Secondary, tertiary, and quartenary protein structure

Question 1

Different models of proteins

Answer 1

Backbone - no R, simple.
Ribbon - shows 2ndary structure α/β.
Wireframe - full representation, complex.
Space filling - surface and shape.

Question 2

Properties of the peptide bond

Answer 2

Resonance with 40% double bond character and an associated charge on the O and N.
- Limits conformational flexibility
— flat/planar bonds that do not rotate (C-N)
— only rotate at the Cα from N-Cα (Φ) and Cα-N (ψ)

Question 3

Dihedral angles

Answer 3

Preferred angle of Φ/ψ, rotation causes carbonyl and R groups to change position relative to eachother - they are constrained to adopt certain angles to minimise steric clashing.

Question 4

α-helix structure

Answer 4

Hydrogen bonds between every five residues (four in-between), 3.6 residues per turn.
R groups point out and determine surface properties - some may be destabilising (steric clashing, repulsions, etc).

Question 5

Proline issues

Answer 5

Restrained angles can’t take on helix angles (Φ), cannot form i-i+4 hydrogen bond because N group lacks a hydrogen.

Question 6

β-sheet

Answer 6

Extended zigzag with characteristic angles. H-bonds are between different areas of the polypeptide, between strands. R-groups extend from both sides.

Question 7

β-sheets parallel vs anti-parallel

Answer 7

Separated N and C termini, same orientation.
Alternating N and C termini, alternation of orientation.
Anti-parallel has linear hydrogen bonds - greater strength that makes entire sheet more stable.

Question 8

Super-secondary structures

Answer 8

Motifs - small regions with defined sequences with common function (EF hand binds calcium)
Domains - sub-regions of the same. chain that fold and function independently (pyruvate kinase is a molecular machine with many functions)

Question 9

Successful Afinsen experiment

Answer 9

Reduce with MPE, denature with urea.
Renature by dialysis before oxidation.

Question 10

Structure is encoded by _____ sequence

Answer 10

native.

Question 11

Free energy funnel of protein folding

Answer 11

Decrease in both energy and entropy as the protein folds into its native conformation, local minima represent structures where protein may get “stuck”.
There are several native structures.

Question 12

Stabilisation of the N state

Answer 12

Hydrophobic effect, enthakpic interactions (H-bonds, VDWs)

Question 13

Intrinsically disordered proteins (D state are stabilised by:

Answer 13

high entropy of the peptide chain

Question 14

Quaternary structure of Hb A

Answer 14

Complex is a heterotetramer

Question 15

Benefits of quaternary structure

Answer 15

Don’t need to synthesis such a big chain, different subunits can be akin apart ad recycled for new purposes, complex interactions of subunits (Hb) are possible.