There are 48 questions in all. Questions 1-8 are essays and problems worth 64 points.
Questions 1-4 and 9-33 are over recent material, and 5-8 and 34-48 are review questions. Multiple choice questions 9-21 and 34-39 are worth 3 points each.
Questions 22-33 and 40-48 are worth 2 points each.
These are equations and constants that you may find useful:

1. The two diagrams below represent two stages in ATP synthesis by ATP synthase. (10)

a. O, L, and T are conformations of the b subunits, and g is another subunit.
O is the open conformation, which has low affinity for ATP (releases ATP and ADP).
L is the loose conformation, which has high affinity (binds) ADP and P_i.
T is the tight conformation, which has very high affinity for ATP.
b. The bond between ADP and P_i is formed, but ATP is not released.
c. The conformation is caused by the rotation of the γ subunit, which is caused by the rotation of the ring of c subunits that are part of F_o.

2. The molecule below is a substrate in the citric acid cycle. (10)
a. Name the enzyme that catalyzes the next reaction and draw the structure of the product.
b. The molecule you drew is also a substrate in the citric acid cycle. Name the enzyme
    for which it is a substrate and draw the structure of the next product. (4)
c. Add all co-substrate coenzymes produced by the two reactions. (2)

3. Skeletal muscle glycogen phosphorylase is regulated both allosterically and covalently.
a. Write the reaction catalyzed by glycogen phosphorylase. (3)
b. Name the enzyme that covalently activates glycogen phosphorylase and write the
    reaction it catalyzes. (5)
c. Glucose-6-P is an allosteric modulator of glycogen phosphorylase. Is it a positive or
    a negative modulator? Why is that reasonable? (2)

a. glycogen_(n+1) + P_i → glycogen_n + glucose-1-P

b. phosphorylase kinase
glycogen phosphorylase b + (2) ATP → glycogen phosphorylase a – P (a) + (2) ADP

c. Negative, which is reasonable because if the concentration of glucose-6-P is high, there is no need to degrade glycogen.

4. Use the two half reactions below.

     a. Write the balanced spontaneous whole reaction.
     Calculate ΔE°′ and ΔG°′ for the whole reaction.(6)

2 cyt a (Fe³⁺) + QH₂ → 2 cyt a (Fe²⁺) + Q + 2 H⁺
ΔE°′ = 0.29 V − 0.10 V = 0.19 V
ΔG°′ = − n F ΔE°′ = − (2) (96480 J/V-mol) (0.19 V) = − 36662 J/mol = − 36.7 kJ/mol

b. The whole reaction summarizes reactions catalyzed by complexes III and IV.

     Electron transport of 2 e⁻ by those complexes causes transport of       6         H⁺ N → P. (2)
c. Based upon your answers to a and b, what is ΔG_T for moving H⁺ N → P? (2)

     36.7 kJ/mol divided by 6 = 6.1 kJ/mol.
Moving H⁺ from N → P must have ΔG°′ < 6.1 kJ/mol.

Questions 5-8 are review essays. Answer THREE of them. Your choice.

5. We studied several enzymes regulated by covalent modification that requires PKA.
a. Write the reaction catalyzed by PKA when pyruvate kinase in the liver is the substrate.
    Which conformation (R or T) is stabilized as a result? (4)
b. What enzyme is required to convert pyruvate kinase to its original conformation?
    Write the reaction catalyzed by that enzyme. (4)

     a. pyruvate kinase + ATP → pyruvate kinase-P + ADP
The T conformation is stabilized.
     b. PP1 (protein phosphatase 1)
pyruvate kinase-P + H₂O → pyruvate kinase + P_i

6. The two diagrams below represent two stages in the mechanism of the reaction catalyzed by citrate synthase. X represents the enzyme.
a. Label the substrate molecules in the diagram on the left. (2)

     b. Name one mechanism that is used by citrate synthase. Explain how you chose that
     mechanism. (2)
Acid-base catalysis, because the His⁺ next to AcCoA loses H⁺ and the Asp⁻   on the other side of AcCoA gains H⁺.

c. Name two other mechanisms used by enzymes and a distinguishing feature of each. (4)
     Metal ion catalysis: a metal ion in the active site helps to position and/or stabilize negatively charged substrates or intermediates.
     Covalent catalysis: a temporary covalent bond is formed between the substrate and the enzyme.
     Induced fit: the enzyme has a conformation change upon binding the substrate that positions the substrate in a favorable orientation.

7. The table below lists solutes and the membranes they must cross. Choose two. Answer parts a and b for your two choices. No ATP is involved in this transport.
a. What type of protein (ion channel, uniport, symport, or antiport) is required, and in
     what direction (out → in, in → out, P → N, or N → P) does it move the solute(s)? If two
     solutes are named, write the direction for the first. (4)
     b. The equation for ΔG_T has two terms: concentration (R T ln c₂/c₁ ) and charge ((Z F ΔV)).
    Which term(s) is/are favorable for the direction in which the solute moves? (4)

*If only the first solute is considered; adding the other solute cancels the charge factor.

8. The last five residues in the β chain of hemoglobin have the sequence A-H-K-Y-H.
a. Draw the sequence at pH 7. Use R to represent the rest of the β chain. (5)
b. What type of interaction involving part of the segment could help to stabilize the T
    conformation when the pH becomes more acidic? Name the residue involved.
     What other residue (not in this segment) might be involved? (3)

NOTE: At pH 7, His side chains should not have a positive charge (because the pK_a is 6.0), Tyr side chains should have no charge (keep H⁺), and Lys side chains should have a positive charge.

b. Increasing [H⁺] means that His side chains are likely to acquire a positive charge and have an ionic interaction with a negatively charged side chain such as Asp (D) or Glu (E).
Other interactions, such as hydrogen bonds and hydrophobic interactions are less affected by changes in pH, and no covalent bond is formed just as a result of changing pH.

     C       9. Glycogen phosphorylase and glycogen synthase both (A) require ATP; (B) are ligases; (C) catalyze reactions involving α-(1→4) glycoside bonds but not reactions of α-(1→6) glycoside bonds; (D) all of the above.

     D       10. The enzyme in glycogen metabolism that produces PP_i is
(A) glycogen synthase; (B) glycogen phosphorylase; (C) phosphoglucomutase;
(D) UDP-glucose pyrophosphorylase; (E) pyrophosphatase.

     B       11. The response to glucagon in a liver cell includes (A) activation of PFK-2;
(B) a decrease in [fructose-2,6-bis-P]; (C) activation of glycogen synthase;
(D) an increase in [ATP].

     B       12. Muscle cell hexokinase is inhibited by                   and has a              K_M, while
liver cell hexokinase (glucokinase) is inhibited by               and has a                 K_M.
(A) ATP / high / glucose-6-P / low;  
(B) glucose-6-P / low / a regulatory protein / high;
(C) glucose-6-P / high / ATP / low; (D) a regulatory protein / low / ATP / high.

     A       13. The response to epinephrine in a muscle cell includes (A) activation of PKA;
(B) inhibition of glycogen phosphorylase; (C) activation of glycogen synthase;
(D) all of the above.

     B       14. Coenzyme Q is reduced by Complex          , accepting                  electrons. It is then oxidized by Complex            .
(A) I / 4 / III;               (B) II / 2 / III;              (C) I / 2 / II;             (D) II / 4 / IV.

     A       15. The ratio of the number of cyt c (Fe²⁺) oxidized by Complex IV to the number of O₂ reduced is (A) 4:1; (B) 2:1; (C) 1:2; (D) 3:2.

     C       16. Which of the following is the correct sequence of electron transport complexes required for the oxidation of succinate? (A) I, II, IV: (B) I, III, IV: (C) II, III, IV;
(D) II, I, III, IV.

     A       17. Antimycin A is an inhibitor of complex III. Treatment with Antimycin A would increase                    concentration and        O₂ consumption
(A) QH₂, reduce; (B) Q, not change; (C) fumarate, increase; (D) QH₂, increase.
Assume you are studying mitochondria that are well supplied with citrate, and the citric acid cycle is functioning normally until you add the treatment.

     C       18. Synthesis of 2 ATP by ATP synthase requires transport of                 from the P side to the N side through ATP synthase and a total of 6 conformation changes by                  β subunits.
(A) 6 e⁻ / 3 ;                    (B) 8 H⁺/ 4;                (C) 6 H⁺ / 2;                 (D) 8 e⁻ / 2.

     B       19. Energy for the synthesis of ATP by ATP synthase is provided directly by              and indirectly by                                 . (A) movement of ADP through the membrane / ATP;
(B) movement of the ring of c subunits / oxidation-reduction reactions;
(C) conformation changes / glycolysis; (D) electron transport / proton transport.

     C       20. Degradation of 1 glucose molecules in the presence of O₂ in a cell that uses glycerol-3-P dehydrogenase results in the net synthesis of       ATP as a result of glycolysis,                  ATP as a result of pyruvate dehydrogenase, and                  ATP as a result of reactions in the citric acid cycle.
(A) 2, 2, 20;          (B) 3, 5, 25;                 (C) 5, 5, 20;                (D) 5, 2, 25.

     D       21. Which of the following conditions reduces ATP synthesis by ATP synthase?
(A) low pO₂; (B) reducing work done by the cell; (C) low concentration of glucose and other energy sources; (D) all of the above.

22-27. Use these molecules. Not all molecules are used. In addition, name the pathway that requires each enzyme.   A pathway may be used more than once. (2 points each)
Assume the citric acid cycle reactions go clockwise (from citrate to oxaloacetate).

Pathways: (K) citric acid (Krebs) cycle; (N) NADH shuttle; (O) glycogen degradation;
(R) regulation of glycolysis and gluconeogenesis; (S) glycogen synthesis.
If a molecule is involved in two pathways, list either. Use each pathway at least once.

    C        22. Intermediate for aconitase                       K      Pathway requiring this enzyme

    F        23. Product of PFK-2                                       R      Pathway requiring this enzyme

    G        24. Substrate of glycogen synthase               S      Pathway requiring this enzyme

    I        25. Substrate of phosphoglucomutase        O (S)    Pathway requiring this enzyme

    B        26. Product of malate dehydrogenase          K (N)    Pathway requiring this enzyme

    D        27. Substrate of glycerol-3-P dehydrogenase in the inner membrane

    N        Pathway requiring this enzyme

28-31. Answer with the appropriate coenzyme that is required by pyruvate dehydrogenase.
(C) CoA-SH; (F) FAD; (L) lipoate; (N) NAD⁺; (T) TPP. (2 each)    Use a coenzyme only once.

     L       28. Required to transfer C₂ to CoA-SH                    C or L    31. Required by E₂

     F       29. Required to oxidize reduced lipoate (dihydrolipoate)

     N or C      30. A co-substrate coenzyme

32-33. Answer with the appropriate hormone: (E) epinephrine; (G) glucagon; (I) insulin.
Use a hormone only once. 2 points each

  E or G   32. Causes an increase in glycogen degradation in skeletal muscle cells

     I       33. Causes an increase in glycolysis in liver cells

The remaining questions cover review material. Questions 34-39 are worth 3 points each.

     D       34. Glutamate has three pK_a's: 2.19, 4.25, and 9.67. The optimal glutamate buffer for pH 4.5 has a ratio of                 for               . Use these molecules:

                 (A) 0.56 / [P]/[O];      (B) 204 / [N]/[O];      (C) 0.25 / [Q]/[P];              (D) 1.8 / [P]/[O].

     C       35. Pyruvate can be converted to lactate, alanine, oxaloacetate, or AcCoA because it is the substrate for four different enzymes. In a mixture such as a cell, what two factors determine the major product?
(A) ΔG°′ for each reaction and V_max for each enzyme;
(B) [pyruvate] and regulation of the enzymes;
(C) k_cat /K_M   for each enzyme and [co-substrate];
(D) V_max for each enzyme and PKA activity.

36-37. Use these graphs on O₂ binding by myoglobin (Mb) and hemoglobin (Hb).

     B       36. The Hill plot shows that line              (Hb) has           , and the other plot shows that
                  has higher affinity for O₂. (A) A, ↑ K_d when pO₂ ↓, Hb;
(B) B, ↑ K_d when pO₂ ↑, Mb; (C) B, ↓ K_d when pO₂ ↑ , Hb;
(D) A, ↓ K_d when pO₂ ↓, Mb.

     B       37. Line C shows that adding CO₂ stabilizes the              conformation, so that the % of                             with O₂ bound              if pO₂ remains the same.
(A) T, Hb molecules, ↑ ; (B) T, hemes, ↓ ; (C) R, Hb molecules, ↑ ; (D) R, hemes, ↓ .

     B       38. PFK-1 is allosterically activated when             binds to a PFK-1                    site, which
                  the [fructose-6-P] required for the apparent K_0.5.
(A) ATP / active / ↑ ; (B) fructose-2,6-bis-P / allosteric / ↓ ;
(C) AMP / allosteric / ↑ ; (D) fructose-1,6-bis-P / active /↑ .

     A       39. Gluconeogenesis             energy, occurs in                 , and is used to                      .
(A) requires / liver cells / provide glucose for cells when blood glucose is low;
(B) produces / all cells / provide ATP for cells when energy supplies are low;
(C) requires / skeletal muscle cells / provide ATP in case of emergency need;
(D) produces / liver cells / provide ATP in the absence of O₂.

40-42. Use these molecules. Not all molecules are used. (2 points each)

     D       40. The product of lactate dehydrogenase when [NADH] is high.

     H       42. α-glucose with its anomeric carbon circled

     G       41. The substrate of FBPase-1

     C       43. Which of the following enzymes catalyzes a reversible reaction that requires metal ion catalysis? (A) chymotrypsin; (B) hexokinase; (C) carbonic anhydrase;
(D) glyceraldehyde-3-P dehydrogenase.

44-45. Answer (A) adenylyl cyclase (AC); (G) Gα; (P) PKA; (D) all of these.
If an answer is true for two enzymes, answer with both.

    A P     44. Catalyzes its reaction several times whenever it is activated.

    G        45. Has hydrolase activity

    D        46. The Michaelis-Menton equation has                in both numerator and denominator and                 only in the numerator.
(A) K_M/ V_max ;   (B) V_max / [S];       (C) K_M / [S];         (D) [S] / V_max .

    C        47. Moving an ion in a spontaneous direction can be performed by
(A) an ion channel only; (B) a carrier protein only; (C) both proteins;
(D) a primary active transporter only.

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