Protein folding Flashcards
A polar group buried in the protein must form what?
A hydrogen bond
What are the delta charges on the donor and the acceptor
+Delta on the donor, which is H
-Delta on the acceptor, which is O
The atoms of a hydrogen bond can approach much closer than a VDW interaction, why?
There is covalent character of the hydrogen bond
The use of hydrogen bonds allows for what?
Increases the compactness and stability of a protein
What are the 3 ways in which hydrogen bonds can form?
a) between backbones so between peptide bonds
b) between backbone and a side chain so between peptide bond and amino acid side chain
c) between side chains
How is close packing of the polypeptide backbone achieved?
achieved by serveral hydrogen bonding patterns
what are the hydrogen bonding patterns for
a) beta sheets
b) alpha helixes
c) reverse turns
a) NH residue i to C=O residue j
b) NH residue i to C=O residue i-4
c) NH residue i+3 to C=O residue i
Alpha helix
a) how many residues per turn?
b) axial per turn
c) where do the side chains project
d) right or left handed
e) All NH and C=O within helix (Except 4 at each end) form what?
f) often what type of -phatic? and what does this allow for?
a) 3.6 residues per turn
b) 5.4 axial per turn
c) side chains project outwards from axis
d) right
e) form favourable internal hydrogen bonds
f) Amphipathic. Allows for burial of hydrophobic side
Beta sheet
a) side chains project from where?
b) Consists of two or more what?
c) The strands can be what?
d) which gives more stability? and how?
e) describe side chains in a B barrel
f) What is the thing called that reverses the direction of the main chain
a) from above and below the sheet
b) B strands
c) parallel or anti
d) anti gives more stabillity as the hydrogen bonds between NH and C=O on other strand allows for a linear formation
e) hydrophobic side chains are packed into the core of the barrel while hydrophilic project outwards
f) beta turns
Beta turns
a) where is it most abundant
b) consist of how many residues?
c) difference between residue i+1 and i+2
d) Where is the hydrogen bond and what does this do?
e) What amino acid is often in position i+1
f) Type 2 turns often have what amino acid in what position? why?
g) what is the difference between type 1 and type 2?
a) on the surface as it redirects the backbone
b) 4
c) different phi and psi angles
d) NH of i+3 and C=O of i, stabilises the turn
e) proline
f) glycine in position i+2 due to less steric hindrance
g) direction of the i+1 carbonyl
