Ramachandran Angles

Question 1

Define primary structure of proteins.

Answer 1

Amino acid sequence in a polypeptide chain.

Question 2

Define secondary structure of proteins.

Answer 2

Refers to local spatial arrangements between short stretches of amino acids in a protein.
(alpha helics, beta pleated sheet.)

Question 3

Define tertiary structure of proteins.

Answer 3

Describes the three-dimensional confirmation of an entire polypeptide chain, and entire protein molecule.

Question 4

Define quaternary structure in proteins.

Answer 4

Refers to the higher order interactions between multiple polypeptide chains, multiple protein molecules that come together to form a single functional unit. (Ribosome)

Question 5

How do we define the confirmation of a peptide unit?

Answer 5

Two main chain torsional angle per residue: phi (circle with line) and psi (trident)

Question 6

What does a peptide unit consist of? (Hint 6)

Answer 6

Alpha C, C, O, N, H, and the next alpha C.

Question 7

What bond is Phi angle referring to? (Circle with line through it.)

Answer 7

The bond (residue) of the alpha carbon to the amino group. (Plane also includes the next alpha carbon, and that alpha carbons carbonyl group)

Question 8

Which bond is Psi angle referring to? (Trident)

Answer 8

The bond (residue) that is the alpha carbon, and the carbonyl group of that amino acid. (Plane also includes amino group and alpha carbon of neighboring amino acid.)

Question 9

What amino acid is this showing? What is it not and why?

Answer 9

Any of 18 amino acids.
Not Glycine: that chart has much more favorable confirmations. (Smallest amino acid!)
Not proline: has special circle side chain with amino group, much more restrictive confirmation criteria. (Least amount of regions allowed for torsion angle).

Question 10

What are the Phi and Psi dihedrals for alpha helices?

Answer 10

Phi: -57
Psi: -47

Question 11

What Phi value can Proline achieve?

Answer 11

Around -60 only (vertical line at -60)