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BIOC192 > Enzymes > Flashcards

Enzymes Flashcards

1
Q

What is a cofactor?

A

A non-protein factor that helps and enzyme catalyse a reaction

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2
Q

What are the 2 classes of cofactor?

A
  • metal ion

- coenzyme

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3
Q

Are metal ion cofactors Lewis acids or bases?

A

Lewis acids = e- acceptors

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4
Q

What is the function of metal ion cofactors?

A

form coordination compounds with precise geometries - good for positioning reactants precisely where they need to be in the active site

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5
Q

What are coenzymes?

A
  • small organic molecules
  • co-substrates (involved at different steps, but not used up in the reaction)
  • carriers (of e-, atoms or functional groups)
  • often derived from vitamins
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6
Q

Describe the cofactor used in glycogen phosphorylation

A

PLP cofactor at active site of glycogen phosphorylate and facilitates its activity

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7
Q

What are advantages of using many weak bonds to bind the S to E?

A

○ Strength in numbers
○ Several bonds required for substrate and specificity
○ Only form if the relevant atoms are precisely positioned
○ Easy to break = reversibility

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8
Q

How is Ea lowered? (3)

A
  1. Ground state destabilisation
    • Ground state energy up
  2. Transition state stabilisation
  3. Alternate reaction pathway with different (lower energy) transition state
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9
Q

How can gs destabilisation and ts stabilisation be achieved?

A

by having an active site that has shape/charge complementarity to the TS, not the substrate

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10
Q

Name the 5 catalytic mechanisms

A
  1. Preferential binding of the transition state.
  2. Proximity and orientation effects.
  3. Acid-base catalysis
  4. Metal ion catalysis.
  5. Covalent catalysis.
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11
Q

What is an analogue?

A

Resembles the transition state but doesn’t disappear, is more stable
- Very effective as drugs

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12
Q

What is an example of an analogue? What is its clinical function?

A

Lipitor = powerful cholesterol lowering drug

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13
Q

How does lipitor work?

A

Inhibits HMG-CoA reductase

  • Natural substrate = has aldehyde group
  • TS analogue = alcohol group -> binds better to Lipitor because it resembles the transition state, rather than the normal substrate
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14
Q

Lipitor can be classified as a…

A

transition state analogue inhibitor of the reaction

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15
Q

Proximity and orientation effects refers to…

A

…that for 2 molecules to react, they need to be in close proximity and at correct orientation

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16
Q

Acid-base catalysis involves…

A

proton (H+) transfer

17
Q

Which amino acids will donate a proton, and at what pH?

A
  • Glu, Asp give up proton at low pH = -ve charge

- Lys, Arg will only donate at high pH

18
Q

What is special about histidine in terms of acid-base catalysis?

A

Histidine can either accept or donate a proton depending on environment
- pKa(His) ~ 6.5 (close to physiological pH) -> can act as acid or base

19
Q

In metal ion catalysis, the metal ion provides…

A
  • Substrate orientation (due to specific coordination geometries)
  • Ability to act as Lewis acids (e- acceptors) to polarize water/other functional groups
  • Provide sites for e- transfer (for catalyzing Redox reactions)
20
Q

What is an example of an enzyme which uses metal ion catalysis?

A

Hexokinase
- Large -ve charge on O’s in TS
- Mg2+ balances the -ve charge of the transition state
.: Decreases energy of transitions state

21
Q

Describe what is formed in covalent catalysis

A

A reactive, short-lived intermediate is formed, covalently attached to the enzyme

22
Q

Define enzyme inhibitor

A

a compound that binds to an enzyme and reduces its activity

23
Q

What are the 2 classes of inhibitors?

A

irreversible and reversible

24
Q

how/where does an irreversible inhibitor bind?

A

binds covalently to the enzyme by reacting with a specific aa side chain in the active site

25
Q

how/where does a reversible inhibitor bind?

A

not covalently bound to the enzyme, can be competitive with the substrate (trying to bind to same place), non-competitive, or a combo of both (= mixed inhibitor)

26
Q

what is the difference between a reversible and irreversible inhibitor?

A

irreversible: binds to enzyme and permanently inactivates it [covalent bond]
reversible: binds to the enzyme but can be released (leaves the enzyme in its original condition)

27
Q

what is a competitive inhibitor?

A

Inhibitor competes directly with the substrate for the active site

28
Q

can a competitive inhibitor be outcompeted by the substrate?

A

yes, infinite [S] outcompetes the inhibitor

29
Q

What changes to kinetic parameters occur when a competitive inhibitor is added?

A 
More substrate needed to get to V = Vmax/2
→ No change in V max
	- No change in y intercept
→ Increase in Km
	- X intercept moves closer to 0
30
Q

What is an example of a competitive inhibitor? (2)

A

• Transition state analogues (e.g. Lipitor)
• Anastrozole - inhibits aromatase
→ Treatment of breast cancer

31
Q

true or false: in non-competitive inhibition, the enzyme can bind substrate or inhibitor, not both

A

false: enzyme can bind substrate or inhibitor or both because inhibitor binds at different site than substrate

32
Q

What is pure non-competitive inhibition?

A

where the binding of I has no effect on the binding of S

33
Q

What changes to kinetic parameters occur when a pure non-competitive inhibitor is added?

A

→ Vmax decreases

→ Km stays the same, because ability of substrate binding to active site is not affected by the enzyme

34
Q

What is mixed inhibition?

A

When inhibitor binding slightly changes substrate affinity

35
Q

What changes to kinetic parameters occur when a mixed inhibitor is added?

A

→ Vmax and Km both change

36
Q

What is the function of glycogen phosphorylase?

A

Takes the terminal sugar off the glycogen (which is stored in muscles) , then used to derive energy

37
Q

How is glycogen phosphorylase activity regulated?

A

by both allosteric activators (AMP) and inhibitors (feedback inhibition of glycogen phosphorylase)

38
Q

A sigmoidal curve shows what about Michaelis-Menten kinetics?

A

That allosteric enzymes break Michaelis-Menten parameters

BIOC192 (11 decks)

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