University of British Columbia Mid-term II March 15 th, 2016 Biochemistry 202 Winter semester, Term 2

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1 University of British Columbia Mid-term II March 15 th, 2016 Biochemistry 202 Winter semester, Term 2 Time: 90 minutes Total Marks: 50 Candidate s Name: (Please print family name first.) Student Number: Candidate s Signature: This examination consists of 4 parts: A, B, C, & D. Part B has 2 questions, part C has 7 questions, & part D has 3 questions. The exam has a total of 7 pages. Please check to ensure that this paper is complete. Answer all questions on this examination paper in the space provided. Read and observe the following rules: 1. Each candidate should be prepared to produce, upon request, his/her library/ams card. 2. No candidate shall be permitted to enter the examination after the expiration of ½ hour, or to leave during the first ½ hour of the examination. 3. Candidates are not permitted to ask questions of the invigilators, except in cases of supposed errors or ambiguities in examination questions. CAUTION - Candidates guilty of any of the following, or similar, dishonest practices shall be immediately dismissed from the examination and shall be liable to disciplinary action: a) Speaking or communicating with other candidates; b) Purposely exposing written papers to the view of other candidates; c) Purposely viewing the written papers of other candidates; d) Using or having visible at the place of writing any books, papers, or other memory aid devices; e) Using or operating electronic devices including but not limited to telephones, calculators, computers, or similar devices other than those authorized by the examiner. Electronic devices other than those authorized by the examiner must be powered down if present at the place of writing. 4. Examination candidates must conduct themselves honestly and in accordance with the established rules for a given examination, which will be articulated by the examiner or the invigilator prior to the examination commencing. Should dishonest behavior be observed by the examiner or invigilator, pleas of accident or forgetfulness shall not be received. 6. Examination candidates must not destroy or damage any examination material, must hand in all examination papers, and must not take any examination material from the examination room. Mark Obtained: /50

Part A. Matching terms. Chose the best answer from the following list below and assign a number. Not all terms will be used. (6 marks) 1. Galactose(β1 4)Glucose 6. Glucose(α1 4)Glucose 2.

If the C5 hydroxyl attacks the carbonyl in an aldohexose, this ring is formed. B. The nucleophile(s) in chymotrypsin. C. Composition of sucrose. Part B. Fill in the blank.

2 Part A. Matching terms. Chose the best answer from the following list below and assign a number. Not all terms will be used. (6 marks) 1. Galactose(β1 4)Glucose 6. Glucose(α1 4)Glucose 2. Serine 7. Benzene 3. Glucose(α1 β2)fructose 8. Furanose 4. Pyranose 9. Serine and water 5. Water 10. Glucose(β1 α2)fructose A. If the C5 hydroxyl attacks the carbonyl in an aldohexose, this ring is formed. B. The nucleophile(s) in chymotrypsin. C. Composition of sucrose. Part B. Fill in the blank. Write in the FULL name of the structure. (4 marks) (No abbreviations) Part C. Multiple Choice. Circle the best answer. (14 marks) 1. Which term BEST describes the two molecules below? a. They are diastereomers. b. They are enantiomers. c. They are epimers. d. They are anomers. 2

3 2. Consider the oxygen-binding profile at three different BPG concentrations of 2mM, 5mM, and 8mM. Which statement is most correct? Hb Oxygen binding 1 Y (fraction saturation) po2 (torr) X Y Z (Hb: Hemoglobin; BPG: 2,3 bisphosphoglycerate) a. Curve X most likely corresponds to 8mM BPG. b. Curve Z most likely corresponds to 2mM BPG. c. Hb has a higher affinity for oxygen at the ph of curve Z. d. Curve Y most likely corresponds to 5mM BPG. e. BPG has no effect on the oxygenation of hemoglobin. 3. Which of the following is NOT true of the reaction mechanism of chymotrypsin: a. Histidine acts as a base catalyst. b. The product fragment with a "new" N-terminal leaves the active site first. c. The tetrahedral intermediate is stabilized by H-bonding from adjacent amino acid R groups in the oxyanion hole. d. Histidine acts an acid catalyst. e. None of the above. I.E., all are true! 4. Which of the following is TRUE about the regulation of pyruvate dehydrogenase complex (PDC)? a. High [NADH] allosterically activates PDC associated kinase. b. High [NADH] allosterically inhibits dihydrolipoyl dehydrogenase (E3). c. High [ADP] allosterically activates PDC associated kinase. d. a and b. e. b and c. f. All of the above. 5. The following structure: a. Cannot undergo mutarotation. b. Stimulates pyruvate kinase. c. Is the α-anomer. d. a and b. e. All of the above. 3

4 6. Arsenite can react with dihydrolipoamide, forming the structure below: Which of the following statements is NOT true about PDC treated with arsenite? a. Most dihydrolipoyl dehydrogenases (E3) would contain FAD. b. Most pyruvate dehydrogenases (E1) would contain hydroxy-ethyl TPP. c. There would be very limited amounts of compounds containing thioesters present in the complex. d. b and c. e. None of the above. I.E., all of the above are true! 7. Which of the following is NOT true of glyceraldhyde-3-phosphate dehydrogenase? a. It catalyzes an irreversible reaction. b. It can oxidize NADH to NAD +. c. The reaction mechanism includes a thioester intermediate. d. a and b. e. All of the above. I.E., none of the above are true! Part D: Short Answer Questions: 1. Given the following reaction: Lactate + NAD + Pyruvate + NADH + H + G o = kj/mole In humans, this is one of the major ways of removing lactate from the blood. It occurs in cytosol of hepatocytes (liver cells) where the NAD+/NADH radio is ~500. Calculate the lowest ratio of lactate/pyruvate that would allow the reaction to be spontaneous at physiological conditions. (4 marks) 4

5 2. Describe the Bohr effect. Your explanation should include a molecular rationale for the effect. (6 marks) 3. African sleeping sickness is a serious disease that kills between 40,000 to 60,000 people a year. It is caused by an infection by a trypanosome (a single celled eukaryotic parasite) with a complicated life cycle. When an individual is bitten by the Tsetse fly, the trypanosome is injected into the blood stream. Once there, the parasite shuts down oxidative phosphorylation and instead relies on glycolysis to meet its energy needs. Unlike humans, trypanosomes contain specialized compartments called glycosomes where most of the glycolytic reactions occur. The last page of this exam illustrates the glycolytic pathway for trypanosomes including the glycosome. Note that this diagram explains glycolysis in both anaerobic and aerobic conditions. Thus, not all of the reactions diagrammed will be occurring for each situation. This pathway is under intense study for development of new drugs to treat African sleeping sickness. 3a. Identify and draw the structure of X, Y, and Z: (6 marks) X: Y: Z: 5

6 3b. Under aerobic conditions, what are the ATP yield and products formed for the catabolism of glucose in trypanosomes? Explain your answer! (5 marks) Hint: Think about electron flow! 3c. Under anaerobic conditions, what are the ATP yield and products formed for the catabolism of glucose in trypanosomes? Explain your answer! (5 marks) Hint: Think about electron flow! 6

7 Where P: Phosphate; DHAP: Dihydroxyacetone phosphate; G-3-P: Glyceraldehyde-3- phosphate; Gly-3-P: Glycerol-3-phosphate; 1,3-BPGA: 1,3-bisphosphoglycerate; 2-PGA: 2-phosphoglycerate; PEP: Phosphoenolpyruvate. Note: Glycerol-3-phosphate oxidase is NOT a proton pump. Equations & Constants: 96,480 kj/ V mole G o = -nf E o R: J/mol K G = G o + RT ln K = o C [C][D] [A][B] Where A & B are reactants and C & D are products 7

3.2 Aerobic Respiration

3.2 Aerobic Respiration Aerobic Cellular Respiration Catabolic pathways Breaks down energy-rich compounds to make ATP Requires oxygen Occurs in different parts of the cell C 6 H 12 O 6 (s) + 6O 2 (g) 6CO