TLB’S Biology Classes

BIOMOLECULES
PART 1
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Are all living organisms made of the same chemicals ?

• All living organisms are made up of a large number of chemical

substances.
• While comparing the chemical constitution of living things with that
of earth’s crust, we will obtain a similar list.
• The only difference between these two lists is that hydrogen and
carbon is present in large amount in living organisms than earth’s
crust.

Chemical Analysis to find the Organic Compounds of Living Organisms

• First take a living tissue like a vegetable or a piece of liver, etc.
• Grind the tissue in tri-chloroacetic acid (Cl3CCOOH) using a mortar

a pestle.
• Strain the thick slurry obtained through a cheese cloth or cotton.
• Now we get a acid soluble filtrate portion known as acid pool and
the acid insoluble precipitate portion known as acid insoluble pool.

• Thousands of organic compounds are present in the acid-soluble1

pool known as ‘biomolecules.’

1
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• The biomolecules which are insoluble in acids and have very high
molecular weight are called biomacromolecules.
Chemical Analysis to find out the Inorganic Compounds
of Living Organisms (Ash Analysis)
• First a small amount of living tissue like leaf, lever, etc is weighed
and dried to get the dry weight.
• Dried tissue is then fully burned.
• During burning, carbon compounds are oxidized to CO2 and H2O.
• The remaining substance left is the ash.
• The ash contains the following inorganic constituents.

• Biomolecules are classified into micromolecules and

biomacromolecules.
MICROMOLECULES
• Chemical compounds which have a molecular weight less than 1000
dalton are called micromolecules or simply biomolecules
•

• They are seen in the acid soluble fraction obtained during chemical
analysis.
BIOMACROMOLECULES

• The biomolecules which are insoluble in acids and have very high
molecular weight are called biomacromolecules.

• They have molecular weight above 10,000 dalton except lipids.

Eg: Proteins, nucleic acids, polysaccharides

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The Molecular Weight of Lipids are Below 800 Dalton but it is

included in Biomacromolecules. Why?
• Lipids are smaller molecular weight compounds.
• It is present as such in cells and also the chief component of cell
membranes and cell organelles.
• While we grind tissue, cell membranes and other membranes are
broken into pieces and form vesicles which are insoluble in acid.
• These vesicles get separated along with the acid insoluble pool and
hence included in the macromolecular fraction.
• Lipids are not strictly macromolecules.
Which is the most abundant chemical in living organisms ?
• If we represent the chemical composition of living tissue from
abundance point of view water is the most abundant chemical in
living organisms.
Average composition of cells

METABOLITES
• The biomolecules which occur in all living cells are called
metabolites. They are classified into two.
1. Primary Metabolites
• Metabolites like carbohydrate, proteins, nucleic acids, lipids, etc. is
present in all animal tissues and are called primary metabolites.
2. Secondary Metabolites
• In plants, fungus and microbial cells in addition to primary
metabolites they posses the substances like alkaloids, flavonoids,
rubber, essential oils, antibiotics, coloured pigments, scents, gums,
spices, etc. These substances are called secondary metabolites.
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 TLB’S Biology Classes

BIOMOLECULES
PART 2
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Proteins
Proteins are polypeptides.

• They are linear chains of amino acids linked by peptide bonds.

• Each protein is a polymer of amino acids.

Peptide bonds
The chemical bond which connect amino acids are known as
peptide bond.

Each peptide bond is formed by the reaction between the carboxyl

group (COOH) of one amino acid with the amino group (NH ) of
2
next amino acid with the elimination of water (dehydration
reaction)
• There are 20 amino acids present.
• They are classified into
1. Essential amino acids and
2. Non-essential amino acids
Essential Amino Acids
• These are amino acids that we get from food or diet
• Dietary proteins are the source of essential amino acids.
Non essential Amino Acids
• These are amino acids synthesized by the body.
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STRUCTURE OF AMINO ACIDS

• Each amino acid has a central carbon atom known as Alpha carbon
atom.
• To the alpha carbon atom, one carboxyl group (COOH), one amino
group (NH2 ), one hydrogen atom and a side chain denoted ‘R’ is
attached.
• The side chains are generally carbon chains or rings to which
various functional groups may be attached.

Examples of Amino Acids

1. Glycine
• This is the simplest amino acid.
• In the position of the R group glycine has hydrogen atom.
2. Alanine
• This is the amino acid in which the side chain is methyl group
(CH3).
3. Serine
• This is the amino acid in which R group is Hydroxy methyl (CH2 -OH).

Based on the number of amino and carboxyl groups Amino acids are
classified into the following groups
1. Acidic Amino Acids:- Eg: Glutamic acid.
2. Basic Amino Acids:- Eg: Lysine.
3. Neutral Amino Acids:- Eg: Valine.
 TLB’S Biology Classes

Amino acids with aromatic ring are called aromatic amino acids.
Examples of aromatic amino acids.
• Tyrosine,
• Phenyl Alanine,
• Tryptophan
Ionisation Nature of Amino Acids
• The amino group (NH2 ) and carboxyl group (COOH) of amino acids
shows ionisation properties. Hence in solution of different pH the
structure of amino acids changes.
• The common nature of amino acids is in zwitter ion form (chemical
compounds that carries a total net charge of Zero are zwitter ions).
• Thus they are electrically neutral but carry formal positive and
negative charges on different atoms.

Functions of Proteins
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.
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Collagen & RuBisCO

• 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.

Structural Levels of Proteins

Proteins exists at 4 structural levels
• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure

1. Primary Structure:
• Primary structure refers to the linear sequence of amino acids in a
protein molecule.
• 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 called as N-terminal amino acid and the last
amino acid is called is C-terminal amino acid.
2. Secondary Structure:
• The right handed helical form of proteins are known as secondary
structure.
• A protein thread does not exist throughout as an extended rigid rod.
• The thread is folded in the form of a revolving staircase known as
helix.
3.Tertiary Structure:
• The polypeptide chains of protein molecules bend and fold to attain
a three dimensional shape called Tertiary structure.
• The structure is helpful for many biological activities.

4. Quaternary Structure:
• More than one polypeptide chains unite together to form the
complicated folded structure called Quaternary structure of
protein.
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Eg: Human haemoglobin

• Adult human Haemoglobin has 4 polypeptide chains.
• Two are identical known as alpha chains and other two are also
identical known as beta chains.
• The alpha and beta chains folded together to form a compact
globular structure of haemoglobin


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BIOMOLECULES
PART 3
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LIPIDS
Lipids are biological molecules which are insoluble in water.
Lipids include
• fattyacids,
• triglycerides,
• glycerol,
• Phospholipids,
• cholesterol etc.

Fattyacids
A fatty acid has a carboxyl group attached to an R group.
The R group could be a methyl (–CH ), or ethyl (–C H ) or
3 2 5
higher number of –CH groups (1 carbon to 19 carbons)
2
Eg. Palmitic acid has 16 carbon atoms including carboxyl carbon;
Arachidonic acid has 20 carbon atoms including the carboxyl carbon.

Based on the type of carbon – carbon bonds, fatty acids are classified into
saturated fatty acids and unsaturated fatty acids.
Saturated Fatty Acids
Fatty acids in which all carbon-carbon bonds are single bonds.
No double bonds are present.
 Eg: Palmitic Acid
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Unsaturated Fatty Acids

Fatty acids in which one or more carbon-carbon double bonds are
present.
 Eg: Linoleic Acid.
Unsaturated fatty acids are more common in nature especially in higher
plants.

Glycerols
Glycerol is a simple lipid.
It is chemically tri-hydroxy propane.
Many lipids have both glycerol and fatty acids.

Triglycerides
 These are esters of fatty acids with glycerol.

Based on the number of fatty acids they may be

• monoglycerides (has one fatty acid chain),
• diglycerides (two fatty acid chain),
• tri-glycerides (three fatty acid chain).
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FATS AND OILS

• Fats that are generally liquid at room temperature are called oils.
• Oils are rich in unsaturated fatty acids and have low melting point.
Phospholipids
• Some lipids have phosphorous and a phosphorylated organic
compound in them

• These are phospholipids.

• They are found in cell membrane.

Eg: Lecithin

Cholesterol
Cholestrol is another form of lipid.
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POLYSACCHARIDES (CARBOHYDRATES)
• These are long chains of sugars.
• It is formed of polymerization of monosaccharides.

Glycosidic bond
• In a polysaccharide individual monosaccharide are linked by
glycosidic bond formed between two carbon atoms of the adjacent
monosaccharides.
POLYSACCHARIDES -EXAMPLES

Cellulose

• Cellulose is a polymeric polysaccharide consisting of only one type

of monosaccharide i.e., glucose.

• Cellulose is a homopolymer.

• Plant cell walls are made of cellulose.

• Paper made from plant pulp is cellulose.

• Cotton fibre is cellulose.
Starch

• Starch is the store house of energy in plants

Inulin

• Inulin is a polymer of fructose

Glycogen

• Glycogen is the stored polysaccharide in animals.

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Complex Polysaccharides
They have as building blocks, amino-sugars and chemically modified sugars

(e.g., glucosamine, N-acetyl galactosamine, etc.).

Exoskeletons of arthropods have a complex polysaccharides called
chitin.
These complex polysaccharides are homopolymers.
 TLB’S Biology Classes

BIOMOLECULES
PART 4
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NUCLEIC ACIDS
Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA) are two types
of nucleic acids.
Nucleotides
 The building blocks of nucleic acids are called nucleotides.
 A nucleotide consists of
• nitrogenous base ,
• pentose sugar and
• phosphate .
 Nitrogenous bases in nucleic acids are pyrimidines and purines
• Pyrimidines have a single heterocyclic ring and purines have two
fused rings.
Pyrimidine bases
Pyrimidine bases are ,
• cytosine ,
• thymine (in DNA) and
• uracil (present in RNA in the place of thymine )
Purine bases
• Adenine and
• guanine are called purine bases .
Sugar in Nucleic acids
• The sugar present in DNA is Deoxy ribose and
• The sugar present in RNA is ribose.
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Nucleoside
• Nitrogenous base and pentose sugar together called nucleoside.
 Eg : Adenosine , guanosine , thymidine , uridine ,and cytidine
are nucleosides.
Examples of nucleotides
• Adenylic acid , thymidylic acid , guanylic acid , uridylic acid
and cytidylic acid are nucleotides.

Phosphodiester bond
• In nucleic acid phosphate is attached to the sugar by an ester bond.
• Phosphate is linked to sugars of two adjacent nucleotide form
Phosphodiester bond.
Watson – crick model of DNA
• This model says that DNA exists as a double helix.
• The two strands of polynucleotide are antiparallel i.e., run in the
opposite direction.
• The back bone is formed by the sugar – phosphate – sugar chain.
• The nitrogen bases interconnect the backbone.
• Adenine of one strand pairs with thymine of the other strand
(A-T base pair) by two hydrogen bonds.
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• Guanine pairs with Cytosine (G-C base pair)by three hydrogen

bonds.
• One full turn of helical stair case has Ten base pairs.
• The total length of a turn is 34A0 and the distance between two base
pairs is 3.4A0.
• This type of DNA is known as B-DNA
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BIOMOLECULES
PART 5
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Metabolism
• All the chemical reactions taking place inside the living organisms are
collectively called metabolism .

Examples

• Removal of CO from amino acids making an amino acid into an

2
amine.
• Removal of amino group in a nucleotide base

• hydrolysis of a glycosidic bond in a disaccharide, etc

Metabolic Pathways

• Metabolic reactions occur in in a series of linked reactions called

metabolic pathways.

Metabolic pathways are divided into two categories – anabolic

pathways and catabolic pathways.
1. Anabolic pathways
• Metabolic pathways which lead to a more complex structure from a
simpler structure is anabolic pathway or biosynthetic pathways.
Examples

• Formation of cholesterol from acetic acid

• Assembly of a protein from amino acids.
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Catabolic Pathways

• Metabolic pathways which leads to a simpler structure from a complex

structure is called catabolic pathways.

Example

• Formation of lactic acid in our skeletal muscle from glucose .

ATP(Adenosine Triphosphate )

• The most important form of energy currency in living systems is the

bond energy in a chemical called adenosine triphosphate (ATP).

ENZYMES
• Enzymes are biological catalysts, which speeds up a chemical reaction
without itself undergoing any permanent change.

• Almost all enzymes are proteins.

Ribozymes
• Ribozymes are some nucleic acids that behave like enzymes
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Active sites
• These are the regions of enzymes which react with the substrate
molecule in chemical reaction.

Rate of Reactions

• When enzyme catalysed reactions are observed, the rate would be

vastly higher than uncatalysed reaction.

Example

Carbonic anhydrase

• It is the enzyme which involved in the formation of carbonic acid in

tissue respiration.
• Carbonic anhydrase catalyse the combination of CO and H O to
2 2
carbonic acid.
• This is the fastest enzyme in the living world , with a speed of 6 lakhs
molecules per second
• (in the absence of the enzyme the reaction rate is only 200 molecules
per hour )

Mechanism of Enzyme Action

• In chemical reactions enzymes convert substrates (S) into products (P).
• During the action of enzymes, the active site of the enzyme combines
with substrate and forms enzyme substrate complex (ES).
• 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.
 TLB’S Biology Classes

• After the expected bond breaking/making is completed, the product is

released from the active site.

Graphical representation of Mechanism of Enzyme Action

• The y-axis represents the potential energy content.
• The x-axis represents the progression of the structural transformation
of substrate into product or the ‘transition state’.
• There is energy level difference between S and P.
• For attaining transition state, Substrate has to attain a higher energy
level.
• Enzymes lower activation energy of the substrate molecules to attain
the transition state.

Activation energy
• The minimum amount of energy that is required to activate atoms or
molecules to a condition in which they can undergo chemical
transformation is known as activation energy.
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Nature of Enzyme Action

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, 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.
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BIOMOLECULES
PART 6
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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.

• 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.
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Enzyme Inhibition
• Activity of the enzyme is inhibited by the presence of certain specific
chemicals which bind with the enzyme.
• The process is called inhibition and chemicals are called inhibitors.
• When the inhibitor closely resembles the substrate in its molecular
structure and inhibits the activity of the enzyme is known as
competitive inhibition.
• Due to the similarity 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.

Example
• Inhibition of succinic dehydrogenase by malonate which closely
resembles the substrate succinate in structure.
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Classification and Nomenclature of Enzymes

• Enzymes have been classified into different groups based on the type of
reactions they catalyse.
• Enzymes are divided into 6 classes
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Apoenzyme
• The protein part of the enzyme is called apoenzyme.

Co-Factors
• The non-protein parts associated with enzyme are called co-factors.
 The co-factors are of three types

• prosthetic group,
• co-enzymes and
• metal ions.
Prosthetic Group
• The organic compounds which are tightly bind to the apoenzyme are
called prosthetic group.
• Eg: the prosthetic group Haem is a part of the enzyme Peroxidase and
Catalase, which catalyse the breakdown of hydrogen peroxide to water
and oxygen.

Co-Enzymes
• The organic compounds which are not firmly bound to the apoenzyme
are called co-enzymes.
• Many co-enzymes are vitamins.
• Eg: NAD (Nicotinamide Adenine Dinucleotide), NADP (Nicotinamide
Adenine Dinucleotide Phosphate) contains the vitamin Niacin.
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Metal Ions
•  A number of enzymes require metal ions for their activity.
•  Eg: Zinc is a co-factor for the proteolytic enzyme carboxy peptidase.