lecture 3 - proteins

Question 1

Why is determining the L and D enantiomers important?

Answer 1

L and D isomers of Thalidomide results in terrible consequences. For example L is teratogenic (causes abnormal physical development) whereas D is an effective sedative

Question 2

The Cahn - Ingold - Prelog rules

Answer 2

SH , OH, NH2, COOH, CHO, CH2OH … Determined by the atom with the larger molecular weight i.e sulphur has a larger molecular weight than O.

Question 3

What isomers do amino acids tend to be? R or S?

Answer 3

All are S except from cysteine which is R due to C-S side chain

Question 4

The CORN rule for determining the D/L isomers of amino acids.

Answer 4

CO= COoh 
R = R group 
N = Nh2 . 

H pointing away.

Question 5

Features of a dipeptide bond

Answer 5

• Peptide bond between a carboxyl and an amino group
• ## By convention amino-terminal is numbered as reside 1 ( sequence written from amino(left) to carboxyl (right)

Question 6

Can the peptide bond/ amide plane rotate?

Answer 6

No

Question 7

Which parts of the polypeptide chain can rotate?

Answer 7

Between the C alpha and N.

Between the C alpha and the CO

Question 8

Definition of a Ramachandran plot

Answer 8

A Ramachandran plot is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure.

Question 9

What is an Alpha helix?

Answer 9

Polypeptide chain adopts a helical structure in 3D

Question 10

what is a Beta pleated sheet?

Answer 10

Polypeptide chain adopts a pleated structure and interacts with adjacent strands

Question 11

How many amino acids residues are there in one turn?

Answer 11

3.6 ( 13 main chain atoms)

Question 12

why is there a Dipole moment t?

Answer 12

All similar charges are pointing in the same direction