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Michaelmas Term 1 > Enzymes and the principles of catalysis > Flashcards

Enzymes and the principles of catalysis Flashcards

1
Q

Describe ATP hydrolysis

A
  • reaction far from equilibrium in vivo
  • thermodynamically favourable
  • spontaneous
  • slow: in the absence of a catalyst, it takes many hours for ATP to be hydrolysed to ADP + Pi
  • liberates free energy used to power the cell
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2
Q

Describe TPI

A
  • uncatalysed reaction rate: one a day
  • reaction rate when catalysed by TPI: 4,300 per
    second
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3
Q

TPI

A

triose phosphate isomerase

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4
Q

Most enzymes accelerate reactions to

A

millions of times faster than the uncatalysed rate

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5
Q

Describe the synthesis of the pyrimidine nucleotide, UMP

A
  • one of the slowest uncatalyzed reactions
  • uncatalysed rate of decarboxylation of orotidine
    monophosphate to UMP is 1 reaction per 45 million
    years
  • catalysed by OMP decarboxylase,
    reaction occurs at a rate of 39 per second
  • rate enhancement of 1.4 x 1017-fold
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6
Q

Describe enzyme catalysis - the basics

A

accelerate the reaction by stabilizing the transition state, reducing the activation energy required to reach it

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7
Q

Describe the transition state

A
  • no longer the substrate but is not yet the product
  • least-stable and most-seldom occupied species along the reaction pathway
  • highest free energy
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8
Q

Enzymes alter

A

reaction kinetics, NOT equilibria

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9
Q

Describe enzyme catalysis - the specifics

A
  • accelerate the attainment of equilibria
  • do not change the standard equilibrium position of the reaction (Keq)
  • at equilibrium, the rate of the forward and reverse reactions are the same, irrespective of the presence of an enzyme
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10
Q

Describe the equilibrium position

A

a function only of the free-energy difference between reactants and products

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11
Q

Describe active sites

A
  • crevice in the enzyme structure
  • key catalytic groups are precisely orientated around the bound substrate
  • water usually excluded unless it is a reactant (crevice mainly lined with hydrophobic amino acids)
  • some hydrophilic residues are present for substrate binding or catalysis
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12
Q

catalytic groups

A

amino acid side chains

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13
Q

binding sites

A

bind and orient substrate(s)

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14
Q

catalytic sites

A

reduce chemical activation energy

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15
Q

Describe covalent catalysis

A
  • covalent bonds formed or broken
  • active site contains a highly reactive group that becomes temporarily covalently attached to the substrate during catalysis
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16
Q

Describe general acid-base catalysis

A

a molecule other than water plays the role of proton donor or acceptor

17
Q

Describe metal ion catalysis

A

metals assist via substrate binding, stabilising negative charges on reaction intermediates to facilitate acidity and enabling oxidation reactions

18
Q

Describe the enhancing proximity of reactants

A

bringing two molecules close together enhances transfer of function

19
Q

Describe chymotrypsin

A
  • catalyses peptide bond hydrolysis
  • attacks the unreactive carbonyl using a powerful nucleophile
20
Q

Describe nucleophile

A
  • a species which is strongly attracted to a region of positive charge in another species
  • contains an electron pair available for bonding
  • either fully negative ions, or have a strongly partial negative (d-) charge somewhere on the molecule
  • ‘excess’ electrons
  • propensity to form a new covalent bond with an electrophile, which accepts the bonding electrons
21
Q

species

A

ion or a molecule

22
Q

Describe a region of positive charge

A

a nucleus

23
Q

Describe a region of positive charge

A

a nucleus

24
Q

Describe the chymotrypsin catalytic triad

A
  • generates nucleophilic serine
  • acid/base catalyst
  • nucleophile
25
Q

Describe the chymotrypsin mechanism

A
  • enzyme-substrate
  • first tetrahedral (oxyanion hole)
  • acyl-enzyme
  • second tetrahedral (oxyanion hole)
  • enzyme-product
26
Q

Describe the Michaelis-Menten model

A
  • E+S -> ES -> E+P
27
Q

k1

A

E+S -> ES

28
Q

k2

A

ES -> E+S

29
Q

k3

A

ES -> E+P

30
Q

Vmax

A
  • [S]/[S] + KM
  • kcat[ET]
31
Q

Describe the kinetic response of enzymes

A
  • changes in substrate concentration means that the system tends towards a steady state
  • concentration of metabolites at steady state is dependent on the KM and Vmax of the enzymes in the system
32
Q

Describe enzyme kinetic parameters

A
  • evolved such that metabolite concentrations at steady state are maintained at relatively low levels (mM – low mM range)
  • metabolism does not exhaust the solvency capacity of the cell

Michaelmas Term 1 (42 decks)

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