Secondary Structure - Biochemistry

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.

In an antiparallel beta sheet, the hydrogen bonding angle is 180 degrees and optimal; this is the most stable angle. In parallel sheets, it is a less stable 150 degrees. Whether a sheet is parallel or antiparallel does not tell us anything about what amino acids it is composed of, so each of the other answers is incorrect.

In an alpha helix, hydrogen bonding occurs every four amino acids, starting from the 1st binding to the 4th in the sequence; the 2nd amino acid binds to the 6th, the 3rd to the 7th, and so on.

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.

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.

Secondary structures in proteins consist of alpha helices and beta sheets. Proline has an additional amino group that interferes with the formation of an alpha helix. Amino acids such as lysine and arginine can form ionic bonds due to their charges. Other amino acids, like isoleucine, tryptophan, or valine disrupt the helix due to big side chains. However, amongst the amino acid mentioned in the answers, proline has the most disruptive effect.

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.

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.

A beta sheet (a secondary structure) has parallel strands when the N-terminal and C-terminal are in the same orientation for all the strands. When the orientation alternates between beta strands they are considered to be anti-parallel. Hydrogen bonds stabilize the structure between polypeptide strands.

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.

Alpha-helices are formed by hydrogen bonding involving an alpha carbon-bound amine group's hydrogen and the carbonyl group attached to the amino acid four amino acids upstream.

A protein motif (aka supersecondary structure) is a defined arrangement of secondary structures within a protein. It is commonly occurring enough to have an identified structure. An example would be the beta-alpha-beta loop. While the arrangement is made up of secondary structure, the overall motif itself can be considered supersecondary or possibly even tertiary, though its components are secondary structures. Motif's do not necessarily have a defined function across different proteins. Protein domains on the other hand, do.

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."

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."

The side chains of the amino acid residues within an alpha helix point "out" and "back" relative to the turns of the helix. Despite differing polarity's of side chains, this pattern holds true. This first reason this pattern is important is in order to minimize steric hindrance. Finally, this pattern allows for a maximization of hydrogen bonding between the side chains and the backbone amides.

Large side chains have increased Van der Waals interactions repelling each other, which is unfavorable. To minimize this steric clash, these residues must be kept far apart, and "They are kept far apart from each other." is the correct answer.

Large residues being near each other in a beta sheet would be very unfavorable. If these large residues alternated in a "every other" manner, they would still be relatively close to each other. Finally, if these residues were kept parallel to each other, they would be on different. But these chains would still be in close proximity to each other, and unfavorable interactions would occur.

The two most common secondary structures within a protein are alpha helixes, and beta-sheets. However, remember that there are multiple types of alpha helixes and beta-sheets, and all have slightly different properties. Overall, alpha helixes and beta sheets are in approximately equal amounts.

Anything not regarded as an alpha helix or a beta sheet is typically referred to as a "irregular structure". This can include random coil, coil structures, Beta-hairpin turns, in addition to a seemingly infinite number of unnamed structures. Overall, there is as much irregular structure as beta sheet and alpha helix within a protein, and the correct answer is 33% for all three.

All the answer choices are different examples of protein supersecondary structures. Beta barrels are commonly found in transmembrane porin proteins.

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).