Enzymes and Catalysis Flashcards

1
Q

In what ways do enzymes interact with substrates?

A

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
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2
Q

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

A

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
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3
Q

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

A

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
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4
Q

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

A

Ionic interactions can pull the substrate and enzyme together favourably

  • Ionic interactions are attractions of opposite charges
  • Larger charge = greater attraction
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5
Q

Describe how chirality influences enzyme/substrate binding

A
  • 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)
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6
Q

How does an enzyme interact with achiral substrates?

A
  • They transform them into chiral products
    • An achiral substrate is therefore called ‘prochiral’
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7
Q

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

A
  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
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8
Q

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

  • Explain the impact of degree of freedom
A

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
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9
Q

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

A
  1. Amide bonds are stable (half life t1/2 = 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
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10
Q

What are cofactors and coenzymes?

A

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
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