Most Enzymes Are Proteins:
With the exception of a small group of catalytic RNA molecules, all enzymes are
proteins. Their catalytic activity depends on the integrity of their native protein
conformation. If an enzyme is denatured or dissociated into its subunits, catalytic
activity is usually lost. If an enzyme is broken down into its component amino
acids, its catalytic activity is always destroyed. Thus the primary, secondary,
tertiary and quaternary structures of protein enzymes are essential to their
How Enzymes Work:
The enzymatic catalysis of reactions is essential to living systems. Under
biologically relevant conditions, uncatalysed reactions tend to be slow – most
biological molecules are quite stable in the neutral pH, mild-temperature, aqueus
environment inside cells. Many common chemical processes are unfavorable or
unlikely in the cellular environment, such as the transient formation of unstable
charged intermediates or the collision of two or more molecules in the precise
orientation required for reaction.
The distinguishing feature of an enzyme-catalysed reaction is that it takes place
within the confines of a pocket on the enzyme called the active site. The molecule
that is bound in the active site and acted upon by the enzyme is called the
substrate. The surface of the active site is lined with amino acid residues with
substituent groups that bind the substrate and catalyse its chemical
Enzymes Affect Reaction Rates, Not Equilibria:
A simple enzymatic reaction might be written:
E + S ES EP E + P
Where E, S and P represent the enzyme, substrate and product; ES and EP are
transient complexes of the enzyme with the substrate and with the product.
The function of a catalyst is to increase the rate of a reaction. Catalysts do not
affect reaction equilibria (A reaction is at equilibrium when there is no net
change in the concentrations of reactants or products).
Any reaction, such as S P, can be described by a reaction coordinate
diagram. Energy in biological systems is described in terms of free energy, G. In
the coordinate diagram, the free energy of the system is plotted against the
progress of the reaction (the reaction coordinate). The starting point for either
the forward or the reverse reaction is called the ground state, the contribution to
the free energy of the system by an average molecule (S or P) under a given set of
The equilibrium between S and P reflects the difference in the free energies of
their ground states. In the reaction coordinate diagram, the free energy of the
ground state of P is lower than that of S, so the standard free energy change (ΔG’˚) for the reaction is negative (the reaction is exergonic) and at equilibrium
there is more P than S (the equilibrium favors (P). The position and direction of
equilibrium are not affected by any catalyst.
Refer to lecture notes 9; ‘Enzymes increase reaction rate’ reaction coordinate
A favorable equilibrium does not mean that the S P conversion will occur at a
detectable rate. The rate of a reaction is dependent on an entirely different
parameter. There is an energy barrier between S and P: the energy required for
alignment of reacting groups, formation of transient unstable charges, bond
rearrangements, and other transformations required for the reaction to proceed
in either direction.
To undergo this reaction, the molecules must overcome this barrier and
therefore must be raised to a higher energy level. At the top of the energy hill is a
point at which decay to the S or P state is equally probable. This is called the
transition state. The transition state is not a chemical species with any significant
stability and should not be confused with a reaction intermediate (such as ES or
EP). It is simply a fleeting molecular movement in which events such as bond
breakage, bond formation, and charge development have proceeded to the
precise point at which decay to either substrate or product is equally likely.
The difference between the energy levels of the ground state and the transition
state is the activation energy, . The rate of a reaction reflects this
activation energy: a higher activation energy corresponds to a slower reaction.
Reaction rates can be increased by raising temperature and/or pressure, thereby
increasing the number of molecules with sufficient energy to overcome the
energy barrier. Alternatively, the activation energy can be lowered by adding a
catalyst. Catalysts enhance reaction rates by lowering activation energies.
A Few Principles Explain the Catalytic Power and Specificity of Enzymes:
Enzymes are extraordinary catalysts. They are also very specific, readily
discriminating between substrates with quite similar structures.
Chemical reactions of many types take place between substrates and enzymes’
functional groups (specific amino acid chains, metal ions, and coenzymes).
Catalytic functional groups on an enzyme may form a transient covalent bond
with a substrate and activate it for reaction, or a group may be transiently
transferred from the substrate to the enzyme. In many cases, these reactions
occur only in the enzyme active site. Covalent interactions between enzymes and
substrates lower the activation energy (and thereby accelerate the reaction) by
providing an alternative, lower-energy reaction path.
Non-covalent interactions help stabilize protein structure and protein-protein
interactions. These same interactions are critical to the formation of complexes
between proteins and small molecules, including enzyme substrates. Much of the
energy required to lower activation energies is derived from weak, non-covalent
interactions between substrate and enzyme. What really sets enzymes apart
from most other catalyst