Problem Set 2 Answers

Multiple Choice:

1) The chirality of an amino acid results from the fact that its carbon:

A) has no net charge. B) is a carboxylic acid. C) is bonded to four different chemical groups. D) is in the L absolute configuration in naturally occurring proteins. E) is symmetric.

2) The uncommon amino acid selenocysteine has an R group with the structure —CH2—SeH (pKa 5). In an aqueous solution, pH = 7.0, selenocysteine would:

A) be a fully ionized zwitterion with no net charge. B) be found in proteins as D-selenocysteine. C) never be found in a protein. D) be nonionic. E) not be optically active. ** Each of these answers in incorrect. A) is partially correct. Selenocysteine would be fully ionized at pH=7.0 but it would have a charge of -1. Therefore it is not a zwitterion.

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 formation of a peptide bond between two amino acids is an example of a(n) ______________ reaction.

A) cleavageB) condensationC) group transferD) isomerizationE) oxidation reduction

5) Which of the following pairs of bonds within a peptide backbone show free rotation around both bonds?

A) C—C and N—C B) C=O and N—C C) C=O and N—C D) N—C and C—C

Problem Set 2 Answers

E) N—C and N—C

6) The most important contribution to the stability of a protein’s conformation appears to be the:

A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it.

B) maximum entropy increase from ionic interactions between the ionized amino acids in a protein.

C) sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein.

D) sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water.

E) stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another.

7) In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the:

A) formation of the maximum number of hydrophilic interactions. B) maximization of ionic interactions. C) minimization of entropy by the formation of a water solvent shell around the protein. D) placement of hydrophobic amino acid residues within the interior of the protein.E) placement of polar amino acid residues around the exterior of the protein.

8) Thr and/or Leu residues tend to disrupt an helix when they occur next to each other in a protein because:

A) an amino acids like Thr is highly hydrophobic. B) covalent interactions may occur between the Thr side chains. C) electrostatic repulsion occurs between the Thr side chains. D) steric hindrance occurs between the bulky Thr side chains. E) the R group of Thr can form a hydrogen bond.

A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n):

A) antiparallel sheet. B) parallel sheet. C) helix. D) sheet. E) turn.

.

Problem Set 2 Answers

10) Which of the following statements concerning protein domains is true?

A) They are a form of secondary structure. B) They are examples of structural motifs. C) They consist of separate polypeptide chains (subunits). D) They have been found only in prokaryotic proteins. E) They may retain their correct shape even when separated from the rest of the

protein.

11) Which of the following statements about aromatic amino acids is correct?

A) All are strongly hydrophilic. B) Histidine’s ring structure results in its being categorized as aromatic or basic, depending

on pH. C) On a molar basis, tryptophan absorbs more ultraviolet light 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 its R group determines whether or not an amino acid

is aromatic.

12) What is the approximate charge difference between glutamic acid and -ketoglutarate at pH 9.5?

A) 0B) ½C) 1D) 1½E) 2

Short Answer:

13) What are the structural characteristics common to all amino acids found in naturally occurring proteins?

Ans: All amino acids found in naturally occurring proteins have an carbon to which are attached a carboxylic acid, an amine, a hydrogen, and a variable side chain. All the amino acids are also in the L configuration.

14) Why do amino acids, when dissolved in water, become zwitterions?

Ans: Near pH = 7, the carboxylic acid group (—COOH) will dissociate to become a

Problem Set 2 Answers

negatively charged —COO– group, and the —NH2 amino group will attract a proton to become a positively charged —NH3

+ group.

15) Leucine has two dissociable protons: one with a pKa of 2.3, the other with a pKa of 9.7. Sketch a properly labeled titration curve for leucine titrated with NaOH; indicate where the pH = pK and the region(s) in which buffering occurs.

Use Glycine titrations as a guide

16) What is the pI, and how is it determined for amino acids that have nonionizable R groups?

Ans: The pI is the isoelectric point. It occurs at a characteristic pH when a molecule has an equal number of positive and negative charges, or no net charge. For amino acids with nonionizable R groups, pI is the arithmetic mean of a molecule’s two pKa values:

pI = 1/2 (pK1 + pK2)

17) Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein, and describe one condition or reagent that interferes with each type of stabilizing force.

Ans: Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen bonds, (c) hydrophobic interactions, and (d) ionic interactions. Agents that interfere with these forces are (a) mercaptoethanol or dithiothreitol, (b) pH extremes, (c) detergents and urea, and (d) changes in pH or ionic strength, respectively.

18) Why are glycine and proline often found within a turn?

Ans: A turn results in a tight 180° reversal in the direction of the polypeptide chain. Glycine is the smallest and thus most flexible amino acid, and proline can readily assume the cis configuration, which facilitates a tight turn.

Problem Set 2 Answers

19) How does the shape of a titration curve confirm the fact that the pH region of greatest buffering power for an amino acid solution is around its pK’s?

Ans: In a certain range around the pKa’s of an amino acid, the titration curve levels off. This indicates that for a solution with pH pK, any given addition of base or acid equivalents will result in the smallest change in pH—which is the definition of a buffer.

20) How can changes in pH alter the conformation of a protein?

Ans: Changes in pH can influence the extent to which certain amino acid side chains (or the amino and carboxyl termini) are protonated. The result is a change in net charge on the protein, which can lead to electrostatic attractions or repulsions between different regions of the protein. The final effect is a change in the protein’s three-dimensional shape or even complete denaturation.