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MT1 - summer - BC University of British Columbia BC gfi‘...

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Unformatted text preview: BC University of British Columbia BC gfi‘ Mid-term Exam — July 21, 2008 2"“ Biochemistry 300 - Summer session w Time: 1.5 hours Total Marks:100 Candidate's Name: (Please print family name first.) Student Number: Candidate's Signature: This examination conslsta of 3 parts A, B, and 0. Part B has 15 questions and part c has 8 questions. The exam has a total of 11 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. hislher librarylAMS card. 2. No candidate shall be permitted to enter the examination after the expiration of ‘A hour. or to leave during the first ‘A hour of the examination. 3. Candidates are not permitted to ask questions of the invigiiators. (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 lrnrnediately dismissed from the examination and shall be liable to disciplinary action: a) Making use of any books. electronic storage devices. papers or memoranda. or cassette recorders other than those authorized by the examiners; b) Speaking or communicating with other candidates: 0) Purposer exposing written papers to the view of other candidates. d) The plea of accident or forgetfulness shall not be received. 4. Smoking is not permitted during examinations. 5. Cellular telephones must be fully turned 93. ———-—————______________ Mark Obtained: I100 Equations 8- Constants: K=°C+273 AG'=AH-TAS F: 96.430 JN mol AG". = -nFAE.,' R: 8.315 Jlmol K as = as“ + RT in 191M [AHB] VI3 = Vmu([S]l([S] + K...» Where A 8: B are reactants and C 8: D are products pH = M. + IogilA‘l/[HAD 1N0 = 1Nmax + (Kntlvrnax)(1’[S]) Part A. Matching terms. Chose from the following list below and assign a number. Not all terms will be used. (20 marks) 1. Synthetase 16. Gibb‘s free energy 2. FMNHz 17- Serine 3. Entropy 1B. FADH; 4. Enthalpy 19. FAD 5. Epimers 20. Holoenzyme 6. Tertiary structure 21. lsoleucine 7. 3-phosphoglycerate 22. Quaternary Structure 8. GlyceraldhydeS-phosphate 23. FMN 9. Activation energy 24. Apoenzyme 10. Histidine 25. Enantiomers 11.Valine 26. Secondary structure 12. Dihydroxyaceton'e phosphate 27. Mutase 13.Anomers 23. Heme group 14.Leucine 29. Synthase 15. Water 30. Transition state A. = G):1 - Gs. B. The spatial arrangement of amino acid residues that are relatively close to one another in the linear sequence. C. The heat content of the system. D. Pairs of molecules, each with more than one asymmetric center. that differ in configuration at only one such center. E. Joins two molecules together without ATP (NTP). F. In the mechanism of chymotrypsin catalysis. it's the second nucleophile. G. An enzyme with its necessary ccfactor(s). ._o °' /—<_ \ P—O on 1/ x . H o o OH OH LEE”. Hi? NH; 330 )CH—ca—co,‘ J. 330 Part B. Multiple Choice. Circle the best answer. (30 marks) 1. What is the [Al/[HA] ratio when a weak acid is in a solution 1 pH unit above its pK.? 1:1. 1:10. 10:1. 1:2. . None of the above. roe-rape 2. Which of the following sugars CANNOT mutarotate? . Glucose—B-phosphate. . GIucose-1—phosphate. Fructose-1 .6-bisphosphate. . chtose-2.6-bisphosphate. . b and d. f. All of the above. magic-n) 3. The tertiary structure of YFP (Your Favorite Protein) is thought to contain a B—strand on its surface. One side of the strand faces the surface of YFP and the other side faces the core. Which of the following sequences of the B~strand is most likely? a. F I M V W G A. b. SLEWKMT. c. TFVENVM. d. TDSQEKC. 4. Regarding pathway regulation by ADP. which of the following is true? a. It stimulates glycolysis by directly activating hexokinase. b. It stimulates glycolysis by directly activating phosphofructokinase. c. It stimulates the Krebs cycle by directly activating isocitrate dehydrogenase. d. All of the above. e. b and c. 5. When the substrate concentration is much greater than K”. the rate of catalysis is almost equal to: a. keg... b. KM. c. Vmax. d- (VmaxiKmflsl- e. None of the above. 6. Which of the following statements about phosphoglycerate mutase is NOT correct? a. As part of the mechanism. the enzyme is transiently phosphorylated in the active site. b. it can covert 2-phosphoglycerate to 3-phosphoglycerate. c. It requires stoichiometric amounts of 2,3-bisphosphoglycerate. d. It catalyzes an intramoiecular shift of a phosphate group. 7. In one of your initial attempts to determine the tertiary structure of YFP, you predict a proline residue to have dihedral angles of phi = -75° and psi = 125°. Based on the Ramachandran plot for proline below, the predicted orientation of the proline residue i5: Praline Very likely. Possible. but not optimal. Not likely. Unable to be determined. 9.0 9'9: 450 -50 G 50 150 8. in solution. glucose: a. Exists primarily in the furanose form. b. Is an aldose. _c. ls almost exclusively a anomer. d. Rapidly converts between D and 1. forms at room temperature. 9. The steps (in order) to covert succinate to oxaioacetate are: a. Oxidation, hydration. oxidation. b. Oxidation. decarboxylation. oxidation. c. Decarboxylation. oxidation. hydration. d. Oxidation. decarboxylation. hydration. 10. Which of the following is NOT true concerning glycolysis in anaerobic muscle? a. There is a net production of NADH. b. There is a net production of ATP. 0. Lactate dehydrogenase is active. d. None of the above (i.e.. all of the above are truei). t1.Which of the following statements is true of enzyme catalysts? a. Their catalytic activity is independent of pH. b. They can increase the reaction rate for a given reaction by a 1000 foid or more. c. They can increase the equilibrium constant for a given reaction by a thousand fold or more. d. They are generally equally active on D and L isomers of a given substrate. a. To be effective. they must be present at the same concentration as their substrate. 12.What would be the expected result of a Lys residue being substituted with a Ser residue in the 2,3-bisphosphoglycerate (BPG) binding site in hemoglobin? a. BPG would bind tighter because of the loss of a positive charge. b. BPG would bind fighter because of a gain of a positive charge. 0. BPG would bind less tightly because of the loss of a positive charge. d. BPG would bind less tightly because of the gain of a positive charge. 13. In yeast, citrate synthase is a homodimer with two active sites. Through a series of experiments. you have determined that 1 nM of enzyme has a VW of 36 plWrnin using citrate as a substrate. Therefore, the turnover number (kw) is: a. 18.000 per minute. b. 36,000 per minute. c. 72.000 per minute. :1. None of the above. 14.The pKa of the carboxyl R group on the amino acid glutamate is 4.1. if the pH is 2. then: a. [R—COOH]>[R-COO‘]. b. [R-COOH] < [R-COO‘]. c. [R-COOH] = [R—COO’]. :1. None of the above, the carboxyi group cannot be ionized. 15. The following statements about the regulation of pyruvate dehydrogenase complex are true EXCEPT: NADH activates the kinase that phosphorylates pyruvate dehydrogenase. Pyruvate inhibits the kinase that phosphorylates pyruvate dehydrogenase. NADH directly inhibits dihydroiipoyl dehydrogenase. Acetyl CoA directly inhibits dihydrolipoyl transacelytase. None of the above (i.e. all are truel). seeps Part 0: Short Answer Questions: 1. Given the following reaction: 1,3-bisphosphoglycerate (1 .3BPG) + ADP ¢> 3-phosphoglycerate (3PG) + ATP 1a. What is the name of the enzyme that catalyzes this reaction? Where in the cell is it found? (2 marks) 1b. Using the table provided below. calculate the AG” of the above forward reaction. Is this a spontaneous reaction at standard state? Why? (4 marks) 1,3 bisphosphoglycerate + H20 —) 3~phosphoglycerate + Pi AG°:: phosphoenolpyruvate + H20 —> Pyruvate + P. AG"; ATP + H20 9 ADP + P; AG”. ATP + H20 -> AMP + PP. (Pyrophosphate) AG"; 3-phosphoglycerate + H20 -) glycerate 4- Pi AG": 49.4 kJImole 451.9 lemole : -30.5 kJImole 45.6 kJImole 40.3 kJImole 1c. In a fasting individual. the following concentrations were observed in liver cells: 6.0 mM ATP 0.1 mM 1.3 blsphosphoglycerate 0.4 mllll ADP 15.0 mil! 3-phosphoglycerate Using the values above. calculate the AG of the forward reaction. Why is this value different than the one calculated in 1b? What is happening with this reaction in liver cells? (5 marks) 2. Proteins can bind to other proteins via a series of weak interactions (in the same way that a substrate can bind to an active site). For the proteins A and B. draw the most likely A:B dimer and comment on the types of interactions that are formed. (4 marks) 3a. An o-helix has a defined structure. Explain how this structure is stabilizedlmaintained. Be very Specific! [4 marks) 3b. Proline residues will cause o-helices to either bend or break. Besides the obvious steric hindrance issues. Why would proline residues disrupt Isl-helices? (3 marks) 4. Papain is a cysteine protease that is found in papaya trees. Papain contains three key conserved residues that are essential for catalysis. These are (Eye-25. His-159. and Aan 58. Based on your knowledge of the mechanism of chymotrypsin proteoiysis, propose a role for each residue. (3 marks) 5. 4-hydroxy—2—nonenal (HNE) rapidly and irreversibly reduces Lipoamide. Discuss the effect that HNE has on the a-ketoglutarate dehydrogenase complex. What would be the status of the bound co—factors when the complex is treated with HNE? (5 marks) 6. Draw out the overall reaction catalyzed by isocitrate dehydrogenase. Make sure to include all names and structures. (4 marks) 7. You are studying an inhibitor of picornavirus RNA polymerase (a cause of the common cold). Through work in your lab, you have confirmed that this enzyme obeys simple Michaeiis-Menten kinetics. Furthermore. a post-doctoral fellow has identified a new inhibitor against the RNA polymerase and provided you with this data: Polymerase + Inhibitor Vt. Mimin 7a. Determine Km and Vm for the Polymerase and the Polymerase + inhibitor. (4 marks) 7b. What type of inhibition is this? How do you know? (3 marks) 8. You are a geologist studying Mt Rainier (eievation: 14 400 feet). As part of your work. you spend two weeks on the summit of the volcano. At sea level [302' In the air (and thus the lungs) 15 approximately 90 Torr however at the summit p02 drops to 55 Torr. The p02 in tissues Is 30 Torr. 8a. In order to acclimatize to the high altitude your body' Increases the concentration of 2 3-bisphosphoglycerate (BPG) In red blood cells The graph (below) shows the 02 binding curves for hemoglobin with normal (5mM) and elevated (BmM) concentrations of BPG. By drawing directly on the graph (1) show the effect altitude has on 02 delivery to tissues with normal concentrations of BPG. and (2) show the effect of increased BPG concentration at high altitude has on 03 delivery In the tissues Does an elevated level of BPG help 02 delivery at high altitudes? (7 marks) 1 0.9 0.8 0.7 I _ .g- l -f- -_r... __'__ 0.3 0.5 t-JlorYfl2 0.4 0.3 0.2 L -L--L--L- fiflfifllfl 0.1 5 g as t -L. : (Mabawpyofthisgraphonfl'renextpage'meeseyoumessupl 10 8b. 0b Smurf! Mt. Rainier' Is eruptinglill You're running down the mountain as fast as you can! This results In increased concentrations of CO; and H” In your muscle tissue Assuming you still have an elevated BPG concentration draw the resulting 02 binding curve for hemoglobin in your muscle on the graph below. (2 marks) I _.'r- __r-. I -nr— --'-- -l I _.-1-- u-r- I -1.- I I I I I ‘EEHIIE Boa-Yo: O 01 fiflflflflflflfl *“ I I I I I u , I. I I I "I' I I -L I I I I 'i' I I -L I I I I “I" I I I ”I" I I -1. I I I I r l n’hisisfliesamegmphasonfliapmlousmei ll ...
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