For multiple choice questions, the correct choice is in the blank. If I think an additional explanation might be helpful, it will immediately follow the question.

You may find these helpful: R = 8.314 J/mole-K; T = 298 K; ΔG°′ = – R T ln K_eq

Multiple Choice Answers:

* Both alanine and methionine are nonpolar. Methionine is a better choice for two reasons:
(a) it's even less polar than alanine; (b) micelle formation is favored for molecules that have a wedge shape, with the broad part of the wedge being the polar part and the narrow point of the wedge being the nonpolar part.

Essays:

21. These two diagrams are two ways of showing the structure of ribonuclease.
Answer either a or b (2). Also answer c and d (8).

The Protein Data Bank has changed the way it represents diagrams, so a similar question now would have different diagrams.

a. Ribonuclease has    3 α      helices. Use H to label the same one on both diagrams.
The 3^rd helix is on the left near the Cys-58 label, the 1^st helix is in the middle, and the 2^nd helix is on the right, just below the Cys-26 label.

b. Ribonuclease has    3 β      sheets. Use S to label the same one on both diagrams.
β-sheet A is the large one in the middle of the protein, B is on the left and includes Cys-72, and β-sheet C is very short, right next to the 2 nd helix.

c. Name two types of information provided only by the diagram on the right.

Primary structure, the number of residues, the residues involved in an α-helix, the residues involved in β-sheets, β-bends, etc.

      You couldn't answer which residues were involved in disulfide bonds, because those are labeled in the ribbon diagram.

      d. Fill in the table below to answer some questions about tertiary structure for ribonuclease.
       Name two types of weak interaction that stabilize tertiary structure. Name an amino acid
       residue (not the same one both times) that might be involved, and the part of the amino
       acid (α-amine, α-carbon, α-carboxyl, or side chain).

22. You need to prepare 1.00 L of a buffer for pH 6.00 with a total concentration of 0.250 M, and you have been told to use a weak acid that has a pK_a = 5.68 and its conjugate base.
a. [A^-] = 0.17 M, and [HA] = 0.08 M
b. A buffer with pK_a = 6.20 is slightly more effective because it has a ratio of [A^-] to [HA] that is closer to 1. That is not the same as having a larger range.

23. The amino acids listed below can be used to make a peptide with the sequence W-E-L-K.
a. Draw the structure of the peptide in the form you would expect to find at pH 3.0. (8)
b. Assuming that all pK_a's in the table still apply for this peptide, what is its pI? (2)

a. At pH 3.0, the glutamate side chain should still be protonated.
b. The pI for this peptide is at the middle of the pH range at which its net charge = 0.
      The net charge = 0 from pH 4.25 – 9.39, so the average = 6.82.

24. The graph represents Θ as a function of pO₂ for hemoglobin (Hb) in the absence of modulators.
a. H⁺ binds to charged side chains, especially His, of the α and β subunits.
             CO₂ binds to the amine terminus of the a and b subunit chains.
             BPG binds to Lys side chains at the middle of the Hb molecule.
b. The line must be to the right, and it should have a sigmoidal shape and go up to the same
             level as the first line.
c. Because the modulators all bind different parts of the globin, there is a cumulative
            negative effect. That is, adding an additional negative modulator helps to stabilize the
            T conformation even more. If you drew a line, it should be further to the right, but it
            should still go most of the way up to the plateau at high pO₂. See Fig. 5-16, for example.
d. Having negative modulators promotes release of O₂ in the tissues, where the
             concentration of the modulators is high.

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