CChheemm 44334433Exam # 2 Oct. 28th, 2005 Name : Answer any seven of questions 1-8 . Each question is worth 15 points for a total of 105 points.1. (i) For the dipeptide Lys-His draw its structure at physiological pH(ii) Identify the only C-N bond with double bond character(iii) Leucine (LEU) has a Pα of 1.30 while closely related Isoleucine (ILE) has a Pα value of0.97. Provide a reason for this difference2. (i) Determinewhich of the following polypeptides, each composed of only one amino acid, ismore soluble in water at pH=7 and explain your reasoning :(-Tyr-)20or (-Lys-)20(ii) Silver ions are capable of reacting with proteins as follows :R-S-H + Ag+-> R-S-Ag + H+When some proteins are heated in the presence of silver ions they are irreversibly destroyed. Explain.(iii) Identify what forces may be responsible for stabilizing the 2o structures A and B in theaccompanying diagram.3. The accompanying diagram represents the denaturation of the protein ribonuclease.(i) Why was urea added and what otherreagent is also necessary to generate the fullydenatured structure shown(ii) Removing these denaturing reagents andexposing the solution to air regenerates thenative structure. What does this tell us about3o structure and why is exposure to airnecessary.(iii) Identify all steps necessaryto generate the scrambled nucleasestructure shown below from thenative structure4. (i) Lysozyme is a small enzyme which hydrolyzes polysaccharide chains using amino acids Glu35and Asp52 as shown below. Identify a pH, giving your reasoning, for this reaction:(ii) The protein α below exists as a dimer, except in aqueous solution where it breaks apartinto two monomers, Explain this 4o structure in terms of forces.αα(iii) The pepsin found in gastric juices ( pH=1.5 ) has a pI pf about 1. What does this tell us aboutthe amino acids that must be present in significant number in pepsin.5. (i) Describe the effects, in terms of the structure and function of hemoglobin (Hb) of: holding your breath decreasing [BPG] from 0.008M (high altitude) to 0.005M (low altitude)(ii) amino groups in the α subunits of hemoglobin can undergo the following carbamoylationreaction. Predict, giving your reasoning, how this can affect the operation of Hb underphysiological conditions :(iii) Under physiological conditions the amino acid lysine does not undergo the carbamoylation reaction shown above. ExplainRNH2CON-H+RNHCONH2HbcyanatecarbamoylationFor Questions 6-8 indicate all answers (i) through (v) that are correct6. Which of the following statements are true of peptides and proteins:(i) phenylalanine is most likely to be found on the surface of a protein(ii) proteins with high proline content will tend to have substantial helix composition(iii) methionine is more likely to be part of a helix rather than part of a β-sheet(iv) renaturation involves reduction followed by refolding of the protein.(v) renaturation involves oxidation followed by refolding of the protein.Comment7. Which of the following statements are true for the pentapeptide : Asp-Met-Glu-Thr-Glu(i) pI of the polypeptide is > 7(ii) pI of the polypeptide is < 7(iii) this polypeptide is an an α-helix at pH > 3(iv) this polypeptide is an an α-helix at pH < 3(v) the N-terminus is Glu and the C-terminus is AspComment8. Which of the following statements are true :(i) the stability of a folded protein molecule comes from favorable entropy contributions fromhydrophobic groups moving to the interior(ii) the stability of a folded protein molecule comes from favorable entropy contributions fromincreased structural complexity(iii) the shape of a specific antibody is determined by the shape of the antigen to which it responds(iv) an antigen can stimulate the production of multiple antibodies(v) disulfide bridges can play a role in stabilizing a polypeptide