2. (12 pts) Given the following metabolic pathway (as it occurs in the cell):

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1 Answer Sheet 1 (Gold) 1. (1 pt) Write your exam ID (A) in the blank at the upper right of your answer sheet. 2. (12 pts) Given the following metabolic pathway (as it occurs in the cell): a. Would you expect enzyme 1 to be regulated? Explain why in 15 words or less. b. If you answered yes to part a, name a molecule that you would expect to act as a positive effector. Name a molecule that you would expect to act as a negative effector. (If you answered no, write NA.) c. Would you expect enzyme 2 to be regulated? Explain why in 15 words or less. d. If you answered yes to part c, name a molecule that you would expect to act as a positive effector. Name a molecule that you would expect to act as a negative effector. (If you answered no, write NA.) e. For the remaining enzymes (3-9), which would you expect to be regulated? List their numbers. 3. (5 pts) True or False? a. Hexokinase has a higher affinity for glucose than glucokinase. b. Hexokinase changes conformation on substrate binding. c. Hexokinase is a lyase. d. Hexokinase is regulated by substrate availability. e. Glucokinase is a multi-subunit protein. 4. (5 pts) a. Define isozyme (10 words or less). b. True or False? Glucosephosphate isomerase and triosephosphate isomerase are isozymes. 5. (5 pts) Which of the following catalytic mechanisms are important in the isomerization of glucose-6-phosphate to fructose-6-phosphate: a. general acid catalysis b. general base catalysis c. covalent catalysis d. electrostatic catalysis e. metal-ion catalysis 2/11

2 Answer Sheet 1 (Gold) 6. (8 pts) Which of the following enzymes can bind ATP? a. hexokinase o. pyruvate dehydrogenase b. glucokinase kinase c. glucosephosphate isomerase p. citrate synthase d. phosphofructokinase-1 q. aconitase e. phosphoprotein phosphatase r. isocitrate dehydrogenase f. phosphofructokinase-2, s. α-ketoglutarate phosphorylated form dehydrogenase complex g. aldolase t. succinyl-oa synthetase h. triosephosphate isomerase u. succinate dehydrogenase i. glyceraldehyde-3-phosphate v. fumarase dehydrogenase w. malate dehydrogenase j. phosphoglycerate kinase x. flavoprotein dehydrogenase k. phosphoglycerate mutase y. 3-phosphoglycerol l. enolase dehydrogenase m. pyruvate kinase z. ATP synthase n. pyruvate dehydrogenase complex 7. (5 pts) An aspiring chef, you decide to try making sauerkraut (sour cabbage) at home. The recipe tells you to tightly pack the shredded & salted cabbage into a container that will not let in air. The container is then left to sit, during which time the cabbage acquires its sour taste. a. Name the process that causes the cabbage to sour, and the compound produced by this process. b. Why is it important that air not be let into the container? (20 words or less) 8. (5 pts) Which of the following statements about pyruvate dehydrogenase complex (and its mechanism) are true? a. The decarboxylase activity of enzyme 1 is due to the nucleophilicity of TPP. b. Enzyme 2 is identical to that of α-ketoglutarate dehydrogenase complex. c. The activity of the complex is important to aerobic and anaerobic metabolism. d. FAD is reduced in the formation of a disulfide bond. e. Lipoic acid is attached to enzyme 2 through a thioester bond. 9. (5 pts) Order the following steps in the reaction mechanism of citrate synthase: a. itroyl-oa is formed. b. The enzyme binds acetyl-oa. c. The intermediate is hydrolyzed. d. The enzyme binds oxaloacetate. e. The enzyme releases citrate and oa. f. The enzyme undergoes a conformational change. g. The enzyme undergoes a second conformational change. 3/11

3 Answer Sheet 1 (Gold) 10. (13 pts) You perform a carbon-labeling experiment to examine metabolism in a newly discovered single-celled eukaryote. You begin by synthesizing glucose with 14 at position 1 and feeding it to the organism. Based on what you know about metabolism in other organisms, where would you expect this carbon to end up in the compounds shown at the right? ircle each carbon that could be labeled. (Be sure to record your answers on the answer sheet.) 11. (3 pts) In the reaction catalyzed by malate dehydrogenase, which compound is the oxidant? 12. (5 pts) Part of the structure of biotin is provided on your answer sheet. Show the reaction step of the pyruvate carboxylase mechanism that results in the carboxylation of biotin. (Draw the activated intermediate and electron movements.) 13. (9 pts) The standard reduction potentials for several half reactions of the electron transport chain are provided below: NAD + + H + +2e - NADH FMN + 2H + + 2e - FMN FAD + 2H + + 2e - FAD oq + 2H + + 2e - oq yt. b (Fe 3+ ) + e - yt. b (Fe 2+ ) yt. c (Fe 3+ ) + e - yt. c (Fe 2+ ) yt. a 3 (Fe 3+ ) + e - yt. a 3 (Fe 2+ ) O 2 + 4H + + 4e - 2 O V V V V V V V V a. alculate the E ' for the transfer of two electrons from complex II to oxygen in a human muscle cell. Show your work. b. alculate the G ' for the transfer of two electrons from complex II to oxygen in a human muscle cell. Show your work. c. What percentage of this free energy change is lost as heat in the electron transport chain (that is, not stored in the proton gradient)? Assume that the G ' of electron transfer G in the cell, and assume that the G of proton transfer across the mitochondrial inner membrane is 20 kj/mol. Show your work. 4/11

4 Answer Sheet 1 (Gold) 14. (6 pts) a. Define antiporter (25 words or less). b. Would you expect to find antiporters in the outer mitochondrial membrane? Explain why or why not (15 words or less). 15. (10 pts) True or False? 16. (3 pts) a. If the membranes of the mitochondrion are ruptured (broken), oxidative phosphorylation cannot occur b. Raising the ph of the fluid in the intermembrane space results in ATP synthesis in the matrix. c. The correct orientation of the enzyme complexes of electron transport is necessary to the formation of the proton gradient. d. Exposing a cell to carbon monoxide will affect its ability to produce ATP. e. Radioactively labeled P i is incorporated into cytosolic ATP only in the presence of a proton gradient across the inner mitochondrial membrane. a. What component of electron transport is diffusible in the membrane? b. Why is this component diffusible in the membrane? (5 words or less.) 5/11

5 Answer Sheet 2 (Blue) 17. (1 pt) Write your exam ID (A) in the blank at the upper right of your answer sheet. 18. (4 pts) Define a hydrogen bond in 25 words or less. 19. (10 pts) a. How many different disaccharides can be formed from two glucose molecules? Show your reasoning. (onsider disaccharides related by mutarotation to be the same.) b. How many different dipeptides can be formed from any two (unmodified) amino acids? Show your reasoning. c. Which type of polymer polypeptide or polysaccharide has more potential for covalent structural diversity? Explain why in 15 words or less. 20. (4 pts) The reaction X 2Z has G ' = +7.1 kj/mol. In which of the following situations would the reaction be spontaneous only in the direction written? a. [Z]/[X] > K eq(x 2Z) j. [Z] 2 > [X] b. [Z]/[X] = K eq(x 2Z) k. [Z] 2 < [X] c. [Z]/[X] < K eq(x 2Z) l. [Z] 2 = [X] d. [Z] > [X] m. [2Z]/[X] > K eq(x 2Z) e. [Z] < [X] n. [2Z]/[X] = K eq(x 2Z) f. [Z] = [X] o. [2Z]/[X] < K eq(x 2Z) g. [Z] 2 /[X] > K eq(x 2Z) p. [2Z] > [X] h. [Z] 2 /[X] = K eq(x 2Z) q. [2Z] < [X] i. [Z] 2 /[X] < K eq(x 2Z) r. [2Z] = [X] 21. (5 pts) Which of the following features of a reaction suggest that it would be used by opposing pathways in a cell? List all that apply. a. The enzyme catalyzing the reaction is found in multiple cellular locations. b. The standard free energy change of the reaction is small in magnitude. c. The standard free energy change of the reaction is large in magnitude. d. The cellular concentrations of products and reactants are nearly equal. e. The reaction in the cell is close to equilibrium. f. The reactants and products of the reaction are at steady state. g. The enzyme catalyzing the reaction is regulated by allosteric effectors. h. The enzyme catalyzing the reaction is subject to simple feedback inhibition. 22. (5 pts) Other than coupling to ATP hydrolysis or phosphoryl transfer (or that of another nucleotide triphosphate), describe a specific way to make a highly unfavorable reaction spontaneous in the cell (20 words or less). 6/11

6 Answer Sheet 2 (Blue) 23. (23 pts) Below is the abstract for a research publication: The isocitrate dehydrogenase of Escherichia coli is an example of a ubiquitous class of enzymes that are regulated by covalent modification. In the three-dimensional structure of the enzyme-substrate complex, isocitrate forms a hydrogen bond with Ser113, the site of regulatory phosphorylation. The structures of Asp113 and Glu113 mutants, which mimic the inactivation of the enzyme by phosphorylation, show minimal conformational changes from wild type, as in the phosphorylated enzyme. alculations based on observed structures suggest that the change in electrostatic potential when a negative charge is introduced either by phosporylation or sitedirected mutagenesis is sufficient to inactivate the enzyme. Thus, direct interaction at a ligand binding site is an alternative mechanism to induced conformational changes from an allosteric site in the regulation of protein activity by phosphorylation. a. What enzyme is being studied in this article? b. What organism does the enzyme come from? c. Where in this organism (cellular location) would the enzyme be present? d. The authors used X-ray crystallography to study the enzyme. What kind of information does this technique provide? e. How many versions (or states) of the enzyme were examined? f. How did the versions (or states) of the enzyme differ? Answer by listing the unique feature of each version or state. g. The abstract states, isocitrate forms a hydrogen bond with Ser113. Based on all of the information in the abstract, what functional group of isocitrate would you expect forms a hydrogen bond with Ser113? Draw this bond. h. How does phosphorylation inactivate the enzyme? Explain in 25 words or less. i. Is the enzyme an allosteric enzyme? 7/11

7 Answer Sheet 2 (Blue) 24. (17 pts) After taking this class, you decide you love biochemistry so much that you want to study it more in graduate school. So you end up being a TA for a class like 153A. On the first exam you grade a titration curve problem. The question asks the students to draw a ph titration curve for the following peptide, and to label the axes of the curve. One student gives this drawing: a. What errors in the drawing would cause you to deduct points? List each error. (1 error or type of error per line; you may not need all of the lines.) If there are no errors, list none. b. The exam also asks the students to calculate the net (average) charge of this peptide at ph 7. What is the correct answer? (Show your work.) 8/11

8 Answer Sheet 2 (Blue) Please note that the answer blanks for this and the following problem may not be located where you first expect, and answer space is limited. Plan accordingly. 25. (25 pts) Bilirubin is a product of the catabolism of heme, and it is the compound that gives urine its yellow color. The structure of bilirubin is shown: a. ircle the atom(s) that were bound the heme iron. b. Put an asterisk (*) next to each atom that can act as an H-bond acceptor. c. Would you expect the carboxyl groups of bilirubin to have a higher or lower pka than that of glycine? Explain why in 25 words or less. Scientists have found that bilirubin can bind isocitrate dehydrogenase, as shown by the plot below: d. What kind of plot is this? e. How is NAD + used (what is its role) in this experiment? f. What does this plot show about the interaction of bilirubin with isocitrate dehydrogenase? (5 words or less.) g. Which of the following values can be determined from this plot? A. [S] H. K' m B. [E] I. V' max. [ES] J. α D. K m K. α' E. V o L. K I F. V max M. K' I G. k cat 9/11

9 Answer Sheet 2 (Blue) 26. (46 pts) Like the breakdown of glucose, the breakdown of lipids provides energy for the cell. a. In what form are lipids stored in the body? (Name the lipid class.) b. A specific example of a lipid is shown below. Name this lipid. This lipid is initially broken down into the following compounds: The parent compound (left) is converted in two steps into an intermediate of glycolysis, then broken down by the subsequent enzymes of glucose catabolism. The initial two steps are shown: c. Name the class and subclass of enzyme 1. d. Name the glycolytic intermediate produced by enzyme 2, and name any additional compound(s) used &/or produced (i.e. indicated by the boxes). Hint: We learned about this reaction in class. e. What is the net production of energy carriers by the complete, aerobic catabolism of the parent compound (including the steps catalyzed by enzymes 1 and 2 above)? Show your reasoning, and then list the net numbers of ATP+GTP, NADH, and FAD produced. (Problem continued on next page.) 10/11

10 Answer Sheet 2 (Blue) (Problem 27 continued) The remaining portions of the original lipid are transported into the mitochondrial matrix, yielding a oa-derivative; this transport requires the hydrolysis of one ATP per molecule. Once in the matrix, these compounds are broken down in a process called β- oxidation, yielding acetyl-oa. The process is repeated again and again until all of the original molecule has been broken down into acetyl-oa. oa-s O R f. Name the enzyme class and subclass (if applicable) for enzymes 3, 4, 5, and 6. enz 3 O oa-s enz 4 O oa-s enz 5 O oa-s enz 6 O oa-s H H H OH O FAD FAD O NAD + R R NADH + H + oa-sh + R O H 3 oa-s R g. Why is this pathway called β-oxidation? Explain in 10 words or less. h. How many acetyl-oa molecules are produced from the complete β-oxidation of the three substituent components of the original lipid? Show your reasoning. i. What is the net production of energy carriers by the complete, aerobic catabolism of these three lipid substituents, including their transport into the matrix, the rounds of β-oxidation, and the catabolism of acetyl-oa? Show your reasoning, and then list the net numbers of ATP+GTP, NADH, and FAD produced. j. ombining your values for parts e and i, and using the new P/O ratios for NADH and FAD, calculate the total (net) number of ATP molecules (or ATP equivalents) produced by the catabolism of the original lipid molecule. Assume that the malate-aspartate shuttle is used. k. The molecular weight of this lipid is roughly 750; that of glucose is 180. How much more ATP can be made, per unit mass, through the catabolism of this particular lipid versus the catabolism of glucose? Show your reasoning, and express your answer as a factor. (For example, 5x more ATP per unit mass from the catabolism of this lipid). 11/11

11 Name (Last, First): Student ID Number: I have read and agree to all instructions and guidelines for this exam. Signed: hemistry and Biochemistry 153A, Winter 2009 Page 2 (28 points) 2. a. First two letters of last name: Date: Answer Sheet 1 (Gold) Final Exam 1, ID: Page 2: Total score Scores / 28 b. positive effector: ; negative effector: c. (15 words or less) Page 3: Page 4: / 23 / 30 d. positive effector: ; negative effector: (15 words or less) Page 5: / 19 e. 3. a. True False 4. a. b. True False c. True False d. True False b. True False (10 words or less) e. True False 5. Page 3 (23 points) a. process: compound: b. (20 words or less) step 1: step 2: step 3: step 4: step 5: step 6: step 7:

12 hemistry and Biochemistry 153A, Winter 2009 Page 4 (30 points) 10. ircle the labeled carbon(s): Final Exam 1 Answer Sheet 1 (Gold) a. b. c. Page 5 (19 points) 14. a. 15. a. True False b. True False b. (25 words or less) (15 words or less) c. True False d. True False e. True False 16. a. b.

13 Name (Last, First): Student ID Number: First two letters of last name: Answer Sheet 2 (Blue) Total score I have read and agree to all instructions and guidelines for this exam. Signed: Date: hemistry and Biochemistry 153A, Winter 2009 Final Exam 1, ID: Page 6 (29 points) 18. Page 6: Scores / 29 Page 7: / a. (25 words or less) Page 8: / 17 b. Page 9: / 25 c. Pages 10, 11: / 46 (15 words or less) Page 7 (23 points) 23. a. (20 words or less) g. name of functional group: drawing: b. c. d. h. e. f. i. (25 words or less)

14 hemistry and Biochemistry 153A, Winter 2009 Final Exam 1 Answer Sheet 2 (Blue) Page 8 (17 points) 24. a. b. Page 9 (25 points) 25. a., b. c. (25 words or less) d. e. f. g. Pages 10 & 11 (46 points) 26. a. b. c. d. ; e. h. i. ATP+GTP: NADH: FAD : f. 3: 4: 5: j. ATP+GTP: NADH: FAD : g. 6: k. (10 words or less)