ENZYME TERMINOLOGY

Transition State:
In a pathway connecting reactants to products, the potential energy increases until it has a maximum value at
the transition state. Once the transition state is crossed, the reaction is downhill in terms of potential energy.
Transition state analog
Transition state analogs are stable compounds whose structures resemble presumed transition states.
Transition states themselves are not stable compounds but transient states in which bonds are forming and
breaking. The dissociation constant for a transition state analog is about 10 -13M. An enzyme is
complementary to the transition state in shape and chemical character.
Activation energy:
The activation energy is the minimum increase in potential energy for reactants to be converted to products,
and hence the minimum energy that reactants must have to be able to react (to reach the transition state). The
requirement that the reactants have sufficient energy, to cross from reactants to products limits the rate of
most reactions.
Binding energy
The tight binding of the enzyme to the transition state lowers the activation energy.
Lock and Key model
Emil Fischer proposed that enzymes were rigid templates that accepted only certain substrates as keys. It is
now accepted that the key is the transition state and not the substrate.
Induced Fit
Activation of an enzyme by a substrate-initiated conformational change is called induced fit. Enzyme
flexibility is involved in substrate specificity and catalytic activity.
Catalytic Triad
A constellation of three amino acid residues, found in many proteolytic enzymes, in which two of the residues
convert the remaining residue, usually a serine or cysteine, into a potent nucleophile.
Initial Velocity:
When substrate is added to the enzyme to initiate a reaction there is initially little or no product present and
the amount of substrate has not decreased significantly. The rate of the reaction during this period is called
the initial velocity Vo.
Diffusion limited reaction
A diffusion limited reaction is one in which every collision between reactants leads to products. The rate of
reaction in this case is limited by the rate of collisions, which is affected just by the rates of diffusion. The
rate constant for collision between molecules in water is about 1 x 10 10 M-1 sec-1. A reaction that occurs with
a rate constant close to this value is said to be diffusion controlled.
Maximal Velocity:
The maximal velocity Vmax, is the maximum rate of reaction catalyzed by an enzyme at very high substrate
concentration. The enzyme is saturated with substrate and almost all enzyme molecules have substrate
bound.
Rate determining step
The rate-determining step in a series of reactions is the slowest step, which therefore ultimately limits the
rate of formation of product.

Michaelis constant:
The Michaelis constant, Km, is the concentration of substrate required for the reaction velocity to be half of
Vmax.
It is also the ratio of rate constants for the reaction model. Under conditions where k-1 is much greater than
k2, Km is equal to the dissociation constant of the enzyme substrate complex and is a measure of the affinity
of the enzyme for its substrate.
k1
E+S
k-1

ES

k2

E+P

Km = (k-1 + k2)/ k1 = [E][S]/[ES]

Michealis Menten (MM) kinetics:
MM kinetics derives from a model with reversible substrate binding to the enzyme, followed by the
chemical transformation. It predicts the behaviour of many enzymes very well.
Catalytic constant, kcat:
The apparent rate constant for an enzyme-catalysed reaction operating at maximum rate is called the
catalytic rate constant, kcat. The maximum rate, Vmax occurs when the enzyme is saturated with substrate.
Vmax = kcat[Eo]. If the enzyme obeys MM kinetics then kcat is the same as k2, the rate constant for the
catalytic step.
Turnover number:
The number of substrate molecules converted into product by an enzyme molecule in a unit time when the
enzyme is fully saturated with substrate. (Equal to kcat)
Catalytic efficiency:
The ratio of the catalytic rate constant to the Michaelis constant, i.e. kcat/Km, is known as the catalytic
efficiency..
Specificity constant:
The catalytic efficiency of an enzyme is the kcat/Km ratio. For comparing reactions of different substrates
with the same enzyme, the relative values of the catalytic efficiencies for different substrates predict the
relative amounts of different products formed. For this reason, kcat/Km is also referred to as the specificity
constant.
Association constant
This is the equilibrium constant for the association of two molecules to form a complex.
For an enzyme forming the enzyme substrate complex:
Kassoc = [ES]/[E][S]
The higher the association complex the greater the affinity of the enzyme for its substrate. Most is present in
the complex.
Dissociation constant
This is the equilibrium constant for the dissociation of a complex (inverse of the association constant). For
example - for an enzyme and its substrate forming the ES complex
Kdiss = [E][S]/[ES]
The lower the dissociation constant, the higher the affinity.

Inhibition constant
The inhibition constant is the dissociation constant for the inhibitor enzyme complex.
The lower the inhibition constant, the greater the affinity of the inhibitor for the enzyme and the stronger the
inhibition
Ki = [E][I]/[EI]
Lineweaver-Burke plot
The double reciprocal plot is a graph of 1/Vo vs 1/[S]. If the enzyme obeys MM kinetics, then this gives a
straight line with slope Km/Vmax, Y-intercept of 1/Vmax and X-intercept of -1/Km.
Eadie-Hofstee plot
This is a graph of Vo vs Vo/[S], which for MM kinetics gives a straight line with slope Km and an intercept of
Vmax.
Competitive Inhibition
This occurs when the inhibiting compound can bind reversibly to the active site of an enzyme and block the
binding of substrate, but the compound itself does not undergo a reaction.
Noncompetitive Inhibition
A reversible noncompetitive inhibitor is a compound whose effects occur through binding to an enzyme
somewhere other than the active site. Thus a noncompetitive inhibitor prevents the chemical reaction from
occurring, but does not do so by competing with substrate for the active site. Reversible noncompetitive
inhibitors are allosteric inhibitors.
Uncompetitive inhihition
An Uncompetitive inhibitor is a compound whose effects occur through binding to an enzyme-substrate
complex, preventing completion of the enzyme reaction and release of product
Irreversible Inhibitors
A molecule that permanently damages the ability of the enzyme to catalyze reactions is called an irreversible
inhibitor. Such inhibitors react covalently with the enzyme. (also called suicide inhibitors or mechanism-based
inhibitors, Trojan horse inhibitors)
Affinity labels (substrate analogs) are molecules that covalently modify active site residues are are structurally
similar to an enzymes substrate.
Group specific reagents react with specific R groups (side chains) of amino acids e.g iodoacetamide reacts with
sulfhydryl groups (-SH)
Allosteric Enzyme
An allosteric enzyme is one which has multiple active sites as well as distinct regulatory sites that control the
flux of biochemicals through a metabolic pathway. The activity of a catalytic centre is altered by the binding of
molecules at the regulatory sites. Multimeric allosteric enzymes can exhibit cooperativity that is the binding
of substrate to one active site increases the activity of another active site in the complex. They do not obey
Michaelis Menten kinetics and exhibit sigmoidal curves of Initial velocity vs Substrate concentration. They are
usually located at the beginning of a metabolic pathway.