4.3 Secondary Structure of Proteins Flashcards
What 2 bonds have free rotation w/in each aa
1) bond btwn alpha carbon and amino nitrogen of that residue
2) bond btwn alpha carbon and carboxyl group of that residue
is the peptide group planar
yes
the angle phi is used to designate which rotation
C-N bonds
the angle psi is used to designate which rotation
C-C bonds
What are some periodic secondary structure
alpha helix and beta pleated sheets
How is the helical conformation very stable?
stabalized by H2 bonds paprallel to the helix axis w/in the backbone of single poptide chain, from N-terminal, C-0 group of each aa residue is H2 bonded to N-H group of the aa four residues away from it in the covalently bonded sequence. helical conformation gives bonds max strength, linear arrangement
How many residues for each turn of the helix
3.6 residues
What can disrupt the alpha helix
proline by creating a bend in the backbone b/c its cyclic structure
Why can’t proline fit into the alpha helix
rotation around the bond btwn the N and aloha carbon is restricted, proline’s amino group cannot participate in intrachain H bonding
What other localized factors can disrupt alpha helix
strong electrostatic repulsion owing to proximity of several charged groups of same sign, cowding (steric repulsion) caused by proximity of bulky side chains
in the alpha helical conformation where do sides lie
all lie outside the helix and crowing can occur if it is bonded to 2 atoms other than hydrogen (VAL, ISO, THR)
How is B-pleated sheet diff than a-helix
peptide backbone in b-sheet is almost completely extended. H2 bonds are perpendicular ot directn of protein chain, not parallel like alpha helix
when are beta sheets parallel
if the peptide chains run in smae direction (if they are aligned in termed of their N and C terminal end)
When are antiparallel pleated sheets formed
when alternating chains run in opposite directions
what gives rise to the name pleated sheets
H2 bonding btwn peptide chains in beta-pleated sheets give rise to a repeated zigzag structure
