BIOMOLECULES

 There is a wide diversity in living organisms in our biosphere.

 Now a question that arises in our minds is:
 Are all living organisms made of the same chemicals, i.e.,
elements and compounds?
 You have learnt in chemistry how elemental analysis is
performed.
 If we perform such an analysis on a plant tissue, animal
tissue or a microbial paste, we obtain a list of elements like
carbon, hydrogen, oxygen and several others and their
respective content per unit mass of a living tissue.

 If the same analysis is performed on a piece of earth’s crust

as an example of non-living matter, we obtain a similar list.
 What are the differences between the two lists?
 In absolute terms, no such differences could be made out.
 All the elements present in a sample of earth’s crust are also
present in a sample of living tissue.
 However, a closer examination reveals that the relative
abundance of carbon and hydrogen with respect to other
elements is higher in any living organism than in earth’s
crust (Table 9.1).
HOW TO ANALYSE CHEMICAL COMPOSITION?
We can continue asking in the same way, what type of organic
compounds are found in living organisms?
How does one go about finding the answer?
To get an answer, one has to perform a chemical analysis.

 We can take any living tissue (a vegetable or a piece of liver,

etc.) and grind it in trichloroacetic acid (Cl3CCOOH) using a
mortar and a pestle.
 We obtain a thick slurry.
 If we were to strain this through a cheesecloth or cotton we
would obtain two fractions.
 One is called the filtrate or more technically, the acid-
soluble pool, and the second, the retentate or the acid-
insoluble fraction.
 Scientists have found thousands of organic compounds in
the acid-soluble pool.

In higher classes you will learn about how to analyse a living

tissue sample and identify a particular organic compound.
It will suffice to say here that one extracts the compounds, then
subjects the extract to various separation techniques till one has
separated a compound from all other compounds.

In other words, one isolates and purifies a compound.

Analytical techniques, when applied to the compound give us an

idea of the molecular formula and the probable structure of the
compound.
 All the carbon compounds that we get from living tissues

can be called ‘biomolecules’.

However, living organisms have also got inorganic elements and
compounds in them.
How do we know this?
A slightly different but destructive experiment has to be done.

 One weighs a small amount of a living tissue (say a leaf or

liver and this is called wet weight) and dry it.
 All the water, evaporates.
 The remaining material gives dry weight.
 Now if the tissue is fully burnt, all the
 carbon compounds are oxidised to gaseous form (CO2,
water vapour) and are removed.
 What is remaining is called ‘ash’.
 This ash contains inorganic elements (like calcium,
magnesium etc).
 Inorganic compounds like sulphate, phosphate, etc., are also
seen in the acid-soluble fraction.
 Therefore elemental analysis gives elemental composition of
living tissues in the form of hydrogen, oxygen, chlorine,
carbon etc. while analysis for compounds gives an idea of
the kind of organic (Figure 9.1) and inorganic constituents
(Table 9.2) present in living tissues.

From a chemistry point of view, one can identify functional

groups like aldehydes, ketones, aromatic compounds, etc.

But from a biological point of view, we shall classify them into

amino acids, nucleotide bases, fatty acids etc.
Amino Acids
Amino acids are organic compounds containing an amino group
and an acidic group as substituents on the same carbon i.e., the
α-carbon.
Hence, they are called α (Alpha)-amino acids.
They are substituted methanes.
There are four substituent groups occupying the four valency
positions.
These are hydrogen, carboxyl group, amino group and a
variable group designated as R group.
Based on the nature of R group there are many amino acids.
However, amino acids which occur in proteins are only of
twenty types.
The R group in these proteinaceous amino acids could be a
hydrogen (the amino acid is called glycine), a methyl group
(alanine), hydroxy methyl (serine), etc. Three of the twenty are
shown in Figure 9.1.

 The chemical and physical properties of amino acids are

essentially of the amino, carboxyl and the R functional
groups.
 Based on number of amino and carboxyl groups, there are
acidic (e.g., glutamic acid), basic (lysine) and neutral (valine)
amino acids.
 Similarly, there are aromatic amino acids (tyrosine,
phenylalanine, tryptophan).
 A particular property of amino acids is the ionizable nature
of –NH2 and –COOH groups.
  Hence in solutions of different pHs, the structure of amino
acids changes.

 LIPIDS

 Lipids are generally water insoluble.

 They could be simple fatty acids.

 A fatty acid has a carboxyl group attached to an R group.
 The R group could be a methyl (–CH3), or ethyl (–C2H5) or
higher number of –CH2 groups (1 carbon to 19 carbons).
 For example, palmitic acid has 16 carbons including carboxyl
carbon.

 Arachidonic acid has 20 carbon atoms including the carboxyl

carbon.

 Types of Fatty Acids

 Fatty acids could be saturated (without double bond) or
unsaturated (with one or more C=C double bonds).

 Another simple lipid is glycerol which is trihydroxy propane.

 Many lipids have both glycerol and fatty acids.

 Here the fatty acids are found esterified with glycerol.

 They can be then monoglycerides, diglycerides and triglycerides.
 These are also called fats and oils based on melting point.


 Oils have lower melting point (e.g., gingelly oil) and hence
remain as oil in winters.

 Can you identify a fat from the market?

 Some lipids have phosphorous and a phosphorylated organic
compound in them.
 These are phospholipids.
 They are found in cell membrane.
 Lecithin is one example.
 Some tissues especially the neural tissues have lipids with more
complex structures.

Nucleic Acids
 Living organisms have a number of carbon compounds in which
heterocyclic rings can be found. Some of these are nitrogen
bases – adenine, guanine, cytosine, uracil, and thymine.
 When found attached to a sugar, they are called nucleosides.
 If a phosphate group is also found esterified to the sugar they
are called nucleotides.
 Adenosine, guanosine, thymidine, uridine and cytidine are
nucleosides.
 Adenylic acid, thymidylic acid, guanylic acid, uridylic acid and
cytidylic acid are nucleotides.
 Nucleic acids like DNA and RNA consist of nucleotides only.
 DNA and RNA function as genetic material.
 PRIMARY AND SECONDARY METABOLITES
 The most exciting aspect of chemistry deals with isolating
thousands of compounds, small and big, from living organisms,
determining their structure and if possible synthesising them.
 If one were to make a list of biomolecules, such a list would have
thousands of organic compounds including amino acids, sugars,
etc.

 For reasons that are given in section 9.10, we can call these
biomolecules as ‘metabolites’.
 In animal tissues, one notices the presence of all such categories
of compounds shown in Figure 9.1.
 These are called primary metabolites.

 However, when one analyses plant, fungal and microbial cells,

one would see thousands of compounds other than these called
primary metabolites, e.g. alkaloids, flavonoids, rubber,
essential oils, antibiotics, coloured pigments, scents, gums,
spices.

 These are called secondary metabolites (Table 9.3).

 While primary metabolites have identifiable functions and play
known roles in normal physiologial processes, we do not at the
moment, understand the role or functions of all the ‘secondary
metabolites’ in host organisms.
 However, many of them are useful to ‘human welfare’ (e.g.,
rubber, drugs, spices, scents and pigments).
 Some secondary metabolites have ecological importance. In the
later chapters and years you will learn more about this.
 BIOMACROMOLECULES
 There is one feature common to all those compounds found in
the acid soluble pool.
 They have molecular weights ranging from 18 to around 800
daltons (Da) approximately.
 The acid insoluble fraction, has only four types of organic
compounds i.e., proteins, nucleic acids, polysaccharides and
lipids.

 These classes of compounds with the exception of lipids, have

molecular weights in the range of ten thousand daltons and
above.
 For this very reason, biomolecules, i.e., chemical compounds
found in living organisms are of two types.

 One, those which have molecular weights less than one

thousand dalton and are usually referred to as micromolecules
or simply biomolecules while those which are found in the acid
insoluble fraction are called macromolecules or
biomacromolecules.
 The molecules in the insoluble fraction with the exception of
lipids are polymeric substances.
 Then why do lipids, whose molecular weights do not exceed 800
Da, come under acid insoluble fraction, i.e., macromolecular
fraction?

 Lipids are indeed small molecular weight compounds and are

present not only as such but also arranged into structures like
cell membrane and other membranes.

 When we grind a tissue, we are disrupting the cell structure.

 Cell membrane and other membranes are broken into pieces,
and form vesicles which are not water soluble.
 Therefore, these membrane fragments in the form of vesicles
get separated along with the acid insoluble pool and hence in
the macromolecular fraction. Lipids are not strictly
macromolecules.

 The acid soluble pool represents roughly the cytoplasmic

composition.
 The macromolecules from cytoplasm and organelles become the
acid insoluble fraction.
 Together they represent the entire chemical composition of
living tissues or organisms.
 In summary if we represent the chemical composition of living
tissue from abundance point of view and arrange them class-
wise, we observe that water is the most abundant chemical in
living organisms (Table 9.4).
 PROTEINS
 Proteins are polypeptides. They are linear chains of amino acids
linked by peptide bonds as shown in Figure 9.3.

 Each protein is a polymer of amino acids.

 As there are 20 types of amino acids (e.g., alanine, cysteine,
proline, tryptophan, lysine, etc.), a protein is a heteropolymer
and not a homopolymer. A homopolymer has only one type of
monomer repeating ‘n’ number of times.
 This information about the amino acid content is important as
later in your nutrition lessons, you will learn that certain amino
acids are essential for our health and they have to be supplied
through our diet.
 Hence, dietary proteins are the source of essential amino acids.
 Therefore, amino acids can be essential or non-essential.
 The latter are those which our body can make, while we get
essential amino acids through our diet/food.
 Proteins carry out many functions in living organisms, some
transport nutrients across cell membrane, some fight infectious
organisms, some are hormones, some are enzymes, etc. (Table
9.5).
 Collagen is the most abundant protein in animal world and
Ribulose bisphosphate Carboxylase-Oxygenase (RuBisCO) is the
most abundant protein in the whole of the biosphere.
 GLUT 4 - Glucose Transporter Type 4
 POLYSACCHARIDES
 The acid insoluble pellet also has polysaccharides
(carbohydrates) as another class of macromolecules.
Polysaccharides are long chains of sugars.

 They are threads (literally a cotton thread) containing different

monosaccharides as building blocks.
 For example, cellulose is a polymeric polysaccharide consisting of
only one type of monosaccharide i.e., glucose.
 Cellulose is a homopolymer.
 Starch is a variant of this but present as a store house of energy
in plant tissues.
 Animals have another variant called glycogen.
 Inulin is a polymer of fructose.
 In a polysaccharide chain (say glycogen), the right end is called
the reducing end and the left end is called the non-reducing end.
 It has branches as
 shown in the form of a cartoon (Figure 9.2).
 Starch forms helical secondary structures.
 In fact, starch can hold I2 (Iodine) molecules in the helical
portion.
 The starch-I2 (Iodine) is blue in colour.
 Cellulose does not contain complex helices and hence cannot
hold I2 (Iodine).
 Plant cell walls are made of cellulose.
 Paper made from plant pulp and cotton fibre is cellulosic.
 There are more complex polysaccharides in nature.
 They have as building blocks, amino-sugars and chemically
modified sugars (e.g., glucosamine, N-acetyl galactosamine,
etc.).
 Exoskeletons of arthropods, for example, have a complex
polysaccharide called chitin.
 These complex polysaccharides are mostly homopolymers.

 NUCLEIC ACIDS
 The other type of macromolecule that one would find in the acid
insoluble fraction of any living tissue is the nucleic acid.
 These are polynucleotides.
 Together with polysaccharides and polypeptides these comprise
the true macromolecular fraction of any living tissue or cell.
 For nucleic acids, the building block is a nucleotide.
 A nucleotide has three chemically distinct components.
 One is a heterocyclic compound, the second is a
monosaccharide and the third a phosphoric acid or phosphate.
 As you notice in Figure 9.1, the heterocyclic compounds in
nucleic acids are the nitrogenous bases named adenine, guanine,
uracil, cytosine, and thymine. Adenine and Guanine are
substituted purines while the rest are substituted pyrimidines.
 The skeletal heterocyclic ring is called as purine and pyrimidine
respectively. The sugar found in polynucleotides is either ribose
(a monosaccharide pentose) or 2’ deoxyribose.
 A nucleic acid containing deoxyribose is called deoxyribonucleic
acid (DNA) while that which contains ribose is called ribonucleic
acid (RNA).

 STRUCTURE OF PROTEINS
 Proteins, as mentioned earlier, are heteropolymers containing
strings of amino acids.
 Structure of molecules means different things in different
contexts.
 In inorganic chemistry, the structure invariably refers to the
molecular formulae (e.g., NaCl, MgCl2, etc.).
 Organic chemists always write a two dimensional view of the
molecules while representing the structure of the molecules
(e.g., benzene, naphthalene, etc.).

 Physicists conjure up the three dimensional views of molecular

structures while biologists describe the protein structure at four
levels.

 Primary Structure
 The sequence of amino acids i.e., the positional information in a
protein – which is the first amino acid, which is second, and so
on – is called the primary structure (Figure 9.3) of a protein.

 A protein is imagined as a line, the left end represented by the
first amino acid and the right end represented by the last amino
acid.
 The first amino acid is also called as N-terminal amino acid.
 The last amino acid is called the C-terminal amino acid.

 Secondary Structure
 A protein thread does not exist throughout as an extended rigid
rod.
 The thread is folded in the form of a helix (similar to a revolving
staircase).
 Of course, only some portions of the protein thread are arranged
in the form of a helix.
 In proteins, only right handed helices are observed.
 Other regions of the protein thread are folded into other forms
in what is called the secondary structure.
 Tertiary structure
 In addition, the long protein chain is also folded upon itself like a
hollow woolen ball, giving rise to the tertiary structure (Figure
9.4 a, b).
 This gives us a 3- dimensional view of a protein.
 Tertiary structure is absolutely necessary for the many biological
activities of proteins.


 Quaternary Structure
 Some proteins are an assembly of more than one polypeptide or
subunits.
 The manner in which these individual folded polypeptides or
subunits are arranged with respect to each other (e.g. linear
string of spheres, spheres arranged one upon each other in the
form of a cube or plate etc.) is the architecture of a protein
otherwise called the quaternary structure of a protein.
 Adult human haemoglobin consists of 4 subunits. Two of these
are identical to each other. Hence, two subunits of Alpha α type
and two subunits of beta β type together constitute the human
haemoglobin (Hb).


 NATURE OF BOND LINKING MONOMERS IN A POLYMER

 In a polypeptide or a protein, amino acids are linked by a peptide
bond which is formed when the carboxyl (-COOH) group of one
amino acid reacts with the amino (-NH2) group of the next
amino acid with the elimination of a water moiety (the process is
called dehydration).

 In a polysaccharide the individual monosaccharides are linked by

a glycosidic bond. This bond is also formed by dehydration.
 This bond is formed between two carbon atoms of two adjacent
monosaccharides.

 In a nucleic acid a phosphate moiety links the 3’-carbon of one

sugar of one nucleotide to the 5’-carbon of the sugar of the
succeeding nucleotide.
 The bond between the phosphate and hydroxyl group of sugar is
an ester bond.
 As there is one such ester bond on either side, it is called
phosphodiester bond (Figure 9.5).
 Nucleic acids exhibit a wide variety of secondary structures. For
example, one of the secondary structures exhibited by DNA is
the famous Watson-Crick model.
 This model says that DNA exists as a double helix.
 The two strands of polynucleotides are antiparallel i.e., run in
the opposite direction.
 The backbone is formed by the sugarphosphate- sugar chain.
 The nitrogen bases are projected more or less perpendicular to
this backbone but face inside.
 A and G of one strand compulsorily base pairs with T and C,
respectively, on the other strand.
 There are two hydrogen bonds between A and T and three
hydrogen bonds between G and C. Each strand appears like a
helical staircase.
 Each step of ascent is represented by a pair of bases.
 At each step of ascent, the strand turns 36°.
 One full turn of the helical strand would involve ten steps or ten
base pairs. Attempt drawing a line diagram.
 The pitch would be 34Å.
 The rise per base pair would be 3.4Å.
 This form of DNA with the above mentioned salient features is
called B DNA.
 In higher classes, you will be told that there are more than a
dozen forms of DNA named after English alphabets with unique
structural features.

 DYNAMIC STATE OF BODY CONSTITUENTS – CONCEPT OF

METABOLISM
 All living organisms, be it a simple bacterial cell, a protozoan, a
plant or an animal, contain thousands of organic compounds.
 These compounds or biomolecules are present in certain
concentrations (expressed as mols/cell or mols/litre etc.).

 One of the greatest discoveries ever made was the observation

that all these biomolecules have a turn over.
 This means that they are constantly being changed into some
other biomolecules and also made from some other
biomolecules.
 This breaking and making is through chemical reactions
constantly occuring in living organisms.
 Together all these chemical reactions are called metabolism.

 Each of the metabolic reactions results in the transformation of

biomolecules. A few examples for such metabolic
transformations are:
 removal of CO2 from amino acids making an amino acid into an
amine, removal of amino group in a nucleotide base;
 hydrolysis of a glycosidic bond in a disaccharide, etc.

 We can list tens and thousands of such examples.

 Majority of these metabolic reactions do not occur in isolation
but are always linked to some other reactions.
 In other words, metabolites are converted into each other in a
series of linked reactions called metabolic pathways.
 These metabolic pathways are similar to the automobile traffic in
a city.
 These pathways are either linear or circular.
 These pathways crisscross each other, i.e., there are traffic
junctions.
 Flow of metabolites through metabolic pathway has a definite
rate and direction like automobile traffic.
 This metabolite flow is called the dynamic state of body
constituents.
 What is most important is that this interlinked metabolic traffic
is very smooth and without a single reported mishap for healthy
conditions.

 Another feature of these metabolic reactions is that every

chemical reaction is a catalysed reaction.
 There is no uncatalysed metabolic conversion in living systems.
 Even CO2 dissolving in water, a physical process, is a catalysed
reaction in living systems.
 The catalysts which hasten the rate of a given metabolic
conversation are also proteins. These proteins with catalytic
power are named enzymes.

 METABOLIC BASIS FOR LIVING

 Metabolic pathways can lead to a more complex structure from
a simpler structure (for example, acetic acid becomes
cholesterol) or lead to a simpler structure from a complex
structure (for example, glucose becomes lactic acid in our
skeletal muscle).
 The former cases are called biosynthetic pathways or anabolic
pathways.
 The latter constitute degradation and hence are called catabolic
pathways. Anabolic pathways, as expected, consume energy.
 Assembly of a protein from amino acids requires energy input.
 On the other hand, catabolic pathways lead to the release of
energy.
 For example, when glucose is degraded to lactic acid in our
skeletal muscle, energy is liberated.
 This metabolic pathway from glucose to lactic acid which occurs
in 10 metabolic steps is called glycolysis.
 Living organisms have learnt to trap this energy liberated during
degradation and store it in the form of chemical bonds.
 As and when needed, this bond energy is utilised for
biosynthetic, osmotic and mechanical work that we perform.
 The most important form of energy currency in living systems is
the bond energy in a chemical called adenosine triphosphate
(ATP).

 THE LIVING STATE

 At this level, you must understand that the tens and thousands
of chemical compounds in a living organism, called metabolites,
or biomolecules, are present at concentrations characteristic of
each of them.

 For example, the blood concentration of glucose in a normal

healthy individual is 4.5-5.0 mM, while that of hormones would
be nanograms/ mL.
 The most important fact of biological systems is that all living
organisms exist in a steady-state characterised by concentrations
of each of these biomolecules. These biomolecules are in a
metabolic flux.
 Any chemical or physical process moves spontaneously to
equilibrium.
 The steady state is a non-equilibrium state.
 One should remember from physics that systems at equilibrium
cannot perform work.
 As living organisms work continuously, they cannot afford to
reach equilibrium. Hence the living state is a non-equilibrium
steady-state to be able to perform work; living process is a
constant effort to prevent falling into equilibrium.
 This is achieved by energy input.
 Metabolism provides a mechanism for the production of energy.
 Hence the living state and metabolism are synonymous.
 Without metabolism there cannot be a living state.

 ENZYMES
 Almost all enzymes are proteins.
 There are some nucleic acids that behave like enzymes.
 These are called ribozymes.
 One can depict an enzyme by a line diagram.
 An enzyme like any protein has a primary structure, i.e., amino
acid sequence of the protein.
 An enzyme like any protein has the secondary and the tertiary
structure.
 When you look at a tertiary structure (Figure 9.4 b) you will
notice that the backbone of the protein chain folds upon itself,
the chain criss-crosses itself and hence, many crevices or
pockets are made.

 One such pocket is the ‘active site’.

 An active site of an enzyme is a crevice or pocket into which the
substrate fits. Thus enzymes, through their active site, catalyse
reactions at a high rate.

 Enzyme catalysts differ from inorganic catalysts in many ways,
but one major difference needs mention.
 Inorganic catalysts work efficiently at high temperatures and
high pressures, while enzymes get damaged at high
temperatures (say above 40°C).

 However, enzymes isolated from organisms who normally live

under extremely high temperatures (e.g., hot vents and sulphur
springs), are stable and retain their catalytic power even at high
temperatures (upto 80°-90°C).
 Taq polymerase and Pfu DNA polymerase
 Thermal stability is thus an important quality of such enzymes
isolated from thermophilic organisms.

 Chemical Reactions
 How do we understand these enzymes? Let us first understand a
chemical reaction. Chemical compounds undergo two types of
changes.
 A physical change simply refers to a change in shape without
breaking of bonds. This is a physical process.
 Another physical process is a change in state of matter: when ice
melts into water, or when water becomes a vapour.
 These are also physical processes.
 However, when bonds are broken and new bonds are formed
during transformation, this will be called a chemical reaction. For
example:

 It is an inorganic chemical reaction.

 Similarly, hydrolysis of starch into glucose is an organic chemical
reaction.

 Rate of a physical or chemical process refers to the amount of

product formed per unit time. It can be expressed as:

 Rate can also be called velocity if the direction is specified.

 Rates of physical and chemical processes are influenced by
temperature among other factors.

 A general rule of thumb is that rate doubles or decreases by half

for every 10°C change in either direction.
 Catalysed reactions proceed at rates vastly higher than that of
uncatalysed ones. When enzyme catalysed reactions are
observed, the rate would be vastly higher than the same but
uncatalysed reaction. For example
 In the absence of any enzyme this reaction is very slow, with
about 200 molecules of H2CO3 being formed in an hour.
 However, by using the enzyme present within the cytoplasm
called carbonic anhydrase, the reaction speeds dramatically with
about 600,000 molecules being formed every second.
 The enzyme has accelerated the reaction rate by about 10
million times.
 The power of enzymes is incredible indeed!

 There are thousands of types of enzymes each catalysing a

unique chemical or metabolic reaction.
 A multistep chemical reaction, when each of the steps is
catalysed by the same enzyme complex or different enzymes, is
called a metabolic pathway. For example,

 is actually a metabolic pathway in which glucose becomes

pyruvic acid through ten different enzyme catalysed metabolic
reactions.
 In our skeletal muscle, under anaerobic conditions, lactic acid is
formed.
 Under normal aerobic conditions, pyruvic acid is formed.
 In yeast, during fermentation, the same pathway leads to the
production of ethanol (alcohol).
 Hence, in different conditions different products are possible.

 How do Enzymes bring about such High Rates of Chemical

Conversions?

 To understand this we should study enzymes a little more.

 We have already understood the idea of an ‘active site’.
 The chemical or metabolic conversion refers to a reaction.
 The chemical which is converted into a product is called a
‘substrate’.
 Hence enzymes, i.e. proteins with three dimensional structures
including an ‘active site’, convert a substrate (S) into a product
(P). Symbolically, this can be depicted as:

 It is now understood that the substrate ‘S’ has to bind the

enzyme at its ‘active site’ within a given cleft or pocket.
 The substrate has to diffuse towards the ‘active site’.
 There is thus, an obligatory formation of an ‘ES’ complex.
 E stands for enzyme.
 This complex formation is a transient phenomenon.
 During the state where substrate is bound to the enzyme active
site, a new structure of the substrate called transition state
structure is formed.
 Very soon, after the expected bond breaking/making is
completed, the product is released from the active site.
 In other words, the structure of substrate gets transformed into
the structure of product(s).
 The pathway of this transformation must go through the so-
called transition state structure.
 There could be many more ‘altered structural states’ between
the stable substrate and the product.
 Implicit in this statement is the fact that all other intermediate
structural states are unstable.
 Stability is something related to energy status of the molecule or
the structure. Hence, when we look at this pictorially through a
graph it looks like something as in Figure 9.6.
 The y-axis represents the potential energy content.
 The x-axis represents the progression of the structural
transformation or states through the ‘transition state’.
 You would notice two things.
 The energy level difference between S and P.
 If ‘P’ is at a lower level than ‘S’, the reaction is an exothermic
reaction.
 One need not supply energy (by heating) in order to form the
product.
 However, whether it is an exothermic or spontaneous reaction
or an endothermic or energy requiring reaction, the ‘S’ has to go
through a much higher energy state or transition state.
 The difference in average energy content of ‘S’ from that of this
transition state is called ‘activation energy’.
 Enzymes eventually bring down this energy barrier making the
transition of ‘S’ to ‘P’ more easy.
 Nature of Enzyme Action
 Each enzyme (E) has a substrate (S) binding site in its molecule so
that a highly reactive enzyme-substrate complex (ES) is
produced. This complex is short-lived and dissociates into its
product(s) P and the unchanged enzyme with an intermediate
formation of the enzyme-product complex (EP).
 The formation of the ES complex is essential for catalysis.

 The catalytic cycle of an enzyme action can be described in the

following
 steps:
 1. First, the substrate binds to the active site of the enzyme,
fitting into the active site.
 2. The binding of the substrate causes the enzyme to alter its
shape, fitting more tightly around the substrate.
 3. The active site of the enzyme which is in close proximity to the
substrate breaks the chemical bonds of the substrate and the
new enzyme- product complex is formed.
 4. The enzyme releases the products of the reaction and the free
enzyme is ready to bind to another molecule of the substrate
and run through the catalytic cycle once again.

 Factors Affecting Enzyme Activity

 The activity of an enzyme can be affected by a change in the
conditions which can alter the tertiary structure of the protein.
 These include temperature, pH, change in substrate
concentration or binding of specific chemicals that regulate its
activity.
 Temperature and pH Enzymes generally function in a narrow
range of temperature and pH (Figure 9.7).
 Each enzyme shows its highest activity at a particular
temperature and pH called the optimum temperature and
optimum pH.
 Activity declines both below and above the optimum value.
 Low temperature preserves the enzyme in a temporarily inactive
state whereas high temperature destroys enzymatic activity
because proteins are denatured by heat.

 Concentration of Substrate
 With the increase in substrate concentration, the velocity of the
enzymatic reaction rises at first.
 The reaction ultimately reaches a maximum velocity (Vmax)
which is not exceeded by any further rise in concentration of the
substrate.
 This is because the enzyme molecules are fewer than the
substrate molecules and after saturation of these molecules,
there are no free enzyme molecules to bind with the additional
substrate molecules (Figure 9.7).


 Competitive Inhibition
 The activity of an enzyme is also sensitive to the presence of
specific chemicals that bind to the enzyme.
 When the binding of the chemical shuts off enzyme activity, the
process is called inhibition and the chemical is called an
inhibitor.
 When the inhibitor closely resembles the substrate in its
molecular structure and inhibits the activity of the enzyme, it is
known as competitive inhibitor.

 Due to its close structural similarity with the substrate, the

inhibitor competes with the substrate for the substrate binding
site of the enzyme.
 Consequently, the substrate cannot bind and as a result, the
enzyme action declines,
 e.g., inhibition of succinic dehydrogenase by malonate which
closely resembles the substrate succinate in structure. Such
competitive inhibitors are often used in the control of bacterial
pathogens.

 Classification and Nomenclature of Enzymes

 Thousands of enzymes have been discovered, isolated and
studied.
 Most of these enzymes have been classified into different groups
based on the type of reactions they catalyse.
 Enzymes are divided into 6 classes each with 4-13 subclasses and
named accordingly by a four-digit number.
 Oxidoreductases/dehydrogenases: Enzymes which catalyse
oxidoreduction between two substrates S and S’ e.g.,


 Transferases: Enzymes catalysing a transfer of a group, G (other

than hydrogen) between a pair of substrate S and S’ e.g.,

 Hydrolases: Enzymes catalysing hydrolysis of ester, ether,

peptide, glycosidic, C-C, C-halide or P-N bonds.

 Lyases: Enzymes that catalyse removal of groups from substrates

by mechanisms other than hydrolysis leaving double bonds.

 Isomerases: Includes all enzymes catalysing inter-conversion of

optical, geometric or positional isomers.
 Ligases: Enzymes catalysing the linking together of 2 compounds,
e.g., enzymes which catalyse joining of C-O, C-S, C-N, P-O etc.
bonds.

 Co-factors
 Enzymes are composed of one or several polypeptide chains.
 However, there are a number of cases in which non-protein
constituents called cofactors are bound to the enzyme to make
the enzyme catalytically active.
 The protein portion of the enzymes is called the Apoenzyme.
 Three kinds of cofactors may be identified: prosthetic groups,
co-enzymes and metal ions.
 Prosthetic groups are organic compounds and are distinguished
from other cofactors in that they are tightly bound to the
apoenzyme.
 For example, in peroxidase and catalase, which catalyze the
breakdown of hydrogen peroxide to water and oxygen, haem is
the prosthetic group and it is a part of the active site of the
enzyme.

 Co-enzymes are also organic compounds but their association

with the apoenzyme is only transient, usually occurring during
the course of catalysis.
 Furthermore, co-enzymes serve as co-factors in a number of
different enzyme catalyzed reactions.
 The essential chemical components of many coenzymes are
vitamins, e.g., coenzyme nicotinamide adenine dinucleotide
(NAD) and NADP contain the vitamin niacin.

 Metal Ions: A number of enzymes require metal ions for their

activity which form coordination bonds with side chains at the
active site and at the same time form one or more cordination
bonds with the substrate,
 e.g., zinc is a cofactor for the proteolytic enzyme
carboxypeptidase.
 Catalytic activity is lost when the co-factor is removed from the
enzyme which testifies that they play a crucial role in the
catalytic activity of the enzyme.