Question 1

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.

Accepted Answer

Proline lacks a hydrogen atom on its amide nitrogen, which is necessary for the formation of hydrogen bonds that stabilize the α-helix structure. This makes it a helix breaker.

Question 2

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.

Accepted Answer

α-helices rarely contain proline residues because proline has a rigid structure that prevents it from adopting the necessary geometry for helix formation.

Question 3

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.

Accepted Answer

The answer of What would you expect about the formation...

Question 4

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

Accepted Answer

Ramachandran determined the allowed values of the phi and psi angles by considering steric hindrance, which dictates the physical feasibility of certain conformations. The pKa values of the amino acids, the hydropathy of amino acids, and hydrogen bonding effects are not directly related to the allowed values of phi and psi angles.

Question 5

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 rotation about the bond between the carbonyl carbon and nitrogen is restricted due to partial double bond character, while other bonds in the backbone can rotate based on steric hindrance or the presence of proline residues.

Question 6

Which represents the backbone 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.

Accepted Answer

The backbone of a protein consists of a repeating unit of nitrogen (N) attached to the alpha carbon (Cα) which is then attached to the carbonyl carbon (C). The amino acid side chain (R) is attached to the Cα and extends outward from the backbone. Therefore, choice C, which represents the repeating units of N-Cα-C, is the best choice.

Question 7

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

Accepted Answer

The distance along a helix axis for one complete turn is called the pitch. The axial distance refers to the distance between two consecutive turns along the helix axis, while the rise is the vertical distance between two consecutive turns. Screw length is not commonly used to describe a helix.

Question 8

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

Accepted Answer

The length along the helix axis for a segment of an ideal α-helix can be calculated by multiplying the rise per amino acid (0.15 nm) by the number of amino acids (30). Thus, 0.15 nm/amino acid * 30 amino acids = 4.5 nm.

Question 9

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.

Accepted Answer

A helical wheel is a diagram that can be used to show the amphipathic nature of a helix, where one side of the helix is hydrophobic and the other is hydrophilic. This is useful for understanding the behavior and interactions of proteins with helical structures. It does not show the pitch of a helix or the characteristics of other types of protein structures.

Question 10

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.

Accepted Answer

A Ramachandran plot displays the allowed angles of phi and psi for a polypeptide backbone, providing information about the local conformation of amino acid residues.

Question 11

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.

Accepted Answer

Linus Pauling is renowned for determining the α-helix structure in proteins like keratin, which was a groundbreaking discovery in the field of molecular biology and biochemistry.

Question 12

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.

Accepted Answer

The side chains of residues in an α-helix extend radially outward from the helix axis, allowing for maximal van der Waals interactions to occur between neighboring amino acids.

Question 13

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

Accepted Answer

The conformation of the backbone of a polypeptide is described by the angles of rotation about the N-Cα (phi, φ) and Cα-C (psi, ψ) bonds. The peptide bond itself is planar and does not rotate due to its partial double bond character.

Question 14

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

Accepted Answer

In an α-helix, the carbonyl group of an amino acid residue forms a hydrogen bond with the amide group of the amino acid residue four positions ahead of it. This pattern is represented by option II in the given structure, where the hydrogen bonds are correctly aligned in the same diagonal direction. Options I, III, and IV have incorrect hydrogen-bonding patterns.

Question 15

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

Accepted Answer

The trans configuration of peptide groups is favored in cells because it minimizes steric hindrance of R groups, allowing the polypeptide chain to fold into a more compact structure. This configuration is also favored during protein synthesis, where the amino acid residues are linked together to form a polypeptide chain. Therefore, choice B and C are both correct. Choice A is incorrect because the cis configuration is also available, but less favored due to its higher energy state. Therefore, the best choice is D, as it combines both B and C as correct explanations.

Question 16

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.

Accepted Answer

Leucine zippers are often found in DNA binding proteins, where they form pairs of helices that wrap around each other. The leucine residues in these helices create an amphipathic structure, which helps to stabilize the interaction between the two helices. Therefore, all three options are correct.

Question 17

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

Accepted Answer

Prolyl cis/trans isomerase enzymes are involved in several human hereditary diseases, such as cyclophilin A in HIV infection and FK506-binding protein in immunosuppression. These enzymes are also found in Arabidopsis, where they regulate flowering by mediating responses to environmental stimuli. Peptidyl cis isomerases and isomerase hydrolases are not specifically implicated in human hereditary diseases or flowering regulation. Proline isomerase is an enzyme that converts the amino acid proline from one form to another and has various functions in different organisms, but is not specifically linked to human hereditary diseases or flowering regulation.

Question 18

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

Accepted Answer

Glycine is the smallest amino acid and lacks a side chain. Its flexibility and ability to rotate freely around the alpha-carbon make it ideal for breaking the repetitive structure of alpha helices, especially at the ends where it can cause a kink.

Question 19

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

Accepted Answer

The formula for calculating the number of turns in an α-helix is:
Number of turns = (length of the helix) / (height of one turn)
Length of the helix = number of amino acids × pitch
So, for this α-helix:
Length of the helix = 15 amino acids × 0.54 nm/turn = 8.1 nm
Height of one turn = rise per amino acid × number of amino acids per turn = 0.15 nm × 3.6 amino acids = 0.54 nm/turn
Number of turns = 8.1 nm / 0.54 nm/turn = 15 turns
However, we need to give the answer in terms of complete turns. As one complete turn corresponds to 3.6 amino acids, the total number of complete turns in this α-helix will be:
Number of complete turns = 15 amino acids / 3.6 amino acids/turn = 4 turns. 
Therefore, the correct answer is B) 4.

Question 20

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.

Accepted Answer

The side chains of amino acids in β-sheets alternate in their orientation, with some pointing up and some pointing down from the plane of the sheet. This creates a distinctive pattern of side chain directionality that is characteristic of β-sheets.

Quiz 4: Proteins: Three-Dimensional Structure and Function

Proline is not often found in α-helices of proteins because it

Which statement is NOT true about an α-helix?

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?

Ramachandran determined the "allowed" values of the phi and psi angles primarily by considering ________.

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

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

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

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 helical wheel can be used to show

What feature does a Ramachandran plot display?

Which was a major scientific accomplishment by Linus Pauling?

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

The conformation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s) ?

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

The trans configuration of most peptide groups is adopted in cells because it

Proteins with alpha helix regions called leucine zippers are

Enzymes implicated in several human hereditary diseases are similar to ones that regulate flowering in Arabidopsis.These enzymes are

The amino acid that destabilizes alpha-helical structures and is usually found at the ends of alpha helices is

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?

Which is not true about β-sheets?