SFP10: Protein Structure And Organisation

Question 1

Name 3 different ways of visualising molecules

Answer 1

Line
Stick
Ball and stick
CPK

Question 2

Why study protein structure?

Answer 2

The 3D structure of proteins is a major determinant of their function (SAR-structure activity relationship)

Question 3

Approx how many families of protein folds are there available at present?

Answer 3

2000

Question 4

How does chirality dictate helix handedness?

Answer 4

As amino acids and residues are chiral about carbon 2 (alpha-carbon)
Earths proteins are L-alpha-amino acids
Helical formation is preferentially right handed

Question 5

True or false… the peptide bond has no rotation

Answer 5

True… it has partial double character

Question 6

Do all atoms lie in the same plane?

Answer 6

Yes

Question 7

What are the two torsion angles in the polypeptide chain also known as?

Answer 7

Ramachandran plots

Question 8

What do torsion angles describe?

Answer 8

The rotations of the polypeptide backbone around the bonds between N-Calpha (Phi, φ) and Calpha-C (Psi, ψ)

Question 9

What is the ideal angle for phi and psi?

Answer 9

Ideal is -60 degrees

Question 10

What is a Ramachandran plot?

Answer 10

A plot of restricted set of allowed psi and phi combinations and backbone conformations