Lecture 5: Ramachandran plots & Secondary structures

Question 1

Phi and Psi dihedral angles - torsion angles

Answer 1

Phi - rotation about N-Ca bond
Psi - “ Ca-C
proline is cyclic and has no degrees of freedom about n-Ca = phi torsion angles is fixed

not all values of Phi and
Psi are permitted i.e. 0
as some combinations cannot occur due to steric hindrance between peptide bonds on either side

Question 2

Ramachandran plots

Answer 2

shows the likelihood of a polypeptide backbone conformation with a particular phi/psi torsion angle pair

Question 3

secondary structure of protein

Answer 3

the a helix
5.4A
3.6 residues aa in a helical turn
N terminal slightly +ve and C terminal -ve
1. citrate synthase - non polar buried in interface between te 2 subunits
2. ADH - amphipathic helix on surface of the alcohol dehydrogenase dimer
3. Troponin C - polar helix surrounded by h2o on all sides

3 10 helix and pi helix

beta sheets
alternate strands run in opposite directions
donor and acceptor atoms of H bonds are in a straight line = stronger hydrogen bonds
r groups protrude either side of the sheet

1.antiparallel 
run perpendicular to the sheet 7A
2.parallel
strands run in same direction
3. mixed
some parallel and some anti parallel

Question 4

how extended is the peptide backbone

Answer 4

both phi and psi angles should be as close to 180 degrees as possible