15. During oxidative phosphorylation, the proton motive force that is generated by electron transport is used to:
(A) create a pore in the inner mitochondrial membrane.
(B) generate the substrates (ADP and Pi) for the ATP synthase.
(C) induce a conformational change in the ATP synthase.
(D) oxidize NADH to .
(E) reduce O₂ to H₂O.

1. Which of the following amino acids has more than one chiral carbon? (A) Cys (B) Thr (C) Tyr (D) Trp (E) Lys

2. Which of the following statements about aromatic amino acids is correct? (A) All are strongly hydrophilic. (B) Histidine is categorized as aromatic. (C) On a molar basis, tryptophan absorbs more ultraviolet light (280 nm) than tyrosine. (D) The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group. (E) The presence of a ring structure in an amino acid determines whether or not it is aromatic.

3. For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have: (A) a net negative charge. (B) a net positive charge. (C) no charged groups. (D) no net charge. (E) positive and negative charges in equal concentration.

4. The six atoms of the peptide group lie in a single plane as depicted in the picture below. In the picture, "R" represent the side chains, and a few atoms are labeled. Which side is closer to the C-terminus of this short peptide. (A) Right side (B) Left side (C) Both sides possible (D) Can't tell from limited information (E) Neither side

5. The bond angles φ and ψ of the short peptide in the picture above are most likely located in the area of Ramachandran plot as below (A) I (B) II (C) III (D) IV (E) I and III

6. Compare the following sequences taken from four different proteins, and select the answer that best characterizes their relationships. 1 PDWLKDNDYLLHGHRPPMPFFRACFKSIFRIHTETGNIWTHLLGFVLFLF 2 PDWLKDNDYLLHGHRPPMPSFRACFKSIFRIHTETGNIWTHLLGFVLFLF 3 PDWLKDNDYLLHGHRPPMPSFRACFKSIFRIHTETGNIWTHLLGFVLFLF 4 PEYMKDNEYILN-YYRADWSIRDAFFSVFSFHNESLNVWTHLIGFIFFVA (A) Protein 3 reveals the greatest evolutionary divergence. (B) Comparing proteins 1 and 2 reveals that these two proteins have diverged the most throughout evolution. (C) Protein 4 is the protein that shows the greatest overall homology to protein 1. (D) Proteins 1 and 4 show a greater evolutionary distance than proteins 1 and 2. (E) The portions of amino acid sequence shown suggest that these proteins are completely unrelated.

7. Which of the following statements about the folding of polypeptides is false? (A) Burial of hydrophobic amino acid R groups to exclude water (B) Alpha helices and beta sheet generally are usually found in different structural layers. (C) Polypeptide segment adjacent to each other in the primary sequence are always far away to each other in the folded structure. (D) Connections between elements of secondary structure do not form knots in most times. (E) Left handed connection between beta strands is very rare.

8. Two heme-binding proteins (myoglobin and hemoglobin), A and B, can bind oxygen. Which of the following statement is correct?. (6, fraction) (A) The plot below describes the behavior of A when it binds oxygen under different pH (B) The plot below describes the behavior of B when it binds oxygen under different pH (C) The plot below describes the behavior of both A and B when they bind oxygen under different pH (D) The curves can't describes the behavior of A or B (E) Hemoglobin does not bind oxygen at pH 7.4

9. The molecule in the right figure is a (A) two glucose linked by β1-4 linkage, part of cellulose (B) two glucose linked by β1-4 linkage, part of amylose (C) two glucose linked by α1-4 linkage, part of amylose (D) two glucose linked by α1-4 linkage, part of sucrose (E) two glucose linked by β1-4 linkage, part of heparan

10. The reaction A + B→C has a ΔG°of -20 kJ/mol at 25°C. Starting under standard conditions, one can predict that: (A) at equilibrium, the concentration of B will exceed the concentration of A. (B) at equilibrium, the concentration of C will be less than the concentration of A. (C) at equilibrium, the concentration of C will be much greater than the concentration of A or B. (D) C will rapidly break down to A + B. (E) when A and B are mixed, the reaction will proceed rapidly toward formation of C.

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