Enzymes
The agents of metabolic function
Almost all are proteins some are RNA
Give cells capacity to exert kinetic control over thermodynamic potential a rxn
may have -G but that doesnt dictate how long the rxn takes use an enzyme to
control speed of rxn
Characterized by three distinct features
1. Catalytic Power
2. Specificity
3. Regulation
1. Catalytic Power
Enzymes can accelerate reactions as much as 10 16 over uncatalyzed rates
e.g., urease: catalyzed rate 3x10 4/sec vs uncatalyzed 3x10-10/sec = ratio of
1014
e.g., OMP decarboxylase: rate inhancement ratio = 10 17
Hydration of CO2
is thermodynamically favored but very slow
introduction of carbonic anyhdrase accelerates reaction 10 million-fold!
However it is specific will not hydrate CO, only CO 2
2. Specificity
Several enzymes hydrolyze proteins but these proteolytic enzymes (digestive
enzymes) are quite specific: some proteases will hydrolyze only peptide bonds
containing a set of amino acids with specific R-groups
e.g., trypsin: will only cleave bond if side chain has Lys or Arg
e.g., thrombin: will only cleave peptide bond if side chain has Arg and Gly
Many proteases will also hydrolyze ester bond (similar to peptide bond- has O
instead of NH) hydrolyzation of ester results in acid and alcohol pdts
Enzymes selectively recognize proper substrates over other molecules
Enzymes produce pdts in very high yields, often over 95%
Specificity is controlled by 3D structure of active site: unique fit of substrate
with enzyme controls selectivity for substrate and pdt yield
3. Regulation
Some enzymes require cofactors / prosthetic groups for fxn
Coenzyme small, vitamin derived organic molecules
Metal ion such as Zn, Mg
Apoenzyme: enzyme without its cofactor
Holoenzyme: apoenzyme plus cofactor
Reactions that are not spontaneous can be made spontaneous by adjusting
concentrations of reactants and products
For real rxns, must consider concentrations, not just refer to G
e.g., DHAP isomerization to GAP
under standard state conditions G = +7.5 kJ/mol (will not occur
spontaneously)
if concentrations are altered: GAP = 3x10-6 M and DHAP = 2x10-4 M, the
G = -2.9 kJ/mol (reaction will proceed)
Transition state (X )
Overall free energy change for rxn (G) related to equilibrium constant (Keq)
Free energy of activation for rxn (G ) related to rate constant (affected by
enzyme)
Transition state is transient molecular structure that is no longer substrate but not
yet pdt
Transition state is least stable and most-seldom-occupied structure along rxn
pathway
Active site is 3D cleft or crevice (active site not composed of adjacent residues in
1 sequence, but residues at various locations in sequence that become adjacent
once folded in 3D structure)
ES complex held together by weak noncovalent interactions
Specificity of ES interactions arises mainly from H-bonding and from the shape of
the active site which rejects molecules that dont have a sufficiently
complementary shape
ES complex binding:
Lock & Key: substrate binds active site with complementary shape
Induced Fit: active site assumes shape complementary to substrate only
after S is bound
Chemical kinetics
Reaction rate (velocity) for A P
V = - A / T (decrease of substrate over time) or P / T (increase of pdt
over time)
1st order rxn (dep on one reactant unimolecular rxn)
o A P : V = k[A]
o Rate constant (k) units: s-1
2nd order rxn (dep on 2 reactant molecules bimolecular rxn)
o 2A P : V = k[A]2
o A + B P : V = k[A][B]
o Rate constant (k) units: M-1s-1
Remember Keq = k1 / k-1 where k1 is forward rate constant, k-1 is reverse rate
constant
Time-dependent concentration changes of [S], [ES], [P], [E]
(remember enzyme is catalyst and cannot be lost or changed during rxn)
Michaelis-Menten Equation
Rate of formation of product when an enzyme (E) combines with a substrate (S) to
form an enzyme-substrate complex (ES) which can proceed to form product (P) or
dissociate into E and S
Assumes formation of ES complex
Assumes that ES complex is in rapid equilibrium with free enzyme
ES
E+P
k1 forward
k-1 reverse
k2
E+S
3. Enzyme Inhibitors
Reversible inhibitors interact with an enzyme via noncovalent associations
rapid equilibrium between enzyme and inhibitor
Competitive Inhibition
If you increase [S] you can
knock inhibitor off enzyme
* Vmax is same but Km is
increased *
-1/KM 1/Vmax
-1/KM(1+[I]/Ki)
Noncompetitive inhibition
* Vmax decreases *
* Km is unchanged *
Uncompetitive inhibition
* Both Vmax and Km are
lowered *
Irreversible inhibitors
Group-specific reagents reagents react with specific side chains of amino acids
e.g., Acetycholinesterase reaction with DIPF (specifies Ser-OH)
Affinity labeling reactive substrate analogs structurally similar to substrate for
enzyme and covalently bind to active-site residues; are more specific for enzyme
active site than group-specific
e.g., Chymotrypsin substrate and inhibitor TPCK similar structure
Suicide inhibitors (mechanism-based inhibitors) modified substrates that provide
most specific means to modify an enzyme active site; inhibitor binds to enzyme as
a substrate and initially processed by the normal catalytic mechanism which then
generates a reactive intermediate that inactivates the enzyme through covalent
modification
e.g., N,N-dimethypropargylamine and (-)Deprenyl inhibition of monoamine oxidase
(MAO) MAO deaminates NTMs (such as dopamine in the case of Parkinsons
disease), inhibition drugs
Transition-state analogs (mimics) potent enzyme inhibitors that mimic the
transition state structure an enzyme binds the transition state more tightly than
the substrate
e.g., Proline isomerization catalyzed by proline racemase enzyme: proline enters
trigonal planar transition state mimicked by pyrrole 2-carboxylic acid (inhibitor)
that binds racemase 160 times stronger than proline
Penicillin
Irreversibly inactivates a key enzyme in bacterial cell wall synthesis
Contains reactive peptide bond in -lactam ring that reacts with enzyme
Cell wall structure: polysaccharide chains are cross-linked with pentaglycine and
tetrapeptide: formation of which is achieved via enzyme Glyopeptide
transpeptidase
Penicillin blocks the last step in cell wall synthesis (cross-linking of different
peptidoglycan strands) by mimicking the terminal D-Ala-D-Ala unit of normal
substrate
Most enzymes are proteins, but
Ribozymes segments of RNA that display enzyme activity in absence of protein
e.g., RNaseP and peptidyl transferase
Abzymes antibodies that recognize the transition state, bind, and catalyze rxn