Exam 1 MAIN Study Guide..

Detailed Page by Page Version (Also try to look at other exam 1 files below)) BSC1010 Exam 1 Detailed Page by page .Study Guide.

Chapter 1

IN ADDITION TO THIS VERY DETAILED STUDY GUIDE ALSO LOOK OVER THE OTHER GENERAL STUDY GUIDES IN THIS SAME FOLDER (BELOW) FOR EACH CHAPTER 1-4 and 5 WHICH HAVE 10-20 OBJECTIVE QUESTIONS AND VOCABULARY LISTS. Page 1. Be able to define the terms biology and evolution. Be able to distinguish what is alive or living versus that which is not based on the seven properties of life.

Page 2. Know figure 1.3 in detail ; know each property of life and its description.

Page 3. Know what is meant by emergent properties what are they? How do they come to be.

Page 4-5. Be able to list the 10 levels of biological organization in correct sequence and be able to describe/define what each level represents. For example ecosystems fall between the higher biosphere level and the lower communities level. By definition we can describe an ecosystems as all the living things in a particular area as well as the non-living components and the interactions between living and living non-living and living and non-living with non living. The sun a nonliving component of most ecosystems can interact with organisms termed producers such as plants leading to the synthesis of organic compounds which are used by the plant and also by consumers which eat plants (page 6) . The organic compounds serve as fuels for the plants and consumers. Utilization of the fuels produces heat which is released back into the ecosystem. When consumers and producers die they return nutrients to the soil a nonliving component. The soil will in turn provide these nutrients to the next generation of producers and consumers. Scientists who study such interactions within ecosystems are called ecologists.

The above was an example of one level of biological organization along with a complete description of the level and examples of events occurring at the level. You should know all the remaining 9 levels of biological organization at this level of detail.

Page 7 Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 8 Know that the cell is the smallest simplest form of life capable of exhibiting the 7 properties of life. Know all cells are surrounded by a membrane that regulates passage of materials between the cell and its surrounding. Know cells are classified into 2 groups eukaryotes and prokaryotes. Know the differences between the 2 types. For example prokaryotic cells are smaller, they are older, they came into existence 3.8 billion years ago whereas eukaryotes first came into existence 2.1 billion years ago. Prokaryotes lack a nucleus, lack a nuclear envelope, lack nuclear pores, lack any nuclear proteins such as the lamin proteins or histones. Most prokaryotes lack any internal membranes such as golgi or vacuoles or endoplasmic reticulum, a few like cyanobacter have some in-folds of their plasma membrane but no separate membrane enclosed organelles. Only eukaryotes have a nucleus and only they have internal separate membrane enclosed organelles like vacuoles and lysosomes and rough ER smooth ER etc...

Page 8 Know about DNA and its function (Also covered in end of chapter 5)

Know that DNA is found in structures called chromosomes in association with proteins. Know that each chromosome consists of a linear or circular strand of DNA which is in turn composed of chains of building blocks called nucleotides. Know that there are 4 nucleotides used in DNA described by the letters A,C G and T (page 9). Linking these 4 nucleotides together in variable sequences creates long chains of nucleotides also known as a DNA chain . To form DNA requires that 2 chains of nucleotides be interwoven as a double helix. Very long chains of connected nucleotides create chromosomes. Know that along the length of a chromosomes long chains of nucleotides ( DNA strands ) are small units called genes. Each gene codes or contains instructions or the blueprint on how to build a specific protein. A chromosome may be 1-200 million nucleotides long, but each gene is only about 10,000 nucleotides long. So a chromosome may have from 100-10,000 genes each coding for a specific protein. When an organism grows and develops from a single fertilized egg it is the creation and actions of these thousands of proteins coded for by the genes that actually carry out the building events and maintenance activities of the cell that will make that single cell become thousands of cells and that will orchestrate the formation of the various bodily structures. The 4 nucleotides of DNA when chained in sequences create words or instructions for the cell on how to build these proteins. Like an alphabet of only four letters words like ACCGGTTGCCCATG which dont mean much to us, such words have very specific meanings to a cell engaged in protein synthesis, just as words created from our 26 letter alphabet have specific meanings for us.

Page 10 Know what the term genome means.

Page 11 Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 12 Know that Diversity is a hallmark of life. Know that there are currently 1.8 million different species of life. Know that taxonomy is the branch of biology that names and classifies species, that groups diverse organisms according to their similarities and their relationships to each other. It also orders them into groups of increasing breadth spanning from the most specific and least inclusive grouping to the broadest and almost all inclusive grouping ie from a species to a domain.

Know the 8 taxon levels of taxonomic grouping in ascending and or descending order. Ie species, genus, family, order, class, phylum, kingdom, domain.

Page 13 know the three domains of life and their descriptions be able to distinguish between the 3, bacteria, archaea, eukarya. Also know the 4 eukaryotic kingdoms and their descriptions, plantae, animalia, fungi, protista (figure 1.15)

Page 14 Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 15 Know what natural selection means Page 16-17 know how new species arise according to the Darwinian model of descent with modification

Page 18 Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 19 Read (BUT MATERIAL WILL NOT BE ON TEST).......... Except for figure 1.24 know this figure and know the steps of the scientific method

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Chapter 2

Page 30 Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 31 Know the section 2.1Matter consists of chemical elements in pure form and in combinations..

Know that chemistry is the study of matter in all of its three states solid, liquid and gas. Know that matter is anything that occupies space and has mass. Know that living organisms are composed of matter. Know that matter can be divided into pure substances and mixtures. Know that pure forms of matter include : elements andcompounds. Know that an element is a pure form of matter that cannot be broken down to other substances by chemical reaction. Know that compounds are also pure forms of matter created by the bonding of two or more different elements in a fixed ratio. The bonding can be ionic or covalent and requires chemical reactivity between valence electrons.

Note: Compounds are newly formed pure substances and have new novel physical properties and chemical properties that differ from the parental elements from which the compound was formed.

Know what a physical property of matter is? (ie boiling point, taste, solubility. Know what a chemical property of matter is Know that mixtures of matter may be homogenous (air) or heterogenous

Page 32 Know the elements of life. Study Table 2.1. Know all the elements and trace elements found in the human body. Know the effects of trace element deficiencies such as iron (Fe) zinc (Zn) and iodine(I) deficiency.

Page 32 The case study on toxic elements. Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 33. Know atomic structure including the definition and location of protons neutrons, electrons, quarks, and neutrinos.

Know what the atomic number, and mass number are. Know how these numbers are represented symbolically on an Element Letter as super or sub scripts. Given a graphical description with atomic number, and mass number be able to find the number of neutrons, protons and electrons.

Know what a cation and an anion are and how they are formed.

Page 34. Know what an isotope is? Know what a radioactive isotope is. Know some uses in medicine and research for radioactive isotopes.

Page 35-36 and PowerPoint and class notes and via Google search. Be familiar with Niels Bohr; who he was; what his contribution to the field of chemistry was.

Know that electrons around the atoms nucleus have potential energy. The ones closest to the nucleus have the least the ones in the outer or valence shells have the most energy. Know that electrons can

only occupy specific energy levels or shells ranging from J-K-L-M-N. or levels 1-5 or higher. As electrons move from outer shells to inner shells theylose energy which is emitted as released energy like light or heat or fluorescence. As electrons move from inner to outer shells they gain or absorb energy which the surrounding environment loses. The electrons on the outer shells (the valence electrons in the valence shell) have the most energy and the most potential to react or form bonds. On the periodic table the rows or periods correspond to the number of energy shells that have electrons in their orbits. So H and He on row 1 or period 1 have only one energy shell with 1 or 2 electrons respectively. Row 2 or period 2 includes Lithium through Neon all of the atoms of these elements have two (2) energy shells. Row 3 or period 3 includes sodium (Na) Argon (Ar) all of the atoms of these elements have 3 energy shells with electrons in orbit. The third shell in this case is the valence shell. The columns on the period table represent groups of atoms of similar size with regard to the radius of the nucleus and similar in their chemical properties. The group number also tells us how many Valence electrons are in the valance shell. For example carbon is in group 4a so carbon has 4 valence electrons available for sharing in covalent bonds. Oxygen has six valence electrons in its valence shell or group 6A so 2 electrons are missing and needed to fill its octet or we say oxygen has a valence of 2; which represents its bonding capacity; it can form 2 bonds by sharing 2 electrons from another atom or atom. Note the number of valence electrons is different then an atoms valence< span> Oxygen has 6 valence electrons but a valence of 2. In the third period phosphorus which is in group 5A does not have a valence of 3 as expected but rather 5 due to hybrid sp orbitation. Hence phosphorous can form 3 single bonds and often forms also a double bond. Arsenic can also do this and in some bacteria arsenic may replace phosphorous in the formation of molecules such as DNA that usually has phosphate groups.

Also know the following:

Page 36-37 Know that electrons have specific configurations within the energy levels they occupy and may be positioned on sublevels or orbitals. On energy level 1 there is one sublevel s which can hold 2 electrons often written as 1s2. On the second energy level further out from the nucleus or the K shell we have s and p sublevels or orbitals. 2 electrons can be found in the s and 6 electrons can be found in the x,y,z, planes of the 3 p orbitals. Or energy level 2 can hold a maximum of 8 electrons. Sometimes filling the s and p of the valence shell is called completing the octet. All stable elements such as the inert gases have complete octets in their valence shells, with all s and p orbitals filled. On energy level 3 which is even further away from the nucleus we have 3 sublevels s, p, and, also d. 2 electrons can occupy the level 3 s orbital or sublevel; 6 electrons can occupy the level 3 p .x-y-z orbitals and 10 can occupy the 5 d orbitals or a total of 18 electrons on level 3 or the L shell.

Also know the following: There are 2 ways to represent electron configurations either by an alphanumeric description i.e [1s22s2 2px22 py22pz23s2 or 1s22s2 2p63s2] or by drawing concentric circles and showing via dots the number of total electrons found within that energy shell. Similar to a bullseye with orbiting electrons on each ring. The second way does not tell us which specific orbitals have electrons but we can guess based on the fact that the s only fits 2 electrons and p orbitals only hold 2 electrons on each axis or 6 total; d orbitals hold 10 electrons and f orbitals at the 4 th energy level hold 14 electrons. Also Level one only has s orbitals Level 2 has sand p Levl 3 has s p and d, level 4 has spdf orbitals. One additional representation is called Lewis dot structure. A letter representing the atom is written and dots representing the paired or unpaired valence electrons are drawn around the written letter. ie :C: Concentric circles or bullseye drawings dont give us the true picture of electron orbit shape; the s orbits for example are really spheres and the p orbits are dumbbell-shaped.

Atoms with unpaired electrons in their valence shell; usually found when an octet of electrons in the s and p orbitals is incomplete, are chemically active and want to form bonds to become stable by completing their octet and leaving no unpaired electrons. Only the inert gases like neon and argon are chemically inert or non reactive.

Because of this most atoms want to form ionic or covalent bonds with other atoms via the valence electrons. The purpose is so that after bonding the atoms involved in the bond will have filled valence shells or complete octets and will become stable compounds or molecules like the inert gases.

Page 38 Know what covalent bonds are.

Top of page 38 know what a molecule is. Know that compounds can form via ionic or covalent bonds but molecules all form via covalent bonds.

Know that covalent bonds can be polar or non-polar. (page 39) Polar covalent bonds form when the difference in the electrotronegativity values of the atoms attempting to bond is > 0.5 and less than 1.9. If this value is <0.5 then the bond will be a non-polar covalent bond. If this value is > 1.9 then the atoms will form an ionic association.

Know that water H2O forms a polar covalent bond leaving partial charges or dipoles that are positive on the 2 hydrogens and dipoles that are negatively charged on the single oxygen. Oxygen which has a strong electronegativity value shares hydrogens electrons unequally holding them >80% of the time. By gaining Hydrogen s electrons the oxygen in water takes on 2 negatively charged electrons and hence takes on a slight negative charge. Each of the two Hydrogens which had their single electron ripped away from heir 1s orbitals; leaving only its nucleus carries a slight positive charge due to the positive charge of the single proton in the nucleus.

In your power points I have a periodic table with electronegativity values that you can look at to predict these types of bonds

A single pair of shared electrons yields a single bond represented graphically by a single line between atoms in the structural formula of the molecule. Ie H3-C-C-H3. Two (2) pair of shared electrons yields a double bond represented graphically by two lines between atoms in the structural formula of the molecule i.e H3-C=C-H3 (Know the difference between structural and molecular formulas)

Page 39 know what ionic bonds are and how they are formed. Be able to show the formation of an ionic bond (this question will be on the tests 100% ) and represent it graphically (this question will be on the tests 100% ). ( Graphically means: Drawing the electron orbitals around the atomic nucleus and showing the transfer of electron from the valence shell of one atom to the receiving valence shell of the other atom and the resulting creations of anion and cation that then attract and from the bond) See figure 2.14 also PAGE 40 AT BOTTOM the text which describes Mg which loses two electrons one gained by one Chlorine and the second gained a second chlorine to form MgCl2. (hthat is one Mg+2 cation bonding with two Chlorine anions Cl-. Cl-

Know ionic compounds unlike covalently bonded molecules, do not have definite size and number of atoms but rather form aggregates of ions that form growing crystal lattices of variable dimension.

Page 40 Know what weak chemical bonds are . For example what is a hydrogen bond how is it formed. What is a dipole dipole bond? What is a van der Waal force? In living organisms many weak bonds are used to give biological macromolecules their specific three dimensional shape. DNA strands are held together via hydrogen bonds. Water molecules stick to each other using hydrogen bonds.

Boiling point and melting points are affected by the strength of inter molecular interactions. Two molecules held together via van der Waals forces wil boil at a much lower temperature than two water molecules held together via hydrogen bonds. The backbone of the alpha helix shape of proteins depends on hydrogen bonds to keep that spiral staircase shape

Page 40-41 Know that even a molecule with non-polar covalent bonds may have very very very weak positive and negative charged regions due to the electrons surrounding each atom and the protons in the nucleus of each atom. Non-polar molecules may interact via these weak electrostaic forces if they are close together and no energy exists in the system to push them apart. These weak interactions are called van der Waals forces or aka London dispersion forces. Molecules like lipids, fats fatty acids oils, waxes all stick to one another using this type of weak force. This type of force is easily disrupted by slight elevations in temperature, which will melt solid forms or boil liquid forms of these non-polar hydrophobic molecules.

Page 41 Know about molecular shape. Know that repulsions from the electrons in the orbitals of the atoms that are bonded into molecules create molecular shape and geometry. Hybrid orbitals of the interacting orbitals of each atom create shapes such as tetrahedral or pyramidal or trigonal or linear forms.

Page 42 Know about the importance of molecular shape to biology and fields such as pharmacy based on the example in figure 2.18 concerning morphine and endorphins.

Page 43 Know that chemical reactions involve reactants and products. The atoms of the reactants are conserved in the production of products. We say that chemical reactions do not create or destroy matter; reactions rearrange matter and bond associations. Reactants appear on the left hand side of a chemical equation followed a right proceeding arrow -> which leads to products on the right hand side of the chemical equation. A reaction may be in equlibrium having an equal likilihood to proceed to the left or to the right.

Chapter 3

Three fourths of the earths surface is covered by water.

Page 46 Know why water is important to life here on earth as well as on other planets. Page 47. Know about the relationship between polar covalent bonds found in water and the dipoles formed on the molecule and how these dipole charges make hydrogen bonding between water molecules possible ( see figure 3.2 page 47).

Know that 4 four hydrogen bonds can form with any single water molecule occurring in approximately a tetrahedral shape in the solid form of water. This arrangement means water molecules are typically always tethered to one another preventing their free kinetic movement and preventing changes in states of water unless significant energy is invested to break all four hydrogen bonds. We say that water has great cohesion, it is held together by its self associations, it sticks easily to itself. Water also sticks to other polar molecules or we say it has good adhesion to polar molecules. These two features makes it possible for water to travel from the roots of a plant to its leaves against gravity. Breaking cohesive water molecules apart along the surface of water is difficult compared to other liquids water has a high surface tension.

Page 48 know the definition of kinetic energy, heat, temperature, calorie, joule, kilocalorie.

Know how water moderates global temperatures (see what follows below):

Know what the term specific heat means. Know that compared to other liquids water has a very high specific heat. It is because of this that the oceans and seas on our planet can absorb extreme levels of solar energy daily absorbing massive amounts of heat but with very little shift in temperature. What gives water this property are the four hydrogen bonds that keep each water molecule tethered so they do not move. In other words the average kinetic energy does not increase much when water is exposed to solar energy because the suns energy may break a hydrogen bond on a water molecule but since that molecule is tethered to three other water molecules it does not move or we say it is not put into motion hence does not gain kinetic energy. A gain in kinetic energy shifts temperatures upward but water which resists kinetic motion due to its four tethers shifts very little in temperature in spite of absorbing a great deal of heat energy from the sun. This makes it possible for the planet to be exposed to solar energy but not have drastic increases in global temperature. Water moderates daily temperatures by absorbing the suns heat but water does not shift much in temperature. The absorbed daytime heat of solar energy is stored in the bodies of water during the day. At night when hydrogen bonds reform in the waters of the world; that stored energy is released back into atmosphere keeping evening temperatures moderate.

In a desert environment where no water is around there are broad shifts in temperature; in the day 130 C ; in the evening 30 C. But in coastal areas near water the range is much narrower with day time temps around 80 and night time temps around 55 C. Water in tose areas absorbs heat in the day so it doesnt go much above 80 . then at night the wate releases the absorbed energy back into the night so nighttime temps stay above 50.

Page 49 know the principles behind evaporative cooling. (the idea that the fastest molecules leave as they evaporate bringing the average kninetic motion down and hence temperatures lower)

Page 50 know why water in its solid from ice is less dense then water in its liquid form

Know exactly how much less dense ice is than liquid water (page 50 1st paragraph in left column of page) 10% less dense for a given volume. We say that in liquid water at the higher temp, water molecules break bonds and slip closer together making them more densely packed. In ice the bonds are rigid no slipping occurs so molecules are held at greater distances from one another as compared to the situation in a liquid sample.

Page 50 know that water is the solvent of life. Know the terms: solvent, solute, solution, aqueous solution Page 51 be able to explain how a solute such as NaCl dissolves when placed in water. In your explanation talk about waters polar covalent bonds, its partial dipole charges and how these charges interact with the Na cation and the Cl anion.

Know the terms hydrophobic and hydrophilic? Can a hydrophobic solute be dissolved in a polar solvent? Why? or Why not?

Molar Concentrations

Know about molarity and how to determine solute concentrations. Know the example on page 51 bottom right hand column where they calculate the number of grams of sucrose that are needed to make a 1 molar solution in 1 liter.

In this regard first be able to calculate the molecular mass of sucrose C12H22O11. In the book this comes out to 342 daltons or 342 grams per mole. (there are 6.02 x 1023daltons in 1 gram) Know where on a periodic table to find the molar mass Know that a mole is equal to 6.02 x 1023 atoms or molecules So 342 grams of sucrose weighed out is the same as 1 one mole or 6.02 x 1023 molecules of sucrose. A 1 molar solution is defined as 1 mole of solute in 1 liter of solvent. Calculating molarity Part 1 : Calculating molar mass of a molecule is often required to do some molarity problems. The video below shows you how to calculate molar mass http://www.youtube.com/watch?v=F9NkYSKJifs Part 2 : Many times molar mass is given and other things are varied. Below are some videos that demonstrate how to solve different molarity problems where the molar mass is given but numbers of moles are sought ; or special volumes are used in the problem http://www.youtube.com/watch?v=raq2Y1yBQrQ

http://www.youtube.com/watch?v=8oTqwBAvbnY http://www.youtube.com/watch?v=S12wa4oe1fE

Based on these examples then: 342 grams of sucrose put in a liter of water will create a 1 Molar sucrose solution. (1 mole in a liter) If we wanted to make a 0.5 liter at 1 molar we would add of 342 grams in 500 ml

If we wanted to make 2.5 liters @ 1 molar, we would add 2 x 342 grams plus 342 grams of sucrose in 2.5 liters of water. To make a 2 Molar solution we would need 2 moles of sucrose in a liter of water. Hence we would add 2 x 342 grams in a liter of water

Page 53 Know what acids and bases are. Know that when acids dissolve in water they donate additional H+ to the solution that joins with water to form H3O+ ions. Acidsincrease the H+ aka H3O+ concentration such that there are more H+ than OH- ions

A substance that reduces the H+ or H3O+ concentration by accepting protons is known as a base.

In pure water the H+ concentration is 10-7 molar and the OH- is perfectly balanced at 10-7 molar. Acids will increase the H+ let say up to 10-2 when this occurs the OH- will correspondingly go down 5 units to 10-12

Instead of using actual concentration we can refer to H+ concentration via a logarithm expression termed the pH or potential hydrogen value

pH = -Log[H+]= negative log of the H+ concentration

Low pH values represent high H+ concentrations because 10-1 is actually greater than 10-6 . The -Log[101 ]= 1 -Log[10-6]=6 So pH 1 equals 0.1 Molar H+ but pH 6 equals .000001 Molar H+

Also every pH value change is based on Log base 10 so each pH change is a 10 fold change.

Page 54 Know Figure 3.10 thoroughly including all examples and their pH values.

Page 54 Know what a buffer is.

Be familiar with amino acids and H2CO3 carbonic acid as natural buffers of the blood stream

Page 55 Read (BUT MATERIAL WILL NOT BE ON TEST) Chapter 4

Page 58 Know that living organisms are made up of chemicals based mostly on the element carbon. This carbon originates in the atmosphere as CO2. Plants take it in and integrate this atmospheric carbon into organic chemicals such as carbohydrates, ie sugars. Animals eat these Carbon products when they eat the plants. Animals restore Carbon to the atmosphere when they respire out CO2. Plants can also do this at the cellular level via cell respiration which produces CO2 which the plant can either release to the environment or use in the synthesis of more sugars. These events represent the carbon cycle.

Page 58 Know that organic chemistry is the branch of chemistry that specializes in the study of carbon compounds such as the sugars produced by plants and metabolized by both animals and plants. CO2 is considered inorganic even though it contains carbon. This is based mostly on the historic principle of vitalism, which assumes organic compounds can only be produced within living organisms and not via artificial synthesis in the lab. Since CO2 can be produced artificially it was and is still considered inorganic. We now know that most organic compounds can also be produced in the lab artificially so by todays standard we would need to alter our definition of what is organic if we wish to not consider CO2 organic. After all CO2 does contain carbon. But the majority of organic compounds also contain hydrogen. These range from hydrocarbons like gasoline to biopolymers such as proteins and lipids.

Page 59 Read (BUT MATERIAL WILL NOT BE ON TEST)

Page 60 Know how to write the molecular formula for hydrocarbons such as methane (CH4), Ethane (C2H6) and ethene (C2H4) (see figure 4.3)

Page 60 Know how to write the stuctural formula for hydrocarbons such as methane (H2-C-H2), Ethane and ethaene (see figure 4.3 for actual drawn structures))

Page 60 Know the difference between a structural formula and a molecular formula.

Page 60 Know that all molecules including hydrocarbons form definite shapes such as tetrahedrons, trigonal planar and linear arrangements. The shapes and isomeric forms of molecules play a role in their biological functionality.

Page 60 know that carbon which has a valence of 4 can form 4 bonds. When it shares these electrons it form s covalent bonds. It is this reason that carbon can from large branched complex molecules. Carbon chains form the skeletons of most organic molecules. These chains are not always linear;some form rings and are called cyclical.

Page 60-63 Know the characteristics of hydrocarbons as an organic compound group.

a) Hydrocarbons are all non-polar hydrophobic compounds (page 61) b) Hydrocarbons all have low melting points and boiling points and low solubility in water. (See PowerPoints and class notes not in textbook) Lacking polar or ionic dipoles or charges these compounds can only interact via van der Waals forces which are weak and easy to break. Hence very low temperatures provide sufficient energy to break these molecules apart and shift them from the liquid state to the vapor state. Also lacking polar or ionic dipoles or charges means no way to interact with water molecules which carry positive and negative partial charges. Hence these hydrocarbons can not interact with water, they can not dissolve in it. c) Hydrocarbons are major components of petroleum or fossil fuel. All hydrocarbons are good fuels . ie butane, propane, octane which serve as lighter fluid, fuel for cook outs; and gasoline respectively (page 61) d) Page 61 .Living organisms have molecules which contain segments that are 100% identical to hydrocarbons like octane (gasoline). The molecules known as FATS or adipose have long hydrocarbon tails attached to a non-hydrocarbon region. Neither petroleum or FAT dissolve in water. FAT is used in living organism as stored fuel. Petroleum likewise functions as a fuel. (See figure 4.6) e) Many biological organic compounds are converted hydrocarbons having a carbon chain skeleton but substituting other atoms for the hydrogen s on the hydrocarbon chain with Oxygen, and Nitrogen. Usually this is in the form of functional groups (page 64). These substitutions change the physical and chemical properties of the hydrocarbon. They become less non-polar and gain

water solubility along with increased Boiling and Melting points and may become less flammable. Example Octanoic acid a fatty organic acid and octane are very different, the latter being 100 times more flammable than the former. f) Page 62 Figure 4.7 and the text on this page: Know the three different types of isomers. Be able to draw examples of each type. Be able to define and compare each type g) Page 63 figure 4.8 know the relationship between eantiomer shape and pharmaceutical efficacy. Example Ibprofen Only the Sor L eantimoer is effective for pain treatment. The D< span> or R form has no effect. Example 2 Allbuterol: only the R enantiomer form aka D form is effective against Asthma; the S or L form does nothing to help asthma.

Page 64- 65 Know all the organic functional groups. Be able to draw all the functional groups or to recognize a functional group from a drawing.

Be able to list examples of molecules that are representative examples of molecules that have a specific functional groups. For example on page 64 in figure 4.9 under Hydroxyl. Ethanol a alcohol is listed as a representative example that contains a hydroxyl group. Ethanol = CH3CH2OH.

Be able to distinguish between aldehydes and ketones (page 64) and give examples of molecules that have these functional groups.

Know any organic molecule that gains a carboxyl group automatically becomes an Organic acid) Carboxyl groups donate the H+ from their OH portion leaving hydrogens electron behind with the C=O and Oxygen. This is written as COO- and H+ anions and cations.

Know any organic molecule that gains an AMINO functional automatically becomes an Organic base) Amino groups accept H+ protons becoming NH3+ or NH4+

Know that sulhydryl groups are seen frequently in protein structures where disulfide bonds form between different protein segments to fold the protein into its 3D shape.

Know that any organic molecule that gains a phosphate group automatically becomes a ACID< span> The phosphate has 3 OH hydroxyls. In solution the H of the OH groups ionizes as a proton into solution leaving the electron behind and makes the phosphate carry a negative charge. Phosphates are important parts of DNA and RNA molecules and of the cell energy molecule known as ATP. Cell membranes are made up of phospholipids. Phosphate groups are important to membrane function providing the hydrophilic part of a membrane that faces out or inside a cell where water is located.

Know that methyl groups are important to the expression of genes. DNA which is methylated does not express genes which means those regions will not be able to code for new proteins.

Page 66 Know about ATP, what it does , and how it works as a cell energy molecule.

Chapter 5

Page 68 Know the 4 classes of critically important large molecules are carbohydrates, lipids, proteins and nucleic acids. The largest are the carbohydrates, proteins and nucleic acids which are called macromolecules. Lipids are smaller and not relatively as large as the others.

Page 68-69 Know that: macromolecules are polymers built from momomers. Know that a polymer: is a long molecule consisting of many identical building blocks (aka monomers) linked by covalent bonds. Analogy is a train which is a chain of identical cars linked together.

Page 69 Know that: The Monomers of large macromolecular polymers are represented by small molecules like amino acids or nucleotides or monosaccharides which are the repeating units that serve as the identical building blocks that are to be linked together to build the macromolecule/polymer.

Page 69 Know that: To connect one monomer to a second monomer chemically requires a process known as a dehydration or condensation reaction. This process removes a water molecule and forms a new covalent bond linking/chaining them together. If this occurs again then the chain will have 3 monomers linked together; if another dehydration occurs then 4 monmers will be linked together via covalent bonds. In this way polymers which may have 100s of such links can be formed. The bonds formed by dehydration that link monomers have many names; in carbohydrates the link between monosaccharides are called glycosidic bonds; in proteins the link between amino acids are called peptide bonds, in nucleic acids the link between nucleotides are called phospoester bonds. All of these are created via dehydration

Page 69 Know that: To disconnect a monomer from a polymer; to remove it off the polymer chain requires the opposite to dehydration ; a reaction called a hydrolysis reaction. In this reaction water is added across a bond restoring the functional groups to the molecules and breaking the covalent bond that links one monemer to a second monomer. When you eat a steak for dinner you are eating protein a macromolecule; apolymer. When that protein reaches your stomach enzymes like pepsin begin to hydrolyze or chemically digest that protein by adding water across the bonds that link amino acids together in the protein. After hydrolysis the only thing that remains are the individual amino acid monomers the polymer is completely disassembled.

Know that is the sequence of monomers that creates macromolecular diversity. Proteins are only built from 20 different monomers but occurring in infinite distinct sequences.

Carbohydrates:

Know/Learn all that follows about Carbohydrates:

Page 69 Know that Carbohydrates consist of sugars and polymers of sugars. The term Carbohydrates means hydrates of carbon indicating that Carbohydrates are combinations of water and carbon. Also in chemistry Carbohydrates are often called polyhydroxy aldehydes and ketones which indicates that sugars the building blocks of Carbohydrate polymers structurally have many Hydroxyl groups and also have atleast one aldehyde group (a carbonyl at the chain terminus) or atleast one ketone group (a carbonyl within the chain)

There are three classifications of Carbohydrates

Page 70

a) Monosaccharides: or simple Sugars (CH2O)n Examples include: Glucose C6H12O6 glucose is main fuel for all cells Galactose C6H12O6 > > > > > > > > > > > > > > > > > > > > > > & lt; span> is a part of lactose can be used as fuel Fructose C6H12O6 > > > > > > > > > > > > > > > > > > > > > > & lt; span> is used to make sucrose it also is very sweet and can be used as fuel Ribose C5H10O4 > > > > > > > > > > > > > > > > > > > > > > & lt; span> is used to make RNA and ATP the energy molecule . also comes as deoxyribose which is used to make DNA.

Other terms to know: Triose: 3 carbon sugar, example: glyceraldehyde Tetrose: 4 carbon sugar, example: Threose, Erythrose Pentose: 5 carbon sugar, example: ribose, ribulose Hexose: 6 carbon sugar example: galactose, glucose, fructose Aldose: sugar with aldehyde group, Example: glucose, galactose Ketose: sugar with ketone group, Example: fructose, ribulose, dihydroxyacetone

Page 71 figure 5.5

b) Disaccharides: 2 monosaccharides linked together via a dehydration reaction forming glycosidic bonds between them. Examples include: Sucrose is made of glucose and fructose linked via alpha 1-2 glycosidic bond. Aka table sugar. Sweet taste. Plants transport sugar from leaves to roots as sucrose. Lactose is made of galactose and glucose linked via a beta 1-4 glycosidic bond. Known as milk sugar. Many peolple who are lactose intolerant can not digest the beta glycosidic bond between the galactose and glucose sugars. Does not taste very sweet Maltose is made of glucose and glucose linked via an alpha 1-4 glycosidic bond. Aka grain or malt sugar. Found in wheat or barley grains used to make Malt liquor and beer..

Page 71-74

c) Polysaccharides: many monosaccharides linked together via a dehydration reaction forming glycosidic bonds between them. Examples include:

Cellulose: Plants use cellulose in their cell walls for support and stability. Cellulose is a simple molecule consisting of, simple linear chains of glucose monomers held via beta glycosidic linkages; it is undigestable in many organisms. Some organisms carry bacteria or protists in gut that allows digestion of cellulose because these organisms make cellulase the enzyme that can digest cellulose. Humans lack enzymes like cellulase and also lack the microorganisms that make cellulase and hence can not digest cellulose Cellulose represents a structural polysaccharide . It is NOT used for fuel or energy by the organism that synthesizes it but rather it uses it as a structural support for cell walls. Microfibers are created from intertwined cellulose chains which are straight and never branched and make strong building materials. paper and cotton are strengthened by cellulose fibrils. Amylose- simple form of starch, simple linear chains of glucose monomers held via alpha glycosidic linkages. Stored in plastids, used as a stored form of energy. Amylose represents a storage polysaccharide . It is used for fuel or energy by the organism that synthesizes it. Plants store sugar for later use as amylose or amylopectin. Animals can eat amylose and amylopectin and digest the alpha glycosidic bonds releasing glucose for use as fuel

Amyolpectin- complex branch/chained form of starch found only in plants. Uses alpha glycosidic links of monomers and alpha 1-6 links. Stored in plastids, used as a stored form of energy. Amylopectin represents a storage polysaccharide . It is used for fuel or energy by the organism that synthesizes it. Chitin- found in fungi cell walls .uses amino sugars such as glucosamine. Glucosamine monemers are linked to one another via 1-4 beta glycosidic bond Also used for sutures and also used as support molecule in an insects exoskeleton/outer skin. Chitin represents a structural polysaccharide . It is NOT used for fuel or energy by the organism that synthesizes it. Glycogen, Stored in liver and muscle; found only in animals, used as a stored form of energy. Highly btanched with alpha 1-4 and alpha 1-6 glycosidic links. Glycogen represents a storage polysaccharide . It is used for fuel or energy by the organism that synthesize it. Animals store sugar for later use as glycogen

Lipids

Page 74

Know the following

Know that lipids all share two important traits: 1) all lipids are nonpolar, 2) all lipids are hydrophobic, (they all mix poorly or not at all with water). They are mostly hydrocarbons but may have some polar bonds with oxygen..

Examples of Lipids include;

Fat or Adipose- Triglycerides Oils or Fatty acids- Long hydrocarbon with carboxyl group, ex. Palm Oil; Coconut Oil Waxes- Bees Wax, Car Wax Pigments- sudan IV, chromolipids, lipofuscins. found in liver cells Anionic detergents, Soaps

Phospholipids- membrane structures Steroids: Cholesterol, Estrogen/Estradiol Testosterone

A. Know that fats are constructed from a glycerol molecule which is an alcohol with three hydroxyl groups and also from 3 fatty acids or oil molecules. The fatty acids are mostly hydrocarbons with 14- 20 carbons in the carbon chain (similar to gasoline or petroleum) but with a carboxyl group on one end. The C-H bonds are non polar along the main axis of each fatty acid and hence water molecules can not form hydrogen bonds with the fatty acids on the fat molecule and so water and fats separate from each other if mixed. To chemically form a fat molecule a dehydration reaction between one of the hydroxyls (OH) on the glycerol and the OH on the carboxyl of the fatty acid occurs removing water and creates an ester bond. This must occur two more times between the other OH groups on glycerol and the other 2 fatty acids. The final fat molecule has 3 fatty acids ester linked to glycerol. It is because of this that FATs carry the chemical name Triacylglycerol or Triglyceride< /b> Functions of Fat: Energy Fuel in stored form Insulation for body Protection of organ systems from blunt trauma

Page 75 Know that the fatty acids attached to glycerol on a fat molecule may be saturated or unsaturated. Solitary Fatty acids (oils) also may be saturated or unsaturated

Know that a saturated fatty acid has no carbon carbon double bonds and has as many hydrogen atoms as possible bonded to the carbons in the fatty acids hydrocarbon chain.

Know that an unsaturated fatty acid has one or more carbon carbon double bonds. i.e. C=C with one fewer hydrogen atoms on each double bonded carbon.

Most naturally produced unsaturated fatty acids fats form cis double bonds with the remaining hydrogens appearing on the same side of the double bond and creating a kink or bend in the molecule. It is this bend that keeps the fatty acid molecules from getting very close to one another and thus

keeps unsaturated fats and fatty acids as liquids at room temperature. Saturated fatty acids dont have this bend or kink so they lay flat on top of each other , very tightly associated and hence saturated fats or fatty acids will formsolids at room temperature

Know that fats made from saturated fatty acids are called saturated fats. Animal fat is usually saturated. Lard and Butter are examples. They are solid at room temperature

Page 76 Know that: Plant and Fish FAT is liquid at room temperature due to the fact that the fatty acids in the triglycerides are unsaturated. Examples: olive oil, cod liver oil. Fish oils containessential fatty acids for humans and also are less likely to cause the cardiovascular problems like saturated and trans fatty acids cause. i.e. Omega 3 fish ol which is unsaturated at carbon 3 position, it is essential for humans and it has all cis configurations around its double bonds.

Hydrogenation puts hydrogen atoms back on to the unsaturated fats fatty acids removing the double bonds. If a plant fat is hydrogenated it becomes solid at room temperature. Example: Peanut butter or Margarine.

In making solid margarine and peanut butter and other hydrogenated vegetable fats, the hydrogenation process is sometimes incomplete creating mostly solid hydrogenated fat but also some incomplete trans rather than natural cis unsaturated fats. The trans fats are difficult to metabolize and can become incorporated easily in atheromas leading to vascular stenosis (blockage) and cardiovascular complications such as stroke and heart attack.

Page 76

Phospholipids Know the following about phospholipids

Know that cells depend on phospholipids as the basis for their membrane structure. Know that each phospholipid consists of a diglyceride with a negatively charged phosphate group and a positively charged base called choline. Glycerol is the backbone of these molecules. Two rather than 3 fatty acids are attached via ester links to glycerol. The third position on glycerol is bonded to a phosphate group via dehydration reaction and a phosphoester link/bond.

Know that the two (2) phospholipid fatty acid tails are nonpolar and hydrophobic but the phosphate and choline base at position 3 are charged and polar and hydrophilic. This arrangement creates a dual nature that fits perfectly with membrane function. Know that Cell membranes consist of a bilayer of phosphoplipids. The charged phosphate and choline parts of these phospholipids face outside or inside the cell where polar water is located. Since the phosphate and choline are charged and hydrophilic they interact naturally with this aqueous environment. The tails of the phospholipids face the interior of the membrane and since they are hydrophobic they exclude water and other polar molecules. In essence, the core of the phospholipid bilayer is like a layer of wax in the middle of the membrane which prevents any large polar molecules and water, to an extent, from passing in or out of the cell. These represent the basic functions of a membrane, which is to regulate passage of materials between the cell and its surrounding. Cells could not exist without phospholipids which creates this boundary between a cell and its environment.

Page 77

Steroids:

In class we watched a video about a pregnant man. In reality this was a pregnant woman who was transgender. By taking steroid hormones like testosterone she was able to make her body express male secondary characteristics such as a deeper voice, hair on the chest and face and legs, breast reduction, shoulder broadening, hip straightening etc.

Page 77 Know that: Testosterone and other steroids like estrogen and the molecule they both are derived from cholesterol, all represent lipids because these molecules are hydrophobic and nonpolar. Know that: Cholesterol and all its derivatives have a 4 ring system with 3 fused six membered rings fused to a single five membered ring. Cholesterol also has a hydrocarbon tail that allows it to insert into the

phospholipid bilayer of animal membranes. Know that: Cholesterol plays a role in animal membrane fluidity and function. Its derivatives estrogen and testosterone are sex hormones that influence development of male or female characteristics. Anabolic steroids which are not natural may lead to heart disease and other health complications. High levels of cholesterol in blood may contribute to atherosclerosis and heart disease. Saturated fats and trans fats elevate cholesterol levels. The liver usually produces cholesterol but we also obtain it from the foods we eat. Page 77

Proteins

Every dynamic of a living being depends on proteins. All cellular activities are carried out by proteins. Every metabolic reaction is catalyzed by Enzymatic proteins. Genes code for proteins; genes contain the blueprint to build all cellular proteins. But it is the proteins themselves that do the actual work of growth development reproduction and energy utilization. Every cell builds thousands of different proteins based on genetic instructions; each with a unique structure and functional purpose.

Page 77 Be able to define what a protein is and how it is distinct from a polypeptide

Know that proteins are polymers built from amino acid monomers. Such polymers are referred to as polypeptides. If the polypeptide by itself has a specific cellular function it is then referred to as a protein Some polypeptides need other polypeptides to join together with them for them to be functional proteins.

Know that all proteins use the same pool of 20 amino acids for their construction Page 78 figure 5.15 Be able to list and or describe 3 organismal functions that proteins typically carry out: i.e. Transport proteins like Hemoglobin which carry oxygen in red blood cells. Or Defensive proteins such as antibodies that tag foreign invaders found in bodily fluids.

Be able to draw the basic structural formula for an amino acid (bottom of page 78 left column). Be able to identify the parts of a drawing of an amino acid with unlabled arrows pointing to its structures.

Page 79 Know the three major classifications of amino acids (below) which are based on the R group or side chains chemistry.

a) 1) Nonpolar hydrophobic non polar side chains, Examples: Valine proline b) 2) Polar- side chains have atoms with partial charges(dipoles) Example: Serine c) 3) Electrically charged- side group carries a full +/- electric charge Example: Aspartate(-) or Lysine(+)

Page 80

Peptide Bonds: Forming polypeptides/proteins

Be able to describe the chemical process required to join/link amino acids together (figure 5.17). A dehydration reaction occurring between the Amino end of one amino acid and the OH on the carboxyl end of a second amino acid produces a peptide bond with water as a byproduct. Peptide bonds are really amide links which all have a carbonyl covalently linked to an amine group (R-H2N-C=O).

When many peptide bonds are formed between 10 or more amino acids we produce a polypeptide. Every polypeptide has an amino terminus and a carboxy terminus at opposite ends. Polypeptides can be as short as 10 and as long as 1000 amino acids chained together. The portions of the linked amino acid chain that includes the amino group; the alpha carbon and the carboxyl groups but NOT THE R OR SIDE CHAIN is called the polypeptide backbone (see page 80 figure 5.17). The backbone is very important to forming the secondary level of protein structure via hydrogen bonding between atoms in the backbone (see page 82 right hand column figure 5.20)

Page 80

Levels of protein structure

A proteins shape/structure determines its functions. Chains of polypeptides which are linear sequences of amino acids must fold into globular or fibrous 3 dimensional proteins of very specific shapes/structures that fit the functions they must perform.

Know all the details of each of the levels of protein structure which follow below:

Primary

Page 80-82

Every polypeptide/protein has its own unique sequence of amino acids. Frederick Sanger was the first scientist to figure out the exact amino acid sequence of insulin.

The alpha chain of insulins sequence based on Sangers work:

H2N-Gly-ile-Val-Glu-Gln_Cys-Cys-Ala_Ser-Val-Cys-Ser-Leu-Tyr-Gln_Leu-Asn-Tyr-Cys-Asn-COOH

We say that the above represents the Primary Structure of insulin; its exact amino acid sequence; it shows which amino acid is 1st 2nd 3rd 4th etc in the specific sequence that represents insulin and only insulin. No other protein in the world has this exact sequence of amino acids.

In 1958 Sanger won the Nobel Prize in Chemistry for his work.

Know that the primary level of protein structure can be critical to normal cell function. Even switching one amino acid in the sequence of a protein can have grave consequences. For example in sickle cell

disease (Page 84 figure 5.21) switching glutamate which is the 6th amino acid in the sequence of the beta globin protein to valine results in causing the final protein (hemoglobin) to stick to itself forming stiff rod like fibers in the red blood cells that stretch the cell making it bend into a sickled shape and sometimes causing the red blood cells to burst.

Secondary

Page 82

To reach the secondary level of protein structure, the atoms in the amino acid chain that include the amino group; the alpha carbon and the carboxyl groups but NOT THE R OR SIDE CHAIN (the polypeptide backbone) (see page 80 figure 5.17) form hydrogen bonds between other atoms in the same backbone (see page 82 right hand column figure 5.20) These are intra molecular weak bond associations. Typically this results in two main structural forms:

a) 1) alpha helices b) 2) beta pleated sheets

Polypeptide chains are variable in their numbers of regions that are alpha helices versus non-helical or sheeted regions. Collagens polypeptides are 100% alpha helix with no beta sheets. Transerythrin (page 83 top illustration) has only one small stretch with a helix and two major sections of beta sheets.

Tertiary

Page 83

In tertiary structure polypeptides fold into a unique 3 dimensional shape

To reach the tertiary level of protein structure the polypeptide in its primary forms and secondary structural regions must interact with one another via amino acid side group interactions. An amino acid on the left side of the polypeptide chain with a positively charged R group/side chain may interact with an amino acid located further down on the right side of the polypeptide chain with a negatively charged R group/side chain (page 83 bottom left illustration). This type of intra molecular interaction is termed an 1) ionicinteraction. The other three possible side chain interactions are 2) disulfide bondsa covalent bond created between thiol groups on opposing amino acid side chains; 3)Polar/dipoledipole interactions such as hydrogen bonds; 4) hydrophobic interactions between non-polar side chains- these interactions usually occur in the interior (core) of a protein away from water or the polar environment of the cells cytoplasm. These interactions are weak bonds such as van der Waals forces aka London Dispersion forces.

Quaternary

Page 83

To reach the Quaternary level of protein structure requires two or more polypeptides interacting to form a functional protein. Each polypeptide by itself is non functional but when joined together in a specific conformation form a functional whole. Examples include Hemoglobin which consist of four polypeptides two alpha chains and two beta chains that when put together in the presence of iron Fe creates a functional protein that can carry oxygen. Collagen is perhaps the second best known example of quaternary protein structure. 3 chains , each completely an alpha helix intertwine to form this important protein which is found as the girders of connective tissue of skin, bone, tendons, and ligaments. The forces that hold the polypeptides to each other are the same as seen in tertiary structure; 1) ionic 2) disulfide bonds; 3) Polar/dipole-dipole interactions such as hydrogen bonds; 4) hydrophobic interactions between non-polar side chains

Page 84

Denaturation

Proteins only function when they are folded into their correct shape. If we heat a protein or expose it to high or low pH we will disrupt the hydrogen bonds and other polar and ionic interactions and van der Waals forces that hold the protein its unique three dimensional shape. The H+ and OH- cations and

anions found in acidic solutions and basic/alkaline solutions strongly disrupt the ionic interactions between +/- charged side chains that hold proteins together in their proper shape. Placing a protein in acid will cause it to unfold/denature exposing its hydrophobic core and making it separate out of solution as a precipitant. If you place a raw egg in lemon juice the proteins will denature and precipitate out as a solid precipitant. This is the same principle as oil separating from water. The non polar (oil like) side chains are exposed in the unfolded/denatured protein. When they contact the polar aqueous solution it causes them to separate and cluster together away from the water as a solid mass of precipitant.

Page 85 Know that in cells proteins often require chaperones to fold correctly in to the proper shape (see figure 5.23)

Page 86 know that X-Ray diffraction is a tool used by chemist to figure out the specific shape of a folded protein

Nucleic acids

Page 87

Know that DNA and RNA are the major nucleic acids found in cells Know that DNA a nucleic acid is found in structures called chromosomes in association with proteins. Know that each chromosome consists of a linear or circular strand of DNA which is in turn composed of chains of building blocks called nucleotides. Know that there are 4 nucleotides used in DNA described by the letters A,C G and T.

Know that each nucleotide consists of a pentose sugar ( 5 carbon sugar); a phosphate group; and a nitrogenous base. The sugars are either deoxyribose which is missing an oxygen atom on its second carbon, or ribose which has a OH hydroxyl on its second carbon. The bases are adenine,guanine cytosine and thymine in DNA or adenine, guanine cytosine and uracil in RNA.

Know that Adenine and Guanine are Purinestwo ringed structures (PuGA) Know that Cytosine Uracil and Thymine are Pyrimidines- one ring structures (PyCUT)

Linking these nucleotides together in variable sequences creates long chains of nucleotides or aka nucleic acids such as a DNA/RNA chains . To form DNA requires that 2 chains of nucleotides be interwoven as a double helix.

When interwoven the two DNA chains pair As with Ts and Gs with Cs

Hence if we know one chains sequence we can infer the second chains sequence.

i.e. if one chain is 5G CCCCATTGCTTA3 then the second chain must be ..3CGGGGTAACGAAT5& amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; amp; lt; /p>

note: the chains run in anti- parallel/opposite directions

When an A from one chain pairs with a T from a second chain it does so by hydrogen bonding

Very long chains of connected nucleotides create chromosomes. Know that along the length of a chromosomes long chains of nucleotides ( DNA strands ) are small units called genes. Each gene codes or contains instructions or the blueprint on how to build a specific protein. A chromosome may be 1-200 million nucleotides long, but each gene is only about 10,000 nucleotides long. So a chromosome may have from 100-10,000 genes each coding for a specific protein. When an organism grows and develops from a single fertilized egg it is the creation and actions of these thousands of proteins coded for by the

genes that actually carry out the building events and maintenance activities of the cell that will make that single cell become thousands of cells and that will orchestrate the formation of the various bodily structures. The 4 nucleotides of DNA when chained in sequences create words or instructions for the cell on how to build these proteins. Like an alphabet of only four letters words like ACCGGTTGCCCATG which dont mean much to us, such words have very specific meanings to a cell engaged in protein synthesis, just as words created from our 26 letter alphabet have specific meanings for us. ..