There are 24 questions in all. Questions 1-20 are multiple choice and are each worth 3 points. Questions 21-24 are essays and problems worth a total of 40 points.

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

              1. CH₃COOH (aq) ↔ CH₃COO^- (aq) + H⁺ (aq). This reaction has K_eq = 1.74 x 10^-5 M.
ΔG for the reaction is (A) positive; (B) negative; (C) = 0; (D) negative, because ΔH is positive.

              2. A solution of                                  in water is most likely to form micelles.
(A) alanine; (B) lysine; (C) methionine; (D) serine.

              4. The [H⁺] for pH 2.8 is                , which is                      than the [H⁺] for pH 4.3 .
(A) 1.6 x 10^-3 M, more; (B) 2.8 M, less; (C) 2.8 x 10^-3 M, more; (D) 0.45 M, less.

              5. The pK_a's for alanine's α-COOH and α-NH₃⁺ are 2.34 and 9.69, respectively. Changing the pH from 2 to 5 causes the net charge of Ala-Ala-Ala-Ala-Ala to change from                 to      .   (A) +5, +4; (B) +1, 0; (C) +5, 0; (D) +3, –2.

              6. Molecules that don't repel each other can precipitate. At what pH is an Ala-Ala-Ala-Ala-Ala solution most likely to precipitate? (A) pH 2.0; (B) pH. 2.3; (C) pH 6.0; (D) 9.7

              7. Write the one-letter abbreviation for molecule U in the blank.

              8. The pH range for which molecule U is the most common form in solution is
(A) 0 – 1.5; (B) 2.0 – 3.0; (C) 4.0 – 6.0; (D) 8.0 – 9.0; (E) ≥ 10.0.

              9. Molecule X is the amino acid                which has been modified by adding                                                   .
(A) valine, phosphate; (B) isoleucine, acetate; (C) glycine, carboxyphosphate;
(D) threonine, phosphate.

              10. The diagram below represents part of a peptide backbone, with bonds labeled A-F .
A, B, D, and F label horizontal (–) bonds; C and E label vertical ( | ) bonds.
Which three letters represent bonds that have free rotation?
 

              11. Which choice is most disrupted by exposing a protein to detergent? (A) peptide bonds; (B) hydrogen bonds; (C) disulfide bonds; (D) hydrophobic interactions.

              12. When the disulfide bonds in ribonuclease A are reduced, and the protein is exposed to urea, it loses its                                                            structure. This can be reversed, if                                                                  first, and then                .
(A) primary and secondary, –S–S– bonds are re-formed, urea is removed;
(B) secondary and tertiary, –S–S– bonds are re-formed, urea is removed;
(C) secondary and tertiary, urea is removed, –S–S– bonds are re-formed;
(D) primary and secondary, urea is removed, –S–S– bonds are re-formed.

              13. Determining the sequence of any protein of more than 50 or so amino acid residues requires treatment with (A) peptide prolyl cis-trans isomerase (PPI); (B) cyanogen bromide or a protease; (C) dithiothreitol reduction, followed by acetylation with iodoacetate to convert –SH to –S–CH₃–COO^-; (D) x-ray crystallography.

              14. The protein that catalyzes reversible disulfide bond formation in order to stabilize the optimal tertiary structure is (A) protein disulfide isomerase; (B) ribonuclease;
(C) chaperonin; (D) prion.

              15. Myoglobin and hemoglobin are different because myoglobin has                   , and hemoglobin has         . (A) only secondary structure, only tertiary structure;
(B) secondary and tertiary structure, quaternary structure;
(C) heme only, a protoporphyrin ring + iron;
(D) only α-helix secondary structure, α-helix and β-sheet secondary structure.

              16. Myoglobin and hemoglobin are also different because myoglobin has              affinity for O₂, and hemoglobin has        binding. (A) higher, hyperbolic;
(B) lower, hyperbolic; (C) higher, cooperative; (D) lower, cooperative.

              17. For both myoglobin and hemoglobin, K_d is equal to (A) n, the Hill coefficient;
(B) [P] + [L]; (C) Θ; (D) P₅₀, the pO₂ at which 50% of binding sites are occupied.

              18. Sequences 1-4 include all 20 amino acids.
(1) H-E-A-R-D; (2) L-I-C-Q-S; (3) M-P-F-V-G; (4) T-W-Y-N-K.
When the sequences are ranked in order of increasing hydrophobicity (most hydrophobic last), they are (A) 2, 3, 4, 1; (B) 1, 4, 2, 3; (C) 4, 3, 1, 2; (D) 3, 2, 4, 1.

              19. As a result of the reaction catalyzed by carbonic anhydrase, increasing [CO₂] causes an increase in (A) [H⁺]; (B) O₂ bound by Hb; (C) pH; (D) all of these.

              20. Normal adult Hb is called Hb A, while Hb Milwaukee has a Glu at β 67 instead of Val. Hb Milwaukee is therefore more likely to
(A) have a different isoelectric point; (B) bind to BPG; (C) clump together and form crystals;
(D) bind CO₂ and stabilize the R conformation.

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).

      a. Ribonuclease has                                  α-helices. Use H to label the same one on both
       diagrams.
b. Ribonuclease has                                 β-sheets. Use S to label the same one on both diagrams
c. Name two types of information provided only by the diagram on the right.

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. Calculate [A^-] and [HA] for the buffer. Show your work . (6)
b. Comment on the effectiveness of the buffer compared to one with a pK_a = 6.20. Explain. (4)

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)

24. The graph represents Θ as a function of pO₂ for hemoglobin (Hb) in the absence of modulators.
a. Name two negative modulators of O₂ binding by Hb and the part of Hb to which each
      binds. Be as specific as possible . (5)
b. Add a line to the graph to show the effect of adding one of the modulators from part a. (1)
c. Describe what would happen if both modulators were added.
       You may also draw a line for this on the graph if it is different from part b. (2)
d. Explain why this is advantageous for Hb function. (2)

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