11. 3D structure of proteins Flashcards
primary structure of proteins
= linear order of AAs from N to C terminus
- linked by peptide bonds
- defines protein structure (how it’s folded)
- determines function
describe peptide bonds
rigid and planar
- rotation is NOT allowed
- trans/cis configuration (trans more stable)
EXCEPT proline (cis & trans equal stability in B turns)
secondary protein structure and 4 types
= folding of protein
- determined by hydrogen bonds
- a helix
- B sheet
- turns
- random coil
helix characteristics
right vs left handed ( whichever direction is coiling to determines)
p = n • h
alpha (a) helix (4)
- 3.6 residues (n=3.6)
- (h=1.5 A)
- (p= 5.4 A)
- right handed !
- R group on outside
C=O —— H-N hydrogen bonds are nearly ________ to helical axis
nearly parallel
primary structure of protein affects _____ of secondary structure
affects stability
residues vs amino acids
residue = amino acids linked by peptide bonds (lost other parts)
AA = has amino group, carboxyl group and side chain (R)
which residues are helix formers vs helix breakers
FORMERS
- Ala, Val, Leu
BREAKER
- Gly
- Pro (just disrupts by bending)
B conformation (pleated B-sheets)
= zig zag structure
- n=2
- rotated 180 relative to ones beside
- non bulky r-chains dominate (Gly,Ala)
in B-sheet where are hydrogen bonds
in between adjacent chains
parallel vs antiparallel B sheets
parallel
- H bonded strands run in SAME direction
- resulting in bent H bonds
antiparallel
- H bonded strands run in opposite directions
- resulting in linear H bonds (stronger)
B turns
allows peptide chain to reverse directions
- 180 turn accomplished over 4 AAs!
•carbonyl C (h bonded) to amide
which residues are prevalent in B turns
Type I - Pro in position 2
Type II - Gly in position 3
rotation around bonds connected to ______ is permitted (backbone)
a (alpha) carbon
