Practice Problems (Chapter 3)

2. Of the 20 standard amino acids, only _____ is not optically active. The reason is that its
side chain _____.
A) alanine; is a simple methyl group
B) glycine; is a hydrogen atom
C) glycine; is unbranched
D) lysine; contains only nitrogen
E) proline; forms a covalent bond with the amino group

4. All of the amino acids that are found in proteins, except for proline, contain a(n) _____
group.
A) amino
B) carbonyl
C) carboxyl
D) ester
E) thiol

5. Which statement 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.

6. Which statement about cystine is CORRECT?

A) Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—
CH2— disulfide bridge between two cysteines.
B) Cystine is an example of nonstandard amino acid, derived by linking two standard
amino acids.
C) Cystine is formed by the oxidation of the carboxylic acid group on cysteine.
D) Cystine is formed through a peptide linkage between two cysteines.
E) Two cysteines are released when a —CH2—S—S—CH2— disulfide bridge is
reduced to —CH2—SH.

8. Which two amino acids differ from each other by only one atom?
A) Ser and Thr
B) Leu and Ile
C) Ala and Ser
D) Asp and Asn
E) Ser and Cys

Page 1
9. Amino acids are ampholytes because they can function as either a(n):
A) acid or a base.
B) neutral molecule or an ion.
C) polar or a nonpolar molecule.
D) standard or a nonstandard monomer in proteins.
E) transparent or a light-absorbing compound.

11. In a highly basic solution, pH = 13, the dominant form of glycine is:
A) NH2—CH2—COOH.
B) NH2—CH2—COO–.
C) NH2—CH3+—COO–.
D) NH3+—CH2—COOH.
E) NH3+—CH2—COO–.

13. At pH 7.0, converting glutamic acid to -carboxyglutamate, will have what effect on the
overall charge of the protein-containing it?
A) It will become more negative
B) It will become more positive.
C) It will stay the same.
D) There is not enough information to answer the question.
E) The answer depends on the salt concentration.

14. At pH 7.0, converting proline to hydroxyproline, will have what effect on the overall
charge of the protein-containing it?
A) It will become more negative
B) It will become more positive.
C) It will stay the same.
D) There is not enough information to answer the question.
E) The answer depends on the salt concentration.

15. What is the approximate charge difference between glutamic acid and -ketoglutarate at
pH 9.5?
A) 0
B) 1/2
C) 1
D) 11/2
E) 2

16. The formation of a peptide bond between two amino acids is an example of a(n) _____
reaction.
A) cleavage
B) condensation
C) group transfer
D) isomerization
E) oxidation-reduction

Page 2
18. An octapeptide composed of four repeating glycylalanyl units has:
A) one free amino group on an alanyl residue.
B) one free amino group on an alanyl residue and one free carboxyl group on a glycyl
residue.
C) one free amino group on a glycyl residue and one free carboxyl group on an alanyl
residue.
D) two free amino and two free carboxyl groups.
E) two free carboxyl groups, both on glycyl residues.

19. At the isoelectric pH of a tetrapeptide:

A) only the amino and carboxyl termini contribute charge.
B) the amino and carboxyl termini are not charged.
C) the total net charge is zero.
D) there are four ionic charges.
E) two internal amino acids of the tetrapeptide cannot have ionizable R groups.

20. Which statement is CORRECT concerning the amino acid composition of proteins?
A) Larger proteins have a more uniform distribution of amino acids than smaller
proteins.
B) Proteins contain at least one each of the 20 different standard amino acids.
C) Proteins with different functions usually differ significantly in their amino acid
composition.
D) Proteins with the same molecular weight have the same amino acid composition.
E) The average molecular weight of an amino acid in a protein increases with the size
of the protein.

21. The average molecular weight of the 20 standard amino acids is 138, but biochemists use
110 when estimating the number of amino acids in a protein of known molecular weight.
Why?
A) The number 110 is based on the fact that the average molecular weight of a protein
is 110,000 with an average of 1000 amino acids.
B) The number 110 reflects the higher proportion of small amino acids in proteins, as
well as the loss of water when the peptide bond forms.
C) The number 110 reflects the number of amino acids found in the typical small
protein, and only small proteins have their molecular weight estimated this way.
D) The number 110 takes into account the relatively small size of nonstandard amino
acids.
E) The number 138 represents the molecular weight of conjugated amino acids.

22. In a conjugated protein, a prosthetic group is:

A) a fibrous region of a globular protein.
B) a nonidentical subunit of a protein with many identical subunits.
C) a part of the protein that is not composed of amino acids.
D) a subunit of an oligomeric protein.
E) synonymous with “protomer.”

Page 3
24. For the study of a protein in detail, an effort is usually made to first:
A) conjugate the protein to a known molecule.
B) determine its amino acid composition.
C) determine its amino acid sequence.
D) determine its molecular weight.
E) purify the protein.

26. By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is
possible to:
A) determine a protein's isoelectric point.
B) determine an enzyme's specific activity.
C) determine the amino acid composition of the protein.
D) preserve a protein's native structure and biological activity.
E) separate proteins exclusively based on molecular weight.

27. To determine the isoelectric point of a protein, first establish that a gel:
A) contains a denaturing detergent that can distribute uniform negative charges over the
protein's surface.
B) exhibits a stable pH gradient when ampholytes become distributed in an electric field.
C) is washed with an antibody specific to the protein of interest.
D) neutralizes all ionic groups on a protein by titrating them with strong base.
E) relates the unknown protein to a series of protein markers with known molecular
weights, Mr.

29. The term specific activity differs from the term activity in that specific activity:
A) is measured only under optimal conditions.
B) is the activity (enzyme units) in a milligram of protein.
C) is the activity (enzyme units) of a specific protein.
D) refers only to a purified protein.
E) refers to proteins other than enzymes.

30. Which type of structure refers to particularly stable arrangements of amino acid residues
in a protein that gives rise to recurring patterns?
A) primary structure
B) secondary structure
C) tertiary structure
D) quaternary structure
E) None of the answers is correct.

31. Which type of structure describes the overall three-dimensional folding of a polypeptide?
A) primary structure
B) secondary structure
C) tertiary structure
D) quaternary structure
E) None of the answers is correct.

Page 4
32. The functional differences, as well as differences in three-dimensional structures, between
two different enzymes from E. coli result directly from their different:
A) affinities for ATP.
B) amino acid sequences.
C) roles in DNA metabolism.
D) roles in the metabolism of E. coli.
E) secondary structures.

33. One method used to prevent disulfide bond interference with protein sequencing
procedures is:
A) cleaving proteins with proteases that specifically recognize disulfide bonds.
B) protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl
groups.
C) reducing disulfide bridges and preventing their re-formation by further modifying
the —SH groups.
D) removing cystines from protein sequences by proteolytic cleavage.
E) sequencing proteins that do not contain cysteinyl residues.

35. Even when a gene is available and its sequence of nucleotides is known, chemical studies
of the protein are still required to determine:
A) the molecular weight of the protein.
B) the amino-terminal amino acid.
C) the location of disulfide bonds.
D) the number of amino acids in the protein.
E) whether the protein has the amino acid methionine in its sequence.

36. The term “proteome” has been used to describe:

A) regions (domains) within proteins.
B) regularities in protein structures.
C) the complement of proteins expressed by an organism's genome.
D) the structure of a protein-synthesizing ribosome.
E) the tertiary structure of a protein.

Page 5
39. Compare the following sequences taken from four different proteins, and select the
answer that BEST characterizes their relationships.
A B C
1 DVEKGKKIDIMKCS HTVEKGGKHKTGPNLH GLFGRKTGQAPGYSYT
2 DVQRALKIDNNLGQ HTVEKGAKHKTAPNVH GLADRIAYQAKATNEE
3 LVTRPLYIFPNEGQ HTLEKAAKHKTGPNLH ALKSSKDLMFTVINDD
4 FFMNEDALVARSSN HQFAASSIHKNAPQFH NLKDSKTYLKPVISET
A) Based only on sequences in column B, protein 4 reveals the greatest evolutionary
divergence.
B) Comparing proteins 1 and 2 in column A 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 2 and 3 show a greater evolutionary distance than proteins 1 and 4.
E) The portions of the amino acid sequence shown suggest that these proteins are
completely unrelated.

40. All of the 20 common amino acids contain an R-group that is attached to the:
A) carboxyl group.
B) amino group.
C)  carbon.
D)  carbon.
E) It depends on the amino acid

41. The amino acid proline is unique because of the R group:

A) has a phosphate attached.
B) is cyclical.
C) is attached to the carboxylic acid carbon.
D) is positively charged.
E) None of the answers is correct.

43. On the molecule below, the arrow is pointing to the _____ carbon.

A) amino
B) 
C) 
D) 
E) carboxylic acid

Page 6
44. Which pair of amino acids can be used to measure the concentration of proteins based on
the absorption of UV light?
A) proline and valine
B) serine and threonine
C) aspartate and glutamate
D) lysine and histidine
E) tyrosine and tryptophan

45. Why can only some amino acids be used to measure protein concentration based on the
absorption of UV light?
A) Only some amino acids are aromatic.
B) Only some amino acids are positively charged.
C) Only some amino acids are strongly hydrophobic.
D) Only some amino acids are strongly hydrophilic.
E) Only some amino acids are negatively charged.

46. The MOST useful way to classify amino acids is by:

A) molecular weight.
B) pKa.
C) polarity.
D) propensity in proteins.
E) alphabetical order.

48. The pKa of lysine's carboxyl group, amino group, and side-chain are 2.2, 9.0, and 10.5,
respectively. If lysine is in a pH 13 solution, what is the net charge on each lysine
molecule?
A) –2
B) –1
C) 0
D) +1
E) +2

49. Amino acids without ionizable R-groups can act as a zwitterion in a(n) _____ solution.
A) nonpolar
B) boiling
C) acidic
D) basic
E) neutral

Page 7
50. According to the diagram, which pH range offers the GREATEST buffering power for
this amino acid?

A) 0.5–1.5
B) 0–1
C) 1–2
D) 2–3
E) 1–3

51. According to the diagram, which estimate is BEST of this amino acid's isoelectric point?

A) 0.5
B) 1
C) 1.5
D) 6
E) 11

Page 8
52. According to the diagram, which pH is the one at which this amino acid will have a net
charge of 0?

A) 11
B) 6
C) 1.5
D) 1
E) 0.5

53. According to the diagram, how many titratable groups does this amino acid have?

A) 0
B) 1
C) 2
D) 3
E) It cannot be determined by this diagram.

Page 9
54. According to the diagram, at pH 1, what is the average net charge on this amino acid?

A) +1
B) + 0.5
C) 0
D) –0.5
E) –1

56. According to the diagram, does this amino acid have a titratable R-group?

A) yes, as evidenced by the steep center of the curve

B) yes, as evidenced by the two relatively flat parts of the curve
C) no, as evidenced by only two relatively flat parts of the curve
D) no, as evidenced by the steepness of the center of the curve
E) It cannot be determined from this graph.

Page 10
57. When the ribosome forms a peptide bond, which two atoms form a covalent bond?
A) the  carbon and the amino nitrogen
B) the amino nitrogen and carboxylic acid carbon
C) the  carbon and the carboxylic acid carbon
D) the amino nitrogen and the  carbon
E) It depends on the amino acids being joined.

58. Which compound is a side-product of a peptide bond formation?

A) water
B) phosphate
C) ammonium
D) carboxylic acid
E) None of the answers is correct.

59. By convention, polypeptides are read in which order?

A) N- to C-terminus
B) C- to N-terminus
C) 5 to 3
D) 3 to 5
E) smallest to largest amino acid by molecular weight

60. Which statement is TRUE about the pKa values for ionizable R-group of amino acids
within a polypeptide?
A) The pKa values for R-groups do not change from free amino acids.
B) The pKa values for R-groups are 1 pH unit higher than free amino acids.
C) The pKa values for R-groups are 1 pH unit lower than free amino acids.
D) The pKa values for R-groups vary depending on the local environment of the side
chain.
E) The pKa values for R-groups depend on how close the R-group is to the N- or C-
terminus of the polypeptide.

61. Which item is NOT a biochemical use/function of peptides of small molecular weight?
A) artificial sweetener
B) hormone
C) poison
D) antibiotics
E) All of the answer choices are correct.

Page 11
62. The structure below is a molecule used in the sweeteners Equal® and NutraSweet®.
When heated, the peptide bond will hydrolyze into methanol, and which two amino acids?

A) asparagine and tyrosine

B) aspartic acid and phenylalanine
C) glutamic acid and phenylalanine
D) aspartic acid and tryptophan
E) glutamic acid and histidine

63. Selective precipitation of a protein from a crude extract is MOST effective by which
molecule?
A) ammonium sulfate
B) urea
C) sodium dodecyl sulfate
D) EDTA (ethylenediaminetetraacetic acid)
E) All of the answers are correct.

64. According to the table, ion-exchange chromatography would be the LEAST effective
method to separate which protein mixture?

Protein MW pI
A 12,500 3.2
B 13,200 5.7
C 13,500 10.5
D 25,200 6.3
E 36,900 5.8
F 78,400 6.1
A) proteins A, B, and C
B) proteins A, C, and E
C) proteins B, E, and F
D) proteins B, C, and E
E) All of the answers are correct.

Page 12
66. A protein with a high percentage of lysine and arginine residues would be BEST purified
and concentrated with which type of column?
A) cation exchange
B) anion exchange
C) size-exclusion chromatography
D) affinity chromatography
E) reverse-phase chromatography

68. If protein A has a pI of 3.1, protein B has a pI of 6.8, and protein C has a pI of 8.9, which
protein would elute FIRST from a cation exchange column at pH 7?
A) protein A
B) protein B
C) protein C
D) All three proteins would elute at the same time from the column.
E) Not enough information about the proteins is given in the problem.

70. Which of the lanes in the gel below would represent an “uninduced” sample?

A) 1
B) 2
C) 3
D) 4
E) 5

72. How are sequential reactions controlled in the Edman degradation procedure?
A) A high salt step is followed by a low salt step.
B) A low salt step is followed by a high salt step.
C) A high pH step is followed by a low pH step.
D) A low pH step is followed by a high pH step.
E) None of the answers is correct.

Page 13
73. The “signature sequence” shown below represents a portion of a protein from four
different organisms. The proteins can be classified as:

A) homologs.
B) orthologs.
C) paralogs.
D) both homologs and orthologs.
E) both homologs and paralogs.

74. Iodoacetamides, maleimides, benzyl halides, and bromomethyl ketones can all be used to
modify the group on residues.
A) amino; basic
B) phenyl; Tyr and Trp
C) carboxyl; acidic
D) sulfhydryl; Cys
E) hydroxyl; Ser and Tyr

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

77. Only one of the common amino acids has no free -amino group. Name this amino acid.

78. Briefly describe the five major groupings of amino acids.

81. Describe the structures of the amino acids phenylalanine and aspartate in the ionization
state you would expect at pH 7.0. Why is aspartate very soluble in water, whereas
phenylalanine is much less soluble?

83. Why do amino acids, when dissolved in water, become zwitterions?

84. As more OH– equivalents (base) are added to an amino acid solution, what titration
reaction will occur around pH = 9.5?

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

Page 14
89. The amino acid histidine has three ionizable groups, with pKa values of 1.8, 6.0, and 9.2.
(a) Which pKa corresponds to the histidine side chain? (b) In a solution at pH 5.4, what
percentage of the histidine side chains will carry a positive charge?

92. Hydrolysis of peptide bonds is an exergonic reaction. Why, then, are peptide bonds quite
stable?

97. For each of these methods of separating proteins, describe the principle of the method,
and tell what property of proteins allows their separation by this technique.
(a) ion-exchange chromatography
(b) size-exclusion (gel filtration) chromatography
(c) affinity chromatography

103. Define the primary structure of a protein.

104. In one or two sentences, describe the usefulness of each of the following reagents or
reactions in the analysis of protein structure:
(a) Edman reagent (phenylisothiocyanate)
(b) protease
(c) reducing agent (dithiothreitol or -mercaptoethanol)

105. A polypeptide is hydrolyzed, and it is determined that there are 3 Lys residues and 2 Arg
residues (as well as other residues). How many peptide fragments can be expected when
the native polypeptide is incubated with the proteolytic enzyme trypsin?

Page 15