Chemical basics of hydrogen bond and proteins?

Answer 1

The peptide linkage in proteins has an NH group (secondary amine) and a CO group (ketone). The O in the CO can form a hydrogen bond with the H in the NH on a different residue. There are two really good conformations to allow a lot of residues to participate in hydrogen bonding. One is the alpha-helix, where the peptide backbone is in a spiral configuration and the hydrogen bond is between peptide linkages a couple of residues apart: counting the first one as 1 and going along the chain, the one it bonds to would be 4. If the helix continues long enough, 2 would bond to 5, 3 would bond to 6, 4 would bond to 7 in addition to its bond with 1, and so forth. Except for the ends, each residue then gets to participate in two hydrogen bonds so the alpha-helix is a particularly stable structure and occurs in many proteins. The other is the beta-sheet, where the residues may be a considerable distance apart along the chain. The backbone is essentially flat, and another segment runs parallel to it; the overall effect is something like a zipper or a set of railroad tracks where the "ties" are hydrogen bonds. It's possible to then put ANOTHER segment parallel on the other side, so again each residue can participate in two hydrogen bonds; beta-sheets are also a particularly common conformation. In a beta-sheet, the two "edge" segments only can hydrogen bond on one side, but there's a structure seen in several proteins called a beta barrel which is, basically, a beta-sheet rolled into a cylinder (the individual segments are then like staves in a barrel, hence the name).