Problem Set 2 Answers

Multiple Choice:
1) The chirality of an amino acid results from the fact that its carbon:
A)
B)
C)
D)
E)

has no net charge.

is a carboxylic acid.
is bonded to four different chemical groups.
is in the L absolute configuration in naturally occurring proteins.
is symmetric.

2) The uncommon amino acid selenocysteine has an R group with the structure CH 2SeH
(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)
B)
C)
D)
E)

a net negative charge.

a net positive charge.
no charged groups.
no net charge.
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)
B)
C)
D)
E)

cleavage
condensation
group transfer
isomerization
oxidation reduction

5) Which of the following pairs of bonds within a peptide backbone show free rotation around
both bonds?
A) CC and NC
B) C=O and NC
C) C=O and NC

Problem Set 2 Answers

D) NC and CC
E) NC and NC

6) The most important contribution to the stability of a proteins 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)
B)
C)
D)
E)

formation of the maximum number of hydrophilic interactions.

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

an amino acids like Thr is highly hydrophobic.

covalent interactions may occur between the Thr side chains.
electrostatic repulsion occurs between the Thr side chains.
steric hindrance occurs between the bulky Thr side chains.
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)
B)
C)
D)
E)

antiparallel sheet.
parallel sheet.
helix.
sheet.
turn.

Problem Set 2 Answers

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

A)
B)
C)
D)
E)

They are a form of secondary structure.

They are examples of structural motifs.
They consist of separate polypeptide chains (subunits).
They have been found only in prokaryotic proteins.
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) Histidines 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)
B)
C)
D)
E)

1
1
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?

Problem Set 2 Answers

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

Problem Set 2 Answers

cis configuration, which facilitates a tight turn.

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 pKs?
Ans: In a certain range around the pKas 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 pHwhich 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 proteins three-dimensional shape or even
complete denaturation.