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). 

Glycine and proline are the two amino acids that are found in beta turns. These 180 degree turns are composed of four total amino acids. 

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

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.

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.

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. 

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.