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Chapter 2 Journey to Microbial

World

Chapter 4 Nutrition and Culture


of Microorganisms

Different chemical reactions and organize

many different molecules into specific


structures is known as metabolism
Catabolism breaks molecular structures down,
releasing energy in the process, and
anabolism uses energy to build larger
molecules from smaller ones.
Metabolic reactions are either catabolic,
which means energy releasing, or anabolic,
which means energy requiring.

All microbial nutrients are compounds

constructed from the chemical elements.


However, just a handful of elements
dominate living systems and are
essential: hydrogen (H), oxygen (O),
carbon (C), nitrogen (N), phosphorus
(P), sulfur (S), and selenium (Se). In
addition to these, at least 50 other
elements, although not required, are
metabolized in some way by
microorganisms

Besides water, which makes up 7080%

of the wet weight of a microbial cell (a


single cell of Escherichia coli weighs just
g), cells consist primarily of
macromoleculesproteins, nucleic
acids, lipids, and polysaccharides.

All cells require carbon, and most

prokaryotes require organic (carboncontaining) compounds as their source


of carbon.
Heterotrophic bacteria assimilate
organic compounds and use them to
make new cell material.
Autotrophic microorganisms build their
cellular structures from carbon dioxide
(CO2) with energy obtained from light or

A bacterial cell is about 13% nitrogen,

which is present in proteins, nucleic


acids,
and
several
other
cell
constituents. The bulk of nitrogen
available in nature is in inorganic form
as ammonia (NH3), nitrate, or nitrogen
gas (N2)

Other Macronutrients: P, S, K,Mg,


Ca, Na
In addition to C, N, O, and H, many other

elements are needed by cells, but in smaller


amounts .
Phosphorus is a key element in nucleic acids
and phospholipids and is typically supplied to
a cell as phosphate (PO4)
Sulfur is present in the amino acids cysteine
and methionine and also in several vitamins,
including thiamine, biotin, and lipoic acid.
Sulfur can be supplied to cells in several
forms, including sulfide (HS2) and sulfate
(SO4)

Potassium (K) is required for the activity

of several enzymes, whereas


magnesium
(Mg) functions to stabilize ribosomes,
membranes, and nucleic acids and is
also required for the activity of many
enzymes.
Calcium (Ca) is not required by all cells
but can play a role in helping to stabilize
microbial cell walls, and it plays a key
role in the heat stability of endospores.

Sodium (Na) is required by some, but not all,

microorganisms, and its requirement is


typically a reflection of the habitat. For
example,seawater contains relatively high
levels of Na, and marine
microorganisms typically require Na for
growth.
By contrast, freshwater species are usually
able to grow in the absence of Na.
K, Mg, Ca, and Na are all supplied to cells as
salts, typically as chloride or sulfate salts.

Micronutrients: Iron and Other


Trace Metals
Microorganisms require several metals

for growth
Chief among these is iron (Fe), which
plays a major role in cellular respiration.
Iron is a key component of cytochromes
and of ironsulfur proteins involved in
electron transport reactions .
Under anoxic conditions, iron is
generally in the ferrous form and
soluble. However, under oxic conditions,

Defined media are prepared by adding precise

amounts of highly purified inorganic or organic


chemicals to distilled water.
Therefore, the exact composition of a defined
medium (in both a qualitative and quantitative
sense) is known.
Major importance in any culture medium is the
carbon source because all cells need large
amounts of carbon to make new cell material

For culturing many microorganisms, knowledge of

the exact
composition of a medium is not essential. In
these instances
complex media may suffice and may even be
advantageous.
Complex media employ digests of microbial,
animal or plant products, such as casein (milk
protein), beef (beef extract), soybeans (tryptic soy
broth), yeast cells (yeast extract), or any of a
number of other highly nutritious yet impure
substances.

An enriched medium, often used for the

culture of otherwise difficult-to-grow


nutritionally
demanding
(fastidious)
microorganisms, starts with a complex
base and is embellished with additional
nutrients such as serum, blood, or other
highly nutritious substances.

A selective medium contains compounds that

inhibit the growth of some microorganisms but


not others. For example, media are available
for the selective isolation
of pathogenic strains of E. coli from food
products, such as ground beef, that could be
contaminated with this organism.

Differential medium is one in which an

indicator, typically a reactive dye, is


added that reveals whether a particular
chemical reaction has occurred during
growth.

Solid and Liquid Culture Media


Liquid culture media are sometimes

solidified by the addition of a gelling


agent.
Solid media immobilize cells,
allowing them to grow and form
visible, isolated masses called
colonies.

Solid and Liquid Culture Media


Microbial colonies are of various shapes

and sizes depending on the organism,


the culture conditions, the nutrient
supply, and several other physiological
parameters, and can contain several
billion individual cells.
Some microorganisms produce
pigments that cause the colony to be
colored. Colonies permit the
microbiologist to visualize the
composition and presumptive

Solid media are prepared in the same way as

liquid media
except that before sterilization, agar, a gelling
agent, is added to the medium, typically at a
concentration of 12%.
The agar melts during the sterilization process,
and the molten medium is then poured into sterile
glass or plastic plates and allowed to solidify
before use.

ENERGY AND THE CELL

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Cells transform energy as they perform work

Cells are small units, a chemical

factory, housing thousands of


chemical reactions.
Cells use these chemical reactions
for
cell maintenance,
manufacture of cellular parts,
and
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Cells transform energy as they perform work

Energy is the capacity to cause change

or to perform work.
There are two kinds of energy.
1. Kinetic energy is the energy of
motion.
2. Potential energy is energy that
matter possesses as a result of its
location or structure.
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Figure 5.10

Energy conversion

Fuel

Waste products

Heat
energy

Carbon dioxide

Gasoline

Combustion
Kinetic energy
of movement

Water

Oxygen
Energy conversion in a car

Heat
energy

Cellular respiration
Glucose

Oxygen

Carbon dioxide
ATP

ATP

Energy for cellular work


Energy conversion in a cell

Water

Figure 5.10_1

Energy conversion

Fuel

Waste products

Heat
energy
Carbon dioxide

Gasoline

Combustion
Kinetic energy
of movement

Water

Oxygen

Energy conversion in a car

Figure 5.10_2

Fuel

Energy conversion

Waste products

Heat
energy

Glucose

Oxygen

Cellular respiration
Carbon dioxide
ATP

ATP

Energy for cellular work


Energy conversion in a cell

Water

Cells transform energy as they perform work

Heat, or thermal energy, is a type of

kinetic energy associated with the


random movement of atoms or
molecules.
Light is also a type of kinetic energy,
and can be harnessed to power
photosynthesis.

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Cells transform energy as they perform work

Chemical energy is the potential

energy available for release in a


chemical reaction. It is the most
important type of energy for living
organisms to power the work of the
cell.

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Cells transform energy as they perform work

Thermodynamics is the study of

energy transformations that occur


in a collection of matter.
Scientists use the word
system for the matter under
study and
surroundings for the rest of the
universe.
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Cells transform energy as they perform work


Two laws govern energy

transformations in organisms.
According to the
first law of thermodynamics,
energy in the universe is constant,
and
second law of thermodynamics,
energy conversions increase the
disorder of the universe.
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Cells transform energy as they perform work

Cells use oxygen in reactions that

release energy from fuel molecules.


In cellular respiration, the
chemical energy stored in organic
molecules is converted to a form
that the cell can use to perform
work.
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Chemical reactions either release or store


energy

Chemical reactions either


release energy (exergonic

reactions) or
require an input of energy and
store energy (endergonic
reactions).

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Chemical reactions either release or store


energy
Exergonic reactions release energy.
These reactions release the energy

in covalent bonds of the reactants.


Burning wood releases the energy in
glucose as heat and light.
Cellular respiration
involves many steps,
releases energy slowly, and
uses some of the released energy to

produce ATP.

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Figure 5.11A

Potential energy of molecules

Reactants

Amount of
energy
released
Energy

Products

Chemical reactions either release or store


energy
An endergonic reaction
requires an input of energy and

yields products rich in potential

energy.
Endergonic reactions
begin with reactant molecules that
contain relatively little potential
energy but
end with products that contain more
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Figure 5.11B

Potential energy of molecules

Products

Amount of
energy
required
Energy
Reactants

Chemical reactions either release or store


energy
Photosynthesis is a type of endergonic

process.
Energy-poor reactants, carbon
dioxide, and water are used.
Energy is absorbed from sunlight.
Energy-rich sugar molecules are
produced.

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Chemical reactions either release or store


energy
A living organism carries out thousands of

endergonic and exergonic chemical


reactions.
The total of an organisms chemical
reactions is called metabolism.
A metabolic pathway is a series of
chemical reactions that either
builds a complex molecule or
breaks down a complex molecule into
simpler compounds.
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Chemical reactions either release or store


energy
Energy coupling uses the
energy released from exergonic

reactions to drive
essential endergonic reactions,
usually using the energy stored in
ATP molecules.

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ATP drives cellular work by coupling exergonic


and endergonic reactions
ATP, adenosine triphosphate, powers nearly

all forms of cellular work.


ATP consists of
the nitrogenous base adenine,
the five-carbon sugar ribose, and
three phosphate groups.

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ATP drives cellular work by coupling exergonic


and endergonic reactions

Hydrolysis of ATP releases energy by

transferring its third phosphate from


ATP to some other molecule in a
process called phosphorylation.
Most cellular work depends on ATP
energizing molecules by
phosphorylating them.

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Figure 5.12A_s1

ATP:

Adenosine

Triphosphate
Phosphate
group
P

Adenine
Ribose

Figure 5.12A_s2

ATP:

Triphosphate

Adenosine

Phosphate
group
P

Adenine
Ribose

H2O

Hydrolysis

ADP:

Adenosine

Diphosphate

Energy

ATP drives cellular work by coupling exergonic


and endergonic reactions

There are three main types of

cellular work:
1.chemical,
2.mechanical, and
3.transport.
ATP drives all three of these types
of work.
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Figure 5.12B

Chemical work

Mechanical work

Transport work

ATP

ATP

ATP

Solute
P

Motor
protein

P
P

Reactants

Membrane protein

P
P
P

Product
Molecule formed

ADP

Protein filament moved

ADP

Solute transported

ADP

ATP drives cellular work by coupling exergonic


and endergonic reactions

ATP is a renewable source of energy

for the cell.


In the ATP cycle, energy released in an
exergonic reaction, such as the
breakdown of glucose,is used in an
endergonic reaction to generate ATP.

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Figure 5.12C

ATP

Energy from
exergonic
reactions

ADP

Energy for
endergonic
reactions

HOW ENZYMES FUNCTION

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Enzymes speed up the cells chemical reactions by


lowering energy barriers
Although biological molecules possess much

potential energy, it is not released


spontaneously.
An energy barrier must be overcome
before a chemical reaction can begin.
This energy is called the activation
energy (EA).

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Enzymes speed up the cells chemical reactions


by lowering energy barriers
We can think of EA
as the amount of energy needed for a

reactant molecule to move uphill to a


higher energy but an unstable state
so that the downhill part of the reaction
can begin.
One way to speed up a reaction is to add
heat,
which agitates atoms so that bonds break
more easily and reactions can proceed
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Figure 5.13A

Activation
energy barrier

Enzyme
Activation
energy
barrier
reduced by
enzyme

Reactant
Energy

Energy

Reactant

Products
Without enzyme

Products
With enzyme

Figure 5.13A_1

Activation
energy barrier

Energy

Reactant

Products

Without enzyme

Figure 5.13A_2

Enzyme
Activation
energy
barrier
reduced by
enzyme

Energy

Reactant

Products

With enzyme

Figure 5.13Q

Energy

b
Reactants

Products
Progress of the reaction

Enzymes speed up the cells chemical reactions


by lowering energy barriers

Enzymes
function as biological catalysts by

lowering the EA needed for a reaction


to begin,
increase the rate of a reaction
without being consumed by the
reaction, and
are usually proteins, although some
RNA molecules can function as
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Animation: How Enzymes Work


Right click on animation / Click play
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A specific enzyme catalyzes each cellular


reaction
An enzyme
is very selective in the reaction it catalyzes and
has a shape that determines the enzymes

specificity.
The specific reactant that an enzyme acts on is
called the enzymes substrate.
A substrate fits into a region of the enzyme called
the active site.
Enzymes are specific because their active site fits
only specific substrate molecules.
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A specific enzyme catalyzes each cellular reaction

The following figure illustrates the

catalytic cycle of an enzyme.

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Figure 5.14_s1

Enzyme available
with empty active
site
Active site

Enzyme
(sucrase)

Figure 5.14_s2

Enzyme available
with empty active
site
Active site

Substrate
(sucrose)
2

Enzyme
(sucrase)

Substrate binds
to enzyme with
induced fit

Figure 5.14_s3

Enzyme available
with empty active
site
Active site

Substrate
(sucrose)
2

Substrate binds
to enzyme with
induced fit

Enzyme
(sucrase)

H2O

Substrate is
converted to
products

Figure 5.14_s4

Enzyme available
with empty active
site
Active site

Substrate
(sucrose)
2

Glucose

Substrate binds
to enzyme with
induced fit

Enzyme
(sucrase)

Fructose
H2O
4

Products are
released
3

Substrate is
converted to
products

A specific enzyme catalyzes each cellular


reaction
For every enzyme, there are optimal

conditions under which it is most effective.


Temperature affects molecular motion.
An enzymes optimal temperature
produces the highest rate of contact
between the reactants and the enzymes
active site.
Most human enzymes work best at 35
40C.
The optimal pH for most enzymes is near
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A specific enzyme catalyzes each cellular


reaction
Many enzymes require nonprotein helpers

called cofactors, which


bind to the active site and
function in catalysis.
Some cofactors are inorganic, such as zinc,
iron, or copper.
If a cofactor is an organic molecule, such as
most vitamins, it is called a coenzyme.

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Enzyme inhibitors can regulate enzyme activity in a


cell

A chemical that interferes with an

enzymes activity is called an inhibitor.


Competitive inhibitors
block substrates from entering the
active site and
reduce an enzymes productivity.

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Enzyme inhibitors can regulate enzyme activity in a


cell

Noncompetitive inhibitors
bind to the enzyme somewhere other

than the active site,


change the shape of the active site,
and
prevent the substrate from binding.

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Figure 5.15A

Substrate
Active site
Enzyme
Allosteric site

Normal binding of substrate


Competitive
inhibitor

Noncompetitive
inhibitor

Enzyme inhibition

Enzyme inhibitors can regulate enzyme activity in a


cell

Enzyme inhibitors are important in

regulating cell metabolism.


In some reactions, the product may act
as an inhibitor of one of the enzymes in
the pathway that produced it. This is
called feedback inhibition.

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Figure 5.15B

Feedback inhibition

Enzyme 1
B

A
Reaction 1

Starting
molecule

Enzyme 2

Enzyme 3
C

Reaction 2

D
Reaction 3
Product

CONNECTION: Many drugs, pesticides, and


poisons are enzyme inhibitors
Many beneficial drugs act as enzyme

inhibitors, including
Ibuprofen, inhibiting the production of
prostaglandins,
some blood pressure medicines,
some antidepressants,
many antibiotics, and
protease inhibitors used to fight HIV.
Enzyme inhibitors have also been developed
as pesticides and deadly poisons for
chemical warfare.
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Figure 5.16

MECHANISM ACTION:

There are 2 main hypotheses explaining of


enzyme action.

Each enzyme is specific for one and ONLY

one substrate (one lock - one key)


active site: part of the enzyme that fits with
the substrate
Note that the active site has a specific fit for
this particular substrate and no other.
This theory has some weaknesses, but it
explains many basic things about enzyme
function.

Substrate: The starting molecules for a chemical

reaction are called the substrates.


Enzyme substrate complex: The enzyme
substrate complex is transitional step when the
substrates of a chemical reaction are bound to
the enzyme.
Active site: The area on the enzyme where the
substrate or substrates attach to is called the
active site.
Enzymes are usually very large proteins and the
active site is just a small region of the enzyme
molecule.

The induced-fit theory assumes that the substrate

plays a role in determining the final shape of the


enzyme and that the enzyme is partially flexible.
This explains why certain compounds can bind to
the enzyme but do not react because the enzyme
has been distorted too much.
Other molecules may be too small to induce the
proper alignment and therefore cannot react.
Only the proper substrate is capable of inducing the
proper alignment of the active site.

In the graphic, the substrate is represented by the

magenta molecule, the enzyme protein is


represented by the green and cyan colors.
The cyan colored protein is used to more sharply
define the active site.
The protein chains are flexible and fit around the
substrate.

The advantages of the induced fit mechanism arise due

to the stabilizing effect of strong enzyme binding.


There are two different mechanisms of substrate
binding; uniform binding which has strong substrate
binding, and differential binding which has strong
transition state binding.
The stabilizing effect of uniform binding increases both
substrate and transition state binding affinity and
differential binding increases only transition state
binding affinity.

Both are used by enzymes and have been

evolutionarily chosen to minimize the G of the


reaction.
Enzymes which are saturated, ie. have a high affinity
substrate binding, require differential binding to
reduce the G, whereas largely substrate unbound
enzymes may use either differential or uniform
binding.

How do enzymes work?


substrate: molecules upon which an enzyme

acts. The enzyme is shaped so that it can only


lock up with a specific substrate molecule.
enzyme
substrate -------------> product

The diagram shows time on the horizontal axis and

the amount of energy in the chemicals involved in a


chemical reaction on the vertical axis.
The point if this diagram again is that without the
enzyme, much more activation energy is required to
get a chemical reaction to take place.

Factors Influencing Enzyme Activity


pH: the optimum (best) in most living things is

close to 7 (neutral).
High or low pH levels usually slow enzyme
activity

Temperature: strongly influences enzyme

activity optimum (best) temperature for maximum


enzyme function is usually about 35-40 C.
Reactions proceed slowly below optimal
temperatures.
Above 45 C. most enzymes are denatured
(change in their shape so the enzyme active site
no longer fits with the substrate and the enzyme
can't function)

METABOLISM
Metabolism is the sum of all biochemical

reactions occurring in living cells.


These reactions can be divided into two main
groups:
1) ANABOLISM

2) CATABOLISM

Involves the synthesis

of complex molecules
from simpler molecules
which requires energy
input.

Involves the

breakdown of complex
molecules into simpler
molecules involving
hydrolysis or oxidation
and the release of
energy.

Energy releasing processes, ones that "generate"

energy, are termed exergonic reactions.


Reactions that require energy to initiate the
reaction are known as endergonic reactions.
All natural processes tend to proceed in such a
direction that the disorder or randomness of the
universe increases

In an exergonic reaction the change is free

energy is represented by a negative number (G), indicating free energy is released during
the reaction.

This kind of reaction is not termed a

spontaneous reaction. In order to go from the


initial state to the final state a considerable
amount of energy must be imparted to the
system.
These kinds of reactions are associated with a
positive number (+G).

The speed V means the number of reactions per

second that are catalyzed by an enzyme.


With increasing substrate concentration [S], the
enzyme is asymptotically approaching its
maximum speed Vmax, but never actually
reaching it.
Because of that, no [S] for Vmax can be given.
Instead, the characteristic value for the enzyme
is defined by the substrate concentration at its
half-maximum speed (Vmax/2).
This KM value is also called Michaelis-Menten
constant.

Vo = Vmax
KM
Vo = Initial reaction velocity

Vmax = Maximum velocity


Km = Michaelis constant
[S] = Substrate concentration

A non protein component of enzymes is called the

cofactor.
If the cofactor is organic, then it is called a
coenzyme.
Coenzymes are relatively small molecules
compared to the protein part of the enzyme.
Many of the coenzymes are derived from vitamins.
The coenzymes make up a part of the active site,
since without the coenzyme, the enzyme will not
function.

In the graphic on the left is the structure for

the coenzyme, NAD+, Nicotinamide


Adenine Dinucleotide.
Nicotinamide is from the niacin vitamin.
The NAD+ coenzyme is involved with
many types of oxidation reactions where
alcohols are converted to ketones or
aldehydes.

Vitamin

Coenzyme

Function

niacin

nicotinamide adenine
dinucleotide (NAD+)

oxidation or
hydrogen transfer

riboflavin

flavin adenine
dinucleotide (FAD)

oxidation or
hydrogen transfer

pantothenic
acid

coenzyme A (CoA)

Acetyl group carrier

vitamin B-12

coenzyme B-12

Methyl group
transfer

thiamin (B-1)

thiaminpyrophosphate
(TPP)

Aldehyde group
transfer

Coenzyme Q10 is a fat-soluble nutrient also

known as CoQ10, vitamin Q10,


ubidecarenone, or ubiquinone.
It is a natural product of the human body that
is primarily found in the mitochondria, which
are the cellular organelles that produce
energy.
It occurs in most tissues of the human body;
however, the highest concentrations are
found in the heart, liver, kidneys, and
pancreas.
Ubiquinone takes its name from a
combination of the word ubiquitous, meaning

Quinones are substances found in all

plants and animals.


The variety found in humans has a 10-unit
side chain in its molecular structure.
Apart from the important process that
provides energy, CoQ10 also stabilizes cell
membranes and acts as an antioxidant.
In this capacity, it destroys free radicals,
which are unstable molecules that can
damage normal cells.

Enzyme inhibitors are molecules that

interact in some way with the enzyme to


prevent it from working in the normal
manner.
There are a variety of types of inhibitors
including: nonspecific, irreversible,
reversible - competitive and noncompetitive.
Poisons and drugs are examples of enzyme
inhibitors.

A nonspecific inhibition effects all enzymes in the

same way.
Non-specific methods of inhibition include any
physical or chemical changes which ultimately
denatures the protein portion of the enzyme and
are therefore irreversible.

Temperature: Usually, the reaction rate increases with

temperature, but with enzyme reactions, a point is


reached when the reaction rate decreases with
increasing temperature.
At high temperatures the protein part of the enzyme
begins to denature, thus inhibiting the reaction.

A competitive inhibitor is any compound which

closely resembles the chemical structure and


molecular geometry of the substrate.
The inhibitor competes for the same active site as
the substrate molecule.
The inhibitor may interact with the enzyme at the
active site, but no reaction takes place.

The inhibitor is "stuck" on the enzyme and

prevents any substrate molecules from


reacting with the enzyme.
However, a competitive inhibition is usually
reversible if sufficient substrate molecules are
available to ultimately displace the inhibitor.
Therefore, the amount of enzyme inhibition
depends upon the inhibitor concentration,
substrate concentration, and the relative
affinities of the inhibitor and substrate for the
active site.

A noncompetitive inhibitor is a substance that

forms strong covalent bonds with an enzyme


and consequently may not be displaced by
the addition of excess substrate.
Therefore, noncompetitive inhibition is
irreversible.
A noncompetitive inhibitor may be bonded at,
near, or remote from the active site. In any
case, the basic structure of the enzyme is
modified to the degree that it ceases to work.

If the inhibition is at a place remote from the active

site, this is called allosteric inhibition.


Allosteric means "other site" or "other structure".
The interaction of an inhibitor at an allosteric site
changes the structure of the enzyme so that the active
site is also changed.

There are approximately 3000 enzymes which

have been characterised.


These are grouped into six main classes
according to the type of reaction catalysed.
At present, only a limited number are used in
enzyme electrodes or for other analytical
purposes.

1.Oxidoreductases
These enzymes catalyse oxidation and

reduction reactions involving the transfer


of hydrogen atoms or electrons.
The following are of particular
importance in the design of enzyme
electrodes.
This group can be further divided into 4
main classes.

oxidases
catalyse hydrogen transfer from the

substrate to molecular oxygen producing


hydrogen peroxide as a by-product. An
example of this is FAD dependent
glucose oxidase which catalyses the
following reaction:
b-D-glucose + O2 = gluconolactone +
H2O2

dehydrogenases
catalyse hydrogen transfer from

the substrate to a nicotinamide


adenine dinucleotide cofactor
(NAD+). An example of this is
lactate dehydrogenase which
catalyses the following reaction:
Lactate + NAD+ = Pyruvate +
NADH + H+

peroxidases
catalyse oxidation of a substrate by hydrogen

peroxide.
An example of this type of enzyme is horseradish
peroxidase which catalyses the oxidation of a
number of different reducing substances (dyes,
amines, hydroquinones etc.) and the concomitant
reduction of hydrogen peroxide.
The reaction below illustrates the oxidation of
neutral ferrocene to ferricinium in the presence of
hydrogen peroxide:
2[Fe(Cp)2] + H2O2 + 2H+= 2[Fe(Cp)2]+ + 2
H2O

oxygenases
catalyse substrate oxidation by

molecular oxygen.
The reduced product of the reaction
in this case is water and not
hydrogen peroxide.
An example of this is the oxidation of
lactate to acetate catalysed by
lactate-2-monooxygenase.

2.Transferases
These enzymes transfer C, N, P or

S containing groups (alkyl, acyl,


aldehyde, amino, phosphate or
glucosyl) from one substrate to
another.
Transaminases, transketolases,
transaldolases and transmethylases
belong to this group.

3.Hydrolases
These enzymes catalyse cleavage

reactions or the reverse fragment


condensations.
According to the type of bond cleaved,
a distinction is made between
peptidases, esterases, lipases,
glycosidases, phosphatases and so
on.
Examples of this class of enzyme
include; cholesterol esterase, alkaline

4.Lyases
These enzymes non-hydrolytically

remove groups from their


substrates with the concomitant
formation of double bonds or
alternatively add new groups across
double bonds.

5.Isomerases
These enzymes catalyse intramolecular

rearrangements and are subdivided into;


oracemases
oepimerases
omutases
ocis-trans-isomerases
An example of this class of enzyme is

glucose isomerase which catalyses the


isomerisation of glucose to fructose.

6.Ligases
Ligases split C-C, C-O, C-N, C-S and C-

halogen bonds without hydrolysis or


oxidation.
The reaction is usually accompanied by
the consumption of a high energy
compound such as ATP and other
nucleoside triphosphates.
An example of this type of enzyme is
pyruvate carboxylase which catalyses
the following reaction:

IEC Classification of Enzymes


Group Name
Type of Reaction Catalyzed
Oxidases or
Oxidation-reduction
Dehydrogenases
reactions
Transfer of functional
Transferases
groups
Hydrolases
Hydrolysis reactions
Addition to double bonds or
Lyases
its reverse
Isomerases
Isomerization reactions
Formation of bonds with
Ligases or Synthetases
ATP cleavage

Enzymes do NOT change the equilibrium position of the

reaction, just the speed at which equilibrium is attained.


Most are globular or soluble.
Stereospecific (can recognize certain isomers only) due to
the fact that amino acids of the active site are chiral
themselves.
Substrate/s bind in hydrophobic cleft (active site) between
several domains where catalysis occurs:
Van der Waals forces
Hydrophobic interactions
Electrostatic interactions

Active site has structure that is complimentary in structure to

the structure of its substrate.

Most are proteins, some are RNA.


Biological catalysts.
E + S ES EP E + P
Not changed by the reaction overall
Much higher reaction rates than uncatalyzed reactions.
Allow for biochemical reactions to occur under very mild

conditions (temperature, near-neutral pH, 1 atm pressure)


High yield of products (few side reactions or by-products)
Very specific reactions (specific for its substrate or a family of
related substrates)
Often a regulated functions:
allosteric activation or inhibition
covalent modification (phosphorylation changes)
enzyme expression controlled or cleavage of proenzyme
controlled.

Preparatory Reaction