BIO 204 - UNIT 1

1) At the subatomic level, what is an ionic bond?

· Ionic bond is the attraction between two opposite charges, cation (positively charged ions) and anion (negatively charged ions). · EX) Na interacts with Cl. Na has a total of 11 electrons, with 1 valence electron. Cl has 17 electrons with 7 electrons in its valence shell. Na transfers its electron to Cl and the two atoms end up with their valence shells complete. One negative electron moves from Na to Cl. Cl now has an extra electron, giving it a negative charge.

1) What distinguishes aldehydes from ketones?

· Ketone is within the carbon skeleton. Carbon is bonded to two other carbons. · Aldehyde is at the end of the carbon skelete. Carbon is bonded to carbon and hydrogen.

1) At the molecular level, explain what is meant by the term "like dissolves like".

A solute will dissolve best in a solvent that has a similar chemical structure to itself.

Secondary Structure of Protein

Alpha helix - delicate coil held together by hydrogen bonding between every fourth amino acid EX) keratin in hair · Local folding, hydrogen bonding · Default structure that usually forms · H-bond between functional groups drive the structure · Bulky R-groups or charged amino acids disrupt H-bonds and prevent the helix structure (ex: proline) Beta pleated sheet - two or more segments of the polypeptide chain lying side by side are connected by hydrogen bonds between parts of two parallel segs of polypeptide backbone. EX) silk protein of spider's web · R groups alternate in orientation (180 degree) · Hydrogen bonds staggered

Monomer of Proteins

Amino acids

Tertiary Structure of Protein

Three-dimensional structure that includes larger folders, ionic bonds, covalent bonds · Ionic bonds, hydrogen, covalent, and hydrophobic interactions drive the formation of this structure · Since the backbone folds back on itself, the distant groups become close enough to interact · Protein folding occurs to maximize interactions, polar molecules interact with water · Most proteins can carry out their function with the tertiary structure

Monomer of Carb

monosaccharide

Monomer of nucleic acids

nucleotides

Trans fats

o Many foods are "hydrogenated" meaning a hydrogen is added to allow them to solidify. EX) peanut butter, margarine § This unnatural process creates saturated fats but also unsaturated fats with trans double bonds à trans fats § Trans fats contribute to many health issues

Collagen

strong fibers outside cells

A DNA

· A DNA is a right-handed helix. o More nucleotides per turn than B DNA o This is what DNA looks like when it is copied to become RNA.

1) At the subatomic level, what is a covalent bond?

· A covalent bond is the sharing of a pair of valence electrons by two atoms. These covalent bonds create molecules. · EX) When two hydrogen atoms approach each other, their 1s orbitals overlap and share their electrons. Each hydrogen is now associated with 2 electrons to complete their valence shell.

1) What is the relationship between the structural diversity found in proteins and the functional diversity they exhibit?

· A protein's specific structure determines how it works. · The function of a protein depends on its ability to recognize and bind to some other molecule. o EX) the ability of an antibody to bind with a foreign substance

Compare the arrangement of phosphate groups in adenosine triphosphate and adenosine diphosphate. What is the biological significance of adenosine triphosphate?

· ATP is attached to a string of three phosphate groups. · ADP is two phosphate groups. · ATP is important to store energy, storage the potential to react with water that releases energy that can be used by the cell.

1) How is the synthesis of large biological macromolecules like carbohydrates and proteins an example of a dehydration reaction?

· Large biological macromolecules - carbohyrdates, prteins, nucleic acids - are chain molecules called polymers. These polymers are long molecules consisting of several monomers linked together. · The monomers are joined together through dehydration to covalently bond the monomers together. o One monomer provides a hydroxyl group, while the other monomer provides a hydrogen.

1) What are monosaccharides and how are pentoses different from hexoses? Which class does glucose fall into?

· Monosaccharides - simple carbohydrates/sugars · Glucose is the most common monosaccharide · Depending on the carbonyl group location, a sugar is either an aldose (aldehyde sugar) or ketose (ketone sugar) o Glucose is an aldose o Fructose is a ketose · Size of carbon skeletons range from 3 to 7 carbons. o Six carbons = hexoses o Three carbons = trioses o Five carbons - pentoses

1) What is a sphingolipid, and how is its structure related to that of a phospholipid?

· Shingolipids are also important components of cell membranes · Similar structure to phospholipid except glucose is replaced with sphingolipid.

1) Explain the observation that a mutation that changes one amino acid in a protein could have A) no effect on the protein's structure/function, B) a moderate effect or C) ablate function altogether. What factors might allow you to predict the potential consequence of any such change?

· Slight changes in primary structure can affect a protein's shape and ability to function. · This depends on which amino acid and the location of the mutation. If the mutation occurs in the area where catalyzation occurs, this may affect function altogether.

1) What is cholesterol, and how does it affect the physical properties of the cellular membranes that it is a part of?

· Sterioids - lipids characterized by a carbon skeleton consisting of four fused rings o Different steroids are distinguished by the particular chemical groups attached to the four fused rings · Cholesterol - type of steroid that is crucial in animals and a precursor to synthesis other steroids (such as sex hormones). o Synthesized in the liver and is obtained from the diet o High levels can contribute to atherosclerosis.

1) What chemical characteristics cause a substance to dissociate a hydrogen ion?

· Strong acids dissociate.

1) What distinguishes structural isomers from stereoisomers like cis/trans isoforms or enantiomers?

· Structural isomers - same molecular formula, but differ in covalent arrangements of carbon skeletons. May also differ in the location of double bonds. · Stereoisomers - same molecular formula, different spatial arrangements o cis: same side o trans: opposite side o rotational restriction occurs · Enantiomers - mirror image isomers that have a chiral carbon bonded to 4 different groups o Different arrangements have different interactions and different biology

1) Explain how the difference in structure between large, structurally simple polysaccharides (think starch or cellulose) and small structurally complex polysaccharides (like those found on the cell surface glycoproteins) is related to their distinct functions.

· Structurally simple polysaccharides serve as storage material and hydrolyzed as needed to provide sugar for cells. - Storage Polysaccharides o This is seen in starch and cellulose. o The simple structure allows for the hydrolyzing of one monomer to provide energy when needed. o Synthesizing starch allows plants to build up surplus gluclose for cellular fuel/energy. This can be later used by hydrolysis, breaking the bond of the glucose monomer. § Amylose (plants) - simpliest form of starch that is unbranched § Amylopectin (plants) - branched with 1-6 linkage at both branch points § Animals and humans can also hydrolyze plant starch, which is used for energy o Glycogen is stored in liver and muscle cells. Functions similar to amylopectin and is extensively branched. § Hydrolysis occurs to release glucose which explains why it is extensively branched - more free ends available for hydrolysis § Glycogen is usually depleted within a day and needs to be replenished by eating

What chemical forces are primarily responsible for the structural stability of the DNA double helix?

· Sugar phosphate backbones are on the outside of he helix · Nitrogenous bases are paired in the interior of the helix · The two strands of polynucleotides are paired by hydrogen bonds between the paired bases.

What is the "sugar-phosphate backbone" of a polynucleotide, and how does it specify both a 3' (three-prime) and a 5' (five-prime) end?

· Sugar-phosphate backbone is the repeating pattern of sugar-phosphate units formed when adjacent nucleotides are joined by phosophodiester linkages (phosphate group links sugar of two nucleotides). · Two ends are very different from each other - one end has a phosphate attached to 5' carbon and the other has a hydroxyl group attached on a 3' carbon · These provide a built-in directionality along its sugar phosphate backbone.

1) What is a sulfhydryl group? What property(ies) does it confer to a molecule it's a part of?

· Sulfhydryl group (thiol) à Bonded to a sulfur hydrogen · SH groups can react and form a cross-link that helps stabilize protein structure.

1) What two chemical moities associate to re-form a water molecule?

· The above reaction is reversible, so hydronium and hydroxide can react to reform water.

1) At the molecular level, what explains water's cohesive and adhesive properties? How is this related to the existence of sequoias that are hundreds of feet tall?

· The cohesive and adhesive properties contribute to the transport of water and dissolved nutrients against gravity in plants. This helps water from the roots reach the leaves through a network of water-conducting cells. · The tallest trees can transport water more than 100m upwards (approx. one quarter of the height of the Empire State Building) · Adhesion of water to cell walls by hydrogen bonds help resist the downward pull of gravity. · Cohesion due to hydrogen bonds between water molecules help hold together the column of water within the cells. Evaporation from leaves pull water upward from the roots through water-conducting cells.

1) How do the conformations of the alpha 1, 4 and beta 1-4 polymers of D-glucose differ? At the biochemical level, what explains the difference in conformation between the two?

· The difference is when glucose forms a ring, the number 1 carbon is positied either below (alpha) or above (beta) the plane of the ring

1) Why does it make some sense that tropical oils and mammal fats should contain a higher prevalence of saturated fatty acids compared to cold-climate plants or cold-blooded animals?

· The main function of fat is energy storage. · Another function is that it provides cushion organs and provides a layer of fat beneath the skin to insulate the body. o This is important especially in whales, seals, and other marine mammals to insulate their bodies in cold ocean waters.

1) What number determines the pH of an aqueous solution, and why is this 7 for pure water?

· The pH of a solution = -log[H+]. · This is 7 for pure water because it denotes the midpoint of the pH scale which is neutral.

1) What is the "NCC backbone" of a polypeptide, and what is meant by an "amino" and a "carboxyl" terminus of a protein?

· The polypeptide backbone is the repeating sequence of atoms in a polypeptide bond. · N-terminus (amino-terminus) - is the end of the polypeptide chain that has a free amino group (left) · C-terminus (carboxyl-terminus) - the end of the polypeptide chain that has a free carboxyl group (right)

1) Why is the collection of lipids in the plasma membrane more accurately referred to as a macromolecular aggregate than a macromolecule (like carbs, proteins and nucleic acids)?

· They are generally not large enough to be considered macromolecules. · They mix poorly or even at all with water because of their hydrophobic nature and mainly containing hydrocarbon bonds.

1) What is the significance of the major and minor grooves of DNA in terms of function and regulation?

· Two portions of the DNA helix: minor groove (shallow) and major groove (wider and deeper) o When proteins interact or bind to DNA, they typically interact with one or the other groove

Hormonal proteins

Function: Coordination of an organism's activites Example: Insulin, a hormone secreted by the pancreas, causes other tissus to take up glucose, thus regulating blood sugar concentration

Defensive proteins

Function: Defensive proteins Example: Antibodies inactivate and help destroy viruses/bacteria.

Structural proteins

Function: Keratin is the protein of hair, horns, feathers, and other skin appendages. Example: Keratin is the protein of hair, horns, feathers, and other skin appendages.

Contractile and motor proteins

Function: Movement Example: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles.

Receptor proteins

Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells

Enzymatic protein

Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules

Storage proteins

Function: Storage of amino acids Example: Casin, the protein of milk, is the major source of amino acids for baby mammals.

Transport proteins

Function: transport of substances Hemoglobin, the iron-containing protein of vertebrae blood, transports oxygen from the lungs to other parts of the body.Other proteins transport molecules across membranes.

Unsaturated fatty acid

Has one or more double bonds, with one fewer hydrogen atom on each double-bonded carbon. o Double bond in fatty acids = cis double bond which creates a "kink" in the hydrocarbon chain o Liquid at room temp - The kinks where the cis double bonds are located prevent the molecules from packing closely together to solidify. o Most plant and fish fats are oils.

1) Is cholesterol a component of all the plasma membrane in all organisms? Explain your answer.

No, cholesterol is only a component in animals.

1) Why are phosphate groups particularly important in a biological context?

Phosphates take part in many important chemical reactions in the cells.

Quaternary Structure of Protein

Protein complex made up of two or more individual polypeptide chains to carry out their functions · aggregation of all polypeptide subunits. · Not all proteins have quaternary structure. · Hemoglobin and collagen are examples of proteins with quaternary structure · Ionic bonding, Hydrogen bonding, Dissulfide bridges, hydrophobic interactions

Saturated fatty acid

Saturated with hydrogen bonds; as many hydrogen atoms as possible bonded carbon o Most animal fats are saturated o Solid at room temp - The "tails" of the fat molecules lack double bonds which give the molecule flexibility to pack together tightly and form a solid. EX) lard and butter

Proteoglycans

creates a network that embeds the collagen

Monomer of Lipids

fatty acids and glycerol

Fibronectin

glycoproteins that bind to the cell-surface receptor proteins called integrins that are built into the plasma membrane. The integrins bind and position themselves to transmit signals between the ECM and cytoskeleton. These work together to integrate changes occurring outside and inside the cell.

Amphipathic

having both hydrophilic and hydrophobic parts

1) How is the structural difference between the alpha 1-4 and beta 1-4 polymers of glucose related to their distinct biological functions?

· Alpha 1-4 allows the linkage of all alpha glucose monomers to be in the same orientation. This is found in starch which allows it to function efficiently to store glucose units. · Beta 1-4 results in th beta glucose monomer to be upside down next to its neighbors. o This is found in cellulose which is straight. Since it is never branched, some of the hydroxyl groups are free to hydrogen-bond with hydroxyls of other cellulose molecules lying parallel. This allows the cellulose to create microfibrils (cable-like building material for plants). o Allows it to function as a strong structure for plants

1) What chemical groups are attached to the alpha carbon in a typical amino acid? Which of these is/are consistent across all kinds of amino acids, and which is/are variable?

· Amino acids share a common structure that have an amino group and a carboxyl group. · The alpha carbon is four different partners - amino group, carboxyl group, hydrogen atom, and variable group (R group).

1) What is an amino group? At physiological pH, what property(ies) does it confer to a molecule it is a part of?

· Amino group (Amine) à Nitrogen bonded to two hydrogens · Acts as base; can pick up an H+ from the surrounding solution

B DNA

· B DNA is the most common structural form in cells; right-handed helix o Two nucleic acids associated with hydrogen bonding to their nitrogenous bases that are tucked in the interior o Sugar phosophate backbones turn along the outside of the helix o 10 nucleotide base pairs along on turn of the helix

1) What happens when a base is added to an aqueous solution, and how does this change the hydrogen ion/hydroxide ion concentrations in the solution?

· Bases reduce the H+ concentration by accepting a hydrogen ion. EX) NH3 + H+ à NH4+ (Base) · Bases reduce the H+ concentration and increase the concentration of OH-.

1) Using carbonic acid/bicarbonate as an example, explain what happens in a buffered system when the concentration of hydrogen ion or hydroxide ion is increased.

· Buffer - substance that minimizes changes in the concentrations of H+ and OH- in a solution. It does this by accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions to the solution when depleted. · Chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator, rxn shifts left or right as other processes in the solution add/remove hydrogen ions. o If H+ concentration in blood begins to fall (pH rises), the reaction proceeds to the right and more carbonic acid dissociates à replenishes hydrogen ions. o If H+ concentration in blood beings to rise (pH falls), the reaction proceeds left and hydrogen ions are removed which form bicarbonate.

1) What is a carbonyl group? What property(ies) does it confer to a molecule it is a part of?

· Carbonyl group (ketone or aldehyde) à Carbon double bonded to oxygen · Sugars with ketone groups are called ketoses, those with aldehydes are called aldoses

1) What is a carboxyl group? At physiological pH, what property(ies) does it confer to a molecule it is a part of?

· Carboxyl group (Carboxylic acid) à Carbon double bonded to oxygen and bonded to OH · Acts as an acid (can donate H+) because the covalent bond between oxygen and hydrogen is so polar

1) What role do chaperonins play in protein folding? Do all proteins require chaperonins? Explain your answer.

· Chaperonins are sheltered protein folding compartments that are required by some proteins to fold correctly · Proteins that need this have specific sequences that signal cells to transport to a chaperonin · Energy from ATP will help close chaperonin · Misfolding can happen which is a serious problem that could cause many diseases - Alzheimer's, Parkinson's, etc.

How are the chemical properties and reactivity of an element related to atomic valence configuration?

· Chemical behavior of an atom depends mostly on the number of electrons in its outermost shell called the valence shell. The electrons in the valence shell are called valence electrons. · Atoms with the same number of electrons in their valence shells exhibit similar chemical behavior. EX) F and CL both have 7 valance elecrons and both form compounds with Na to form NaF (used in toothpaste) and NaCl (table salt). · Atom with completed valence shell = unreactive, and will not readily interact with other atms. - Noble Gases · All other atoms are chemically reactive because they have incomplete valence shells.

1) What are disaccharides? Name one commonly found in nature and describe its "function" (in a biological context).

· Disaccharides are double sugars, consisting of two monosaccharides joined by a covalent bond (glycosidic linkage) . · EX) maltose is a disaccharide formed by linking of two molecules of glucose (used in making beer · EX) sucrose (made from glucose and fructose) · Must be broken down into monosaccharides to be used for energy by organisms.

1) DNA can be described as a right-handed double helix with complementary,anti-parallel strands. Explain what is meant by each of these terms.

· Double helix - formation of a DNA molecule from two polynucleotides (or strands) that wind around an imaginary axis. · The two sugar-phosphate backbones run in opposite 5' à 3' directions from each other - which form an arrangement called anti-parallel strands

1) What is meant by the dynamic equilibrium of association/dissociation in pure water?

· Dynamic equilibrium is when water molecules dissociate at the same rate they are being reformed from H+ and OH-. At this point, the concentration of water molecules greatly exceed the concentration of the H+ and OH-.

1) Why is understanding enantiomers important from a biological perspective?

· Enantiomers - mirror images of each other and differ in shape due to the presence of assymetric carbon (one attached to 4 different atoms or groups of atoms) · There are left-handed and right-handed versions of the molecule and only on isomer is biologically active because it may be the only one form that can bind to specific molecules in an organism. · Some isomer molecules and arrangements can bind to a carbon or receptor, while others can not. · These isomers are important in the pharmaceutical industry because the two enantiomers of a drug may not be equally effective. o EX) methamphetamine has two enantiomers - one that is a highly additive stimulant and the other with weaker effects used as an over-the-counter vapor inhaler for treatment of nasal congestion. o This shoes that specific arrangement of atoms is important and has effects on the body.

1) Why does the bulk of the plant material we eat go undigested (compared to, say, the plant matter eaten by a cow)?

· Enzymes that digest starch by hydrolyzing its alpha linkages are unable to hydrolyze (break) the beta linkages of cellulose. Only a few organisms possess enzymes that are able to digest cellulose. · Cellulose in most animals and humans can't be digested, but it does help to stimulate the lining and secrete mucus to aid the passage of food through the tract. Insoluble fiber = cellulose · Cows have cellulose digesting prokaryotes and protists in its gut which hydrolyze the cellulose of hay and grass to convert to glucose and nourish the cow.

1) What four elements are the principal atomic constituents of biological molecules, and how do they differ in terms of their covalent interactions?

· Four elements - Oxygen, Carbon, Hydrogen, and Nitrogen. (OCHN) · Each atom can share valance electrons and has a bonding capacity corresponding to the # of covalent bonds the atom can form (usually the same number of unpaired electrons). · The attraction of an atom for electrons in a covalent bond - electronegativity. More electronegative atoms strongly pull shared electrons toward itself. o Nonpolar covalent bond - when two atoms of the same element have the same electronegativity o Polar covalent bond - when an atom is bonded to a more electronegative atom o Oxygen is the most electronegative element between the four. The electrons are closer to the oxygen nucleus than with hydrogen or other elements when covalently bonded. o Carbon and hydrogen have similar electronegativity, so their bond is less polar.

What are functional groups in general? Why is it important to understand their structure and properties in a biological context?

· Functional groups are chemical groups directly involved in chemical reactions. · Each have certain properties - shape/charge, etc · Most important in biological processes - hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, and methyl o First 6 are chemicall reactive o All except sulfhydryl are hydrophilic and increase solubility of organic comounds in water

Why are sulfhydryl groups particularly important in a biological context?

· Gives ability to oxidize with other sulfhydryl groups to form dissulfide bridges to create more stability in the protein. · Hair protein cross-links maintain the straightness or curliness of hair.

What are monosaccharides?

· Glucose is major nutrients for cells · In cellular respiration, cells extract energy from glucose molecules by breaking them down in a series of reactions · Some glucose carbon skeletons are used for synthesis of amino acids or fatty acids, while others are incorporated into disaccharides or polysaccharides.

1) What is the structure of glycerol? Of a fatty acid? How are these molecules related to triacylglycerols?

· Glycerol - an alcohol where each of its carbons contains a hydroxyl group. · Fatty acid - long carbon skeleton usually 16 or 18 carbons in length. The carbon at one end is part of a carboxyl group. The remaining skeleton include the hydrocarbon chain. o These C-H bonds make fatty acids hydrophobic. · A triacylglycerol is created by joining three fatty acids to a glycerol by an ester linkage. - AKA triglyceride o Ester linkage - dehydration rxn between hydroxyl group and carboxyl group

1) What is "special" about the three amino acids we highlighted (glycine, proline and cysteine)?

· Glycine (G) - smallest, not chiral, bonded only to H · Cysteine ( C ) - contains sulfhydryl functional groups. Two of these groups can become oxidized and create sulfide bonds which is important to stabilize structure · Proline (P) - Bonded to both the alpha carbon and amino nitrogen group, which changes the property of the amino group

1) What drives the formation of stable ions? Why is a sodium ion more stable chemically than the sodium atom?

· Having a full valence shell and filling the octet rule drives the formation of stable ions. · The sodium ion is more stable because the sodium atom is once valence electron in its shell. When it loses the electron, the valence shell is complete and it is closer to becoming a noble gas.

1) At the molecular/biochemical level, why does heating up your egg in a skillet cause the egg white to turn white and solidify? Are all proteins equally sensitive to heat? Explain your answer.

· Heating up an egg causes the protein to denature. · Most proteins are equally sensitive to heat. Protein in blood tends to denature at very high body temps which is why high fevers are fatal to babies. · Denaturation - when the pH, salt concentration, temperature, or other aspects of its environments are altered which causes the weak chemical bonds and interactions within a protein to be destroyed. The protein unravels and loses its shape. o Denatured proteins become biologically inactive

1) What happens when a water molecule dissociates?

· Hydrogen atom leaves its electron behind and transfers with one single proton. The water molecule that lost the hydrogen becomes OH- and the water molecule that gained the hydrogen becomes H3O+

1) What is a hydrogen bond? Is it more similar to an ionic bond or a covalent bond? Why?

· Hydrogen bond - the attraction between hydrogen and an electronegative atom (F, O, N) · Similar to covalent bonds because they share electrons.

1) What determines if a compound is hydrophilic or hydrophobic?

· Hydrophilic - substance that has an affinity for water o Some compounds can be hydrophilic without dissolving · Hydrophobic - substances that repel water o Nonionic and nonpolar (can't form a hydrogen bond) o Oil molecules are hydrophobic due to the prevalence of bonds between carbon and hydrogen, which share electrons almost equally.

1) What type(s) of chemical interactions stabilize a polypeptide's tertiary structure? Which of these forces are "strong" and which are "weak"?

· Hydrophobic interactions (somewhat misleading) - polypeptide folds into its functional shape, amino acids with hydrophobic (nonpolar) side chains usually end up in clusters at the core of the protein, out of contact with water · Hydrogen bonds between polar side chains and ionic bonds between positively and negatively charged side chains help stabilize the structure · Disulfide bridges help reinforce the shape. o Disulfide bridges - two cysteines that have sulfhydryl groups (-SH) are brought close together by the folding of the protein. Creates a S-S bond.

1) What is a hydroxyl group? At physiological pH, how are its chemical properties different from the OH component of the carboxyl group? What property(ies) does it confer to a molecule it is a part of?

· Hydroxyl group (Alcohol) à Bonded to an OH group · Is polar due to electronegative oxygen. Forms hydrogen bond with water and can dissolve compounds.

1) What are the nitrogenous bases, and which are purines and which are pyrimidines?

· Nitrogenous bases have one or two rings that include nitrogen atoms. · Called nitrogenous bases because the nitrogen atoms tend to take up a H+ from the solution, thus acts like a base. · Two families of nitrogenous bases: pyrimidine and purines o Pyrimidine - has one six-membered ring of carbon and nitrogen atoms § Cytsosine ( C ), thymine (T), and uracil (U) o Purines - larger, with six-membered ring fused to a five-membered ring § Adenine (A) and guanine (G) o DNA - adenine, guanine, cytosine, thymine o RNA - adenine, guanine, cytosine, uracil

1) What determines if an amino acid is classified as "polar," "nonpolar," "charged-acidic," or "charged-basic"?

· Non-polar - R group consists of nonpolar group that is hydrophobic · Polar - R group consists of polar group that is hydrophilic · Charged-acidic - R group that is generally negative in charge due to the presence of a carboxyl group. à hydrophilic · Charged-basic - R group that is generally positive in charge. à hydrophilic

1) What are the parts of a ribonucleotide, and how is the structure of a deoxyribonucleotide different?

· Nucleotide - Generally composed of three parts: 5-carbon sugar (pentose), nitrogen-containing (nitrogenous) base, and one to three phosophate groups. o The beginning portion that has three phosphate groups - those are lost when it becomes a polymer o Other portion without phosphate group - nuceloside · Ribonucleotide - monomer of ribonucleic acid (RNA) o Nitrogenous base has ribose attached · Deoxyribonucleotide - monomer of deoxyribonucleic acid (DNA) o Nitrogenous base has deoxyribose attached § Deoxyribose lacks an oxygen atom on the second carbon in the ring (deoxy)

1) What is a phosphate group, and what property(ies) does it confer to the molecule it's a part of?

· Phosphate group à Phosphorous double bonded to one oxygen and single bonded to three other oxygens. · Contributes negative charge (1 - positioned inside chain, 2 - when at the end). · Confers on the molecule the ability to react with water, releasing energy

1) What is a phospholipid, and how is its structure related to but distinct from that of a triacylglycerol?

· Phospholipid is a fat molecule that has two fatty acids attached to glycerol rather than three. The third hydroxyl group of glycerol is joined to a phosphate group, which has a negative electrical charge. · Phospholipid has two ends that show different behaviors and work to create the phospholipid bilayer. This creates a boundary between the cell and its external environment and establishes separate compartments within eukaryotic cells. o Hydrophilic heads - Phosphate group and attachments form and have an affinity for water o Hydrophobic tails - hydrocarbon tail that repels water o When added to water, phospholipids self-assemble and create the bilayer that shields their hydrophobic tail from water. The hydrophilic heads are on the outside of the bilayer.

1) In the opposite--or hydrolytic--reaction, where is the "hydrolysis" occurring (using carbohydrates as an example)?

· Polymers disassemble to monomers through hydrolysis - which reverses the dehydration reaction. The hydrolysis breaks the bond between the monomers. · Hydrolysis can occur in the process of digestion in our bodies. It can be involved in the breakdown of molecules, such as lipids.

1) What is the primary structure of a polypeptide and in what sense does it "dictate" higher levels of protein structure?

· Primary structure of poly peptide - sequence of amino acids similar to the order of letters in a very long word · The precise primary structure is not random, it is inherited genetic information. · This dictates the secondary and tertiary because of the chemical backbone and the side chains (R groups) of the amino acids it contains which determine how the other structures will form.

1) How are the structure and properties of proteoglycans related to their function as part of the extracellular matrix?

· Proteoglycans consist of a small core protein with many carb chains covalently attached (95% carb chains) · The proteoglycan complex (several proteoglycans) embed collagen (the strong fibers outside cells). · The extracellular matrix acts a "cell wall" similar to the cell wall of plants which consists of collagen, fibronectin, and proteoglycans.

1) What is quaternary structure? Do all proteins have quaternary structure? Explain your answer.

· Quaternary structure - aggregation of all polypeptide subunits. · Not all proteins have quaternary structure. · Hemoglobin and collagen are examples of proteins with quaternary structure

1) Explain why ribonucleic acids are considered to be functionally more complex than deoxyribonucleic acid. What is the relationship between the structural complexity exhibited by cellular ribonucleic acids and this functional complexity?

· RNA molecules exist as single strands which allow for complementary base pairing to occur between regions of two RNA molecules. This base pairing allows for three-dimensional shapes that are necessary for the RNA function. · Transfer RNA (tRNA) - brings amino acids to the ribsome during the synthesis of a polypeptide o About 80 nucleotides in length o Its functional shape results from base pairings between nucleotides where complementary stretches of the molecule can run antiparallel to each other · RNA molecules are more variable in shape

1) What are the principal motifs in the secondary structure of proteins, and what type(s) of chemical interactions stabilize these structural motifs?

· Secondary structure has coils and folds. Two main structures: o Alpha helix - delicate coil held together by hydrogen bonding between every fourth amino acid EX) keratin in hair o Beta pleated sheet - two or more segments of the polypeptide chain lying side by side are connected by hydrogen bonds between parts of two parallel segs of polypeptide backbone. EX) silk protein of spider's web

Primary Structure of Protein

· Sequence of amino acids similar to the order of letters in a very long word; Every protein has a unique sequence · The precise primary structure is not random, it is inherited genetic information. · This dictates the secondary and tertiary because of the chemical backbone and the side chains (R groups) of the amino acids it contains which determine how the other structures will form. · One amino acid is added one at a time until entire chain is complete

1) Even though a methyl group contributes no polarity or charge to a molecule it's a part of, one small methyl group added on to a molecule can nonetheless completely alter that molecule's biological function. Explain this observation.

· Shape and structure play a huge role in the functions of a molecule. This explains why adding a methyl group can alter the biological function since there would be an additional functional group added to the structure.

1) Why is it accurate to depict water as "sticky" molecules?

· Water has three properties that factor into the "sticky" molecules: cohesion, adhesion, and surface tension · Water molecules stay close to each other due to hydrogen bonding which hold the substance together - cohesion. This contributes to the transport of water within plants to reach from the root to its leaves. · Adhesion - the clinging of one substance to another. Adhesion of water by hydrogen bonds to molecules of a cell wall helps counter the downward pull of gravity. · Surface tension - measure of how difficult it is to stretch or break the surface of a liquid. Since water has hydrogen-bonds next to and below, but to the air above - it behaves as though it was coated with an invisible film. EX) Spider can walk across a pond without breaking the surface of the water.

1) At the molecular level, what explains the fact that water is an excellent solvent? Why is this important in a biological context?

· Water is a very versatile solvent because of the polarity of water. · The oxygen of the water molecule is partially negative, so it is attracted to a cation. · The hydrogen regions are partially positive, so they will attract the anions. · EX) NaCl - Oxygen will attract Na, while Hydrogen will attract Cl · Many compounds are soluble in water, which makes water the solvent of life.

1) At the molecular level, what explains water's high specific heat and heat of vaporization (compared to similarly sized non-polar substances)? How is this related to the relative stability of earth's temperature and our ability to moderate temperature changes in our bodies?

· Water is able to moderate/stabilize air temp by absorbing heat from the air that is warmer and releasing stored heat to air that is cooler. It is an effective heat beak because it can absorb or release heat with only a slight change in its own temp. - This is due to the high specific heat of water. · Water is a high specific heat at 1 calorie per gram versus ethyl alcohol which has a specific heat of 0.6 cal/g. · Water's high specific heat is due to hydrogen bonding. o Heat is released when a hydrogen bond forms o The calorie of heat causes a relatively small change in temp because the heat is used to disrupt hydrogen bonds before the water molecules can begin to move faster · The high specific heat tends to stabilize ocean temps, creating a favorable environment for marine life. Since water covers most of Earth, it keeps temperature fluctuations on land and in water within limits that permit life. o EX) ocean can absorb heat from the sun in the daytime and warm up only a few degrees, while it can also warm the air when cooling at night. · In addition, since organisms are made primarily of water - they are able to resist changes in their own temperature than if they were made of a liquid with a lower specific heat. · Heat of vaporization - quantity of heat a liquid must absorb for 1g of it to be converted from liquid to gas. Water has a high heat of vaporization relative to other liquids (about double). · Heat of vaporization causes evaporative cooling (as liquid evaporates, the surface of the liquid that remains cools down) which contributes to the stability of temp in water which prevents organisms from overheating. o Evaporation of sweat from human skin dissipates body heat and helps prevent overheating when excess heat is generated.

1) What is a "weak acid," and why is it weak relative to a "strong acid"?

· Weak acids are acids that reversibly release and accept back hydrogen ions. Strong acids dissociate completely when mixed with water. This is due to the electronegativity of the strong acids and the attraction between the water molecules and the electronegative atoms in the strong acid.

1) What happens when an acid dissociates, and how does this affect the hydrogen ion/hydroxide ion concentrations in the solution?

· When acids dissolve, they donate additional H+ to the solution which result in an acidic solution.

1) Explain why the polymerization of mononucleotide triphosphates into nucleic acids does not require outside energy input whereas the dehydration synthesis of polysaccharides from monosaccharides does.

· When the phosphate group is removed from the OH, it is an energy releasing reaction. The substrait mononucleotide supplies the energy to make the reaction happen which is why it doesn't require outside energy.

1) At the molecular level, what explains the fact that unlike most substances, frozen water is less dense than liquid water? How is this related to Earth's fitness for life?

· When water is frozen, the molecules become locked into a crystalline lattice where the water molecule hydrogen bonds keep all molecules far enough apart to make ice less dense than liquid water. When the ice melts, the molecules slip closer together and become more dense. · The fact that ice is less dense than water give it the ability to float on water. This is an important factor to the environment for life. The ice insulates the ocean below it and allows life to exist under the frozen surface. The frozen surface also allows for animals to live on.

Z DNA

· Z DNA is a left-handed helix. o Staggered orientation o Difference in structure would affect the types of proteins that binds o Not much known about the function of this DNA.

1) At the molecular/biochemical level, how can pH changes lead to denaturation of a protein?

· pH too low or too high - protein will lose its negative charge which will repel and prevent protein from aggregating and could cause unfolding