Chapter 6—Proteins: Secondary, Tertiary, and Quaternary Structure
MULTIPLE CHOICE
1. Amino acid side chains capable of forming hydrogen bonds are usually located on the protein ____
and form hydrogen bonds primarily with the ____.
a.
surface, water solvent
b.
interior, water solvent
c.
surface, other amino acid side chains
d.
interior, other amino acid side chains
e.
all are true
2. ____ amino acids are almost never found in the interior of a protein, but the protein surface may
consist of ____ amino acids.
a.
Nonpolar, both polar and nonpolar
b.
Nonpolar, mostly nonpolar
c.
Polar, both polar and nonpolar
d.
Polar, only polar
e.
Polar, only nonpolar
3. Electrostatic interactions among amino acid residues on proteins may be damped out by high
concentrations of:
a.
water.
b.
organic solvents.
c.
salts.
d.
heat.
e.
all of the above.
4. An electrostatic interaction might occur within a protein between which of the following amino acid
pairs at typical physiological pH?
a.
Ser/Asn
b.
Asp/Glu
c.
Arg/Cys
d.
Lys/Asp
e.
Val/Ile
5. ____ between tightly packed amino acid side chains in the interior of the protein are a major
contribution to protein structure.
a.
Hydrogen bonds
b.
Electrostatic interactions
c.
Covalent ester bonds
d.
Van der Waals interactions
e.
All are true
Garrett/Grisham 5e Test Bank 2
6. A hydrophobic interaction might occur within a protein between which of the following amino acid
pairs?
a.
Ser/Ile
b.
Val/Leu
c.
Tyr/Cys
d.
Lys/Asn
e.
His/Val
7. All of the information necessary for folding the peptide chain into its “native” structure is contained in
the ____ of the peptide.
a.
amino acid sequence
b.
amino acid composition
c.
configuration
d.
amino acid side chain charges
e.
all are true
8. Amino acid sequence is:
a.
primary structure.
b.
secondary structure.
c.
tertiary structure.
d.
quaternary structure.
e.
regular structure.
9. Secondary and higher orders of structure are determined by all EXCEPT:
a.
hydrophobic interactions.
b.
ionic bonds.
c.
van der Waals forces.
d.
hydrogen bonds.
e.
peptide bonds.
10. If an aspartic acid residue were present in the interior of a globular protein, it would most likely be
_________.
a.
deprotonated and thus negatively charged
b.
tightly associated with the R-group of a lysine residue
c.
react with a cysteine to form a thioester
d.
react with a serine to form an ester
e.
none of the above
11. Planarity of the peptide bond means that no rotation occurs about the _____ bond while rotation is
allowed about the ____ and ____ bonds.
a.
C(O)-N; C-C; N-C
b.
C(O)-N; C-C(O); N-C
c.
C-C(O); C(O)-N; N-C
d.
N-C; C–C(O); C(O)-N
e.
none of the above
12. A Ramachandran plot shows:
a.
the amino acid residues which have the greatest degree of rotational freedom.
b.
the sterically allowed rotational angles between R groups and -carbons in a peptide.
c.
the sterically allowed rotational angles between C and the amide nitrogen (C−N) as well
as between C and the amide carbonyl carbon (C−CO).
d.
the sterically allowed rotational angles about the amide nitrogen (NH) and CO.
e.
the amino acid residues that form -helix, -sheet, etc.
13. Alpha helices are stabilized primarily by:
a.
hydrogen bonds between the main chain peptide bond component atoms.
b.
electrostatic interactions between R-groups.
c.
hydrophobic interactions between the -carbons of the main chain.
d.
hydrogen bonding between the R-groups.
e.
hydrophobic interactions between R-groups and the solvent water.
14. In the majority of -helixes, each peptide carbonyl is hydrogen bonded to the peptide N−H group ____
residues farther ____ the chain.
a.
2, down
b.
4, up
c.
3, down
d.
2, up
e.
4, down
15. ____ and ____ act as helix breakers due to their unique structure, which fixes the value of the C−N−C
bond angle.
a.
Histidine, lysine
b.
Proline, hydroxyproline
c.
Arginine, lysine
d.
Serine, threonine
e.
Tyrosine, serine
16. If the following section of a polypeptide is folded into an -helix, to which amino acid is the carbonyl
group of alanine hydrogen bonded?
ala-ser-val-asp-glu-leu-gly
a.
serine
b.
aspartic acid
c.
glutamic acid
d.
leucine
e.
valine
17. When the peptide (AEFFLAMEP) forms an -helix, which amino acid residue would be closest to
being in the same position on the same face of the helix as is the initial alanine residue?
a.
F(3)
b.
A(6)
c.
E(8)
d.
P(9)
e.
L(5)
18. Antiparallel -sheets have:
a.
sheets that progress from N to C termini in the same direction.
b.
usually all of their hydrophobic residues on one side of the sheet.
c.
all hydrophobic residues.
d.
all hydrophilic residues.
e.
fibers that can be stretched or extended, but are not flexible.
19. –Turns in a peptide chain form a tight loop with hydrogen bonding of the carbonyl oxygen with:
a.
side chain amine of lysine two amino acids down the chain.
b.
amide proton on the next amino acid down the chain.
c.
amide proton of the glutamine side chain.
d.
amide proton of the residue three positions down the chain.
e.
amide proton of asparagine side chain.
20. Polylysine is a random coil when the pH is less than 11, while it forms an -helix if the pH is raised to
greater than 12. This is because at pH 12:
a.
the lysine residues are negatively charged which electrostatically stabilizes the helix.
b.
the positive charges on the lysine residues stabilizes the -helix.
c.
the lysine residues are neutral which eliminates electrostatic repulsion between the R
groups.
d.
the high concentration of OH− ions in solution reduces the electrostatic repulsion between
the R-groups.
e.
the lysine side chain changes configuration with pH.
21. The amino acid residue most likely to be found in a beta turn is:
a.
glycine.
b.
alanine.
c.
valine.
d.
glutamic acid.
e.
leucine.
Garrett/Grisham 5e Test Bank 5
22. ____ –sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and
____ -sheets are usually arranged with all their hydrophobic residues on one side of the sheet.
a.
Antiparallel, parallel
b.
Antiparallel, antiparallel
c.
Parallel, antiparallel
d.
Parallel, parallel
e.
None of the above
23. Which of the following amino acids would generally not be found in an -helix?
a.
Ala
b.
His
c.
Leu
d.
Ser
e.
Met
24. Tertiary structure is defined as:
a.
the sequence of amino acids.
b.
the folding of a single polypeptide chain in three-dimensional space.
c.
hydrogen bonding interactions between adjacent amino acid residues into helical or
pleated segments.
d.
the way in which separate folded monomeric protein subunits associate to form oligomeric
proteins.
e.
all are true.
25. Tertiary structure of proteins depends on all of the following EXCEPT:
a.
protein structure depends on primary structure.
b.
-helices and –sheets often associate and pack close together.
c.
secondary structures form whenever possible.
d.
proteins are stable as a single-layer structure.
e.
peptide segments between secondary structures are short.
26. The “Greek Key” topology is composed of ____.
a.
Adjacent -helices oriented in the same direction
b.
Adjacent -helices oriented in the opposite direction
c.
Discreet regions of -sheet oriented in an antiparallel fashion
d.
Discreet regions of -sheet oriented in an antiparallel fashion
e.
Parallel -sheet structures connected by -helices
27. Fibrous proteins contain polypeptide chains ____ producing long fibers or large sheets.
a.
with an abundance of aromatic amino acids
b.
with an abundance of hydrophilic amino acids
c.
organized approximately parallel along a single axis
d.
with amino acids arranged in a repeating (-a-b-c-d-)n sequence
e.
all are true
28. –Keratin has all of the following characteristics EXCEPT:
a.
primary component in hair, claws, fingernails, and horns of animals.
b.
consists of four helical strands arranged as twisted pairs of two-stranded coiled coils.
c.
has associated hydrophobic strips on the two coiled coils.
d.
presence of properly placed polar amino acids help to solubilize -keratin.
e.
has covalent disulfide bonds to stabilize the structure.
29. The “permanent” part of adding wave in hair is primarily due to:
a.
rearrangement of hydrogen bonds between hair fibers.
b.
reestablishment of new ionic interactions between hair fibers.
c.
breaking and reforming peptide bonds in the hair polypeptides.
d.
rearrangement of hydrophobic interactions in hair fibers.
e.
reduction and re-oxidation of disulfide bonds in hair fibers.
30. Silk fibers consist of ____ proteins consisting of alternating ____ and ____ or ____ residues.
a.
fibroin; glycine; proline; leucine
b.
-keratin; alanine; glycine; serine
c.
fibroin; glycine; alanine; threonine
d.
-keratin; cysteine; alanine; proline
e.
fibroin; glycine; alanine; serine
31. Collagen has the following characteristics EXCEPT:
a.
Tropocollagen is the basic structural unit.
b.
There is about 33% glycine in collagen.
c.
Both intermolecular and intramolecular crosslinks help to stabilize the collagen fibrils.
d.
Modification of prolines occurs prior to collagen synthesis.
e.
Inextendable fibrous protein are components of connective tissues.
32. The unique composition of collagen is accommodated in a structure called a(n):
a.
-pleated sheet.
b.
triple helix.
c.
helix-turn-helix motif.
d.
coiled coils.
e.
all are true.
33. Prolyl hydroxylase has all of the following characteristics EXCEPT:
a.
requires citric acid.
b.
is activated by Fe2+.
c.
hydroxylates proline residues in proteins.
d.
requires molecular oxygen.
e.
requires -ketoglutarate.
34. A major stabilizing factor in the triple helix is a ____ structure such that ____ residues from the three
strands stack along the center of the triple helix.
a.
linear, glu
b.
linear, gly
c.
staggered, lys
d.
staggered, gly
e.
stacked, pro
35. In hemoglobin, a ____ protein, the space between the helices is filled efficiently and tightly with
mostly ____ amino acid chains and with ____ side chains facing the outside of the protein structure.
a.
globular, hydrophobic, polar
b.
globular, polar, nonpolar
c.
fibrous, hydrophobic, nonpolar
d.
fibrous, polar, nonpolar
e.
none are true
36. Why should the core of most globular and membrane proteins consist almost entirely of -helix and –
sheets?
a.
Hydrogen bonded structures must be kept away from water solvent.
b.
Highly polar N−H and C=O moieties of the peptide backbone must be neutralized in the
hydrophobic core of the protein.
c.
Hydrogen bonding only occurs in the core of proteins.
d.
Trapped water stabilizes the helix and sheet structures.
e.
None are true.
37. The outward face of a(n) ____ consists mainly of polar and charged residues, whereas the inner face
contains mostly nonpolar, hydrophobic residues.
a.
-sheet
b.
configuration
c.
-turn
d.
amphiphilic helix
e.
all are true
38. A –barrel would most likely be composed of ____.
a.
parallel -sheets connected by regions of -helix
b.
parallel -sheets connected by -turns.
c.
parallel -sheets connected by regions of random coil.
d.
parallel -sheets connected disulfide bonds.
e.
both a and c are correct.
39. Flexible, disordered segments of proteins are commonly high in the amino acid:
a.
leu
b.
lys
c.
ser
d.
pro
e.
asp
40. Which of the following would be the most rapidly occurring event giving rise to protein motion?
a.
hinge-bending movement between protein domains
b.
tyrosine ring flip
c.
cis-trans isomerization of proline
d.
protein conformational change
e.
both b and c are equally rapid
41. Which statement is correct about the −− motif?
a.
The two -strands are antiparellel.
b.
The peptide segment connecting the -strands usually contains no more than five amino
acids.
c.
The peptide segment connecting the two -strands commonly contains proline.
d.
The cross-over connection itself contains an -helical segment.
e.
none are correct.
42. All are true about the tertiary structure of the enzyme triose phosphate isomerase EXCEPT:
a.
Its -strands are parallel.
b.
Its -helices are in the interior of the molecular structure.
c.
It contains a –barrel in the center of its structure.
d.
It is composed entirely of alternating -helices and -strands.
e.
All are true.
43. All are classes of globular proteins according to type and arrangement of secondary structure
EXCEPT:
a.
small metal- and disulfide-rich proteins.
b.
parallel or mixed -sheet.
c.
antiparallel -sheet.
d.
antiparallel -helix.
e.
all are true.
44. ____ are examples of antiparallel -helix proteins.
a.
Triose phosphate isomerase
b.
Pyruvate kinase
c.
Flavodoxin
d.
Hemoglobin
e.
Papain
45. ____ is an example of a disulfide-rich protein.
a.
Insulin
b.
Glyceraldehyde-3-phosphate dehydrogenase
c.
Hemoglobin
d.
Triose phosphate isomerase
e.
All are true.
46. ____ are proteins that help other proteins to fold.
a.
Immunoglobulins
b.
Phospholipases
c.
Synthetases
d.
Molecular chaperones
e.
Proteases
47. All are structural and functional advantages to quaternary structure EXCEPT:
a.
cooperativity.
b.
stability.
c.
bringing catalytic sites together.
d.
genetic economy and efficiency.
e.
all are true.
48. All of the statements about the tertiary structure of the enzyme triose phosphate isomerase are correct
EXCEPT:
a.
Its -strands are parallel.
b.
Its -helices are in the interior core of the molecular structure.
c.
It contains a –barrel in the center of its structure.
d.
It is composed entirely of alternating -helices and -strands.
e.
Hydrophobic residues are buried between concentric layers.
49. Arrange the steps involved in folding of globular proteins into a proper sequence.
A.
“Molten globule” formation of assembled domains.
B.
Formation of domains through cooperative aggregation of folding nuclei.
C.
Adjustment in the conformation of domains.
D.
Rapid and reversible formation of local secondary structure.
E.
Final protein monomer formation.
a.
A, B, C, D, E
b.
B, C, E, A, D
c.
D, C, B, A, E
d.
D, B, A, C, E
e.
B, D, C, A, E
50. Which of the following does not contribute to the spontaneous nature of the protein folding process?
a.
formation of hydrogen bonds and electrostatic interactions
b.
loss of translational freedom as portions of the protein interact
c.
formation of hydrophobic interactions
d.
both a and c
51. Which of the following proteins does not have quaternary structure?
a.
immunoglobulins
b.
insulin
c.
glycogen phosphorylase
d.
myoglobin
e.
alcohol dehydrogenase
52. Which of the following items was one of the crucial elements of the Anfinsen experiment with
ribonuclease A?
a.
hydrophobic interactions were disrupted by the addition of -mercaptoethanol
b.
correct formation of disulfide bonds was achieved even with urea present
c.
removal of -mercaptoethanol resulted in complete denaturation of the protein
d.
the presence of 8 cysteine residues means that there are 105 different disulfide bond
possibilities
e.
none of the above
53. In the tertiary structure of a protein, an electrostatic interaction could form between the R-groups of
which two amino acids?
a.
Gln and Lys
b.
Asp and Thr
c.
Leu and Asp
d.
Glu and Arg
e.
Arg and His
54. In the tertiary structure of a protein, a hydrophobic interaction could form between the R-groups of
which two amino acids?
a.
Ala and Ser
b.
Asn and Tyr
c.
Leu and Val
d.
Val and His
e.
Pro and Gln