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Chapter 1:Cell and its structure

Concept of cell
History of cellular discovery
Cell Theory

1839
Plant Cell Organization
Plant cell size
Plant cell size
Plant cell
Cell: It’s the structural & functional unit of
life.
Organization of a typical plant cell

Plant Cell
Non-living
Protoplast
materials
Plant cell composition
Protoplast: Protoplasm +Non living Substance
Non Living Substances: • 3. Excretory Substances- Tannin
1. Storage Substances- proteins Resin
lipids Latex
Organic acid
carbohydrates Glue
2. Secretory Substances- enzymes Alkaloid
pigments Glue
nectar Volatile oil
Minerals
Protoplasm:
Cell membrane+ Cytoplasm+ Nucleus
Cytoplasm:
1. Cell organelles: mitochondrion
plastid
endoplasmic reticulum
Golgi body
lysosome
ribosome
microtubules
centrosome
2.Cell matrix
3. Cell vacuole
Cell wall
 Cell Wall
• It is a tough ,flexible or rigid
layer that surrounds the plasma
membrane of plant cell.

• It was first discovered and

named by Robert Hooke in 1665.

• Its permeable in nature.

Cell Wall(Physical Structure)
Cell Wall(Physical Structure)
• It consists of two layers-primary cell wall and secondary cell wall.
• In between these two layers, there is a common layer known as
middle lamella.
• Primary cell wall is formed on the middle lamella by deposition of
cellulose, hemicellulose and glycoprotein.
• Secondary cell wall is formed on the primary cell wall after full
maturation of the cell.
• This layer is comparatively thicker, generally cellulose and lignin are
deposited on it.
• The cell wall starts to develop during the telophase of mitotic cell
division.
Cell Wall(Physical Structure)
Cell Wall(Chemical Structure)
• Polysaccharides
• Protopectins
• Glycoproteins
• Xyloglucon
• Cellulose , hemicellulose, lignin,
pectin-primary wall
• Cellulose, cutin, suberin,wax,
calcium oxalate ,inorganic salts -
secondary wall
Cell Wall: Vascular tissue have no secondary
cell wall
Chemical • Cell Wall of higher plants are
Plant Composition of composed of cellulose and
cell wall polysaccharides.
Bacteria Peptidoglycan or • Cellulose exits as micelles units
Mucoprotein in the cell wall. Each micelles
Fungi Chitin and other unit comprises of several
polysaccharides thousands of Beta D Glucose.
Algae Glycoproteins and
Polysachharides
Glycoprotein S-
Archaea(Single layers,Pseudopeptidoglyc
celled organism) an or Polysachharides
 Plasmodesmata
• In many places of the wall the
cellulose layer remain absent and
small pits are formed. These are
called pit fields.
• These pits remain opposite of the
adjacent wall’s pits. The middle
lamella then is known as pit
membrane.
• In middle lamella minute pores
remain through which the
protoplasm of both cells get
connected by microfibrils. Each of
these are called plasmodesma .
Cell Wall
• 1.middle lamella is made mostly of • 5.The secondary cell wall is made
PECTIC ACIDS. of
• 2.During telophase microfilaments, CELLULOSE,LIGNIN,SUBERIN,WAX.
microtubules, endoplasmic • 6.It is thicker, almost 5-10
reticulum forms fragmoplast in the micrometer.
equator zone and combine with • 7.It contains pit field, pit
vesicles of golgi body and create membrane, pit pair and
this layer of cell wall. plasmodesma.
• 3.Primary cell wall is made of • 8.In ultrastructure the cell wall is
CELLULOSE,HEMICELLULOSE and made of fibrils.
GLYCOPROTEIN.
• 4.The primary cell wall is 1-3
micrometer thick.
Ultrastructure of cell wall
Protoplasm
Protoplasm
Cell membrane/Plasmalemma/Plasmamembrane
• The cell membrane is a living, elastic, selectively permeable and
ultrathin membrane.
• It is a bilayer membrane.
• Its width is 70- 100A.
• The most accepted model about the structure of cell membrane is-

Fluid –mosaic model theory

Cell Membrane{According to FLUID MOSAIC
MODEL}
• 1.It is the membrane found in all
cells which separates the cell from
the outside environment.
• 2.In plant cell, a cell wall remains
attached to the outer surface of it.
• 3.It can be folded and each folding
is called microvillus.
• 4.If the microvillus goes deep
inside the protoplasm then it is
called pinocytic vesicle.
• 5.It is a semi permeable
membrane.
Fluid Mosaic Model Theory
• S. J. Singer and Garth Nicolson proposed this model in 1972.
• The main component of cell membrane is a bimolecular lipid layer
that actually consists of two rows of phospholipids molecules.
• Each phospholipid molecule has a water-soluble polar head and two
fat-soluble non polar tails.
• The polar head of phospholipid is hydrophilic and it faces the exterior.
• The non polar tail is hydrophobic and always try to avoid water and
face the inside of the bilayer.
Fluid Mosaic Model Theory
Fluid Mosaic Model Theory
• The phospholipid bilayer are
different types of embedded
proteins and cholesterol
molecules which look like
Mosaic.
• The plasma membrane is fluid in
nature because of its
hydrophobic components such
as lipid and membrane proteins
that move laterally or sideways.
Fluid Mosaic Model Theory
• Peripheral Protein Molecule-

Some protein molecules exist

outside the lipid layer.
• Integral Protein Molecule-

Some protein molecules partially

or entirely pass across the lipid
layer.
Fluid Mosaic Model Theory
• Oligosaccharide molecules
attached to same protein and
lipid molecules of cell
membrane to form glycoprotein
and glycolipid.
• Carbohydrate molecules are
considered to be responsible for
the transition of some
substances inside and outside
the cell.
Fluid Mosaic Model Theory
• Flip flop movement:

Transverse diffusion or flip-

flop involves the movement of a
lipid or protein from one
membrane surface to the other.
Cell membrane structure summary
• 1.AmphiphilicPhospholipid
bilayer
• 2.Peripheral,Integral and
Transport Proteins
• 3.Glycocalyx sugar
layer(glycolipid and
glycoprotein)

• 4.Lipids(Cholesterol)
Cytoplasmic organelles
Cytoplasmic Organelles: Chloroplast-the
green coloured plastid
• It remains covered by a double
layered membrane.
• It has a transparent, granular,
homogenous protein and starch
containing watery medium
called stroma.
• There are small stacks of sac like
discs(10-100) present within the
stroma called grana.[40-80 per
chloroplast]
Cytoplasmic Organelles: Chloroplast-the
green coloured plastid
• There are disc like sacs known as
thylakoids.

• The thylakoids elongated like

tubular organs and connected
with the grana side by side are
called lamellum.
Cytoplasmic Organelles: Chloroplast-the
green coloured plastid
• The round bodies containing
necessary enzymes for ATP
synthesis present in the
thylakoid membrane are called
ATP synthases.
• The regions containing about
300-400 molecules of
chlorophyll-a, chlorophyll-b,
carotene and xanthophyll
aggregated in pigment system
are known as photosynthetic
units or quantosome.
Chloroplast function
Cytoplasmic Organelles: Mitochondrion
• There are two membranes of 50-
70 Angstrom.
• The outer membrane defines the
external shape.
• The inner membrane has many
folds called cristae.
• The volume enclosed by the
inner membrane is called the
matrix.
Cytoplasmic Organelles: Mitochondrion
• The matrix contains enzymes
that participate in the TCA cycle
or Kreb’s cycle and ribosomes,
matrix granules and
mitochondrial DNA.
• ATP syntheses and ETS are also
present in the inner surface and
combindly called oxisomes.
• The round stalked sac like bodies
ornamented in the cristae are
called ATP synthases.
Cytoplasmic Organelles: Mitochondrion
• Mitochondrial matrix contains
small, double stranded and
circular DNA.
• It also contains 70 S (sub unit)
ribosomes.
• Chemically there are 60-65%
protein,25-30% lipid,0.5% DNA
and RNA and trace amount of
sulfur, iron,copper,vitamins etc.
 Mitochondrion
• 1.MEMBRANE: • 4.OXYSOME:
• Double layered lipoprotein The circular ,granular, usually stalked object
present on the inner surface
• Outer membrane smooth and contain transparent
protein 5.ATP SYNTHASE:
• Gap between the two layers is 6-8nm. Its like a machine. It receives electron to
• 2.CHAMBERS: produce ATP from ADP.
6.ETS:
• Space between two membrane is the outer
membrane It is present in the inner membrane
• This chamber is filled with coenzyme enriched fluid Generates proton gradient
• Space covered by inner membrane in the central 7.DNA:
region is the inner chamber
Small ,double stranded but circular
• It contains jelly like homogenous liquid matrix. 8.RIBOSOME:
• 3.CRISTAE: 70 S ribosome
• These are the finger like projections of the inner
membrane creating folding towards the center.
• Remains transversely in the inner chamber
• Creates partial compartments and the space inside is
called intracristal space
Mitochondrion function
Cytoplasmic Organelles: Ribosomes
• These are the minute granular
bodies without any membrane.
• All types of ribosomes consist of
two unequal sub units.
• In normal condition the sub
units remain freely suspended in
the cytoplasm but during protein
synthesis the two sub units
come together.
• In eukaryotic 80S and in
prokaryotic 70S.
Ribosome
• 1.It is the molecular machine responsible for • 6.Structure:
protein synthesis. • Two separate RNA –Protein complex called
• 2.It looks like a hamburger with a puffy bun Subunits are present.
on the top and RNA as the patty.
• No membrane.
• 3.Its Protein, RNA ratio is 1:1 but few Mg, Ca, • Large subunit is situated on the top and binds
Mn ions are also found in its chemical tRNAs.
structure.
• 4.In Prokaryotic cells Ribosomes originate • Small subunits are at the bottom and binds
from DNA but in eukaryotic cells it is mRNA.
produced from nucleus in two sub units. • In prokaryotic the size is 70S.(50S,30S)
• 5.It is found in all cells but more in cells but in eukaryotic its 80S(60S,40S).
specialized for protein synthesis.
• There are 4 binding sites and each one is
basically a sequence of nucleotides.
• During Protein synthesis the sites are visible.
Ribosome sites
• 1.Aminoacyl-tRNA site: It is the
charged tRNA which delivers amino
acid to the ribosome.It is the acceptor
site.
• 2.Peptidyl-tRNA site: It bears the
peptide chain.it is the holding site.
• 3.Exit site: It is the final transitory step
for the tRNA.
• 4.mRNA site: It is the site where
mRNA get attached to the ribosome.
Basically mRNA provides the message
or codon and ribosome read it
through and create a peptide chain.
Ribosome functions
Cytoplasmic Organelles: Golgi body
Cytoplasmic Organelles: Golgi body
• Three types of structural
components are found in it.
• Cisternae- these are parallel
arranged elongated or flat tubular
structure of irregular length.
• Vacuole-these are round plate
parts present near the cis –
cisterna.
• Vesicles-these are the
comparatively smaller sac like
bodies present below the trans-
cisterna.
Cytoplasmic Organelles: Lysosome
Cytoplasmic Organelles: Lysosome
• These are generally round in shape.
• These remain covered by a three
layered unit membrane.
• These are made up of lipoprotein.

• Several Hydrolase enzymes are

present inside these.(50 types)
• Each lysosome contains a specific
type of enzyme.
Cytoplasmic Organelles: Endoplasmic
Reticulum
• It’s a complex network of
membrane bound tubular or sac
like body which remain extended
from the nuclear membrane to
the cell membrane.
• It is a unit, membrane bound
and three layered.
• It may be of three types-
cisternae, vesicles and tubules.
Cytoplasmic Organelles: Endoplasmic
Reticulum
Cytoplasmic Organelles: Centriole
• It is the transparent round
organelle near the nuclear
membrane which functions in
the formation of spindle system
and aster rays during cell
division.
• The dense matrix of the
centrosome is known as the
centrosphere.
Cytoplasmic Organelles: Centriole
Cytoplasmic Organelles: Cell Vacuole
Cytoskeleton
Cytoskeleton
Peroxisome
Cytoplasm: Protoplasm - Nucleus
• It’s the live, semi- transparent,
granular, colloidal, colourless
and flexible constituent of cell.
• It contains all the cell organelles,
solid non living materials, stored
foods, organic acids, water etc.
• Its 98% water.
Nucleus: Nuclear membrane+ Nucleoplasm
+Nucleolus+ Chromatin Fiber
Nucleus
Chromosomes
• The elongated thread like
structures existing in coiled
network within nucleoplasm of
nucleolus are the nuclear
reticulum or chromatin fibers.
• The nuclear reticulum during cell
division become condense and
more tightly coiled wide threads
called chromosomes.
 Chromosome
• It is an organized structure of
DNA,RNA and protein that is found
in the nucleus of eukaryotic cell.
• The number of the chromosomes
is constant and unchangeable for a
particular species.
• Higher plant and animal cells
contain two sets of chromosomes
and they are called diploids(2n).
• The gametes contain half the
number of chromosomes or single
set of chromosomes and known as
haploids(n).
Chromosomes
• Each chromosome at the
mitotic metaphase stage
contains two longitudinal
halves which are called
chromatids or daughter
chromosomes.
• In the anaphase stage the
chromatids of a
chromosome separate
from each other and
move to the opposite
poles.
Chromosome terminology
Chromosome
Chromosome
Chromosomes
• The length of
chromosomes vary from
3.5- 30 micrometer.
• The diameter also varies
from 0.2-2.0 micrometer.
• Human chromosome has
an average length of 4-6
micrometer.
• In mitotic metaphase
stage chromosomes have
the most thick, short and
clear look.
Chromosomes
• Pellicle is the outer thin covering or • The primary constriction or
sheath of the chromosome. centromere is comparatively narrow
• Matrix is made up of proteins, small and divides the chromosome into two
quantities of RNA and lipid. arms.
• Chromonemata are the coiled threads • The secondary constrictions are found
that form the bulk of the in some chromosomes in addition
chromosome. with the primary ones.
• Chromomeres are linearly arranged • If secondary constriction is present in
bead like and compact segments. the distal region of an arm ,it would
pinch off a small fragment called
satellite.
• The terminal regions on either side of
chromosomes are called telomeres.
Chromosomes: The regulators of cell division
• Chromosomes are mainly • DNA contribute 45%
composed of nucleic acids acid and • RNA contribute 0.2-1.4%
protein.
• There are two types of nucleic • The alkaline proteins have low ionic
acids –DNA and RNA. properties and the ratio of the
protein and DNA is 1:1
• There are two types of protein – • The acidic proteins have high ionic
Alkaline or Histone protein and properties.
Acidic or Non–Histone protein.
• There are trace amount of lipid, • #Histones are water soluble
enzymes ,calcium, magnesium, iron proteins in which alkaloid amino
etc. present. acids are predominant.
• #The rest of the proteins remaining
after the histones are classified as
non histone.
DNA
DNA: Deoxyribonucleic acid-polymer of
Deoxyriobonucleotide
• Physical Structure-
• Two polynucleotide strands
are enter twined and look
like a spiral shaped ladder
• Two strands are
complementary
• Each strand is made up of
four types of nucleotides.
• The backbone of each
strand consists of
deoxyribose and phosphate
group.
Genetic materials / Hereditary materials
• Nucleic acid is a complex organic
polymer of nucleotides.
• Nucleotide has three parts-

1.pentose sugar
2.inorganic phosphoric acid
3.nitrogenous base.
Genetic materials / Hereditary materials
• Pentose sugar has two
types of 5 carbon sugar.

• Ribose sugar is found in

RNA.

• Deoxyribose sugar is
found DNA.
Genetic materials / Hereditary materials
• The inorganic
phosphoric acid is
attached to the
sugar molecule in
place of the –OH
group on the 5
number carbon.
Genetic materials / Hereditary materials
• There are two types
of nitrogenous bases.
• 1. Purines have two
rings of atoms.
• 2. Pyrimidines have a
single ring of atoms.
• A nucleic acid has any
four types of nitrogen
bases.
DNA: Deoxyribonucleic acid-polymer of
Deoxyriobonucleotide
• The nucleotides are
joined to one another
in a chain by covalent
bonds between the
sugar of one
nucleotide and the
phosphate of the next,
resulting in an
alternating sugar-
phosphate backbone.
DNA :Chemical structure
• The nitrogenous bases of the two
separate polynucleotide strands are
bound together, according to base
pairing rules (A with T and C with G),
with hydrogen bondsto make double-
stranded DNA. The complementary
nitrogenous bases are divided into
two groups, pyrimidines and purines.
In DNA, the pyrimidines are thymine
and cytosine; the purines are adenine
and guanine.
• 5’ end indicates the carbon has a
phosphate group and 3’ indicates the
carbon has a hydroxyl group.This
asymmetry gives a DNA strand a
direction.
DNA
RNA: Its the nucleic acids transcribed from the DNA and
containing ribose and Uracil as special sugar and base
respectively.
• Types of RNA:
• 1.Messenger RNA(mRNA):It is transcribed from the DNA and carries the
genetic information from the nucleus to ribosome.
• 2.Transfer RNA(t RNA): It combines with specific amino acid in the
cytoplasm and carries it to the ribosome.
• 3.Ribosomal RNA(r RNA): It constitutes the ribosome.
• 4.Genetic RNA( g RNA): It carries genetic information and regulates the
hereditary characters.
• 5.Minor RNA: There are some small RNA molecules in the cell as the small
cytoplasmic RNA(sc RNA), nuclear RNA(sn RNA),guide RNA (gRNA).
RNA
Non genetic RNA types
• 1.Ribosomal RNA:
• About 80%
• Synthesized in nucleolus
• Located in Ribosome
• In low ionic concentration remains
coiled
• In high ionic concentration forms
helix
• Provides a mechanism for decoding
mRNA into amino acids
• Interacts with tRNA during
translation
Non genetic RNA types
• 2.Messenger RNA:
• About 3-5%
• Synthesized by transcription
• Synthesized from nuclear DNA
• Single stranded
• Created as a complementary strand
of DNA
• Acts as the template for formation
of protein
• Carries coding information to the
sites of protein synthesis
Non genetic RNA types
• 3.Transfer RNA:
• About 10-15%
• Located in cytoplasm
• Clover leaf shaped
• 5 arms and 4 loops
• 3’ end has the sequence CCA
where amino acid get attached
• Opposite position has Anticodon
loop with 3 bases where tRNA gets
attached to mRNA
• Carries specific amino acid from
cytoplasm to the ribosome
Gene: The region of DNA that controls a
hereditary characteristic
• Each chromosome of each • A gene may determine of a
species has a definite number characteristic of an individual by
and arrangement of genes. specifying a polypeptide chain that
• Genes can be as short as 1000 forms a protein or part of a protein.
base pairs or can be several • Action of gene may be defined as the
hundred thousand pairs long. process of protein synthesis of genes.
• The total amount of gene in a • A structural gene, an operator gene and
set of chromosomes of all type a promoter gene take part in protein
of an organism is known as synthesis. These genes are called
genome. together as operon.
• The gene ,which regulates the operon,
is called the regulator gene
Central Dogma
DNA replication
DNA Replication: The process of producing two
identical copies from one original molecule.
• The semi conservative model • 3.Stability of the single strand
was proposed by Watson and • 4. Formation of replication fork
Crick.
• 5.Attachement of RNA primer at
• The main steps in the the ORI region
mechanism of DNA replication
are: • 6.Elongation of the daughter
DNA chain
• 1.Identification of point of origin
of replication(ORI) • 7.Attachement of the Okazaki
segments and termination of
• 2. Unwinding of the mother DNA replication
molecule and dissolving bonds
between the bases • 8.DNA proof reading and repair
DNA replication fork
DNA Replication: The process of producing two
identical copies from one original molecule
Sl Enzyme Function in DNA replication

1 DNA Gyrase Relieves strain of unwinding by DNA helicase

2 DNA Helicase Dissolves the hydrogen bonds between two strands and unwinds the helix

3 SSBP (Single Strand Unites with a single helix and prevents its rewinding
Binding Proteins)

4 Primase Works in RNA primer attachment

5 DNA Polymerase Builds a new duplex DNA strand by adding nucleotides in the 5’to
3’direction,performs proof reading and error correction.

6 Telomerase Lengthens telemetric DNA by adding repetitive nucleotide sequences

7 DNA Ligase Reanneals the semi-conservative strands and joins Okazaki fragments

8 Topoisomerase Relaxes the DNA from its super-coiled nature

Transcription: Formation of messenger RNA
• Initiation. The DNA molecule
unwinds and separates to form a
small open complex. RNA
polymerase binds to the promoter
of the template strand.
• Elongation. RNA polymerase
moves along the template strand,
synthesizing an mRNA molecule. In
eukaryotes there are three RNA
polymerases: I, II and III. The
process includes a proofreading
mechanism.
Transcription: Formation of messenger RNA
• Termination.In eukaryotes it is
more complicated, involving the
addition of additional adenine
nucleotides at the 3' of the RNA
transcript (a process referred to
as polyadenylation).
• Processing. After transcription the
RNA molecule is processed in a
number of ways;introns are
removed and the exons are spliced
together to form a mature mRNA
molecule consisting of a single
protein-coding sequence.
Transcription: Formation of messenger RNA
• Promoter:The specific base • Introns: The regions in the newly
sequence recognized by the RNA formed pre mRNA which do not
polymerase in the initiation contain genetic message.
phase. • Exons: the remaining regions of
• Cistron:The specific region of the a newly formed pre RNA other
DNA molecule that unwinds in than introns.
initiation phase. • Splicing: The process where
• Terminator:It’s the specific base newly formed pre RNA are
sequence in the DNA which RNA spliced together to form a
polymerase faces at the end of mature mRNA.
the transcription.
Translation: Amino acids formation process
1.Activation of amino acid
2.Transfer of activated amino acid
to tRNA
3.Initiation of protein synthesis
4.Elongation of the polypeptide
chain
5. Chain termination
Translation: The process in which mRNA takes
part in protein synthesis.
• There are 20 amino acids taking • Two steps in charging:
part in protein synthesis. • 1.An amino acid reacts with ATP
• A tRNA specifically links to an in presence of specific enzyme
amino acid and the process is to form the activated
known as charging. aminoacyle adenylic acid.
• This process is done by direction • 2.The complex reacts with a
of an enzyme called aminoacyl specific tRNA and the amino acid
tRNA synthetase. is transferred to the 3’ end of
tRNA and the enzyme leaves the
complex.
Translation
Terminology
• Brownian movement: The random • Ion Channel : Integral protein
movement caused by the uneven molecules of the cell membrane
bombardment of particle. work as the channel to pass water
• Cyclosis: The protoplasm in plant soluble molecules
cell has a movement around the • Endosymbiont: The mitochondria
central vacuole. and the chloroplasts.
• Unit membrane: Cell membranes
and cell organelles consist of more
then one layer but the layers work
collectively as a unit.
Terminology
• Autophagy is a self-
digesting mechanism responsibl
e for removal of damaged
organelles, malformed proteins
during biosynthesis, and
nonfunctional long-lived
proteins by lysosome. ... The
molecular mechanism of autoph
agy involves several conserved
Atg (autophagy-related)
proteins.
Terminology
• A polyribosome (or polysome or
ergasome) is a complex of an
mRNA molecule and two or
more ribosomes that act
to translate mRNA instructions
into polypeptides.