ACS Biochemistry Exam Questions With Complete Solutions

ACS Biochemistry Exam Questions With Complete Solutions Metabolism (catabolism and anabolism) - ANSWERS Metabolism: sum of total chemical reactions in an organism, also the method by which cells extract and use energy from their environment. Catabolism: The process by which stored nutrients and ingested foods are converted to a usable form of energy. It produces simple products CO2, H2O, NH3, and building blocks such as sugars and fats that are used in anabolism. Anabolism: the process by which simple products and building blocks of catabolism are used to create complex biological products that contribute to organismal growth and development. It also uses the energy produced in catabolism to do biological work. Properties of cells - ANSWERS Metabolism: undergoing catabolic and anabolic processes. Reproduction: cell populations grow via asexual reproduction. Mutation: during growth and reproduction, cells sometimes make mistakes, leading to mutations and evolution. Respond to environment: metabolic pathways respond to signals, including light, touch, hormones, and nutrients, that can turn the pathways on or off. Speed and efficiency: cell operations are highly specific to maximize targeting and efficiency. Similar building blocks: most species are very similar at the cellular level. What accounts for water's unique properties? - ANSWERS Hydrogen bonding The unique properties of water (specific heat, heat of vaporization, solubility) - ANSWERS 1) high specific heat, or heat required to raise the temperature of the unit mass of a given substance by one degree. For water to increase in temperature, water molecules must be made to move faster, or get higher KE, and doing this requires breaking hydrogen bonds, which absorbs heat. So, as heat is applied, most of it goes to breaking the bonds not upregulating KE, thus making water harder to heat than substances where no bonds need to be broken. 2) High heat of vaporization, or the amount of heat needed to turn one g of a liquid into vapor, without a temperature rise in the liquid. Important for sweat because it ensures that when the liquid evaporates from our skin, the heat required for the transition is kept in the gas, causing a net cooling effect on the skin. 3) Unique solubility properties: "like dissolves like". Water dissolves polar molecules and ions, and can act as an H-bond donor or receptor 4) Amphoteric, it can act as an acid (donating electrons) or a base (accepting electrons). The conjugate acid of water is the hydronium ion, H3O+, and the conjugate base of water is the hydroxide ion, OH-. Keq for water at 25 degrees C and in pure water - ANSWERS At 25 degrees C: Keq= Kw= [OH-][H3O+]= 1*10^-14 In pure water: [OH-]=[H3O+]= 1*10^-7 Calculation for pH and pKa - ANSWERS pH= -log[H3O+] pKa= -log(Ka) Normal blood pH range - ANSWERS 7.35-7.45 The Hydrophobic Effect - ANSWERS When non-polar molecules aggregate in the presence of water, minimizing the entropy decrease water must go through to order themselves around the border of the non-polar molecule. Reducing the surface area water must organize around increases entropy, which is favorable. The aggregation is responsible for the formation of a variety of lipid structures in the body, including cell membranes. Buffers - ANSWERS Composed of a weak acid (HA) and its conjugate base (A-). Added acid reacts with A-, and added base reacts with HA, giving a limited overall pH change. Two main reactions: 1) When excess base is added: OH-+HA-->H2O+A- 2) When excess acid is added: H+ + A- -->HA **So, the net result is more of the weak acid and its conjugate base** When are buffers optimal? What equation can we use for this? - ANSWERS When [HA]= [A-], occurring when pH=pKa Henderson- Hasselbalch allows use to calculate pH at given pKa, and vice versa: Blood Buffering - ANSWERS Components: 1) carbonic acid (H2CO3) (weak acid). pKa= 6.1. 2) Bicarbonate Ion (HCO3-), conjugate base of carbonic acid 3) H+ (hydrogen ion) If OH- (base) is added, Carbonic acid buffers it into bicarbonate ion and water. If H+ (acid) is added, bicarbonate ions and H+ buffer it to carbonic acid. Amino Acids, peptides, and polypeptides - ANSWERS the building blocks of proteins, a chain of which is called a peptide. There are 20 standard amino acids that act as the monomers to make protein polymers! A long peptide is called a polypeptide! Proteins are composed of one or more polypeptide chain. Peptide bonds - ANSWERS Between the C and N of C=O and N-H of two adjacent amino acids. What wavelength is indicative of aromatic amino acids? - ANSWERS 280 nm, with tryptophan absorbing more, tyrosine absorbing a bit less, and phenylalanine absorbing a lot less. Stereochemistry of amino acids - ANSWERS Every carbon except for glycine is a chiral center, giving two possible structures for each: L and D (except for glycine). L is the only one found in nature. Acid-Base properties of amino acids - ANSWERS Each has at least two ionizable protons (from the COOH and NH3 groups), but most have others. COOH pKa: 2.34 NH3 pKa: 29.60 PI - ANSWERS the isoelectric point, or the pH at which an amino acid or peptide has no net charge. - At pH= PI, the predominant species is the zwitterion - At pH<PI, the predominant species is net positive - At pH>PI, the predominant species is net negative **At PI, amino acid or peptide cannot migrate through an electric field, so this is a way we can separate amino acids (by PI via electric field!)** How to calculate PI, or isoelectric pint - ANSWERS Average pKa values involving the neutral species For glycine, that only has COOH and NH3 pKa's, the PI is the average between 2.34 and 9.60, so 5.97! Essential Amino Acids - ANSWERS Those that cannot be made in the body and thus must be obtained via the diet. Some can be made from others, so it isn't a hard line, but: Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine are all essential. **Cysteine can be made from methionine, tyrosine can be made from phenylalanine, etc.** Amino acid name post-peptide bond - ANSWERS residues Peptide directionality - ANSWERS From N to C Protein makeup - ANSWERS One or more polypeptide chains, and optional prosthetic groups that make a conjugated protein. The folding of the chains is what delineates function of the protein itself. 4 protein structure levels, and their components - ANSWERS Primary structure: amino acid reside sequences Secondary structure: alpha helix and beta sheet folded segments Tertiary structure: polypeptide chains in 3-D shapes Quaternary structure: Assembled subunits comprised of multiple chains Amino Acids with ionizable side chains - ANSWERS Terminal carboxyl group: pKa of 3.1 Aspartic Acid/Glutamic Acid: pKa of 4.1 Histidine: pKa of 6.0 Terminal amino group: pKa of 8.0 Cysteine: pKa of 8.3 Tyrosine: pKa of 10.9 Lysine: pKa of 10.8 Arginine: pKa of 12.5 Protein Native conformation - ANSWERS The low-energy structure a given protein will fold into. Determining primary structure of proteins (steps) - ANSWERS 1) Determine how many chains are present 2) Cleave one chain into small pieces using an enzyme with a known preferred cleavage site 3) Characterize each piece 4) Perform a second round of cleavage and characterization 5) Determine how the pieces fit together How can one determine the number of chains are present in a protein? - ANSWERS Determine the number of N or C termini. Ex: Sanger's Reagent interacts with the amino terminal (binds to it via a C-NH bond) to show how many are present in the protein. Cyanogen Bromide, Trypsin, and Chymotripsin - ANSWERS All are enzymes used to delineate primary structure of proteins using expected cleavage sites. Cyanogen Bromide: cleaves methionine residues on the carboxyl side. Trypsin: Cleaves after Arginine or Lysine, on the carboxyl side. Chymotripsin: Cleaves after aromatics (F/Y/W) on the carboxyl side. A key method in characterizing polypeptide fragments - ANSWERS Edman degradation: the polypeptide is treated with phenylisothiocyanate, which reacts with the N-terminal amino acid to give an N-terminal PTC derivative of the protein. This derivative forms by addition of the terminal N—H bond across the C = N of the phenylisothiocyanate. The N terminal is then cleaved under acidic conditions, resulting in the removal of exactly one amino acid monomer for identification. How are protein native structures stabilized? - ANSWERS By weak non-covalent bonding and di-sulfide bonds Protein Denaturation - ANSWERS The loss of protein structure due to unfolding. It can happen as a result of heat or chemicals breaking hydrogen bonds and other weak non-covalent bonds that hold the proteins together. What type of bond characterizes the secondary structure of proteins? - ANSWERS Peptide Bonds. They are planar, and exist between the C=O of one amino acid and the N-H of the other (the C binds to the N). The trans structure is preferred by nature due to the steric hinderance of the cis form. Peptide backbone: two polypeptide angles having free rotation - ANSWERS Angle about the C-N bond: PHI Angle about the C-C=O bond is PSI Some measures of phi and psi are more common than others. **Rotation around the peptide bond is NOT permitted, but rotation around these bonds is** Favorable measures of phi and psi in peptide bonds - ANSWERS Angle about the C-N bond, Phi, is favorable at 180, and most unfavorable at 0. Angle about the C-C=O bond, Psi, is also favorable at 180 and most unfavorable at 0. Ramachandran Diagrams - ANSWERS G. N. Ramachandran, in his 1950s experiments, used peptide models to systematically vary phi and psi. Phi and psi angles that cause atoms to collide correspond to sterically impractical conformations of the polypeptide backbone. The plots resulting from these systematic angle variations and subsequent conformations is called Ramachandran Diagram, with green regions showing favorable angle conformations (THAT INDICATE SECONDARY STRUCTURES). The two most commonly preferred secondary structures (minimize steric hindrance): alpha helixes and beta sheets. Rules for secondary protein structure (proposed by Linus Pauling, Robert Corey, and Herman Branson) - ANSWERS 3 principles: 1) planar peptide bonds gave allowed torsion angles 2) Hydrogen bonds are maximized in favorable structures 3) Linear hydrogen bonds are most effective Alpha Helix (what they are, and how they are de-stabilized) - ANSWERS Type of secondary protein structure. They are typically right-handed, with stabilizing hydrogen bonds between each -NH and -CO of peptide bonds four residues apart. They are de-stabilized by runs of similarly charged amino acids and too many bulky amino acids, such as proline and glycine. Beta Sheets - ANSWERS Type of secondary protein structure. They have multiple strands (typically 2-15) that interact via inter-chain hydrogen bonds between -NH and -CO of peptide bonds. Successive R groups on opposite sites of the sheets project into the surrounding space. There are two sub-types: 1) Anti-parallel: characterized by two peptide strands running in opposite directions held together by hydrogen bonding between the strands 2) Parallel: characterized by two peptide strands running in the same direction held together by hydrogen bonding between the strands **Anti-parallel sheets are stronger because the hydrogen bonds are linear, which means better orbital overlap** Connecting Elements for both alpha helixes and beta sheets - ANSWERS Random coils: polymer conformation where the monomer subunits are oriented randomly while still being bonded to adjacent units. Turns, bends, and loops: connect α helices and β strands. The most common types cause a change in direction of the polypeptide chain allowing it to fold back on itself to create a more compact structure. (Ex: type-1 beta bends typically include cis-Pro) Flexible, disordered segments: no one defined structure, it can change circumstantially What do bulky side chains prefer in terms of secondary protein structure? - ANSWERS Beta sheets, because they can stick out the side rather than be incorporated into the helix. Amino acids that are "Structure breakers" - ANSWERS Glycine and Proline Fibrous proteins (what they are, their role, and their solubility) - ANSWERS Elongated molecules with a single major type of secondary structure. Many have structural roles (like skin, bones, and connective tissue). They are rich in hydrophobic residues, so they are generally water insoluble. Four major examples of fibrous proteins - ANSWERS Collagen, Elastin, Keratin, and Fibroin What fibrous protein are tendons made up of, and why? - ANSWERS Tendons require strength, resilience, and elasticity. They serve as biological springs, until they are stretched past their breaking point. They are primarily made up of collagen, as a result (80% collagen when dried). Collagen is a tough yet flexible fiber that is able to recover quickly after stretching (unless the stretch passes its breaking point). It is simultaneously long-lasting and incredibly flexible, making it the perfect material for connective tissue. Tropocollagen, and its key amino acids - ANSWERS The fundamental unit of collagen (Mr=300,000). Its sequence is GLY-X-Y, where X and Y are often OH-Pro or Pro, or sometimes OH-Lys and His. Collagen structure: its components, and its basic structural unit. - ANSWERS Its compontents: Quaternary structure stabilized by hydrogen bonds. Its basic unit is a left-handed helix polypeptide chain, which is combined with two others into a triple-stranded collagen molecule (all right handed helixes, with glycine side chains lining the interior), which is further combined to give a collagen fibril quaternary structure. These hydrogen bonds arise from -OH groups added on to Pro and Lys, with Vitamin C required for their hydroxylation! So that's why scurvy is induced via lack of Vitamin C- collagen cannot fully form and teeth fall out, muscles and tendons loosen, etc. Its basic structural unit: a left-handed helix. There are no stabilizing hydrogen bonds within the helix, instead Proline leads to extended chains due to steric repulsion. Collagen Cross-links (what they do, steps and residues involved). - ANSWERS Cross-links between fibrils stabilize collagen's structure. Steps: 1) Collagen assembles into fibrils 2) Lysyl oxidase catalyzes formation of covalent links between collagen. **They involve Lys and His!** Collagen (what it is, where it is found) - ANSWERS A key type of fibrous protein found in the body. The most abundant protein in mammals, found in ligaments, cartilage, tendons, bones, skin, and teeth. It is a family of 26 genetically distinct proteins. What fibrous protein are blood vessels made out of, and why? - ANSWERS They are mostly elastin. They require the ability to expand and contract with each heart beat- they must be extensible but also resilient. So, elastin is the perfect material. It is common for tissues requiring flexibility to have a network of elastic fibers interwoven with collagen (the elastic fibers being 50% elastin by mass). Elastin Structure - ANSWERS Alternating hydrophilic and hydrophobic domains give elastin its key ability to stretch and compress like a rubber band: the hydrophobic domains are like a plate of spaghetti in the related state- they are gathered away from water. Upon being stretched, the molecules uncoil into an extended conformation, but immediately coil back to a hydrophobic clump once the force is removed! This combination gives elastin its rubber band-like ability. Elastin Cross-links - ANSWERS Lysine cross-links ensure the molecule returns to its original state after stretching. What fibrous protein makes up skin, and why? - ANSWERS Skin requires elasticity, resilience, strength, and protection- so keratin is key, along with elastin and collagen. Alpha Keratin (what composes, and its fundamental structure) - ANSWERS Composes skin, hair, wool, feathers, nails, claws, quills, horns, hooves, etc. Fundamental structure is an alpha helix. Two alpha helixes coil together to give a two-chain coil, which then bovines with another two-chain coil to give a protofilament, which then further combine to give a protofibril. Alpha Keratin Cross links - ANSWERS Helicies and fibers are cross-linked by disulfide linkages. When getting a perm, straight hair is given a chemical treatment that reduces the disulfide bonds to S-H groups, then the desired style is given, then the S-H bonds are oxidized back to disulfide bonds, in the desired style, holding it in place. What fibrous protein makes up spider webs, and why? - ANSWERS Spider webs require high tensile strength and low-density (rates of strength to density exceed that of steel). As a result, the protein fibroin makes up the majority of spider webs: it is flexible, light, and high-strength. In spider webs, it combines with the gummy protein sericin to cement it together. Silk Fibroin structure - ANSWERS It has the repeating structure GLY-ALA-GLY-ALA. It is an anti-parallel (strong) beta sheet, with amorphous regions surrounding bulky residues. Fibrous vs. globular proteins - ANSWERS Fibrous proteins have a single major type of secondary structure, while most other proteins are folded compactly and have a mix of secondary structures. Myoglobin - ANSWERS The oxygen carrying protein of red muscle. Hemoglobin - ANSWERS The oxygen carrying protein of the blood. An average human has 2L hemoglobin, has 5-6L of blood, and uses 600L O2 per day. Myoglobin vs. hemoglobin: structures - ANSWERS Myoglobin (Mb) and the two chains of hemoglobin (Hb) are homologous proteins, meaning they had a common ancestor, with random mutations over evolutionary time resulting in key changes. Homologous proteins often have similar sequences, and similar 3-D structures, as is the case here. They have similar secondary and tertiary structures, both having about 78% alpha helix makeup (8 alpha helixes). They both have one heme group, with a non-polar interior. However, they differ in their quaternary structure: Myoglobin has none, while hemoglobin has 2 alpha chains and 2 beta chains combined into one structure with heme at the center of each, attached to iron. How does hemoglobin bind oxygen, and what are some competitive inhibitors? - ANSWERS Hemoglobin binds O2 reversibly using its heme prosthetic group, attached to Fe2+. Other ligand compete favorably with O2, like CO, NO, and H2S. What determines the amount of oxygen bound to hemoglobin (saturation)? - ANSWERS The partial pressure of oxygen, or PO2. Normal arterial O2 pressures, typically around 100 mmHg, give 97% hemoglobin saturation. However, when blood travels to tissues, PO2 is much lower than in the lungs, typically around 20-40mmHg. This cues hemoglobin to release oxygen to the tissues, leaving it about 50% saturated (2 oxygen molecules have been released). How to measure cooperativity - ANSWERS The degree of cooperativity is measured by the Hill coefficient, or n. When n>1, positive cooperativity (each successive loss or reaction makes following ones easier to conduct). When n<1, negative cooperativity (each successive loss or reaction makes following ones harder to conduct). When n=1, there is no cooperativity (each successive loss or reaction has no impact on further conduction). Hemoglobin vs. Myoglobin: cooperativity - ANSWERS Hemoglobin has n=2.8, making it extremely cooperative. This gives it a sinusoidal curve for % saturation vs. PO2. Binding the first O2 is difficult: requires 18 mmHg. However, the second is easier, it requires 26 mmHg. From there, the last two are much easier. Myoglobin, on the other hand, is not cooperative. This gives it a hyperbolic curve for % saturation vs. PO2. Origin of Hemoglobin's Cooperativity - ANSWERS Structures of oxygenated (R state) and de-oxygenated (T state) hemoglobin differ. The T state, or the de-oxygenated form of hemoglobin, is more stable in the absence of O2 because of several key interactions (including ion pairs) that do not exist in the R state.