Biochemistry I – Final Exam Fall, 2007 Name:____________________ 1 Final Exam Face Page This exam consists of 11 pages (including the face page) and a total of 200 pts. The following equations and constants may be useful: Ligand Binding: ! Y =[ML][M] + [ML] ! Y =[L]KD+ [L] ! Y =KA[L]1+ KA[L] Scatchard Plot: Y/[L] vs Y or ν/[L] vs ν Y/[L] = (-1/KD) Y + 1/KD ν/[L] = (-/KD) ν+ n/KD Hill Plot: log(Y/(1-Y)) vs log[L] Hill Equation: log(Y/(1-Y)) = log Kπ + nhlog[L] Enzyme Kinetics: For ( E + S <--> ES  E + P ) VMAX = kcat[ET] KM = (k-1+kcat)/K1 Michaelis-Menton equation: ! v =VMAX[S]KM+ [S] Steady State Equation for Enzyme Inhibition: ! v =VMAX"'[S]""'KM+ [S] Double Reciprocal Plot: ! 1v=KMVMAX1[S]+1VMAX Competitive Inhibition: ! 1v="KMVMAX1[S]+1VMAX Noncompetitive Inhibition: ! 1v="KMVMAX1[S]+"'VMAX α=1+[I]/KI α’=1+[I]/KI’ α'=1 for competitive inhibition α'>1 for noncompetitive inhibition ! "=slope([I] > 0)slope([I] = 0) ! "'=y # int([I] > 0)y # int([I] = 0) General Thermodynamics T = 300K and pH = 7.0 unless otherwise stated. R = 8.3 J/mol-K S = R ln W ΔG° = ΔH° - TΔS° ΔG° = -RT ln KEQ ΔG = ΔG° + RT lnKBiochemistry I – Final Exam Fall, 2007 Name:____________________ 2 Part A: Please circle the best answer (2 pts each). 1. The side chain of the amino acid Histidine, with a pKa of 6.0, is a) 99% deprotonated at pH 7.0. b) 99% protonated at pH 7.0. c) 9% deprotonated at pH 7.0. d) 9% protonated at pH 7.0. 2. Amino acid side chains likely to be directly involved in enzyme catalysis are a) Trp, His and Phe. b) Asp, Leu and Val. c) Asp, His and Cys. d) His, Ser and Pro. 3. β-pleated sheets are stabilized primarily by hydrogen bonds a) between residues n and n+4 in the same strand. b) between side chains on adjacent polypeptide strands. c) between backbone atoms on adjacent residues in the same strand. d) between backbone atoms on neighboring polypeptide strands. 4. H-bonding between potential main chain donors and acceptors is a) maximized in α-helices but not in β-sheets. b) maximized in β-sheets but not in α-helices. c) maximized in both α-helices and β-sheets. d) minimized in both α-helices and β-sheets. 5. The side chain of which of the following amino acids is most likely to occur in the middle of a membrane-spanning α-helix? a) Arginine b) Aspartate c) Phenylalanine d) Lysine 6. The largest driving force for protein folding is a) configurational entropy. b) van der Waals interactions between non-polar side chains. c) H-bonding between main chain atoms. d) the hydrophobic effect. 7. The largest driving force for formation of the DNA double helix is a) configurational entropy. b) van der Waals interactions between the bases. c) H-bonding between the bases. d) the hydrophobic effect. 8. The largest driving force for formation of a phospholipid bilayer is a) configurational entropy. b) van der Waals interactions. c) H-bonding between the head groups and water. d) the hydrophobic effect.Biochemistry I – Final Exam Fall, 2007 Name:____________________ 3 9. The standard free energy change, ΔG°, for a reaction is negative a) if the products are more stable than the reactants. b) if the reactants are more stable than the products. c) if the activation barrier is reduced by an enzyme. d) only when the reaction is coupled to ATP hydrolysis. 10. An enzyme will efficiently catalyze a reaction in cells if a) the ΔG° for the reaction is negative. b) the ratio of products to reactants is much less than 1. c) the ratio of products to reagents is much less than KEQ. d) a reaction further downstream in the pathway is inhibited. 11. A homo-dimer that binds its ligand with KD1<KD2 has a Hill coefficient a) greater than 1. b) less than 1. c) equal to 1. d) equal to 0. 12. The assembly of a phospholipid bilayer a) requires a non-polar solvent. b) requires ATP hydrolysis. c) occurs spontaneously in water. d) requires cholesterol. 13. Membrane fluidity is increased by ______ the fatty acyl chain length or by ______ the degree of saturation of the fatty acyl chains. a) increasing, increasing. b) increasing, decreasing. c) decreasing, decreasing. d) decreasing, increasing. 14. A regulated step in a metabolic pathway is a) usually a reversible step. b) usually an irreversible step. c) always the most upstream step in the pathway. d) always cooperative. 15. A six carbon fatty acid generates more ATP than glucose because a) the fatty acid generates more NADH molecules per glucose. b) the fatty acid starts off more oxidized than glucose. c) the fatty acid cannot enter the TCA cycle. d) the fatty acid is a preferred substrate for the F1/Fo ATP synthase. 16. RNA is less stable than DNA because a) the 3’ -OH on the ribose in RNA can attack a 5’ phosphate group. b) the 2’ -OH on the ribose in RNA can attack a phoshodiester linkage. c) the N-glycosidic linkage in RNA is less stable than in DNA. d) only 2 hydrogen bonds are formed between the bases in RNA. 17. DNA polymerization is made spontaneous by a) the inherently exergonic formation of a phosphodiester bond. b) cleavage of a phosphoanhydride bond. c) transfer of 2 electrons from NADH. d) the generation of DNA into Okazaki fragments.Biochemistry I – Final Exam Fall, 2007 Name:____________________ 4 18. The editing of mistakes in DNA polymerization is carried out by a) an RNA polymerase called primase. b) a 5’3’ exonuclease acitivty in DNA polymerase. c) a 3’5’ exonuclease activity in DNA polymerase. d) a DNA helicase. 19. The processivity of DNA polymerase is mediated by a) the helicase. b) the gyrase. c) the β-sliding clamp. d) DNA ligase. 20. Okazaki fragments are necessary intermediates in DNA replication because a) DNA can only be synthesized in the 5’ to 3’ direction. b) DNA can only be synthesized in the 3’ to 5 direction. c) DNA synthesis requires unwinding of the DNA duplex. d) DNA polymerase can only incorporate 1000 nucleotides before falling off the DNA. 21. Sequence specific interactions between a DNA-binding protein and the major groove of DNA are likely to be mediated by a) H-bonds between base edges and polar side chains. b) electrostatic interactions between base edges and charged side chains. c) H-bonds between phosphate backbone and polar side chains. d)