IT - Enzymes I

Question 1

What is a common protein structure found in 10% of enzymes?

Answer 1

(ba)8-barrel

Question 2

What is the building block of (ba)8-barrel?

Answer 2

Repeating motif of beta-strand followed by alpha-helix (8 times)

Question 3

How does (ba)8-barrel differ from b-barrel?

Answer 3

(ba)8-barrel has parallel beta-strand direction (↑↑) and alpha-helix, while b-barrel has anti parallel beta-strands (↑↓)

Question 4

What is the function of TIM enzyme in glycolysis?

Answer 4

Convert DHAP to G3P

Question 5

Does TIM require regulation?

Answer 5

No, it needs to be fast, not regulated

Question 6

Does TIM move protons?

Answer 6

No, it performs internal redox reaction - oxidation of C1 and reduction of C2 in G3P

Question 7

DHAP –> G3P mechanism (2)

Answer 7

DHAP –> Enediol

• Abstraction of proton by base B1 at C1
• Donation of proton by acid A1 at C2=O

Enediol –> G3P

• Donation of proton by acid A2 at C2
• Abstraction of proton by base B2 at C1OH

Question 8

Does a higher free energy of E+G3P compared to E+DHAP prevent conversion?

Answer 8

No, it just means the equilibrium favors DHAP.

Conversion still happens because G3P is constantly removed.

Question 9

What occurs in a general reaction between Y and X? (3)

Answer 9

• DG of Y → X is negative and thus favourable, leading to formation of X
• DG of X → Y is positive and thus not favourable

however, some Y is formed from X (because of the thermal energy)

Question 10

How is equilibrium, the number of Y molceules being converted to X mole? (3)

Answer 10

• at equilibrium, the rate for conversion of Y → X is exactly equal to the conversion of X → Y
• at equilibrium, there is a large excess of X over Y
• the excess of X over Y compensates the slow rate in the conversion of X → Y

Question 11

What is the highest energy barrier for TIM in the forward reaction?

Answer 11

Product release (TS4), which is close to the diffusion limit (fast)