SPL: proteins and protein structure

Question 1

Explain the main properties of the main chain part of amino acids - pH, optical activity and peptide bonds.

Answer 1

pH:

• pH 1 - NH3+RCCOOH
• pH 7 - NH3+RCCOO- (zwitterion)
• pH 11 - NH2RCCOO-

Optical activity:

• L-isomer - found in amino acids
• D-isomer - rare in nature

Peptide bonds:

• Formed by condensation - producing water molecule

Question 2

Describe the 4 basic classifications of R groups among the 20 amino acids, giving examples of each.

Answer 2

• 6 hydrophillic - serine, threonine, tyrosine, asparagine, glutamine, cysteine
• 9 hydrophobic - glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, proline, tryptophan
• 2 acidic - aspartate, glutamate
• 3 basic - lysine, arginine, histidine

Question 3

Define the primary, secondary, tertiary and quaternary structure of a protein.

Question 4

Describe the main features of an alpha-helix, beta-sheet, and a loop.

Question 5

Describe the 3 main classes of supersecondary structures found in proteins.

Answer 5

1. All alpha-helix proteins - e.g. globin fold of myoglobin/haemoglobin
2. All beta-sheet proteins - e.g. immunoglobulin fold of antibodies
3. Mixed alpha-beta proteins - e.g. “TIM” fold