C483 Practice Final Exam

Last Name___________________________ First Name: _______________________

Please make sure there are 16 pages to this exam, including data and scratch pages.

Part A is composed of 25 multiple choice problems worth 2 points each. Circle the letter next to the correct answer. Multiple answers for the same question receive no credit.

Part B is composed of 17 short answer problems worth 3 points each.

Part C is composed of five problems worth 55 points total. Score:

Multiple Choice: _________/50

Short answers _________/51

Question 43 _________/10

Question 44 _________/10

Question 45 _________/10

Question 46 _________/10

Question 47 _________/15

Bonus _________/4

Total: __________/160

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Part A. (2 points each) Questions 1-8 focus on the most recent material.

1. ______ Which statement concerning nitrogen metabolism reactions in humans is FALSE? A. Ammonia is released in the liver mitochondria when glutamate is oxidized to -ketoglutarate. B. Glutamate synthetase is a “mop up” enzyme for free ammonia, requiring no ATP. C. Transaminase enzymes require PLP as a cofactor. D. Transaminases catalyze a reaction that is neither an oxidation nor reduction.

2. ______ A carbon atom carried by THF can be derived from which amino acid? A. alanine B. aspartate C. glutamate D. serine

3. ______ Which of these is the purpose of the citrate/pyruvate shuttle? A. Produce NADPH in the cytosol

B. Take NADH into the matrix C. Carry acetyl CoA into the cytosol. D. Produce pyruvate under anaerobic conditions

E. More than one of the above

4. ______ The reaction that makes dUMP into dTMP is a target for cancer treatment according to which of these mechanisms? A. Thymidylate synthase can be inhibited by a mechanism based inhibitor. B. Dihydrofolate reductase, which catalyzes the regeneration of THF from DHF, can be inhibited by a competitive inhibitor. C. Both A and B. D. Neither A nor B.

5. ______ Which of the following is not a tissue specific function of the liver? A. regeneration of pyruvate from alanine. B. regeneration of pyruvate from lactate. C. formation of urea. D. -oxidation.

E. release of glucose to the blood.

6. ______ Which hormone is not matched with its effect? A. Glucagon leads to activation of glycogen phosphorylase. B. Glucagon stimulates gluconeogenesis. C. Insulin stimulates hormone sensitive lipase to hydrolyze fat stores in adipose.

D. Insulin leads to increase of glucose transport from blood into the cell.

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7. ______ Each of these amino acids is paired with its catabolic intermediate except A. serine pyruvate B. proline succinyl CoA C. asparagine oxaloacetate D. arginine alpha-ketoglutarate

8. ______ Proline biosynthesis starts with the metabolic intermediate A. oxaloacetate B. -ketoglutarate C. pyruvate D. 3-phosphoglycerate

9. ______ The aggregation of nonpolar molecules or groups in water is thermodynamically favorable due to the A. increased entropy of the water molecules. B. decreased enthalpy of the system. C. increased entropy of the nonpolar molecules when they associate. D. very strong van der Waals forces among the nonpolar molecules or groups.

10. ______ The coding strand DNA sequence that would code for Leu-Pro-His would be:A. 5’-CUUCCUCAU-3”B. 5’-UACUCCUUC-3’C. 5’-CTTCCTCAT-3’D. 5’-TACTCCTTC-3’

11. ______ Glycine has pKa values of 2.1 and 9.0. For which pH would it BEST serve as a buffer?

A. 2.3B. 3.1C. 5.5D. 8.3E. 11

12. ______ The net charge of cysteine in a solution at pH 8.3 is:A. -1B. -0.5C. +0.5D. +1E. +1.5

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13. ______ Because hemoglobin is tetramericA. it binds oxygen more tightly than myoglobin.B. its oxygen binding curve is a rectangular hyperbola.C. it cannot be regulated by allosteric control.D. it can bind oxygen cooperatively.E. None of the above.

14. ______ The enzyme that catalyzes the transformation of pyruvate to oxaloacetate can be categorized as this type of enzyme:

A. OxidoreductaseB. TransferaseC. HydrolaseD. LyaseE. Ligase

15. ______ An enzyme inhibitor causes no change in the apparent KM value, but Vmax goes down. It must be

A. a competitive inhibitor. B. an irreversible inhibitor. C. an uncompetitive inhibition. D. a noncompetitive inhibitor.E. a mechanism based inhibitor.

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16. ______ Triacylglycerols are not found in cell membranes because they are A. not amphipathic. B. too rigid.C. not abundant in cells.D. charged at biological pH.

17. ______ The spontaneity of a neutral organic molecule crossing a membrane depends on A. the membrane potential.B. the concentration gradient.C. The membrane potential and the concentration gradient.D. neither the membrane potential nor the concentration gradient.

18. ______ Which of these signal transduction components is a second messenger?A. glucagonB. G-protein coupled receptorC. cAMPD. glucagon binding proteinE. receptor tyrosine kinase

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19. ______ Which of the statements concerning a near-equilibrium reaction is TRUE?A. The concentrations of reactants and products are nearly equal under cellular conditionsB. The enzyme catalyzed reaction is most likely regulated.C. The standard free energy of the reaction must be near zero.D. The flux through the reaction is affected by changes in reactant concentration.

20. ______Which statement is false concerning the fate of glucose-6-phosphate in a muscle cell?A. G-6-P can be incorporated into glycogen.B. G-6-P can enter the pentose phosphate pathway. C. G-6-P can be converted to glucose.D. G-6-P can enter glycolysis.

21. ______ The net effect of the eight steps of the citric acid cycle is toA. completely oxidize an acetyl group to carbon dioxide.B. convert pyruvate to acetyl CoA.C. produce a citrate moleculeD. produce 6 ATP for every pass through the cycle.E. More than one of the above

22. ______ The standard reduction potential for the reaction of oxaloacetate and NADH to produce malate is

A. + 0.149 VB. - 0.149 VC. + 0.481 VD. - 0.481 V

23. ______ In humans, a full rotation of the ATP synthase rotor requires _____ protons and forms ___ ATP.

A. 3, 8B. 8, 3C. 2, 10D. 10, 2

24. ______ Which of these molecules is not correctly matched to its role in nitrogen metabolism?

A. glutamine: produced in nitrogen “mop up” reactionsB. glutamate: formed in transamination reactions from other amino acidsC. alanine: carries nitrogen from liver to the muscleD. arginine: part of the urea cycleE. aspartate: a nitrogen donor in urea synthesis

25. ______ Which reaction does not require the cofactor TPP?A. decarboxylation of -ketoacids in branched amino acid catabolismB. pyruvate acetyl CoAC. transketalase of the pentose phosphate pathway.D. aspartate + -ketoglutarate oxaloacetate + glutamate

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Part B: (3 points each) Questions 26-30 focus on the most recent material.

26. Match each of the following processes with their cellular location: fatty acid catabolism, urea cycle, ketogenesis, amino acid synthesis and degradation, fatty acid synthesis, glycolysis

Matrix: ___________________________________________________________________

Cytosol: _______________________________________________________________

Both: _________________________________________________________________

27. What are two key differences between the isozymes hexokinase and glucokinase that allow them to have different activity with the same reaction?

28. Which of the following compounds are glucogenic? Circle every compound that is glucogenic, and put an X through compounds that are not.

Odd chain fatty acid lysine ketone bodies

Even chain fatty acid alanine glycerol

29. Circle all the reactions necessary to transform 3-phosphoglycerate into serine and put an X through the ones that are not necessary.

Decarboxylation Redox Carboxylation

Hydrolysis condensation transamination

30. Circle the one letter abbreviation of the THREE amino acids that are major carriers of nitrogen from peripheral tissue to the liver. If you circle more than three, you will get zero points.

A D E G R Q

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31. For the chymotrypsin (serine protease) active site, match the structure with one of the following catalytic strategies it performs: acid/base catalysis, covalent catalysis, stabilization of high energy intermediate

Serine sidechain of the catalytic triad: _____________________________

Histidine sidechain of the catalytic triad: _____________________________

Oxyanion hole: _______________________________

32. Draw lysine at its isoelectric point.

33. The oxidation of malate is the last step of the citric acid cycle. The reaction has a large positive standard free energy, but occurs spontaneously in the cell. Explain.

34. If this Michaelis-Menton graph were produced using a [E]T of 30 nM, estimate kcat and KM:

kcat = _____________________ KM = _____________

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35. Draw the structure of the C-3 epimer of -D-glucose.

36. What is the net change in high energy bonds in the reaction below? Predict the standard free energy of this reaction to be positive, negative, or near zero.

37. How many of each of these molecules are net produced when one acetyl CoA goes through one full round of the citric acid cycle?

NADH _______ CO2 _________ oxaloacetate __________

38. Calculate the free energy change when glucose is phosphorylated by ATP to form glucose-1-phosphate.

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39. Draw an oxygen binding curve for hemoglobin (be sure to label the axes.). Bisphosphoglycerate stabilizes the tense state of hemoglobin—would an increase in its concentration cause your curve to shift left or right?

left or right? ___________________

40. How many net ATP can be produced from full anaerobic catabolism of a molecule of glucose released from glycogen in a muscle cell?

41. Choose one protein from this list that matches with each statement below: G-actin, tubulin, keratin, collagen, myosin

Coiled-coil that makes up hair ____________________

Globular monomer that only hydrolyzes ATP when polymerized ________________

ATP binding motor that moves muscle __________________

42. The sequence of a protion of a protein was determined to be …PAIWCVVIWMQFIAVWMI… Is this sequence most likely the sequence of A.) a hairpin turn, B.) -sheet on the surface of a globular protein, or C.) a transmembrane -helix? Explain.

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43. CHOOSE 1 OF THE FOLLOWING problems. Provide a full enzyme mediated arrow mechanism for the reaction using the necessary cofactor (see final page for structures.)

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44. What is the pH of a 0.10 M acetate/acetic acid buffer (pKa= 4.7) in which acetic acid is 86.4% in its protonated form?

Draw the asp-val-tyr tripeptide in its most prevalent ionization state/states in this buffer. What is the approximate net charge on this tripeptide?

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45. Explain the logic of these pathway regulations:

A. Phosphofructokinase, not hexokinase, is the main regulation site of glycolysis.

B. SuccinylCoA inhibits the entry of acetyl CoA into the citric acid cycle.

C. NADH inhibits pyruvate dehydrogenase.

D. Citrate inhibits the citric acid cycle and activates acetyl-CoA carboxylase.

E. Insulin leads to activation of glycogen synthase.

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46 A. Certain microorganisms with an incomplete citric acid cycle decarboxylate -ketoglutarate to produce succinate semialdehyde. A dehydrogenase then converts succinate semialdehyde to succinate. Fill in the missing structures in the boxes.

B. These reactions can be combined with other standard citric acid cycle reactions to create a pathway from citrate to oxaloacetate. Give structures or names of intermediates in this pathway.

C. How does this alternative pathway compare to the standard citric acid cycle in its ability to make free energy available to the cell?

4 point bonus: Which cofactor would you expect to be necessary for an amino acid racemase? Explain the role of the cofactor in one sentence.

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47. A. A molecule of glucose that you eat can eventually be transformed into part of a fatty acid that you store. Circle the pathways/cycles below that are part of this overall flow of carbon atoms. Cross out any that are not.

Gluconeogenesis, beta-oxidation, citric acid cycle, glycolysis, urea cycle, fatty acid synthesis

B. Trace the metabolic path of this glucose molecule through the enzymes it encounters along the way to being made into fat. Write all the enzymes in the list below into the proper places in the figure below. If the enzyme is not used, write its name in the “not used” box. If it is used, write the enzyme in the order that the carbon atoms from glucose encounter the enzymes.

Pyruvate dehydrogenase, fumarase, aldolase, lactate dehydrogenase, pyruvate kinase, acetyl CoA carboxylase, fatty acid synthase, hexokinase, carnitine acyltransferase, ATP synthase

B. What is the minimum number of glucose molecules that would be necessary to be the carbon source for synthesis of a 16-carbon fatty acid through this pathway?

C. How many net glucose can be made from one molecule of a 16-carbon fatty acid?

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pKa values for peptides: carboxy terminus: 3.2 amino terminus: 9.0

Amino acid Sidechains: Asp 3.9 Cys 8.4 Arg 12.5 Glu 4.1 Tyr 10.5 His 6.0 Lys 10.5

G = RT ln[X ] final

[X ] initial + ZF G = -nFEo’

R = 8.314 J/ mol . K F = 96,485 J/V . mol

pH = pKa + log [A-]/[HA] v = (Vmax[S])/KM + [S]

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Scratch paper: Nothing on this page will be graded.

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