Chapter 6
Eduard Buchner – Coined term ‘Enzymes’
Cell-free yeast Ferment sugar alcohol
Fermentation was continued even when removed from cells
Catalytic activity depend on integrity of native protein conformation
Molecular weight = 12,000 to 1,000,000
Cofactor is an inorganic compound
Coenzyme complex or organic/metallorganic acts as a carrier of functional
groups
VOCAB
Prosthetic group - coenzyme that is tight/covalently bound to enzymatic
protein
Holoenzyme - Catalytically active enzyme bound coenzyme subdidvison of a
prosthetic group
Apoenzyme or apoprotein - the protein part of a holoenzyme
Active site - specific place for substrate
Substrate -Goes to the active site by enzymatic movement
Ground state – Starting point
Transition state – the point at which decay of substrate and product are
equally likely (Peak)
Biochemical free energy – standard change at 7.0 pH
Activation energy – difference btwn the ground and transition state
Rate limiting step – slowest point of the rxn
Rxn Intermediate – anything on the pathway with a finite chemical lifetime
(ES,EP)
Specificity – to tell differences btwn substrate and competing fake by binding
energy
Entropy – Large restrictions in the relative motions of two substrates
Desolvation – Replacement of the solvation shell structured around substrate
and enzyme weak bonds
Induced fit – enzyme changes its shape when the substrate binds
Enzymes classified by their Rxns they catalyze
Oxidoreductases – Transfers electrons by H atoms
Transferases - group transfer
Hydrolases – Transfer of functional groups to water
Lyases – Cleaved c-c,c-o,c-n by elimination leaving addition of groups/
rings to double bonds
Isomerases – Transfer of groups within molecules to yield ISOmeric
forms
Ligases – Formation of c-c,c-o,c-n bonds by condensation coupled to
cleave ATP or similar cofactors
Translocases – movement of molecules across membranes or their
separation within membranes
Enzymes affect rxn rate
E + S ↔ ES ↔ EP ↔E + P -- E,S,P are enzymes substrate and product,
transitional complexes being ES and EP
Catalyst do not affect rxn equilibria
Enzymes accelerate the interconversion S and P
Enzymes are not used up completely
Activation energy – lower EA to increase rates for rxns needed for cell
survival
Rxn equilibria are linked to the standard free-energy change for the reaction
Reacting rates ↔ activation energy
Keq – Describes an equilibrium such as S↔P
[ P]
K’eq= [S ]
For unimolar reaction S P
Rate equation
V=k[S] V=Velocity / rate of rxn k = rate constant
First order Rxns – Rate depends on substrate only (k units reciprocals S-1)
Second order – Rate depends on concentration of two different molecules or
compounds
Transition-state theory
kT − ∆ G ∓/ RT
k= ee relationship btwn k and ∆ G ∓ inverse and
h
exponential
Enzymes enhance rates in the range of 5 to 17 orders of magnitude
Examples; Carbonic anhydrase 107 Cyclophilin 105
Binding energy ∆ G B Non-covalent enzyme substrate interaction
Hydrogen – hydrophobic effect
Covalent interactions of substrates and enzymes -- use to lower
activation energy
Full effect of substrate and enzymes is formed only when substrate reaches
transition state
Unfavorable binding and favorable results in lower NET activation energy
Weak binding btwn E and S drive enzymatic catalysis
Active site -- Optimized when substrate in a cavity and removed from water
Binding energy – contrains substrate in the proper orientation to rxn
Barriers to rxn ; entropy in solution, solvation shell that surround and
stabilizes, proper alignment of catalytic function
Distortion of a substrate causes unfavorable free-energy change
Binding energy compensates thermosynamically to keep balance
Catalytic functional groups aid in cleavage formation bonds by
Acid/base , Covalent , Metal ion Catalysis’
Acid- base
Protons are transferred between enzyme and substrate
sometimes with an intermediate
Catalysis uses H3O or OH ions in the water
Mediated by weak acids or bases that is NOT water
Occurs in Glutamine, asparagine, arginine, lysine, cystine,
histidine, serine, and tyrosine for their enzymatic
Covalent Catalysis – Transient covalent bond forms between the enzyme and
the substrate
Catalysis only results when the new pathway has lower activation
energy
New steps must be faster that OG reaction
Metal Ions Catalysis
Help orient the substrate for rxn
Stabilize charged rxn transition states
Mediate oxidation-reduction rxns – by reversible changes in the
metal ions oxidation state
o Nearly 1/3 of all known enzymes require 1+ metal ions for
catalytic activity
6.3
Enzyme kinetics = the discipline focused on determining RATE OF RXN and
how it changes in experimental conditions.
Presteady- Initial period during which ES
builds
Steady – period when ES and other
Intermediates remain constant
Steady kinetics – the traditional analysis
of reaction rates
Initial rate (initial velocity);