Lecture 13. Enzymes and Catalysis Flashcards

1
Q

What does Eyring’s equation show ?

A

The rate of reaction can be related to Gibbs free energy of the transition state for that reaction

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2
Q

What is the activation state ?

A

The energy required to get to the transition state from starting materials

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3
Q

What happens as the activation energy increases ?

A

The rate constant (k) becomes smaller

The reaction becomes slower

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4
Q

What can catalysts do ?

A
  1. Reduce the activation energy for a reaction

2. Provide an alternative mechanism with a lower overall activation energy

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5
Q

Why are enzymes crucial for life ?

A

Activation energies for uncatalysed metabolic processes are so big that very high temperatures would be requires to achieve the same rates

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6
Q

What does a large difference in the activation energy result in ?

A

A larger difference in k catalysed and k uncatalysed

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7
Q

What can enzymes provide ?

A

A large reduction in the activation energy

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8
Q

What are the four categories by which enzymes catalyse reactions ?

A
  1. Proximity and orientation effects
  2. Acid base catalysis
  3. Covalent catalysis
  4. Transition state stabilisation
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9
Q

What type of cost does binding a substrate to an enzyme require ?

A

Entropic cost

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10
Q

What is required for a substrate to bind tightly to an enzyme ?

A

Favourable enthalpy

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11
Q

What does binding of substrate molecules to enzymes allow ?

A

The enzyme to exert control over the conformation and shape of the substrate molecule

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12
Q

What does free rotation around single bonds in acyclic systems result in ?

A

A huge number of thermally accessible conformations

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13
Q

Which type of reaction (intramolecular or intermolecular) are generally faster ?

A

Intramolecular

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14
Q

Why are intramolecular reactions generally faster ?

A

The reactants are already in the molecule

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15
Q

What can contribute to influencing the rate of acceleration ?

A
  1. Different functionality from different amino groups
  2. Shape and form of protein
  3. Interactions with the amide backbone
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16
Q

In bimolecular reaction what are proximity and orientation effects thought to account for ?

A

Accelerations up to 10^8 fold over the background uncatalysed reaction

17
Q

How can protonation affect functional groups in substrate molecules ?

A

Turn them into better leaving groups

18
Q

How does protonation affect carbonyl groups ?

A

Makes them more electrophilic

19
Q

What can deprotonation do to functional groups ?

A

Make them into better nucleophiles

20
Q

What does acid/base catalysis do by appropriate amino acid side chains ?

A

Accelerating enzymatic processes

21
Q

What amino acid cannot be chiral ?

A

Glycine

22
Q

What amino acids have carboxylic side chains ?

A

Aspartic acid and glutamic acid

23
Q

What happens if aspartic acid and glutamic acid are protonated in the active sites ?

A

They can act as proton donors

24
Q

What happens if aspartic acid and glutamic acid are deprotonated ?

A

They can stabilise adjacent positive charges and perhaps act as bases (proton acceptors)

25
Q

What happens when the pH of an environment corresponds to the molecules pKa ?

A

The compound will be 50% ionised

26
Q

What can nucleophilic sides chains react directly with and form ?

A

Substrates forming covalent bonds between the enzyme and the substrate

27
Q

What happens to the covalent bonds formed between the enzyme and substrate ?

A

Cleaved in later steps, regenerating the unmodified enzyme

28
Q

What can lysine react with ?

A

Carbonyl groups in substrates to form imines/iminium ions

29
Q

What does thioester formation occur with ?

A

Cysteine side chains

30
Q

What can favorable reactions between the enzyme and substrate do ?

A

Stabilise the transition state and lower the activation energy

31
Q

What are some methods of understanding how an enzyme works ?

A
  1. Kinetic studies
  2. Detection of intermediates
  3. Chemical modification
32
Q

What is x-ray crystallography used for?

A

A very powerful technique that allows for the 3D structure of the enzyme to be solved

33
Q

How would you obtain the structure of the enzyme-substrate complex ?

A

Grow crystals and soak in substrates

34
Q

What is the problem of growing and soaking the crystals in substrate ?

A

Enzyme turnover is generally much faster than the timescale of crystallisation and data aquisition

35
Q

How would you solve the problem of a quick enzyme turnover in x-ray crystallography ?

A
  1. Use an unreactive substate mimic
  2. If the enzyme requires two substrates, try two crystals one with each substrate
  3. Complex of the enzyme with the product
36
Q

What can the use of x-ray crystallography in conjunction with computational modelling do ?

A

Reverse some of the tricks that are used to obtain crystal structures

37
Q

What is site directed mutagenesis ?

A

Amino acids are exchanged for others

38
Q

Which amino acids should you mutate ?

A

Target key structural/catalytical residues

39
Q

In site directed mutagenesis, how would you make as little disruption as possible to the enzyme structure ?

A
  1. Remove the reactive group

2. Replace with something of similar size (ideally smaller) and polarity/charge distribution