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Bio chem > Lecture 9 - Enzymes > Flashcards

Lecture 9 - Enzymes Flashcards

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1
Q

Enzymes are central to life

Describe what enzymes are and do

A

catalysts - Increase rate of reaction

Proteins - Catalytic RNA, Ribozyme, Ribosome

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2
Q

Enzymes do not

A

change free energy level of products and reactants.

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3
Q

Enzymes Fight against entropy by…

A

Keeping cells organised,
control gradients,
control pH

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4
Q

Liver cells

A

Responds to insulin
Turn sugar into glycogen or
mobilise glycogen into sugar

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5
Q

ΔG = 0

A

At equilibrium

Substrates & Products equal concentration

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6
Q

is life at equilibrium?

A

no

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7
Q

ΔG < 0

A

Products dominate
Energy released spontaneous
- ΔG
Want to drive

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8
Q

ΔG > 0

A

Energy required
substrates dominate.
+ ΔG

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9
Q

what is needed to maintain cellular integrity?

A

energy

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10
Q

ΔG = ΔH - TΔS

A

Gibbs free energy
Enthalpy
Entropy

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11
Q

To favour forward reaction (ΔG < 0)

A

Enthalpy decrease (ΔH < 0)

Entropy increase (ΔS > 0)

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12
Q

Cellular integrity means

A

decrease in entropy (ΔS) in cell.

Energy required somewhere else.

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13
Q

Enzymes control

A

where and when energy is released to maintain the cell.

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14
Q

To keep reactions going

A

ΔG < 0

Negative

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15
Q

Kinetics

A

How quickly is it going to reach the equilibrium

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16
Q

timescale for life

A
  • Reactions pass through high- energy transition states.
  • Activation energy (ΔGo‡) required to reach transition state. determines rate.

• Free energy change (ΔGo)
sets ratio [P]/[S] at equilibrium.

• Activation energy of back
reaction = ΔGo + ΔGo‡

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17
Q

What determines rate?

A

Activation energy (ΔGo‡) required to reach transition state.

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18
Q

Reaction that favours products

A

Moves forward

Negative ΔG

How fast its going to get there is governed by the transition state

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19
Q

Higher the barrier / hill on graph Free energy vs Progress of reaction

A

Slower reaction

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20
Q

higher activation energy

A

Back reaction slower

Products favoured over reactants

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21
Q

enzymes lower

A

activation energy

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22
Q

How do Enzymes catalyse thermodynamically favourable reactions?

A

lowering the activation energy.

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23
Q

Catalyzed version by enzyme

A

Has lower activation energy

Faster reaction

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24
Q

Rate enhancement

A

differs from ΔG

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25
Q

Aldolase

A

+ΔG

big rate enhancement

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26
Q

Adenylate kinase

A

ΔG near 0

big rate enhancement

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27
Q

Cleavage of DNA phosphodiester backbone

A

-ΔG

Stable for 1000 years uncatalyze

Catalyze by ribonuclease A in less than a millisecond

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28
Q

‘Isozymes’ differ in

A

sequence but catalyse the same reaction.

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29
Q

Classes of enzymes

A
  1. Oxidoreductases (Redox)
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
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30
Q

Transferases

A

Transfer of a functional group.

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31
Q

Hydrolases

A

Hydrolysis reactions (using H2O).

Breaks down peptide bonds
Eg protease

Burn ATP

32
Q

Lyases

A

Non-hydrolytic breaking or making of bonds (not using H2O).

33
Q

Isomerases

A

Transfer of atoms/groups within a molecule to yield an isomeric form.

34
Q

Ligases

A

Join two molecules together (i.e. form a new bond; usually coupled to ATP cleavage.

35
Q

Enzyme–substrate binding occurs at

A

Active site

36
Q

Enzyme active site

A

has amino acid side chains projecting into it.

binds substrate via weak interactions.

determines specificity of reaction.

37
Q

Enzyme–substrate binding example

A

Hexokinase binding glucose

38
Q

Types of enzyme substrate bonds

A
  • Ionic bonds
  • Hydrogen bonds
  • van der Waals interactions
  • Covalent bonds
39
Q

Ionic bonds

A

Interactions of + and - charges

salt bridges

Make use of charged side chains (Asp, Glu, Arg, Lys).

40
Q

H bonds

A

Side chain or backbone O and N atoms act as h bond donors and acceptors.

Stabilise α helix, b strand, protein structures, protein substrate interactions

41
Q

van der Waals interactions

A

Between any protein and substrate atoms in close
proximity

2 atoms close up to each other

weakest

Abundant

42
Q

Covalent bonds

A

Strong bonds

Rare

43
Q

2 models for enzyme substrate binding

A

Lock and key

Induced fit

44
Q

Lock and key model

A

Complementary
No change in conformation required

Active site perfect shape for substrate to bind

Shape of substrate and conformation of active site are complementary

45
Q

Induced fit

A

Enzyme undergoes conformational change upon binding to substrate.

Shape of active site becomes complementary to shape of substrate only after substrate binds to enzyme.

46
Q

glucose and hexokinase binding model

A

Induced fit

47
Q

Enzymes are

A

dynamic (not static).

48
Q

Enzymes show

A

geometric and stereospecificity

49
Q

If shape of active site

is asymmetric,

A

enzyme distinguish between identical groups on substrate.

two CH2COO- groups.

50
Q

weak interactions ensure

A

specificity and reversibility:

51
Q

specificity.

A

Several bonds are required for substrate binding

52
Q

Weak bonds can only form

A

relevant atoms are precisely positioned.

53
Q

Molecular complementarity between enzyme and substrate is

A

critical.

54
Q

How is Activation energy (ΔGo‡) lowered?

A
  1. Ground state destabilisation.
  2. Transition state stabilisation.
  3. Alternate reaction pathway with a different (lower-energy) transition state.
55
Q

Ground state destabilisation and Transition state stabilisation is achieved by?

A

having an active site that has

shape/charge complementarity to transition state, not substrate.

56
Q

Strategies for Catalysis not exhaustive and exclusive

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,
57
Q

Cofactors with activated groups examples

A

electrons, hydride ion (H-), methyl groups (CH3), amino groups (NH2).

58
Q

For two molecules to react they need to be:

A

close together
In right orientation

Proximity and orientation

59
Q

what drives covalent catalysis?

A

Nucleophilic attack on an electrophile

60
Q

Electrophiles

A

Protons (H+)
Metal ions
Carbonyl carbon atom
Cationic imine (Schiff base)

61
Q

Example of nucleophilic attack; requires

A

correct orientation and ionisation.

62
Q

Cofactors

A

Non protein factors

Help enzymes catalyze reactions

63
Q

2 classes of cofactor

A

Metal ion

Coenzymes

64
Q

Metal ion catalysis

A

Specific coordination geometry orients substrates.

As Lewis acids, metals accept an electron pair to polarise
H2O and functional groups.

Transfer electrons in redox reactions.

65
Q

Enzymes that use Mg2+

A

Hexokinase
DNA polymerase
Pyruvate kinase

66
Q

What does Hexokinase use as a cofactor?

A

Mg2+

67
Q

Hexokinase uses Mg2+ as a cofactor and establishes

A

orientation of phosphates of ATP by octahedral coordination of Mg2+ ion.

68
Q

Hexokinase

Electron Withdrawing Lewis acid

A

stabilises electrons on

oxygen, making phosphorous a better electrophile.

69
Q

Hexokinase

A

Uses ATP

Has Mg2+ which binds to phosphate of ATP to help establish geometry and withdraw electrons as a lewis acid

Electron withdrawing lewis acid

70
Q

Coenzymes

A
  • small organic molecules.
  • co-substrates.
  • carriers (of electrons, atoms, or functional groups).
  • derived from vitamins.
71
Q

Pyruvate dehydrogenase

A

Provides acetyl-CoA in aerobic conditions

Multienzyme complex composed of 30 copies of enzyme E1, 60 copies of E2 and 12 copies of E3, each with cofactors.

Net reaction is an oxidative decarboxylation.

72
Q

Many cofactors of pyruvate dehydrogenase

A 
CoA (coenzyme A)
FAD
NAD+
TPP
Lipoic acid
73
Q

what dictates speed of reaction?

A

Activation energy of transition state

74
Q

What lowers activation energy?

A

Enzymes

75
Q

Enzyme Active sites are

A

highly specific for one reaction, particularly to shape of transition state.

76
Q

Many enzymes require

A

cofactors which confer specific abilities, e.g. redox activity.

Bio chem (36 decks)

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