Question 1

Ramachandran determined the ʺallowedʺ values of the phi and psi angles primarily by considering . A) pK_avalues of the amino acids B) the hydropathy of amino acids C) steric hindrance D) hydrogen bonding effects

Accepted Answer

Ramachandran determined the allowed values of phi and psi angles primarily by considering steric hindrance, which refers to the physical constraints that prevent certain angles due to the size and shape of atoms in the peptide backbone.

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

Accepted Answer

NMR (Nuclear Magnetic Resonance) spectroscopy is a powerful technique used to determine the tertiary structure of proteins in solution by providing detailed information about the spatial arrangement of atoms within the protein.

Question 3

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

Accepted Answer

α-helices are a type of secondary structure in proteins.

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.

Accepted Answer

The trans configuration in peptide bonds minimizes steric hindrance of R groups, which can interfere with the proper folding of proteins. Additionally, the cis configuration can create steric clashes with adjacent atoms, making it less favorable. Therefore, nearly all peptide bonds are in the trans configuration.

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

Accepted Answer

Peptide bonds have a partial double bond character between the carbon and nitrogen due to resonance, making the C-N bond shorter than typical C-N single bonds. Additionally, the C=O bond in the peptide linkage is slightly longer than a typical C=O double bond due to resonance delocalization.

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

Accepted Answer

Fibrous proteins, such as collagen and keratin, have elongated, filamentous shapes and are well suited for providing structural support. Enzymes (B) catalyze biochemical reactions, globular proteins (C) have a more compact, globular shape and have a wide range of functions, and β-strand (D) is a secondary structure that is found in both globular and fibrous proteins.

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_αonly C) N-C_α, C_α-C and C-N bonds D) N-C_αand C_α-C bonds only

Accepted Answer

The conformation of a polypeptide backbone is described by the rotation angles around the N-Cα (phi, φ) and Cα-C (psi, ψ) bonds. The peptide bond (C-N) is planar and does not rotate.

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

Accepted Answer

NMR (Nuclear Magnetic Resonance) is a technique used to analyze the macromolecular structure of proteins in solution. It is a highly sensitive spectroscopic technique that can provide detailed information about the structure, dynamics, and interactions of proteins. NMR is particularly useful for studying intrinsically disordered proteins and protein complexes in solution. Other techniques listed, such as X-ray crystallography, SDS-PAGE, and affinity chromatography, are useful for protein analysis but are not specifically designed for analyzing macromolecular structure in solution.

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

Accepted Answer

Dorothy Crowfoot Hodgkin received the Nobel Prize in Chemistry in 1964 for her work on the structure of vitamin B12. She also solved the structure of penicillin and developed techniques for studying large proteins.

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.

Accepted Answer

The peptide bond is actually shorter than a typical carbon-nitrogen bond due to partial double-bond character.

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

Accepted Answer

X-ray crystallography is a technique used to determine the three-dimensional structure of proteins by analyzing the diffraction patterns of X-rays passing through a crystallized sample of the protein.

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.

Accepted Answer

Oligomeric proteins involve the association of two or more polypeptide chains.

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.

Accepted Answer

The bond between the carbonyl carbon and nitrogen (called the peptide bond) has restricted rotation due to the partial double-bond character, which creates a planar geometry. Other bonds in the backbone are free to rotate depending only on steric hindrance or the presence of proline residues. The bond between the nitrogen and alpha carbon in proline residues also has restricted rotation due to the formation of a cyclic structure.

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.

Accepted Answer

Computers are used to calculate the atomic positions from X-ray diffraction patterns, which are used to determine the three-dimensional structure of proteins.

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.

Accepted Answer

The fact that the structures determined by X-ray crystallography are similar to those determined by NMR, which is a technique that can be used to study proteins in solution, suggests that the X-ray structures represent the structures in solution. The solubility of the protein crystals (B) and the requirement for proteins to align in a regular pattern to form a crystal (C) are not direct evidence that the crystal structures represent the solution structures. Option D is incorrect as proteins can have multiple conformations depending on their environment and interactions.

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

Accepted Answer

The native conformation refers to the three-dimensional shape that a protein adopts under physiological conditions. This shape is typically the most stable and functional form for the protein to perform its biological functions. Option A is incorrect as minimal configuration is not a specific term used in protein structure. Option C refers to the linear sequence of amino acids in a protein, which is not the same as the final three-dimensional shape. Option D refers to a specific type of stereoisomerism, which is not directly related to protein structure.

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

Accepted Answer

Repeating units of N-Cα-C form the backbone of a protein.

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

Accepted Answer

A Ramachandran plot displays the allowed angles of phi (φ) and psi (ψ) for a polypeptide backbone, which are the dihedral angles that describe the conformation of the backbone in protein structures.

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

Accepted Answer

Eclipsed ethane and staggered ethane are different conformations of the same molecule, ethane, differing by rotation around the carbon-carbon bond.

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

Accepted Answer

A change in conformation of a molecule involves rotation about bonds only, without breaking or forming new covalent bonds or inversion about a center of symmetry.

Quiz 4: Proteins: Three-Dimensional Structure and Function

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

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

To what level of structure do α-helices belong?

Nearly all peptide bonds are in the trans configuration because

In peptide bonds, the bonds between

Structural proteins that typically assemble into large cables or threads to provide mechanical support to cells or organisms are classified as proteins.

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

is a technique used to analyze the macromolecular structure of proteins in solution.

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.

Which statement is not true about the peptide bond?

Which technique is commonly used to determine the three-dimensional conformation of a protein?

What does it mean to say a protein is oligomeric?

What is true about the rotation about bonds in a protein backbone?

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

Which is evidence that structures for proteins determined by X-ray crystallography represent the structures in solution?

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

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

What feature does a Ramachandran plot display?

Which pair represents different conformations?

A change from one conformation of a molecule to another involves .