Lecture 5 -The peptide bond and secondary protein structure

Question 1

What do peptide bonds remove?

Answer 1

The ionisable α-carboxyl and α-amino groups of the amino acids

Question 2

Native conformations: what are they and what is their significance?

Answer 2

A protein in its normal, stable state

This conformation determines a protein’s biological function

Question 3

The two key factors in determining protein structure

Answer 3

1 - Possible rotations around bonds

2 - Weak, non-covalent bonds (hydrogen bonding, electrostatic attraction, hydrophobic/hydrophilic interaction, disulfide bridges)

Question 4

Key properties of the alpha helix structure

Answer 4

Right-handed, turning clockwise from the N-terminus

• 3.6 amino acids per turn
• Rise - each residue advances by 0.15nm
• Pitch - the advance on the helix per turn (0.54nm)

Question 5

Beta-pleated sheets: what are the amino acids in this form like and what forms are there?

Answer 5

Almost fully extended amino acid chains

Parallel and anti-parallel sheets

Question 6

Parallel beta-pleated sheets

Answer 6

Hydrogen bonds occur at a slanted angle causing the sheet to be slightly bent

Question 7

Antiparallel beta-pleated sheets

Answer 7

Hydrogen bonds occur directly in a straight line, forming a full sheet

Question 8

Loops and turns

Answer 8

Allow proteins to fold in on themselves for a compact structure

Loops - Often contain hydrophilic residues and are found on protein surfaces
Turns - loops containing 5 residues or less

Question 9

Superseciondary structures

Answer 9

• Helix-loop-helix
• Coiled-coil
• Helix bundle
• β α β Unit
• Hairpin
• β Meander
• Greek key
• β Sandwich

Question 10

Coiled-coil: what is it and what is it used for?

Answer 10

Two amphipathic α helices that interact in parallel through their hydrophobic edges

Some DNA proteins and some structural proteins

Question 11

Helix bundle: what is it?

Answer 11

Several α helices that associate in an antiparallel manner to form a bundle

Question 12

β α β Unit: what is it and what is it used for?

Answer 12

Two parallel β strands linked to an intervening α helix by two loops

Many different proteins

Question 13

Hairpin: what is it?

Answer 13

Two adjacent antiparallel β strands connected by a β turn

Question 14

β Meander: what is it?

Answer 14

An antiparallel sheet composed of sequential β strands connected by loops or turns

Question 15

Greek key: what is it?

Answer 15

4 antiparallel strands (strands 1,2 in the middle, 3 and 4 on the outer edges)

Question 16

β Sandwich: what is it?

Answer 16

Stacked β strands or sheets

Question 17

Helix-loop-helix: what is it?

Answer 17

Two helices connected by a turn

Mainly used in proteins that bind to DNA