DD - Protein Structure (1)

Question 1

What are the 3 Corey-Pauling rules associated with the secondary structure?

Answer 1

RULE 1- There can be no rotation around the planar peptide bond
RULE 2- Other parts of the chain must be flexible
RULE 3- Structure must have the maximum number of stabilising forces between residues

Question 2

What are the 2 main secondary structures?

Answer 2

1. Alpha helix
2. Beta sheet

Question 3

What bonds allow for the formation of alpha helix sheets?

Answer 3

Hydrogen bonds form from NH of one residue to C=O residue (x+4 amino acids away)

Question 4

What amino acid usually tends to be at the start and end of an alpha helix?

Answer 4

START: Proline- can form part of the capping box
END: Proline/Glycine

Question 5

What amino acid do peptide bonds kink around to form BENDS

Answer 5

Proline

Question 6

What amino acid increases the flexibility of the alpha helix?

Answer 6

Glycine

Question 7

How do Amphipathic Helices form?

Answer 7

Due to the separation of hydrophobic and polar residues to either side of the helix

Question 8

How are Beta Pleated Sheets structured?

Answer 8

Beta strands form laterally allowing for at least 3 hydrogen bonds to form between strands

Question 9

Why are anti-parallel strands more stable than parallel strands in a beta-pleated sheet?

Answer 9

More hydrogen bonds can form and they form directly opposite each other

Question 10

How are random coils important for protein structure and function?

Answer 10

-Act to help bind ligands
-Connect 2 domains allowing flexible linkage

Question 11

How do B-turns form?

Answer 11

Hydrogen bonds form from C=O of one residue to NH residue (3 amino acids away)