Test Bank for Biochemistry A Short Course 4th Edition John L. Tymoczko
TEST BANK FOR BIOCHEMISTRY
A SHORT COURSE JOHN L.
TYMOCZKO
Chapter 3 Amino Acids
Matching Questions
Use the following to answer questions 1–10:
Choose the correct answer from the list below. Not all of the answers will be used. Answers may be
used more than once.
1. a) l amino acids
2. b) water
3. c) protons
4. d) zwitterions
5. e) arginine
6. f) serine
7. g) tyrosine
8. h) cysteine
9. i) glutamate
10. j) histidine
11. k) proline
12. l) asparagine
13. m) d amino acids
1. ____________: Chiral type of amino acids found in proteins.
Ans: a
Section: 3.1
2. ____________: Another name for dipolar molecules.
Ans: d
Section: 3.1
3. ____________: Disulfide bonds are formed by pairs of this amino acid.
Ans: h
Section: 3.2
4. ____________: The amino acid with a side-chain pK
a
Ans: j
Section: 3.2
just below neutral pH.
5. ____________: The amino acid with a side group that has a terminal carboxamide.
Ans: l
Section: 3.2
6. ____________: The amino acid with an imidazole side chain.
Ans: j
Section: 3.2
7. ____________: An amino acid that must be supplied by the diet.
Ans: j
Section: 3.3
8. ____________: The amino acid with a negatively charged side chain at neutral pH.
Ans: i
Section: 3.2
9. ____________: The amino acid with a sulfhydryl side chain.
Ans: h
Section: 3.2
10. ____________: The amino acid with the abbreviation Ser.
Ans: f
Section: 3.2
Fill-in-the-Blank Questions
11. The amino acid that contains a weakly acidic “phenolic” group is .
Ans: tyrosine Section 3.2
12. are amino acids with neutral R groups containing an electronegative atom.
Ans: Polar amino acids Section 3.2
13. The amino acid with the smallest-size side chain allowing greatest flexibility in a protein is .
Ans: glycine Section 3.2
14. The charge of glycine when the pH is < 2.0 is .
Ans: +1 Section 3.1
15. Between the amino and the carboxyl functional group, the has the lowest affinity for a proton.
Ans: carboxyl Section: 3.1
16. The amino acid with an indol ring is .
Ans: tryptophan Section: 3.2
17. is an amino acid with a hydrophobic side chain containing a thioether.
Ans: Methionine Section: 3.2
18.
The group is the functional group that makes an amino acid more reactive than nonpolar amino acids
valine, alanine, and phenylalanine.
Ans: hydroxyl Section: 3.2
19.
Ans: nonessential Section: 3.3
20. is often seen in a child with a protein-deficient diet.
Ans: Edema Section: 3.3
Multiple-Choice Questions
21. What charged group(s) is/are present in glycine at a pH of 7?
A) –NH
3
+
B) –COO
C) –NH
2
+
D) A and B
–
E) A, B, and C
Ans: D Section: 3.2
22. At a pH of 12, what charged group(s) is/are present in glycine?
A) –NH
3
B) –COO
C) –NH
2
D) A and B
+
+
–
E) A, B, and C
Ans: B Section: 3.2
23. In what pH range is zwitterionic alanine the predominate structure?
A) 0–2
B) 9–14
C) 8–10
D) 2–4
E) 2–9
Ans: E Section 3.2
24. Which amino acids contain reactive aliphatic hydroxyl groups?
A) serine and methionine
B) serine and threonine
C) methionine and threonine
D) cysteine and methionine
E) cysteine and threonine
Ans: B Section: 3.2
25. Name three amino acids that are positively charged at a neutral pH.
A) lysine and arginine
B) histidine and arginine
C) cysteine and arginine
D) lysine and proline
E) glutamine and histidine
Ans: A Section: 3.2
26. What would interactions between side chains of aspartate and arginine at neutral pH be?
A) hydrophobic
B) ionic
C) hydrogen bonding
D) steric
E) covalent
Ans: B Section: 3.2
27. Which amino acid has a side chain with a hydroxyl group?
A) serine
B) alanine
C) tryptophan
D) histidine
E) glutamine
Ans: A Section: 3.2
28. Which amino acid has a carboxyl group in its side chain?
A) glutamine
B) galanine
C) cysteine
D) glutamate
E) None of the above.
Ans: D Section: 3.2
29. What would the overall charge of a peptide of the following peptide sequence at pH 1 be (Asp-Gly-Arg-Hi
A) −1
B) 0
C) 1
D) 2
E) 3
Ans: E Section: 3.2
30. Which of the following amino acids would most likely be soluble in a nonpolar solvent such as benzene?
A) valine
B) histidine
C) glutamine
D) glycine
E) All of the above.
Ans: A Section: 3.2
31.
Below is a list of five tripeptides identified by their single letter codes. They are listed as A, B, C, D, and E.
tripeptide contains an amino acid capable of forming covalent disulfide bonds?
A) FNC
B) RGK
C) VIL
D) MDE
E) SYT
Ans: A Section: 3.2
32.
Below is a list of five tripeptides identified by their single letter codes. They are listed as A, B, C, D, and E.
tripeptide is negatively charged at physiological pH?
A) FNC
B) RGK
C) VIL
D) MDE
E) SYT
Ans: D Section: 3.2
33.
Below is a list of five tripeptides identified by their single letter codes. They are listed as A, B, C, D, and E.
tripeptide has the most polar side chains?
A) FNC
B) RGK
C) VIL
D) MDE
E) SYT
Ans: E Section: 3.2
34. Where are Trp and Phe found in a globular protein and why?
A) exterior due to the hydrophilic effect
B) interior due to the hydrophobic effect
C) exterior forming polar H-bonds with water
D) interior forming ionic bonds with other amino acids
E) exterior forming ionic-polar bonds with water
Ans: B Section: 3.2
35. Amino acids contain all of the following functional groups except:
A) indole.
B) thioester.
C) phenyl.
D) sulfhydryl.
E) amine.
Ans: B Section: 3.2
Short-Answer Questions
36. What is the advantage of having multiple functional groups in proteins?
Ans:
The rich diversity of functional groups in proteins can contribute independently to protein structu
accounts for the diversity in function as well.
Section: Introduction
37. What is the advantage of protein interaction and assembly with other proteins?
Ans:
When proteins interact or assemble, new functions and specificity become available. These prot
interactions provide multifunctional activity and specificity.
Section: Introduction
38. Draw the general structure of an amino acid at pH 7.0 with the side group shown as an “R.”
Ans: The figure should look like either one of the structures shown in the left margin on p. 38.
Section: 3.1
39. Why is the central carbon on an amino acid so important?
Ans:
This is the chiral center of the molecule and is linked to each important functional group of an am
Section: 3.1
acid.
40. Draw the structure of alanine, aspartic acid, and histidine when the pH is 1.0, 7.0, and 12.0.
Ans:
Use the figures in your book and the pK
a
Section: 3.2
for each functional group to determine the ionization sta
each amino acid.
41.
What is the net charge of each the following amino acid: alanine, aspartic acid, and histidine when the pH
7.0, and 12.0?
Ans:
For alanine, the charges are: 1, 0, and −1. For aspartic acid, the charges are: 1, −1, and −2. For
Section: 3.2
histidine, the charges are: 2, 0, and −1.
42.
A gene is mutated so the amino acids glycine and glutamate are now alanine and leucine, respectively. Wh
the potential results of each of these mutations? Assume that the mutations are not near each other in the
primary sequence and have no impact on the other.
Ans:
The glycine-to-alanine mutations are similar and will have little or no effect. Glutamate and leucin
very different chemistries and will impact the function and structure of the protein, as one is charg
water soluble, and the other is hydrophobic and nonpolar.
Section: 3.2
43. What are the four ways amino acids can be classified?
Ans: hydrophobic, polar, positively charged, and negatively charged
Section: 3.2
44. What are the three aromatic amino acids?
Ans: phenylalanine, tyrosine, and tryptophan
Section: 3.2
45. Which amino acid side chains are capable of ionization?
Ans: The amino acids are aspartate, glutamate, histidine, cysteine, tyrosine, lysine, and arginine.
Section: 3.2
46. Which are the branched amino acids, and what impact do they have on protein shape?
Ans:
These are the aliphatic, hydrophobic amino acids, valine, leucine, and isoleucine. They are hydro
which drives the hydrophobic interactions in the interior of a protein. These are also bulky amino
that will lend to steric strain if forced close to each other in a peptide.
Section: 3.2
47. Draw a titration curve for glycine.
Ans: Use the information from Section 2.5 and the graph from Figure 3.2.
Section: 3.2
48. What do serine, threonine, and tyrosine have in common?
Ans:
Each has a hydroxyl (–OH) group, which makes the first two amino acids more water soluble an
Section: 3.2
increases the reactivity of all three amino acids.
49. Which amino acid is responsible for stabilizing the structure of a protein by forming pairs of sulfhydryl grou
Ans: cysteine
Section: 3.2
50. What functions make histadine an important amino acid?
Ans:
The pK
a
Section: 3.2
of the imidazole ring is near physiological pH. This means that the side group may be ch
and protonated or neutral and deprotonated. This results in an amino acid that can either lend or
a proton or charge in the active site of an enzyme.
51. Which amino acids have a side chain that includes a modified carboxyl group, carboxaminde?
Ans: asparagine and glutamine
Section: 3.2
52.
Which ionizable group has the lowest affinity for protons: the terminal a-carboxyl group, the aspartic acid
group, or the terminal a-amino group?
Ans: the terminal a-carboxyl group
Section: 3.2
53.
Malnourished children with Kwashiorkor display a distended stomach, giving the illusion of being full. Why
this happen?
Ans:
This is a nutritional state where there is an extremely low or poor protein intake in the diet. The o
Section: 3.3
shift of the blood, which is poor in protein content, causes water to flow into the tissues.
54. What is the difference between nonessential and essential amino acids?
Ans:
The former are amino acids that humans can generate de novo, or from scratch. The latter cann
Section: 3.3
made and must be ingested for the mature formation of proteins.
55. List the essential amino acids.
Ans: histadine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valin
Section: 3.3
Chapter 4 Protein Three-Dimensional Structure
Matching Questions
Use the following to answer questions 1–10:
Choose the correct answer from the list below. Not all of the answers will be used.
1. a) amino
2. b) water
3. c) protons
4. d) DNA
5. e) secondary structure
6. f) tertiary structure
7. g) Ramachandran
8. h) RNA
9. i) domain
10. j) cystine
11. k) proline
12. l) Sanger
13. m) d amino acids
14. n) cysteine
56. When a peptide bond is formed between two amino acids, a(n) ____________molecule is lost.
Ans: b
Section: 4.1
57. ____________: Codes for the sequence of amino acids.
Ans: d
Section: Introduction
58. According to convention, ____________ is the terminus drawn on the left side of a peptide.
Ans: a
Section: 4.1
59. Two amino acids undergo oxidation to form a dimer called ____________.
Ans: j
Section: 4.1
60.
Changes in ____________ create amyloid fibers, which are insoluble and are the source of mad cow dise
Alzheimer disease, and Parkinson disease.
Ans: e
Section: 4.5
61. ____________: Compact regions that may be connected by a flexible segment of polypeptide chain.
Ans: i
Section: 4.3
62.
____________: This amino acid residue disrupts the α helix because its side chain contains a unique ring
structure that restricts bond rotations.
Ans: k
Section: 4.2
63.
The plot that allows one to investigate the likely orientation of certain amino acid pairs is called the
____________.
Ans: g
Section: 4.1
64. ____________: The type of structure to which α helices, β sheets, and turns are referred.
Ans: e
Section: 4.2
65. The overall 3D-structure of a single polypeptide chain is referred to as ____________.
Ans: f
Section: 4.3
Fill-in-the-Blank Questions
66. The of a disulfide bridge results in a separation of two protein chains.
Ans: oxidation Section 4.1
67. The peptide bond is also known as a(n) .
Ans: amide bond Section 4.1
68. Peptides differ from proteins in .
Ans: the number of amino acid residues Section 4.1
69. Due to the side chain steric clash, almost all peptide bonds are in their configuration.
Ans: trans Section 4.1
70. The secondary structure that is stabilized by CO and NH hydrogen bonding within the peptide chain is the
Ans: alpha helix Section 4.2
71. The indicates the left- or right-handedness of an α helix.
Ans: screw sense Section 4.2
72. is a fibrous protein and is the primary component of wool and hair.
Ans: α-keratin Section 4.2
73. Every third residue in the protein collagen is .
Ans: glycine Section 4.2
74. Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as .
Ans: β-mecaptoethanol Section 4.3
75. The β-sheet structure occurs when the two strands are oriented in opposite directions (N → C).
Ans: antiparallel Section 4.3
76.
A protein whose peptide backbone is mostly extended and hydrogen bonded to different strands of the pro
composed mostly of the secondary structure.
Ans: β-sheet Section 4.3
77. A protein is considered to be when it is converted into a randomly coiled structure without its normal ac
Ans: denatured Section 4.4
78. is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.
Ans: Collagen Section 4.3
79. Collagen contains , a modified amino acid.
Ans: hydroxyproline Section 4.3
80. Compact, globular proteins are typically water and consist mostly of secondary structure.
Ans: soluble; an alpha helical Section 4.3
81. refers to the spatial arrangement of subunits and the nature of their interactions.
Ans: Quaternary structure Section 4.3
Multiple-Choice Questions
82. What determines a protein’s function?
A) its structure
B) its gene sequence
C) N-terminal amino acids
D) None of the above.
E) All of the above.
Ans: A Section: Introduction
83.
What is the approximate mass of a protein containing 200 amino acids? (Assume there are no other prote
modifications.)
A) 20,000
B) 11,000
C) 22,000
D) 222,000
E) None of the above.
Ans: C Section: 4.1
84. Key properties of proteins include:
A) a wide range of functional groups.
B) an ability to possess either rigid or flexible structures as dictated by functional requirements.
C) the ability to interact with other proteins.
D) A and B.
E) All of the above.
Ans: E Section: 4.1
85. Why is the peptide bond planar?
A) Bulky side chains prevent free rotation around the bond.
B) It exhibits partial double-bond character, preventing rotation.
C) Hydrogen bonding between the NH and C=O groups limits movement.
D) None of the above.
E) All of the above.
Ans: B Section: 4.1
86. The configuration of most α-carbon atoms of amino acids linked in a peptide bond is:
A) cis.
B) circular.
C) parallel.
D) trans.
E) perpendicular.
Ans: D Section: 4.1
87. What structure(s) did Pauling and Corey predict in 1951?
A) α helix
B) β sheet
C) β turn
D) A, B, and C
E) A and B
Ans: E Section: 4.2
88. Which of the following protein(s) contain examples of α-helical character?
A) keratin
B) ferritin
C) myosin
D) tropomyosin
E) All of the above.
Ans: E Section: 4.2
89.
Which of the following amino acid residues would most likely be buried in the interior of a water-soluble, g
protein?
A) aspartate
B) serine
C) phenylalanine
D) lysine
E) glutamine
Ans: C Section 4.3
90. Where are β turns and loops often found?
A) in a hydrophobic pocket
B) on the interior cleft
C) at the protein interface with ligand
D) on the surface of proteins
E) None of the above.
Ans: D Section: 4.3
91. The folding of a protein into its native shape can best be described as:
A) a random event.
B) a random event catalyzed by ribosome proteins to maintain a low energy structure.
C) a series of controlled folds with a few random-shaped structures.
D) a series of repeatable random events where the lowest energy structure is maintained.
E) an event where the highest possible energy state is stabilized with discrete folding intermediates.
Ans: D Section: 4.5
92. Your study group is trying to identify differences in the four levels of protein structure. Which of the followi
would you say is true of important stabilizing forces in secondary structure but not tertiary structure?
A) The structure is stabilized by ionic attractions between oppositely charged side chains.
B) The structure is stabilized by H-bonding between polar side chains.
C) The structure is stabilized by hydrophobic interactions between nonpolar side chains.
D) The structure is stabilized by H-bonding between the oxygen of the backbone carbonyl and the hydrog
the backbone amine.
E) None of these differentiate between secondary and tertiary structure.
Ans: D Sections: 4.2 and 4.3
93.
A clinician friend comes to you and tells you she has a patient that she thinks has some sort of defect in t
collagen structure. She wants to know what kinds of structural differences there might be. Which of the fo
is NOT true for defects leading to scurvy or brittle bone disease?
A) Proline residues are not hydroxylated.
B) Glycine is replaced by other amino acids.
C) Proyloyl hydroxylase activity is deficient.
D) Accumulation of defective collagen causes cell death.
E) All of the above are true.
Ans: E Section: 4.2
94. All of the following would disrupt quaternary structure except:
A) increase the temperature.
B) decrease the pH.
C) add 8 m Urea.
D) treat with ascorbic acid (vitamin C).
E) treat with β-mercaptoethanol.
Ans: D Section: 4.4
95. Which of the following secondary structures would you expect to find on the surface of a globular protein?
A) α helix
B) β sheet
C) loops between two α-helices
D) none of the above because water would disrupt the hydrogen bonding that stabilizes these structures
E) A, B, and C as long as the polar and charged amino acid side chains face the surface of the protein
Ans: E Section: 4.2
96.
The metamorphic protein lymphotactin undergoes changes in _____what_______ structure in order to ca
its full biochemical activity?
A) primary and therefore also tertiary
B) primary, secondary, and tertiary
C) quaternary (subunits separate and carry out individual activities)
D) secondary and tertiary
E) primary, secondary, tertiary, and quaternary
Ans: D Section: 4.5
Short-Answer Questions
97. How does a protein’s amino acid sequence influence the tertiary structure?
Ans:
A protein will spontaneously fold into a three-dimensional structure determined by the amino acid
sequence.
Section: Introduction
98. What is the advantage of protein interaction and assembly with other proteins?
Ans:
When proteins interact or assemble, new functions and specificity become available. Protein
interactions allow new binding sites at the assembly interface, and provide multifunctional activit
specificity, such as that found in polymerases and signal transduction.
Section: Introduction
99. How does the protein backbone add to structural stability?
Ans:
The protein backbone contains the peptide bond, which has NH molecules and C=O (ketone) gro
Hydrogen-bond formation between the hydrogen on the nitrogen and the oxygen support the pro
conformation.
Section: 4.2
100. Why are all the theoretical combinations of phi and psi not possible?
Ans: Steric hindrances of the side chains make certain combinations and angles impossible.
Section: 4.2
101. Describe some of the features of an α helix.
Ans:
Section: 4.2
The α helix is a coil stabilized by intrachain hydrogen bonds between the carbonyl oxygen of a re
and the amide hydrogen of the fourth residue away. There are 3.6 amino acids per turn. The hyd
bonds are between amino acid residues that have two intervening residues. Thus, these amino a
residues are found on the same side of the coil. The helix is almost always right-handed, althoug
handed helices are, in theory, possible.
102. What is the “hydrophobic effect” as it relates to protein structure?
Ans:
The three-dimensional structure of a water-soluble protein is stabilized by the tendency of hydro
Section: 4.3
groups to assemble in the interior of the molecule.
103. What are the key characteristics that make the peptide bond important to protein folding/structure?
Ans: The resonance of the amide bond creates a planar, rigid region of the peptide backbone with the
groups on opposite sides of the peptide bond. This results in a limit to the types and angles of
Section: 4.1
conformation, allowing a predictable folding pattern.
104. What are prions?
Ans:
Prions are proteins that can assume (after infection or by other causes) a new protein structure t
Section: 4.5
self-propagating. Prion diseases have several variants, at least one of which is fatal to humans.
105.
In the ribonuclease experiments performed by Anfinsen, what was the significance of the presence of the
reducing agent β-mercaptoethanol?
Ans:
The reducing agent reduced incorrectly paired disulfide bonds, allowing them to reform with the
Section: 4.5
pairing until the most stable conformation of the protein had been obtained.
106. What is the advantage of having certain regions of partially correct folded regions?
Ans:
If some regions interact preferentially, lending stability to certain conformations as the protein fol
Section: 4.3
can impact the overall structure of the protein.
107.
A primary sequence of a protein contains a run of reasonably small amino acids, containing few branched
acids or serines. This sequence ends in a proline. What can you deduce from this information?
Ans:
The sequence is likely an α helix. The smaller amino acids do not sterically hinder the side group
the outside of the helix and the absence of amino acids that would interfere with the helix are all
evidence for this secondary structure. The proline is likely to be the end of the sequence.
Section: 4.2
108.
What is the sequence of amino acids found in collagen? What is the significance of the sequence and wh
complication of scurvy?
Ans:
Section: 4.2
Gly-Pro-Pro. The small side group of the glycine allows for a tight screw turn for this atypical heli
prolines are important to stabilize tight three-amino-acid helices. In addition, the prolines are also
hydroxylated by an enzyme that requires ascorbic acid to maintain activity. Without the hydroxyla
collagen by prolylhydroxylase, the collagen superstructure is less stable and results in adverse f
of the connective tissues (scurvy).
109.
Prion diseases are often latent; that is, those with prion diseases are asymptomatic for many years after t
initial infection. What causes this latency?
Ans: Prion diseases are protein based; more specifically, protein-structure based. Because it takes tim
convert the prion protein from the soluble, mostly helical form to the beta-strand, insoluble form,
lag time before enough proteins are converted to the polymer, which causes cell injury This
Section: 4.5
characteristic of prion diseases makes it difficult to diagnose before it is too late.