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Proteins & Enzymes > Enzyme Mechanisms > Flashcards

Enzyme Mechanisms Flashcards

1
Q

proteases catalyse…

A

hydrolysis of peptide bond. Have different specificities for the AA preceding scissile bond

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2
Q

scissile bond

A

bond broken in a peptide by an enzyme

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3
Q

catalytic triad arose by

A

convergent evolution

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4
Q

AA side chains alone cannot catalyse these reactions:

A

redox reactions, group transfer reactions (metal ions, cofactors, coenzymes help)

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5
Q

coenzyme

A

small molecule usually derived from a vitamin (e.g. FAD, NAD+)

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6
Q

vitamins are essential

A

cannot be made in human cells

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7
Q

haem, lipoic acid, ubiquinone, molybdenum cofactor

A

can be made in human cells

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8
Q

oxidoreductase

A

oxidation-reduction reactions. Dehydrogenases, oxidases, reductases

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9
Q

tranferases

A

transfer of functional groups. Kinases, phosphorylases

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10
Q

hydrolases

A

hydrolysis reactions. Phosphatases, proteases

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11
Q

lyases

A

group elimination to form double bonds. Decarboxylases, synthases, aldolases

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12
Q

isomerases

A

isomerisation. Racemases, mutases

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13
Q

ligases

A

bond formation coupled with ATP hydrolysis. Synthetases, carboxylases.

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14
Q

NAD

A

nicotinamide adenine dinucleotide phosphate

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15
Q

FAD

A

flavin adenine dinucleotide

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16
Q

pyruvate dehydrogenase is multi-enzyme complex - contains E1. E2 & E3

A

Mr = 4-10 millions Da. Uses 5 coenzymes in conversion of pyruvate –> acetyl CoA

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17
Q

TPP

A

thiamine pyrophosphate

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18
Q

carbanion on TPP is stabilised by thiazole ring because…

A

of electron withdrawing properties of the S & the positive charge on the N

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19
Q

coenzyme A

A

forms final product (is not just attached to enzyme), is not regenerated like the catalytic coenzymes. Acetyl group is added by pyruvate dehydrogenase complex

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20
Q

thioester linkage

A

high energy bond

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21
Q

E2 (dihydrolipoyl transacetylase) catalyses… (transfer of acetyl group to CoA.)

A

Coenzyme A + acetyllipoamide –> acetyl CoA + dihydrolipoamide. Lipoamide is in reduced form after transfer reaction. Enzyme needs to regenerate before next round of catalysis - E3.

22
Q

E3 (dihrydrolipoyl dehydrogenase) catalyses… (regeneration of lipoamide by oxidation of dihydrolipoamide)

A

dihydrolipoamide + FAD –> lipoamide + FADH2 - NAD+ -> FAD + NADH + H+

23
Q

E3 residues involved in catalysis of oxidation of dihydrolipoamide…

A

Cys41 & Cys46 (which form a disulfide bridge)

24
Q

E1 (pyruvate dehydrogenase) catalyses…

A

oxidative decarboxylation of pyruvate

25
Q

Importance of having large enzyme complex = coordination of reactions

A

Allows coordinated catalysis of a complex multi-step reaction, proximity of reaction centres increases overall rate, increases effective concentration of reactants, intermediates remain tethered to complex, minimises side reactions. (5 points)

26
Q

Ethanol fermentation: pyruvate decarboxylase & alcohol dehyrdogenase

A

Pyruvate decarboxylase produces acetaldehyde. This is converted to ethanol by alcohol dehydrogenase (ADH)

27
Q

pyruvate replenishes…

A

oxaloacetate (in gluconeogenesis)

28
Q

Biotin & carboxybiotinyl enzyme - biotin consists of..

A

imidazoline ring that is cis-fused to a tetrahydrothiophene ring bearing a valerate side chain

29
Q

TCA cycle has pathways converting

A

lactate, pyruvate & other intermediates to oxaloacetate

30
Q

in carboxybiotinyl enzyme, N1 of biotin ureido group is…

A

carboxylation site

31
Q

pyruvate carboxylase has 2-phase reaction mechanism

A

1st produces carboxybiotinyl enzyme, 2nd produces oxaloacetate

32
Q

TPCK

A

resembles substrate for chymotrypsin but is chemically modified to is reacts irreversibly with the enzyme, when bound in the active site

33
Q

serine proteases contain catalytic triad

A

His, Ser, Asp. (His identified by affinity-labeling using substrate analogue.

34
Q

specificity of serine proteases determined by

A

nature of S1 pocket & P1 residue of substrate

35
Q

2 first steps of catalytic mechanism of serine protease

A
  1. nucleophilic attack by Ser195 forming tethrahedral intermediate, His57 acts as general base & Asp102 exerts electrostatic force. 2. decomposition of tetrahedral intermediate to give acyl-enzyme intermediate; protonated His57 acts as general acid to form amine leaving group.
36
Q

2 last steps of catalytic mechanism of serine protease

A
  1. His57 acting as general base promotes nucleophilic attack by H2O on acyl-enzyme, 2nd tetrahedral intermediate formed. 4. decomposition of intermediate to give resting enzyme & carboxylic acid. Protonated His57 acts as general acid.
37
Q

in serine proteases, oxyanion hole acts to stabilise transition states

A

favourable binding interactions between oxyanion species & AA side chains. Favourable binding interactions lower activation energy

38
Q

zymogen

A

large precursor molecules in pancreas that show little activity

39
Q

(zymogen) proteases are activated by

A

proteolytic cleavage in duodenum

40
Q

trypsinogen activated by cleavage after Lys15

A

catalysed by enteropeptidase (a serine protease) under hormonal control. Trypsin then catalyses its own activation (autocatalytic)

41
Q

inappropriate activation in pancreas is prevented by synthesis of

A

pancreatic trypsin inhibitor which binds tightly to trypsin

42
Q

proelastase activated in similar manner to

A

trypsinogen

43
Q

hexokinase - an example of induced fit

A

movement of lobes upon substrate binding squeezes out water, preventing possible hydrolysis of ATP in competing side reaction

44
Q

lysozyme destroys bacterial cell walls by hydrolysing β(1-4) linkages between…

A

NAG & NAM sugar units (NAG = N-acetylglucosamine. NAM = N-acetylmuramic acid)

45
Q

lysozyme also hydrolyses polyNAG found in…

A

chitin of fungi cell walls

46
Q

sugar in subsite D of HEW lysozyme adopts..

A

half-chair conformation (is energetically unfavourable as ΔG is +, so other subsites must have - ΔG)

47
Q

Phillips mechanism for lysozyme

A
  1. Glu35 acts as general acid & protonates the bridge O of glycosidic bond. 2. The glycosidic bond cleaves leaving a positively charged D-ring oxonium ion which is stabilised by favourable electrostatic interaction with the negatively charged Asp52 carboxylate and enzyme-induced distortion of the D-ring to enhance resonance stabilisation. 3. water provides OH- that combines with oxonium ion & a H+ to reprotonate Glu35.
48
Q

Hydrolysis of peptide bond favoured by 3 factors:

A
  1. Presence of nucleophile to attack carbonyl group. 2. Presence of charges to polarise carbonyl group + stabilise tetrahedral intermediates. 3. Presence of proton donor to make NH- group a better leaving group.
49
Q

zymogen

A

larger precursor molecule that shows little activity

50
Q

trypsinogen activated by cleavage after… Is catalysed by…

A

Lys15. Enteropeptidase (under hormonal control).

51
Q

Trypsin catalyses its own activation; is…

A

autocatalytic

52
Q

Inappropriate activation of trypsin prevented by…

A

pancreatic trypsin inhibitor which tightly binds trypsin

Proteins & Enzymes (6 decks)

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