Deck 6: Proteins: Secondary, Tertiary, and Quaternary Structure

Question 1

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 α-carbons of the main chain.
D) hydrogen bonding between the R-groups.
E) hydrophobic interactions between R-groups and the solvent water.

Answer 1

A

Question 2

β-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.

Answer 2

D

Question 3

If the following section of a polypeptide is folded into an α-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

Answer 3

C

Question 4

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; Cα-Cβ; N-Cα
B) C(O)-N; Cα-C(O); N-Cα
C) Cα-C(O); C(O)-N; N-Cα
D) N-Cα; Cα-C(O); C(O)-N
E) none of the above

Question 5

In the majority of α-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

Question 6

____ 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

Question 7

____ and ____ act as helix breakers due to their unique structure, which fixes the value of the C_α−N−C bond angle.

A) Histidine, lysine
B) Proline, hydroxyproline
C) Arginine, lysine
D) Serine, threonine
E) Tyrosine, serine

Question 8

When the peptide (AEFFLAMEP) forms an α-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)

Question 9

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

Question 10

Amino acid sequence is:

A) primary structure.
B) secondary structure.
C) tertiary structure.
D) quaternary structure.
E) regular structure.

Question 11

____ 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

Question 12

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

Question 13

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

Question 14

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 α-carbons in a peptide.
C) the sterically allowed rotational angles between Cα and the amide nitrogen (C_α−N) as well as between Cα and the amide carbonyl carbon (C_α−CO).
D) the sterically allowed rotational angles about the amide nitrogen (NH) and CO.
E) the amino acid residues that form α-helix, β-sheet, etc.

Question 15

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

Question 16

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.

Question 17

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.

Question 18

Antiparallel β-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.

Question 19

Polylysine is a random coil when the pH is less than 11, while it forms an α-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 α-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.

Question 20

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

Question 21

Which of the following amino acids would generally not be found in an α-helix?

A) Ala
B) His
C) Leu
D) Ser
E) Met

Question 22

Tertiary structure of proteins depends on all of the following EXCEPT:

A) protein structure depends on primary structure.
B) α-helices and β-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.

Question 23

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 α-ketoglutarate.

Question 24

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

Question 25

The outward face of a(n) ____ consists mainly of polar and charged residues, whereas the inner face contains mostly nonpolar, hydrophobic residues.

A) β-sheet
B) configuration
C) β-turn
D) amphiphilic helix
E) all are true

Question 26

α-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 α-keratin.
E) has covalent disulfide bonds to stabilize the structure.

Question 27

The unique composition of collagen is accommodated in a structure called a(n):

A) β-pleated sheet.
B) triple helix.
C) helix-turn-helix motif.
D) coiled coils.
E) all are true.

Question 28

____ β-sheets characteristically distribute hydrophobic side chains on both sides of the sheet, and ____ β-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

Question 29

Which statement is correct about the β−α−β motif?

A) The two β-strands are antiparellel.
B) The peptide segment connecting the β-strands usually contains no more than five amino acids.
C) The peptide segment connecting the two β-strands commonly contains proline.
D) The cross-over connection itself contains an α-helical segment.
E) none are correct.

Question 30

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.

Question 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.

Question 32

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

Question 33

Flexible, disordered segments of proteins are commonly high in the amino acid:

A) leu
B) lys
C) ser
D) pro
E) asp

Question 34

Silk fibers consist of ____ proteins consisting of alternating ____ and ____ or ____ residues.

A) fibroin; glycine; proline; leucine
B) α-keratin; alanine; glycine; serine
C) fibroin; glycine; alanine; threonine
D) β-keratin; cysteine; alanine; proline
E) fibroin; glycine; alanine; serine

Question 35

Why should the core of most globular and membrane proteins consist almost entirely of α-helix and β-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.

Question 36

A β-barrel would most likely be composed of ____.

A) parallel β-sheets connected by regions of α-helix
B) parallel β-sheets connected by β-turns.
C) parallel β-sheets connected by regions of random coil.
D) parallel β-sheets connected disulfide bonds.
E) both a and c are correct.

Question 37

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

Question 38

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

Question 39

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.

Question 40

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.

Question 41

Discuss the structure of fibroin proteins.​

Question 42

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 β-sheet.
C) antiparallel β-sheet.
D) antiparallel α-helix.
E) all are true.

Question 43

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 β-mercaptoethanol
B) correct formation of disulfide bonds was achieved even with urea present
C) removal of β-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

Question 44

____ 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.

Question 45

Which of the following proteins does not have quaternary structure?

A) immunoglobulins
B) insulin
C) glycogen phosphorylase
D) myoglobin
E) alcohol dehydrogenase

Question 46

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.

Question 47

Discuss cooperativity in proteins.​

Question 48

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

Question 49

Explain the role of hydrophobic interactions in protein folding.​

Question 50

Describe β-turns in peptide chains.​

Question 51

____ are examples of antiparallel α-helix proteins.

A) Triose phosphate isomerase
B) Pyruvate kinase
C) Flavodoxin
D) Hemoglobin
E) Papain

Question 52

Enumerate the characteristics of the α-helix structure of proteins.​

Question 53

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

Question 54

____ are proteins that help other proteins to fold.

A) Immunoglobulins
B) Phospholipases
C) Synthetases
D) Molecular chaperones
E) Proteases

Question 55

All are true about the tertiary structure of the enzyme triose phosphate isomerase EXCEPT:

A) Its β-strands are parallel.
B) Its α-helices are in the interior of the molecular structure.
C) It contains a β-barrel in the center of its structure.
D) It is composed entirely of alternating α-helices and β-strands.
E) All are true.

Question 56

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

Question 57

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

Question 58

All of the statements about the tertiary structure of the enzyme triose phosphate isomerase are correct EXCEPT:

A) Its β-strands are parallel.
B) Its α-helices are in the interior core of the molecular structure.
C) It contains a β-barrel in the center of its structure.
D) It is composed entirely of alternating α-helices and β-strands.
E) Hydrophobic residues are buried between concentric layers.