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
psi vs phi angles and are both what (2)
phi - the bond between alpha carbon and amide (N)
psi- the bond between the alpha carbon and carbonyl (C=O)
both 180 and contribute to secondary structure
tertiary protein structure
= 3D shape of polypeptide (1)
- protein shape = function
- stabilized by weak interactions!
•hydrophobic interactions
•H bonds
•ionic interactions
•didulfide bridges
what are structural motifs (folds)
arrangement of 2 or more secondary structure elements + connections!!!
what are domains
formed by combination of different motifs
- have specific functions
- 3 degree structure
fibrous proteins
- polypeptide chains side by side
- insoluble
- made from one type of secondary structure
- fulfill structural roles
globular proteins
- water soluble
- made of one or different types of secondary structures
describe alpha keratin and its structure
a keratin
- found in hair, fingernails, claws, horns etc
made up of a dimer of RIGHT handed alpha helices
- primary structure has nonpolar residues
• rich in Cys residues forming disulfide bonds
what are disulfide bonds and why are they important in protein structure
bonds that form between two cysteine residues
- to stabilize tertiary structure
which proteins fibrous or globular are more abundant (what else is this protein also good at)
globular
- more diverse functions than fibrous
ex. enzymes
compare a-helices vs B sheets in structure and size
a-helices = more compact so produce a shorter structure
human serum albumin
585 AA
myoglobin
functions as oxygen storage protein in muscles
-nonpolar inside
-polar outside
quaternary protein structure
- multiple proteins
(2 or more polypeptides held together)
ex. hemoglobin
supramolecular structures
consist of several types of proteins
ex dna around histone proteins
protein folding (conformation) is determined by the _________
amino acid sequence
(want to hide hydrophobic AAs inside)
ramachandran plot
plot of psi (Poseidon) and phi (eye) angles
