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Building a phenotype - lectures > EnYems And > Flashcards

EnYems And Flashcards

1
Q

Why must metabolism be accelerated by enzymes?

A

To operate on a time scale relevant to life

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2
Q

What does thermodynamics NOT a tell you

A

Speed of a reaction

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3
Q

What does he say (3 things) about this reaction:

ATP ADP + Pi

A
  1. Thermodynamically favourable so it’s spontaneous (-🔺G)
  2. Incredibly slow in absence of catalyst
  3. However in the context of ATP this is also a good thing because we don’t want to deplete energy store really quickly
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4
Q

How much does Triose Phosphate Isomerase (TPI), an enzyme in glycolysis speed up the reaction

  • what’s the rate of the uncatalysed reaction
  • catalysed reaction
  • rate enhancement
A

Uncatalysed: one product/day

Catalysed: 4300 products/second

Rate enhancement: 1000 million fold

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5
Q

Slowest uncatalysed reaction

A

Synthesis of UMP (a pyramiding nucleotide)

1 reaction per 45 million years

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6
Q

When the synthesis of UMP is catalysed

Catalysed
Reaction enhancement

A

Catalysed - 39 products/ second

Rate enhancement: 1.4x10^17 fold

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7
Q

What is the synthesis of UMP catalysed by

A

OMP decarboxylase (decarboxylates orotidine monophosphate to UMP)

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8
Q

Why are uncatalysed reactions so slow

A

Because they go from a substrate to product via an intermediary state (the transition state)

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9
Q

Transition state

A

Transitory molecular structure that is no longer the substrate but not yet the product

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10
Q

What’s the least stable species in a reaction?

A

The transition state

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11
Q

What has the highest free energy in a reaction?

A

The transition state

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12
Q

What will free energy be like in a spontaneous reaction

A

Free energy of products will be lower than free energy of reactants

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13
Q

What does an enzyme do in terms of free energy?

A

It reduces the free energy of the transition state

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14
Q

How do enzymes accelerate a reaction in terms of transition state and activation energy?

A

They stabilise the transition state , reducing the activation energy required to reach it

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15
Q

Enzymes affect the ___ NOT the ___

A

Enzymes affect the KINETICS not the THERMODYNAMICS

Delta G remains the same

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16
Q

Two unaltered things when an enzymes acts

A
  1. 🔺G

2. Equilibrium position

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17
Q

What does an enzyme do in terms of equilibrium

A

Accelerates how long it takes to reach equilibrium

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18
Q

Simplistic analogy of how enzymes stabilise transition state

A

Enzyme complementary to transition state

But leaving enough room so that once the conformational change occurs the substrate is completely complementary to the enzyme (magnets arranged so they anticipate the shape of the broken sticks)

Because then by being completely complementary and snug with the transition state it makes the transition state more stable which reduces free energy required to reach it

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19
Q

What part of an enzyme shares similar features in all enzymes

A

The active site

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20
Q

General features of the active site

A
  1. Crevice in the enzyme structure
  2. AA side chain catalytic groups
  3. Water excluded
  4. Hydrophilic side chains
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21
Q

What are catalytic groups on enzymes

A

Within active site key AA side chains known as catalytic groups are precisely orientated and around the bound substrate

22
Q

What is meant by water is excluded in the active site of an enzyme

A

Crevice is mainly lined with hydrophobic amino acids so water excluded unless it’s a reactant

23
Q

What is meant by there are SOME amino acids with hydrophilic side chains in the enzyme active site?

A

There are a few and these polar residues acquire special properties essential for substrate binding or catalysis

24
Q

What is meant by some hydrophilic residues in active site of enzyme

A

Some but they acquire special properties essential for substrate binding or catalysis

25
Q

What’s the driving force behind protein folding

A

Hydrophobic residues make protein fold to have a hydrophobic core

26
Q

Why are proteins preferred as a catalyst rather than RNA

A

proteins can fold specifically due to hydrophobic action of residues

Proteins can be made of 20 different amino acids which all provide improved chemistry for a catalyst

27
Q

Why are proteins better catalysts than RNA

A

Proteins can fold because of natural hydrophobic action

Improved chemistry set of 20 AA side chains

28
Q

Covalent catalysis

A

Breaking or making of covalent bonds between enzyme and substrate

(Typically active site has a highly reactive group that become temporarily covalently attached to the substrate)

29
Q

Acid base catalysis

A

A molecule other than water acts as an acid (proton donor) or a base (proton acceptor)

30
Q

In the context of enzymes metal ions are usually

A

Positively charged

31
Q

How can metal ions assist catalysis (3)

A
  1. Help bind substrate
  2. Stabilise negative charges on reaction intermediates
  3. Increase acidity of interacting molecules (promotes the molecules role in acid base catalysis)
32
Q

Catalysis by enhanced proximity of reactants

A

Bring two molecules close together can enhance transfer of function groups

33
Q

4 mechanisms enzymes commonly employ to catalyse specific reactions

A
  1. Covalent catalysis
  2. General acid base catalysis
  3. Metal ions catalysis
  4. Enhanced proximity
34
Q

Acid-base catalysis example

How does chymotrypsin catalyse the hydrolysis of peptide bonds with this mechanism?

A

Chymotrypsin attacks the unreactive carbonyl in the peptide bond with a nucleophile.

And forms a covalent bond

35
Q

What is the nucleophile in chymotrypsin that aids catalysis the peptide bond

A

Serine 195 residue

36
Q

What’s the catalytic triad (chymotrypsin action)

A

Asp 102
His 57
Set 195

37
Q

How does the serine 195 in chymotrypsin become a nucleophile?

+ how is the catalytic triad involved

A

His attracts H in serine OH group

Serine now a nucleophile because it’s lost the H from its OH group so is just the O- (forms a charged alkoxide ion)

Asp forms H bond with His to allow His to more easily accept to H from the Ser

38
Q

Then sweetlove illustrates a catalytic mechanism using

A

Chymotrypsin as an example

Looks at how it uses covalent and acid base catalysis

39
Q

Example of base catalysis in chymotrypsin action

A

Chymotrypsin uses histidine residue as a base catalysis to increase nucleophilicity of Seine

40
Q

What can the kinetics of many enzyme catalyse reactions be mathematically described by?

A

Michaelis-Menten model

41
Q

Why is it useful to know Vmax and Km

A

If u know what Vmax and Km are then u get define mathematically what the enzyme will do for any given substrate concentration

42
Q

How to get Vmax and Km

A

Use purified enzyme and do experiments

43
Q

When [S] and Km are the same what is the velocity ?

A

Half of the V max

44
Q

What is Km a measure of

A

Affinity at which enzyme binds substrate

45
Q

Lose Km means what

A

Tighter it’s binding it’s substrate and so faster reaction will go go a given substrate concentration

46
Q

Why are enzyme kinetics important?

A

Allows us to make predictions about how enzyme systems behave

47
Q

Sumamry of the confusing bit!

A
  • Enzymes control rate of reactions
    • If rate of one recation is faster than another so that more product is used than made by the supplying reaction then it wouldn’t wortk
    • So enzymes keep all reactions at a steady state
    • Enzyme kinetics have evolved so that metabolite concentrations are all at a steady state
    • This is important because it keeps metabolite concnetrations in a low range otherwise the cell would become staurated and there wouldn’t be enough water to sufficiently hydrate everything
48
Q

Example of enzyme kinetics being an important tool for biotechnology

A

involved in biosynthesis of lysine (animal food addidative). If they’ve got all these constants then they can try and optimise the system.

EG. Try and optimise Kms of enzymes to engineer different affinity of substrate and see how it would affect production of lysine

49
Q

In a system of enzymes the kinetic response of enzymes to changes in substrate concentration means …

A

the system tends towards a steady state

50
Q

Vmax and Km are selected by evolution because

A

need to keep metabolite concentrations at steady state relatively low so solvency capacity of cell is not exhausted

Building a phenotype - lectures (36 decks)

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