Enzyme Catalysis

Question 1

Acid Base Catalysis

Answer 1

• electron transfer in reactions creates a high energy intermediate state caused by charge separation
• this is unfavorable and raises energy of activation
• bases and acts donate or release proteins to create lower energy states by neutralising charges
• this reduces the energy of activation

Question 2

general acid/base catalysis

Answer 2

• rate of reaction dependent on the concentration of all acids/bases present in the reaction, not only the proton concentration
• general bases: Asp, Arg, His

Question 3

specific acid/base catalysis

Answer 3

• rate of reaction dependent on only proton/hydroxide io concentration

Question 4

concerted general acid/base catalysis

Answer 4

• both processes occur simultaneously

- bond breakage at the same time as bond formation

Question 5

Keto-Enol Tautomerisation

Answer 5

• uncatalysed reaction has charge separation with a high energy carbanion TS
• this is disfavored and reduces spontaneity
• acids can protonate negative oxygen or bases can deprotonate TS: reduces energy
• draw mechanisms*

Question 6

Enzyme Catalyzed Concerted Keto-Enol Tautomerisation

Answer 6

• concerted mechanism: acid protonates carbonyl group as base deprotonates carbon
• uses amino acid side chains as acids or bases
• enzymes are more effective due to their concerted mechanism
• side chains form conjugates and are reset by water
• enzyme shows activity dependent on the pH of solution, as the side chains can protonate/deprotonate to either become active or inactive

Question 7

Regulation of Residue pKa

Answer 7

• eg. glutamine has a normal pKa of 3/4
• if near a hydrophobic region: uncharged favored, pka is raised
• if near a positive charge: negative charged form is stabilized, lowering pka
• if near a negative charge: negative charged form is destabilized, pka is raised

Question 8

Covalent Catalysis

Answer 8

rate acceleration through transient formation of catalytic substrate covalent bond

• 3 stages
  1. nucleophilic reaction between catalyst and substrate
  2. withdrawal of electrons from reaction center by electrophilic catalyst
  3. elimination of catalyst
• nucleophile must be deprotonated

Question 9

Activation of Carbonyl Groups to form Schiff Base

Answer 9

Schiff Base:

• C double bonded to NR3 is more reactive because the system is more polarisable
• protonated form is even more reactive due to resonance and increase polarizability
• pi cloud shifted over the N to make C extremely electrophilic to aid catalysis

Question 10

Roles of Covalent Catalysis

Answer 10

1. group transfer reactions

2. increase substrate reactivity: activate it so that product can be formed

Question 11

Good Covalent Catalyst

Answer 11

• highly nucleophilic
• good leaving group (highly polarizable)
• Asp, Lys, Cys, His, Ser

Question 12

Acetoacetate Decarboxylase

Answer 12

uncatalysed: forms enolate ion
charged: stabilised by Lys residue to reduce charge accumulation in TS to lower free energy
- enamine formed, which is neutral so the structure is more stable
* see mechanism*

Question 13

Electrostatic Catalysis

Answer 13

the presence of charges/oriented dipoles within the active site can stabilise the TS via solvation

• closer charges maximises electrostatic catalysts
• micro environment of enzyme can be fine tuned to improve charge stabilisation
  eg. non polar residues enhance the energy of interaction

Question 14

Metal Ion Catalysis

Answer 14

1. metalloenzymes: tightly bound
2. metal activated enzymes: loosely bound

• neutralise negative charges, but are extremely effective due to their large charges and high concentrations

Question 15

Roles of Metal Ions

Answer 15

• electrostatic stabilisation and charge isolation: highly effective because of high charge that is pH independent
• redox reactions
• binding and orientation of substrates: act as lewis acids to form dative covalent bonds
• promote nucleophilic catalysis: activate bound H20

Question 16

FeS clusters

Answer 16

• redox active cofactors allow electron transfer
• Fe2+ found is FeS clusters ligated by residues
• involved in electron transfer
• found in Complex I: ubiquinone oxidoreductase
• electron transfer from UQ to UQH2
• iron cluster chain allows electron hopping

Question 17

Oxidising Water in Photosynthesis

Answer 17

• two molecules of water oxidised to oxygen and four protons/electrons
• OEC (oxygen evolving clusters): contains manganese ions that exist in multiple oxidation states
• they are used to soak up and store electrons that are then used to fix carbon dioxide

Question 18

Activating Water

Answer 18

• hydroxide ions are excellent nucleophiles but exist at low concentrations
• metal ions promote nucleophilic catalysis by ionising water
• ion’s charge makes its bound water more acidic than free water
• pka of water is lowered to form metal ion bound OH: a potent nucleophile

Question 19

Carbonic Anhydrase

Answer 19

Carbon dioxide + water to give a proton and HCO3-

• has Zn2+ ion tetrahedrally coordinated by three His side sides and the oxygen of a water molecule
• OH stabilised by charge interaction and accumulates

Question 20

Orientation and Proximity Effects

Answer 20

• rate enhancement obtained by taking 2 reactants out of solution and placing them next to each other in the active site to raise local reactant concentration
• correct orientation of orbitals: stereoelectronic assistance
• unfavorable entropy offset by favorable binding energy because of complementation

Question 21

Preferential TS binding

Answer 21

• enzyme complementary to TS more than substrate
• stabilization of TS leads to lowering of free energy of activation
  ‘induced fit’ model

Question 22

Coulumbic Energy of Interaction

Answer 22

• dependent on permitivity of medium
• proportional to inverse of distance between charges
• maximum in a vacuum