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2 Exam - 1999 1. (5 points) In the following table indicate by an X whether the amino acids contribute to hydrophobic, ionic and hydrogen bonding interactions in a protein at pH 7.0. Amino Acid Asp Leu Tyr Hydrophobic X X Ionic X Hydrogen bonds X X 2. (8 points) Blood that has been stored for some time is depleted of BPG. What problems, if any, would this cause upon transfusion into a patient? Why? The BPG-depleted red cells contain Hb that binds O2 too strongly and would not deliver O2 to the tissues. 3. (12 points) A. (6 pts) Curve A corresponds to the oxygen saturation curve of normal hemoglobin. On this figure (a) draw the oxygen saturation curve corresponding to R state hemoglobin and label "R" and (b) draw the oxygen saturation curve corresponding to T state hemoglobin and it label "T". B. (6 pts) This Hill plot represents the oxygen saturation curve for Hb at pH 6.8 in the absence of BPG. Draw the oxygen saturation curve at pH 6.8 in the presence of BPG and label "+BPG, pH 6.8"; draw the oxygen saturation curve in the absence of BPG at pH 7.2 and label "-BPG, pH 7.2". "-BPG, pH 7.2" is higher affinity, curve to the left. "+BPG, pH 6.8" is lower affinity, curve to the right. 4. (5 points) Would you expect the and subunits of hemoglobin to have more or less hydrophobic amino acids than myoglobin. Why? More need to have hydrophobic amino acids for subunit interactions. 5. (8 points) In deoxy hemoglobin a Cl- is bound between the -amino group of the amino terminal amino acid (Val) of the 2 chain and an Arg of the 1 chain. This Cl- is absent in oxy hemoglobin. How can the presence of this Cl- explain, as least partly, the Bohr effect? The Cl- can only be bound if the amino group is protonated and this stabilizes the protonated form of the amino group. Thus, proton uptake would favor the deoxy state the Bohr effect. 6. (12 points) A protein containing 100 amino acids has a -sheet between the first few amino acids at the amino terminal and the last few amino acids at the carboxyl terminal with a hydrogen bond between the amino terminal amino acid and the carboxyl terminal amino acid. The sequence of the two ends is A-F-S-I-L ........... V-A-L-V-T. A. (4 points) Is the -sheet parallel or antiparallel? It must antiparallel for the amino and carboxyl terminals to form a hydrogen bond. B. (4 points) Which amino acids are hydrogen bonded in the sheet? A-T, F-V, S-L, I-A, L-V C. (4 points) Is the -sheet amphipathic? No. Almost all the amino acids are hydrophobic. 7. (5 points) Why would hydrophobic be forces more important in stabilizing folding intermediates than hydrogen bonds? Hydrogen bonds are too liable because they can be disrupted by water; hydrophobic interactions actually depend on proper folding of the protein. 8. (8 points) A. (4 points) How does calcium facilitate muscle contraction? The binding of calcium to troponin C causes the troponin C-tropomyosin complex to move so that the myosin head can bind to actin. B. (4 points) How many subunits are there in an antibody molecule (type IgG, as shown in class)? How many immunoglobulin domains? There are 4 subunits (2 heavy chains and 2 light chains) and 12 immunoglobulin domains. 9. (12 points) A. (6 points) A protein contains two domains that are connected by a loop of 12 amino acids. In the crystal structure of the protein the atoms of the amino acids in this loop cannot be detected, whereas all the amino acids in the two domains are readily detected. Explain this observation. The amino acids in the loop are mobile do not have a fixed conformation therefore are not fixed in the crystal and don't diffract (give a signal). B. (6 points) Would an AlaPro mutation most likely affect the structure of the domains or the loop? Why? The substitution would most like disrupt the domains by terminating the -helix. It is unlikely that the substitution would affect the loop. 10. (5 points) Name the domains depicted below: Domain Domain 11. (8 points ) Explain why the aggregates of HbS that form at body temperature (37 C) dissociate when the temperature is lowered to 0 C. For aggregation to occur, G = H-T S, must be negative at 37 C. Aggregation is driven by hydrophobic interactions for which S is positive (favorable). At high temperature the entropy term predominates and aggregation is favored; at low temperature G for aggregation must be unfavorable, presumably because the unfavorable the enthalpy term becomes predominate. 12. (12 points) Amino acid substitutions at the - interface may change the relative stabilities of the R and T forms of hemoglobin. For example, in one mutant form of hemoglobin the hydrogen bond that is primarily responsible for stabilizing the R state is lost. A. (6 points) Would you expect this hemoglobin to have a higher or lower than normal O2 affinity? Explain. Lower. The protein will remain in the T state since the R state is no longer stabilized B. (6 points) Why does this hemoglobin have a Hill coefficient of 1.0? There is no conversion of T to R, so no cooperativity is observed.

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