Enzyme Catalysis Flashcards
Acid Base Catalysis
- 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
general acid/base catalysis
- 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
specific acid/base catalysis
- rate of reaction dependent on only proton/hydroxide io concentration
concerted general acid/base catalysis
- both processes occur simultaneously
- bond breakage at the same time as bond formation
Keto-Enol Tautomerisation
- 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*
Enzyme Catalyzed Concerted Keto-Enol Tautomerisation
- 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
Regulation of Residue pKa
- 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
Covalent Catalysis
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
Activation of Carbonyl Groups to form Schiff Base
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
Roles of Covalent Catalysis
- group transfer reactions
2. increase substrate reactivity: activate it so that product can be formed
Good Covalent Catalyst
- highly nucleophilic
- good leaving group (highly polarizable)
- Asp, Lys, Cys, His, Ser
Acetoacetate Decarboxylase
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*
Electrostatic Catalysis
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
Metal Ion Catalysis
- metalloenzymes: tightly bound
- metal activated enzymes: loosely bound
- neutralise negative charges, but are extremely effective due to their large charges and high concentrations
Roles of Metal Ions
- 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
FeS clusters
- 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
Oxidising Water in Photosynthesis
- 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
Activating Water
- 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
Carbonic Anhydrase
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
Orientation and Proximity Effects
- 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
Preferential TS binding
- enzyme complementary to TS more than substrate
- stabilization of TS leads to lowering of free energy of activation
‘induced fit’ model
Coulumbic Energy of Interaction
- dependent on permitivity of medium
- proportional to inverse of distance between charges
- maximum in a vacuum
