05. Forms and functions of enzymes

Question 1

What is an enzyme?

Answer 1

A protein catalyst that increases velocity of chemical reaction and is not consumed in the reaction it catalyses (remains chemically unchanged).

Question 2

The active site is a cleft, indentation of the enzyme molecule. What are the 3 advantages of having an active site as a cleft?

Answer 2

1. The indentation/cleft has a 3D conformation to confer specificity
2. Since the cleft is indented inside, it limits access to non-substrate molecules
3. It positions specific amino acid residues(on the active site) for catalysis.

Question 3

Enzymes are known to confer specificity to their substrates. Why is specificity important in biological reactions (e.g. glycolysis with 10 steps and 9 enzymes to catalyse)

Answer 3

With specificity, it ensures high yield at the end of the 10 steps of glycolysis process to ensure efficient usage of resources.

Question 4

The lock and key hypothesis is not a very good model to explain the substrate specificity of enzymes. Explain why.

Answer 4

• Lock and key hypothesis states that the substrate must be an exact fit to the active site of the enzyme, which is not efficient since there are many substrates with similar shapes/functional groups.

-Lock and key hypothesis also fails to explain the stabilisation of transition state that enzymes can achieve (bc transition state is different shape and does not produce an exact fit to active site;; so it doesnt make sense that the enzyme can stabilise the transition state if it is not exact shape)

Question 5

What model can be used to explain specificity of enzymes instead? What does this model state?

Answer 5

Induced fit model, where the active site is not an exact fit, but when substrate binds to it, the active site undergoes a structural change to bind to substrate better.

Question 6

Enzymes can catalyse reactions involving only 1 substrate. True or False?

Answer 6

False, most enzymes can catalyse reactions involving > 1 substrate with similar shapes / chemical bonds etc.

Question 7

What are cofactors and what are the 2 main groups of cofactors?

Answer 7

Cofactors are the non-protein portion of the enzyme which is required for enzyme activity.

Types of cofactors:
1. Metal ions (inorganic)
2. Coenzymes (organic)

Question 8

What are the 2 groups of coenzymes (organic cofactors) and do they bind loosely/tightly?

Answer 8

1. Cosubstrate : binds transiently, can detach from active site once catalysis is done
2. Prosthetic group : binds tightly
   - just like a prosthetic leg where it needs to fit tightly to persons thighs for them to walk
   - heme in hemoglobin/globulin : prosthetic group –> need to bind tightly in order to deliver O2

Question 9

What is the equation of Gibb’s free energy?

Answer 9

∆G = ∆H-T∆S,

∆H : enthalpy change (heat given off/taken in)
∆S : disorder of a system
T : temp (in K)

Question 10

What does the ∆G tell us about the spontaneity of the reaction?

Answer 10

∆G<0 : reaction is spontaneous and can occur
∆G>0 : reaction is non-spontaneous and is unlikely to occur

Question 11

what is the main limitation of ∆G?

Answer 11

∆G only tells us if the reaction can occur, but does not tell us anything about the rate of the reaction.

Question 12

How do enzymes increase the ROR?

Answer 12

They provide an alternative pathway with a lower activation energy (by lowering the energy of transition state)

• thus more molecules have energy ≥ Ea, ROR increases.

Question 13

What are the 2 kinds of catalytic mechanisms?

Answer 13

1. Acid-base catalysis
2. Metal ion catalysis

Question 14

What is the idea behind acid-base catalysis?

Answer 14

Residues in the active site can act as acids or bases by donating a proton to substrate / removing a proton from substrate to make substrate more reactive.

Question 15

What is the idea behind metal ion catalysis in contributing to catalytic activity? [4]

Answer 15

1. Metal ions stabilize the negative charge of substrates so the other substrate can react with it better.
2. Metal ions bind to substrates to orientate them properly for reaction. (metal ions form ionic bonds with electroneg atoms on substrate and thus holding it in place)
3. Polarisation of substrates. (Donates or accepts protons to make substrates more reactive)
4. metal ions can mediate redox reactions

Question 16

Is it possible to totally replace metal ions with positively charged amino acid groups to stabilise the negative charges and orientate substrate molecules properly? Why?

Answer 16

No.

1. Metal ions are unaffected by pH. If there was a change in pH, positively charged amino groups will no longer be able to perform their function as they may lose positive charge.
2. Positively charged amino groups usually have a +1 charge. However, for metal ions, they usually have charges greater than +1, which allows them to stabilise negative charges better.

Question 17

what is the effect of temperature on enzyme activity.

Answer 17

as temp increase, ROR increases.
-for every 10°C increase, ROR doubles.

Beyond optimal temperature, enzyme activity quickly declines to 0 as heat causes molecule to vibrate fast and molecular interactions between side chains are disrupted, causing enzymes to denature and lose their tertiary structure.
- Tertiary structure gone = activity gone.

Question 18

How can change in pH affect enzyme activity?

Answer 18

Enzymes only work across small pH range. If the pH is out of the buffering capacity of residues involved (pKa ± 1), it can break intra and intermolecular bonds, altering conformation of enzyme and altering its activity (enzyme activity decreases drastically)