L3-BCMB2002_secondary-Gooley Flashcards
(26 cards)
Positive torsion angle is when C-D ____ A-B, using a ____ rotation
Eclipse, counter-clockwise
With omega angles, there is __ ________ around the peptide bond (_____)
no rotation, rigid
Omega
CC-NH
Phi
CN-CC
Psi
NC-CN
Why are the phi psi pairs of angles not evenly distributed over the plot?
Steric clashes of the atoms of the L-amino acids
To avoid a clash b/n the side chain of a residue and the carbonyl oxygen of the preceding group, phi is most frequently _____
Negative
RAMACHANDRAN PLOT - forbidden regions are due to _____ ____
steric hindrances
RAMACHANDRAN PLOT - Most favored regions are ___ and ___
Alpha and beta
Regular secondary structures:
Repeating phi psi angles for sequential residues
Irregular secondary structures:
Non-repeating phi psi angles for sequential residues which has markedly different angles (Beta - turn)
Alpha-helices is ____ handed (in both directions) where side chains are pointed ___ from helix
Right, away
Alpha-helices is also called 3.6^13 as __
there are 3.6 residues in a turn and 13 atoms in a H bond ring
Alpha helices: All NH and C=O within the helix (except ___) form favourable ____ ___ bonds
Those at the ends, internal hydrogen
Alpha helices: Carbonyls are ____ aligned to NH: a small net dipole movement
oppositely
Alpha helices are often ____
Amphipathic (has both polar and apolar side)
Alpha helices: phi psi angles are
-57, -47
B-Sheet consists of ____ B-strands
2 or more
B-sheets: phi psi angles are:
-130, +130
B-sheets: H bonds of ____ strands are more stable
Antiparallel
B-sheets: outer NH and C=O of a sheet are ___ ___ bonded
Not hydrogen
B-sheets: side chains are pointed __ or __ with respect to the sheet
up, down
B-turns are abdundant, mostly __ ______, consisted of _ residues, and _____ backbone - reversing mainchain
4, on surface, redirect
Residues i+1 and i+2 have __ phi psi angles
different
