MCB 450 Spring 2012 Problem sets Lecture 4 (chapts 4&5)

Q1. Amino acid side chains capable of forming hydrogen bonds are usually located on the protein ___________ and form hydrogen bonds primarily with the ___________________. a. surface, water solvent b. interior, water solvent c. surface, other amino acid side chains d. interior, other amino acid side chains e. all are true Ans. a Q.2 An electrostatic interaction might occur within a protein between which of the following amino acid pairs at typical physiological pH? a. Ser/Asn b. Asp/Glu c. Arg/Cys d. Lys/Asp e. Val/Ile Ans. d Q3. All of the information necessary for folding the peptide chain into its native structure is contained in the __________________of the peptide. a. amino acid sequence b. amino acid composition c. configuration d. amino acid side chain charges e. all are true Ans. e Q4. Secondary and higher orders of structure are determined by all EXCEPT: a. hydrophobic interactions. b. ionic bonds. c. van der Waals forces. d. hydrogen bonds. e. peptide bonds. Ans. e Q5. The resonance structure which forms the "amide plane" contains which atoms? a. C H-NH-CO-C-C H b. C H-NH-CO c. C -NH-CO-C d. NH-CO

e. Ans. c

NH-CO-C

Q6. In the majority of -helixes, each peptide carbonyl is hydrogen bonded to the peptide N-H group ______ residues farther _____ the chain. a. 2, down b. 4, up c. 3, down d. 2, up e. 4, down Ans. b Q7. When the peptide (AEFFLAMEP) forms an -helix, which amino acid residue would be closest to being in the same position on the same face of the helix as is the initial alanine residue? f. F(3) g. A(6) h. E(8) i. P(9) j. L(5) Ans. c Q8. Polylysine is a random coil when the pH is less than 11, while it forms an -helix if the pH is raised to greater than 12. This is because at pH 12: a. the lysine residues are negatively charged which electrostatically stabilizes the helix. b. the positive charges on the lysine residues stabilizes the -helix. c. the lysine residues are neutral which eliminates electrostatic repulsion between the R groups. d. the high concentration of OH- ions in solution reduces the electrostatic repulsion between the R-groups. e. the lysine side chain changes configuration with pH. Ans. c Q9. Tertiary structure is defined as: a. the sequence of amino acids. b. the folding of a single polypeptide chain in three-dimensional space. c. hydrogen bonding interactions between adjacent amino acid residues into helical or pleated segments. d. the way in which separate folded monomeric protein subunits associate to form oligomeric proteins. e. all are true. Ans. b Q10. -Keratin has all of the following characteristics EXCEPT:

a. b. c. d. e. Ans. d

primary component in hair, claws, fingernails, and horns of animals. consists of four helical strands arranged as twisted pairs of two-stranded coiled coils. has associated hydrophobic strips on the two coiled coils. principal constituent of connective tissues in animals. has covalent disulfide bonds to stabilize the structure.

Q11. Arrange the steps involved in folding of globular proteins into a proper sequence. A. B. C. D. E. a. b. c. d. e. Ans. d Q12. Why is Proline an -helix destabilizating residue? Give 2 reasons. 1. Free rotation about C-N bond prohibited (since the C of Proline is involved in the ring structure) 2. N has no H atom and hence cannot participate in H-bonding Q13. Describe the forces involved in protein folding. Large increase in entropy of water molecules compensates for the loss of conformational entropy of the protein molecule and hence drives the protein folding process forward. Q14. A protein was purified to homogeneity. Determination of the mass by gel-filtration (separates according to size) yields 60-kDa species. Chromatography in the presence of urea yields a 30-kDa-species. When the chromatography is repeated in the presence of urea yields a 30 kDa-species. When the chromatograph is repeated in the presence of urea and -mercaptoehtanol, a single molecular species of 15 kDa results. Describe the structure of the molecule. Treatment with urea disrupts noncovalent bonds. Thus, the original 60-kDa protein must be made of two 30kDa subunits. When these subunits are treated with urea and -mercaptoethanol, a single 15-kDa species results, suggesting that disulfide bonds link the 30-kDa subunits. "Molten globule" formation of assembled domains. Formation of domains through cooperative aggregation of folding nuclei. Adjustment in the conformation of domains. Rapid and reversible formation of local secondary structure. Final protein monomer formation. A, B, C, D, E B, C, E, A, D D, C, B, A, E D, B, A, C, E B, D, C, A, E

Q15. Electrostatic interactions among amino acid residues on proteins may be damped out by high concentrations of: a. water. b. organic solvents. c. salts. d. heat. e. all of the above. Ans. c Q16. A hydrophobic interaction might occur within a protein between which of the following amino acid pairs? f. Ser/Ile g. Val/Leu h. Tyr/Cys i. Lys/Asn j. His/Val Ans. b Q17. Although they have very different functions, hen egg white lysozyme and __________ share similar sequence homology and similar tertiary structure. a. trypsin b. -lactalbumin c. thrombin d. hemoglobin e. chymotrypsin Ans. b Q.18 Acid hydrolysis of an octapeptide yielded the following amino acids in equimolar ratios: Ala, Asp, Leu, Lys, Met, Phe, Tyr, Val Dansyl chloride treatment of the original octapeptide, followed by acid hydrolysis, yielded dansyl-Ala. Treatment of the original octapeptide with CNBr yielded a dipeptide containing Leu and Phe, and another product. Treatment of the original octapeptide with chymotrypsin, yielded Leu, a dipeptide containing Tyr and Ala, and a pentapeptide. Treatment of the original octapeptide with trypsin gave two tetrapeptides, both of which remained near the origin upon electrophoresis at pH 6.0. Give a sequence consistent with the foregoing data. Partial credit will be given for each clue that you can correctly interpret. _______ - _______ - _______ - _______- _______ - _______- _______ - _______

Ala-Phe-Asp-Lys-Ala-Phe-Met-Arg Dansyl chloride treatment of the original octapeptide, followed by acid hydrolysis, yielded dansyl-Ala. Ala is at N-terminus Treatment of the original octapeptide with CNBr yielded Arg and a peptide. Met is in position 7 and Arg at C-terminus. Treatment of the original octapeptide with trypsin gave two tetrapeptides. Lys is at position 4. Treatment of the two tryptic tetrapeptides (from the clue above) with chymotrypsin gave four dipeptides. Phe is at positions 2 and 6. Three of these dipeptides remained near the origin upon electrophoresis at pH 6.0, and one moved toward the cathode (the negative pole). Asp is at position 3 and Ala at position 5

Q19. Determine the sequence of a peptide consisting of 14 amino acids on the basis of the following data. Coma between residues means the order is not known. Amino acids within a bracket are part of the same peptide: Note: Chymotrypsin can also cleave the peptide bound on the carboxyl side of leucine at a slower rate. Amino acid composition (4S, 2L, F, G I, K, M, T, W, Y) Amino terminal analysis: S Carboxypeptidase A digestion: L Trypsin digestion: (3S, 2L, F, I, M, T, W) (G, K, S, Y) Chymotrypsin digestion: (F, I, S) (G, K, L)(L,S) (M,T) (S,W) (S,Y) Amino-terminal analysis of (F, I, S) peptide: S Cyanogen bromide treatment: (2S, F, G, I, K, L, M, T, Y) (2S, L, W) First amino acid: S Last amino acid: L Cyanogen Bromide cleavage: M in 10th position, carboxyl residue are: (2S, L, W) Amino-terminal residues: (G, K, Y, S), tryptic peptide, ends in K Therefore amino terminal is: SYGK Chymotrypsin peptide order: (S-Y),(G,K,L),(F,I,S),(M-T),(S-W),(S-L) Sequence: SYGKLSIFTMSWSL

Q20. Why do proteins precipitate in high salt concentration? If the salt concentration becomes too high, the salt ions interact with the water molecules. Eventually, there are not enough water molecule to interact with the protein, and the protein precipitates.