Exam 4 Fall 2007
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There are 40 questions in all. Questions 1-4 are each worth 10 points, 5-7 are each worth 8 points, and most of the remaining questions are each worth 3 points. Exceptions are noted. Questions 8-27 cover recent material, and 28-39 are review.

These are equations and constants that you may find useful:

ΔGT = R T ln (c2/c1) + Z F ΔV

R = 8.315 J/mole-K

T = 298 K

ΔG = ΔG°′ + R T ln Keq

F = 96,480 J/V-mole

ΔV = − 0.070 V

General note: "Write a reaction" means to write the names, but you don't need to draw the molecules. "Draw a reaction" means you need to show the molecules.

1. Most cells use glucose as their preferred energy source. Answer these questions for a cell that uses the malate shuttle and has O2 present. Read the directions first .
a. What is the net energy yield from one glucose?
     Answer by listing the total high energy coenzymes produced in each pathway (the
     direct yield) and converting NADH and FADH2 into number of ATP (the oxidative
     phosphorylation yield). Write 0 if none was produced.
     Substrate level phosphorylation means ATP and/or GTP produced directly in the
     pathway; the shaded cells are ones where you don't need to write anything.

pathway

substrate level phosphorylation

Number NADH

Number FADH2

glycolysis
direct yield

     

glycolysis
oxidative phosphorylation yield

     

pyruvate dehydrogenase

     

pyruvate dehydrogenase
oxidative phosphorylation yield

     

citric acid cycle

     

citric acid cycle
oxidative phosphorylation yield

     

Total number of ATP

 

     b. What happens to the energy yield when UCP1 is present and active? Be specific about
     the part of the energy yield that changes and how it changes. (2)
Note: UCP1 was the topic of an assignment this semester.

2. ATP synthase is probably the one most important enzyme you'll study.
a. Describe the structure and function of Fo.
b. Describe the structure and function of F1.
c. If you haven't already explained this, how are the functions of Fo and F1 related?

3. The molecules below are all intermediates in citric acid cycle reactions. Choose two and answer the questions.
a. Name the enzyme that catalyzes the reaction.
b. Draw the structures of the substrate(s) and product for the reaction.
     If you need more room, draw the structure(s) below.
c. What is unusual and/or important about either the enzyme or the reaction?

a.

a.

a.

           

substrate

product

substrate

product

substrate

product

4. Phosphorylase kinase and glycogen synthase are both substrates for PKA.
a. Choose one and write the reaction catalyzed by PKA. Indicate whether the enzyme you
    chose becomes more active (R) or less active (T) as a result of the reaction. (4)
b. Write the reaction the other enzyme (the one not used in part a) catalyzes. (4)
c. Why is it significant that both enzymes are modified by PKA? (2)

5. You have been asked to design a dipeptide buffer for pH 4 using two different amino acids. The relevant pKa's of the three best choices are given below.
a. Which dipeptide would be the best buffer?
b. Does it matter what the sequence is (which residue is first)? If it does, what is the best
    sequence? If it doesn't matter, why not?
c. The pH can be adjusted to 4 using either HCl or NaOH. At that pH, what is the most
    common form of the optimal dipeptide? Draw it.

amino acid

aspartate

glutamate

histidine

α-COOH pKa

1.88

2.19

1.82

α-NH3+ pKa

9.60

9.67

9.17

side chain pKa

3.65

4.25

6.00

6. The reaction catalyzed by malate dehydrogenase in the cytosol has ΔG°′ = − 29.7 kJ/mol. This is the reverse of the citric acid cycle, which is always written as a reversible reaction.
a. What is Keq for the cytosol reaction?
b. How are conditions in the matrix different from the cytosol, so that a reaction with
    ΔG°′ = 29.7 kJ/mol can occur?

7. The Gs protein pathway is named for the G protein.
a. How is Gα activated?
b. What does Gα activate, and how?
c. How is Gα inactivated?

8-9. Use the diagram, which represents glycogen synthesis, and the molecule on the right.
R, S, and T are intermediates in glycogen synthesis, while N, O, and P are enzymes.
Molecule R connects glycolysis and glycogen synthesis.

              8. Which blank (R, S, or T) is the molecule?

              9. Enzyme                  (N, O, or P) requires UTP and releases PPi.

              10. Glycogen synthase is                active when blood glucose level is                as a result of                                binding its receptor. (A) more, low, glucagon;
(B) more, high, glucagon; (C) more, high, insulin; (D) less, high, insulin.

              11. The branching and de-branching enzymes are very similar, except that the
                 enzyme also has                 activity. (A) branching, phosphorylase;
(B) debranching, hydrolase; (C) debranching, transferase; (D) branching, ligase.

              12. Pyruvate kinase in liver cells is regulated covalently and allosterically. It is
                 by being phosphorylated and is                  by increased fructose-1,6-bis-P.
(A) activated, activated; (B) activated, inhibited; (C) inhibited, activated;
(D) inhibited, inhibited.

              13. Increasing the ratio of [ATP]:[AMP] in                      cells inhibits                     .
(A) liver, PFK-1; (B) skeletal muscle, lactate dehydrogenase;
(C) liver, glyceraldehyde-3-P dehydrogenase; (D) all of the above.

14-16. Answer with these choices: (A) PFK-1; (B) PFK-2; (C) FBPase-1; (D) FBPase-2.
If two answers are correct, write both . (2 points each)

              14. A hydrolase

              15. Activated by
                    fructose-2,6-bis-P

              16. Regulated covalently

              17. When epinephrine binds a liver cell receptor,                                    is                      as
a result of activating the G-protein pathway. (A) adenylyl cyclase (AC), activated;
(B) glycogen synthase, inhibited; (C) FBPase-1, activated; (D) all of the above.

              18. The coenzyme on the right is required by               of pyruvate dehydrogenase in order to
(A) E1, remove CO2; (B) E2, transfer C2 to CoA-SH;
(C) E2, oxidize CoA-SH; (D) E3, oxidize FADH2.

19-21. Use these molecules. Not all molecules are used. Do not use a choice more than once .

(A)

(B)

(C)

(D)

(E)

(F)

              19. This is the product of fumarase.

              20. This is the product of a redox reaction that also produces NADH.

              21. This is the substrate of a redox reaction that produces FADH2.

              22. The enzyme                 is allosterically                                       by                        .
(A) citrate synthase, activated, ATP; (B) isocitrate dehydrogenase, inhibited, Ca2+;
(C) α-ketoglutarate dehydrogenase, inhibited, NADH; (D) all of the above.

23-25. Answer (A) Complex I; (B) Complex II; (C) Complex III; (D) Complex IV.
If two answers are correct, answer with both letters.

              23. Oxidizes succinate                                                    24. Reduces cyt c (Fe3+)

              25. Moves 4 H+ from N to P for every 2 e− transferred.

26. Use these half reactions.

Half reaction

E°′ (V)

Half reaction

E°′ (V)

1/2 O2 + 2 H+ + 2 e− → H2O

0.82

fumarate + 2 H+ + 2 e− → succinate

0.03

cyt c (Fe3+) + e− → cyt c (Fe2+)

0.25

pyruvate + 2 H+ + 2 e− → lactate

− 0.19

Q + 2 H+ + 2 e− → QH2

0.10

NAD+ + 2 H+ + 2 e− → NADH + H+

− 0.32

              26. The correct whole reaction for complex IV, with ΔE°′, is
(A) 2 cyt c (Fe3+) + 1/2 O2 + 2 H+ → 2 cyt c (Fe2+ ) + H2O, and ΔE°′ = 1.07 V;
(B) 2 cyt c (Fe2+) + 1/2 O2 + 2 H+ → 2 cyt c (Fe3+) + H2O, and ΔE°′ = 0.32 V;
(C) 2 cyt c (Fe2+) + 1/2 O2 + 2 H+ → 2 cyt c (Fe3+) + H2O, and ΔE°′ = 0.57 V;
(D) 2 cyt c (Fe3+) + H2O → 2 cyt c (Fe2+) + 1/2 O2 + 2 H+, and ΔE°′ = 0.57 V.

              27. Four different complexes (I – IV) are involved in electron transport. All four
(A) transport protons across the membrane from the N side to the P side;
(B) include more than one coenzyme or cytochrome involved in redox reactions;
(C) transport electrons across the membrane from the N side to the P side;
(D) either oxidize or reduce coenzyme Q.

              27. When 6 NADH are oxidized,                   cyt c (Fe3+) are eventually reduced, resulting in the synthesis of                H2O.
(A) 6, 6; (B) 12, 6; (C) 12, 12; (D) 12, 24.

              28. Antimycin A inhibits cytochrome c1, which transfers e− to cytochrome c. In the presence of antimycin A,         can be oxidized, but              concentration increases.
(A) NADH, succinate; (B) succinate, QH2; (C) QH2, cyt c (Fe2+); (D) cyt c (Fe2+), QH2.

              29. Citric acid (C6H8O7) has three pKa's: 3.13, 4.76, and 6.70. The optimal citrate buffer for pH 5.0 has a ratio of                    for                                          .
(A) 1.74, Na2C6H6O7 / NaC6H7O7; (B) 0.24, Na2C6H6O7 / NaC6H7O7;
(C) − 0.24, Na2C6H6O7 / NaC6H7O7; (D) 0.020, Na3C6H5O7 / Na2C6H6O7.

              30. Which of these amino acids has the one-letter abbreviation L?

(A)

(B)

(C)

(D)

31-32. Red blood cells contain carbonic anhydrase, which catalyzes H2O + CO2 ↔ HCO3− + H+, and the Cl−–HCO3− transporter, which is an antiport. ΔGT for Cl− into the cell = 45 J/mol
ΔG°′ for the reaction catalyzed by carbonic anhydrase ∼ 0.

              31. The major factor that determines the direction of HCO3− transport (into or out of the cell) is (A) ΔV for the cell membrane; (B) the concentration gradient;
(C) the charge on HCO3−; (D) the charge on Cl−.

              32. Increasing [CO2] leads to increasing                , stabilizing the                conformation of hemoglobin, and                    O2.
(A) pH, T, releasing; (B) [H+], T, binding; (C) [H+], T, releasing; (D) pH, R, binding.

              33. Which mechanism of catalysis does pyruvate dehydrogenase use for two of its three enzymes? (A) acid-base; (B) covalent; (C) metal ion.

              34. A branch point is a molecule, such as glucose-6-phosphate, that can go in several directions. The kinetic constant value that best indicates the destination of a branch point molecule is (A) a high KM; (B) a low Vmax; (C) a high kcat/KM; (D) a high Vmax.

              35. PFK-1 is allosterically regulated. Therefore, you know that the structure of PFK-1
(A) has more than one active site; (B) has cooperative binding;
(C) changes conformation; (D) all of the above.

              36. What happens to succinate dehydrogenase in the presence of malonate?
(A) It is allosterically inhibited; (B) Its KM increases;
(C) Its Vmax increases; (D) all of the above.

              37. The Ca2+ ATPase moves Ca2+ against its electrochemical gradient, which requires
(A) 2 Ca2+ forming a Ca2+ – ATP 4− complex that is moved across the membrane;
(B) transferring phosphoryl to part of the carrier and changing conformation;
(C) opening a calcium channel in response to epinephrine; (D) all of the above.

              38. Which amino acid side chain rotates out of the nicotinic ACh receptor when ACh binds? (A) glutamate; (B) glycine; (C) leucine; (D) tyrosine.

              39. The reason GAPDH (glyceraldehyde-3-phosphate dehydrogenase) is important is that it (A) produces NADH before ATP is produced; (B) produces ATP;
(C) catalyzes an irreversible reaction in glycolysis; (D) is the committed step.

              40. Lactate dehydrogenase converts lactate to pyruvate when (A) [ATP] is high;
(B) [O2] is high; (C) [ATP] is low; (D) [O2] is low.

 

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