Protein structure

Question 1

Primary structure

Answer 1

• The order of amino acids - polypeptide chain

Question 2

Secondary structure

Answer 2

• Dominated by the main chain amide-amide hydrogen bonds
• Partial double bond character on the nitrogen to the carbon - no rotation around the nitrogen and carbon, places a dipole on the molecule
• Alpha helix - promoted by small amino acids, disfavoured by restricted and bulky amino acids
• Beta sheets - can be parallel or antiparallel, promoted by bulky amino acids

Question 3

Ramachandran plots

Answer 3

• Tells us what is sterically possible
• Finds the potential stable conformations and conformations that were sterically disallowed due to atomic collision
• Dark regions correspond to the favourable conformations (no steric clashing)
• The conformations correspond to specific secondary protein structures

Question 4

Tertiary structure

Answer 4

• Based off of the side chains