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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
Aldolase
+ΔG big rate enhancement
26
Adenylate kinase
ΔG near 0 big rate enhancement
27
Cleavage of DNA phosphodiester backbone
-ΔG Stable for 1000 years uncatalyze Catalyze by ribonuclease A in less than a millisecond
28
‘Isozymes’ differ in
sequence but catalyse the same reaction.
29
Classes of enzymes
1. Oxidoreductases (Redox) 2. Transferases 3. Hydrolases 4. Lyases 5. Isomerases 6. Ligases
30
Transferases
Transfer of a functional group.
31
Hydrolases
Hydrolysis reactions (using H2O). Breaks down peptide bonds Eg protease Burn ATP
32
Lyases
Non-hydrolytic breaking or making of bonds (not using H2O).
33
Isomerases
Transfer of atoms/groups within a molecule to yield an isomeric form.
34
Ligases
Join two molecules together (i.e. form a new bond; usually coupled to ATP cleavage.
35
Enzyme–substrate binding occurs at
Active site
36
Enzyme active site
has amino acid side chains projecting into it. binds substrate via weak interactions. determines specificity of reaction.
37
Enzyme–substrate binding example
Hexokinase binding glucose
38
Types of enzyme substrate bonds
* Ionic bonds * Hydrogen bonds * van der Waals interactions * Covalent bonds
39
Ionic bonds
Interactions of + and - charges salt bridges Make use of charged side chains (Asp, Glu, Arg, Lys).
40
H bonds
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
van der Waals interactions
Between any protein and substrate atoms in close proximity 2 atoms close up to each other weakest Abundant
42
Covalent bonds
Strong bonds | Rare
43
2 models for enzyme substrate binding
Lock and key | Induced fit
44
Lock and key model
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
Induced fit
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
glucose and hexokinase binding model
Induced fit
47
Enzymes are
dynamic (not static).
48
Enzymes show
geometric and stereospecificity
49
If shape of active site | is asymmetric,
enzyme distinguish between identical groups on substrate. two CH2COO- groups.
50
weak interactions ensure
specificity and reversibility:
51
specificity.
Several bonds are required for substrate binding
52
Weak bonds can only form
relevant atoms are precisely positioned.
53
Molecular complementarity between enzyme and substrate is
critical.
54
How is Activation energy (ΔGo‡) lowered?
1. Ground state destabilisation. 2. Transition state stabilisation. 3. Alternate reaction pathway with a different (lower-energy) transition state.
55
Ground state destabilisation and Transition state stabilisation is achieved by?
having an active site that has | shape/charge complementarity to transition state, not substrate.
56
Strategies for Catalysis not exhaustive and exclusive
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
Cofactors with activated groups examples
electrons, hydride ion (H-), methyl groups (CH3), amino groups (NH2).
58
For two molecules to react they need to be:
close together In right orientation Proximity and orientation
59
what drives covalent catalysis?
Nucleophilic attack on an electrophile
60
Electrophiles
Protons (H+) Metal ions Carbonyl carbon atom Cationic imine (Schiff base)
61
Example of nucleophilic attack; requires
correct orientation and ionisation.
62
Cofactors
Non protein factors Help enzymes catalyze reactions
63
2 classes of cofactor
Metal ion | Coenzymes
64
Metal ion catalysis
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
Enzymes that use Mg2+
Hexokinase DNA polymerase Pyruvate kinase
66
What does Hexokinase use as a cofactor?
Mg2+
67
Hexokinase uses Mg2+ as a cofactor and establishes
orientation of phosphates of ATP by octahedral coordination of Mg2+ ion.
68
Hexokinase | Electron Withdrawing Lewis acid
stabilises electrons on | oxygen, making phosphorous a better electrophile.
69
Hexokinase
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
Coenzymes
* small organic molecules. * co-substrates. * carriers (of electrons, atoms, or functional groups). * derived from vitamins.
71
Pyruvate dehydrogenase
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
Many cofactors of pyruvate dehydrogenase
``` CoA (coenzyme A) FAD NAD+ TPP Lipoic acid ```
73
what dictates speed of reaction?
Activation energy of transition state
74
What lowers activation energy?
Enzymes
75
Enzyme Active sites are
highly specific for one reaction, particularly to shape of transition state.
76
Many enzymes require
cofactors which confer specific abilities, e.g. redox activity.

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