Protein Structure

Question 1

What are the main features of alpha helices and how does the right-handed form differ to the left?

Answer 1

Residues adopt successive phi and psi of -60 and -50.
13 atoms per H bond loop. H bonds form between CO of one residue and NH of n+4.
Left handed have phi and psi of -57 and -47 BUT place side chains next to CO which is bulkier than NH.

Question 2

How are alpha helices polar?

Answer 2

Amides point down so amino end is positive
Carbonyls point up so carboxyl end is negative
First and last NH and CO groups are not H bonded so polar surfaces (all H bonds same direction).

Question 3

Why are beta sheets twisted?

Answer 3

L amino acids form sheet.
Sheets introduce unfavourable distortions in INTERCHAIN H BONDS. Twist conserves these but compromises optimisation of the conformational energy of PPC.

Question 4

How do parallel and antiparallel beta sheets differ?

Answer 4

Parallel = AAs in strands run in same biochemical direction
Antiparallel = H-bonds parallel - slightly more stable due to enhanced VDWs.
(but both satisfy all possible main chain H-bonds).

Question 5

Outline the structure of a Rossman fold

Answer 5

Up to 7 parallel beta strands
1st 2 strands are connected by alpha helices
Structures between additional strands vary.