There are 30 questions in all. Questions 1-25 are multiple choice and are each worth 2 points. Questions 26-30 are essays and problems worth a total of 50 points.

These are equations and constants you may find helpful: ΔG = − n F ΔE&Deg;′
R = 8.314 J/mole-K; T = 298 K;                  F = 96,480 J/V-mole
ΔG = R T ln (C₂/C₁) + Z F ΔV                      ΔG = ΔG°′ + R T ln ([products]/[reactants])

              1. Which sequence would you expect to see for a transmembrane α-helix?
(A) –K–S–A–Y–T–L–G–F–I–; (B) –P–S–I–A–Y–W–G–L–N–;
(C) –F–I–C–L–H–A–V–L–G–; (D) –I–A–E–Q–K–V–C–P–G–.

              2. H₃PO₄has three pK_a's: 2.14, 6.86, and 12.4. If you prepare a buffer for pH 6.5, the acid (HA) would be                                   , the base (A⁻) would be                           , and the ratio of their concentrations ([A⁻]/[HA]) would be               .
(A) H₃PO₄, H₂PO₄⁻, 0.36; (B) H₂PO₄⁻, HPO₄²⁻, 2.29;
(C) H₃PO₄, H₂PO₄⁻, − 0.36; (D) H₂PO₄⁻, HPO₄²⁻, 0.70.

              3. Which level of protein structure is stabilized to a significant degree by hydrogen bonds between backbone atoms?
(A) primary; (B) secondary; (C) tertiary; (D) quaternary.

              4. The tertiary structure of proteins like ribonuclease is determined by their
(A) primary structure; (B) secondary structure; (C) disulfide bonds;
(D) phosphorylation.

5-6. Use these graphs on O₂ binding by myoglobin (Mb) and hemoglobin (Hb).

              5. The Hill plot shows that line                (Hb) has           , and the other plot shows that
                    has higher affinity for O₂. (A) A, cooperativity, Hb;
(B) B, cooperativity, Mb; (C) B, cooperativity, Hb; (D) A, cooperativity, Mb.

              6. Line C shows that the addition of CO₂ stabilizes the                          conformation, so that the % of                                      with O₂ bound           if pO₂ remains the same.
(A) T, Hb molecules, increases; (B) T, hemes, falls; (C) R, Hb molecules, increases;
(D) R, hemes, falls.

              7. The coenzyme TPP is a             coenzyme required for reactions that involve                 .
(A) co-substrate, adding –COO⁻ ; (B) co-substrate, removing –COO⁻ ;
(C) prosthetic, adding –COO⁻ ; (D) prosthetic, removing –COO⁻ .

              8. Which of the following enzymes is an example of a ligase?
(A) hexokinase; (B) pyruvate decarboxylase; (C) succinyl-CoA synthetase;
(D) pyruvate dehydrogenase.

9-12. Use these diagrams which show two stages in a bisubstrate reaction.
X represents the backbone of the enzyme.

              9. Which mechanism of catalysis does this enzyme use? (A) acid-base; (B) covalent;
(C) metal ion; (D) all of the above.

              10. The active site of the enzyme includes the residues (A) D and H; (B) N and H;
(C) S and H; (D) D and P.

              11. This reaction                                            with a                          intermediate.
(A) is a ping-pong reaction, succinyl-CoA; (B) is a ping-pong reaction, citroyl-CoA; (C) involves a ternary complex, succinyl-CoA;
(D) involves a ternary complex, citroyl-CoA.

              12. The enzyme that catalyzes this reaction is classified as a/n (A) oxidoreductase;
(B) isomerase; (C) lyase; (D) transferase.

13-15. Use (A) allosteric regulation; (C) covalent modification; (P) proteolysis;
(B) both allosteric and covalent; (D) both covalent and proteolysis.

              13. This requires an enzyme that recognizes a specific S, T, or Y side chain.

              14. Inhibition involves stabilizing a T conformation.

              15. The enzyme's affinity for its substrate is related to its K_0.5.

              16. Which two molecules are isomers that are both required for glycolysis?
(A) alanine and pyruvate; (B) dihydroxyacetone and glyceraldehyde;
(C) oxaloacetate and α-ketoglutarate; (D) glyceraldehyde and pyruvate.

              17. The energy yield from converting 2 α-ketoglutarates to 2 malates in the citric acid cycle is (A) 3 NADH + 1 FADH₂ + 1 GTP; (B) 6 NADH + 2 FADH₂ + 2 GTP;
(C) 4 NADH + 2 FADH₂; (D) 4 NADH + 2 FADH₂ + 2 GTP.

              18. The malate/α-ketoglutarate carrier in the inner mitochondrial membrane
(A) requires ATP and uses primary active transport;
(B) changes conformation and is therefore saturable;
(C) is a symport that uses secondary active transport;
(D) is a channel for organic molecules, which allows rapid diffusion.

              19. K_M, K_0.5, and K_T are all (A) rates for initial conditions; (B) solute concentrations required for a rate to be half the saturated rate; (C) rate constants for enzymes that are also receptors; (D) rate constants for carriers that are also enzymes.

              20. The substrate for G_sα is (A) ATP; (B) adenylyl cyclase (AC); (C) GTP; (D) PKA.

              21. For each glucose in the presence of O₂, the pay-off phase of glycolysis has an energy cost of         , a total energy yield of                , and ends with                       .
(A) 2 ATP, 4 ATP + 2 NADH, 2 pyruvate; (B) 2 ATP, 4 ATP + 0 NADH, 2 lactate; (C) 0 ATP, 4 ATP + 2 NADH, 2 pyruvate; (D) 0 ATP, 4 ATP + 0 NADH, 2 lactate.

              22. PDH requires the co-substrate coenzyme                , which is modified to                        , and the prosthetic coenzyme           , which is                              during the reaction.
(A) FAD, FADH₂, TPP, acetylated; (B) CoA-SH, AcCoA, lipoate, reduced;
(C) NAD⁺, NADH, CoA-SH, oxidized; (D) ATP, ADP, biotin, oxidized.

              23. When insulin binds its receptor, glycogen                        increases, because                           becomes more active when phosphate is                                .
(A) synthesis, glycogen synthase, removed by PP-1;
(B) synthesis, PKA, added by c-AMP;
(C) degradation, phosphorylase kinase, added by PKA;
(D) degradation, glycogen phosphorylase, removed by PP-1.

              24. When the protein PFK-2/FBPase-2 is phosphorylated, the active site
                     becomes                  active, and fructose-2,6-bis-phosphate is                      .
(A) PFK-2, more, synthesized; (B) PFK-2, less, synthesized;
(C) FBPase-2, more, synthesized; (D) FBPase-2, more, degraded.

              25. Fructose-2,6-bis-phosphate               PFK-1 and                 FBPase-1, so that                                  is more likely to occur. (A) activates, inhibits, gluconeogenesis;
(B) activates, inhibits, glycolysis; (C) inhibits, activates, glycolysis;
(D) inhibits, activates, gluconeogenesis.

26. Use the small peptide below and the pK_a's given for each amino acid residue. The residues are numbered 1-5, starting on the left. (10)
a. Write the 3-letter abbreviations and the 1-letter abbreviations in the table.
b. At what pH range is the peptide shown?
c. Assume that all functional groups use the specified pK_a's. What change occurs when
       the pH goes from 5 to 3? Be specific about the group that changes and how it changes.
d. In fact, at least one group probably has a modified pK_a . What group, how does the pK_a
       change, and why?

28. The reaction catalyzed by isocitrate dehydrogenase has ΔG°′ = − 20.9 kJ/mol.
a. What is the ratio of [products]/[reactants] when ΔG = 0?
b. Write the reaction catalyzed by isocitrate dehydrogenase. (You do not need to draw
       any molecules.)
c. Describe one condition that would cause ΔG to increase to 0, and explain how that
      affects the activity of isocitrate dehydrogenase.

29. Electron transport is associated with pumping protons against their electrochemical gradient. Answer a and b; answer either c or d.
a. Fill in the table to indicate the number of protons pumped by each Complex as a
      result of oxidizing 1 NADH.

      b. Given ΔV = − 0.20 V (P → N), [H⁺] P = 1 x 10⁻⁷ M, and [H⁺] N = 5.8 x 10⁻⁸ M,
       what is ΔG_T for moving H⁺ across the membrane by Complex IV?
c. How many ATP's can be made as a result of oxidizing 4 NADH? Show your labeled
       work for solving the problem.
d. Describe one condition that would change the answer to part c. You should be clear
      about whether the number of ATP's made would increase or decrease as a result of
      the change.

Answer one number 30 or the other but not both.

30. PKA directly or indirectly regulates the activity of several enzymes involved in glycolysis, gluconeogenesis, and glycogen metabolism. (10)
a. Write the reaction PKA catalyzes.
b. How is PKA activated? Be specific. You do not need to describe the entire pathway,
      but you should name the initial cause and describe the final activation step.
c. In general, what is the relationship between activating PKA and regulation of
      carbohydrate metabolism?

30. Draw the reactions of the citric acid cycle and include the energy produced.
Write the name of each enzyme that catalyzes an oxidation-reduction reaction.

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