SURBHI STUDY CIRCLE BIOLOGY 11TH

BIOMOLECULES
All living organisms are made up of similar elements, it doesn’t matter that they are microscopic or
large organism. They are made up of same elements or compounds intermixed in different
composition. In living organisms Carbon and Hydrogen are in abundance with respect to other
elements

HOW TO ANALYSE CHEMICAL COMPOSITION?

• Take any living tissue 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
• Filtrate or the acid-soluble pool, that fraction which passed through cheesecloth.
• Retentate or the acid-insoluble fraction.
• Scientists have found thousands of organic compounds in the acid-soluble pool.
• All the carbon compounds that we get from living tissues can be called ‘biomolecules’.
• Living organisms have also got inorganic elements and compounds in them.
• Wet weight – weight of living tissue/structure.
• Dry Weight – weight of structure after drying it. (Wet weight – water).
• Ash – 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). (Dry weight – carbon compound)
• A List of Representative Inorganic Constituents of Living Tissues
• Sodium (Na+), Potassium (K+), Calcium (Ca+2), Magnesium (Mg+2) Water (H2O)
• Compounds NaCl, CaCO3, PO4–3, SO4–2

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-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-one (21) types.
 R group = hydrogen e.g., glycine
 R group = methyl group e.g., alanine
 R group = hydroxy methyl e.g., serine.
 The chemical and physical properties of amino acids are essentially of the amino, carboxyl and
the R functional groups.
 Acidic amino acid – glutamic acid etc. In this there are more acidic group than amino group.
 Basic amino acid – lysine. Amino group is more than carboxylic group
 Neutral amino acid – valine. AG=CG
 Aromatic amino acids – tyrosine, phenylalanine, tryptophan. Contain a benzene derivative.
 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.

1
 SURBHI STUDY CIRCLE BIOLOGY 11TH

LIPIDS
 Lipids are generally water insoluble. They could be simple fatty acids or a derivative of glycerol or both.
 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).
 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.

NUCLEOTIDES
 Many carbon compounds have heterocyclic rings like nitrogen bases -adenine, guanine, cytosine, uracil, and
thymine.
 When found attached to a sugar, they are called nucleosides.(nucleoside = sugar + nitrogen base). Adenosine,
guanosine, thymidine, uridine and cytidine are nucleosides.
 If a phosphate group is also found esterified to the sugar they are called nucleotides. (Nucleotides = nucleosides +
phosphate). 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

Primary metabolites – Biomolecules which are present in all organisms and have identifiable functions and play
known roles in normal physiological processes.
Secondary metabolites – In plants, fungus and microbes many compounds other than primary metabolites are
present. e.g., alkaloids, flavonoids, rubber, essential oils, antibiotics, coloured pigments, scents, gums, spices. The
role or functions of all the secondary metabolites are not known yet. Many of them are useful to ‘human welfare’
(e.g., rubber, drugs, spices, scents and pigments). Some secondary metabolites have ecological importance.

BIO-MACROMOLECULES
• 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. (Micromolecules) (Mw= <1000 daltons)
• 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. (Macromolecules) (Mw= >1000 daltons)
• The molecules in the insoluble fraction with the exception of lipids are polymeric substances.
• Lipids are 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.

2
 SURBHI STUDY CIRCLE BIOLOGY 11TH

PROTEINS
 Proteins are polypeptides. They are linear chains of amino acids linked by peptide bonds.
 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 hetero-polymer and not a homo-polymer.
 A homo-polymer has only one type of monomer repeating ‘n’ number of times.
 Amino acids can be essential or non-essential. Essential amino acids are supplied in diet while our body prepares
non-essential amino acids.
 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.
 Collagen is the most abundant protein in animal world.
 Ribulose bisphosphate Carboxylase-Oxygenase (RUBISCO) is the most abundant protein in the whole of the
biosphere. EX- GLUT-4 it enables glucose transport into cells.

POLYSACCHARIDES
 Polysaccharides are long chains of sugars. They are threads (literally a cotton thread) containing different
monosaccharides as building blocks.
 Cellulose is a polymeric polysaccharide consisting of only one type of monosaccharide i.e., glucose. Cellulose is a
homo-polymer.
 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-I2
is blue in colour. Cellulose does not contain complex helices and hence cannot hold I2.
 Plant cell walls are made of cellulose. Paper made from plant pulp is cellulose. Cotton fibre is cellulose.
 There are more complex polysaccharides in nature. They act 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 hetero-polymers.

NUCLEIC ACIDS
 Present in acid insoluble fraction of all living tissues.
 These are polynucleotides. For nucleic acids, the building block is a nucleotide. A nucleotide has three chemically
distinct components. One is a heterocyclic compound (N2 bases, the second is a monosaccharide and the third a
phosphoric acid or phosphate.)
 Adenine, Guanine, Uracil, Cytosine, and Thymine are N2 containing bases. Adenine and Guanine are substituted
purines while the rest are substituted pyrimidines.
 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 are hetero-polymers containing strings of amino acids. Biologists describe the protein structure at four
levels.

3
 SURBHI STUDY CIRCLE BIOLOGY 11TH
PRIMARY STRUCTURE
 It is linear structure of protein.
 The left end represented by the first amino acid and the right end represented by the last amino acid.
 The first aminoacid is also called as N-terminal amino acid. The last amino acid is called the C-terminal amino
acid.

SECONDARY STRUCTURE
 The linear protein thread is folded in the form of a helix (similar to a revolving staircase).In proteins, only right
handed helices are observed.

TERTIARY STRUCTURE
The long protein chain is also folded upon itself like a hollow wollen ball, giving rise to the tertiary structure. This
gives us a 3-dimensional view of a protein. Tertiary structure is absolutely necessary or 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.
 e.g., Adult human haemoglobin consists of 4 subunits. Two of these are identical to each other. Hence, two
subunits of α type and two subunits of 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 as there is
one such ester bond on either side, it is called phospho-diester bond.
• Nucleic acids exhibit a wide variety of secondary structures. One of the secondary structures exhibited by DNA is
the famous Watson - Crick Model.

CONCEPT OF METABOLISM
• Living organisms contain thousands of organic compounds. These compounds or biomolecules are present in
certain concentrations (expressed as mols/cell or mols/litre etc.).
• 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 through chemical reactions. Together all these
chemical reactions are called
• These metabolic reactions result in the transformation of biomolecules like 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.
• Majority of these metabolic reactions are always linked to some other reactions or the metabolites are converted
into each other in a series of linked reactions called metabolic pathways.

4
 SURBHI STUDY CIRCLE BIOLOGY 11TH
• Flow of metabolites through metabolic pathway has a definite rate and direction. This metabolite flow is called
the dynamic state of body constituents.
• Another feature of these metabolic reactions is that every chemical reaction is a catalysed reaction. There is no
uncatalysed metabolic conversion 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) = anabolic pathways, or lead to a simpler structure from a complex structure (for example,
glucose becomes lactic acid in our skeletal muscle) = catabolic pathways.
• Anabolic pathways, as expected, consume energy. While, catabolic pathways lead to the release of energy, which
is stored in the form of chemical bonds in ATP (adenosine triphosphate).

THE LIVING STATE

• Many chemical compounds or metabolites, or biomolecules, are present at concentrations characteristic of each of
them.
• e.g., the blood concentration of glucose in a normal healthy individual is 4.5-5.0 mM, while that of hormones
would be nanograms/ mL.
• 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. Because systems at equilibrium cannot perform work.
• 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.
 An enzyme like any protein has a primary structure, secondary and the tertiary structure.
 In tertiary structure, 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. Inorganic catalysts work efficiently at high
temperatures and high pressures, while enzymes get damaged at high temperatures (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).
Thermal stability is thus an important quality of such enzymes isolated from thermophilic organisms.

CHEMICAL REACTIONS
 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. When bonds are broken and new bonds are formed during transformation, this will be called a chemical
reaction.
 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.
 Rate can also be called velocity if the direction is specified.
 Rates of physical and chemical processes are influenced by temperature among other factors.

5
 SURBHI STUDY CIRCLE BIOLOGY 11TH
• A general rule 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 un-catalysed ones. e.g.,
• 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 carbonic anhydrase, the reaction speeds about 600,000 molecules being
formed every second.
• 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,
• This reaction is actually a metabolic pathway in which glucose becomes pyruvic acid through ten different
enzyme catalysed metabolic reactions.

HOW DO ENZYMES BRING ABOUT SUCH HIGH RATES OF CHEMICAL CONVERSIONS?

 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-
 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).
 There could be many more ‘altered structural states’ between the stable substrate and the product. all other
intermediate structural states are unstable. Stability is something related to energy status of the molecule or the
structure.
 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 easily.

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:
 First, the substrate binds to the active site of the enzyme, fitting into the active site.
 The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate.
 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.
 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.

6
 SURBHI STUDY CIRCLE BIOLOGY 11TH

FACTORS AFFECTING ENZYME ACTIVITY

• Factors affecting Enzyme activity are 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.
• Each enzyme shows its highest activity at a particular temperature and pH called the optimum temperature and
optimum pH.
• 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.
• 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.

COMPETITIVE INHIBITION
• 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

 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

7
 SURBHI STUDY CIRCLE BIOLOGY 11TH
 Enzymes are composed of one or several polypeptide chains. However, there are a number of cases in which
non-protein constituents called co-factors are bound to 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 apo-enzyme.
 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.