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.
a) amino
b) water
c) protons
d) DNA
e) secondary structure
f) tertiary structure
g) Ramachandran
h) RNA
i) domain
j) cystine
k) proline
l) Sanger
m) D amino acids
n) cysteine
1.
When a peptide bond is formed between two amino acids, a(n) ____________molecule is lost.
2.
____________: Codes for the sequence of amino acids.
Ans:
d
Section: Introduction
3.
According to convention, ____________ is the terminus drawn on the left side of a peptide.
Ans:
a
Section: 4.1
4.
Two amino acids undergo oxidation to form a dimer called ____________.
Ans:
j
Section: 4.1
5.
Changes in ____________ create amyloid fibers, which are insoluble and are the source of mad
cow disease, Alzheimer disease, and Parkinson disease.
Ans:
Section: 4.5
6.
____________: Compact regions that may be connected by a flexible segment of polypeptide
chain.
Ans:
Section: 4.3
Ans:
b
Section: 4.1
Chapter 4 Protein Three-Dimensional Structure
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7.
____________: This amino acid residue disrupts the α helix because its side chain contains a
unique ring structure that restricts bond rotations.
8.
The plot that allows one to investigate the likely orientation of certain amino acid pairs is called
the ____________.
Ans:
g
Section: 4.1
9.
____________: The type of structure to which α helices, β sheets, and turns are referred.
Ans:
Section: 4.2
10.
The overall 3D-structure of a single polypeptide chain is referred to as ____________.
Ans:
Section: 4.3
Fill–in-the-Blank Questions
11.
The of a disulfide bridge results in a separation of two protein chains.
Ans: oxidation Section 4.1
12.
The peptide bond is also known as a(n) .
Ans: amide bond Section 4.1
13.
Peptides differ from proteins in .
Ans: the number of amino acid residues Section 4.1
14.
Due to the side chain steric clash, almost all peptide bonds are in their configuration.
Ans: trans Section 4.1
15.
The secondary structure that is stabilized by CO and NH hydrogen bonding within the peptide
chain is the .
Ans: alpha helix Section 4.2
16.
The indicates the left- or right-handedness of an α helix.
Ans: screw sense Section 4.2
17.
is a fibrous protein and is the primary component of wool and hair.
Ans: α-keratin Section 4.2
18.
Every third residue in the protein collagen is .
Ans: glycine Section 4.2
19.
Disulfide bonds in proteins can be reduced to free sulfhydryl groups by reagents such as .
Ans: β-mecaptoethanol Section 4.3
Ans:
k
Section: 4.2
Chapter 4 Protein Three-Dimensional Structure
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20.
The β–sheet structure occurs when the two strands are oriented in opposite directions (N →
C).
21.
A protein whose peptide backbone is mostly extended and hydrogen bonded to different strands
of the protein is composed mostly of the secondary structure.
Ans: β-sheet Section 4.3
22.
A protein is considered to be when it is converted into a randomly coiled structure without its
normal activity.
Ans: denatured Section 4.4
23.
is the major fibrous protein present in skin, bone, tendon, cartilage, and teeth.
Ans: Collagen Section 4.3
24.
Collagen contains , a modified amino acid.
Ans: hydroxyproline Section 4.3
25.
Compact, globular proteins are typically water and consist mostly of secondary structure.
Ans: soluble; an alpha helical Section 4.3
26.
refers to the spatial arrangement of subunits and the nature of their interactions.
Ans: Quaternary structure Section 4.3
Multiple-Choice Questions
27.
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
28.
What is the approximate mass of a protein containing 200 amino acids? (Assume there are no
other protein modifications.)
A) 20,000
B) 11,000
C) 22,000
D) 222,000
E) None of the above.
Ans: C Section: 4.1
Ans: antiparallel Section 4.3
Chapter 4 Protein Three-Dimensional Structure
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29.
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.
30.
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
31.
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
32.
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
33.
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
34.
Which of the following amino acid residues would most likely be buried in the interior of a
water-soluble, globular protein?
A) aspartate
B) serine
C) phenylalanine
D) lysine
E) glutamine
Ans: C Section 4.3
Ans: E Section: 4.1
Chapter 4 Protein Three-Dimensional Structure
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35.
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.
36.
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
37.
Your study group is trying to identify differences in the four levels of protein structure. Which
of the following 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 hydrogen of the backbone amine.
E) None of these differentiate between secondary and tertiary structure.
Ans: D Sections: 4.2 and 4.3
38.
A clinician friend comes to you and tells you she has a patient that she thinks has some sort of
defect in the collagen structure. She wants to know what kinds of structural differences there
might be. Which of the following 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
39.
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
Ans: D Section: 4.3
Chapter 4 Protein Three-Dimensional Structure
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40.
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
41.
The metamorphic protein lymphotactin undergoes changes in _____what_______ structure in
order to carry out 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
42.
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.
43.
What is the advantage of protein interaction and assembly with other proteins?
multifunctional activity and specificity, such as that found in polymerases and signal
transduction.
Section: Introduction
44.
How does the protein backbone add to structural stability?
oxygen support the protein conformation.
Section: 4.2
45.
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
46.
Describe some of the features of an α helix.
amino acids per turn. The hydrogen bonds are between amino acid residues that have two
Ans: E Section: 4.2
Chapter 4 Protein Three-Dimensional Structure
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47.
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
hydrophobic groups to assemble in the interior of the molecule.
Section: 4.3
48.
What are the key characteristics that make the peptide bond important to protein
folding/structure?
types and angles of conformation, allowing a predictable folding pattern.
Section: 4.1
49.
What are prions?
Ans:
Prions are proteins that can assume (after infection or by other causes) a new protein
structure that is self-propagating. Prion diseases have several variants, at least one of
which is fatal to humans.
Section: 4.5
50.
In the ribonuclease experiments performed by Anfinsen, what was the significance of the
presence of the reducing agent β-mercaptoethanol?
obtained.
Section: 4.5
51.
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 folds, they can impact the overall structure of the protein.
Section: 4.3
52.
A primary sequence of a protein contains a run of reasonably small amino acids, containing few
branched amino acids or serines. This sequence ends in a proline. What can you deduce from
this information?
interfere with the helix are all evidence for this secondary structure. The proline is likely
Section: 4.2
53.
What is the sequence of amino acids found in collagen? What is the significance of the sequence
and what is the complication of scurvy?
addition, the prolines are also hydroxylated by an enzyme that requires ascorbic acid to
coil. The helix is almost always right-handed, although left-handed helices are, in theory,
possible.
Section: 4.2
Chapter 4 Protein Three-Dimensional Structure
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54.
Prion diseases are often latent; that is, those with prion diseases are asymptomatic for many
years after their initial infection. What causes this latency?
polymer, which causes cell injury This characteristic of prion diseases makes it difficult
to diagnose before it is too late.
collagen superstructure is less stable and results in adverse flexibility of the connective
Section: 4.2