Enzymes and Catalysis

Question 1

In what ways do enzymes interact with substrates?

Answer 1

Substrates usually interact with the protein amide backbone and side chains, and must also physically fit into the binding site

3 main molecular interactions:

1. Hydrogen bonding
2. Hydrophobic forces
3. Ionic interactions

Question 2

How does hydrogen bonding play a role in enzyme/substrate binding?

Answer 2

If the substrate is incorrect or not oriented properly, the interaction will be unfavourable due to the loss of hydrogen bonds

• Note that H bonding is strongest when the H is more acidic and the lone pair is more basic
• Also note that H bonding adds 5-10 kcal of energy per mole but NOT to the substrate-protein binding energy

Question 3

How do hydrophobic forces play a role in enzyme/substrate binding?

Answer 3

The expulsion of water from non-polar regions is entropically favoured as it creates disorder

• Hydrophobic regions come together not due to attraction but because the process is entropically driven

Question 4

How do ionic interactions play a role in enzyme/substrate binding?

Answer 4

Ionic interactions can pull the substrate and enzyme together favourably

• Ionic interactions are attractions of opposite charges
• Larger charge = greater attraction

Question 5

Describe how chirality influences enzyme/substrate binding

Answer 5

• Amino acids are chiral, so enzymes are chiral molecules
• Chiral molecules interact differently with other chiral molecules (enzymes can recognise one stereoisomer over the other)

Question 6

How does an enzyme interact with achiral substrates?

Answer 6

• They transform them into chiral products
  
  • An achiral substrate is therefore called ‘prochiral’

Question 7

Enzymes accelerate rates of reactions by reducing activation energy. State 6 ways this can be done

Answer 7

1. Orient the reacting functional groups
2. Provide a solvent environment that favours the chemical reaction
3. Perform a complex reaction in a series of smaller steps
4. Bind the transition state very well to stabilise
5. Act as acid or base catalysts
6. Form covalent bonds with the substrate after initial binding
   
   • I.e., changing the reaction from inter to intramolecular

Question 8

How do proximity and orientation influence enzyme/substrate reaction rates?

• Explain the impact of degree of freedom

Answer 8

Enzymes can increase reaction rates by bringing substrates/reactants together in close proximity

• Degree of freedom: number of possible ways two bonds can be moved away from each other

Question 9

Why must hydrolysis of peptides in our body be enzyme catalysed?

Answer 9

1. Amide bonds are stable (half life t_1/2 = 500 years)
2. Hydrolysis requires a base to form a tetrahedral intermediate
   
   • An enzyme must bring the base (Enz-OH) as biological pH = 7
   • The tetrahedral intermediate must be stabilised by hydrogen bonding to an enzyme backbone
3. The amide is a poor leaving group and requires protonation by an enzyme

Question 10

What are cofactors and coenzymes?

Answer 10

Many enzymes require additional non-protein components called cofactors

• Cofactors can be inorganic ions (ex., Mg2+, Zn2+) or small organic molecules called coenzymes (vitamins)
  
  • Coenzymes may donate/accept a portion of their structure to/from the starting material, intermediate, or product