Secondary Structure
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Biochemistry › Secondary Structure
How many amino acids are per turn in an alpha helix secondary structure?
3.6
7.2
10.4
1.8
0.4
Explanation
Polypeptide chains in proteins fold to attain a more compact secondary structure. The two forms of secondary structures are alpha helices and beta sheets. Amino acids that are separated by three or four residues in a polypeptide chain within a secondary alpha helix structure are spatially close and can form hydrogen bonds.
Which of the following amino acids is least likely to be found in the middle of an alpha helix?
Proline
Glutamic acid
Methionine
Serine
Explanation
Proline is bound to two alkyl groups thus giving it a planar configuration, giving the nitrogen only the ability to accept hydrogen bonds not donate them. While this is not a problem at the beginning of an alpha helix this can disturb the bonds if place further down the chain. Thus proline is often referred to as the "alpha helix buster."
Which of the following are true of beta bends in protein structures?
I. Beta bends are secondary protein structures.
II. Beta bends consist of sequences of four amino acids.
III. In beta bends amino acids proline and glycine are common.
IV. Hydrogen and ionic bonds stabilize beta bends.
I, II, III, and IV
I, II, and III
II and III
I and IV
I, II, and IV
Explanation
Beta bends are part of secondary protein structures. They serve as a link between alpha helices and beta sheets. Beta bends are composed of proline and glycine, amino acids that usually are not found in alpha helices.
What is the only level of protein structure that does not involve covalent bonding?
Secondary structure
Primary structure
Tertiary structure
Quaternary structure
Explanation
Covalent bonding is when two nonmetals share electrons in order to form a bond. This type of bonding can be observed in the primary (peptide bonds), tertiary (disulfide bonds), and quaternary (disulfide bonds) levels of protein structure. The secondary structure of proteins only uses hydrogen bonding as the folding force.
Referring to the secondary structure of proteins, proline is necessary for which of the following?
The beta bend needed for parallel beta sheet secondary structures
For the hydrogen bonding, stabilizing antiparallel beta sheet
For hydrogen bonding interactions in alpha helices
For proper polypeptide chain subunit interactions
For the beta bend of antiparallel beta sheets
Explanation
Proline is necessary for the beta bend (along with a glycine). This beta bend is needed for the polypeptide to turn 180 degrees and come back to form a parallel beta sheet. Proline disrupts the hydrogen bonding of alpha helices, and is not needed for antiparallel beta sheets, since there is no beta turn required.
What type of bonds are the "backbone" of secondary protein structure?
Hydrogen bonds
Peptide bonds
Van der Waals interactions
Amide bonds
Amino acid bonds
Explanation
Hydrogen bonds stabilize interactions among the amide and carboxyl groups in the main chain of the polypeptide. These interactions may induce the formation of alpha-helices and/or beta-pleated sheets.
Which of the following statements are true about motifs in a protein structure?
I. The most common motif is beta-alpha-beta, when an alpha helix connects two parallel strands of a beta sheet.
II. Motifs are usually composed of more than one form of secondary structure.
III. Motifs are supersecondary structures.
IV. Motifs are combinations of alpha helices and beta sheets.
I, II, III, and IV
I and II
III only
III and IV
I, II, and III
Explanation
Motifs are supersecondary protein structures. Motifs are combinations of secondary structures such as alpha helices and beta sheets.The beta-alpha-beta and the beta hairpin motifs are some of the most common.
The stabilization of secondary structure in polypeptides is conferred by which of the following?
The amino acid backbones
The R-groups of the amino acids
Disulfide bonds
Metal cations
The phosphate groups
Explanation
Alpha helices and beta sheet, the dominant secondary structural motifs in polypeptides are formed by hydrogen bonds between the carbonyl and amino groups of the amino acid backbone.
With respect to proteins, alpha structures are __________ and beta structures are __________.
helices . . . pleated sheets
parallel . . . antiparallel
left . . . right
primary . . . secondary
L . . . D
Explanation
Alpha helices and beta pleated sheets are two forms of secondary structure. Alpha helices can be either right handed (counterclockwise) or left handed (clockwise). Beta pleated sheets can be either parallel (amino and carbonyl groups do not line up) or anti parallel (amino and carbonyl groups line up).
What is the hydrogen bonding pattern within an alpha helix?
Lone pair on C=O of residue i to hydrogen on N-H of residue i+4.
Lone pair on C=O of residue i to hydrogen on N-H of residue i+3.
Lone pair on C=O of residue i to hydrogen on N-H of residue i+2.
Hydrogen of N-H of residue i to hydrogen on N-H of residue i+3.
Hydrogen of N-H of residue i to hydrogen on N-H of residue i+4.
Explanation
Within an alpha helix, the structure is stabilized by hydrogen bonding between the lone pair on a carbonyl oxygen to a hydrogen of an amino backbone group. Remember, hydrogen bonding must occur between a lone pair of an electronegative atom and a hydrogen connected to an electronegative atom. Two of the answer choices suggest that the hydrogen bonding occurs between two hydrogen atoms, which is not possible.
Finally, the alpha helix contains 3.6 residues per turn. As such, the correct answer is "Lone pair on C=O of residue i to hydrogen on N-H of residue i+4."