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
how are hydrogen bonds diff from ones in alpha helix
H2 bonds are perpendicular to direction of protein chain not parallel as in alpha helix
How are super secondary structures in proteins form
combination of alpha and beta strands combined in many ways
Describe the beta alpha beta unit
two parallel strands of beta sheets are connected by a stretch of alpha helix. Less stable than anti parallel
Describe the alpha alpha (helix-turn-helix) unit
consists of 2 antiparallel alpha helices
Where is energetically favorable contacts in helix-turn-helix
energetically favourable contacts exists btwn the side chains in the 2 stretchs of helix
What is a beta meander
an antiparallel sheet formed by a series of tight reverse turns connecting stretches of the polypeptide chain
what is a greek key
antiparallel sheet formed when polypeptide chain double nack on itself in a pattern similar to a decorative design from classical period
What is a motif
a repetitive supersecondary structure
what is collagen
a component of bone and connective tissue, most abundant in vetebrates. organized in water-insoluble fibers
What is a collagen fiber consist of
3 polypeptide chains wrapped around each other in a ropelike twist or triple helix
describe the 3 chains of collagen
each of 3 chains had a repeating sequence of 3 aa residues X-PRO-GLY or X-HYP-GLY (hyp-hydroxyproline)
What is hair pin super secondary structure
Anti parallel beta sheets
What are tim barrels
Beta barrels comprised of alternating beta alpha beta units. Seen in private kinase
