Lecture 29- Enzymes II

Question 1

“Perfect enzyme” (6)

Answer 1

An enzyme where the chemical activity it carries out is so efficient the limiting step is finding the substrate.
Reaction rate is limited by diffusion.
Speed at which enzyme finds substrate is fixed by the structure of the enzyme.
Evolution can only work on the chemistry of an enzyme- speed them up.
Diffusion limited rate = K3/Km = 108M-1s-1.
K3= catalytic rate = Vmax/[end]total
EZ = Intermediate.

Question 2

So why has evolution not made all the other enzymes “perfect”? (2)

Answer 2

It wouldn’t be helpful to have all the enzymes working full out all the time, as all the nutrients would be degraded.
Enzyme activity needs to be controlled e.g. allosteric, phosphorylation.

Question 3

Example of “perfect” enzymes (2)

Answer 3

Carbonic anhydrase is an example of a perfect enzyme, an example of a diffusion-limited enzyme.

In glycolysis, this enzyme is called TIM (triosephosphate isomerase). This enzyme interconverts two products.
On breakdown of fructose 1,6 bisphosphate you get two products, but only one is useful which is glyceraldehyde-3-phosphate. The other molecule has to be converted to G3P, TIM catalyses this reaction.

Question 4

Proteases (6)

Answer 4

Breaks down proteins, hydrolyses the peptide bonds of their protein substrate.
Specificity means selectivity.
Various classes: serine, aspartyl, cysteine and metallo.
Serine proteases are very reactive as they have the catalytic triad, there are other residues nearby able to H bond with serine and histidine present. Moves a proton making serine more reactive.
Side chains make OH more reactive.
Serine proteases have a conserved 3D structure with a charge relay system, the different proteases can accommodate to different side chains.

Question 5

Serine proteases - examples (4)

Answer 5

Chymotrypsin and trypsin are involved in digestion.
Chymotrypsin has a very reactive serine which attacks the peptide bond by forming an acyl-enzyme intermediate.
Wants the square side chain to be Phe, Trp or Tyr, so the binding pocket is hydrophobic.

Trypsin can only hydrolyse the peptide bond if the square side chain is positively charged, so a lysine or arginine. This is because in the binding pocket of trypsin there is a binding site for the Lys/Arg and it has a negatively charged residue. This allows enzyme to bind to the protein and cleave the peptide bond.

Elastin important in lung function.
Elastase wants a small residue; its binding pocket is very small so only small residues can get through and bind.

Question 6

Catalytic triad

Answer 6

A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes

Question 7

Enzymes as Nano-Machines - Example 1 (6)

Answer 7

Mitochondria.
Outer membrane is permeable to many substrates while the inner membrane is impermeable to many substrates Inc. protons.
Inner membrane: electron transport chains –> respiratory chain.
Protons are generated and exported out of mitochondria.
In oxidative phosphorylation, protons are pumped into IMS and as inner membrane is impermeable to protons, you can set up a protein gradient. You are storing energy as well as there being a charge difference (a potential difference across the membrane).
On inner mitochondrial membrane, we have ATP synthase which acts as a motor and activated by a rotating spindle (proton driven). There are three active sites. We can drive this motor by protons, as the motor spins we produce ATP.

Question 8

Enzymes as Nano-Machines - Example 2 (2)

Answer 8

Topoisomerase II is also a Nano-machine, it is a molecular clamp that unlinks tangled chromosomes. It uses ATP to work the clamp.