Reproduction

Immunity

Coordination

Synthesis

It is important to realize that cell organelles are involved in many of these life processes, as well as the organ systems of complex organisms. Cellular Communication Neurotransmitters and hormones allow communication between nerve cells and other body cells as well. If nerve or hormone signals are changed, this disrupts communication between cells and will adversely effect organism homeostasis. Additionally, the DNA molecule contains the instructions that direct the cells behavior through the synthesis of proteins.

Cell Membrane Receptors Cell Membrane Receptors 7

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Many cell membranes havereceptor molecules on their surface. These receptor sites play an important role in allowing cells and organs to communicate with one another. Hormonal Regulation Hormones provide a primary way for cells to communicate with each other. A hormone is a chemical messenger with a specific shape that travels through the bloodstream influencing another target cell ortarget organ. Upon reaching the cell the hormone is targeted for, the hormone often activates a gene within a cell to make another necessary compound. One example of this is provided by the pituitary gland. This gland at the base of the brain makes a hormone called LH (luteinizing hormone). This hormone travels through the bloodstream and stimulates the ovary to produce yellow tissue that produces the hormone progesterone, which maintains the thickness of the uterus lining. The graphic below illustrates how this kind of hormonal regulation can work in a plant cell. Animal cell hormonal regulation involves a similar mechanism. A Hormonal Feedback Mechanism

The diagram at the right illustrates how a hormone can bind to receptors on a cell membrane and trigger that cell to produce a needed compound.

Nervous Regulation Nerve cells or neurons also allow cells to communicate with each other. Neuron communications are one way organism can detect and respond to stimuli at both the cellular and organism level. This detection and response to stimuli helps to maintain homeostasis in the cell or organism. Neurons may stimulate other nerve cells or muscle cells, thus causing the later to contract and produce movement. Structure and Function of a (Neuron) Nerve Cell

Week 4 Molecular Biology & Genetics

Structures and their Functions 1. dendrite -- neuron branch which detects stimuli (changes in the environment) 2. cyton -- cell body of the neuron where normal metabolic activities occur 3. axon -- longest dendrite covered by a myelin sheath which provides electrical insulation -- carries nerve message or impulse to the terminal branches 4. terminal branches -- release nerve chemicals calledneurotransmitters which stimulate adjacent dendrites on the next neuron or a muscle cell Any change in nerve or hormone signals will change the communication between cells and organs in an organism and thus may cause problems for organisms stability and ability to maintain homeostasis. Cell Transport Cell Membrane The cell membrane or plasma membrane performs a number of important functions for the cell. These functions include the separation of the cell from its outside environment, controlling which molecules enter and leave the cell, and recognition of chemical signals. The cell membrane consists of two layers of phospholipids with proteins embedded within these layers. The surface of the cell contains molecules which recognize other molecules which may attach to or enter the cell.

Cell Membrane Structure

Week 4 Molecular Biology & Genetics

Membrane Processes The processes of diffusion and active transport are important in the movement of materials in and out of cells. Diffusion Diffusion or passive transport is the movement of materials from a region of higher to a region of lower substance concentration. The diagram at the right shows the movement of molecules from higher concentration on side A to a lower concentration on side B.

Active Transport In active transport, molecules move from a region of lower concentration to a region of higher concentration. As this process does not naturally occur, the cell has to use energy in the form of ATP to make active transport occur.

Cell Chemistry Many organic and inorganic substances dissolved in cells allow necessary chemical reactions to take

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Week 4 Molecular Biology & Genetics place in order to maintain life. Large organic food molecules such as proteins and starches must initially be broken down through the life process of digestion in order to enter cells. Organic Molecules and Digestive End Products Organic Molecule carbohydrates proteins lipids (fats) Digestive End Product(s) simple sugars (glucose) amino acids fatty acids and glycerol

Photosynthesis Vocabulary: chloroplasts, chlorophylls, chromotography, enzymes, guard cells, photosynthesis, stomate Biochemical Processes Almost all life on Earth ultimately depends upon the Sun for its energy. The process of photosynthesis converts the Sun's energy to sugars which living things may use as an energy source. These sugars are converted to a form living things can use by a process called respiration. Thousands of chemical reactions occur in living things. These reactions are aided by compounds called enzymes. Enzymes and some other kinds of molecules have specific shapes which allow them to function.

Photosynthesis The energy for life comes primarily from the Sun. Photosynthesis is the major way the energy of the Sun is converted to sugars which provide for the energy needs of living systems. Plants and many microorganisms use solar energy to combine the inorganic molecules carbon dioxide and water into energy-rich organic compounds such as glucose sugar and release oxygen to the environment. A Representation of Photosynthesis The overall process of photosynthesis in a plant or algal cell is shown in the graphic below. Plants use use water and the energy provided by sunlight to combine carbon dioxide into glucose sugar with oxygen being released as a waste product.

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Equation for Photosynthesis carbon dioxide + water (sunlight) (enzymes) glucose + oxygen

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chloroplasts: organelles that carry on photosynthesis in green plant cells chlorophylls: the variety of green pigments within the chloroplasts Chromatography While chlorophyll is the chief pigment responsible for photosynthesis in green plants, many plants contain other colored pigments as well. These chlorophyll and colored pigments may be separated according to their various chemical charges by a technique known as chromatography. In this technique, a mixture of plant pigments is separated by placing a drop or two of pigment on a special paper called chromatography paper which is dipped in a chemical allowing the different plant pigments to move based on their charges. A picture of a completed chromatography may be viewed in the graphic at the right.

Homeostasis by Plants

Maintenance of Water

plants need to regulate water loss and carbon dioxide intake for photosynthesis and other life activities when plants do not keep enough water in their cells, they wilt and die

stomate: a microscopic hole in a plant leaf which allows gases to enter and leave and water vapor to leave as well. Stomata is the plural of stomate.

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guard cells: open and close the stomate.

the ability of the guard cell to close during periods of limited water availability for the plant allows the plant to maintain water homeostasis

___________________________________________________________________________ Cell Respiration Vocabulary: active site, antibodies, ATP, catalyst, cellular respiration, denatured, enzymes, hormones, hydrolysis, pH, specific, substrate, synthesis, temperature Respiration In all organisms, organic compounds such as glucose can be used to make other molecules. These molecules include proteins, DNA, starch, and fats. The chemical energy stored in bonds can be used as a source of energy for life processes. Stored energy is released when chemical bonds are broken during cellular respiration and new compounds with lower energy bonds are formed. Cells usually transfer this energy temporarily in phosphate bonds of a high-energy compound called ATP. (adenosine triphosphate) In all organisms, the energy stored in organic molecules may be released during cellular respiration. This energy is temporarily stored in ATP molecules. In many organisms, the process of cellular respiration is concluded in mitochondria, in which ATP is produced more efficiently, oxygen is used, and carbon dioxide and water are released as wastes. The energy from ATP is used by the organism to obtain, transform, and transport materials, and to eliminate wastes.

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Equations for Cell Respiration glucose + oxygen carbon dioxide + water + 36 ATP The energy from ATP is then used by the organism to obtain, transform, and transport materials, and to eliminate wastes. water + ATP ADP + P + Energy (ATP-ase) Note: ADP is adenosine diphosphate. This reaction is reversible and ADP can be converted back to ATP in cellular respiration. Types of Reactions hydrolysis: reaction in which large molecules are broken down into smaller molecules. Chemical digestion is an example of a hydrolysis reaction synthesis: the combining of simpler molecules to form a more complex molecule Biochemical processes, both breakdown (hydrolysis) and synthesis, are made possible by enzymes. Enzymes and other molecules, such as hormones and antibodies, have specific shapes that influence both how they function and how they interact with other molecules. Enzyme Structure and Function catalyst: inorganic or organic substance which speeds up the rate of a chemical reaction without entering the reaction itself. enzymes: organic catalysts made of protein.

most enzyme names end in -ase enzymes lower the energy needed to start a chemical reaction (activation energy), thus speeding the reaction

How do enzymes work? substrate: molecules upon which an enzyme acts. The enzyme is shaped so that it can only lock up with a specific substrate molecule. enzyme substrate -------------> product

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Lock and Key Theory

Each enzyme is specific for one and ONLY one substrate (one lock - one key) active site: part of the enzyme that fits with the substrate Note that the active site has a specific fit for this particular substrate and no other. This theory has some weaknesses, but it explains many basic things about enzyme function. Since the enzyme may unhook from the substrate, it may be reused many times. Factors Influencing Enzyme Activity pH: the optimum (best) in most living things is close to 7 (neutral). High or low pH levels usually slow enzyme activity

Temperature: strongly influences enzyme activity

optimum (best) temperature for maximum enzyme function is usually about 35-40 C. reactions proceed slowly below optimal temperatures 16

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above 45 C. most enzymes are denatured (change in their shape so the enzyme active site no longer fits with the substrate and the enzyme can't function)

Concentrations of Enzyme and Substrate When there is a fixed amount of enzyme and an excess of substrate molecules, the rate of reaction will increase to a point and then level off. This leveling off occurs because all of the enzyme is used up and the excess substrate has nothing to combine with. If more enzyme is available than substrate, a similar reaction rate increase and leveling off will occur. The excess enzyme will eventually run out of substrate molecules to react with. Enzymes and other molecules, such as hormones, receptor molecules, and antibodies, have specific shapes that influence both how they function and how they interact with other molecules. __________________________________________________________________________ Cell Division Vocabulary: anaphase, asexual reproduction, binary fission, budding, cell cycle,chromatids, chromatin, chromosomes, clones, cloning, cytokinesis, DNA, DNA replication, heredity, interphase, metaphase, mitosis, prophase, replication, sporulation, synthesis, telophase Asexual Reproduction Species are maintained in existence through the life spans process of reproduction. Asexual reproduction produces genetically identical offspring from a single parent cell. The process of mitosis is associated with asexual reproduction and the growth and repair of cells in sexually reproducing organisms. Reproduction and development are necessary for the continuation of any species. Asexual reproduction is a method of reproduction with all the genetic information coming from one parent.

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Some Methods of Asexual Reproduction 1. binary fission -- involves an equal division of both the organism cytoplasm and nucleus to form two identical organisms -- the diagram of the protist at the right is example of this

2. budding -- involves one parent dividing its nucleus (genetic material) equally, but cytoplasm unequally -- the diagram of a yeast at the right is an example of this

3. sporulation (spore formation) -- is reproduction involving specialized single cells coming from one parent -- the diagram of mold spores being formed at the right is an example of this

Asexual reproduction is sometimes called cloning. Cloning is the production of identical genetic copies. All forms of asexual reproduction are variations of the cell division process of mitosis. Mitosis is associated with asexual reproduction, as well as growth and repair in sexually reproducing organisms.

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Mitosis Mitosis is the method used for cell division and reproduction in cells not involved in sexual reproduction. This process starts with one replication (copying of the chromosome material) and one division of the chromosome material. This results in the chromosome numbers in the two cells produced being the same as in the parent cell. This process is represented in the graphic which follows. An Overview of the Process of Mitosis

The Cell Cycle The cell cycle is the lifespan of a cell. It is divided into three parts: Interphase, Mitosis, and Cytokinesis. Interphase is divided into three parts. G1 - or the first growth phase, is the stage in a cells life when normal cell functioning is occurring. A cell will remain in this stage unless it receives a signal to reproduce. Cells can receive signals from neighboring cells during development of a multicellular organism, or it may receive a signal for repair of neighboring cells or a cell may receive a

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signal to divide if the cell becomes too large for intracellular transport to occur effectively. When a cell receives the signal to divide, it moves into the second stage of interphase called synthesis. Synthesis is the longest part of the cell cycle because this is the stage when a cells DNA replicates. DNA replication involves separating the double helix, complimentary nucleotides finding their match (Adenine joins with Thymine, Cytosine joins with Guanine) and two identical strands of DNA forming. Once this is accomplished, and proteins have confirmed its success, a cell moves into the third phase of interphase called G2, or the second growth phase. Here, organelles replicate and the cell grows in anticipation of dividing into two smaller cells. If everything goes according to plan, a cell is ready to move into the mitotic stage of the cell cycle. Mitosis is the division of the nucleus stage. It is a choreographed mechanism to efficiently and accurately divide the two identical copies of DNA into the newly forming cells and it is done the same way in every living cell. The four parts of this cycle are prophase, metaphase, anaphase and telophase (PMAT). In prophase, the DNA which is in long, stringy chromatin form condenses and coils up intochromosomes. The identical pieces of DNA are joined together with a centromere. During this phase, the nuclear membrane in eukaryotes begins to disintegrate. Inmetaphase, the paired chromatids line up (chromosomes) single file down the equator of the cell. In anaphase, the sister chromatids separate and identical chromatids each move to opposite poles. Telophase is when the chromosomes begin to uncoil again back into chromatin and new nuclear membranes begin to form in eukaryotes. The final stage of the cell cycle begins in telophase when the cells cytoplasm begins to divide. In animal cells, the cell membrane pinches in during this stage calledcytokinesis. In plant cells, a cell plate forms between the newly forming nuclei as the cell wall can't pinch in. This continues until two new cells are formed with identical DNA.

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2 Key Results of Mitosis 1. The same chromosome number is retained from generation to generation. 2. Each daughter cell receives an exact copy of the chromosomes of the parent cell. (clones) Asexual Heredity Every organism requires a set of coded instructions for specifying its traits. For offspring to resemble their parents, there must be a reliable way to transfer information from one generation to the next. Heredity is the passage of these instructions from one generation to another. The DNA molecule provides the mechanism for transferring these instructions. In asexually reproducing organisms, all the genes come from a single parent. As asexually produced offspring are produced by the cell division process of mitosis, all offspring are normally genetically identical to the parent.

Genetics Review Intro to Genetics Vocabulary: sexual reproduction, gamete, egg/ovum, sperm, gonads, fertilization, differentiation, meiosis, replication, crossing over, variations, natural selection, recombination, external fertilization, external development, internal fertilization, internal development Sexual Reproduction Process The process of sexual reproduction involves two parents. Both parents normally contribute one gamete or sex cell to the process. This process assures that the genetic information given to the offspring will be obtained equally from each parent. The female gamete is called the egg or the ovum and the male gamete is called a sperm. These gametes are formed in specialized reproductive structures called gonads. The sperm is much smaller than the egg, but is capable of moving on its own power using a whip-like tail called a flagellum.

Sperm and Egg (fertilization)

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The sperm and egg This process forms a zygote which contains develop into a characteristics of both Process of Fertilization

unite in a process called fertilization. single celled structure called a the complete genetic information to complete new organism having parents.

This zygote will then divide by mitosis and form the specialized cells, tissues, and organs of the organism. This development of specialized structures from the zygote is called differentiation. Meiosis The process of meiosis produces gametes or sex cells. While some parts of this cell division process are similar to the asexual cell division process of mitosis, there are several key differences. Meiosis produces gametes, while mitosis produces other cell types. The process of meiosis halves the chromosome number from the original parent cell in the four cells it forms. It does this by having two cell divisions forming four cells, where mitosis has only one cell division forming two cells. Both processes start out with one doubling or replication of the chromosome material. The graphic below will help to visually illustrate some of the key events of meiosis.

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Process of Meiosis

Another important way that meiosis differs from mitosis is the exchange of chromosome pieces which occurs in the first division of this process. This exchange of chromosome pieces is called crossing over. Crossing over assures that the cells produced as a result of meiosis will be different from and exhibit variations from the parent cell that produced them. This process is chiefly responsible for the variations seen in members of the same species of sexually reproducing organisms. These variations are the driving force for the process of natural selection. The process of crossing over and how it produces variation when these chromosomes are recombined in the process of fertilization is illustrated in the graphic below.

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Crossing Over and Genetic Recombination

Comparative Reproduction and Development Different organisms possess different adaptations for reproduction and development. Organisms which spend their lives or a large proportion of their lives in the water tend to lay their eggs in great numbers (thousands) in the water and wait for the male of the species to release sperm near them to fertilize them. The fertilization which occurs in the water in this case outside the body of the organism is called external fertilization. These young organisms then develop outside the mother in the water once this has occurred, which is called external development. A disadvantage of this 24

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process is that the eggs and developing young have little or no parental protection. Many fish and amphibians like frogs undergo fertilization and development in this manner. Reptiles and birds engage use the process of internal fertilization to fertilize their eggs. In this situation, the male of the species inserts his sperm inside the female, who then lays her fertilized eggs outside her body. The process of development is then external. Reptiles and especially birds tend to lay fewer eggs and provide much more parental protection for their developing young. Organisms (with some exceptions) which use the process of internal fertilization tend to spend much of their lives on land. Mammals like humans have both their fertilization and initial stages of development occur within the female organism. This is referred to as internal fertilization and internal development. These organisms tend to release very few eggs, but those eggs and the developing organism are very well protected by one or both parents. DNA/RNA Vocabulary: genes, DNA, replication, mutation, gamete, heredity, complementary base pairing, chromosomes, asexual, mitosis, crossing over, genetic recombination, natural selection, cancer, adenine, guanine, cytosine, thymine, template, RNA, mRNA, rRNA, tRNA, transcription, regulation DNA All Organisms have a set of instructions that determine their characteristics. These instructions are called genes and contain the instructions for life that are passed from parents to offspring during reproduction. The inherited instructions that are passed from parent to offspring exist as a code. The DNA molecule which makes up our genes contains this code. Asexual v. Sexual Heredity The DNA molecules must be accurately replicated before being passed on. Asexually reproducing organisms normally pass on this genetic code identically between the parent and offspring, while the offspring of sexual reproduction produce offspring that resemble their parents, but exhibit some variations from them.

Mutations Changes in DNA or mutations which occur in non sex cells of a sexually reproducing organism will not be passed on to their offspring.Mutations which occur in sex cells or gametes will be frequently be passed on to their offspring. Protein Synthesis Once the coded information contained in the DNA molecule is passed on, it is used by a cell to make proteins. The proteins that are made become cell parts and carry out most functions of the cell. The subtle differences in DNA between different human beings and different species results in the production of different proteins. This is a major reason why we show individual differences.

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DNA Structure and Function DNA provides the set of coded instructions required by every organism for specifying its traits. The DNA molecule also provides for a reliable way for parents to pass their genetic code from one generation to the next. Heredity refers to this passage of these instructions from one generation to another. DNA is a double stranded molecule which has the shape of a twisted ladder. This shape is called an alpha helix. The sides of this twisted ladder are composed of alternating phosphate and deoxyribose sugar units, while the rungs of the ladder are composed of pairs of nitrogenous bases. These bases are called adenine (A), thymine (T), guanine (G), and cytosine (C). These bases exist in pairs on the rungs of the ladder with A always pairing with T and G pairing with C. This principle is sometimes called complementary base pairing. (The saying G CAT provides a means of remembering this idea.

Structure of the DNA molecule

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Location of DNA

Gene-Chromosome Model Hereditary information is contained in genes, which are composed of DNA, located in the chromosomes of each cell. Chromosomes are found in the nucleus of each cell. The Gene Chromosome Model

Each gene carries a separate piece of information. An inherited trait of an individual can be determined by one genes, but is usually determined by the interaction of many different genes.

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A single gene can influence more than one trait. A human cell contains many thousands of different genes coding for many different traits. Changes in the sequence of the DNA molecule and therefore the gene are called mutations. A mutation may change the manner in which a trait is expressed by an organism.

Asexual Heredity Every organism requires a set of coded instructions for specifying its traits. For offspring to resemble their parents, there must be a reliable way to transfer information from one generation to the next. Heredityis the passage of these instructions from one generation to another. TheDNA molecule provides the mechanism for transferring these instructions. In asexually reproducing organisms, all the genes come from a single parent. As asexually produced offspring are produced by the cell division process of mitosis, all offspring are normally genetically identical to the parent. Sexual Heredity In sexually reproducing organisms, the new individual receives half of the genetic information from its mother through the egg and half from its father from his sperm. Sexually produced offspring resemble, but are not identical to, either of their parents. Some reasons for these variations between sexually reproduced offspring and their parents include crossing over when gametes are formed in each parent and genetic recombination, which is the combining of the genetic instructions of both parents into a new combination in the offspring when fertilization occurs. Genetic Recombination

Note that two of the four offspring in the punnett square at the right have a completely different genetic makeup than that of either parent The processes of crossing over and genetic recombination will result in offspring exhibiting variation from the original parents. The variations shown between different sexually produced offspring provide the driving force for the process of natural selection.

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Heredity and Environment The characteristics of an organism can be described in terms of combinations of traits. Traits are inherited, but their expression can be modified by interactions with the environment. Examples of this include the lack of color in completely shaded grass, even though it still possesses the genetic makeup to appear green and the change in fur color of returning fur in a shaven Himalayan hare at cold temperatures. Effect of Cold on Himalayan Hare Fur Color

The application of an ice pack to a region of shaved hair results in black hair growing back instead of the original white color. The many body cells in an individual can be very different from one another, even though they are all descended from a single cell and thus have identical genetic instructions. This is because different parts of these instructions are used in different types of cells, influenced by the cells environment and past history. Poor health habits can have an adverse effect on the development and expression of many genes in human cells, resulting in sickness or even death. Mutation A mutation is a change in the genetic material of an organism. Mutations

Mutations which occur in non sex cells of sexually reproducing organisms will not be passed on to the offspring, although they may result in disease or death for the organism involved. One possible consequence of a mutation in a non sex cell is uncontrolled mitotic cell division or cancer. Mutations which occur in sex cells or gametes may be passed to the offspring. Along with crossing over and genetic recombination, mutation provides for a source of variation in sexually reproducing individuals.

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DNA In all organisms, the coded instructions for specifying the characteristics of the organism are carried in DNA. The genetic code is contained in the four nitrogenous bases of DNA; adenine, guanine, cytosine, and thymine. These bases are often indicated only by using their beginning letters A, G, C, and T. Each individual DNA strand serves as a template or model for the formation of other DNA molecules by replication. RNA DNA codes for the formation of RNA in the nucleus of the cell. RNA is short for another kind of nucleic acid called ribonucleic acid. RNA is very similar in structure to DNA except for three small differences. These differences include the fact that RNA is a single stranded molecule, lacks the base thymine (T) as it is replaced by the base uracil (U), and its five carbon sugar ribose has one more oxygen atom than the sugar in DNA. Three different types of RNA exist, mRNA or messenger RNA, tRNA or transfer RNA, and rRNA or ribosomal RNA. Protein Synthesis Cells store and use coded information. The genetic information stored in DNA is used to direct the synthesis of the thousands of proteins that each cell requires. The chemical and structural properties of DNA are the basis for how the genetic information that underlies heredity. DNA is encoded in the sequence of nitrogenous bases which directs the formation of proteins in the cell. How does this process work? First, the DNA code is copied on to the mRNA (messenger RNA) codon. A codon is a sequence of three nitrogenous bases. This process is calledtranscription. This mRNA codon is then carried from the nucleus out to the ribosome. Messenger RNA attaches to another kind of RNA called tRNA (transfer RNA). Transfer RNA attaches to amino acids and carries them to the ribosome. This assembly of amino acids due to the code provided to RNA by the original DNA molecule is what produces proteins for the cell. Remember a protein is a long molecule formed from amino acid subunits. Protein Synthesis

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In summary, the code of DNA directs the synthesis of RNA, which in turn directs the making of proteins on the ribosomes. This is sometimes referred to as being the central dogma or idea of biology. There are 64 possible combinations of triplets (sequences of 3 nitrogenous bases) which code for the 20 different possible amino acids. As the DNA of different organisms and most individuals (except for identical twins) is different, this means the proteins produced by different humans and other organisms exhibit differences. It is these differences which make us unique individuals. The work of the cell is carried out by the many different types of molecules it assembles, mostly proteins. Protein molecules are long, usually folded chains made from 20 different kinds of amino acids in a specific sequence. This sequence influences the shape of the protein. The shape of the protein, in turn, determines its function. Offspring resemble their parents because they inherit similar genes (DNA sequences) that code for the production of proteins that form similar structures and perform similar functions. Cell Regulation Cell functions are regulated. Regulation occurs both through changes in the activity of proteins and through the selective expression of individual genes, as humans and other organisms have genes which direct the expression of other genes. This regulation allows cells to respond to their environment and to control and coordinate cell growth and division. Genetic Engineering Vocabulary: selective breeding, recombinant DNA, artificial selection, inbreeding, hybridization,

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genetic engineering, restriction enzyme, cloning, genetic mapping, Human Genome Project Genetic Engineering Throughout recorded history, humans have used selective breeding and other methods to produce organisms with desirable traits. Our current understanding of genetics and heredity allows for the manipulation of genes and the development of new combinations of traits and new varieties of organisms. This includes various aspects of DNA technology, including recombinant DNA technology. Scientists have also developed many ways of determining the genetic makeup of different organisms, including humans.

Selective Breeding For thousands of years new varieties of cultivated plants and domestic animals have resulted from selective breeding for particular traits. Some selective breeding techniques include artificial selection, where individuals with desirable traits are mated to produce offspring with those traits. A variation of this process traditionally used in agriculture isinbreeding, where the offspring produced by artificial selection are mated with one another to reinforce those desirable traits.Hybridization is a special case of selective breeding. This involves crossing two individuals with different desirable traits to produce offspring with a combination of both desirable traits. An example of this are Santa Gertrudis cattle, which were developed by breeding English shorthorn cattle, which provided for good beef, but lacked heat resistance, with Brahman cattle from India which were highly resistant to heat and humidity. The Santa Gertrudis breed of cattle has excellent beef, and thrives in hot, humid environments. An Example of Selective Breeding

English shorthorn Brahman cattle: Good resistance to heat cattle: Good beef but poor heat resistance. but poor beef.

Santa Gertrudis cattle: Formed by crossing Brahman and English shorthorns; has good heat resistance and beef.

Genetic Engineering In recent years new varieties of farm plants and animals have been engineered by manipulating their genetic instructions to produce new characteristics. This technology is known as genetic

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engineering or recombinant DNA technology. Different enzymes can be used to cut, copy (clone), and move segments of DNA. An important category of enzyme used to cut a section of a gene and its DNA from an organism is known as a restriction enzyme. When this piece of DNA, which has been cut out of one organism, is placed in another organism, that section of gene will express the characteristics that were expressed by this gene in the organism it was taken from. An Example of Genetic Engineering

Inserting, deleting, or substituting DNA segments can alter genes. An altered gene may be passed on to every cell that develops from it. Knowledge of genetics, including genetic engineering, is making possible new fields of health care. Genetic engineering is being used to engineer many new types of more efficient plants and animals, as well as provide chemicals needed for human health care. It may be possible to use aspect of genetic engineering to correct some human health defects. Some examples of chemicals being mass produced by human genes in bacteria include insulin, human growth hormone, and interferon. Substances from genetically engineered organisms have reduced the cost and side effects of replacing missing human body chemicals. While genetic engineering technology has many practical benefits, its use has also raised many legitimate ethical concerns. Other Genetic Technologies Cloning involves producing a group of genetically identical offspring from the cells of an organism. This technique may greatly increase agricultural productivity. Plants and animals with desirable qualities can be rapidly produced from the cells of a single organism. Genetic mapping, which is the location of specific genes inside the chromosomes of cells makes it possible to detect, and perhaps in the future correct defective genes that may lead to poor health. Thehuman genome project has involved the mapping of the major genes influencing human traits, thus allowing humans to know the basic framework of their genetic code Knowledge of genetics is making possible new fields of health care. Genetic mapping in combination with genetic engineering and other genetic technologies may make it possible to correct defective

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genes that may lead to poor health. There are many ethical concerns to these advanced genetic technologies, including possible problems associated with the cloning of humans. Another down side to genetic mapping technologies it is possible that some organizations may use this genetic information against individuals. Human Genome

Vocabulary: karyotype, sex chromosome, autosome, pedigree, sex-linked gene, DNA fingerprinting, gene therapy Humans are identified by their 46 chromosomes (23 pairs of homologous chromosomes). We receive 23 chromosomes via the egg cell from our mother and 23 chromosomes via the sperm cell from our father. Sperm and egg cells are haploid, meaning that they contain only a single set of chromosomes. When the sperm and egg unite during fertilization, the resulting cell (the zygote) has 46 chromosomes. A zygote is diploid because it contains both sets of homologous chromosomes. Karyotypes A karyotype is a photograph of chromosomes in order from largest to smallest in pairs. By looking at a karyotype, you can decipher whether the person is male or female, and often you can see if there

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Week 4 Molecular Biology & Genetics are any chromosome abnormalities. For example, if a person has Down's Syndrome, their karyotype

The red circle highlights the extra chromosome. The red arrow is pointing to the sex chromosomes (XX). This karyotype is of a female with Down's Syndrome. would have an extra 21st chromosome. See the karyotype below. Sex Chromosomes Two of our 46 chromosomes are known as sex chromosomes and are identified as the 23rd pair in a karyotype. Females have two large X chromosomes and males have one X and one small Y chromosome. The other 22 pairs of chromosomes are known as autosomes. Pedigrees A pedigree is a chart that scientists use to show the relationships within a family. A genetic counselor may use a pedigree to see how traits are passed from one generation to the next, making inferences about the genotypes of the different individuals. Pedigrees are usually used to trace a single-gene trait through a family (ex: white forelock). Many traits are either polygenic (controlled by many genes) or are influenced by the environment. This means that the expression of your genes can be affected by the environment you are exposed to (ex: your nutrition plays a large role in what your height and weight will be).

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Week 4 Molecular Biology & Genetics There are many genetic disorders that humans can inherit. Some of them include PKU, Down's Syndrome, sickle cell anemia, and Huntington's disease. There are many ways to diagnose genetic disorders including blood tests, amniocentesis, urine tests, and karyotype analysis. Sex-Linked Genes Genes that are found on the sex chromosomes (the X and Y) are known as sex-linked genes. Many genetic disorders are found on the X chromosome. Females would need two recessive copies on their X chromosomes for disorders like hemophilia and colorblindness to be expressed. Since males only have one X chromosome, all alleles located on the X chromosome are expressed. Due to the male's single X chromosome, disorders like colorblindness are found more commonly in males. DNA Fingerprinting To identify individuals, scientists use a method called DNA fingerprinting. The DNA that is chosen to be analyzed serves little to no function to the individual, but these sections can vary greatly from person to person. DNA is cut by a restriction enzyme and undergoes gel electrophoresis, which separates the DNA by size. The resulting banding pattern is unique to each person, and the information is extremely useful in convicting criminals or in overturning wrongful convictions.

Gene Therapy Since scientists completed work on the Human Genome Project in 2000, we can use the information gathered to help treat genetic disorders.Gene therapy is when a faulty gene is replaced with a proper working gene. A similar scenario would be adding a gene in where one is missing. This can be accomplished with the help of a virus, since they are able to enter the DNA of a cell. First the virus is modified so it cannot cause disease. Next, a piece of DNA containing the normal functioning gene is inserted into the DNA of the virus. Lastly, the patient is "infected" with the virus (that has the modified DNA), introducing the proper working gene.

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Ethical Issues As we develop new technology and are able to alter the human genome, many ethical issues arise. Should we use the knowledge we have to just cure diseases, or is it alright to start changing whatever it is we don't like about ourselves? Should we be able to choose the traits we want for our babies before they are even born? Where do we draw the line?

Review provided by regentsprep.org and The NYS Core Curriculum

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Microbiology & Genetics Regents Questions August 2011

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June 2011

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Jan 2011

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