all living organisms need energy to grow and reproduce maintain their structures and respond to their

environments

metabolism has a central role on such processes

animals consume food to replenish energy their metabolism breaks down the carbohydrates lipids
proteins and nucleic acids to provide chemical energy for these processes

plants convert light energy from the sun into chemical energy stored in molecules during the process of
photosynthesis

plants can synthesize most of the organic matter on earth by assimilating inorganic elements from the
environment into organic molecules driven by energy from sunlight such process is photosynthesis

respiration by plants and heterotrophic organisms converts the same amount of carbon present in
organic compounds back into carbon dioxide. These processes are important not only for the plants but
also for animals which receive their carbon and nitrogen solely from organic compounds and thus
completely rely on plant resources to obtain nutrition

photosynthesis and respiration are metabolic processes

__________________________________________________________________________________

Metabolism is the processes by which cells and organisms acquire, rearrange, and free resources
in ways that sustain life

-involves several chemical and physical processes occurring in a cell or in the organism and takes place
through a sequence of reactions catalyzed by enzymes thus constituting metabolic pathways, and the
metabolic intermediates are known as metabolites.

most of the metabolites are produced only in specialized organs or cell types and only at certain phases
of development or under specific growth conditions

there are two principal types of metabolites: primary and secondary

primary metabolites are the compounds that are present in many organisms and are directly involved
in their growth development and reproduction like carbohydrates proteins lipids and vitamins

secondary metabolites meanwhile are the end products of primary metabolism that include steroids
antibiotics and essential oils, which provide protection to plants against herbivores and microbial
infection used as medicines pigments flavorings and seed dispersal agents
Metabolism also may be subdivided according to the type of transformation that occurs:

catabolism is a set of processes by which complex chemical compounds are broken down to release
energy and create smaller chemical building blocks which are then used as building materials for
synthesis of cellular components required for cell structure and function

anabolism by contrast consists of the processes that synthesize larger or more complex chemical
compounds from smaller chemical building blocks using energy

anabolic pathways are associated with the growth and repair processes characteristic of living
organisms

whereas catabolism is destructive anabolism is constructive

the catabolic and anabolic reactions that proceed in cells are accompanied by energy changes and it is
the study of these changes that constitutes the field of bioenergetics

metabolic pathways can be linear or branched or cyclic :

branched pathways yield several useful final compounds from one precursor molecule or convert
multiple starting substances into one product (FOR EXAMPLE GLYCOLYSIS)

cyclic pathway one of the starting compounds of the pathway is reproduced in a sequence of reactions
and re-enters the same metabolic pathway (FOR EXAMPLE KREBS CYCLE)

metabolic pathways synthesize end products required by the cell or organism and such product may be
used as part of the structure of the cell or in cases where it is secreted from the cell it may be
incorporated into extracellular elements like the pectin of the middle lamellae of plant cell walls

the end product may also function in the cell as a regulatory agent for other reactions like in the case of
hormones end products may also be stored as reserves such as starch glycogen and certain lipids a

metabolic pathway may also function to provide energy rich compounds such as atp and they may be
used in other energy requiring reactions
intermediates of a metabolic pathway may also be drawn upon and used as substrates for other
metabolic sequences for example many of the krebs cycle intermediates are withdrawn and utilized for
biosynthesis of other compounds the table shows the common metabolic pathways in cells
plants show a lot of genetic variation in metabolism

several different organic compounds have been found in plants which include compounds associated
with the metabolic pathways that absorb nutrients from the environment in energy metabolism and in
biosynthetic pathways that provide the basic constituents of the plant cell proteins membranes and cell
walls

generally in plant cells, metabolic processes are regulated by two means:

 first is compartmentalization of metabolic reactions in separate cell organelles

 second is the mechanisms regulating the activity of enzymes catalyzing the metabolic
reactions
 Concepts of THERMODYNAMICS

living organisms are highly ordered and structured systems where metabolic functions are carried out
speedily and with great precision

the cell is an extremely organized biochemical machine wherein hundreds of reactions may be occurring
simultaneously

energy is needed to enable all chemical reactions to proceed organisms have developed mechanisms for
storing chemical energy and using it to drive energy consuming reactions

the fundamental laws of physics and chemistry apply to living organisms and explain at a molecular level
how organisms operate

the information necessary to establish proper reactions acting on proper materials is stored both in the
nucleus and in plastids and mitochondria

however after death, decay is a process by which complex molecules of an organism break down and
thus become more disorganized or disordered and scattered this disorder or randomness is known as
entropy

entropy generally refers to a form of energy which cannot perform work; this increase in
entropy cannot be prevented

thermodynamics is a study of energy and heat-related changes

the laws of thermodynamics govern all energy changes in the universe right from nuclear reactions to
the buzzing sound of a bee

a general understanding of thermodynamic principles is necessary because these principles provide a

quantitative framework for understanding energy transformations in biology

in addition to energy transformations thermodynamics also helps to describe the capacity of a system
to do work

work may be defined in several different ways

in biology the concept of work is applied more broadly embracing a variety of work functions against a
wide spectrum of forces encountered in cells and organisms

in addition to mechanical work such as muscular activity the biologist is concerned with such diverse
activities as chemical synthesis the movement of solute against electrochemical gradients osmosis and
ecosystem dynamics - these and a host of other essential activities of living things can all be described in
thermodynamic terms
  First law of thermodynamics (law of conservation of energy)
-states that energy can change from one form to another but it can neither be created nor can be
destroyed

the total amount of energy in the universe remains constant; energy is never lost in our action

an apparent decrease in one form of energy will be balanced by an increase in some other form of
energy

 Second law of thermodynamics (ENTROPY)

-states that disorder or entropy in the universe is continuously increasing disorder and randomness
are the natural scheme of things in our universe and in all energy exchanges and conversions

if no energy enters or leaves the system under study, the potential energy of the final state will always
be less than the potential energy of the initial state this is because entropy is related to the energy of
molecular motion it follows that the more molecules are free to move about- that is the more random
or less ordered or chaotic system - the greater will be their entropy.

as physiologists our concern with entropy is primarily that it represents energy that is not available to do
work in this context the second law can then be restated as :

the capacity of an isolated system to do work continually decreases, thus it is never possible
to utilize all the energy of a system to do work

to explain further the laws of thermodynamics let us take the classic example of aerobic respiration
where complete oxidation of glucose molecule yields carbon dioxide and water

to accommodate the first law of thermodynamics it should be asserted that the left hand side of the
reaction exactly balances the right hand side in terms of energy yet this reaction occurs without any
outside energy source and the second law predict that the products must somehow contain less intrinsic
energy than the reactants during the reaction some energy is released in various forms such as heat
the laws of thermodynamics apply only to closed systems - that is to systems where or in which no
energy is leaving or entering

in terms of their thermodynamics animals must function as open systems

o without an energy input, the blood coursing through an animal circulatory system will slow to a
halt
o without an energy input, vital molecules in animals tissues will become more disorganized by
spontaneously breaking down or by other processes eventually, therefore many vital molecules
will lose their critical structural and functional properties
o without an energy input, positive and negative ions will distribute themselves randomly across
an animal's cell membranes this randomization of electrical charges among other things will
make nerve impulses impossible

the second law of thermodynamics dictates that if an animal were required to function as an isolated
system, all forms of order within its body would decay. this loss of order would eventually kill the animal
because order is essential for life

animals require energy from the outside because energy is necessary to create and maintain their
essential internal organization so life is a completely open system where both energy and matter
continuously flow in and out

food that is processed provide energy to the cells to move their muscles to repair things that break
down all the time inside our bodies

the fact that things break down so easily is indeed a consequence of the second law so life is in no way a
violation of the second law it actually fits it very well

In biological systems, no significant temperature differences exist within a cell or different organs. Under
these circumstances, the energy is not liberated as such but is distributed in the reacting molecules. In
many of these, energy-liberating reactions are coupled with energy-consuming reactions. In most of
these coupled reactions, the overall process proceeds spontaneously.

to maintain the biological order homeostasis is required to overcome the tendency towards increasing
disorder living cells or organisms tend to reduce their own entropy - that is the reduce randomness or
disorganization in their components - and thus build up and maintain their highly organized state by
expanding energy
the sun is the ultimate source of all energy on this planet

in different parts of the cell the macromolecules may be broken down into smaller molecules so that the
carbon, hydrogen, and oxygen atoms may be rearranged substituted, deleted or supplemented to form
a vast array of entirely different molecules releasing energy that is necessary for cell functioning

in addition to water, energy is an absolute requirement for the maintenance and replication of life
regardless of its form

energy to build and preserve order in the face of a constantly deteriorating environment is a
fundamental need of all organisms

energy is the capacity to do work either actively or stored for later use

energy can exist in multiple forms such as mechanical energy, heat, sound, electric current, light or
radioactive radiation so there are several ways for measuring energy

the most convenient is expressed in terms of heat because the remaining other forms of energy can be
changed into heat

the unit of heat normally used in biological studies is a kilocalorie which is equivalent to 1000 calories
one calorie is a heat required to raise a temperature of one gram of water by one degree Celsius

however it should not be confused with calories for a term connected to diet and nutrition -the Calorie
with a capital C

Free Energy
-is the amount of energy available to break chemical bonds that tend to hold the atoms in a molecule
together and subsequently form other chemical bonds in any system

-it is the thermodynamic parameter that determines the direction in which physical and chemical
changes must happen and their ability to perform work

In a molecule within a cell where pressure and volume usually do not undergo change, the free energy is
symbolized by a letter G or Gibb’s free energy in honor of Josiah Willard Gibbs the 19th century physical
chemist who introduced the concept:

G= H - TS
G is equal to the energy contained in a molecule's chemical bond called enthalpy (H) minus the energy
unavailable because of this order or randomness called entropy (S) times the absolute temperature (T)
in degrees kelvin

two kinds of energy are identified

free energy which is available to do work and entropy which is not

except in a limited number of situations it is free energy ,the energy available to do work, that is of
greatest interest to the biologist

It is neither convenient nor relevant to measure absolute energies (either G or S), but changes
(designated by the symbol Δ) in energy during the course of a reaction can usually be measured with
little difficulty as, for example, heat gain or loss, or work.

chemical reactions break some bonds in the reactants and form new bonds in the products thus
resulting in changes in free energy

when a chemical reaction occurs under conditions of constant temperature pressure and volume, as it
happens in most biological reactions,the change in free energy (given the symbol delta g) is simply
equal to the change in enthalpy minus the temperature multiplied to the change in entropy

Δ G= Δ H - T Δ S

the change in free energy or ΔG is a fundamental property of chemical reactions changes in free energy
can tell us much about a reaction

in some reactions ΔG is positive this means that:

 the products of the reaction contain more free energy than the reactants
 enthalpy is higher or entropy is lower in the system
 such reactions do not proceed spontaneously they require extra energy for the reaction to
proceed and are thus endergonic or energy consuming

in some reactions ΔG is negative this means that:

 the products contain less free energy than the reactants and the excess energy is released
 enthalpy is lower or entropy is higher or both
 such reactions tend to proceed spontaneously as a difference in entropy is greater than the
difference in enthalpy between reactants and products and thus such reactions are exergonic or
energy yielding

biological organisms overcome metabolic restrictions imposed by thermodynamically unfavorable

reactions that exhibit a positive g by coupling them or linking them to reactions with a negative g thus
the free energy released by the exergonic reaction provides the necessary energy to ensure that the
endergonic reaction proceeds. However, in order that this system of coupled reactions will occur
spontaneously, the net free energy change must always be negative (-ΔG) thus the concept of such
coupled reactions was critical to our understanding of how life and overall endergonic process is
maintained without defying the laws of thermodynamics

TO MAINTAIN THE BIOLOGICAL ORDER, HOMEOSTASIS IS REQUIRED TO OVERCOME THE TENDENCY

TOWARDS INCREASING DISORDER
The relationship between free energy and the capacity to do work is not restricted to chemical
reactions. Any system at equilibrium has a capacity to do work, the maintenance of such a steady state
but non-equilibrium condition is called homeostasis. Indeed homeostasis, that reflects the capacity to
avoid equilibrium despite changing environmental conditions, is an essential characteristic of all living
organisms - when g equals zero no useful work can be done and life ceases to exist.

catabolic pathways
 lead to an increase in entropy
 exergonic
 released energy is then stored as ATP and reduced coenzymes (NADH, NADPH, FADH2) which
are required to drive anabolic pathways

anabolic pathways
 lead to a decrease in entropy
 endergonic
 Energy is supplied in the form of ATP molecules and the reduced coenzymes

Adenosine Triphosphate or ATP is the most used energy intermediate in the biological world

an animal uses its absorbed chemical energy to carry out three major types of physiological work:

1. Biosynthesis

an animal synthesizes its body constituents such as its proteins and lipids by use of absorbed energy.
As this process takes place some of the absorbed energy that is used remains in chemical form because
the products of biosynthesis are organic molecules with significant chemical energy content.

During growth chemical energy accumulates in the body in the form of biosynthesized products that are
used to assemble new cells and tissues. Some of the chemical energy accumulated in body tissues
through growth may be used by an animal as food energy during times of fasting or starvation.
Ultimately all the chemical energy accumulated in body tissues becomes food for predators or decay
organisms when the animal dies

2. Maintenance

an animal’s maintenance functions are all the processes that maintain the integrity of its body,
examples include circulation, respiration, nervous coordination, gut motility, and tissue repair. With only
trivial exemptions the energy used for maintenance is degraded entirely to heat within the body

3. For generation of external work

Animals perform external work when they apply mechanical forces to objects outside their bodies.
Much of the absorbed chemical energy used to fuel external work is degraded to heat within the body
However when external work is performed some energy leaves the body as mechanical energy
transmitted to the environment. The fate of that energy depends on whether it is stored. Energy of
external work is stored if it is converted into increased potential energy of position when a bicyclist
ascends to the top of a hill part of his energy of external work is stored as increased potential energy of
possession because his body and bike moved a higher position in earth's gravitational field.
Enzymes
-are protein catalysts that play two principal roles:

 speed chemical reactions

 often regulate reactions

Enzyme molecules are huge in size thus enzymes have a very low diffusion rate and make a colloidal
system in water. The large colloidal nature of enzymes provide greater surface areas to the reactants
which come into closer contact with one another, thus facilitating chemical reactions.

Every enzyme contains somewhere within its tertiary configuration, a characteristic cluster of amino
acids forming one or more active sites, where the substrate molecule binds and the actual catalytic
event occurs. The active site is usually a cleft or groove or pocket, with chemical and structural
peculiarities that accommodate the entire substrate with high specificity.

Structurally, the active site can be considered to be composed of four main components:

1. The Binding site : attracts and positions the substrate and cofactors and bind it to the enzyme.

2. The Catalytic site : where reactions occur through bond-breaking and bond-forming

3. Structural residues : keep the enzyme’s active site in proper configuration to allow it to perform its
function effectively.

4. Non-essential residues : present close to the surface of an enzyme and can be replaced or eliminated
without loss of any function.

Therefore, the structure of the active site is responsible for the catalytic activity and as well as the
specificity of the enzyme.

The binding of the substrate and enzyme molecules is typically stabilized entirely by weak bonds, not
covalent bonds. If an enzyme requires two or more substrates, the enzyme molecule has an active site
specific for each.

Enzymes, based on their occurrence in cells, fall into two categories:

1. Constitutive enzymes:

 maintained at a constant level because the structural genes for these enzymes are
continuously expressed, e.g., enzymes of glycolysis.
 present in a tissue in relatively high and steady amounts regardless of conditions

2. Inducible enzymes:

 found lacking in the cells but their structural genes can be activated by the presence of specific
inducer molecules in the cell, e.g., nitrate reductase (NR), isocitrate lyase, malate synthase.
 present at low levels (or not at all) in a tissue, unless their synthesis is activated by specific
inducing agents.
The differentiation of tissues in an animal’s body exemplifies the control of constitutive enzymes on a
long timescale. Tissues become different in their sets of functional metabolic pathways during
development, and they remain different throughout life, because of long-term (often epigenetic)
controls on gene expression. For example, the bone marrow cells and skin cells of mammals differ in
whether they express the genes that code for the enzymes required for hemoglobin synthesis. All the
genes are relatively steadily expressed—and the enzymes are therefore constitutive—in marrow cells
but not skin cells. Accordingly, the marrow cells have a functional metabolic pathway for hemoglobin
synthesis at all times throughout life, whereas skin cells do not.

Knowing how enzyme function is important in order to understand the overall cellular metabolism,
the effect of drugs/toxins on metabolism, and genetic diseases.

To appreciate the extreme importance of enzymes, it is crucial to recognize that the vast majority of the
biochemical reactions that occur in animals do not take place on their own at significant rates under
physiological conditions. Cells are biochemically complex enough that, in principle, tens of thousands of
reactions might occur in them. However, because reactions in general require catalysis to occur at
significant rates, the particular reactions that do take place in a cell—out of all those that could take
place—depend on the cell’s own biosynthesis of enzyme proteins. Enzymes represent one of the
foremost means by which cells take charge of their own biochemistry.

When we say that an enzyme is a catalyst, we mean it is a molecule that accelerates a reaction without,
in the end, being altered itself.

The substrates of an enzyme are the initial reactants of the reaction that the enzyme catalyzes;
the products of the enzyme are the compounds produced by the reaction.

This complexing of enzyme and substrate, which usually is stabilized by noncovalent bonds, is essential
for catalysis because the enzyme can alter the readiness of the substrate to react only if the two are
bonded together.

Substrate is converted to product while united with the enzyme, forming an enzyme–product complex,
also usually held together by noncovalent bonds. The enzyme–product complex then dissociates to yield
free product and free enzyme.
In a cell, a collision between an enzyme molecule and substrate molecule does not necessarily result in
the formation of an enzyme– substrate complex. The two molecules may instead collide and “bounce
apart” (i.e., separate).

The outcome of a collision depends on a property of the enzyme called enzyme–substrate affinity,
which refers to the proclivity of the enzyme to form a complex with the substrate when the enzyme
and substrate meet.

An enzyme that is highly likely to form complexes with substrate molecules it contacts has a
high enzyme–substrate affinity.

Conversely, an enzyme that is unlikely to form complexes has a

low enzyme–substrate affinity.

Two hypotheses have been proposed to describe the mechanism of enzyme action:

The Lock and Key hypothesis and the Induced-Fit hypothesis.

 The Lock and Key hypothesis

Emil Fischer (1894) introduced the ‘lock and key’ hypothesis of enzyme action. He proposed that
enzymes possess a well-defined 3-D structure that precisely fits the substrate molecule just as the key
fits a lock. For a key to operate, it must be supplied with the appropriate lock and the same principle
holds good for enzyme and substrate combination to yield products. This is one explanation for the
precise specificity of enzymes towards their respective substrates.

However this analogy is flawed in two important respects:

 First, the binding between the substrate and the corresponding active site on an enzyme is
principally chemical and electrochemical in nature, not mechanical.
 Second, the lock-and-key analogy erroneously suggests mechanical rigidity. In fact, as we have
seen, the active site and other regions of an enzyme molecule are flexible and change
conformation when enzyme–substrate binding occurs. They also change conformation when
product is released.
 Induced Fit hypothesis

According to Daniel Koshland (1958), a slight rearrangement of chemical groups occurs in both enzyme
and substrate upon formation of an ES complex. Enzymes are therefore best regarded as rather
‘flexible’ molecules whose shape can change slightly under the influence of electrical charges present on
the substrate.
Reaction velocity (reaction rate)

the amount of substrate that is converted to product per unit of time.

 At relatively low substrate concentrations, the reaction velocity increases as the substrate
concentration increases. However, this process does not go on indefinitely: As the substrate
concentration is raised, the reaction velocity eventually reaches a maximum.

The reason for this overall behavior is precisely that substrate must combine with enzyme molecules to
form product. When the substrate concentration is low, all of the available enzyme molecules are not
occupied by substrate at any given time and the amount of substrate available is therefore the
limiting factor in determining the reaction velocity. Raising the substrate concentration increases the
reaction velocity by using more of the available enzyme molecules. At high substrate concentrations,
however, the amount of enzyme is the limiting factor in determining the reaction velocity. When the
substrate concentration is high, the population of available enzyme molecules becomes saturated,
meaning that each enzyme molecule is occupied by a substrate molecule nearly all of the time.
Increasing the substrate concentration, therefore, cannot increase the reaction velocity further.

The rates of reactions in an uncatalyzed cell at normal cellular temperature are very low as the reactant
molecules lack adequate kinetic energy to exceed the activation energy barrier.

In general, reactions can be accelerated by two means:

(i) Providing the reacting molecules with excess energy in the form of heat. With an increase in
temperature, a greater number of reactants will gain sufficient energy of activation to the
intermediate form and get converted to the product.
(ii) (ii) Lowering down the activation energy barrier by using a catalyst or an enzyme.

Activation energy can be defined as ‘the extra energy needed to break existing bond(s) and initiate a
chemical reaction’.

The catalytic effectiveness of an enzyme depends partly on the activation energy of the enzyme-
catalyzed reaction. To understand the implications of activation energy, it is necessary to recognize that
a substrate molecule must pass through an intermediate chemical state termed a transition state
to form a product molecule. Thus one can think of any reaction, whether or not it is enzyme catalyzed,
as involving first the conversion of the substrate to a transition state, and second the conversion of the
transition state to the product.

For a substrate molecule to enter the transition state, its content of energy must increase. The amount
by which it must increase is the activation energy of the reaction. Molecules gain the energy they need
by random collisions with other molecules. Any particular substrate molecule has a continuously
fluctuating energy content as it gains and loses energy through intermolecular collisions; as its energy
content rises and falls, it undergoes reaction when its energy content is boosted by an amount at least
equal to the activation energy. An enzyme accelerates a reaction by lowering the activation energy.
The extent to which it lowers the activation energy is one factor that determines the enzyme’s
catalytic effectiveness.

Enzyme Regulation

Enzymes must be regulated to adjust their activity levels to cellular needs. There are various control
mechanisms in cells which help in enzyme regulation.

A. Substrate-level regulation

includes the effect of substrate and product concentrations on the reaction rate. According to the
Michaelis–Menten equation, an increase in concentration of the substrate results in higher rates of
reaction. Conversely, an increase in product concentration reduces the speed at which substrate is
converted to product.

B. Allosteric regulation

All enzymes capable of allosteric regulation exist in two different interchangeable states.

In one state, the enzyme has a high affinity for its substrate, whereas in the other state, it has low
affinity for its substrate.

Such enzymes with two interconvertible forms are called ‘allosteric enzymes’. These enzymes are multi-
subunit proteins with several catalytic and regulatory/allosteric subunits. Each catalytic subunit contains
an active site to which the specific substrate binds, and every regulatory subunit has one or more
allosteric sites to which the specific effector molecule binds, which may either inhibit or stimulate the
enzyme, depending on which form of the enzyme (low affinity or high affinity) is favoured by effector
binding. The binding of effector molecules at the allosteric site will cause changes in conformation of the
enzyme molecule that may in turn alter the rate (kinetics) of the enzyme reaction.

Although binding sites for allosteric modulators do not occur in all enzymes, they are a common feature
of enzymes that play regulatory roles.

An enzyme molecule that has its catalytic activity increased by a modulator is said to be upregulated;
conversely, one that has its catalytic activity decreased is said to be downregulated.

When an allosterically modulated enzyme is the rate-limiting enzyme in a metabolic pathway, the entire
pathway may be upregulated or downregulated by allosteric modulation. The downregulation of an
entire pathway occurs, for example, during the phenomenon known as feedback inhibition (end-
product inhibition), a common process in which a product of a metabolic pathway decreases the
catalytic activity of a rate-limiting enzyme earlier in the pathway.
Covalent Modulation

The most important processes of covalent modulation are phosphorylation and dephosphorylation—
the covalent attachment and removal of orthophosphate groups (HPO42–).

When a phosphate group forms a covalent bond with an enzyme that is covalently modulated, the
enzyme’s activity is modulated because the shape of the protein changes, leading to changes in the
catalytically important properties of the molecule.

Often phosphorylation and dephosphorylation act as a very rapid type of on–off switch. That is, for
example, an enzyme molecule might be completely inactive (“turned off”) when it lacks a phosphate
group and become activated (“turned on”) when it bonds with a phosphate group.

The transition between the downregulated “off” form and the upregulated “on” form can occur almost
instantaneously. A crucial property of covalent modulation is that, unlike allosteric modulation, it
requires the action of enzymes to catalyze the making and breaking of covalent bonds. The enzymes
that catalyze phosphorylation belong to a large class called protein kinases, which are enzymes that
covalently bond phosphate to proteins using ATP as the phosphate donor. The enzymes that catalyze
dephosphorylation are protein phosphatases, which break covalent bonds between proteins and
phosphate, liberating phosphate in the simple form of inorganic phosphate ions.
Enzyme Inhibition

Enzyme inhibition is important for several reasons:

1. It plays a vital role as a control mechanism in cells.

2. It is important in understanding the mode of action of drugs, poisons, antibiotics, pesticides, and such.

3. It is useful to enzymologists as a tool in the studies of reaction mechanism or properties of enzymes

A. Irreversible Inhibitors

Irreversible inhibitors such as, alkylating agents, nerve gas poison (diisopropyl fluorophosphate),
organophosphates, and pesticides, bind to the enzyme in a covalent manner resulting in irrevocable
loss of catalytic activity. These bind to acetylcholine esterase, an enzyme crucial to the transmission of
nerve impulses, thereby leading to rapid paralysis of vital function. Many natural toxins, e.g., alkaloid
physostigmine, a potent inhibitor of acetylcholine esterase, are toxic to animals.

Plants also use irreversible inhibitors as part of their range of defences against predators and pathogens.
An example is mimosine, an alkaloid originally isolated from the sensitive plant, Mimosa pudica. It is
toxic to browsing animals because it irreversibly inhibits enzymes of DNA synthesis in susceptible cells.

B. Reversible inhibitors

Reversible Inhibitors bind to the active site of an enzyme non-covalently in a dissociable manner.

1. Competitive inhibitors compete with the substrate for access to the active site of an enzyme
because of their resemblance to substrate molecules. However, a higher substrate concentration
can reverse the effect of competitive inhibition.
2. Non-competitive inhibitors bind to the enzyme surface at a location other than the active site,
thus inhibiting catalytic activity. Increasing the concentration of substrate will not restore the
original rate of reaction.
The catalytic nature of enzymes often receives such exclusive attention that enzymes are viewed merely
as molecules that speed things up. At least as important, however, is the role that cellular enzymes play
as agents of regulation of cell function. The biochemical tasks in a cell are typically accomplished by
sequences of enzyme-catalyzed reactions called metabolic pathways.

Enzymes participate in the regulation of cell function in two principal ways:

 First, the types and amounts of enzymes synthesized by a cell determine which metabolic
pathways are functional in the cell; any particular pathway is functional only if the cell
synthesizes (through gene expression) all the enzymes the pathway requires.
 Second, the catalytic activities of the enzyme molecules that actually exist in a cell at any given
time can be modulated as a way of controlling the rates at which the functional metabolic
pathways operate.

Enzymes exist either as a single unit (monomeric) or aggregates (oligomeric) of several subunits. Each
subunit may have an active site where substrate molecules bind during enzymatic reaction.
Cofactors are classified into prosthetic groups and coenzymes depending upon their association with
the enzymes.

Role of cofactors:

 In some cases, the cofactor completes the active site of the enzymes or modifies it in such a
manner that substrate binding can occur.
 Cofactors act as a donor of electrons or atoms to the substrate and following the reaction
return to their former state.
 Cofactors may serve as temporary recipients of either one of the reaction products/
electron/proton, again being recycled to their former state sometime after the main reaction is
completed.
 Finally, the cofactor, together with the side chains of residues at the active site, may serve to
polarize the substrate and prime it for catalytic alteration.

Coenzymes: The loosely associated, organic cofactors are designated as coenzymes.

Coenzymes generally act as donor/acceptor of atoms that are either incorporated into or withdrawn
from the substrate molecule. Coenzymes have important role in oxidation–reduction reactions.
Factors Affecting Enzymatic Reactions

 Temperature

Temperature In living organisms, the rate of reaction generally becomes double for every 10°C increase
in temperature, within the normal range of environmental temperatures. An increased thermal activity
because of increase in temperature causes a greater reaction rate but eventually leads to denaturation
of enzymes.

 pH and ionic strength

Small deviation in pH has a marked impact on the structural configuration and ionic strength of
enzymes because of various functional groups (−SH, −NH, −OH, −COOH) associated with them. In
addition, many substrates, products, effectors and cofactors are also altered by pH and ionic strength.
Much larger changes in pH cause denaturation of the proteinaceous enzyme itself, due to interference
with weaker non-covalent links building its 3-D structure.

Different enzymes have different pH optima, with the maximum activity between pH of 6.0 and 8.0.

 Substrate concentration

With increased substrate concentration, the rate of enzymatic reactions will increase because the
maximum active sites of enzyme will be occupied and the enzyme is said to be working at maximum
efficiency, all other factors being constant. Any further increase in substrate concentration will have no
impact on the reaction because of the limiting effect of enzyme concentration thereby showing
hyperbolic kinetics.

 Enzyme concentration

The rate of an enzymatically controlled reaction increases linearly with the enzyme concentration under
constant conditions. This constant rise in the rate of the reaction halts at a point and becomes constant
because of the limiting effect of the substrate concentration.
Enzymes are primary instruments of physiological change in all five of the time frames identified

Three of the time frames, you will recall, refer to changes in animal physiology that are responses to
changes in the external environment.

1.) acute physiological responses by individuals, the responses that occur rapidly after the
environment changes. Allosteric modulation and covalent modulation of existing enzymes are
major mechanisms of acute enzyme responses. For instance, if an animal is frightened by a
predator and runs rapidly away, allosteric upregulation of phosphofructokinase by accumulation
of adenosine monophosphate (AMP) in its muscle cells will immediately increase the rate at
which glucose is processed to manufacture more ATP to sustain muscular work (see Figure
2.19).
2.) chronic (long-term) physiological responses of individuals, depends on reconstructions of
physiological systems requiring hours, days, or longer periods to complete. Environmentally
induced changes in the expression of enzyme-coding genes constitute a major mechanism of
chronic responses. For an example, consider a fish acclimated to toxin-free water. If the fish
encounters toxins, it will be unable to defend itself immediately using P450 enzymes, because
the enzymes must be synthesized, a process requiring many hours or days. In the long term,
however, the fish will assume a new phenotype—characterized by superior toxin defenses—
because of induction of its P450 enzymes.

3.) evolutionary change depends on shifts of gene frequencies in entire populations over multiple
generations. Genes that code for enzymes are frequently known to evolve by mutation, natural
selection, and other mechanisms on both long and short scales of evolutionary time, as we have
seen in In this way, populations of animals take on new catalytic and regulatory phenotypes by
comparison with their ancestors.

Individual animals also undergo periodic physiological changes— such as changes between day and
night—under control of internal biological clocks. Enzymes often mediate these changes, as shown by
the fact that—in the tissues of animals—the catalytic activities of many enzymes rise and fall in rhythms
that parallel the daily day–night cycle even when the animals have no external information on the
prevailing time. Some of these enzymes affect the abilities of animals to metabolize particular
foodstuffs. Others affect capabilities for detoxifying foreign chemicals, including medications as well as
toxins. Thus food metabolism and responses to foreign agents vary between day and night because of
internally programmed enzyme changes.