This document is the instructions for a final exam on Biochemistry I. It provides information on the exam format, length, and academic integrity policy. It then lists 20 amino acids and provides space for the student to write their score. The exam consists of true/false questions, multiple choice questions, and short answer questions covering topics like protein folding, chromatography, enzyme kinetics, and protein sequencing.
This document is the instructions for a final exam on Biochemistry I. It provides information on the exam format, length, and academic integrity policy. It then lists 20 amino acids and provides space for the student to write their score. The exam consists of true/false questions, multiple choice questions, and short answer questions covering topics like protein folding, chromatography, enzyme kinetics, and protein sequencing.
This document is the instructions for a final exam on Biochemistry I. It provides information on the exam format, length, and academic integrity policy. It then lists 20 amino acids and provides space for the student to write their score. The exam consists of true/false questions, multiple choice questions, and short answer questions covering topics like protein folding, chromatography, enzyme kinetics, and protein sequencing.
This document is the instructions for a final exam on Biochemistry I. It provides information on the exam format, length, and academic integrity policy. It then lists 20 amino acids and provides space for the student to write their score. The exam consists of true/false questions, multiple choice questions, and short answer questions covering topics like protein folding, chromatography, enzyme kinetics, and protein sequencing.
Undergraduate Honors Program of Nano Science and Engineering ENPN10015: Biochemistry I
Fall 2022
Final exam
Instructions: • You will have the entire class to complete this exam (1 hour 50 minutes)
• Only answer in the space provided. Only the answers in the provided space will be graded.
• For short answer questions, please be concise. Write legibly. Any illegible writing will result in points taken off.
• Questions are on both sides of the exam. Make sure you answer them all.
Academic integrity: Integrity of scholarship is essential for an academic community. The University expects that both faculty and students will honor this principle and in so doing protect the validity of University intellectual work. All academic work must be completed by the individual student whom the work is assigned to, without unauthorized help.
2 (1.5 points each) True or False (please indicate your answer above the line for each question).
1. _________ Proteins with higher contact orders tend to fold with slower rates.
2. _________ Chaotropic agents such as urea are used to denature proteins by inserting charges
3. _________ Molecular chaperone protein GroELS complex degrades misfolded proteins
4. _________ Amino acid analysis by strong acid hydrolysis followed by chromatography cannot be used to quantify each of the 20 amino acids present in the sample.
5. _________ Trypsin is used to fragment polypeptides as it hydrolyzes large hydrophobic amino acid residues
6. _________ Both H+ and 2,3-Bisphosphoglycerate (2,3-BPG) are heterotropic effectors for hemoglobin
7. _________ Specific activity of crude protein from tissue extracts is generally higher than that of purified protein
8. _________ Rate of an enzyme catalyzed reaction increases with the substrate concentration indefinitely
9. _________ Transition analogues will bind to an enzyme more tightly than a substrate analogue
10. _________ Apparent Km in a competitive inhibition is always higher than true Km as long as there is inhibitor present
(3 points each) Multiple Choice (please indicate your answer above the line for each question)
1. _________ Which of the following protein chromatography methods is typically used to separate proteins based on their sizes? a. Affinity chromatography b. Hydrophobic interaction chromatography c. Ion exchange chromatography d. Gel filtration chromatography e. None of the above
2. _________ Which of the following is thermodynamically unfavorable as protein folds?
a. Conformational entropy of the protein b. Salt bridge formation between carboxyl and amino groups within the protein c. Hydrogen bonding between amide hydrogen and carboxyl oxygen d. Entropy of surrounding water molecules e. None of the above 3 3. _________ Which of the following is true regarding chemical synthesis of oligopeptides a. Synthesis starts from the N-terminus b. Growing peptide chain is suspended in a viscous solution c. Amino group of the growing chain must be protected throughout reaction d. All of the above e. None of the above
4. _________ Which of the following BEST describes the oxyanion stabilization by chymotrypsin? a. General acid-base catalysis b. Covalent catalysis c. Electrostatic catalysis d. Proximity and orientation e. None of the above
5. _________ Which of the following cofactor is frequently associated with ATP binding and stabilization? a. Fe2+ b. Heme c. Mg2+ d. Mn2+ e. Cu2+
6. _________ Which of the following is FALSE as hemoglobin switches from the T-state to the R-state? a. the heme group goes from a flat conformation to a slightly puckered conformation b. the ferrous ion is pulled into the plane of the heme group c. the F8 (proximal) histidine rotates about 8 to better align with the ferrous ion d. movement of the F8 histidine causes a shift in the F helix, thus weakening interactions with other subunits e. None of the above
7. _________ Which of the following equation best represent the oxygen binding curve of myoglobin where y is the proportion of myoglobin sites occupied; x is partial pressure of oxygen; and K is a constant a. y = 1/x b. y = x/(K + x) c. y = Kx d. y = 1/Kx e. y = (K + x)/x
8. _________ Which of the following is true regarding the effectors of hemoglobin-oxygen binding? a. increase in blood pH will cause hemoglobin to bind more tightly to oxygen b. increased CO2 from increased muscle activity will result in an increase in the R state of hemoglobin c. increased Cl- will cause the formation of a salt bridge between two Lys residues, one on an subunit, the other on a subunit d. the binding site of 2,3-BPG contains several Asp and Glu residues which are repelled by the similar charge, pushing the two subunits away from each other e. all of the above
4 9. _________ An enzyme catalyzes a reaction with Vmax of 100 μmol/min at a given enzyme concentration with Km of 10 mM for its substrate. Which of the following initial rate most likely matches a reaction catalyzed by this enzyme at the same enzyme concentration with substrate concentration of 100 mM? a. 10 μmol/min b. 50 μmol/min c. 100 μmol/min d. 500 μmol/min e. 1000 μmol/min
10. _________ Which of the following best describes an enzyme that catalyzes the reaction below
a. Oxidoreductase b. Transferase c. Hydrolase d. Lyase e. Ligase
11. _________ Which of the following best describes an enzyme that catalyzes the reaction below
a. Oxidoreductase b. Transferase c. Hydrolase d. Lyase e. Ligase
12. _________ Malonic acid, a three carbon diacid, is a _____________ inhibitor to succinate dehydrogenase which typically react succinic acid, a four carbon diacid. a. Competitive b. Uncompetitive c. Mixed d. Irreversible e. None of the above
5 Short Answers
1. (6 points) Briefly explain the role of disulfide bonds in protein folding. Are disulfide bonds necessary for protein folding? If so, why? If not, why are do they appear in nature?
2. Ion exchange chromatography is a frequently used method to separate proteins.
a. (3 points) What is the basis of separation by ion chromatography? (i.e. Separation is based on what property of the analyte molecules)
b. (3 points) How to adjust the mobile phase composition to increase the elution speed?
c. (3 points) What kind of chemical functional group is used for making a weak cation exchanger for ion exchange chromatography?
6 3. Chymotrypsin is a protease that targets large amino acid residues. The active site of chymotrypsin is shown below
a. (5 points) Show how an oxyanion intermediate is formed and how it is stabilized.
b. (5 points) Briefly explain why His57 is necessary for the deprotonation of Ser195, which is the active nucleophile.
7 4. Michaelis-Menten equation is used to describe the initial rate of an enzyme-catalyzed reaction
a. (3 points) Write out the Michaelis-Menten equation in terms of Km and kcat, and describe the meaning of each constant terms
b. (3 points) Describe how to experimentally obtain the Michaelis-Menten constants.
c. (3 points) Briefly describe what are the assumptions/conditions made while deriving the Michaelis- Menten equation
d. (4 points) Briefly explain how to generate a Lineweaver-Burk plot and why it may be useful.
8 5. (5 points) Briefly describe the difference between Edman degradation and Sanger’s reagent. Which method is better and easier to use for protein sequencing? And why?
6. (6 points) Draw an oxygen binding curve to illustrate what you think would happen to a myoglobin that has a mutation in its distal histidine. And briefly explain your expected curve.
