CHAPTER 9 BIOMOLECULES

9.1 HOW TO ANALYSE CHEMICAL COMPOSITION?

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 are organic compounds containing an amino group and an
acidic group as substituents on the same carbon i.e., the -carbon. Hence,
they are called -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, those
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. A particular
property of amino acids is the ionizable nature of NH 2 and COOH groups.
Hence in solutions of different pHs, the structure of amino acids changes.
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 CH 2 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.
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., gingely oil)
and hence remain as oil in winters. 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. 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.
9.2 PRIMARY AND SECONDARY METABOLITES
If one were to make a list of biomolecules, such a list would have thousands
of organic compounds including amino acids, sugars, etc. 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.
9.3 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).
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. 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.
9.5 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. Starch forms helical secondary structures. In fact,
starch can hold I2 molecules in the helical portion. The starch-I 2 is blue in
colour. Cellulose does not contain complex helices and hence cannot hold I 2.
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.
9.6 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).
9.7 STRUCTURE OF PROTEINS
Proteins, as mentioned earlier, are heteropolymers containing strings of
amino acids. 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 Nterminal amino acid. The last amino acid is called the C-terminal amino acid.
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. 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. 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 type and two subunits of type together constitute
the human haemoglobin (Hb).
9.8 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 sugar-phosphatesugar 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 34. The rise per base pair would be 3.4.
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.
9.9 DYNAMIC STATE OF BODY CONSTITUENTS CONCEPT OF
METABOLISM
A few examples for such metabolic transformations are: removal of CO 2 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.
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.
9.10 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 utilized 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).
9.11 THE LIVING STATE
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. 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.
9.12 ENZYMES
Almost all enzymes are proteins. There are some nucleic acids that behave
like enzymes. These are called ribozymes. An enzyme like any protein has
the secondary and the tertiary structure. Inorganic catalysts work efficiently
at high temperatures and high pressures, while enzymes get damaged at
high temperatures (say above 40C). 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 80-90C). Thermal stability is thus an important
quality of such enzymes isolated from thermophilic organisms.
9.12.1 Chemical Reactions
When enzyme catalyzed reactions are observed, the rate would be vastly
higher than the same but uncatalysed reaction. In the absence of any
enzyme this reaction is very slow, with about 200 molecules of H 2CO3 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. For example,
Glucose 2 Pyruvic acid
C6H12O6 + O2 2C3H4O3 + 2H2O
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.
9.12.2 How do Enzymes bring about such High Rates of Chemical
Conversions?
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.
9.12.3 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 induces the enzyme to alter its shape, fitting
more tightly around the substrate. 3. The active site of the enzyme, now in
close proximity of 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.
9.12.4 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). 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.

9.12.5 Classification and Nomenclature of Enzymes

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
Transferases: Enzymes catalysing a transfer of a group, G (other than
hydrogen) between a pair of substrate S and S
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.
9.12.6 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 the enzyme to make the enzyme catalytically active. In these
instances, 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. 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.
SUMMARY
Although there is a bewildering diversity of living organisms, their chemical
composition and metabolic reactions appear to be remarkably similar. The
elemental composition of living tissues and non-living matter appear also to
be similar when analysed qualitatively. However, a closer examination
reveals that the relative abundance of carbon, hydrogen and oxygen is higher
in living systems when compared to inanimate matter. The most abundant
chemical in living organisms is water. There are thousands of small molecular
weight (<1000 Da) biomolecules. Amino acids, monosaccharide and
disaccharide sugars, fatty acids, glycerol, nucleotides, nucleosides and
nitrogen bases are some of the organic compounds seen in living organisms.
There are 20 types of amino acids and 5 types of nucleotides. Fats and oils
are glycerides in which fatty acids are esterified to glycerol. Phospholipids

contain, in addition, a phosphorylated nitrogenous compound. Only three

types of macromolecules, i.e., proteins, nucleic acids and polysaccharides are
found in living systems. Lipids, because of their association with membranes
separate in the macromolecular fraction. Biomacromolecules are polymers.
They are made of building blocks which are different. Proteins are
heteropolymers made of amino acids. Nucleic acids (RNA and DNA) are
composed of nucleotides. Biomacromolecules have a hierarchy of structures
primary, secondary, tertiary and quaternary. Nucleic acids serve as genetic
material. Polysaccharides are components of cell wall in plants, fungi and
also of the exoskeleton of arthropods. They also are storage forms of energy
(e.g., starch and glycogen). Proteins serve a variety of cellular functions.
Many of them are enzymes, some are antibodies, some are receptors, some
are hormones and some others are structural proteins. Collagen is the most
abundant protein in animal world and Ribulose bisphosphate CarboxylaseOxygenase (RuBisCO) is the most abundant protein in the whole of the
biosphere. Enzymes are proteins which catalyse biochemical reactions in the
cells. Ribozymes are nucleic acids with catalytic power. Proteinaceous
enzymes exhibit substrate specificity, require optimum temperature and pH
for maximal activity. They are denatured at high temperatures. Enzymes
lower activation energy of reactions and enhance greatly the rate of the
reactions. Nucleic acids carry hereditary information and are passed on from
parental generation to progeny.