Biology Chapter 3 – Enzymes And Metabolic Reaction

OBJECTIVES

 State the factors that affect chemical reactions

 Explain the role of enzymes in metabolic reactions
 Describe the mode of action of enzymes
 Describe the methods by which enzymes are regulated
 Distinguish between competitive and non-competitive enzyme inhibition
 Understand the practical applications of enzymes.
Factors Affecting Chemical Reactions:
Every chemical reaction has a specific equilibrium point and that equilibrium point is related to the
free energy released by the reaction under specified conditions. The free energy released by a
chemical reaction is directly related to its equilibrium.

 Exergonic Reaction: The further towards completion the point of equilibrium lies, the more
free energy is given off and the reaction is called an exergonic reaction (ΔG is negative).
 Endergonic Reaction proceeds hardly at all towards its completion point and free energy is
needed to help the reaction (ΔG is positive)
 Activation energy is the energy needed to push the reacting molecules over the energy barrier
Enzyme: An enzyme is a protein molecule that acts as a catalyst.
The binding of a substrate to the enzyme active site produces an enzyme–substrate complex. The
enzyme and the substrate are held together by hydrogen bonding, ionic attraction and covalent
bonding.
Formation of enzyme–substrate complex results in a lower activation energy than in an un-catalysed
reaction
Catalyst: A catalyst is a chemical agent that speeds up a reaction without being consumed by the
reaction. A catalyst is a substance that lowers the activation energy required for a reaction by forming
a temporary association with the molecules that are reacting.

The effects of having a catalyst present in a chemical reaction are as follows:

 Little added energy is needed to start the chemical reaction. Q Reactions proceed more rapidly
with a catalyst than without
 Reactions proceed more rapidly with a catalyst than without
 A catalyst allows equilibrium of a reaction to be reached much faster
The Role of Enzymes in Metabolic Reactions:

 Enzymes are protein molecules that serve as catalysts and supply the activation energy for
molecules to react with one another.
 An enzyme is not permanently altered or used up during a chemical reaction. Enzymes are
recycled and can catalyse more reactions.
 Enzymes allow cells to carry out chemical reactions rapidly at the normal metabolic temperatures
of cells.
 There are many different types of enzyme and cells synthesise those that they need for their
biological activities and functions. The molecule on which an enzyme acts is its substrate
 Biology Chapter 3 – Enzymes And Metabolic Reaction

Mode of Action of Enzymes:

An enzyme has an active site that binds its specific substrate. The polypeptide chains of an enzyme
are folded to form a pocket on the enzyme surface. The enzyme substrate fits precisely into this
pocket.
Active Site: The pocket of the enzyme where the substrate fits is the active site. The active site of an
enzyme has a precise three-dimensional shape and the correct orientation and array of bonding types
(polar, non-polar, hydrophilic and hydrophobic) to ensure the substrate binds correctly.
The active site holds the substrate on the enzyme and orients the substrate correctly so that the
reaction can occur. The binding of a substrate to the active site produces an enzyme–substrate
complex. The enzyme–substrate complex gives rise to the chemical reaction which produces product
and free enzyme. When the enzyme reaction is completed, the free enzyme is in the same chemical
form that it was in before the reaction started. The formation of the enzyme– substrate complex results
in a lower activation energy than that of the corresponding un-catalysed reaction.
The enzyme-catalysed reaction occur at the active site. Enzymes are flexible protein molecules and
when the substrate binds to the active site, the enzyme changes shape exposing the parts that react
with the substrate.
The change in enzyme shape caused by substrate binding is called Induced Fit.
Induced-fit Hypothesis:
In an enzyme–substrate reaction, the substrate complexes with the active site which then undergoes a
slight change in shape in order to accommodate the substrate. This is called the induced-fit hypothesis
because the enzyme is induced to undergo a slight alteration in shape to achieve an optimum fit for
the substrate. The change in shape of the active site facilitates the enzyme reaction and after the
reaction is completed, the product is released. The enzyme active site returns to its original shape and
is ready to bind another substrate molecule.
When a substrate binds to the active site, induced fit brings the reactive protein side-chains of the
enzyme into alignment with the substrate so that catalysis can occur.
In order to speed up the rate of a chemical reaction, enzymes use these mechanisms:

 Orienting the substrate so that the right atoms for bond formation are closely aligned with the
enzyme
 Adding a charge to the substrate to make it more chemically reactive
 Inducing strain (‘stretching’) on chemical bonds in a substrate so they are less stable and more
reactive.
Enzyme Specificity:
The specificity of an enzyme results from the exact three-dimensional shape and structure of its active
site
Molecules with shapes different from the enzyme substrate, or with different functional groups and
properties, cannot fit properly to bind to the active site. Amino acids involved in binding at the active
site do not need to be adjacent to each other on the enzyme’s primary protein structure. When the
enzyme protein folds into its tertiary structure, the folding brings together parts of the molecule that
were far apart.
 Biology Chapter 3 – Enzymes And Metabolic Reaction

Factors Affecting Enzyme Activity:

Substrate concentration affects the rate of enzyme action. The rate of an enzyme-catalysed reaction
increases as the substrate concentration increases and the rate of increase of the reaction gradually
levels off.
When further increases in the substrate concentration do not produce a significant increase in the rate
of enzyme action the maximum rate has been attained. When the maximum rate is achieved the
enzyme is saturated. At saturation, all of the enzyme molecules are bound to substrate molecules and
the enzyme is working as fast as it can. The concentration of an enzyme is usually much lower than its
substrate and even though enzyme molecules work at an incredibly fast rate, a high concentration of
substrate molecules can temporarily outstrip the enzyme’s capacity. The maximum rate of an
enzymatic reaction is a measure of the efficiency of the enzyme.
Enzyme efficiency is the number of molecules of substrate that are converted to their products in a
unit of time (second) when there is excess substrate present.
Enzyme Co-factors:
Some enzymes require non-protein molecules called cofactors to function. There are three types of
cofactor: inorganic ions, coenzymes and prosthetic groups
Inorganic ions temporarily bind to certain enzymes and are essential for their catalytic activity.
Coenzymes are carbon-containing molecules that temporarily bind to a substrate or the active site of
an enzyme while catalysis is happening.
PH: The rates of most enzyme-catalysed reactions are dependent on the pH of the medium in which
they occur. Enzymes have an ideal pH at which enzyme activity is optimal. Deviations from the
optimal pH reduce enzyme activity
Temperature: Temperature generally increase the rate of enzyme-catalysed reactions because as
temperature increases the substrate molecules (reactant) have enough energy to provide activation
energy for the chemical reaction. The increase in temperature increases the kinetic energy of the
enzyme and substrate molecules; hence they have a greater chance of colliding with each other. High
temperatures can inactivate or denature the protein structure of enzymes because the bonds in the
protein molecule are broken. The shape of the enzyme changes during denaturation therefore it can no
longer bind its substrate efficiently

Enzyme Regulation:
Homeostasis: Homeostasis is the
maintenance of stable internal conditions
within an organism. Organisms must regulate
their metabolism, of which an important
component is the rate of enzyme activity.
 Biology Chapter 3 – Enzymes And Metabolic Reaction

Metabolism: Metabolism consists of a sequence of enzyme-catalysed reactions called a pathway.

These pathways convert raw materials that are ingested or synthesised in the plant or animal body into
forms that can be used by living cells.
In a metabolic pathway, the product of one chemical reaction is the substrate for the next chemical
reaction.
Groups of enzymes in a common pathway can be segregated (grouped together) within the cell
making it easy for the product of one reaction to pass directly to the next enzyme for modification.
This ‘assembly-line arrangement’ also ensures that there is little build up of intermediate chemical
reaction products
In each metabolic pathway, there is always one regulatory enzyme. The regulatory enzyme sets the
rate of the overall enzyme sequence in response to signals from the cell. In most metabolic pathways,
the first enzyme is the regulatory enzyme.
Anabolic pathways synthesise important chemical building blocks (e.g. sugars, amino acids, fatty
acids) from which macromolecules are constructed. The formation of polymers from monomers is
also an anabolic reaction.
Catabolic pathways break down molecules and free the potential energy that was stored inside them.
Cells regulate anabolic and catabolic pathways in accordance with their needs.
Allosteric regulation of enzyme activity occurs when the function of the active site is affected by the
binding of a molecule at a site on the enzyme that is separate and distinct from the active site. The
substrate binds to the active site and, simultaneously, the allosteric molecule binds to the allosteric
site. When the allosteric molecule binds, it may inhibit enzyme activity or it may increase enzyme
activity.
Enzyme Inhibitors: Enzyme inhibitors are molecules that bind to enzymes and slow down or stop
enzyme-catalysed reactions.
Irreversible inhibitors bind to certain side-chains of the polypeptides that make up the active site of
an enzyme thereby destroying the ability of the enzyme to interact with its substrate.
Pyrethroids are chemical compounds that bind irreversibly to the enzymes that control the gated
sodium channels in the plasma membrane of the nerve axons responsible for generating action
potentials in insects. Thus, these enzymes are irreversibly inhibited by pyrethroids and the insects
become paralysed.
Nicotine is a naturally occurring chemical found in tobacco. It affects a wide variety of biological
functions ranging from gene expression, regulation of hormone secretion and inhibition of enzymes
When a person smokes, nicotine enters the bloodstream through the alveoli of the lungs; it travels to
the brain where it exerts its effects on the body via neurotransmitters
 Biology Chapter 3 – Enzymes And Metabolic Reaction

Competative and Non-Competative Inhibition

 Competitive and non-competitive inhibition are both reversible.

 Competitive inhibitors compete with the enzyme substrate for the active site.
 Competitive inhibition is reversible.
 Competitive inhibitors have a structure similar to that of the genuine substrate but, when they bind
to the enzyme active site, no catalysis occurs.
 Competitive inhibitors simply block the genuine substrate from entering the active site.
 Competitive inhibition can be overcome by a sufficiently high concentration of the genuine
substrate. When the concentration of the competitive inhibitor is reduced, it detaches from the
active site and the enzyme can then bind a genuine substrate molecule.
Example of Competitive Inhibition:
The enzyme succinate dehydrogenase is found in all mitochondria and catalyses the conversion of the
compound succinate into the compound fumarate. Succinate dehydrogenase is subject to competitive
inhibition by oxaloacetate. Oxaloacetate has a similar chemical structure to succinate and therefore it
can act as a competitive inhibitor of the enzyme by binding to its active site
Non-competitive Inhibitors

 Non-competitive inhibitors bind to the enzyme at a site distinct from the active site.
 This binding may cause a conformational change in the enzyme that alters the three-dimensional
structure of the active site.
 Examples of non-competitive inhibitors are metals such as lead, mercury and copper. T
 The active site may still be able to bind substrate but the rate of product formation is reduced.
Summary of the Properties of Enzymes:

 They are biological catalysts

 They lower the activation energy barrier for the reaction each catalyses
 They form enzyme–substrate complexes
 They change shape to accommodate substrate (induced fit)
 Their catalytic activity is influenced by temperature and pH
 They have optimal conditions that favour maximum enzyme activity and product formation
 They are subject to competitive inhibition, non-competitive inhibition and irreversible
inhibition
 They may require cofactors (non-protein molecules for catalytic activity)