L4: Protein Structure To Protein Function

Question 1

Describe structure of collagen fibre

Answer 1

• Right hand twist of 3 left hand twist (3 residues per turn) helical polypeptide chains
• Amino acid sequence: Gly-X-Y or Gly-X-HyY (X= any a.a., Y = lysine, proline)
• Staggered packing of individual collagen molecules in collagen fibrils (light and heavy staining)

Question 2

How is collagen fibre stabilised

Answer 2

1. Interchain H-bond

2. Sheath of water molecules of solvation

Question 3

Post translational modification after protein synthesis

Answer 3

1. Lysine —> Hydroxylysine, Proline —> Hydroxyproline
2. Vitamin C as co-factor for lysyl and prolyl hydroxylase
3. Hydroxylysine: attachment of disaccharide
4. Hydroxyproline: H-bond formation

Question 4

Structure of haemoglobin

Answer 4

• 2 alpha and 2 beta chains
• Heme group tightly bound in hydrophobic binding pocket
• Fe2+ bound to heme group with proximal histidine and oxygen on two sides
• Proximal histidine bind to Fe2+
• Oxygen binds between distal histidine and Fe2+ of heme group
• Heme group form porphyrin ring system
• Oxygen binding to Fe2+ pulls it back into plane of porphyrin ring —> stabilised

Question 5

Myoglobin vs Haemoglobin

Answer 5

Myoglobin: monomeric with 1 heme, facilitate oxygen diffusion in muscle
Haemoglobin: tetrameric with 4 hemes

Question 6

Why haemoglobin binds to successive oxygen with increasing affinity

Answer 6

1. Successive addition of oxygen trigger T to R state conformational change which further open up the binding sites for oxygen.
2. T —> R state:
   - oxygen pulls subunits outwards
   - breaking ions pairs between alpha1-beta2 interface
   - T state has a lower affinity for oxygen. Deoxyhaemoglobin are more stable in T state.

Question 7

3 factors which lower affinity of haemoglobin for oxygen

Answer 7

1. Hydrogen ions (pH)
   - Hydrogen ions are allosteric effectors of haemoglobin
   - Bohr effect: oxygen binds well at higher pH (lungs), released well at lower pH (tissue)
   - decrease in pH, decrease in affinity, shift right in oxygen-dissociation curve
2. 2,3 BPG:
   - allosteric effects
   - bind to beta subunits, pull subunits together
   - decrease in affinity for O2, stabilisation of T state
3. CO2:
   - form carbamates with N-terminal —> release protons —> lower pH
   - stabilisation of deoxy form of haemoglobin