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NAME: ____________________________________________ Solar ID: ______________________________________________
INSTRUCTIONS FOR Midterm 1 (pages 2-11): (100 points total)
a. Answer questions 1-26 on the Opscan sheet. Only one answer per question. b. Answer questions 27-30 on the exam paper. c. Use a number 2 pencil. d. Fill in NAME (LAST, FIRST, and MI), and IDENTIFICATION NUMBER (Solar ID number) using the bubbles on the Opscan sheet. e. Check that the correct bubble bubble under “TEST VERSION” is filled filled in on the Opscan sheet. (1 for Version 1). f. Fill in NAME (LAST, FIRST, and MI) and IDENTIFICATION NUMBER (Solar ID number) on the top of EVERY page of the exam paper. g. Hand in BOTH the OPSCAN and EXAM PAPER after completing the exam.
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1. You monitor the progress of a thermodynamic process and observe that the process occurs spontaneously at all temperatures but at a very slow kinetic rate. Which of the following statements about this process can be said with complete confidence? (3 points) A. The process has only a slightly negative !G value. B. The process has a negative !H and a negative !S value. C. The process has a positive !H and a positive !S value. D. The process has a negative !H and a positive !S value. E. The process has only a slightly positive !G value.
2. You measure the equilibrium constants (Keq) for a chemical reaction carried out at a variety of different temperatures (T). By plotting Keq (y-axis) vs (1/T) (x-axis), the data can be fit by a straight line that intercepts the y-axis at a positive value. Which of the following statements about the chemical reaction is most accurate? (3 points) A. The reaction is exergonic. B. The reaction results in the release of heat from the system to the surroundings. C. The reaction results in an increase in the number of energetically equivalent arrangements.
D. The reaction is spontaneous at all temperatures be low the value of the x-intercept. E. The reaction is endergonic.
3. Transferring benzene from a non-polar solvent to an aqueous solvent is accompanied by negative values of !S for the process and aggregation of the benzene molecules. What is the best explanation for this observation? (3 points) A. The benzene molecules form strong interactions with each other that drive aggregation and increase order in the system. B. Formation of ordered water cages around the benzene molecules is an entropically unfavorable process that can be minimized by aggregation of the benzene molecules.
C. The water molecules of the aqueous solvent are forming weak hydrogen bonds with the benzene that are enthalpically favored. D. The entropy of the aqueous solvent increases as the water molecules form ordered water cages around each benzene molecule.
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E. Aggregation produces a large negative !H that can overcome the negative !S so that the overall !G for the process is negative.
4.You wish to carry out a biochemical reaction in a solution that can maintain a pH value close to pH 7 and resist changes in pH as the reaction progresses. Which of the following compounds would be most useful for this purpose? (3 points) A. A weak acid that exists in approximately equal concentrations of the free acid and conjugate base forms at pH 7.
B. A weak acid whose titratable group is close to being fully deprotonated at pH 7. C. A weak acid whose titratable group is close to being fully protonated at pH 7. D. A polyprotic acid that has multiple titratable groups with a wide distribution of pKa values for each group. E. A strong acid that can donate protons to water molecules and form hydronium ions.
5. You carry out an isoelectric focusing experiment on a mixture of amino acids containing: Asp, His, and Lys. The pH gradient in the experiment runs from low pH (left) to high pH (right). What is the order of migration of the amino acids in the experiment from left to right after equilibrium is reached? (3 points)
A. Asp, Lys, His B. His, Lys, Asp C. Asp, His, Lys
D. Lys, His, Asp E. His, Asp, Lys
6. Which of the following steps is NOT used in the sequencing of proteins by Edman degradation. (3 points)
A. Reaction of the free amino groups of the polypeptide with phenylisothiocyanate. B. Addition of anhydrous trifluoroacetic acid followed by aqueous acid. C. Incubation of the polypeptide with strong acid for several hours to hydrolyze all peptide bonds in the protein and liberate the modified N-terminal amino acid.
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D. Identification of the PTH-amino acid by hydrophobic interaction chromatography. E. Re-addition of PITC to react with the new amino terminus of the polypeptide.
7. You wish to purify your protein of interest by cation exchange chromatography for use in an enzymatic reaction. You have previously determined the isoelectric point of your protein to be 8.5 Dissolving your protein in which of the following solutions is most likely to produce interaction of your protein with the stationary phase while still retaining enzymatic activity after purification? (3 points) A. A solution buffered at pH 2 containing low concentrations of salt. B. A solution buffered at pH 6 containing low concentrations of salt.
C. A solution buffered at pH 10 containing high concentrations of salt. D. A solution buffered at pH 10 containing low concentrations of salt. E. A solution buffered at pH 6 containing high concentrations of salt.
8. Gel filtration chromatography preserves the quaternary structure of proteins. You carry out a gel filtration experiment on a mixture of proteins with different quaternary structures. Which of the three proteins will emerge first from the column? (3 points) A. A trimeric protein composed of identical protomers with a molecular weight of 20 kDa per protomer. B. A dimeric protein composed of different protomers with molecular weights of 10 kDa and 40 kDa. C. A trimeric protein composed of identical protomers with a molecular weight of 40 kDa per protomer.
D. A monomeric protein with a molecular weight of 10 kDa. E. Whichever protein has the largest number of charged amino acid side chains.
9. You are given a Ramachandran plot calculated from the tertiary structure of your protein. What information about the protein’s structure CANNOT be ga ined from this plot? (3 points) A. The likely involvement of each residue in particular secondary structure elements. B. The values of rotation around the backbone N-C" and C"-C bonds for each residue. C. The likely number of residues that form hydrogen bonds between their backbone carbonyl oxygen atom (n position) and a hydrogen atom bonded to the amide nitrogen of the residue four places ahead of them (n+4 position).
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D. The number of residues whose backbone atoms exist in conformations that are ‘favored’ versus those in ‘allowed’ conformations. E. The values of rotation around the C "-C# bond for each residue.
10. Which of the following characteristics is NOT a reason for the observed high tensile strength of keratin? (3 points) A. The presence of hydrophobic amino acid residues in the a and d positions of the 7-residue pseudorepeat in the primary structure. B. The formation of disulfide bonds between cysteine residues across different protofilaments. C. Dimerization of two keratin polypeptides to form a coiled-coil arrangement. D. The arrangement of 3 residues per turn of the helix versus 3.6 residues per turn for a regular "-helix.
E. The association of protofilaments to form larger microfibrils.
11. Which of the following statements about X-ray crystallography is INCORRECT? (3 points) A. Models are constructed by mea suring the diffraction of x-rays from molecules of protein as they move freely in solution.
B. The arrangement of atoms in the protein crystal determines the pattern of d iffracted x-rays in a diffraction experiment. C. A model constructed from data to 1.0 Å resolution will normally have greater confidence in the position of the atoms than from data determined to 3.0 Å resolution. D. X-ray crystallography provides a 3-dimensional image of the distribution of electrons in the protein crystal. E. X-ray crystallography can be used to determ ine the primary, secondary, and tertiary structures of proteins.
12. Which of the following statements about tertiary structure is correct? (3 points) A. Tertiary structure is less conserved in evolution than primary structure. B. Hydrophobic side chains are more likely to be found on the outside surface of a protein than in the central core.
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C. The function of a protein can be inferred by analysis of conserved motifs in the tertiary structure.
D. Knowledge of the tertiary structure of a protein gives no information on the secondary structure. E. Protein domains are formed by the assembly of multiple protomers into an oligomer.
13. Which of the following is NOT a part of the GroEL/ES refolding mechanism? (3 points) A. Hydrolysis of ATP molecules bound to subunits of the cis ring after enclosing a misfolded protein. B. Reduction of disulfide bonds to allow the misfolded protein to refold more easily. C. A change in the conformation of the subunits of the cis ring after binding of the GroES cap. D. Mechanical alteration of the misfolded polypeptide structure to promote refolding. E. Removal of the misfolded protein away from the other cellular components to prevent aggregation during refolding.
14. Which of the following statements about protein folding is FALSE? (3 points) selecting 1 of the 2 false answers will give 3 points*
A. The information needed to define the tertiary structure of a protein is encoded in the sequence of amino acids residues. B. The unfolded polypeptide chain is incapable of finding the correct tertiary structure without the assistance of chaperones such as GroEL/ES.
C. Protein folding is a cooperative process with the formation o f small amounts of structure driving larger formation. D. Formation of the final tertiary structure is normally much faster than the formation of the secondary structure elements.
E. The Anfisen experiment revealed that protein folding is a spontaneous and reversible process.
15. Which of the following is the best explanation for the acceleration of a chemical reaction by an enzyme. (3 points) A. Reduction of the Gibbs free energy of the reaction products. B. Reduction of the number of intermediate steps in the reaction. C. Decreasing the concentration of the transition state of the r eaction. :
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D. Increasing the free energy of activation of the reaction. E. Stabilizing the highest free energy species that is formed during the course of the reaction.
16. You measure the rate of a reaction between two substrate molecules to form a single molecule of product. A critical acid catalysis step is carried out by a lysine side chain in the enzyme’s active site and the rate enhancement for the enzyme-catalyzed reaction is 1 x109. A mutant enzyme bearing a substitution of the catalytic lysine to an alanine binds the substrate molecules in the same way and gives a rate enhancement of ~104. What is the best explanation for this result? (3 points) A. The rate enhancement for the mutant enzyme results from the holding of the two substrates together in the active site in a position that allows them to react more readily than in solution.
B. The rate enhancement for the mutant enzyme results from the ability of the alanine side chain to donate a proton and help catalyze the reaction. C. The rate enhancement for the mutant enzyme results from the ability of alanine to form the covalent intermediate that is an essential step of the reaction. D. The rate enhancement for the mutant enzyme results from the nucleophilicity of the alanine side chain. E. It is not possible for an enzyme lacking the major catalytic side chain to enhance the rate of a reaction. The data must be incorrect.
17. Which type of catalytic mechanism is NOT employed by lysozyme to accelerate the cleavage of peptidoglycan? (3 points) A. Formation of a covalent intermediate between the enzyme and the substrate. B. Donation of a proton by an acid C. Removal of a proton by a base. D. Preferential binding to the transition state. E. Stabilization of an unstable negative charge by a divalent cation.
18. Which of the following statements about the binding of substrate by lysozyme is TRUE? (3 points) A. Lysozyme can bind equally well to a heteropolymer of alternating N-acetylglucosamine and Nacetylmuramic acid residues and a homopolymer of N -acetylglucosamine residues.
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B. Peptidoglycan binds to lysozyme in a substrate-binding cleft that fits seven residues of peptidoglycan. C. Binding of peptidoglycan to lysozyme distorts the NAM residue in the ‘D’ position into a ‘chair’ conformation D. The enzyme forms hydrogen bonds between the backbone atoms of the polypeptide chain and the substrate that help stabilize a less stable conformation of a single sugar residue. E. Binding of peptidoglycan to lysozyme is dependent on the formation of covalent bonds between the substrate and enzyme.
19. The tripeptide below is shown in the major ionization state at pH 7. What would be the most common overall charge on the peptide at pH 5? (3 points)
A. +1 B. 0 C. -1 D. +2
20. You conduct an SDS-PAGE experiment on a mixture of three tripeptides with the sequences: ArgTrp-Trp, Ala-Ala-Ala, and Asp-Phe-Phe. Which of the following statements about the results of the experiment are correct? (3 points) A. Arg-Trp-Trp will migrate the furthest because of the overall positive charge on the peptide. B. Asp-Phe-Phe will migrate the furthest because of the overall negative charge on the peptide. C. Arg-Trp-Trp will migrate the furthest because it has the highest molecular weight.
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D. Ala-Ala-Ala will migrate the furthest because it has the lowest molecular w eight. E. Ala-Ala-Ala will migrate the furthest because it has the most ne utral pI value.
Answer the following seven questions with either TRUE (A) or FALSE (B). (2 points each)
20. The 280 nm extinction coefficients for two proteins containing the same number of residues but with different primary structures will always be identical. F 21. The pattern of shorter peptides produced by incubation of chymotrypsin with two separate polypeptides containing the same number of residues but w ith different primary structures will always be identical. F 22. Proline residues are rarely found in "-helices because of their inability to form salt bridges with other residues in the helix. F 23. It is possible to predict the involvement of a residue in an anti-parallel #-strand from the values of $ and % for that residue. T 24. All proteins have primary, secondary, tertiary, and quaternary structures. F 25. 2-dimensional nuclear magnetic resonance can be used to determine interatomic distances in protein molecules. T 26. The development of electrospray mass spectrometry was important for protein sequencing as it allows macromolecules to remain intact during the mass spectrometry experiment. T
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27. You treat a pentapeptide (5 residues) with trypsin to produce a dipeptide and a tripeptide. These products are then reacted with dansyl chloride followed by aque ous acid and the products dansylalanine and dansyl-tryptophan are identified. Only the tripeptide product absorbs light at 280 nm. Reaction of a fresh batch of the pentapeptide with cyanogen bromide results in the formation o f a two products: a tetrapeptide containing a homoserine lactone and a free valine. Mass spectrometry reveals that the original pentapeptide contains no lysine residues. What is the sequence of the original pentapeptide in single letter code? (8 points (3 points for correct composition; 5 points for correct sequence))
__A__ - __R__ - __W__ -__M__-__V__
The following 3 questions show amino acids in their un-ionized form that have been modified by the action of enzymes. Each amino acid has been modified at a single position. For each amino acid, circle the atoms that have been added by the enzyme AND give the name of the amino acid before it was modified. N.B. In each case, only a single proton was removed from the original amino acid during modification. (6 points each)
28.
______ serine _/ alanine ____________
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29.
______aspartic acid_____________
30.
_____threonine______________
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