CChheemm 44334433 Exam #2 2008 Name : Answer any seven of questions 1-8 . Each question is worth 15 points for a total of 105 points. 1. For the dipeptide Val-His: (i) Draw its structure at pH values of 1, 5 and 11 (ii) Determine, showing your method, its isoelectric point or pI (iii) Pyruvic acid (pKA = 3.00 ) and Succinic acid ( 1st pKA = 5.0, 2nd pKA = 7.0) are shown on the right. Determine, giving your reasoning, which will function as a more effective buffer at physiological pH and draw the structure of the anion acting as a buffer component. 2. The side chains of the amino acid cysteine can undergo the following reaction, useful in detection : (i) If you wish to perform the above reaction on a cysteine containing protein identify, giving your reasoning, what reagents would first have to be added to the protein. (ii) Give two other amino acids that might be detected using iodoacetate, molecule I in (i) above. (iii) You are told that the peptide shown below contains an a helix 10 amino acids long. Without needing to calculate any running averages identify those amino that form the a-helix and circle those amino acids that might be pointing towards the inside of the larger protein. ISCH2COHOIOOHCCH2HS3 (i) For the tripeptide shown to the right the pKa of the His sidechain is 6.0, the PKa of the carboxyl group is 2.0 and that of the amino group is 9.0 . Complete the plot of the fraction of protein protonated (y-axis, 1 to 0) vs. the pH of the environment (x-axis, 0 to 12) (ii) Replacement of a buried Tyrosine residue by a glycine residue lowers the melting temperature (TM) of a protein to 342 K. Decide, giving your reasoning, whether the effect on TM is due to a change in ∆H or ∆S. (iii) An enzyme has a glutamic acid residue in its active site. In order for the enzyme to be fully active, this glutamate side-chain must be negatively charged. Draw, using the graph on the right, the pH dependence of the enzyme activity. Justify your graph, preferably with a sample calculation. 4 (i) The core of a globular protein consists entirely of six valine residues. The melting curve for this protein, as well as a number of variants is shown to the right. The thermodynamic parameters, for the reaction going from the Native to Unfolded state, are shown in the table below. Determine , giving your reasoning, what these values tell you about the forces responsible for the native structure(ii) A protein contains an Ile residue that is buried in its non-polar core. This residue has been changed to either a Val, Ala, or Gly. The melting curves for all four of these proteins are shown on the right, . Given that the protein with Ile has the highest TM identify, giving your reasoning, which of the other melting curves belongs to which mutant protein. (iii) For the proteins listed in the table identify, giving your reasoning : a) the the protein with the highest pI b)the protein with the lowest pI c) the protein that is most soluble in an aqueous solution of pH=2.0 5 .(i) Explain, using diagrams how the CO2 transport mechanism shown on the lower right contributes to the Bohr effect in Hb. (ii) On the right is the oxygen binding curve for normal Hb. Draw the binding curves you would expect for (a) fetal Hb and (b) normal Hb in the presence of high [BPG] (iii) A crocodile’s Hb does not normally bing BPG but does instead bind bicarbonate. What evolutionary advantage does this molecular adaptation give the crocodile. NHNNH3+βαR for mT for mHb CO2 transport schemeNH3++ HCO3-NHCOO-+H++ H2OFor Questions 6-8 indicate all answers (i) through (v) that are correct. 6. Which, if any, of the following statements are true for binding plot of myoglobin (Myo), normal hemoglobin (Hb-normal) and a mutant hemoglobin (Hb-mutant) shown on the right: (i) The mutant hemoglobin favors the R state (ii) The myoglobin shown preferentially adopts the Tense, or T, state (iii) The mutant hemoglobin binds less oxygen in the lungs but releases oxygen more efficiently in the tissues (iv) The normal hemoglobin binds more oxygen in the lungs but releases oxygen less efficiently in the tissues (v) A loss of any of the positively charged amino acids in the central cavity of Hb (page 229 of your text) could have produced the mutant Hb whose plot is shown above Comment: 7. The 3o structure for a protein is shown, as is a melting curve for the protein with an Ile at position 18 and a melting curve for a mutant with Ala at position 18. Which of the following statements are true : (i) intra-chain hydrogen bonds are utilized to stabilize region A (ii) substituting Ala for Ile at position A explains the melting curves (iii) substituting Ala for Ile at position B explains the melting curves (iv) substituting Ala for Ile at position 18 affects the melting curve by changing ∆H (v) substituting Ala for Ile at position 18 affects the melting curve by changing ∆S Comment 8. For the the immune response shown which of the following statements are true : (i) the antibodies are eliciting a response by stimulating the production of antigens (ii) the antibody structure includes variable and constant regions connected by disulfide bridges (iii) the antibody alters the antigen shape to produce antigens specific to the antibody (iv) the antigen alters the antibody shape to produce antibodies specific to the antigen (v) by first denaturing the antigen one can will normally stimulate a greater production of antibodies