Chapter 3 Amino Acids, Peptides, and Proteins
Multiple Choice Questions
1. Amino acids
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. Amino acids
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
3. Amino acids
Two amino acids of the standard 20 contain sulfur atoms. They are:
A) cysteine and serine.
B) cysteine and threonine.
C) methionine and cysteine
D) methionine and serine
E) threonine and serine.
4. Amino acids
All of the amino acids that are found in proteins, except for proline, contain a(n):
A) amino group.
B) carbonyl group.
C) carboxyl group.
D) ester group.
E) thiol group.
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5. Amino acids
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.
6. Amino acids
Which of the following statements 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 a 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 cystines are released when a —CH2—S—S—CH2— disulfide bridge is reduced to —CH2—
SH.
7. Amino acids
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.
8. Amino acids
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
9. Amino acids
Amino acids are ampholytes because they can function as either a(n):
A) acid or a base.
B) neutral molecule or an ion.
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C) polar or a nonpolar molecule.
D) standard or a nonstandard monomer in proteins.
E) transparent or a light-absorbing compound.
10. Amino acids
Titration of valine by a strong base, for example NaOH, reveals two pK’s. The titration reaction
occurring at pK2 (pK2 = 9.62) is:
A) —COOH + OH– → —COO– + H2O.
B) —COOH + —NH2
→ —COO– + —NH2+.
C) —COO– + —NH2+ → —COOH + —NH2.
D) —NH3+ + OH– → —NH2 + H2O.
E) —NH2 + OH– → —NH– + H2O.
11. Amino acids
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–.
12. Amino acids
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.
13. Amino acids
At pH 7.0, converting a 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.
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14. Amino acids
At pH 7.0, converting a 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. Amino acids
What is the approximate charge difference between glutamic acid and -ketoglutarate at pH 9.5?
A) 0
B) ½
C) 1
D) 1½
E) 2
16. Peptides and proteins
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
17. Peptides and proteins
The peptide alanylglutamylglycylalanylleucine has:
A) a disulfide bridge.
B) five peptide bonds.
C) four peptide bonds.
D) no free carboxyl group.
E) two free amino groups.
18. Peptides and proteins
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.
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19. Peptides and proteins
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. Peptides and proteins
Which of the following is correct with respect to 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. Peptides and proteins
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. Peptides and proteins
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.”
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23. Peptides and proteins
Prosthetic groups in the class of proteins known as glycoproteins are composed of:
A) carbohydrates.
B) flavin nucleotides.
C) lipids.
D) metals .
E) phosphates.
24. Working with proteins
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.
25. Working with proteins
In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel-
filtration) chromatography?
A) cytochrome c Mr = 13,000
B) immunoglobulin G Mr = 145,000
C) ribonuclease A Mr = 13,700
D) RNA polymerase Mr = 450,000
E) serum albumin Mr = 68,500
26. Working with proteins
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 on the basis of molecular weight.
27. Working with proteins
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 bases.
E) relates the unknown protein to a series of protein markers with known molecular weights, Mr.
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28. Working with proteins
The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric
focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing
SDS, and electric current is again applied. In this second step:
A) proteins with similar isoelectric points become further separated according to their molecular
weights.
B) the individual bands become stained so that the isoelectric focus pattern can be visualized.
C) the individual bands become visualized by interacting with protein-specific antibodies in the
second gel.
D) the individual bands undergo a second, more intense isoelectric focusing.
E) the proteins in the bands separate more completely because the second electric current is in the
opposite polarity to the first current.
29. Working with proteins
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. Peptides and proteins
Which of the following refers to particularly stable arrangements of amino acid residues in a protein
that give rise to recurring patterns?
A) Primary structure
B) Secondary structure
C) Tertiary structure
D) Quaternary structure
E) None of the above
31. Peptides and proteins
Which of the following 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 above
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32. The covalent structure of proteins
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. The covalent structure of proteins
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.
34. The covalent structure of proteins
A nonapeptide was determined to have the following amino acid composition: (Lys)2, (Gly) 2, (Phe) 2,
His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then
hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was
exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of
the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4-Dinitrophenyl-
histidine was recovered from the pentapeptide, and 2,4-dinitrophenylphenylalanine was recovered
from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a
tetrapeptide. The tetrapeptide was composed of (Lys) 2, Phe, and Gly. The native sequence was
determined to be:
A) Gly–Phe–Lys–Lys–Gly–Leu–Met–Phe–His.
B) His–Leu–Gly–Lys–Lys–Phe–Phe–Gly–Met.
C) His–Leu–Phe–Gly–Lys–Lys–Phe–Met–Gly.
D) His–Phe–Leu–Gly–Lys–Lys–Phe–Met–Gly.
E) Met–Leu–Phe–Lys–Phe–Gly–Gly–Lys–His.
35. The covalent structure of proteins
Even when a gene is available and its sequence of nucleotides is known, chemical studies of the
protein are still required to determine:
A) 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.
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36. The covalent structure of proteins
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.
37. The covalent structure of proteins
A major advance in the application of mass spectrometry to macromolecules came with the
development of techniques to overcome which of the following problems?
A) Macromolecules were insoluble in the solvents used in mass spectrometry.
B) Mass spectrometric analyses of macromolecules were too complex to interpret.
C) Mass spectrometric analysis involved molecules in the gas phase.
D) Most macromolecules could not be purified to the degree required for mass spectrometric
analysis.
E) The specialized instruments required were prohibitively expensive.
38. The covalent structure of proteins
Identify the pair of peptides below that cannot be distinguished by tandem mass spectrometry.
A) VTSPLYANEGK and VTCPLYANEGK
B) VTSPLYANEGK and VTSPLYADEGK
C) VTSPLYANEGK and VTSPIYANEGK
D) VTSPLYANEGK and VSTPLYANEGK
E) All of the above
39. Protein sequences and evolution
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 amino acid sequence shown suggest that these proteins are completely unrelated.
Chapter 3 Amino Acids, Peptides, and Proteins
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Short Answer Questions
40. Amino acids
Page: 72 Difficulty: 1
What are the structural characteristics common to all amino acids found in naturally occurring
proteins?
41. Amino acids
Page: 75 Difficulty: 1
Only one of the common amino acids has no free -amino group. Name this amino acid and draw its
structure.
42. Amino acids
Pages: 74–77 Difficulty: 2
Briefly describe the five major groupings of amino acids.
43. Amino acids
Pages: 73–75 Difficulty: 2
A B C D E
__________________________________________________________________
Tyr-Lys-Met Gly-Pro-Arg Asp–Trp-Tyr Asp-His-Glu Leu-Val-Phe
Which one of the above tripeptides:
____(a) is most negatively charged at pH 7?
____(b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and
hydrolyzed in acid?
____(c) contains the largest number of nonpolar R groups?
____(d) contains sulfur?
____(e) will have the greatest light absorbance at 280 nm?
Chapter 3 Amino Acids, Peptides, and Proteins
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44. Amino acids
Pages: 73–75 Difficulty: 2
Draw 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?
45. Amino acids
Pages: 77–78 Difficulty: 3
Name two uncommon amino acids that occur in proteins. By what route do they get into proteins?
Pages: 78–79 Difficulty: 1
Why do amino acids, when dissolved in water, become zwitterions?
47. Amino acids
Page: 79 Difficulty: 1
As more OH– equivalents (base) are added to an amino acid solution, what titration reaction will
occur around pH = 9.5?
Page: 80 Difficulty: 3
In the amino acid glycine, what effect does the positively charged —NH3+ group have on the pKa of
an amino acid’s —COOH group?
49. Amino acids
Page: 79 Difficulty: 3
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?
Chapter 3 Amino Acids, Peptides, and Proteins
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50. Amino acids
Page: 79 Difficulty: 2
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.
51. Amino acids
Page: 80 Difficulty: 2
What is the pI, and how is it determined for amino acids that have nonionizable R groups?
52. Amino acids
Page: 80 Difficulty: 2
The amino acid histidine has a side chain for which the pKa is 6.0. Calculate what fraction of the
histidine side chains will carry a positive charge at pH 5.4. Be sure to show your work.
53. Amino acids
Page: 80 Difficulty: 2
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?
Chapter 3 Amino Acids, Peptides, and Proteins
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54. Amino acids
Page: 81 Difficulty: 2
What is the uniquely important acid-base characteristic of the histidine R group?
55. Peptides and proteins
Page: 82 Difficulty: 1
How can a polypeptide have only one free amino group and one free carboxyl group?
56. Peptides and proteins
Page: 82 Difficulty: 1
Hydrolysis of peptide bonds is an exergonic reaction. Why, then, are peptide bonds quite stable?
57. Peptides and proteins
Page: 82 Difficulty: 2
Draw the structure of Gly–Ala–Glu in the ionic form that predominates at pH 7.
58. Peptides and proteins
Page: 82 Difficulty: 2
The artificial sweetener NutraSweet®, also called aspartame, is a simple dipeptide,
aspartylphenylalanine methyl ester, on which the free carboxyl of the dipeptide is esterified to methyl
alcohol. Draw the structure of aspartame, showing the ionizable groups in the form they have at pH 7.
(The ionizable group in the side chain of aspartate has a pKa of 3.96.)
59. Peptides and proteins
Page: 84 Difficulty: 1
If the average molecular weight of the 20 standard amino acids is 138, why do biochemists divide a
protein’s molecular weight by 110 to estimate its number of amino acid residues?
Chapter 3 Amino Acids, Peptides, and Proteins
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60. Peptides and proteins
Page: 84 Difficulty: 2
Lys residues make up 10.5% of the weight of ribonuclease. The ribonuclease molecule contains 10
Lys residues. Calculate the molecular weight of ribonuclease.
Pages: 86–87 Difficulty: 2
Why do smaller molecules elute after large molecules when a mixture of proteins is passed through a
size-exclusion (gel filtration) column?
62. Working with proteins
Pages: 86–87 Difficulty: 2
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
63. Working with proteins
Pages: 86–88 Difficulty: 2
A biochemist is attempting to separate a DNA-binding protein (protein X) from other proteins in a
solution. Only three other proteins (A, B, and C) are present. The proteins have the following
properties:
pI
(isoelectric Size Bind to
point) Mr DNA?
––––––––––––––––––––––––––––––––––––––––––
protein A 7.4 82,000 yes
protein B 3.8 21,500 yes
protein C 7.9 23,000 no
protein X 7.8 22,000 yes
––––––––––––––––––––––––––––––––––––––––––
What type of protein separation techniques might she use to separate:
Chapter 3 Amino Acids, Peptides, and Proteins
35
(a) protein X from protein A?
(b) protein X from protein B?
(c) protein X from protein C?
64. Working with proteins
Pages: 88–89 Difficulty: 2
What factors would make it difficult to interpret the results of a gel electrophoresis of proteins in the
absence of sodium dodecyl sulfate (SDS)?
65. Working with proteins
Pages: 90–91 Difficulty: 2
How can isoelectric focusing be used in conjunction with SDS gel electrophoresis?
66. Working with proteins
Pages: 91–92 Difficulty: 3
You are given a solution containing an enzyme that converts B into A. Describe what you would do
to determine the specific activity of this enzyme solution.
67. Working with proteins
Pages: 91–92 Difficulty: 2
As a protein is purified, both the amount of total protein and the activity of the purified protein
decrease. Why, then, does the specific activity of the purified protein increase?
68. Peptides and proteins
Page: 84 Difficulty: 1
Chapter 3 Amino Acids, Peptides, and Proteins
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Define the primary structure of a protein.
69. The covalent structure of proteins
Pages: 94–100 Difficulty: 2
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)
70. The covalent structure of proteins
Pages: 96–97 Difficulty: 2
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?
71. The covalent structure of proteins
Pages: 94–95 Difficulty: 2
The following reagents are often used in protein chemistry. Match the reagent with the purpose for
which it is best suited. Some answers may be used more than once or not at all; more than one reagent
may be suitable for a given purpose.
(a) CNBr (cyanogen bromide) (e) performic acid
(b) Edman reagent (phenylisothiocyanate) (f) chymotrypsin
(c) Sanger reagent (FDNB) (g) trypsin
(d) reducing agent (dithiothreitol) (h) iodoacetamide
___ hydrolysis of peptide bonds on the carboxyl side of Lys and Arg
___ cleavage of peptide bonds on the carboxyl side of Met
___ breakage of disulfide (—S—S—) bonds
___ modification of sulfhydryl groups of Cys
___ determination of the amino acid sequence of a peptide
___ determining the amino-terminal amino acid in a polypeptide
72. The covalent structure of proteins
Pages: 94–97 Difficulty: 2
Conjugated proteins contain chemical substituents in addition to amino acids. List three classes of
conjugated proteins and identify the type of prosthetic group associated with each one.
Chapter 3 Amino Acids, Peptides, and Proteins
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73. The covalent structure of proteins
Pages: 94–97 Difficulty: 2
Provide a brief definition for a polymorphic protein.
74. The covalent structure of proteins
Pages: 94–97 Difficulty: 2
A biochemist wishes to determine the sequence of a protein that contains 123 amino acid residues.
After breaking all of the disulfide bonds, the protein is treated with cyanogen bromide (CNBr), and it
is determined that that this treatment breaks up the protein into seven conveniently sized peptides,
which are separated from each other. It is your turn to take over. Outline the steps you would take to
determine, unambiguously, the sequence of amino acid residues in the original protein.
75. The covalent structure of proteins
Pages: 94–97 Difficulty: 3
You are trying to determine the sequence of a protein that you know is pure. Give the most likely
explanation for each of the following experimental observations. You may use a simple diagram for
your answer.
(a) The Sanger reagent (FDNB, fluorodinitrobenzene) identifies Ala and Leu as amino-
terminal residues, in roughly equal amounts.
(b) Your protein has an apparent Mr of 80,000, as determined by SDS-polyacrylamide gel
electrophoresis. After treatment of the protein with performic acid, the same technique
reveals two proteins of Mr 35,000 and 45,000.
(c) Size-exclusion chromatography (gel filtration) experiments indicate the native protein has
an apparent Mr of 160,000.
66. 76. The covalent structure of proteins
Page: 101 Difficulty: 2
Describe two major differences between chemical synthesis of polypeptides and synthesis of
polypeptides in the living cell.
Chapter 3 Amino Acids, Peptides, and Proteins
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77. Protein sequences and evolution
Page: 102–104 Difficulty: 2
Distinguish between homologs, paralogs, and orthologs as classes of related proteins.
78. Protein sequences and evolution
Page: 105 Difficulty: 2
How are “signature sequences” useful in analyzing groups of functionally related proteins?