Pop quiz: alpha helices are stabilized by hydrogen bonds between the carbonyl group of residues i and the amide group of residue
s i+4 of the next helical turn. But the first and last turns don’t have a turn before or after them, respectively, which leaves the usual alpha-helical interactions for several residues unfulfilled. Based on the hydrogen bonding requirements at the beginning of an alpha helix, which of the following amino acids do you predict is very common just before the start of a helix to stabilize the first helical turn? A) Gly
B) Phe
C) Ser
D) Arg
E) Ala
Alpha helix is a secondary structure of proteins, it is made of 3.6 aminoacids residues per turn, this structure is possible thanks to local hydrogen bonding between C=O and N-h groups. The result is a cylindrical structure with a hydrogen-bonded backbone and the outside studded with side chains.
Glycin has an -H in its side chain, this makes it a too flexible molecule, therefore it's unusual to find them in alpha-helical structures because their presence could cause the helix to deform. Large R-groups can also affect this stability, phenylalanine has a bulky aromatic side group, this discards it as a stabilizer. Serine has a hydrogen bond donor or acceptor as a side chain, due to the proximity to the main chain it competes with the main chain to form NH and CO bonds. Alanine is the most common amino acid in alpha-helix structures because it has a short and no charged R group (unlike arginine that even when it's short it has a charged R-group), this makes it flexible enough to keep the structure stabilized.
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