Ch. 6 - Biochemistry Questions

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

c. glutamic acid

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

c. organized approximately parallel along a single axis

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.

c. salts

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.

c. the lysine residues are neutral which eliminates electrostatic repulsion between the R groups.

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 (Cα-N) as well as between Cα and the amide carbonyl carbon (Cα-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.

c. the sterically allowed rotational angles between Cα and the amide nitrogen (Cα-N) as well as between Cα and the amide carbonyl carbon (Cα-CO).

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

d. D, B, A, C, E

____ are examples of antiparallel α-helix proteins. a. Triose phosphate isomerase b. Pyruvate kinase c. Flavodoxin d. Hemoglobin d. Papain

d. Hemoglobin

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

d. Lys/Asp

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.

d. Modification of prolines occurs prior to collagen synthesis.

____ are proteins that help other proteins to fold. a. Immunoglobulins b. Phospholipases c. Synthetases d. Molecular chaperones e. Proteases

d. Molecular chaperones

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.

d. The cross-over connection itself contains an α-helical segment.

____ 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

d. Van der Waals interactions

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.

d. amide proton of the residue three positions down the chain.

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

d. amphiphilic helix

____ is an example of a disulfide-rich protein. a. Insulin b. Glyceraldehydes-3-phosphate dehydrogenase c. Hemoglobin d. Triose phosphate isomerase e. All are true.

a. Insulin

________ 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

c. Parallel, antiparallel

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

a. amino acid sequence

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

a. globular, hydrophobic, polar

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.

a. glycine.

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.

a. hydrogen bonds between the main chain peptide bond component atoms.

Amino acid sequence is: a. primary structure. b. secondary structure. c. tertiary structure. d. quaternary structure. e. regular structure.

a. primary structure

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.

a. requires citric acid.

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

a. surface, water solvent

____ 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 non polar b. Nonpolar, mostly non polar c. Polar, both polar and non polar d. Polar, only polar e. Polar, only nonpolar

c. Polar, both polar and non-polar

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

b. 4, up

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. d. Hydrogen bonding only occurs in the core of proteins. d. Trapped water stabilizes the helix and sheet structures. e. None are true.

b. Highly polar N-H and C=O moieties of the peptide backbone must be neutralized in the hydrophobic core of the protein.

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.

b. Its α-helices are in the interior core of the molecular structure.

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.

b. Its α-helices are in the interior of the molecular structure.

____ and ____ act as helix breakers due to their unique structure, which fixes the value of the Cα-N-C bond angle. a. Histidine, lysine b. Proline, hydroxyproline c. Arginine, lysine d. Serine, threonine e. Tyrosine, serine

b. Proline, hydroxyproline

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

b. Val/Leu

Flexible, disordered segments of proteins are commonly high in the amino acid: a. leu b. lys c. ser d. pro e. asp

b. lys

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.

b. the folding of a single polypeptide chain in three-dimensional space.

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.

b. triple helix.

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.

b. usually all of their hydrophobic residues on one side of the sheet.

The resonance structure which forms the "amide plane" contains which atoms? a. CαH-NH-CO-CαH b. CαH-NH-CO c. Cα-NH-CO-Cα d. NH-CO e. NH-CO-Cα

c. Cα-NH-CO-Cα

The "Greek Key" topology is composed of ____. a. Adjacent α-helices oriented in the same direction b. Adjacent α-helices oriented in the opposite direction c. Discreet regions of β-sheet oriented in an antiparallel fashion d. Discreet regions of β-sheet oriented in an antiparallel fashion e. Parallel β-sheet structures connected by α-helices

c. Discreet regions of β-sheet oriented in an antiparallel fashion

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)

c. E(8)

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. principal constituent of connective tissues in animals. e. has covalent disulfide bonds to stabilize the structure.

d. principal constituent of connective tissues in animals.

Tertiary structure of proteins depends on all 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.

d. proteins are stable as a single-layer structure.

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

d. staggered, gly

Planarity of the peptide bond means that rotation is allowed about the bond linking the ____ and the carbon of the peptide bond, and also about the bond linking the ____ to the adjacent α-carbon. a. α-carbon, carbonyl carbon b. β-carbon, carbonyl carbon c. carbonyl carbon, nitrogen of the peptide bond d. α-carbon, nitrogen of the peptide bond e. none are true-carbon.

d. α-carbon, nitrogen of the peptide bond

____ form between two normal β-structure hydrogen bonds and are comprised of two residues on one strand and one residue on the opposite strand. a. α-Helix b. Parallel β-sheet c. β-Turn d. β-Bulge e. α-Turn

d. β-Bulge

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.

e. all are true

All are true for collective motions of proteins EXCEPT: a. are movements of groups of atoms covalently linked in such a way that the group moves as a unit. b. include trypsin ring flips c. include cis-trans isomerization of prolines. d. involve the flexible antigen-binding domains of immunoglobulins. e. all are true.

e. all are true

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.

e. all are true.

A β-barrel would most likely be composed of ____. a. parallel β-sheets connected by 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.

e. both a and c are correct

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. α-keratin; cysteine; alanine; proline e. fibroin; glycine; alanine; serine

e. fibroin; glycine; alanine; serine

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.

e. peptide bonds

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.

e. reduction and re-oxidation of disulfide bonds in hair fibers.