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BIOC192 > Lecture 10: HOW DOES AN ENZYME CATALYSE A REACTION? 1 > Flashcards

Lecture 10: HOW DOES AN ENZYME CATALYSE A REACTION? 1 Flashcards

1
Q

What are the strategies for catalysis?

A

Acid-base catalysis, covalent catalysis, redox and radical catalysis, geometric effects, stabilisation of the transition state and cofactors with activated groups

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2
Q

What is redox and radical catalysis driven by?

A

Metal ions

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3
Q

What are the geometric effects?

A

Proximity and orientation

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4
Q

what are some examples of activated groups of cofactors?

A

Electrons, hydride ions (H-), methyl groups (CH3), amino groups (NH3) with the ability to carry things

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5
Q

What do many enzymes do?

A

Use more than one strategy

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6
Q

What does covalent catalysis involve?

A

The formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme

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7
Q

What does the enzyme in covalent catalysis have?

A

A nucleophilic side chain

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8
Q

How is the enzyme regenerated in covalent catalysis?

A

By a hydrolysis reaction

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9
Q

What is covalent catalysis driven by?

A

Nucleophilic attack on an electrophile

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10
Q

For two molecules to react they need to be …

A

Close together and in the correct orientation

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11
Q

What does nucleophilic attack require?

A

Correct orientation and ionisation

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12
Q

What does nucleophilic attack depend on?

A

The R groups and how good the leaving group is

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13
Q

What does nucleophilic attack form?

A

A trigonal planar intermediate

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14
Q

What should allow nucleophilic attack to occur faster?

A

Stabilising the transition state

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15
Q

What does hexokinase use as a cofactor?

A

Mg2+

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16
Q

What is established in hexokinase?

A

Orientation of phosphates of ATP by octahedral coordination of Mg2+ ion

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17
Q

What is the Mg2+ cofactor known as?

A

An electron withdrawing Lewis acid which stabilises oxygen, making phosphorus a better electrophile (leaving group)

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18
Q

What does acid-base catalysis involve?

A

Ionisable groups and proton transfer

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19
Q

What amino acids have ionisable groups?

A

Glu, Asp (COOH)

Lys, Arg (NH3+)

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20
Q

What do amino acid groups need to be in for the catalytic mechanism to proceed?

A

In the correct ionisation state

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21
Q

What may ionisation be part of?

A

activation to the transition state

22
Q

What is enzyme activity dependent on?

A

pH

23
Q

Why is enzyme activity ph dependent?

A

Because transfer of protons is involved

24
Q

What does each enzyme have?

A

A characteristic optimal pH at which its rate is highest

25
Q

What is histidine particularly suitable to?

A

Acid-base catalysis reactions

26
Q

What is the pKa of the imidazole group in histidine?

A

~6.5 which is close to physiological pH

27
Q

What can histidine do?

A

Depending on the environment of the active site His can donate or accept a proton

28
Q

What does chymotrypsin do?

A

Cleave proteins

29
Q

What catalysis strategies does chymotrypsin use?

A

Acid-base, covalent, geometric effects and stabilisation of the transition state

30
Q

What are proteases?

A

Hydrolyases

31
Q

What are the substrates in a reaction using chymotrypsin?

A

A polypeptide and water

32
Q

What are the products in a reaction using chymotrypsin?

A

Two shorter peptides, or individual amino acids

33
Q

What does chymotrypsin act in?

A

Digestion

34
Q

What do other proteases do?

A

Make hormones, remove defunct proteins we no longer need, or activate enzymes (as in blood clotting)

35
Q

What do divergent evolution serine proteases have?

A

Same structure with unique specificities

36
Q

What is in the specificity pocket of chymotrypsin?

A

2 glycines (small)

37
Q

What is in the specificity pocket of trypsin?

A

Negative aspartic acid which attracts positively charged polypeptides

38
Q

What is in the specificity pocket of elastase?

A

Valine and threonine with large side chains

39
Q

What do convergent serine proteases have?

A

The same catalytic triad occurs in different order and different structures.

40
Q

What should proteases have if they shared a common ancestor?

A

Share order and structure

41
Q

What does the catalytic triad in chymotrypsin include?

A

Serine, histidine and aspartic acid

42
Q

What is the first part in the action of chymotrypsin?

A

his57, polarised by Asp102, withdraws a proton from Ser195 making there serine hydroxyl a good nucleophile to attack the sissile bond

43
Q

What is the sissile bond?

A

The bond which is broken

44
Q

What happens after his57, polarised by Asp102, withdraws a proton from Ser195 making there serine hydroxyl a good nucleophile to attack the sissile bond?

A

Nucleophilic attack forms a covalent, tetrahedral intermediate which is stabilised by the oxyanion hole, lowering the activation energy

45
Q

what happens after Nucleophilic attack forms a covalent, tetrahedral intermediate which is stabilised by the oxyanion whole, lowering the activation energy?

A

The tetrahedral intermediate decomposes, driven by general acid catalysis from his57

46
Q

What happens as a result of the first tetrahedral intermediate decomposing?

A

Half of the polypeptide chain remains covalently attached to the enzyme in an acyl-enzyme intermediate and the other half can leave the active site

47
Q

What happens after the first half leaves the active site?

A

Water replaces one of the products in the active site

48
Q

What happens after water replaces one of the products in the active site?

A

Polarised by His57 acting as a general base (OH-), water makes a nucleophilic attack forming a second tetrahedral intermediate, again stabilised by the oxyanion hole

49
Q

What happens after Polarised by His57 acting as a general base (OH-), water makes a nucleophilic attack forming a second tetrahedral intermediate, again stabilised by the oxyanion hole?

A

Whit His57 acting as a general acid, this intermediate decays to form a carboxylate

50
Q

What happens as a result of the second intermediate decaying to form a carboxylate?

A

The second product can leave the active site and the active site has been regenerated and is ready for another round of catalysis

BIOC192 (38 decks)

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