Deck 4: Proteins: Three-Dimensional Structure and Function

Question 1

Ramachandran determined the ʺallowedʺ values of the phi and psi angles primarily by considering .

A) pK_a values of the amino acids
B) the hydropathy of amino acids
C) steric hindrance
D) hydrogen bonding effects

Answer 1

steric hindrance

Question 2

NMR is often used for the determination of the of proteins.

A) molecular weight
B) isoelectric point
C) tertiary structure
D) pK_a

Answer 2

tertiary structure

Question 3

To what level of structure do α-helices belong?

A) primary
B) secondary
C) tertiary
D) quaternary

Answer 3

secondary

Question 4

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.

Question 5

In peptide bonds, the bonds between

A) C and N are shorter than typical C-N bonds.
B) C and N are longer than 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

Question 6

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

Question 7

The conformation of the backbone of a polypeptide is described completely by the angles) of rotation about which bonds)?

A) the peptide bond only
B) N-C_α only
C) N-C_α, C_α-C and C-N bonds
D) N-C_α and C_α-C bonds only

Question 8

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

Question 9

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

Question 10

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.

Question 11

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

Question 12

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 protein has multiple α-helices.

Question 13

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.

Question 14

Computers are used to advance the understanding of three dimensional protein structure by

A) determining the specific sequence of amino acids.
B) finding repeating subunit patterns.
C) calculating atomic positions from X-ray diffraction patterns.
D) collimating X-ray beams.

Question 15

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 one conformation is ever possible for a protein so it is irrelevant whether the protein is in a crystal or in solution.

Question 16

The is the single shape a protein adopts under physiological conditions.

A) minimal configuration
B) native conformation
C) primary structure
D) most stable enantiomer

Question 17

Which represents the backbone of a protein? Note: R = amino acid side chain N = nitrogen
C_α = alpha carbon C = carbonyl carbon

A) R₁R₂R₃R₄R₅
B) repeating units of N-C
C) repeating units of N-C_α-C
D) repeating units of C_α-C

Question 18

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 pK_a

Question 19

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

Question 20

A change from one 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

Question 21

The distance along a helix axis for one complete turn is called the .

A) axial distance
B) rise
C) screw length
D) pitch

Question 22

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.

Question 23

Which is true about the side chains of residues in an α-helix?

A) They extend above or below the pleats.
B) They extend radially outward from the helix axis.
C) They point toward the center of the helix.
D) They hydrogen bond extensively with each other.

Question 24

Which structure below indicates the proper hydrogen-bonding pattern between amino acids in an α-helix? Dashed lines represent the hydrogen bonds.)

A) I
B) II
C) III
D) IV

Question 25

Proline is not often found in a-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.

Question 26

How many monomers are there in an oligomeric protein designated αβ₂γ₂?

A) 2
B) 3
C) 4
D) 5
E) not given

Question 27

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

Question 28

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

Question 29

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

Question 30

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 an oligomer or not.
D) Increased efficiency by the sharing of the same subunit with the same function among different proteins.

Question 31

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

Question 32

An ideal α-helix has a pitch of 0.54 nm and a 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

Question 33

Which was a major scientific accomplishment by Linus Pauling?

A) Determined the 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.

Question 34

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

Question 35

Which is not an example of an oligomeric protein?

A) cytochrome c
B) potassium channel protein
C) MS2 capsid protein
D) hemoglogin
E) bacterial photosynthetic reaction center

Question 36

A helical wheel can be used to show

A) the pitch of a helix structure.
B) the amphipathic nature of a helix.
C) DNA binding.
D) pleated sheets.

Question 37

A b sandwich forms when

A) two hydrophobic sides of b-sheets interact.
B) two hydrophilic sides of b-sheets interact.
C) an a-helix separates two b-sheets.
D) two amphipathic a-helices interact.

Question 38

Which is not true about β-sheets?

A) The side-chains of all 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 for those in the α-helix.
D) In antiparallel sheets the hydrogen bonds between adjacent strands are nearly perpendicular to the backbones of the strands.

Question 39

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.

Question 40

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

Question 41

Proteins segments which fold first can promote the folding of other sections 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.

Question 42

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

Question 43

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

Question 44

Chaperones are proteins which

A) renature and denatured proteins.
B) help cells repair damage due to heat shock.
C) assist protein self assembly.
D) use ATP to fold proteins.
E) All of the above

Question 45

Hemoglobin is

A) a tetramer of 4 myoglobin proteins.
B) a tetramer of four globin chains 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 myoglobin proteins.
E) an erythrocyte.

Question 46

Antibodies bind antigens at

A) light chains.
B) heavy chains.
C) hypervariable regions.
D) glycoprotein regions.
E) All of the above

Question 47

Proteins with high T_m 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

Question 48

All proteins possess primary, secondary, tertiary and quaternary structure.

Question 49

The main property of myoglobin and hemoglobin that makes them an efficient system for oxygen delivery from lungs to muscles is

A) hydrophobicity.
B) different binding affinities for oxygen.
C) movement of the protein shapes.
D) cooperativity.
E) All of the above

Question 50

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.

Question 51

In addition to self assembly, 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

Question 52

Protein folding can be followed 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

Question 53

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 and hemoglobin are identical.

Question 54

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 irreversibly inactivated and must be targeted by the cell for degradation.

Question 55

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

Question 56

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

Question 57

The T_m of a protein is temperature at which it

A) is completely denatured.
B) liquifies.
C) is half denatured.
D) resists denaturation.

Question 58

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.

Question 59

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) Chaotropic agents cannot denature the native conformation.
E) All of the above

Question 60

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 of oxygen.
D) A and B above

Question 61

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

Question 62

In oligomeric proteins all the subunits are always identical.

Question 63

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

Question 64

Using simple computer algorithms biochemists can easily predict the tertiary structure of a protein from its sequence.

Question 65

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

Question 66

The subunits of a multisubunit proteins are always identical.

Question 67

Chaotropic agents denature by disrupting stabilizing hydrophobic interactions, while detergents denature by penetrating and disrupting hydrophilic interactions.

Question 68

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

Question 69

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

Question 70

Water can easily penetrate and even pass through the interior of a folded protein.

Question 71

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

Question 72

Heat shock proteins are those stable at higher temperatures.

Question 73

β-strands are a type of secondary structure.

Question 74

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

Question 75

Once denatured, proteins cannot be renatured or restored to the native state.

Question 76

The amount of energy required to denature a protein is often small.

Question 77

Proline exists in the cis configuration more frequently than any other amino acid.

Question 78

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

Question 79

Chaperones are proteins which prevent incorrect folding of proteins as well as preventing some proteins from aggregating.

Question 80

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