COEP Technological University, Pune

A Unitary Public University of Government of Maharashtra

Department of Applied Sciences & Humanities
(School of Transdisciplinary Sciences & Management)
Wellesley Road, Chhatrapati Shivajinagar, Pune - 411005.

BIOLOGY FOR ENGINEERS - CLASSNOTES

UNIT 2: ORGANIZATION OF LIVING MACHINES

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Biomolecules and manufacturing of Biopolymers:

 Carbohydrates (structure-based function and engineering applications)

 Lipids (structure-based function and engineering applications)
 Proteins (structure-based function and engineering applications)
 Nucleic Acids (structure-based function and engineering applications)
Organization of life forms: Cell to organism

Energy dynamics in biological system

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A living organism’s body is built of and run by thousands of different types of molecules. As
these are made chiefly by the living organisms they are known as biomolecules.
Biomolecules have distinct properties and functions responsible for their selection and
continuation in the course of evolution.
Many of the small molecules with low molecular weight, simple structure and high
solubility are known as micromolecules (or monomers e.g. water, mineral, simple sugars,
nucleotide etc.) form the building units for larger macromolecules (or polymers.e.g.
protein, lipids etc.). The biomolecules are classified into organic and inorganic types based
on their composition.
Thus, all cells are made up of biomolecules, these are organized in physico-chemical
organizations and in isolation they do not have living characteristics. Biomolecules
produce, maintain and perpetuate the living state and are continuously transformed i.e.
synthesized and broken down.

1
Water, minerals and gases are important groups of inorganic bimolecules while lipids,
carbohydrates, proteins and nucleic acids are the four important classes of organic
compounds.

WATER
Physical & Chemical Properties of Water:
 Water is cohesive & adhesive
 Water has high specific heat
 Water has high thermal conductivity
 Water has high boiling point
 Water is good evaporative coolant
 Water has high freezing point and is less dense as a solid than liquid
In the biological reactions, two important features are observed,
 polarity (+ ve charge for H and – ve for O extend polarity to water molecule; water
molecules form cluster around electrically charged molecules like PO 4 or COOH, that are
water soluble hence known as hydrophilic while water does not react with non
charged molecules like lipids that are insoluble known as hydrophobic) and
 ionization ability (water molecule dissociates to form H and OH ions)

Significance of water in living system

 Life has doubtless origin from the water.
 Water is the most abundant substance in living system making up more than 70% of the
weight for most of the living organisms.
 Water provides liquid medium for colloidal protoplasm for chemical reactions and
transport mechanism in the cell.
 The water molecule and its ionization products, H and OH influence the structure,
properties and self assembly of all cellular components.
 Aqueous solutions of weak acids & bases with their salts act as buffer in pH change in
biological system. It facilitates chemical reactions in the cells.

2
 The non covalent interactions responsible for the strength & specificity of biomolecules
are decisively influenced by the solvent property of water. It is known as Universal
solvent for most of the organic & inorganic molecules.
 It absorbs heat and maintains body temperature.
 In green plants, it is a source for H + ve ions as a source of energy.
 Removal of waste material thus helps in maintaining homeostasis
MINERALS
Minerals are the nutrients required especially for the growth of plants that are absorbed
from the soil. Some of these minerals are required in larger quantity and some in trace
levels for the plant growth. Accordingly they are known as micro or macronutrients
respectively. The role of some minerals in the cell metabolism is as follows,

Mineral Function Minera Function

l
N, S Synthesis of Amino acids, P Present in compounds like
proteins phospholipids, ATP, nucleotides
etc.
K, Na Constituents of Body fluids, Ca Plays significant role in Blood
nerve cells, blood plasma coagulation & cell wall
formation, propulsion of nerve
impulses
Fe Formation of haemoglobin Mg Formation of chlorophyll,
enzymes, structural integrity of
ribosomes
I Functioning of thyroid glands Cu, Mo Activation of enzymes

3
Ions are required to maintain osmotic concentration of cellular as well as extra cellular
fluids.
Gasses are significant for the basic cellular processes.
Gas Function
O2 Essential for respiration for all aerobic bacteria, combustion process,
photosynthesis byproduct
N2 Constituents of proteins, nucleic acid, fixation & release of nitrogen by
bacteria for plants
CO2 Used in photosynthesis, excess is dissolved in water

4
Carbohydrates –These are hydrates of carbon made up of C, H, O
Reducing sugars – Sugars with free aldehyde / ketone group
Non- reducing sugars- e.g. aldehyde region of glucose reacting with ketone region of
fructose – form glycosidic bond – non – reducing sugar as free aldehyde / ketone groups
are masked.
Aldoses: Glucose, Ribose, Deoxiribose, Mannose, Galactose etc.
Ketoses: Fructose, Ribulose, Xylulose etc.
According to number of monomers present in carbohydrate molecule
Monosaccharide: Water soluble
 Trioses (Dihydroxy acetone, glyceraldehydes)
 Tetroses (Threose, Erythrose)
 Pentoses (Ribose, Deoxyribose, Xylose, Ribulose, Arabinose)
 Hexoses (Glucose – also called blood sugar, grape sugar and Dextrose can be
polymerized in to glycogen in animals and starch in plants; Fructose – Fruit sugar;
Galactose, Mannose)
 Heptose (Sedoheptulose)
Oligosaccharides: 2-9 monomers
 Disccharides (Maltose, Sucrose, lactose etc)
 Trisaccharides (Raphinose, Pectin, Innulin)
 Polysaccharides (Starch, Cellulose, Glycogen, Chitin, Agar)
Homo-polymers: All the monomers same in given polysaccharides (Starch, Hemicellulose,
Cellulose, Glycogen)
Hetero-polymers: Two or more monomers in given polysaccharides (Agar, Chitin)
Monomers are linked by glycosidic bond during polymerization
Types & Function of Polysaccharides:
Storage polysaccharides: Starch, inulin stored in roots, tubers of plants; Glycogen: In
animals and bacteria

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Inulin is the smallest polysaccharide: not metabolized in human body filtered through
kidney.  used in kidney testing.
Structural polysaccharides: Cellulose, Hemicellulose, Pectin – (in plants), Chitin (plant
fibres & animal exoskeleton like insects, spiders, crabs etc.)
Chondrin sulphate in cartilage, tendon ligament
Hyaluronic acid – (glucoronic a.+ acetyl glucosamine) cementing subs. between animal
cells. In diff body fluid – vitreous humor of eye,
sinusoidal fluid CSF e.g. Keratan Sulphate in cornea, skin, cartilage, bone, hair, nail
Mucopolysaccharide – slimy substances e. g. Hyaluronic acid
Agar – used in culture media, medicine, capsules and chromatography
Algin –used in Ice creams, cosmetics.
Carrageenin – used as a emulsifier, clearing agent – fruit juice.
Funori –used as adhesilve in hair curling
Heparin – used in blood bank as blood anti-coagulant
Husk of Plantago ovata – used as purgative / laxative
Aloegel – used as inflammation - relief, in hand lotion, shampoo, hair conditioner,
sunscreen lotion.

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PROTEINS:
Proteins make up more than 50 % of the dry mass of animals and bacteria and perform
important functions in living organisms. They contain the elements carbon, oxygen,
hydrogen, nitrogen and usually sulfur that makes a monomer of protein i.e. amino acid. All
organisms contain 20 common amino acids as biological molecules.
Essential amino acids: can not be synthesized by animals, so must be taken in diet. In man
such amino acids are 8, in other animals are 7.
Non Essential Amino acids: Can be synthesized by animals, so may not be taken in diet
Each amino acid (AA) has a carboxyl group (-COOH), amino group (-NH2) and a hydrogen
atom bounded to a central carbon atom. The sequence of amino acids (linked by peptide
bond) determines the overall shape and properties of proteins. Depending on number of
amino acids in a chain oligopeptide (1-10 AA), Polypeptides (11-50 AA) and protein (>50
AA).
Various categories made for the classification of proteins based on the composition,
structure etc. are as follows;
Structural organization of proteins:
PrimaryProteins: two dimensional, simple chain of AA with peptide (covalent) bond e.g.
Insulin
Secondary Proteins: Various functional groups exposed on outer surface interact with
hydrogen bonds
 - helix – e.g. keratin, hair, fur, clans, hooves
 – pleated – B. keratin of feathers, silk fibroin
 Collagen helix – 3  – helices coiled around one another
Tertiary Proteins: Additional bonds between functional groups, twisting of secondary
protein, weak covalent and high energy disulphide bonds are formed e.g. Myoglobin
Quaternary Proteins: Formed as a result of 2-more
polypeptide chain and have specific orientation

7
Types of proteins according to structure:
Fibrous – collagen fibres, keratin, elastin, fibrin, fibroin, actin, myosin, bl. clot.
Globular – glutelin, protemine, globulin, albumin, glutenin, orygemin.
Intermediate – (myosin), fibrinogen.
Types of proteins according to chemical nature
Simple – only a.a. Albumin, globulin, protanine, fish, prolamine (corn, pl, wheat), histone
(corn, wheat), glutelin (glutenin), keratin.
Conjugated – protein + non protein (prosthetic group) e.g. Nucleoprotein (nucleic acid),
chromoprotein (Hb, cytochrome), metallo (with metals Zn, Fe ), lipoprotein,
glycoprotein etc.

Properties of proteins:
 Number: According to length,, number & types of polypeptides – thousands of proteins
 Specificity: High specificity in the individual but shared with related species or group
 Molecular weight – ACTH (4500 daltons) to Pyruvate Dehydrogenase (4,600,000
daltons)
 Solubility: Some are insoluble due to large size, many form colloidal solution with water
 Amphoteric nature: Show both acidic & basic properties.
 Electrical reaction: Isoelectric point at which pH is neutral (Curdling of milk at pH 4.7
due to isoelectric point at acidic pH 4.7)

8
 Denaturation: Permanent or temporary loss of three dimensional structure caused due
to UV, heat, strong acid & alkali, high salt concentration; within limit renaturation occur.
Role of protein:

Type of protein Example Function

Enzymes Amylase Converts starch into sugar
Structural Keratin, Collagen Hair, wool, nail, horn, hoofs, tendons,
cartilage
Haemoglobin Blood clotting
Hormones Insulin, glucagons Regulate glucose metabolism
Contractile Actin, myosin Contractile filaments in muscle, cilia &
flagella (in lower organisms)
Amphoteric All proteins Maintain acid-base equilibrium
Storage Ferritin, albumin Stores iron in spleen & egg yolk
Casin Milk
Transport Haemoglobin Carried oxygen in blood
Serum albumin Carries fatty acid in blood
Energy All proteins Provides energy stored in peptide
bonds
Metaloprotein Cytochrome Electron transport
Receptor Adrenalin Conduction of nerve stimulus
Nucleoprotein Histones & non- Stabilization of DNA coiling
histone
Immunological Antibodies Forms complexes with foreign
proteins
Toxins Venum (Neurotoxin) Blocks the nerve function
Proteins are masterpieces of molecular engineering and they are tailored to their functions
by millions of years of natural selection.

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LIPIDS:
Lipids are the organic compounds that share a distinguishing property of non polarity and
so do not dissolve in water. They mostly contain carbon and hydrogen with very small
portion of oxygen compare to carbohydrates. Some of them also incorporate phosphorus
and nitrogen. Basically they are polymers of fatty acids & glycerol.
As lipids are insoluble in water they are vital components of the membrane that separate
living cells from each other and their surrounding.
Lipids offer unique way to store energy as they possess very high proportion of energy rich
carbon-hydrogen bonds in a concentrated form within the cells. They contain six times
more energy than the carbohydrates and have become increasingly important as food
reserves for organisms. (e.g. migratory birds).
Fatty Acids: Simplest form of lipids consisting of a long hydrocarbon chain (non polar
hydrophobic) with a carboxyl group at the end (which is hydrophilic). Because of this
characteristic orientation, fatty acids significantly contribute in the structure of cell wall.
Fats & Oils: These are the energy store reserves for the plant & animal cells. Fats are
formed by the condensation of fatty acid molecules and are characteristically non polar.
They are classified into saturated (butter, coconut oil) which are solid at room
temperature and without double bond and unsaturated (from olive, corn, safflower,
peanut etc.) which are liquid at room temperature and with double bond. Usually, animals
use saturated fatty acids against the plants with unsaturated fatty acids.
Phospholipids: These are similar to fats except one or two fatty acids are replaced by
phosphate group which in turn are linked to nitrogen containing group.
Steroids: They differ from lipids in structure but insoluble in water. Cholesterol is most
commonly known steroid forming essential component of animal cell membrane. It also
served as a raw material for the production of vitamin D and steroid hormones.
In general the steroids carry chemical messages between the cells.
Properties:
 Saturated & unsaturated
 Insoluble in water and soluble in organic solvents like alcohol
 Low specific gravity hence float on water

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 On hydrolysis give fatty acids and glycerol
 Neutral fats or triglycerides are colour less, odder less, taste less
 Rancidity: Naturally occurring unsaturated fats undergo partial hydrolysis by the action
of enzyme lipase. Oxidation at double bond produces aldehydes and carboxylic acids.
This develops foul test and odder to the fats.Types of Lipids –
1. Simple Lipids – These are neutral or true fats. Solid at room temperature, on hydrolysis
give three faty acids and one glycerol e.g. waxes

R C O R  esters of fatty acids with different alcohols.

e.g. tripalmitin, diplamitin are hard fats, solid at room temp.
2. Compound / Conjugated lipids –
Phospolipids – Cephalin – act as insulation for nerves
Lecithin – cell permeability
Glycolipds – Cerebrosides – brain cells – cell mem. gangliosides – grey matter.
Sphingomyelins –in myelin sheath.
Sphingosine  amino alcohol.
Lipoproteins – found in milk, egg yolk, blood plasma, tissues, cell surfaces.
Cutin – from cuticle.
Suberin – due to it cell wall impermeable to H2O.
Chromolipds – e.g. carotenoids.
3. Derived Lipids –Formed from hydrolysis of simple & comp. lipids, Include f.a., steroids,
prostaglandins, terpenes.
Prostaglandins – Hormone – like unsaturated fatty acids / local hormones, present in
amniotic and tissue fluid
 Circulate in blood
 Cause acid production in stomach
 Stimulate contraction of smooth muscles.
Steroids – solid wax like alcohols e.g. ergosterol – yeast. Cholesterol - animal cell mem.,
blood, bite. When bl. level of chole. rises – Cholesterol and its esters form bond with fats
secreted by endothelium of arteries. And thus deposited on wall of arteries.

11
It is precursor for hormone progesterone, testosterone, cortisol, estradiol, androsteron
Produces bile salts, vitamin D by action of U V rays of sunlight.
 React with protein in nucleus
 Trigger changes in gene expression and metabolism
Role of lipids:
 Reserved food: In plants oilseeds like groundnuts, mustard, coconut are the stores of
fats. Animals contain adipocytes which are the cells containing the fat droplets as stored
food.
 Structural component: Phospholipids, glycolipids and sterols are the structural
components of the cell membranes.
 Synthesis: Take part in the synthesis of steroids, hormones, Vit D etc.
 Energy source: Rich source of energy. 9.3 kcal/gram
 Insulation: Provide electrical and thermal insulation. Deposited below the skin and
around the internal organs to lessen the heat loss. Also work as shock absorbers.
 Solvent: Fats are the solvents for fat soluble vitamins like A, D, K, E.
 Waxes are water proof agents e.g. fur, feathers, insect exoskeleton, bee wax, ear wax
(cerumen), skin wax (sebum), paraffin wax & plant waxes

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NUCLEIC ACIDS :
1streported by Friedrich Miescher. from pus cells nuclei. Called them nuclein. Altman called
N.A. Feulgen developed staining tech. of N.A. with fusch.
DNA – Deoxyribo nucleic acid
Made up of three components –
i) Deoxyribose sugar – (pentagonal shape with 5 C atoms)

ii) Nitrogen containing bases –

Purine – Adenine (A), Guanine (G).
Pyrimidine – Cytosine (C), Thymine (T)

Pentose suger + N base  nucleoside

Glycosidic bond between 1st C of sugar and nitrogen at 3rd position in pyrimidine base and
9th position in purine base.
iii) Phosphoric acid –
OH – 3 acid groups.
OH

O P OH

OH

Nucleoside + P group at 5’ position by phosphor-diester bond.

Nucleoside + Phosphate group  nucleotide.
Amount of DNA measured by picogram = 10-12 g., 1 Pg DNA has 31 cm length.
Human cell – contains 5.6 Pg DNA – 174 cm long.

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Chain of nucleotides – poly nucleotide chain
5’ 3’
P
‫׀‬ S A T S
‫׀‬
P
‫׀‬
P
‫׀‬ G C S
S
‫׀‬
P
‫׀‬
P
‫׀‬ T C
S
‫׀‬ S

‫׀‬ P
P
‫׀‬ C C
S
‫׀‬ S

‫׀‬ P
↓
3´
Characteristics / Properties – DNA
 It has several thousand Nucleotides.
 Back bone of it by alternate d sugar and PO4 gr.
 Nitrogen bases are inside at right angle to longitudinal axis.
 PO4 gr. Attached 5th , 3rd C atom.
 By phosphodiester bond.
 2 chains joined by weak H bond – A = T, G = C specific pairing. H of one base linked
to O2 / N2 of another base.
 2 strands anti parallel i.e. 3’, 5’ phosphor ------- link in opp. direction.
 Pairing specific  2 chain complementary.
i.e. sequence of N2 bases in one chain will decide it on other chain.
 Diameter of DNA – 20 A

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  Erwin Chargaff’s rule – regardless of source - purine, pyrimidine components
occur in equal amounts in a DNA mole.

1) A = T, G = C from this it is also

seen
A C
= =1
2) T G
3) A +G = T + C
4) A + C = G + T but
5) A + T not always G + C necessarily.

James Waston & Francis Crick – suggested three dimensional molecular model based on
X ray crystallography technique; according to this model DNA comprises of
1) 2 right Handed helices.
2) Each turn has – 10 nitrogen base pairs
3) One spiral each 3.4 A
4) Distance between 2 nitrogen bases 3.4A
Denaturation and Renaturation of DNA –
1) If DNA solution heated / exposed to alkaline PH or acidic PH, H bonds break and 2
strands uncoil this is known as denaturation or DNA melting.
2) If above solution gradually cooled / neutralized – new base pair formation begins, it
becomes thermally / chemically stable finally double stranded DNA formed which is
called as renaturation.
Linear DNA with ends free with histones (eukaryotes) and circular DNA 2 ends
covalently linked without histones (prokaryots).
Repetitive DNA –

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 The part of DNA which contains same sequence of N bases repeated several times in
tandem ( one behind another)
e.g. A A T C G G A A T C G G A A T C G G
 It occurs specifically near telomeres (ends), centromeres,
 Area with long sequence of repetitive DNA is called satellite DNA as it separates out
during density gradient ultra centrifugation.
 Microsatellite DNA  1 – 10 base pairs repeat units
Minisatellite DNA  11 – 60 base pairs repeat units, it is hypervariable (it is known as
VNTR variable Number of Tandom Repeats discovered by Jeffreys et al., specific for
each individual therefore used in DNA finger printing.
Palindromic DNA –
DNA duplex has areas with sequence of nucleotides same reading forward or backward
from central axis of symmetry GACTGCGTCAG
AND MADAM DNA
(Restriction endo-nuclease commonly recognize DNA sequences that are palindromes.

RNA – Ribo Nucleic Acid –

It is also made up of three components;
i) Ribose sugar – Pentose sugar
ii) Nitrogen containing bases – Purine – Adenine, Guanine & Pyrimidine – Cytosine, Uracil.
Sugar + N. B.  Nucleoside
Genetic in some pl. viruses TMV yellow MV animal viruses – influenza, poliomyelitis, HIV;
Animal, Plant viruses  single stranded
Reovirus of some plant  Double stranded.
Non- genetic RNA –
Mainly in nucleolus, cytoplasm, ribosome, mitochondria, chloroplast, in association with
chromo.
Found both in pro & eukaryots
Synthesis in N on one of the DNA strand by transcription.
Thus carries genetic inf. from DNA.

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Structure – Single stranded. Hence does not follow Chargaff’s rule.
Types – three types of RNA - all are synthesized in nucleus
1) m – RNA / messenger / template: linear, longest molecule with 900 – 1500
nucleotides
Function: To carry genetic information in the form of codons from DNA to site of protein
synthesis i.e. ribosomes.
2) r – RNA / ribosomal RNA – folded.
Function:
 Proper orientation of m RNA
 Formation of ribosomal complex by the attachment of smaller & larger subunit and
further ribosomal complex with m RNA
 relese of t RNA from ribosome complex after transfer of AA to polypeptide chain
3) t - RNA / transfer RNA/ soluble RNA (can’t be precipitated by ultracentrifugation)
Structure: According to shape two models are explained viz. clover leaf and hair pin
Function:
 To bring AA at the site of protein synthesis
 Transfer of AA to polypeptide chain

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 LEVELS OF ORGANIZATION OF LIFE

Cell as basic unit of life, prokaryotic and eukaryotic cells, microbes, plant and animal cells;
CELL ORGANELLES
Present in all eukaryotic cells. Absent in prokaryotic cells, secondarily lost in mammalian
RBC.
MITOCHONDRION
Also called as power houses, energy coins. Present in all eukaryotic cells, except
mammalian RBC where secondarily lost.
No. per cell variable, 1 in primitive eukaryotes, 5,00,000 insect flight muscles.
Size 1.5—10 μm in length, 0.25 μm in diameter.
Shape cylindrical common, may be spherical, tubular, branched, discoidal.
Ultrastructure :--
1) 2 membranes : Outer – limiting,
permeable, smooth, Inner – selectively
permeable thrown into folds called cristae /
trabeculae.
2) In between two membranes peri –
mitochondrial space, filled with homogenous
fluid called cytosol, contains H2O, minerals.
3) Inner mitochondrial cavity has dense,
homogenous gel like matrix with high conc.
of soluble proteins, nucleotides, lipids,
circular DNA called mitochondrial/mt DNA,
ribosomes of 70s type, K+, HPO4, Mg++, Mn++, Cl
—
, SO4—, RNA (3 types), riboflavin vitamin.
4) Inner cavity divided into many compartments due to cristae, which are more in active
cells. Inner membrane has 2 faces, outer face called C/cytosl face, inner M/matrix face. On
inner surface of inner membrane i.e. at M face, numerous knob like elementary particles /
F1 paticles / oxysomes / Fernandez – Moran subunits.

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 Oxysome :- composed of base, stalk, head piece.
Head piece – contains F1 – subunit, spherical, contains enzyme ATPase / ATP synthatase
Function – oxidative phosphorylation, oxidation of food, ATP release.
Base – contains Fo – particle / subunit , rectangular ,embedded in inner mitochondrial
membrane, contains coezymes of ETC.
Stalk – contains F5, F6 subunit.
Mitochondria:- self duplicating, New one formed by division of existing one.
Semi autonomous organelle –
Mitochondria – have own genetic information, in mitochondria DNA is independent of
cell’s nuclear DNA., capable of self replication, capable of forming 3 types of RNA.
Mitochondria has its own ribosomes. Hence can, form its own structural proteins. Few
subunits of mitochondria & enzymes are formed by itself from ribosomes. Remaining
subunits from cytosol. Hence mitochondrion is a semiautonomous organelle.

Functions:-
1) Power house / storage batteries / ATP mills of cells.
2) Bring about oxidation of carbohydrates, fats., proteins.
3) Capable of self – replication.
4) Site for synthesis of haemoglobin( protein in blood), myoglobin ( protein in
muscles).
5) Site for thermiogenesis (heat production).

PLASTIDS – FOOD FACTORIES & STORE HOUSES

On the basis of colour pigments plastids are classified in to chloroplasts (green),
chromoplast (Yellow, orange etc.) and amyloplasts (White)
Chloroplast: Present in green parts of plant like leaves, skin of raw fruits, flower in bud
condition, young stem.
Shape – Cup shaped, Spiral ,Girdle,Branched,Starlike ,Reticulate, Spherical, Oval,
Discoidal in higher plants. Number –1 to several hundreds. Size – 4 – 6 m.

Ultra structure –
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1) Covered by 2 membranes. Outer one permeable with less proteins. Inner one semi
permeable with more proteins.
2) Periplastidial space of 25 – 75 A between 2 membranes.
3) Matrix / stroma – Ground substance, colourless, granular with proteins, lipids, 70 s
ribosomes, circular DNA, (called as chloroplast/ct – DNA), RNA (3types), enzymes.
4) In stroma no. of membranous sheets called lamellae. Lamellae form closed oval sacs
called thylakoids.
5) Each thylakoid has intra thylakoid space / loculus. In loculus no. of para crystalline
rounded bodies called quantosomes present which trap quantum of light. Each quantosome
contains 230 chlorophyll pigment molecules. In higher plants quantosomes contain
chlorophyll a & b, carotene, xanthopyll. Thylakoids also contain various electron carriers
like cytochrome f, b, ferredoxin, plastocyanin, plastoquinone.
In eukaryotes – thylakoids are superimposed like a pile of coins and form granum. In each
granum 10 – 100 (average 20 – 50) thylakoids. In each chloroplast about 40 – 60 grana .
Adjacent grana interconnected by stroma lamellae / frets / intergranal lamellae.
Semi – autonomous organelles
Circular DNA, 70 S ribosome, RNA (3 types) present, hence can form another chloroplast
using some enzymes from cytoplasm.

Functions- 1. Photosynthesis.
2. O2 replenished in atmosphere.
3.Starch storage.
4.Natural greenery

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Endoplasmic Reticulum – (ER)

ER has inter connected membrane bound vacuoles / cavities , concentrated in endoplasmic

portion of cytoplasm (Cytoplasm has 2 regions – outer homogenous--ectoplasm, inner
granular – endoplasm ), hence called ER,
Occurrence –
Well developed in fully differentiated, metabolically active eukaryotic cells – e.g. liver,
pancreas. Absent in prokaryotic cells, secondarily lost in matured mammalian erythrocytes
(RBC).
Ultra structure –Composed of 3 shapes
1) Cisternae – Near nucleus. Long, flattened, saclike, unbranched tubules. Lie one upon the
other, interconnected & studded with ribosomes.
2) Vesicles – oval / rounded, vacuolar structures, scattered in cytoplasm.
3) Tubules – branched, form reticular structure along with cisternae and vesicles. Near cell
membrane. .
Types:-
1) Agranular / Smooth ER – SER
Ribosomes absent on outer membrane.
Present near cell membrane. Generally in
the form of tubules.
2) Granular / Rough ER / RER –
Ribosomes attached to outer membrane.
Generally in the form of cisternae.
Functions of Endoplasmic Reticulum–
2) Fluid filled vacuolar system. Acts as endoskeleton; gives support to colloidal
protoplasm.
3) Active, passive transport of material.
4) Divides cytoplasm into many compartments, thus cell activities take place separately in
each compartment. Various organelles remain stationed.
5) Increase surface area for absorption / chemical reactions within cell.
6) Contain variety of enzymes.

21
Golgi Complex: Molecular sorting & finishing area
Ultrastructure -
Present in three shapes / forms --
a) Cisternae - Flat / curved , piled up one above other, with swollen ends. Outer convex
surface associated with nuclear membrane/ ER. It is called – forming / cis / entry face
Inner concave surface, called maturing / trans / exit face.
b) Vacuoles –Formed by fusion of small vesicles / large parts of broken cisternae.
Generally associated near concave surface.
c) Vesicles – Pinched off from edges of cisternae hence near edges / concave surface.
Chemical composition – Proteins – 60%, Phospholipids – 40% , Enzymes.
Origin – mostly from SER as cisternae connected to E.R.

Functions –
1) Secretion – Mainly secretion of enzymes, hormones, glycoprotein, Ab( antibody).
2) Storage and Synthesis – Store proteins, lipids in the form of glycoprotein & glycolipid.
3) Packing and forwarding center for enzymes, mucus, hormones in small vesicles.
4) Cell plate formation in cell division.
5) Formation of primary lysosomes – Hydrolytic enzymes are formed in ER, then
come to cisternae, packed and budded off as primary lysosome.

22
Lysosomes : Sacs of hydrolytic enzymes
Structure – These are small membrane bound (unit membrane) vesicles. Contain
hydrolytic enzymes.
*** Hydrolytic enzymes are stored in crystalline / fluid form. Membrane of lysosome is
impermeable to enzyme. But ruptures during O 2 deficiency / exposure to poisonous
substances. Then enzymes are released and cell itself is destroyed. Hence lysosomes are
also known as suicidal bags of cells.***

Types of Lysosomes
1) Primary lysosome - / storage granules – Derived from G.C. Contain only hydrolytic
enzymes in inactive form. In the form of small vesicles.
2) Secondary lysosome / Digestive vacuoles / Heterophagosomes – Pinosome
( vacuole with liquid) / phagosome (vacuole with solid) fuse with primary
lysosome. Hence contain enzyme + material to be digested.
3) Residual Bodies / Tertiary lysosome / Telolysosome – Undigested mateial remain in.
Now called residual body. Come near plasma membrane, throw out their contents
out side thro’ ephagy / exocytosis. If contents not discharged, the cells are loaded
with it, cause nephritis, hepatitis, arthritis, gout, lung fibrosis.
4) Autophagosomes / Autolysosomes – Cell organelles like ER, Mitochondria get worn
out. Its degradation by lysosome called as autophagy. Primary lysosome + worn out
cell organelle form autophagosomes.
Function –
1) Digestion – by hydrolytic enzymes.
Extracellular – enzymes are released in surrounding medium by exocytosis.
Intracellular – by formation of secondary lysosomes or autophagosomes. E.g.
phagocytes in higher animals, degeneration of tail in tadpole larva of frog by enzyme
cathepsin.
Heterophagy – digestion of foreign substance,
Autophagy – digestion of self substances. Thus lysosomes are self disposal units, also
bring about physiological rejuvenation. Digestion of reserve food during starvation is
also called as Autophagy.

23
 2) Initiate cell division by removing repressors of this process.
3) By breaking thyroglobulins, thyroid hormone(thyroxin) is produced.
4) In joint disorder like gout, arthritis -- macrophages come here & release lysosomes
which causes inflammation.
5) Accidental / pathological release of lysosome enzyme causes chromosome breakage,
abnormal distribution of chromosomes during mitosis, which may lead to blood
cancer.

Ribosomes: Work benches for protein analysis

Occurance -- both in pro and eukaryotic cells, except mature RBC.

Types of Ribosomes – According to size, sedimentation coefficient (S = 1  10-13 cm

/sec /dyne / gm) 2 types.
1) 70 S ribosoms –found in mitochondria, chloroplast of eukaryotic & prokaryotic cells
2) 80 S ribosomes – “ in eukaryotic plant & animal cells.

Structure – Not covered by unit membrane, but porous, hydrated, 2 subunits. Larger &
smaller. 70 S ribosome has 50 S and 30 S subunits & 80 S ribosome has 60 S and 40 S
subunits which are separated by a narrow cleft. 2 subunits remain separated, join only

24
during protein synthesis. In high conc. of Mg ++ ions  2 subunits remain united &
called as dimmer. Smaller sub unit fits like a cap on larger subunit. Larger subunit – dome
– shaped, 2 binding sites Peptidyl / P site / donar site, Amino – acyl / A site / acceptor site.
It has protuberance, ridge and stalk. Smaller subunit – ellipsoidal shape, cap like. It has a
platform, cleft, head & base.
Polyribosome / polysomes – It is chain of ribosomes as formed during protein synthesis on
m-RNA.

Functions –
1) Protein factories / engines of cell as site of protein synthesis.
2) Free ribosome produce non – secretary proteins like enzymes for intra cellular use (e.g.
in muscle cells, skin cells)
3) Bound ribosome like present on RER synthesize secretory proteins e.g. enzymeA
After synthesis of proteins, proper folding of proteins is assisted by specific proteins
chaperons which also assist transport of proteins into organelles like mitochondria

Nucleus: Genetic message centre

Ultrastructure-
Contains nuclear membrane, nucleolus, nucleoplasm, chromatin
Nuclear membrane / karyotheca / Nuclear envelop / Nucleolemma.
 It is an outer envelop
 Present in all eukaryotic N Absent during late cell division.
 Consists of 2 unit membrane, between them perinuclear space of 75 A.
 Outer membrane continuous with RER, studed with ribosome on outer side.
 Nuclear openings or pores in it to maintain nucleo – cytoplasmic connection.
 Outer membrane called as ectokaryotheca, inner called as endokaryotheca.
 Each nuclear pore has cylindrical annulus with pore complex.
• Through pore complex / basket movement of substances takes place.
 mRNA come out through them into cytoplasm.
 Dissociates during early cell division, reappears at end of cell division.

25
Nucleous –
Appears spherical, dense, colloidal, no limiting membrane. No. 2 -- 5
Parts – i)Granular region -- protein granules ii)Fibrillar region – proteinaceous fibrils
iii)Amorphous matrix – less dense called ‘pars amorpha’. iv)Chromatin fibres are
perinucleolar and intranucleolar.
Nucleoplasm – nuclear sap / nucleoplasm / karyolymph.
Transparent., semi – solid, granular, acidophilic.Composed of – Nucleic acids, enzymes,
minerals.
Chromatin –
Hereditary part. Network of fibres. During cell division organizes as chromosome.
.Heterochromatin – Show thick regions, darkly staining where DNA is condensed. Lies near
nuclear membrane. Contain late replicating genes. Inactive genetically.
Euchromatin – Thin regions, less darkly staining, DNA loose, genetically active.
Chromatin thread composition – DNA, RNA, proteins (histones., non – histones.)
Functions --
1) Contain hereditary material in the form of chromosomes
2) Transfer genetic characters from one generation to another
3) Control cell division
4) Control all physiological activities of the cell.

26
 EVOLUTION OF BIOLOGICAL MACHINES

Major changes that occurred when prokaryotes gave rise to eukaryotes -

 Cells acquired more DNA.
 DNA folded compactly into discrete complexes with specific proteins to divide it equally
between daughter cells at cell division.
 Specialized proteins stabilize folded DNA (chromosomes).
 A system of intracellular membranes and a double membrane surrounding the DNA
was developed.
 Early eukaryotic cells enveloped aerobic bacteria or photosynthetic bacteria to form
endosymbiotic associations that became permanent. Some aerobic bacteria evolved into
mitochondria of modern eukaryotes and some photosynthetic bacteria became plastids
like chloroplasts and likely ancestors of modern plant cells.
 It was advantageous to cluster together for acquiring greater motility, efficiency, or
reproductive success than their free-living, single-celled competitors.
 Specialization within the colony – to cellular differentiation.
 It led to even more complex and highly differentiated organisms, in which some of them
carried out the sensory functions, others the digestive, photosynthetic or reproductive
functions so forth.

Principles of generating diverse body plans and design in nature:

The major events include the changes in

a. Size of organisms
b. Form and complexity
c. Expansions in diversity
d. Production of many shapes of macroscopic life.

The evidences for the process of evolution are usually obtained from fossil records which is
also the data at the time of origin.
Inferences about direction of evolution:
a. Multicellularity evolved independently many times and in all parts of life i.e. plants,
animals and microorganisms.
b. Multicellularity evolved from different unicellular ancestors.
c. These multicellular organisms have new body plans and physiologies
d. They represented more complex features.
These complex forms then diversified so that varied kinds appeared over a long period.

Figure: Evolution of eukaryotes through endosymbiosis:

27
Size and multicellularity:
For first 2500 million years of life on the earth, most species were generally much smaller
and rarely exceeded 1mm in size. The bacterial microfossils obtained from 3500 million
years had 5mm diameter.
The early microfossils of eukaryotes were 40-200 mm in size for first 600-800 million
years

Cellular dimension are limited by oxygen diffusion:

A bacterial cell is 1-2 mm long and animal/plant cell is 5-100 mm long. The upper limit of
cell size is set by the rate of diffusion of solute molecules in aqueous system.
Consider the example of a bacterial cell-
It depends upon oxygen consuming reactions for energy production. So it has to obtain
molecular oxygen by diffusion across its plasma membrane. The cell is small and the ratio
of its surface area to its volume is large hence every part of its cytoplasm is easily receiving
the diffused oxygen.

28
But as cell size increases, surface-to-volume ratio decreases. The rate of consumption of
oxygen is faster than that of its diffusion because if the metabolism of the cell. So when the
cell size goes on increasing, the oxygen demand for metabolism increases to such a point
that the metabolism becomes impossible. This puts a theoretical upper limit for the cell size
and cell cannot increase above this point.
Complexity: It is referred to as number of different cell types or the no./ functional
specialization of parts.

There are four types of complexity –

1. the number of different physical parts e.g. genes, cells, organs and organisms in a
system..
2. the no. of different interactions between the above mentioned parts
3. the no. of levels
4. the no. of parts or interactions in a specific condition

Diversity: Actually the diversity of life has expanded from its origin but it doesn’t cause
continuous increase. For the organisms those are made entirely of soft tissues or of small
size, it cannot be said whether the total diversity increased or decreased over a long period
of time.

29
 Levels of Organization
Within multi-cellular organisms there is division of labor. Division of labor means that the
work (labor) of keeping the organism alive is divided (division) among the different parts
of the body. Each part has a job to do and as each part does its special job, it works in
harmony with all the other parts.
The arrangement of specialized parts within a living thing is referred to as levels of
organization.
First Level :-Cells
Cells of course, are the first level of organization
Second Level:- Tissues
Tissues are the second level of organization. In any multi-cellular organism, cells rarely
work alone. Cells that are similar in structure and function are usually joined together to
form tissues. There are four basic/major types of tissues in the human body: Muscle tissue
( skeletal, smooth, cardiac muscles), nerve tissue ( brain, spinal nerves, cranial nerves),
connective tissue ( bone, cartilage, blood), and epithelial tissue ( skin, other body parts
coverings).
Third Level :- Organs
Organs are the third level of organization.
When a bunch of different types of tissues work together, they form an organ. E.g. Brain,
liver, stomach, heart etc.
Fourth Level :- Organ System
Organ systems are the fourth level of organization.
Each organ in human body is a part of an organ system, a group of organs that work
together to perform a major function. E.g. heart, blood vessels are parts of circulatory
system, likewise digestive, excretory, respiratory systems.
Fifth Level :-- Organism/Individual
Organisms with many systems form fifth level of organization.

30
 Single cell to multi cellular organism

 Unicellular organisms formed colonies by remaining together after each cell

division.
 Division of labor, made it possible to exploit resources in better way.
 For formation of multicellular organism, cells remain bound together. In animals
extracellular organic matrix binds cells together as cell wall, plasmodesmata are
absent.
 Such fundamental arrangement is seen in epithelial tissue sheets.
 From a group of cells, some cells differentiated from others and adopt different
structure, chemistry, function usually in response to cues from neighbouring cells.
 Cells have memory i.e. cell and its progeny usually persist in their differently
specialized state even after disappearance of original stimuli.
 Final character of animal not determined by its final environment but entire
sequences of influences to which cells are exposed during development.
 As body grows and matures, progressively finer details of the adult body pattern
become specified, complex organisms are formed in long developmental history.
 Though more and more complex organisms are formed, early developmental stages
very similar though adult stage radically different.
 Specialization of cells depend on gene expression and not on loss or acquisition of
genes. As specialization also involves loss of genetic material. E.g. RBC – lost
nucleus during differentiation.
 In eukaryotes sophisticated mechanisms for controlling gene expression has
evolved.
 Groups of genes activated or repressed in response to external and internal signals.
 Radical differences of character between cell types reflect stable changes in gene
expression.

31
Energy Dynamics in Biology –
a. Photosynthesis and energy assimilation: aerobic and anaerobic
systems. Applications
b. Respiration and Electron Transport Chain: Mitochondria and
respiration, ATP generation.
Bioenergetics: Thermodynamic principles applied to biology, negative
entropy changes in biological systems, Free Energy, Chemical Equilibrium

32
 1) PHOTOSYNTHESIS

(PHOTOSYNTHETIC ELECTRON TRANSFER, CALVIN CYCLE)

Introduction:

Solar energy is the prime source of energy to entire living world. 2] All living organisms
require energy for their life processes. 3] Solar energy can’t be utilized by organisms.

Important Features of Photosynthesis:

1) It is an intracellular process. 2) It takes place only in green cells of plant 3) During

this process organic food is synthesized. 4) It utilizes solar or light energy. 5) It uses CO 2
& H2O as raw materials. 6) Solar energy is converted into chemical energy. 7) Only 1 to
5% of solar energy received by earth is utilized in photosynthesis. 8) It is redox reaction
where water is oxidized to oxygen & CO 2 is reduced to carbohydrates. 9) At first simple
sugar like glucose is formed & then complex food like starch, proteins, fats are formed.
10) Chlorophyll acts as a catalyst.

Definition:- It is a biochemical process in which organisms prepare complex organic

food from simple, inorganic substances like CO 2 & H2O with the help of chlorophyll &
light energy, releasing O2 as by product.

Overall reaction: -

6CO2 + 12H2 O ----------------- C 6H12O6 + 6H2O + 6O2

Photosynthesis is an anabolic (biosynthetic ) & endergonic ( E dependent ) process.

Pigments and their role :--1] Photosynthetic pigments of chloroplast in higher plants
are chlorophyll & carotenoids.

2] Chlorophyll : - Each chlorophyll molecule looks like a kite or tennis racket with head
& tail. Head is made up of 4 pyrol rings with Mg in center. It is hydrophilic Tail is made
up of phytol which is long chain alcohol. It is lipophilic, hydrophobic.

3] Chlorophyll a : - It is bluish green, with molecular formula C 55 H 72 O 6 N 4 Mg,

absorbs – blue, yellow, red wave lengths of light.

4] Chlorophyll b – It is yellowish green, molecular formula C 55H70O6N4Mg ,absorbs –

blue, orange wave lengths of light.

33
5] Carotenoids are carotenes & xanthophylls. Carotenes are yellowish orange with
molecular formula C40H56. Xanthophylls are yellow with molecular formula C40H56O2
Carotenoids are long chain hydrocarbons. They don’t have definite shape.

6] All photosynthetic pigments trap light energy in form of photons.

7] Chlorophyll b, Crotenes & Xanthophylls transfer trapped light energy to chlorophyll a

by resonance transfer, do not participate actively in photosynthesis. Hence they are
called as accessory pigments/antennae pigments/light gatherers. These accessory
pigments avoid photo-oxidation of reaction center in intense light.

8] Chlorophyll a collects light energy from these pigments. It also absorbs light energy.
It uses light energy for formation of ATP. Hence it is called as active pigment. It acts as a
center of chemical reaction. It shows fluorescence.

9] Middle region of quantosomes are called as photocentres or reactive centers.

10) Chlorophyll a has two pigment systems called photosystems i.e. PSI , PSII are
involved . PS I absorbs far red light of wavelength 700 nm & PSII absorbs short red light
of wavelength 680 nm. Each system has its own type of chlorophyll a i.e. P700 & P680.
Both system work in cooperation to capture radiant energy.

PS I – 670 , 683, 700. P – 700 is Reaction center. PSII – 680, 673. P – 680 is Reaction
center. PSI – lies on outer surface of thyllacoid, PSII – lies in inner surface of thyllacoid.
Mechanism of Photosynthesis --
Reaction of photosynthesis takes place in two phases i.e. photochemical phase &
biochemical phase.

I] Primary Process / Photochemical phase / Light reaction

1) It takes place in presence of solar energy i.e. light & only in granna of chloroplast.
Hence it is light reaction.
2) Light energy is converted into chemical energy with formation of ATP &
NADPH2. Hence it is photochemical phase.
3) ATP is formed by addition of 1 inorganic phosphate to ADP with the help of
energy. This is called as phosphorylation.
4) Energy required for phosphorylation is obtained from light in form of photons.
Hence it is called as photophosphorylation.
5) During this process eֿ s are transfered through a system of eֿ acceptors.
6) Two pathways are there of eֿ transfer i.e. cyclic & non cyclic

(A) Cyclic eֿ transfer / Cyclic photophosphorylation

(1)It involves PS I (Pigment system I). (2) Light strikes chlorophyll-a i.e.P – 700
trap(3) It absorbs quantum of light energy. (4)As a result it is exited i.e. its energy level

34
increases.(5) Hence it emits a pair of high energy electrons. (6)Energy rich eֿ leave
chlorophyll molecule & hence the chlorophyll molecule becomes +vely charged (ionized)
i.e. unstable.(7)Electrons move through various electron acceptors such as FRS(Z) ,
ferredoxin, cytochrome b6, cytochrome f & plastocyanin.(8)As energy rich electrons
move through electron acceptors, they loose some of their energy which is used for
synthesis of ATP from ADP & inorganic phosphate. (9)Finally de-energised electrons
return to unstable chlorophyll a molecule which becomes stable. (In one millionth of a
second) (10)Thus the electrons lost by chlorophyll molecules return to the same
chlorophyll molecule. Hence it is called as cyclic electron transfer.

Cyclic electron transfer occurs when light intensity is low, CO2, O2 low.

B] Non cyclic photophosphorylation / Non cyclic e– transfer

1) It involves pigment system I & II i.e. PS I & PS II

35
2) Light strikes chlorophyll – a of PS I & PSII i.e. P-- 700 trap & P680 trap.
3) They absorb quantum of light energy .
4) As a result they are exited i.e. their energy level increases.
5) Hence they emit a pair of high energy electrons
6) Energy rich e–s leave chlorophyll a molecule which becomes + vely charged
(Ionised) i.e. unstable.
7) These e–s from PS I system move through various e – acceptors such as FRS,
ferredoxin and finally accepted by NADP, that from PS II through plastoquinone,
cytochrome b6 , Cytochrome f, plastocyanin.
8) As energy rich electrons move through electron acceptors, they loose some of
their energy which is used for synthesis of ATP from ADP & inorganic phosphate.
9) In presence of light & chlorophyll a molecule photolysis of water takes place &
two electrons , two H + ions & O 2 are released. O2 is released outside. These
electrons are accepted by chlorophyll –a of PS II & it becomes stable. H ions are
accepted by NADP.
10)Two electrons emitted from PSII are accepted by chlorophyll- a of PS I after it
emits two e – s when light strikes on it. Thus chlorophyll-- a of PS I becomes
stable.
11)Finally two H + ions released by photolysis & two e – s released by PSI combine
together & reduce NADP to NADPH2

12)Thus e– s emitted from one pigment system don’t return to it. Hence it is called as
non cyclic e– transfer.

FRS – ferredoxin reducing system

Ferredoxin – Fe containing flavo protein

Cytochromes – Fe containing proteins

Platocyanin – Cu “ “

36
 Significance of Non cyclic e – transfer :-

1] In this pathway ATP & NADPH2 are formed.

2] ATP acts as an energy donar in dark reaction

3] NADPH2 acts as a hydrogen donar in dark reaction
4] Photolysis of water takes place.
5] Oxygen is liberated as bi product.
6] It is more efficient than cyclic photophosphorylation.

Cyclic Photohosphorylation Non cyclic Photophosphoryltion

1. e–s return to same chlorophyll 1. e–s don’t return to same chlorophyll
molecule from which they are molecule from which they are emitted.
emitted. 2. Photolysis of water take place.
2. Photolysis of water doe not take 3. O2 is evolved as bi product.
place. 4. NADPH2 is formed
3. O2 is not evolved 5. NADP takes part as e - acceptor
4. NDPH2 is not formed 6. Both pigment systems I & II are involved.
5. NADP doesn’t take part.
7. More efficient as more energy is formed.
6. Only pigment system I is involved
8. Primary acceptor is FRS (Z) &
7. Less efficient as less energy is
plastoquinone .
formed.
9. It takes place in green plants.
8. Primary acceptor is FRS (Z)
10.Occurs in normal light, aerobic condition,
9. It takes place in photosynthetic
sufficient CO2
bacteria
10. Occurs in low intensity light,
anaerobic condition, less CO2 available

37
II) Secondary Process / Biochemical Phase / Dark Reaction
1) It takes place in stroma of chloroplast, independent of chlorophyll
2) Light is not required for it. Hence it is known as dark reaction.
3) ATP, NADPH2 formed during light reaction are used in dark reaction for reducing
& fixing CO2 in carbohydrate i.e. hexose sugar. Hence it is also known as CO2

fixation or synthetic phase.

4) Energy in ATP is used for various reactions.

5) Enzymes & coenzymes necessary for dark reaction are present in stroma of
chloroplast.
6) Blackman in 1950 observed this reaction first. Hence it is also called as
Blackman’s reaction

38
7) Melvin Calvin & Benson traced path of carbon during dark reaction. They were
awarded Nobel prized in 1961.
8) During their experiment they fed unicellular algae chlorella & Scenedesmus with
radio active carbon isotope i.e. C¹4O 2 Algae were allowed to carry photosynthesis.
At different time intervals algal cell extract was chemically analysed by paper
chromatography to find out compound containing C ¹4. On the basis of products
obtained they suggested a cycle for dark reaction which is called as Calvin Cycle.
It has three phases

A] Carboxylation Phase B] Reduction Phase C] Regeneration & Synthetic Phase.

A] Carboxylation Phase.

i) Atmospheric CO2 is taken by stroma of chloroplast.

ii) RuMP ( Ribulose Mono Phosphate ) – 5 carbon compound is
present in stroma. It is phosphroylated into RuDp (RuDP—Ribulose
Di Phosphate) It is called as CO2 acceptor
iii) RuDP absorbs atmospheric CO2 & forms unstable 6 C compound.
iv) 6 C compound immediately undergoes hydrolysis & splits into 2
molecules of 3C compound i.e. 3 PGA. This is first stable compound
in Calvin Cycle. Hence it is also called as C3 Cycle.
B] Reduction Phase –

i) 3PGA is phosphorylated to 1, 3 DPGA( Di Phospho Glyceric Acid )

ii) 1, 3 – DPGA is reduced to 3 – PGAL ( Phospho Glyceraldehyde ) by using
hydrogen from NADPH2 & in this reaction one inorganic phosphate is
released. The process is reverse of oxidation in glycolysis. Hence it is
known as glycolytic reversal.
C] Regeneration & Synthetic Phase

i) 10 molecules of 3 – PGAL are used for regeneration of RuMP through

various phases with formation of 10C, 9C, 8C …… compounds.
ii) Two molecules of 3PGAL are used to form hexose sugar i.e. glucose which
is converted into starch by polymerization.

Action spectrum – rate of photosynthesis at different wavelengths of light.

Absorption spectrum – absorption of light of different wave lengths.

Quantun requirement – no. of photons/quanta required to release 1 molecule of

O2

Emerson & Lewis showed that it is 8 quanta.

Red drop – sudden fall in photosynthesis yield beyond red region of spectrum.
Showed by Emerson & Lewis.

39
 Emerson’s enhancement effect – if simultaneously shorter & longer wave lengths
are provided, rate of photosynthesis is higher than total rate from the beams
separately.

RESPITATION

Introduction - Living beings need regular supply of energy for vital functions or
activities like cell division, transport of materials, locomotion, digestion etc .

Definition :– It is an intracellular oxidation -- reduction reaction in which complex

organic substances are broken down stepwise to release chemical energy in the form of
ATP & CO2 & H2O are given out as byproducts.

Important features :-- Overall Reaction

C6H12O6 + 6O2↓ → 6CO2↑ + 6H2O + E (38ATP, 277.44 Kcal)

 In biochemical process the reaction is not so simple.

 Free molecular oxygen does not combine directly with substrate like in combustion.

 Hydrogen is gradually removed from the substrate & the electrons released (H2 →
2H + 2e‾ ) are transferred through a series of e‾ carriers to generate energy in the
form of ATP ( exergonic -- energy producing, catabolic – breakdown process )

 The process occurs at cellular temperature.

 Gases are exchanged in liquid medium by blood, tissue fluid etc.

 CO2 & H2O are given out as byproducts.

 All energy in glucose molecule is not converted into ATP but some of it is lost as heat
energy.

ATP –The Energy Currency of the Cell

These are bio-molecules which store energy in biologically usable form.

ATP – Adenosine Tri Phosphate

It is composed of a) Adenosine – which is made up of adenine [Nitrogen base] +

Ribose Sugar [Pentose sugar] b) 3 phosphate groups
α β γ
Adenine----- Ribose sugar-----PO4 ~ PO4 ~ PO4

40
 Second & Third phosphate groups are attached to ribose sugar by high energy
bonds, when cell needs energy it breaks the third high energy bond & even the
second phosphate bond of ATP forming ADP & AMP respectively
ATP → ADP + iP + E

All living cells generate ATP by using energy trapped in glucose molecule during
photosynthesis. During this process glucose molecule is oxidized. In this reaction
CO2 & H2O are given out as by products. This is called as cellular respiration.
Energy released is trapped in ATP molecule by attaching phosphate group. This is
called as phosphorylation. As glucose molecule is oxidized it is called as oxidative
phosphorylation.

Significance : 1] It stores energy in biological usable form. 2] It supplies energy

in

various cellular activities by breaking phosphate bond in between 2nd & 3rd and

even 1st & 2nd phosphate groups. 3] It acts as a phosphate donar in various
biochemical reactions.

 Cellular respiration is oxidation of food material into CO2 and H2O.

 During this oxidation E released is trapped in ATP ( 1ATP traps 7.28 k cal)for
using in all cell activities.

This oxidation occurs in three phases.

1) Glycolysis – Breakdown of glucose to pyruvic acid (pyruvate). It occurs in

cytosol i.e. cytoplasm. Hence mitochondria are not necessary. In occurs in
prokaryotes as well as eukaryotes. As O 2 is also not required it is common to
aerobic as well as anaerobic organisms. In glycolysis 2 ATP and 2 NADH + H +
also formed.

2) Citric Acid Cycle / Krebs cycle -

 Decarboxylation of pyruvic acid to CO2 and H2O along with formation of NADH +
H+ and FADH2.

 In eukaryotes it occurs in mitochondrial matrix. Matrix has complex mixture of

soluble enzymes for decarboxylation of pyruvic acid.

At the end 3CO2 , 4 NADH + H+, 1 FADH2 are formed (when 2e – are removed
from malic acid transferred to NAD + reducing it to NADH + H +, same way 2 e –
removed from saccinic acid and reduces FAD. To FADH2

41
 Outer membrane – contains many complexes of integral membrane proteins that
form channels – porins through which many molecules and ions move in and out
of mitochondria.

 e – from NADH and FADH2 are transferred to next phase i.e. respiratory chain.

3) Electron Transport Chain / Respiratory Chain -

 Inner membrane of mitochondria contains complexes of integral membrane

proteins.

NADH dehydrogenase complex

Succinate dehydrogenase complex

Cytochrome c reductase complex

Cytochrome c oxidase cpmplex

ATP synthase complex

 It also consists ubiquinone, cytochrome a,b,c, which shuttle electrons from one
complex to another.

Inner membrane is selectively permeable.

(NADH carries e – from catabolic reactions to respiratory chain.

NADPH supplies e – to anabolic reactions.)

 Stepwise transfer of e – from NADH, Ubiquinone, Cytochromes and then finally

to O2 to form H2O takes place. Neither NADH nor NADPH can cross inner
mitochondrial membrane, but the e – carried by them can shuttle across.

 During e – transfer E is released.

 It is used to transfer/ pump H + (protons) from matrix into inter membrane space
by active transport.

 Thus matrix becomes – vely charged and inter membrane space +vely charged.

 Gradient of protons formed across the inner membrane forms a miniature

battery. (Mitochondria contain 3 classes of cytochromes – a,b,c which absorb
different light spectra)

42
 [Plastoquinone is like ubiquinone. Ubiquinone ( Coenzyme Q)  small,
hydrophobic, hence freely diffusible in lipid bilayer of inner mitochondrial
membrane and can shuttle reducing equivalents between other less mobile
electron carriers in the membrane. Cytochromes  proteins with iron – heme
group; show strong absorption of visible light.)

 In mitochondrial respiratory chain, e – move as follows – NADH / FADH2 

Co.Q  Cytochrome b  Cytochrome C1  Cytochrome C 
Cytochrome a  Cytochrome a3  O2.

FADH2
AH2

FAD

ATP ATP ATP

A NAD CoQ Fe+++ Fe+++ Fe+++ Fe+++ Fe+++ 1/2 O2

Cyt b Cyto C1 Cyt C Cyt a Cyt a3

NADH
CoQH2 Fe++ Fe++ Fe++ Fe++ Fe++ H2O
AH2 + H+

2H+

ADP + iP ADP + iP ADP+ iP

Chemiosmosis in Mitochondria:-

 As e – pass from NADH + H+ / FADH2 down the gradient to O2, E is released.

 This E is used to pump H + (protons)from matrix into inter membrane space

against conc. / electrochemical gradient by active transport

 As proton conc. increases in inter membrane space; a strong diffusion gradient is

set up.

 These protons can only exit through ATP synthase complex into matrix .

43
 E is released as protons flow down their conc. gradient through specific protein
channels in inner membrane. This free E is utilized for ATP synthesis. The
process catalyzed by a membrane protein complex ATP synthase. ATP synthase
is present in elementary particles of inner membrane. Mitochondrial ATP
synthase is an F-type ATP ase . ATP synthase has two distinct components : F1 →
peripheral membrane protein & Fo → integral to above membrane. Fo has a
proton pore through which protons leak as fast as they are pumped by e‾
transport. Without a proton gradient the F1 depleted vesicles can’t make ATP. On
the other hand isolated F1 catalyze ATP hydrolysis ( reversal of synthesis) hence
originally called as F1 ATP ase. When purified F1is added back to depleted
vesicles, it reassociates with Fo plugging its proton pore & restoring membrane’s
capacity to couple e‾ transfer & ATP synthesis.

 This transfer of protons along concentration gradient from inter membrane space
to matrix is called chemiosmosis. It is an example of facilitated diffusion.

 Peter Mitchell proposed chemiosmotic model. According to this model

transmembrane differences in proton concentration are the reservoir for E
extracted biological oxidation reactions.

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 Inhibitors of e – transfer to O2, like cyanide, CO, antimycin A, block ATP
synthesis and vice versa. (oligomycin inhibits ATP synthase activity. ) Thus these
two processes show obligatory coupling.

Mitochondrial DNA:-
 Human mitochondrion contains 5 – 10 circular DNA molecules – mt – DNA.
 Mutation in mt – DNA causes human diseases; affecting mainly brain and
muscles.
 In mammals 99.99% of mt DNA is inherited from mother. This is because in
zygote paternal mitochondria are only about 100, while maternal are 100,000.

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 BIOENERGETICS

Living cells and organisms must perform work to stay alive and to reproduce
themselves. The synthetic reactions that occur within cells, like synthetic processes in
any factory, require the input of energy. Energy is also consumed in the motion of a
bacterium or an Olympic sprinter.

Although the characteristic composition of an organism changes little through time, the
population of molecules within the organism is far from static. Small molecules,
macromolecules, and supra-molecular complexes are continuously synthesized and then
broken down in chemical reactions that involve a constant flux of mass and energy
through the system. The hemoglobin molecules carrying oxygen from your lungs to
your brain at this moment were synthesized within the past month; by next month they
will have been degraded and entirely replaced by new hemoglobin molecules. The
amounts of hemoglobin in the blood remain nearly constant because the rate of
synthesis balances the rate of its breakdown, the constancy of concentration is the result
of a dynamic steady state, a steady state that is far from equilibrium. Maintaining this
steady state requires the constant investment of energy; when the cell can no longer
generate energy, it dies and begins to decay toward equilibrium with its surroundings.

Metabolism –The sum of all chemical transformations taking place in a cell

/organism.

Metabolic pathways – A series of enzyme catalyzed reactions. Each step in it brings

about specific, small chemical change like removal, transfer / addition of a particular
atom / functional group.

Metabolites – Metabolic intermediates which convert precursors into products.

Intermediary metabolism – Combined activities of all metabolic pathways that

interconvert precursors, metabolites & products of low molecular weight

Catabolism --The degradative phase of metabolism in which organic nutrient

molecules (carbohydrates, fats, and proteins) are converted into smaller, simpler end
products (such as lactic acid, CO 2, NH3). Catabolic pathways release energy, some of
which is conserved in the formation of ATP and reduced electron carriers (NADH,
NADPH, and FADH2); the rest is lost as heat.

Anabolism –(also called biosynthesis ) Small, simple precursors are built up into
larger and more complex molecules, including lipids, polysaccharides, proteins, and
nucleic acids. Anabolic reactions require an input of energy.

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Bioenergetics - The quantitative study of the energy transductions that occur in living
cells and study of the nature and function of the chemical processes underlying these
transductions. Biological energy is not in the form of heat mechanical or light energy
therefore word thermodynamics is not used but word bioenergetics is used. This energy
is termed as free energy and defined as energy available for work. It symbolizes change
in energy and not the absolute energy.

Two approaches to study physical or chemical processes:

Kinetic molecular approach: In this, process is studied in terms of molecules

and atoms.

Thermodynamic approach: Process id studied by considering energy changes

involved. Thermodynamics means study of heat flow. But actually not only
relation between heat and work but also deals with all kinds of inter conversion of
one kind of energy in to the other. Most of the energy forms are ultimately
converted in to heat.

Thermodynamics help to forecast whether certain physical or chemical

transformations are possible or not. Under given set of conditions of
temperature, pressure, concentration etc. But it can not give any information of
time required for completion of change as well as rate of reaction.

If the system exchanges neither matter nor energy with its surroundings, it is said
to be isolated. If the system exchanges energy but not matter with its
surroundings, it is a closed system; if it exchanges both energy and matter with
its surroundings, it is an open system.

A living organism is an open system; it exchanges both matter and energy with its
surroundings. Living organisms derive energy from their surroundings in two
ways:

1) They take up chemical fuels (such as glucose) from the environment and
extract energy by oxidizing them; or

2) They absorb energy from sunlight.

Homogenous system – System with same chemical composition throughout.

Heterogenous system – System with two or more phases which are

homogenous themselves but separated from each other by definite boundary. (ice
and water)

State of a system: Variable of a state are temperature, pressure, volume,

composition

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 Gas Equation: PV = nRT

Therefore if 2 values are known the third can be determined thus state of a simple
homogenous system can be defined. Physical properties of a system are of two
types:

Extensive properties: Depend on quantity of matter in the system under

consideration e.g. mass, volume, energy

Intensive properties: Depend on nature of substance and independent of its

amount e.g. temperature, pressure, viscocity, refractive index

Thermodynamic equilibrium: It is said to achieved when observable

properties like temperature, pressure, volume does not change with time. For
thermodynamic studies a system must be in in 3 types of equilibria which must
exist symeltaniously.

a) Thermal equilibrium

b) Chemical equilibrium

c) Mechanical equilibrium: No movement of particles of the constituents of

system itself and between itself and surroundings.

Isothermal process: Temperature remains same

For Exothemal process – heat evolved give out immediately to surroundings to

maintain the temperature. For endothermic process required amount of heat
enters the system from surroundings to maintain the temperature.

Adiabatic process – heat neither enters nor leaves the system during the
process.

Thermodynamic laws and living organisms

The molecular complexity and orderliness of structure of living organisms is

much higher in contrast to the randomness of non living matter.

The first law of thermodynamics, fully valid for biological systems

Photosynthetic cells absorb light energy and use it to drive electrons from water
to carbon dioxide, forming energy-rich products such as glucose (C 6H12O6),
starch, and sucrose and releasing O2 into the atmosphere:

Light 6 CO2 + 6 H2O  C6H12O6 + 6 O2

(light-driven reduction of CO2)

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Non – photosynthetic cells and organisms obtain the energy they need by
oxidizing the energy-rich products of photosynthesis and then passing electrons
to atmospheric O2 to form water, carbon dioxide, and other end products, which
are recycled in the environment:

C6H12O6 + O2  6 CO2 + 6 H2O + energy

(energy-yielding oxidation of glucose)

DNA, RNA, and proteins are informational macromolecules. In addition to using

chemical energy to form the covalent bonds between the subunits in these
polymers, the cell must invest energy to order the subunits in their correct
sequence. It is extremely improbable that amino acids in a mixture would
spontaneously condense into a single type of protein, with a unique sequence.
This would represent increased order in a population of molecules; but according
to the second law of thermodynamics, the tendency in nature is toward ever-
greater disorder in the universe: the total entropy of the universe is continually
increasing. To bring about the synthesis of macromolecules from their
monomeric units, free energy must be supplied to the system (in this case, the
cell).

Second law of thermodynamics

How living organisms can create and maintain their intricate orderliness in an
environment that is relatively disordered and becoming more with the time ?
Living organisms do not constitute exceptions to thermodynamic laws. Their high
degree of molecular orderliness must be paid for in some way since it can not
arise spontaneously from disorder.

Living organisms have following characteristic properties such as,

1) Use free energy: Living organisms absorb useful form of energy that is free
energy from surrounding under specific temperature and pressure and return
less useful form of energy to the environment in equal amount. The useful form
of energy returned by the living organisms is heat or other form that is quickly
randomized in the environment and thus increase the entropy.

2) Open system: living organisms are not in equilibrium with the environment

3) Steady state: Cell is non equilibrium open system, a machine for extracting
free energy from the environment which it causes to increase in randomness. The

49
 rate of transfer of energy and matter from environment in to system is equal to
transfer of energy and matter from system to environment.

4) Non equilibrium: Open system in steady state can do work in non

equilibrium. Process under non equilibrium can be regulated. This is orderly
state of an open system.

5) Isothermal system: The living system is essentially isothermal that is at any

given time all parts of the cell have the same temperature. Furthermore, there are
no significant differences in pressure between one part of the cell and another.
For this reason, cells are unable to use heat as a source of energy, since, heat can
do work at constant pressure only if it passes from a higher to a lower
temperature zone.

6) Isothermal chemical engines: energy absorbed from environment id

transformed to carry out synthesis of cell components, osmotic work, transport of
material into cell, nerve conduction, muscle contraction etc. which takes place at
constant struggle against the tendency to produce entropy. Synthesis of large and
information rich macromolecules, the information of intricately structured cells,
development of an organization, all these are powerful anti entropic doom
imposed on all natural phenomenons. Under the second law of thermodynamics,
living organisms choose the least evil – they produce entropy at a minimum rate
by maintaining steady state.

An attempt to produce a machine which could produce more mechanical work

than the equivalent energy used is failed. This compels to accept the first law of
thermodynamics in biological systems.

Mathematical formulation of first law

Suppose some amount of heat is put in the system, Since heat can not be lost it
must remain either partial or whole in the system, or can used up by the system
in doing mechanical work.

In general case, when both happen,

Heat absorbed = increase of internal energy + work done by the

system

If final and initial internal energy of the system is E2 and E1 respectively, then
increase internal energy is ∆E = E2- E1

If heat absorbed is q and work done is w then

∆E = E2 – E1 = q – w (this is first law of thermodynamics)

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 Although the heat absorbed / the work done by the system might vary the path by
which the change is affected ∆E is always same.

Second law of thermodynamics:

1. First law explains the equivalence between heat and work but imposes no
condition on their mutual convertibility. It never explains under what
circumstances and to what extent it is possible to convert one form of energy in to
other.

2. It also explains about the amount of heat lost by a hot body must be equivalent
to the gain by cold body. But is does not explains that heat has to flow
spontaneously from hot to cold body and not in reverse direction.

3. Different forms of energy can be readily and completely converted in to heat

but not possible to convert back heat completely in to work. Hence, there must be
some other law besides the first law that governs the direction of flow of heat and
extent of its convertibility in to work. This limitation forms the basis for second
law of thermodynamics. The total entropy of a system must increase if
the process has to occur spontaneously.

Entropy: The quantitative expression for randomness or disorder of the

components of a chemical system is expressed as entropy, S.

When the products of a reaction are less complex & more disordered than the
reactants, the reaction proceeds with a gain in entropy. Any change in
randomness of the system is expressed as entropy change, S, which by
convention has a positive value when randomness increases. J. Willard Gibbs,
who developed the theory of energy changes during chemical reactions, showed
that the free energy content, G, of any closed system can be defined in terms
of three quantities:

Enthalpy, H – heat content of reacting system, reflecting the number and kinds
of chemical bonds in the reactants & products; Entropy, S; and the absolute
temperature, T (in degrees Kelvin).

The definition of free energy is G = H – TS.

When a chemical reaction occurs in biological system at constant temperature &

pressure, the free-energy change, G, is determined by the enthalpy change, H,
reflecting the kinds and numbers of chemical bonds and non covalent
interactions broken and formed, and the entropy change, S, describing the
change in the system’s randomness:

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 G / ∆F = H – T S (F → Heltmoz free E, T→ absolute temp.)

Also ∆G / ∆F = ∆E – T ∆S ( E/Q → internal energy)

Hence total energy of the system is ∆E = ∆G + T ∆S

If ∆G is negative, the reaction would proceed spontaneously with loss of free

energy that is exergonic reaction. If in addition, ∆G is of great magnitude, the
reaction goes virtually to completion and is essentially irreversible.

If ∆G is positive, the reaction can not occur spontaneously and would proceed
only if the free energy can be gained that is endergonic.

If ∆G is zero, the system is at equilibrium and no net change takes place.

Relationship between equilibrium constant and standard free energy change in a

model reaction. Thus, in a reaction, A + B ↔ C + D

[C] [D]

∆G = ∆G0+ RT ln ---------------------

[A] [B]

When the concentration of [A] [B] [C] [D] ∆G is 0.1 M, ∆G 0 known as standard
free energy change. At equilibrium, ∆G0 = 0

[C] [D]

i.e. ∆G = ∆G0+ RT ln ---------------------

[A] [B]

For biochemical reactions, a standard state is defined as having a pH of 7. the

standard free energy change at this standard state is denoted by ∆G 0 since the
equilibrium constant under standard condition is;

K’eq = [C] [D] / [A] [B]

Substituton gives ∆G0 = - RT ln K’ eq

Thus, the standard free enrgy change can be calculated from the equilibrium
constant K’ eq it is important to note that ∆G may be larger or smaller than ∆G0’
depending on the concentration of various reactants.

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