INTRODUCTION

Good day, in this presentation, we are going to talk about enzymes. Enzymes are defined as
large molecules that speed up chemical reactions without increasing their activation energy. In
other words, they are also catalysts, which provide shortcuts for reactions, which then allow
them to use less activation energy. In this presentation, we shall be focusing on four aspects of
enzymes.

Nomenclature of Enzymes
The name of an enzyme is frequently derived from the reaction it catalyzes or from the
substance or class of substance(otherwise known as substrate) on which it acts. Most enzyme
names end with "-ase". Several enzymes, however, have earlier names that were given to them
before their functions were fully known such as pepsin, trypsin, and chymotrypsin.

Enzymes that catalyze an oxidation reaction are often called oxidase, while those that catalyze
a hydrolysis reaction are hydrolase.

Sometimes, the substrate is added to identify the enzyme, such as that of glucose oxidase and
pyruvate carboxylase. In some instances, only the substrate and not the reaction type is given in
the name like urease and lactase. In these names, the reaction involved is hydrolysis.

There are 6 major enzyme classifications based on their reaction type.

1. Oxidoreductases catalyze oxidation-reduction reactions. It requires a coenzyme that
oxidizes or reduces as the substrate is reduced or oxidized. An example of this is lactate
dehydrogenase.
2. Transferases catalyze the transfer of functional groups. There are two major subtypes,
namely, transaminases that catalyze the transfer of amino groups, and kinases that catalyze the
transfer of phosphate groups. An example is aspartate aminotransferase or aspartate
transaminase.
3. Hydrolases catalyze hydrolysis reactions. They are central in the process of digestion.
An example is acetylcholinesterase.
4. Lyases catalyze group elimination to form double bonds that do not involve hydrolysis or
oxidation. An example is Aconitase.
5. Isomerase catalyzes isomerization reactions. Only one reactant and one product are
operative in isomerase reactions. An example is phosphohexose isomerase.
6. Ligase - catalyze bond formation coupled with ATP hydrolysis. They require the input of
energy obtained by a hydrolysis reaction. An example is Tyrosine-tRNA synthetase

Models of Enzyme Activation

Before we learn about the two models of enzyme, lets first discuss how enzymes are activated.
Enzymes are activated once a substrate is attracted and binds to an enzyme active site. An
enzyme active site is that small portion or part of the enzyme that is involved in the reaction. It is
3D crevice formed due to the bending and folding of the protein, known as its secondary or
tertiary structure. The substrate is the molecule which the enzyme acts upon. Once these two
interact it yields a product known as the enzyme-substrate complex. This is what gives it its
catalyzing properties. The substrate is attracted to the active site by the same forces that
maintain the tertiary structure of the enzyme. Forces such as electrostatic interaction, hydrogen
bonds, and hydrophobic interactions.

Now there are two common models of enzyme activation. The first one is the lock-and-key
model, the first and simplest model created. It claims that the active site is a fixed and rigid
crevice that only accept a substrate with the same “shape” or geometrical conformation. It is
known as the lock-and-key model because the active site here represents the lock while the
substrate represents the key. If the key, or the substrate, is not the same exact shape or does
not compliment the shape of the lock, it will not be able to bind with the active site and no
enzyme-substrate complex will be formed. Therefore no catalysis will occur. Only the substrate
that exactly fits will be able to bind to the active site.

Second is the induced fit model, where it takes into account the “flexibility” of the active site.
This model is more applicable to numerous enzymes and is a more through explanation since it
takes into account the flexibility of the active site. It states that the active site is not rigid or
static, rather it is constantly changing in shape. It allows for small-changes in the shape of the
active site to accommodate for the substrate. They do not have to be the same exact shape all
together, the active site can “adapt” or “adjust” itself so that the substrate can bind to them. Just
like how a glove is flexible and adapts to the shape of the hand because of its flexibility, the
active site is also capable of making minor changes in its shape to take in the substrate.

Models of Enzyme Specificity

Enzyme Specificity
Enzyme specificity is the degree to which an enzyme’s activity is limited to a particular
substrate, group of substrates, type of chemical bond, or type of chemical reaction.

In an enzyme, an active site is present. It is a small, three-dimensional region within the

enzyme. It is the specific region in the enzyme where the substrate molecule binds and where
the catalytic event occurs.

The active site in each enzyme is limited in number and this determines the extent of enzyme
specificity. It also demonstrates specificity which allows it to discriminate between possible
substrate molecules. The shape of the active site closely mirrors a particular substrate. There is
a “close fit” of the correct substrate to the active site.

Categories of Enzyme Specificity

1. Absolute specificity - In this category of specificity, the enzyme catalyzes only one type
of reaction. It is also not common and is the most restrictive of all specificities. The
enzyme catalase exhibits absolute specificity. It only accepts the substrate hydrogen
peroxide.
2. Group specificity - Here, the enzyme acts on molecules as long as the reactive
functional group is present. An example would be the enzyme chymotrypsin which
catalyzes peptide bonds near aromatic amino acids.
3. Linkage specificity - In linkage specificity, the enzyme acts on a certain type of
chemical bonding. It is the most general of the common specificities. Enzymes
phosphatases are linkage specific. It hydrolyzes phosphate-ester bonds in all types of
phosphate esters.
4. Stereochemical specificity - the enzyme acts on a particular stereoisomer. For
instance, the L-amino acid oxidase catalyzes the oxidation of the L-amino acid, but not
the D-amino acid.

Regulations of Enzyme Specificity

The regulations of enzyme specificity involve the concept of energy conservation. There are five
regulations of enzyme specificity.
 1. Allosteric enzyme is an enzyme with two or more protein chains, otherwise known as a
quaternary structure. It also has two kinds of binding sites, namely a substrate and a
regulator. Regulators are substances that bind at regulatory sites of allosteric enzymes.
It has two types: positive and negative.
a. A positive regulator increases enzyme activity, and the shape of the active site is
changed so that it can be prepared to accept substrates.
b. Meanwhile, a negative regulator (also known as non-competitive inhibitor)
decreases enzyme activity, and changes to the active site are made so that
substrates would not be readily accepted.
2. Feedback control is the process in which activation or inhibition of the first reaction in a
reaction sequence is controlled by a product of the reaction sequence.
a. To illustrate, consider a biochemical process within a cell that occurs in several
steps, each step catalyzed by a different enzyme. The product of each step is the
substrate for the next enzyme.

If the final product (D) is a negative regulator of the Enzyme 1:

3. At low concentrations of D, the reaction sequence proceeds rapidly.

4. At higher concentration of D, the activity of Enzyme 1 becomes inhibited (by feedback),
and eventually the activity stops.
a. At the stopping point, there is sufficient D present in the cell to meet its needs.
When the concentration of D decreases through use in other cell reactions, the
activity of Enzyme 1 increases and more D is produced.

5. Proteolytic enzyme is an enzyme that catalyzes the breaking of peptide bonds that
keep the primary structure of a protein. As they would eventually destroy the tissues that
produce them, these enzymes are produced in an inactive form and are later converted
to active form when necessary. Majority of the digestive and blood-clotting enzymes are
proteolytic.
6. Zymogen is the inactive precursor of a proteolytic enzyme. To activate it requires an
enzyme-controlled reaction that removes some part of the zymogen structure. This
would change the three-dimensional structure of the zymogen, which would also affect
the site conformation.
7. Covalent modification is a process in which enzyme activity is manipulated by
changing the structure of an enzyme by means of either attaching or removing a
chemical group from a certain amino acid within the enzyme’s structure.