Chapter 4 Book Questions - Proteins: Three-Dimensional Structure and Function

Which pair represents different conformations?
A. Cis-1,2-dichloroethene and trans-1,2-dichloroethene.
B. L-glycine and D-glycine.
C. Eclipsed ethane and staggered ethane.
D. Pentane and 2-methylbutane.

C. Eclipsed ethane and staggered ethane.

4-Introduction

Which is a reasonable number of different polypeptides found in humans?
A. 2000
B. 20,000
C. 2,000,000
D. 2,000,000,000

B. 20,000

4-Introduction

Proteomics is
A. the study of large sets of proteins, such as the entire complement of proteins produced by a cell.
B. the manipulation of protein sequences to develop new proteins.
C. the copying of proteins to generate a lot of molecules from a small sample.
D. the specific study of the energy costs for protein synthesis.
E. the study of DNA/protein complexes.

A. the study of large sets of proteins, such as as the entire complement of proteins produced by a cell.

4-Introduction

A change from on conformation of a molecule to another involves _______.
A. rotation about bonds only
B. breaking and reforming of covalent bonds
C. inversion about a center of symmetry
D. Any of the above

A. rotation about bonds only

4-Introduction

The _______ is the single shape a protein adopts under physiological conditions.
A. minimal configuration
B. native conformation
C. primary structure
D. most stable enantiomer

B. native conformation

4-Introduction

Structural proteins that typically assemble into large cables or threads to provide mechanical support to cells or organisms are classified as __________ proteins.
A. fibrous
B. enzyme
C. globular
D. β-strand

A. fibrous

4-Introduction

To what level of structure do α-helices belong?
A. primary
B. secondary
C. tertiary
D. quaternary

B. secondary

Section 4-1

Which statement is false about a globular proteins that performs its biological function as a single independent polypeptide chain?
A. Its tertiary structure is likely stabilized by the interactions of amino acid side chains in non-neighboring regions of the polypeptide chain.
B. It could contain α-helices that are stabilized my hydrogen bonding.
C. It likely has extensive quaternary structure to maintain its globular shape.
D. Non-covalent forces are the primary source of stability for the secondary and tertiary structure.

C. It likely has extensive quaternary structure to maintain its globular shape.

Section 4-1

What does it mean to say a protein is oligomeric?
A. In vivo it establishes an equilibrium between two or more active conformations.
B. It has more than fifty amino acids.
C. The active protein involves the association of two or more polypeptide chains.
D. The proteins has multiple α-helices.

C. The active protein involves the association of two or more polypeptide chains.

Section 4-1

Computers are used to advance the understanding of three-dimensional protein structure by
A. determining the specific sequence of amino acids.
B. calculating atomic positions from X-ray diffraction patterns.
C. collimating X-ray beams

C. collimating X-ray beams

Section 4-2

Which technique is commonly used to determine the three-dimensional conformation of a protein?
A. Isoelectric focusing.
B. The Edman degradation
C. SDS-PAGE
D. X-ray crystallography

D. X-ray crystallograpy

Section 4-1

In 1962 Kendrew and Perutz won a Nobel Prize for
A. solving the structure of collagen by NMR.
B. determining the structure of the α-helix.
C. performing the first sequence of a protein.
D. determining the structure of myoglobin and hemoglobin by X-ray crystallography.

D. determining the structures of myoglobin and hemoglobin by X-ray crystallography.

Section 4-2

Which statement is false about the determination of protein structures?
A. NMR can generate sets of structures which may represent protein fluctuations.
B. The structures found by NMR and X-ray crystallography are usually very different.
C. It is often difficult to produce quality protein crystals for X-ray analysis.
D. NMR spectroscopy exposes protein solutions to a magnetic field.

B. The structure found by NMR and X-ray crystallography are usually very different.

Section 4-2

___________ received a Nobel Prize in 1964 for determining the structure of vitamin B12. He/she also solved the structure of penicillin in 1947 and developed many techniques used in the study of large proteins.
A. Max Perutz
B. Linus Pauling
C. Rosalind Franklin
D. Dorothy Crowfoot

D. Dorothy Crowfoot

Section 4-2

__________ is a technique used to analyze the macromolecular structure of proteins in solution.
A. X-ray crystallography
B. SDS-PAGE
C. Affinity chromatography
D. NMR

D. NMR

Section 4-2

NMR is often used for the determination of _________ of proteins.
A. molecular weight
B. isoelectric point
C. tertiary structure
D. pKa

C. tertiary structure

Section 4-2

Which is evidence that structures for proteins determined by X-ray crystallography represent the structures in solution?
A. Their similarity to structures determined by NMR.
B. The protein crystals are soluble in water.
C. The proteins must align in a regular pattern to form a crystal.
D. Only on conformation is ever possible for a protein so it is irrelevant whether the protein is in a crystal or in solution.

A. Their similarity to structures determined by NMR.

Section 4-2

Which statement is not true about the peptide bond?
A. The peptide bond has partial double-bond character.
B. The peptide bond is longer than the typical carbon-nitrogen bond.
C. Rotation is restricted about the peptide bond.
D. The carbonyl oxygen and the amide hydrogen are most often in a trans configuration with respect to one another.

B. The peptide bond is longer than the typical carbon-nitrogen bond.

Section 4-3

In peptide bonds, the bonds between
A. C and N are shorter than typical C-N bonds.
B. C and N are longer that typical C-N bonds.
C. C and O are longer than typical C=O bonds.
D. C and O are shorter than typical C=O bonds.
E. Both A and C.

E. Both A and C

Section 4-3

Nearly all peptide bonds are in the trans configuration because
A. cis peptide bonds are weaker
B. trans peptide bonds are stronger
C. cis peptide bonds prevent R groups from interacting.
D. trans peptide bonds minimize steric hindrance of R groups.

D. trans peptide bonds minimize steric hindrance of R groups

Section 4-3

Which represent the back bone of a protein?

Note: R = amino acid side chain
N = nitrogen
Cα = alpha carbon
C = carbonyl carbon

A. R1R2R3R4R5.
B. Repeating units of N-C.
C. Repeating units of N-Cα-C.
D. Repeating units of Cα-C.

C. Repeating units of N-Cα-C.

Section 4-3

What is true about the rotation about bonds in a protein backbone?
A. The rotation is free about all bonds in the backbone, except for the bond between the nitrogen and the alpha carbon in proline residues.
B. The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues.
C. All bonds in the backbone have restricted rotation and partial double-bond character.
D. The rotation is free only about the peptide bond. The other bonds are restricted by steric hindrance and the presence of proline residues.

B. The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues.

Section 4-3

The trans configuration of most peptide groups is adopted because it
A. is the only one available.
B. is favored in protein synthesis.
C. minimizes steric hindrance of R groups.
D. Both B and C.
E. All of the above.

D. Both B and C.

Section 4-3

Enzymes implicated in several human hereditary diseases are similar to ones that regulate flowering in Arabidopsos. These enzymes are
A. peptidyl cis isomerases.
B. proline isomerase.
C. prolyl cis/trans isomerase.
D. isomerase hydrolase.

C. prolyl cis/trans isomerase.

Section 4-3

The conformation of the backbone of a poly peptide is described completely by the angle(s) of rotation about which bond(s)?
A. The peptide bond only.
B. N-Cα only.
C. N-α, Cα-C and C-N bonds.
D. N-Cα and Cα-C bonds only.

D. N-Cα and Cα-C bonds only.

Section 4-3

What feature does a Ramachandran plot display?
A. Allowed angles of phi and psi for a polypeptide backbone.
B. Preferred amino acids in an α-helix.
C. The hydropathy of amino acids.
D. The variation of pH versus volume of base added during titration to determine the pKa.

A. Allowed angles of phi and psi for a polypeptide backbone.

Section 4-3

Ramachandran determined the "allowed" values of the phi and psi angles primarily by considering ____________.
A. pKa values of the amino acids
B. the hydropathy of amino acids
C. steric hindrance
D. hydrogen bonding effects

C. steric hindrance

Section 4-3

The distance along a helix acis for on complete turn is called the ________.
A. axial distance
B. rise
C. screw length
D. pitch

D. pitch

Section 4-4

The amino acid that destabilizes alpha-helical structure and is usually found at the ends of the alpha helices is
A. glycine
B. alanine
C. asparagine
D. glutamate

A. glycine

Section 4-4

Which was the major scientific accomplishment by Linus Pauling?
A. Determined that α-helix structure in keratin.
B. Discovered β-strands and described their assembly into sheets.
C. Determined the three-dimensional structure of hemoglobin and myoglobin.
D. Determined the structure of penicillin.

A. Determined that α-helix structure in keratin.

Section 4-4

An ideal α-helix has a pitch of 0.54 nm and rise of 0.15 nm. What is the length along the helix axis for a segment of an ideal α-helix that contains 30 amino acids?
A. 200 nm
B. 4.50 nm
C. 16.20 nm
D. 55.5 nm

B. 4.50 nm

Section 4-4

How many complete turns are there in an ideal α-helix that contains 15 amino acids and has a pitch of 0.54 nm and a rise of 0.15 nm?
A. 1
B. 4
C. 8
D. 59

B. 4

Section 4-4

Proline is not often found in α-helices of proteins because it
A. has a small, uncharged side chain.
B. has a very bulky side chain.
C. lacks a hydrogen atom on its amide nitrogen.
D. interacts with adjacent amino acids.

C. lacks a hydrogen tom on its amide nitrogen.

Section 4-4

Which structure below indicated the proper hydrogen-bonding pattern between amino acids in an α-helix? (Dashed lines represent the hydrogen bonds.) See question 34 for picture.
A. I
B. II
C. III
D. IV

B. II

Section 4-4

Which statement is NOT true about an α-helix?
A. It is usually right-handed.
B. It is a type of secondary structure.
C. It frequently contains proline residues.
D. It is stabilized by hydrogen bonding.

C. It frequently contains proline residues.

Section 4-4

Which is true about the side chains of residues in an α-helix?
A. They extend above or below the pleats.
B. They extend radically outward from the helix axis.
C. They point toward the center of the helix.
D. They hydrogen bond extensively with each other.

B. They point toward the center of the helix.

Section 4-4

What would you expect about the formation of an α-helix for a segment of a protein chain that contains lysine approximately every fourth residue with all other residues being mostly hydrophobic?
A. Helix formation would be favored at low pH.
B. Helix formation would be favored at high pH.
C. Helix formation would be favored at neutral pH.
D. Helix formation would never occur regardless of pH.

B. Helix formation would be favored at high pH.

Section 4-4

A helical wheel can be used to show
A. the pitch of helix structure.
B. the amphipathic nature of a helix.
C. DNA binding.
D. pleated sheets.

B. the amphipathic nature of a helix.

Section 4-4

Which is not true about β-sheets?
A. The side-chains of amino acids point to the same side of the sheet.
B. The polypeptide chains in the sheet are nearly fully extended.
C. The range of allowed phi and psi angles is broader than those in the α-helix.
D. In antiparallel sheets the hydrogen bonds between adjacent strands are nearly perpendicular to the backbones of the strands.

A. The side-chains of all amino acids point to the same side of the sheet.

Section 4-5

Proteins with alpha helix regions called leucine zippers are
A. often found in DNA binding proteins.
B. amphipathic helices.
C. part of pairs of helices that are wrapped around each other.
D. All of the above.

D. All of the above.

Section 4-5

A β-sandwich forms when
A. two hydrophobic sides of β-sheets interact.
B. two hydrophilic sides of β-sheets interact.
C. and α-helix separates two β-sheets.
D. two amphipathic α-helices interact.

A. two hydrophobic sides of β-sheets interact.

Section 4-5

Loops and turns in proteins are
A. regions that let a polypeptide chain fold back on itself.
B. stretches on non-repeating three dimensional structures in proteins.
C. regions causing direction change in the polypeptide backbone.
D. All of the above.

D. All of the above.

Section 4-6

Tertiary structure of proteins describe
A. polypeptide folding,
B. bringing amino acids far apart in primary structure close together.
C. stabilizing protein structure by non-covalent interaction.
D. disulfide bridges.
E. All of the above.

E. All of the above.

Section 4-7

Supersecondary structures that contain recognizable combinations of α-helices, β-strands and loops (e.g. the Greek Key) are called _______.
A. domains
B. folds
C. homologous regions
D. motifs

D. motifs

Section 4-7

How many monomers are there in an oligomeric proteins designated by αβ2γ2?
A. 2
B. 3
C. 4
D. 5
E. Not given.

D. 5

Section 4-8

The principle forces holding subunits of an oligomeric protein to each other are __________.
A. peptide bonds
B. hydrophobic interactions
C. covalent bonds
D. disulfide bonds

B. hydrophobic interactions

Section 4-8

Which factor does not help to explain why many proteins exhibit quaternary structure?
A. Oligomers are usually more stable than the free monomers.
B. Active sites can be formed when the protein chains associate.
C. The subunits always are able to maintain the same three-dimensional structure whether they are associated into a oligomer or not.
D. Increased efficiency by the sharing of the same subunits with the same function among different proteins.

C. The subunits always are able to maintain the same three-dimensional structure whether they are associated into an oligomer or not.

Section 4-8

Protein subunits in a multisubunit protein are held to each other primarily by
A. covalent bonds.
B. hydrophobic interactions exclusively.
C. both strong and weak interactions.
D. hydrophobic and other weak interactions.
E. All of the above.

D. hydrophobic and other weak interactions.

Section 4-8

A tetrameric protein contains
A. four different subunits.
B. four identical subunits.
C. three subunits and one prosthetic group.
D. A or B only.
E. A, B, or C.

D. A or B only.

Section 4-8

A protein has a molecular weight of 5600 daltons; its subunits are about 1960 daltons. There are ___ protein chains per oligomer.
A. 4
B. 3
C. 2
D. 1
E. Cannot determine from the information given.

B. 3

Section 4-8

Which is not an example of an oligomeric protein?
A. Cytochrome c.
B. Potassium channel protein.
C. MS2 capsid protein.
D. Hemoglobin.
E. Bacterial photosynthetic reaction center.

A. Cytochrome c.

Section 4-8

__________ is used to estimate the molecular weight of oligomeric proteins, while __________ is used to determine molecular weight of each chain.
A. Melting point; SDS-gel electrophoresis
B. SDS-gel electrophoresis; gel-filtration chromatography
C. Acrylamide gel electrophoresis; isoelectric focusing
D. Gel-filtration chromatography; SDS-gel electrophoresis
E. SDS-gel electrophoresis; NMR

D. Gel-filtration chromatography; isoelectric focusing

Section 4-8

Many proteins have multiple subunits because
A. an active site is shared by different subunits.
B. they are more stable and flexible in movement.
C. different combinations can perform different functions.
D. All of the above.
E. A and C above.

D. All of the above.

Section 4-8

Protein folding can be following in the laboratory by measuring
A. viscosity.
B. electrophoretic mobility and gel filtration.
C. UV absorption and light rotation.
D. A, B, and C above.
E. A and C above.

E. A and C above.

Section 4-8

Which demonstrates that the primary structure of a protein determines its tertiary structure?
A. How the disulfide bonds hold it in the correct shape.
B. Proteins can refold even when the amino acid sequence is changed.
C. Proteins refold when the amino acid sequence is the same as in the native conformation.
D. Chaotrophic agents cannot denature the native conformation.
E. All of the above.

C. Proteins refold when the amino acid sequence is the same as in the native conformation.

Section 4-9

Protein X can bind to either protein A or protein B to form a complex. The association constants are 108 M-1 (X with A) and 106 M-1 (X with B). Which statement is true?
A. In the presence of excess X, it takes fewer molecules of A than B to generate a given amount of complex.
B. The dissociation constant of the complex XA is higher than that of complex XB.
C. B must be a larger protein than A.
D. The values of the association constants indicate that both complexes XA and XB are very unstable in small cells like E. coli.

A. In the presence of excess X, it takes fewer molecules of A than B to generate a given amount of complex.

Section 4-9

In addition to self assemble, some proteins fold with the help of
A. energy stabilizers.
B. weak chemical interactions.
C. other proteins.
D. low entropy pickets.
E. All of the above.

C. other proteins.

Section 4-9

Interactomes describe interactions between
A. DNA and RNA
B. RNA polymerase and RNA.
C. DNA polymerase and DNA.
D. Proteins with other proteins.

D. Proteins with other proteins.

Section 4-9

Which statement is true about disulfide bonds and protein folding?
A. Disulfide bonds have no influence on protein folding since they only form after the protein adopts its native conformation.
B. Proteins occasionally adopt nonnative conformations and form improper disulfide bonds that can be reversed by the enzyme protein disulfide isomerase.
C. The folding of the native conformation is influenced more strongly by the formation of disulfide bonds than by the primary structure of a protein.
D. If a protein forms an improper disulfide bond it is irreversible inactivated and musty be targets by the cell for degradation.

B. Proteins occasionally adopt nonnative conformations and form improper disulfide bonds that can be reversed by the enzyme protein disulfide isomerase.

Section 4-10

The Tm of a protein is temperature at which it
A. is completely denatured.
B. liquifies.
C. is half denatured.
D. resists denaturation.

C. is half denatured.

Section 4-10

Proteins with very high Tm values are generally stable at
A. room temperature (21°C).
B. 50° to 60°C.
C. temperatures below 50°C.
D. temperatures above 60°C.
E. All of the above.

E. All of the above.

Section 4-10

Proteins segments which fold first can promote the folding of other secretions of the protein into the native conformation by a process known as
A. renaturation.
B. stabilization.
C. hydrophobic interaction.
D. disulfide bridge formation.
E. cooperativity.

E. cooperativity.

Section 4-11

Chaperones are proteins which
A. renature any denature proteins.
B. helps cells repair damage to to heat shock.
C. assist protein self assembly.
D. use ATP to fold proteins.
E. All of the above.

E. All of the above.

Section 4-11

Hemoglobin is
A. a tetramer of 4 myoglobin proteins.
B. a tetramer of four globin chaions and one heme prosthetic group.
C. a dimer of subunits each with two distinct protein chains (alpha and beta).
D. a dimer of subunits each with two myglobin proteins.
E. an erythrocyte.

C. a dimer of subunits each with two distinct protein chains (alpha and beta).

Section 4-13

Hydrophobic amino acid sequences in myoglobin are responsible for
A. covalent bonding to the heme prosthetic group.
B. the folding of the polypeptide chain.
C. the irreversible binding go oxygen.
D. A and B above.

B. the folding of the polypeptide chain.

Section 4-11

Collagen is a protein made of a triple helix that is stabilized by
A. disulfide bridges.
B. intrachain hydrogen bonds.
C. interchain hydrogen bonds.
D. covalent bonds.

C. interchain hydrogen bonds.

Section 4-12

The main property of myglobin and hemoglobin that makes then an efficient system for oxygen delivery from lungs to muscles is
A. hydrophobicit.
B. different binding affinities for oxygen.
C. movement of the protein shapes.
D. cooperativity.
E. All of the above.

B. different binding affinities for oxygen.

Section 4-13

A hyperbolic binding curve differs from a sigmoidal binding curve in that the hyperbolic curve
A. has a single equilibrium constant for oxygen binding.
B. binds more oxygen after the initial proteins first bind oxygen.
C. shows cooperativity.
D. binds up to four molecules of oxygen.
E. All of the above.

A. has a single equilibrium constant for oxygen binding.

Section 4-13

Cooperative binding of oxygen by hemoglobin
A. is induced by hemoglobin.
B. is a result of different affinities for oxygen by each subunit protein.
C. is induced by oxygenation.
D. is a result of interaction with myoglobin.

C. is induced by oxygenation.

Section 4-14

Which statement is false about the heme group?
A. When oxygen binds to heme, the iron ion is oxidized from Fe2+ to Fe3+.
B. If exposed to air, a free heme group (not associated with hemoglobin) is readily oxidized converting Fe2+ to Fe3+ and can no longer bind oxygen.
C. The heme group is tightly, but non-covalently, held in myoglobin molecule.
D. The chemical structure of the heme groups in myoglobin are identical.

A. When oxygen binds to heme, the iron ion is oxidized from Fe2+ to Fe3+.

Section 4-14

Conditions in the tissues which enhance the delivery of oxygen by hemoglobin are the presence of
A. carbon dioxide.
B. 2,3 BPG
C. protons.
D. All of the above.
E. A and B above.

D. All of the above.

Section 4-14

Antibodies bind antigens at
A. light chains.
B. heavy chains.
C. hypervariable regions.
D. glycoprotein regions.
E. All of the above.

C. hypervariable regions.

Section 4-15

Antibodies are suitable for diagnostic tests because
A. they can be made radioactive.
B. they can be readily purified.
C. they are found in very small quantities.
D. they bind very specifically to antigens.
E. they are found everywhere.

D. they bind very specifically to antigens.

Section 4-15

T/F: All proteins possess primary, secondary, tertiary and quaternary structure.

False.

Section 4-1

T/F: β-strands are a type of secondary structure.

True.

Section 4-1

T/F: Water can easily penetrate and even pass through the interior of a folded protein.

False.

Section 4-2

T/F: NMR has the advantage of using proteins in solutions, but it is difficult to determine the structures of very large proteins with this technique.

True.

Section 4-2

T/F: Proline exists in the cis configuration more frequently than any other amino acid.

True.

Section 4-3

T/F: All amino acids can readily interconvert between the cis and trans forms by rotation about the peptide bond.

False.

Section 4-3

T/F: α-helices easily form on the surface of water-soluble proteins due to the stabilizing effect of hydrogen bonding with water.

False.

Section 4-4

T/F: Proline is the least common amino acid in α-helices due to its inability to fully participate in intrahelical hydrogen bonding.

True.

Section 4-4

T/F: A fold in a protein is a combination of secondary structures that form the core of a protein domain.

True.

Section 4-7

T/F: Homologous proteins can be identified not only by sequencing, but also by comparing similarities in tertiary structure.

True.

Section 4-7

T/F: In oligomeric proteins all the subunits are always identical.

False.

Section 4-8

T/F: The subunits of a multisubunit proteins are always identical.

False.

Section 4-8

T/F: Proteins often consist of multiple subunits so that they may have different functions under different conditions.

True.

Section 4-8

T/F: The amount of energy required to denature a protein is often small.

True.

Section 4-10

T/F: Once denatured, proteins cannot be renatured or restore to the native state.

False.

Section 4-10

T/F: Chaotropic agents denature by disrupting stabilizing hydrophobic interactions, while detergents denature by penetrating and disrupting hydrophilic interactions.

False.

Section 4-10

T/F: Disulfide bond formation between two cysteine residues appropriately located in a polypeptide chain drives protein folding into the proper configuration.

False.

Section 4-10

T/F: The native structures of proteins are more stable than the non-native conformations; they occupy a low-energy well when folded.

True.

Section 4-11

T/F: Using simple computer algorithms, biochemists can easily predict the tertiary structure of a protein form its sequence.

False.

Section 4-11

T/F: The association of hydrophobic side chains in the interior of proteins helps to stabilize helices and pleated sheet domains.

True.

Section 4-11

T/F: Chaperones are proteins which prevent incorrect folding of proteins as well as preventing some proteins from aggregating.

True.

Section 4-11

T/F: Heat shock proteins are those stable at higher temperature.

False.

Section 4-11

T/F: Ascorbic acid is necessary for the formation of hydroxyproline and hydroxylysine residues before they are incorporated into the collagen protein molecule.

False.

Section 4-12

T/F: The porphyrin prosthetic group is held into the interior of globin molecules by covalent bond to specific amino acids residues.

False.

Section 4-13

T/F: The hydrophobic crevice of globin prevents complete electron transfer to the oxygen so that the electron returns to the iron atom when oxygen dissociates.

False.

Section 4-13

T/F: Myoglobin has a gfreater affinity fgor oxygen than hemoglobin.

True.

Section 4-13

T/F: Cooperative binding and allosterism of hemoglobin allow oxygen to be unloaded at low partial pressures of oxygen in the tissues.

True.

Section 4-14