MIDTERM Bioc 202 2022 (1)

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University of British Columbia Midterm Exam June 6 th , 2022 Biochemistry 202 Time: 150 min Total Marks: 100 Candidate’s Name: please print family name e.g. Krisinger first name e.g. Mike Student Number: Candidate’s Signature: This examination consists of 14 pages. Please check to ensure all pages are present. Answer all questions on this examination paper in the space provided. If you require additional paper use the blank area on page 14. Read and observe the following rules: 1 . Each examination candidate must be prepared to produce, upon the request of the invigilator or examiner, his or her UBC card for identification. 2. Examination candidates are not permitted to ask questions of the examiners or invigilators, except in cases of supposed errors or ambiguities in examination questions, illegible or missing material, or the like. 3. No examination candidate shall be permitted to enter the examination room after the expiration of one-half hour from the scheduled starting time, or to leave during the first half hour of the examination. Should the examination run forty-five (45) minutes or less, no examination candidate shall be permitted to enter the examination room once the examination has begun. 4. Examination candidates must conduct themselves honestly and in accordance with established rules for a given examination, which will be articulated by the examiner or invigilator prior to the examination commencing. Should dishonest behavior be observed by the examiner(s) or invigilator(s), pleas of accident or forgetfulness shall not be received. 5. Examination candidates suspected of any of the following, or any other similar practices, may be immediately dismissed from the examination by the examiner/invigilator, and may be subject to disciplinary action: i. speaking or communicating with other examination candidates, unless otherwise authorized; ii. purposely exposing written papers to the view of other examination candidates or imaging devices; iii. purposely viewing the written papers of other examination candidates; iv. using or having visible at the place of writing any books, papers or other memory aid devices other than those authorized by the examiner(s); and, v. using or operating electronic devices including but not limited to telephones, calculators, computers, or similar device other than those authorized by the examiner(s)—( electronic devices other than those authorized by the examiner(s) must be completely powered down if present at the place of writing ). 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 without permission of the examiner or invigilator. 7. Notwithstanding the above, for any mode of examination that does not fall into the traditional, paper-based method, examination candidates shall adhere to any special rules for conduct as established and articulated by the examiner. 8. Examination candidates must follow any additional examination rules or directions communicated by the examiner(s) or invigilator(s). Page 3 4 5-7 8 9 10 11 12 13 TOTAL MARK Possible 12 16 24 8 5 8 9 8 10 100

BIOC 202, Midterm, June 6 th , 2022 Page 2 Equations & Constants : K = ºC + 273 ∆G = ∆H - T∆S F: 96,480 J . V -1 . mol -1 ∆G’ o = -nF∆E’ o R: 8.315 J . mol -1 . K -1 ∆G = ∆G’ o + RT ln [C][D] At equilibrium, K’ eq =[C] eq [D] eq [A][B] [A] eq [B] eq kDa: 1000g/mol Where A & B are reactants and C & D are products. 1 m = 1 × 10 10 Å V o = V max ([S]/([S] + K m )) 1/V o = 1/V max + (K m / V max )(1/[S]) pH = pK a + log ([A - ]/[HA]) E = K . q 1 . q 2 where: E is energy (J . mol -1 ) D . r K = 1.39 × 10 -4 J . m . mol -1 q = charge D = Dielectric constants. Note D H 2 O = 80; D hexane = 2 r = distance between point charges (m) 1 Å = 1 x 10 -10 m Typical p K a Values for Various Amino Acid Residue R groups as well as the N and C termini Found in Proteins: Group Typical p K a Terminal a -carboxyl group 3.1 Aspartic acid 3.7 Glutamic Acid 4.3 Histidine 6.0 Terminal a -amino group 8.0 Cysteine 8.2 Tyrosine 10.1 Lysine 10.5 Arginine 12.5 Ramachandran Plot of L-alanine:

BIOC 202, Midterm, June 6 th , 2022 Page 3 Part A: Structure Recognition Marks (12) 1. Name the compounds or structures shown on page 3 on the line provided next to the capital letters below . Abbreviations or misspelt names will receive only partial credit. Be as specific as you can. Valiant efforts will receive partial credit. (Note: 2 marks each for each A to F) A, B. _______________________________________ _________________________________________ C. _____________________(Structure in the circle?) E. _______________________________________ D. _______________________________________ F. _______________________________________ A, B. C. D. E. F. ? - - - + 3

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BIOC 202, Midterm, June 6 th , 2022 Page 4 Part B: Matching Terms Marks (16) 1. Choose from the following list below and assign ONE number in the space provided next to the capital letters . Not all terms will be used. Terms can be used more than once. (Note: 2 marks each for A to H) 1. K M 17. increase 2. decrease 18. cofactor 3. thermodynamics 19. [S] 4. just as likely as 20. associated inhibitor 5. G S - G substrate 21. competitive inhibitor 6. prosthetic group 22. Less likely than 7. V max 23. uncompetitive inhibitor 8. more likely than 24. G X - G substrate 9. G products - G substrate 25. peptide bond 10. stay the same 26. an exergonic reaction 11. an endergonic reaction 27. an endothermic reaction 12. G uncatalyzed - G catalyzed 28. water 13. lower, higher, lower 29. large hydrophobic residue 14. higher, lower, higher 30. [I] 15. higher, lower, lower 31. suicide inhibitor 16. carbonyl carbon 32. tetrahedral intermediate A. ______ The oxyanion hole of chymotrypsin helps bind and stabilize the ______________ when converting substrate into product. B. ______ Conditions in actively respiring tissues relative to the lung are ____ [O 2 ], _____ [CO 2 ], _____ pH. C. ______ Binding energy is best defined by _________________. D. ______ A parameter that stays constant when the enzyme concentration is doubled for a given enzyme catalyzed reaction. E. ______ An inhibitor that forms a tight, often covalent interaction at the active site. F. ______ A reaction where ΔG > 0. G. ______ If the R-group of a lysine residue was brought in close proximity to the C-terminus of the polypeptide (at pH 7), the pK a of the R-group would ___________________.

BIOC 202, Midterm, June 6 th , 2022 Page 5 H. ______ The sequence EKDKE is ___________________ KEDKR to form a β-strand. Part C: multiple choice. Marks (24) Circle the best answer. (Note: 2 marks each) 1. All hexose sugars are best described as a set of _________. a. isomers b. enantiomers c. anomers d. pyranoses e. aldoses f. two of the above 2. Carbon monoxide (CO) is toxic to humans because: a. it binds to myoglobin and causes it to denature. b. it is rapidly converted to toxic CO 2 . c. it binds to the globin portion of hemoglobin and prevents the binding of O 2 . d. it binds to the Fe in hemoglobin and prevents the binding of O 2 . e. it binds to the heme portion of hemoglobin and causes heme to dissociate from hemoglobin. 3. Patients with chronic hypoxia (low O 2 levels) due to decreased lung function may adapt by increasing their circulating BPG levels. Predict which of the following will be true for such a patient. Note: p 50 refers to the partial pressure of O 2 at which the O 2 -carrying proteins are 50% saturated. a. p 50 for O 2 will be decreased. b. p 50 for O 2 will be increased. c. The R-state of hemoglobin will be favored. d. O 2 binding to hemoglobin will be hyperbolic. e. Two of the above 4. Glutamine is a polar molecule. Consider glutamine at pH 7. What is the maximum number of water molecules that, in theory, one glutamine molecule could hydrogen bond with? a. 0 b. 1 c. 2 d. 3 e. 4 f. 12 g. 13 5. Consider the molecule shown in question A,B of Part A (Structure Recognition). What is the net charge of the dominant species at pH 1? a. -3 b. -2 c. -1 d. 0 e. +1 f. +2 g. +3

BIOC 202, Midterm, June 6 th , 2022 Page 6 6. Which of the following is NOT true of the peptide backbone drawn below: Cα−C O −N−Cα−C O −N−Cα 1 2 3 4 a. The atoms attached to bond 4 are in trigonal planar conformation. b. The angle of rotation of bond 3 is termed psi (ψ). c. Rarely, bond 1 is in the cis isomer. d. Although bond 2 can freely rotate, not all angles of rotation are possible. e. None of the above, i.e. all are true! 7. When the R groups of an arginine and an aspartate residue are in close proximity in three-dimensional space: a. An ionic attraction could form. b. A single hydrogen bond could form. c. Two hydrogen bonds could form. d. a and b. e. All of the above. 8. Which of the following best describes the forces that cause the monomer units of a quaternary structure to come together properly? a. Hydrophobic, electrostatic and covalent bonds. b. Hydrophobic, electrostatic and hydrogen bonds. c. Hydrophobic, electrostatic, hydrogen bonds and disulfide bonds. d. Electrostatic and hydrogen bonds. e. Only hydrogen bonds. 9. Which of the following is the best explanation of the hydrophobic effect? a. It is caused by an affinity of hydrophobic groups for each other. b. It is caused by the affinity of water for hydrophobic groups. c. It is an entropic effect, caused by the desire of water molecules to increase their entropy by forming highly ordered structures around the hydrophobic groups. d. It is an entropic effect, caused by the desire of water molecules to increase their entropy by excluding hydrophobic groups, which they must otherwise surround by highly ordered structures. e. It is an entropic effect caused by the desire of hydrophobic groups to increase their entropy by associating with other hydrophobic groups. 10. Which of the following sequences would most likely form part of an amphipathic β-sheet? a. Asn-Leu-Ala-Asp-Ser-Phe-Arg-Gln-Ile b. Gln-Ile-Thr-Phe-Thr-Leu-Gln-Val-Ser c. Lys-Gln-Asn-Glu-Pro-Arg-Ala-Asn-Glu d. Ala-Phe-Leu-Val-Ile-Trp-Phe-Val-Ala

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BIOC 202, Midterm, June 6 th , 2022 Page 7 11. Consider a 100-amino acid residue long protein. If just three (3) phi and psi angle combinations were sampled at each residue, how many backbone structures could the protein adopt theoretically? Assume all peptide bonds are in trans. a. 3 100 = 5.15 x 10 47 structures b. 3 99 = 1.72 x 10 47 structures c. 100 x 3 = 300 structures d. 99 x 3 = 297 structures e. An infinite number of structures 12. Consider a 100-amino acid residue long protein without any post-translational modifications. The average MW of an unmodified amino acid is 128 g/mol. What is the best estimate of the molecular mass of this protein? Hint: remember your peptide bond formation! a. 12,800 Da b. 11,000 Da c. 11,018 Da d. 12.8 kDa e. 12,800 g/mol

BIOC 202, Midterm, June 6 th , 2022 Page 8 Part D: Short Answer Questions – Answer in the provided space. If you use abbreviations for enzymes or metabolites please define them. Abbreviations for nucleotides, cofactors and amino acids are acceptable. Marks (48) ( 4 ) 1. An enzyme is found that catalyzes the reaction: A ⇋ B Researchers find that the K M for the substrate A is 1.5 μM, and the k cat is 20 min -1 . In an experiment, [E t ] = 5 nM, and the measured V o = 0.02 μM min -1 . What was the [A] in the experiment? ( 4 ) 2. Draw a reaction coordinate diagram for the conversion of substrate, A to product, B. In your diagram include the free energy profile of the uncatalysed reaction and also the reactions catalyzed by enzyme E1 and enzyme E2, noting that enzyme E1 converts A to B faster than enzyme E2. Remember to label the X- and Y-axis, any relevant species and complexes.

BIOC 202, Midterm, June 6 th , 2022 Page 9 ( 5 ) 3. Biomolecules can be separated with a laboratory technique called Ion-Exchange Chromatography. This method separates ions and polar molecules based on their affinity for the ion exchanger. The Ion- Exchange Chromatography column shown below is composed of positive charges as shown. You are working with a peptide with sequence: Glu-Asp-Met-Val-Ala-Phe-Arg-Asn-His You treat your peptide with chymotrypsin at pH 7. After incubating the peptide for 1 hr at 37° C the reaction mixture was immediately added to the ion-exchange chromatography column shown below. Predict the order of ALL molecules that will elute (i.e. flow) from the column. Define all molecules. Explain your answer. + + + + + + + + + + + + + + + +

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BIOC 202, Midterm, June 6 th , 2022 Page 10 4. You are working on characterizing a potential reversible thrombin inhibitor. Previous work in your lab has established that thrombin obeys Michaelis-Menten kinetics and has a K M of 0.1 mM and a V max of 0.4 μmol/sec when 20 nmol thrombin was used with a test peptide substrate. ( 4 ) 4a. You are working with the thrombin inhibitor called WEAVER. Carrying out a series of kinetic assays on 20 nmol thrombin and 5 μmol WEAVER, you have created a double reciprocal plot (below). Calculate K M , V max , and k cat for thrombin treated with inhibitor WEAVER. Please show your work! Using your data, discuss the type of inhibition and how inhibitor WEAVER inhibits thrombin. ( 4 ) 4b. Another competitor is also racing to get a thrombin inhibitor developed. Your competitor is working with the thrombin inhibitor called CLARK. Carrying out a series of kinetic assays on 2.0 nmol thrombin and 5 μmol CLARK, your competitor has created a double reciprocal plot (below). Calculate K M , V max , and k cat for thrombin treated with inhibitor CLARK. Please show your work! Using your data, discuss the type of inhibition and how inhibitor CLARK inhibits thrombin. -0.02 -0.01 0.00 0.01 0.02 0.03 1 2 3 4 5 6 7 8 1/[peptide substrate] (1/mM) 1/Vo (s/ μ mol) Double reciprocal plot for thrombin (20 nmol) + 5 μ mol inhibitor WEAVER -20 -10 0 10 20 30 10 20 30 40 50 60 70 80 1/[peptide substrate] (1/mM) 1/Vo (s/ μ mol) Double reciprocal plot for thrombin (2.0 nmol) + 5 μ mol inhibitor CLARK

BIOC 202, Midterm, June 6 th , 2022 Page 11 ( 3 ) 5. What is thought to be the dominant mechanism of protein folding? Why can folding not be random? Hint: combinations of ϕ and ψ angles. ( 3 ) 6a. Consider a holoenzyme consisting of a proteolytic enzyme and a protein cofactor a pH 7. An important ionic interaction exists between a Glu of the enzyme active site and an Arg residue of the bound cofactor. The rest of the binding interface is largely hydrophobic with a dielectric constant, D = 8. Draw what this binding interface looks like. Amino acid side chain structures are NOT required for full marks. ( 3 ) 6b. For apoenzyme formation, 20 kJ/mol of energy is required to break the ionic interaction and help dissociate the cofactor from the enzyme. What is the distance in angstroms between the Glu and Arg in the holoenzyme?

BIOC 202, Midterm, June 6 th , 2022 Page 12 ( 4 ) 7. Name the four types of non-covalent interactions that stabilize tertiary and quaternary structures of proteins. ( 4 ) 8. Consider the tripeptide: Glu-Leu-Asp. It has several ionizable groups including one with a p K a = 9.3. A biochemist makes up 100 mL of a 0.1 M solution of the tripeptide at a pH of 8.4. He then adds 60 mL of 0.1 M NaOH. What is the pH of the resulting solution?

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BIOC 202, Midterm, June 6 th , 2022 Page 13 ( 4 ) 9. Calculate the actual, physiological D G for the reaction: Phosphocreatine + ADP à creatine + ATP at 37 ° C, as it occurs in the cytosol of neuron, with phosphocreatine at 4.7 mM, creatine at 1 mM, ADP at 0.73 mM, and ATP at 2.6 mM. Note D G’ ° values for ATP hydrolysis = -30.5 KJ/mol and phosphocreatine hydrolysis = -43.0 KJ/mol ( 4 ) 10a. Draw the C-3 epimer of a -D-glucopyranose. Then show how mutarotation can occur by drawing the open chain form and the product configuration after mutarotation. ( 2 ) 10b. How is this spontaneous process of mutarotation prevented in a cell?