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Bio chem > Lecture 10 - Enzyme Catalyse a reaction > Flashcards

Lecture 10 - Enzyme Catalyse a reaction Flashcards

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1
Q

Strategies for Catalysis (6)

A
  1. Acid-base catalysis
  2. Covalent catalysis
  3. Redox and radical catalysis (metal ions)
  4. Geometric effects (proximity and orientation)
  5. Stabilisation of the transition state
  6. Cofactors with activated groups, e.g. electrons, hydride ion (H-), methyl groups (CH3), amino groups (NH2).
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2
Q

Do many enzymes use more than one from the strategies for catalysis list?

A

Yes
not exclusive
not exhaustive

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3
Q

For two molecules to react they need to be:

A

Close together

right orientation

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4
Q

Covalent catalysis

A

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

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5
Q

what drives covalent catalysis?

A

Nucleophilic attack on an electrophile

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6
Q

Good electrophiles

A

Positive

Centres that able to form additional bonds

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7
Q

Good electrophiles examples

A 
Carbonyl carbon atom
Cationic imine (Schiff base)
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8
Q

Good nucleophiles

A

Things that attack electrophiles

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9
Q

Good nucleophiles examples

A 
Hydroxyl group (need to be deprotonated)
Sulfhydryl group (need to be deprotonated)
Amino group (uncharged state)
Imidazole group (uncharged state)
Found in enzyme active sites
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10
Q

what does a nucleophilic attack require?

A

correct orientation

Ionisation

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11
Q

acid-base catalysis

A

Involves ionisable groups and proton transfer.

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12
Q

what may be part of the activation to the transition state?

A

Ionisation

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13
Q

why do Groups need to be in correct ionisation state?

A

For catalytic mechanism to proceed.

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14
Q

Ionisable group that can easily lose a proton

A

Glu

Asp

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15
Q

Ionisable group that can easily gain a proton

A

Lys

Arg

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16
Q

Ionisable groups that most active in acid base catalysis and assist with forming better nucleophiles

A

Glu Asp

Lys Arg

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17
Q

Enzyme activity is

A

pH dependent.

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18
Q

what do each enzyme have at which its rate is highest?

A

characteristic optimal pH

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19
Q

what do Amino acid sidechains need to be in?

A

correct ionisation state for catalytic mechanism to proceed.

20
Q

what example is suitable to acid base catalysis, types of reactions?

A

Histidine

21
Q

Histidine

Imidazole pKa

A

~ 6.5 – close to physiological pH

22
Q

what can the active site His depending on environment do?

A

Donate or accept proton

23
Q

Divergent evolution of serine proteases

incl examples

A

Same structure, unique specificities (pocket)

Chymotrypsin, Trypsin, Elastase

24
Q

Convergent evolution of serine proteases

A

Same catalytic triad occurs in different order and in different structures.

25
Q

Catalytic triad

A

Asp, his, ser

Convergent evolution

Occur in 3 different order and structure in 3 different proteins

26
Q

In Chymotrypsin: acid - base and covalent catalysis.

what does the Catalytic triad comprise of?

A

serine, histidine and aspartic acid.

27
Q

In Chymotrypsin: acid - base and covalent catalysis.

How does Serine Hydroxyl become a good nucleophile?

A

Sharing proton with histidine

28
Q

In Chymotrypsin: acid - base and covalent catalysis.

What does Serine Hydroxyl attack?

A

Scissile bond

29
Q

In Chymotrypsin: acid - base and covalent catalysis.

What does the Oxyanion hole do?

A

Stabilise tetrahedral intermediate

30
Q

In Chymotrypsin: acid - base and covalent catalysis.

what is polarised by Asp102?

A

His57

31
Q

In Chymotrypsin: acid - base and covalent catalysis.

what does His57 withdraw proton from?

A

Ser195

becomes nucleophilic

32
Q

In Chymotrypsin: acid - base and covalent catalysis.

what does Non-polar environment of Asp102 do?

A

raises its pKa.

Oxyanion hole stabilise tetrahedral intermediate.

33
Q

In Chymotrypsin: acid - base and covalent catalysis.

What drives decomposing of tetrahedral intermediate?

A

acid catalysis from His57.

34
Q

In Chymotrypsin: acid - base and covalent catalysis.

what happens to both halves of polypeptide ‘acyl-enzyme intermediate’?

A

Half polypeptide remains covalently attached to the enzyme.

other half can leave the active site.

35
Q

In Chymotrypsin: acid - base and covalent catalysis.

what replaces one of the products in the active site in Acyl-enzyme intermediate?

A

Water

36
Q

In Chymotrypsin: acid - base and covalent catalysis.

what is Polarised by His57 as a general base?

A

water

37
Q

In Chymotrypsin: acid - base and covalent catalysis.

what does water make?

A

nucleophilic attack

38
Q

In Chymotrypsin: acid - base and covalent catalysis.

when water makes a nucleophilic attack what does it form?
incl how its stabilised

A

second tetrahedral intermediate

Stabilised by oxyanion hole

39
Q

In Chymotrypsin: acid - base and covalent catalysis.

what acts as acid when 2nd intermediate decays?

A

His57

40
Q

In Chymotrypsin: acid - base and covalent catalysis.

what does 2nd intermediate form when it decays?

A

Carboxylate

41
Q

In Chymotrypsin: acid - base and covalent catalysis.

what happens when 2nd intermediate decays?

A

2nd product leave the active site.

Active site has been regenerated and is ready for
another round of catalysis.

42
Q

Aspartic protease mechanism examples

A

HIV protease and pepsin

43
Q

what is versatile?

A

Acid-base catalysis

44
Q

Catalytic triad occurs by

A

convergent and

divergent evolution.

45
Q

Stabilisation of electrophilic targets invites

A

nucleophilic attack.

46
Q

Stabilisation of an intermediate is

A

crucial to many reactions.

47
Q

Covalent catalysis can be resolved by

A

complementary half reaction.

Bio chem (36 decks)

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