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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
Importance of having large enzyme complex = coordination of reactions
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
Ethanol fermentation: pyruvate decarboxylase & alcohol dehyrdogenase
Pyruvate decarboxylase produces acetaldehyde. This is converted to ethanol by alcohol dehydrogenase (ADH)
27
pyruvate replenishes...
oxaloacetate (in gluconeogenesis)
28
Biotin & carboxybiotinyl enzyme - biotin consists of..
imidazoline ring that is cis-fused to a tetrahydrothiophene ring bearing a valerate side chain
29
TCA cycle has pathways converting
lactate, pyruvate & other intermediates to oxaloacetate
30
in carboxybiotinyl enzyme, N1 of biotin ureido group is...
carboxylation site
31
pyruvate carboxylase has 2-phase reaction mechanism
1st produces carboxybiotinyl enzyme, 2nd produces oxaloacetate
32
TPCK
resembles substrate for chymotrypsin but is chemically modified to is reacts irreversibly with the enzyme, when bound in the active site
33
serine proteases contain catalytic triad
His, Ser, Asp. (His identified by affinity-labeling using substrate analogue.
34
specificity of serine proteases determined by
nature of S1 pocket & P1 residue of substrate
35
2 first steps of catalytic mechanism of serine protease
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
2 last steps of catalytic mechanism of serine protease
3. 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
in serine proteases, oxyanion hole acts to stabilise transition states
favourable binding interactions between oxyanion species & AA side chains. Favourable binding interactions lower activation energy
38
zymogen
large precursor molecules in pancreas that show little activity
39
(zymogen) proteases are activated by
proteolytic cleavage in duodenum
40
trypsinogen activated by cleavage after Lys15
catalysed by enteropeptidase (a serine protease) under hormonal control. Trypsin then catalyses its own activation (autocatalytic)
41
inappropriate activation in pancreas is prevented by synthesis of
pancreatic trypsin inhibitor which binds tightly to trypsin
42
proelastase activated in similar manner to
trypsinogen
43
hexokinase - an example of induced fit
movement of lobes upon substrate binding squeezes out water, preventing possible hydrolysis of ATP in competing side reaction
44
lysozyme destroys bacterial cell walls by hydrolysing β(1-4) linkages between...
NAG & NAM sugar units (NAG = N-acetylglucosamine. NAM = N-acetylmuramic acid)
45
lysozyme also hydrolyses polyNAG found in...
chitin of fungi cell walls
46
sugar in subsite D of HEW lysozyme adopts..
half-chair conformation (is energetically unfavourable as ΔG is +, so other subsites must have - ΔG)
47
Phillips mechanism for lysozyme
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
Hydrolysis of peptide bond favoured by 3 factors:
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
zymogen
larger precursor molecule that shows little activity
50
trypsinogen activated by cleavage after... Is catalysed by...
Lys15. Enteropeptidase (under hormonal control).
51
Trypsin catalyses its own activation; is...
autocatalytic
52
Inappropriate activation of trypsin prevented by...
pancreatic trypsin inhibitor which tightly binds trypsin

Proteins & Enzymes (6 decks)

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