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Yr 1 - Proteins & Enzymes > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What are most enzymes?

A

Nearly all are proteins, but some RNA molecules act as enzymes too

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2
Q

How do enzymes increase rate of reaction?

A

Enzymes lower the activation energy of a reaction

Provide catalytically competent groups for a specific reaction mechanism by binding substrates in an orientation that is optimised for the reaction.

Stabilises transition state of reaction to promote reaction towards product

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3
Q

What is the activation energy?

A

Energy required for a reaction to occur

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4
Q

Why is a 1:1 ratio between enzymes and substrates not needed?

A

Enzymes are not reactants so are not used up during reaction

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5
Q

How do enzymes affect reaction equilibrium?

A

Enzymes increase the rate at which the reaction equilibrium is reached, but do not shift the position of equilibrium.

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6
Q

What is the active site?

A

Region of enzyme that binds to the substrate and where the conversion to product takes place

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7
Q

How are active sites formed?

A

3D space formed by crucial amino acid residues (these residues can lie far apart in linear polypeptide chain)

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8
Q

What does the unique 3D arrangement that forms active sites provide?

A

Substrate specificity

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9
Q

Why are do active sites only bond substrates via weak interactions (and reversible covalents)?

A

Don’t want strong as will be difficult to release substrate

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10
Q

What is the basic enzymatic reaction?

A

E + S –> ES –> E+P
ES catalysed by k1
- ES –> E+P catalysed by k3
- ES –> E + S catalysed by k2

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11
Q

What is k1?

A

Rate of formation of enzyme-substrate complex

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12
Q

What is k2 and k3?

A

The rates of dissoci§ation of enzyme-substrate complex

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13
Q

Initial velocity (V0) at low substrate concentration is directly proportional to what?

A

[S]

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14
Q

At high [S], what happens to the velocity and the rate?

A

At high [S] the velocity tends towards a maximum value (maximum reaction velocity Vmax)

The rate becomes independent of [S]

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15
Q

What is Km?

A

The Michaelis Constant

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16
Q

What is Km equal to?

A

Equal to the [S] at which the reaction rate is half of Vmax

i.e. the substrate concentration when the reaction rate is half of the maximum

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17
Q

What does Km measure?

A

Measure of affinity of enzyme for its substrate (in terms of [S]) –> the same regardless of the amount of enzyme

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18
Q

What does a low Km mean?

A

High affinity

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19
Q

What does a high Km mean?

A

Low affinity

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20
Q

Why does a low Km indicate a high affinity?

A
  • Enzyme normally saturated with substrate
  • Only low [S] required to saturate enzyme
  • Will act at a more or less constant rate regardless of variations of [S]
21
Q

Why does a high Km indicate a low affinity?

A

 Enzyme not saturated with substrate
 Higher [s] required to saturate enzyme
 Activity will vary as [S] varies; rate of formation of product depends on availability of substrate

22
Q

How does increasing amount of enzyme affect Vmax?

A

Higher Vmax

23
Q

To determine the amount of enzyme present in a sample, what must be ensured?

A

o Ensure limiting factor is enzyme

o [S] must be high enough to ensure enzyme is acting at Vmax

24
Q

To determine the conc of a substrate in a sample, what must be ensured?

A

o Substrate must be limiting factor
o [S] must be below Km
o Rate of formation of product increases steeply with increasing [S]

25
Q

In the Lineweaver-Burk Plot, what is the y intercept? What is the gradient? What is the x intercept?

A

o y intercept = 1 / Vmax
o gradient = Km / Vmax
o x intercept = -1 / Km

26
Q

How does increasing the substrate conc affect reaction?

A

Increasing = increasing rate to a certain point; once all enzymes have bound, any substrate increase will have no effect on rate of reaction

27
Q

How does increasing enzyme conc affect reaction?

A

Increasing = increases rate as long as there is substrate available to bind to.

28
Q

How does increasing temp affect reaction?

A

Too low and too high slows reaction

29
Q

What is an enzyme inhibitor?

A

An enzyme inhibitor is a molecule that binds to an enzyme and decreases its activity.

30
Q

What is a competitive inhibitor?

A

An inhibitor that resembles substrate competes with substrate for active site (Either substrate or inhibitor can bind to enzyme (not at same time)

31
Q

How can competitive inhibitors be overcome?

A

By a higher substrate conc

32
Q

What is effect of competitve inhibitors on Km?

A

Km is raised by interfering with binding of substrate: affects affinity of substrate for enzyme and increases [S] required to achieve Vmax

33
Q

What is effect of competitve inhibitors on Vmax?

A

Unchanged –> inhibitor swamped out at high [S]

34
Q

When will competitive inhibitors exert inhibitory effects?

A

At lower conc

35
Q

What are non-competitive inhibitors?

A

o Inhibitor binds to a site other than the active site: inhibitor and substrate can bind simultaneously (independent site)
o Inhibitor alters conformation or accessibility of the active site

36
Q

Are non-competitive inhibitors affected by high [S]?

A

No

37
Q

What is effect of non-competitive inhibitors on Vmax?

A

Vmax decreases –> no matter how much substrate you add, a proportion of enzyme is switched off

38
Q

What is effect of non-competitive inhibitors on Km?

A

Unchanged –> binding of substrate to uninhibited enzyme is unaltered

39
Q

What is job of acetylcholine esterase?

A

Switches off motor impulses passing through nervous system

40
Q

What happens if acetylcholine esterase gets blocked (e.g. snake venom)?

A

Impulses don’t get switched off and keep going. Nerve impulses controlling muscle movement cause spasm: lungs go into spasm, stop breathing & suffocate

41
Q

How do NSAIDs (COX inhibitors) work?

A

Covalent modification of serine residue in active site via competitive irreversible inhibition

42
Q

What does methotrexate inhibit?

A

Methotrexate inhibits dihydrofolate reductase (an important enzyme in making nucleotides for DNA&RNA)

43
Q

What is methotrexate used to treat?

A
  • In low doses is used in inflammation (arthritis)
  • In high doses is used in cancer treatment: starved of building blocks for making DNA that fuels cancer. However, this treatment (chemotherapy) has negative effect on immune cells/hair cells as these all divide quickly so require DNA
44
Q

How does methotrexate bind?

A
  • Binds in its active site
  • Reversible (non-covalent) inhibition
  • Competitive
45
Q

What do COX enzymes do?

A

Turn lipids into prostaglandins

46
Q

Compare the binding of ibuprofen and aspirin?

A

Ibuprofen

  • Binds to active site non-covalently therefore is reversible
  • Binding is competitive

Aspirin

  • Covalent modification of a serine residue in active site therefore is irreversible
  • Inhibitor binding is competitive
47
Q

What are IC50 values?

A

Inhibitor concentration at which 50% of activity remains

48
Q

What do IC50 values tell us?

A

Tell us about relative effectiveness of inhibitors

Measure effectiveness of different inhibitors by measuring effects at different concentrations
o With standard amount of enzyme & substrate

Yr 1 - Proteins & Enzymes (8 decks)

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