What in the primary structure of a protein dictates whether
a structure will form alpha-helix or beta-sheet for secondary
structure?
The side groups can influence how stable a particular
secondary structure might be. For instance, if there are
two glutamic acids 4 residues apart in an alpha helix, they
would be placed near each other, one over the other, but
they would repel each other because of their like electrical
charges. In a beta sheet, on the other hand, they would not
be near each other. So situations like this influence just
what form of secondary structure is preferred for a given
region.
Does the formation of secondary structures have to do with the polarity of its
side chains? Why do most proteins have extensive regions folded into
alpha-helices and beta-pleated sheets?
No. The secondary structures tend to form because of interaction between
backbone atoms only. However, side chain interaction could either add to this
stabilty or detract from it so as to prevent its formation. For
example suppose you had a stretch of polypeptide with glutamates and aspartates
at every 4th or 5th position. An alpha helix structure for this stretch would
position these negatively charged groups above and below each
other, close to one another. One could imagine that the electrical repulsion
between these like charges would disallow the formation of such an alpha-helix.
One could make an analogous argument about a beta sheet.
In lecture, you've said that "side chain interactions play a major role
in allowing or disallowing such secondary structures to form." What sort of
side chain reactions prevent beta-pleated sheets from forming?
Interaction between side chain can pull the polypeptide chain out of a
secondary structure. Imagine a horizontal beta pleated sheet with a glutamic
acid side chain sticking up on one side of the sheet, and now another
part of the polypeptide chain oriented above it with an arginine held above the
sheet . If the arginine is far enough above it, it could attract the gluatmate
carboxyl, thus pulling that residue up out of the sheet. The
whole sheet could be weakened by this distortion, and the structure could be
resolved by some alternative more stable arrangement, notinvovling secondary
structure.
In reference to beta pleated sheets--what is meant by parallel or
anti-parallel?
Parallel refers to two polypeptide chains that are both lined up in the same
direction, e.g., considered as sections, N terminal on the left and C-terminal
on the right for both. Antiparallel is the opposite case, where one strand can be
written N to C and its neighbot C to N, and so on for more strands to make a
sheet. Beta sheets can form either way, but the antiparallel case is more common, as
the polypetide just keeps b doubling back on itself to form the sheet. See the
ribbon models of protein 3-D structure in your texts.