ENZYMES

Enzymes 2. Transferases catalyze the transfer of a

 Are proteins that speed up reactions group of atoms, such as from one molecule
produced by the living cell to another.
 Used in diverse areas like food 3. Hydrolases catalyze hydrolysis reactions.
manufacturing, paper, leather, agriculture, 4. Lyases catalyze the addition of two groups
and different industries. They are also useful to a double bond or the removal of two
in disease diagnosis nowadays. groups from adjacent atoms to create a
 large molecules that increase the rates of double bond.
chemical reactions without themselves 5. Isomerases catalyze isomerization
undergoing any change. Without enzymes to reactions.
act as biological catalysts, life as we know it 6. Ligases, or synthetases, catalyze the
would not be possible. joining of two molecules.
 The vast majority of all known enzymes are
globular proteins, Factors affecting enzymatic reactions
 an enzyme cannot alter the equilibrium for a Effect of temperature- Enzymes have an
reaction; it can only accelerate the reaction optimum temperature at which they function most
rate, by decreasing the activation energy of efficiently. enzymes normally function as catalysts
the reaction at constant (ambient or body) temperature.
 Nearly all enzymes are proteins denature at high temperature and lose activity.
 Substrates-chemical reactants to which an Effect of pH-pH sensitivity of enzymes results
enzyme binds are the enzyme’s from the effect of pH on the ionic charge of amino
 The location within the enzyme where the acid side chains of enzymes. Various solutes,
substrate binds is the enzyme’s active site. including substrates, products, metal ions and
regulatory molecules, also affect the rate of
Properties of an Enzyme enzymatic reactions
 Enzymes, also called a biological catalyst,
accelerate biochemical reactions without Specificity
affecting the nature of the product.  Enzymes are highly selective, catalyzing only
 All enzymes are proteins with a molecular specific substrates (substances where enzyme
weight ranging from about 12,000 to more acts) and specific reaction, thus this property
than 1 million. of enzyme is collectively known as specificity.
 Enzymes react at optimum pH and Enzymes can be Bond specific (relative
temperature, usually ranging from 25-45°C, specificity), group-specific (structural
with 37°C as the highest enzymatic action. specificity), substrate-specific (absolute
At 60°C, enzymes are inactivated in a liquid specificity), stereoscopic specific (optical
medium. specificity), geometric specific and co-factor
 Enzymes have high catalytic activity, specific.
speeding up reactions as much as 1021 over  The reaction that the enzyme catalyzes, is
uncatalyzed levels under optimum determined chemically by the amino acid
temperature and pH conditions. Catalytic residues in the catalytic center of the enzyme.
power is defined as the ratio of the enzyme- In general, the active site of the enzyme is
catalyzed Rate of a reaction to the composed of the substrate binding site and the
uncatalyzed rate. catalytic site.
 Substrate specificity is determined by the
How Are Enzymes Named and Classified? size, structure, charges, polarity, and
 Enzymes are commonly given names derived hydrophobicity of the substrate binding site.
from the reaction that they catalyze and/or the  All enzymes are assigned a four-digit enzyme
compound or type of compound on which they classification (EC) number to organize the
act different enzymes that catalyze the many
 Enzymes can be classified into six major thousands of reactions.
groups according to the type of reaction they  first digit indicates membership of one of
catalyze the six major classes of enzymes
1. Oxidoreductases catalyze oxidations and  next two digits indicate substrate subclasses
reductions. and sub- subclasses
 ENZYMES

 fourth digit indicates the serial number of  The functional role of coenzymes is to act as
the specific enzyme transporters of chemical groups from one
reactant to another
Mechanisms of Enzyme Action
Lock-and-Key Model Enzyme Kinetics
- The simplest and most frequently referenced  The Michaelis–Menten equation: a simple
is the lock-and-key model model of an enzymatic reaction
- This model assumes that the enzyme is a  In 1913, long before the structure of proteins
rigid three-dimensional body. The surface was known, Leonor Michaelis and Maud
that contains the active site has a restricted Leonora Menten developed a simple model for
opening into which only one kind of the kinetics of enzyme catalyzed reactions
substrate can  The Michaelis–Menten model assumes that
Induced-Fit Model the substrate S binds to the enzyme E, forming
- American biochemist, Daniel Koshland, an essential intermediate, the enzyme-
introduced the induced-fit model in which he substrate complex (ES), which then undergoes
compared the changes occurring in the shape reaction on the enzyme surface and
of the cavity upon substrate binding to the decomposes to E + P (product).
changes in the shape of a glove when a hand  The first step in the enzymatic reaction is the
is inserted reversible process of binding of substrate to
- the enzyme modifies the shape of the active the enzyme forming enzyme-substrate
site to accommodate the substrate complexes. The second step is a catalytic
Catalytic Power of Enzymes process where the enzyme catalyzes a reaction
- Enzymes have high catalytic activity, to form a product. This reversible reaction is
speeding up reactions as much as 1021 over caused by two possible fates of transition
uncatalyzed levels under optimum state: 1) may lose energy to return to reactant
temperature and pH conditions. Catalytic (substrate) form; or 2) may lose energy to
power is defined as the ratio of the enzyme- produce a product. These now lead to two
catalyzed Rate of a reaction to the equilibria. Remember that an enzyme only
uncatalyzed rate. accelerates the rate of a reaction and it
catalyzes both the reverse and forward
Co-enzymes and Co-factors reaction.
 Coenzymes serve as intermediate carriers of  The catalytic activity of an enzyme can be
functional groups in the conversion of determined through an enzyme assay. An
substrates to products. Some coenzymes are enzyme assay measures either the
tightly bound and are difficult to separate disappearance of a substrate or the appearance
referred to as prosthetic groups of the enzyme. of a product. This involves two processes:
 Holoenzymes- combined form of protein and fixed time assay and kinetic assay. In a fixed
the co-enzyme. Enzymes with covalently or time assay, the amount of reaction is measured
noncovalently bound coenzymes.  The in a fixed amount of time while in the kinetic
prosthetic group forms a complex with protein assay, the progress of the reaction is monitored
that is catalytically active continuously. Do take note that enzyme assay
 Apoenzyme – a catalytically inactive protein is very sensitive to changes in variables such
without a prosthetic group. heat labile or as temperature & pH, which is why it is
unstable part of the holo-enzyme. gives important to control conditions precisely.
necessary three-dimensional structures  The enzymatic reaction has what we call a
required for the enzymatic chemical reaction. Saturation point, where all enzyme molecules
 Prosthetic groups- are tightly bound, often are bound to their substrate. As a consequence,
covalently linked, to an enzyme and remain an additional substrate could no longer
associated with the enzyme during the entire increase the rate of reaction due to the fact that
catalytic cycle. all enzymes have been used up.
 Some enzymes require inorganic (metal) ions,  To illustrate this mechanism, Figure 5.3 shows
frequently termed cofactors, for their activity, a saturation curve of the enzymatic reaction.
e.g., blood-clotting enzymes that require Ca The reaction velocity, V, refers to the number
2+, and oxidoreductases, which use iron, of reactions that are catalyzed by an enzyme
copper, and manganese. per second. The maximum rate (Vm) at which
a reaction can occur is its Saturation point.
 ENZYMES

The term first-order kinetics is given when the of substrate, however, it binds to other parts
substrate concentration is low where the rate of the enzymes called allosteric site causing
of reaction is dependent on the substrate and conformational change to the active site of
zero-order kinetics is given when the substrate the enzyme.
concentration is high because the rate of  an additional substrate concentration does
reaction is not dependent on the concentration not overcome this type of inhibition.
of the substrate. Furthermore, it does not affect Km and
 In the first-order kinetics, ½ Vmax and Km are affects the rate of the catalyzed reaction.
important. The affinity of an enzyme to its
substrate is determined by which the reaction Uncompetitive Inhibition
velocity (V) is one-half of the maximum  This type of inhibition occurs when the
velocity (Vm) for the given reaction. Km is substrate causes the binding of inhibitor or
referred to as the Michaelis constant which cause a change in the structure of the
denotes the concentration of substrate enzymes that allow the inhibitor to bind.
producing a rate of ½ Vmax. Therefore, an increase in substrate
 Observe that there is an approximately linear concentrations causes an increase in the
relationship between the substrate and the degree of inhibition. Just like competitive
velocity of the reaction at a low substrate inhibition, Km is increased but Vm is
concentration and that in high concentrations, decreased because the presence of
the velocity is nearly independent of the increased substrate caused the inhibitors to
substrate. Nearly all enzymes behave using work better.
this figure thereby the Michaelis-Menten
Equation is used to interpret enzyme kinetics. Phosphorylation
 Another mechanism to inhibit enzyme
Enzyme Inhibition reaction is phosphorylation which is
 Enzymes need therefore to be regulated in its mediated by kinase enzymes. Kinase
function and this is called Enzyme Inhibition. enzymes can either inactivate or activate
Enzyme inhibitors cause a decrease in enzyme an enzyme by cleaving the phosphate
activity by binding to the enzymes. group from ATP and binds it to the
 The inhibition of enzymes can be reversible enzyme.
and irreversible.
 Inhibitors that are tightly bound to the active Zymogens
site of an enzyme causes irreversible  Zymogens are enzymes secreted in an
inhibition. inactive state. This is beneficial because
 While reversible inhibition has inhibitors that enzymes can be transported to different
are transiently bound to the active site locations without performing its function.
(competitive inhibition) or allosteric site (non- The addition of amino acids makes these
competitive inhibition) of the enzyme. enzymes inactive. In order to become
active, amino acids must be acted upon by
Competitive Inhibition other enzymes.
 prevent the substrate from binding at the
active site of the enzyme by mimicking a
portion of the substrate thereby preventing a
catalytic reaction.
 cause an apparent increase in Km, without
changing Vmax
 the rate of the enzyme catalyzed reaction in
the presence of a competitive inhibitor can
be increased by increasing the substrate
concentration, since substrate, at higher
concentration, competes more effectively
with the inhibitor.
Noncompetitive inhibitors
 cause an apparent decrease in Vmax
 do not bind at the active site of the enzyme,
therefore, will not compete with the binding