BIOCHEMISTRY

Lesson 2
 THE CELL

❖All organisms are made up of cells.

“ It is the basic structural, functional and

biological unit of life.”

❖It was discovered by Robert Hooke in

1665.
❖The word cell comes from a Latin
word 'cellula' meaning small room.
❖Cells are the building block of life,
where all the chemical processes
occur.
❖They take up the biological molecules,
convert them into energy or use them
to carry out specialized functions.
❖It also contains the hereditary material
which determine the genetic
characteristics.
❖The cell theory was developed by
Matthias Jacob Schleiden and
Theodor Schwann. It states that..
“All organisms are composed of one
or more cells, and that all cells
come from pre-existing cells. The
vital functions of an organism occur
within the cells and that all cells
contain hereditary information
necessary for cell functions and for
transmitting from one generation to
the next.”
❖Every living things (animals, plants,
bacteria, fungi, protozoans) are made
up of cell.
• Some organisms are made up of just
one cell. ( Unicellular organism.
e.g. Bacteria)
• While some organisms are made up of
many cells. (Multicellular organisms
e.g. Animal cell)
❖The human body is built with about
30 to 40 trillion cells specializing in
different functions.
❖Many identical cells joins together and
forms a tissue.
❖Various tissues, that perform a
particular function, organized together
which forms the organ.
❖Various organs joined together forms
an organ system.
TYPES OF CELL

1. Eukaryotic cell

2. Prokaryotic cell
 1. EUKARYOTIC CELL

• Eukaryotic cells are those cells which

have a true nucleus.
• It has a nuclear membrane within which
there is well defined chromosomes.
• It has other membrane bound
organelles like mitochondria,
endoplasmic reticulum, Golgi
bodies etc.
• Organisms with eukaryotic cells are
called as Eukaryotes.
• They may be single-celled or
multicellular organisms. e.g. cells
of plant, animals, fungi.
 2. PROKARYOTIC CELL
• Prokaryotic cells are those cells whose
nucleus is not distinct and their DNA
is not organized into chromosomes.
• They lack most of the membrane bound
organelles.
• Prokaryotic cells are also called
Prokaryotes.
• They are usually unicellular
organisms.
e.g. bacteria.
 EUKARYOTIC CELL
• A typical Eukaryotic cell, as seen under
light microscope has two major parts:

The cell membrane

The cytoplasm and its

organelles
• The different substances that make up
the cell are collectively called as
Protoplasm.
 1. CELL MEMBRANE
• It is a thin, elastic, semi permeable
membrane of 7.5 to 10
nanometers thickness.
• It is a living membrane made up of
phospholipid bilayer embedded
with proteins.
• It is a flexible membrane and so it can
fold in or out.
• It is made up of 55 % proteins, 25 %
phospholipids, 13 % cholesterol, 4%
lipids and 3% carbohydrates.
Functions of the cell membrane
• It protects the cell contents from the
surrounding environmement.
• It provides a shape to the cell.
• It is semi permeable and allows
transport of certain substances into
and out of the cell.
• It helps in forming cell junctions.
2. CYTOPLASM AND ITS ORGANELLES
• In eukaryotes, the protoplasm
surrounding the nucleus is called
cytoplasm.
• It is a clear gelatinous fluid that fills the
cell and surrounds the organelle.
• It contains 90 % water, dissolved
substances, minerals, sugar, irons,
vitamins, amino acids, proteins and
enzymes.
• Cytoplasm is the seat for many
pathways like glycolysis and HMP
(Hexose monophosphate) pathway.
• The cytoplasm contains well
organized structures called
organelles which vary in size
from a few nanometers to many
micrometers and they are
specialized to carry out one or
more vital functions of the cell.
• Cytoplasm vs cytosol?
• The organelles include...
–Mitochondria

–Endoplasmic reticulum

–Golgi apparatus

–Ribosomes

–Lysosomes

–Peroxisomes

–Centriole

–Vacuole
• These are tiny, sausage shaped
structures of diameter 0.5 to 1
micrometer.
• It is called as “Power house of the cell” as
it generates energy in the form of
AdenosineTriphosphate (ATP) which is
required by all the cells.
• It is found both in plant and animal
cells.
• It has a double membrane envelope:
an inner membrane and an outer
membrane.
• The inner membrane is folded and pleated
(double fold) and it is called cristae.

• It provides large surface area for different

biochemical processes as it contains many
oxidative enzymes.
• Within this membrane are the proteins involved
in electron transport chain, ATP synthase and
transport proteins.
• It is impermeable to molecules and ions but
allows the free passage of carbon dioxide,
oxygen and water.
• The metabolites are transported across
the membrane with the help of
transport proteins.
• The outer membrane is a smooth
phospholipid bilayer enveloping the
mitochondria.
• It had enzymes like monoamine
oxidase and NADH reductase. (NADH-
Nicotinamide adenine dinucleotide +
Hydrogen)
• An intrinsic protein called porin form
the channels that makes the membrane
permeable to solutes and metabolites.
• It allows the free passage of substances
with molecular weight of less than 10,000.
• The membranes create two
compartments.
–The space between the outer and inner
membrane is called the intermembrane space.
–It is here that oxidative phosphorylation occus.
(Releasing energy by oxidizing nutrients for ATP
synthesis)
–The inner cavity of mitochondria is called the
matrix.
• It is packed with many enzymes like
pyruvate dehydrogenease, pyruvate
carboxylase, enzymes for oxidation of
fatty acids, aminoacids and enzymes of
citric acid cycle.
• It also contains the mitochondrial
genome, mitochondrial ribosomes,
tRNAs, dissolved oxygen, carbon
dioxide and water.
• FUNCTIONS:-
–It is the seat for the Kreb's cycle
(citric acid cycle)
–It contains enzymes for Oxidative
phosphorylation which helps in
producing energy rich ATP molecules
–It provides intermediates for
synthesis of cytochrome,
chlorophyll, hemoglobin and
steroids
–Amino acids like glutamate
are synthesized in it from
alpha ketoglutarate and oxalo
–Many fatty acids are synthesized in
the matrix
–Calcium can be stored in the
mitochondria and released whenever
required.
• It is a network of tubular and vascular
structures extending from outer
membranes of nucleus to the cell
membrane.
• It is seen to be spread throughout the
cytoplasm and it provides a large
surface area for various physiological
activities.
• The inside of the vesicles and tubules
is filled with an endoplasmic matrix.
• When the ribosomes are attached on
the outer surface of mebrane of the
endoplasmic reticulum, it is called as
Rough endoplasmic reticulum
(RER).
• It lies adjacent to the cell nucleus and
its membrane is continuous with the
membrane of the nucleus.
• When there are no ribosomes attached
to the endoplasmic reticulum, it is
called as Smooth endoplasmic
reticulum (SER).
• Functions:-
–RER helps in transporting proteins from
ribosomes to Golgi bodies.
–Proteins that enters RER undergoes
processing, folding and sorting
–SER is involved in the synthesis of
lipids, including cholesterol and
phospholipids
–In some cells, SER helps in the synthesis
of steroid hormones from cholesterol
–In the cells of liver, SER helps in
detoxifying drugs and harmful chemicals.
• It is a stack of membranous sac, like a pile of
discs.
• It is present between endoplasmic reticulum
and cell membrane.
• Like endoplasmic reticulum, it is a
single membrane bound structure.
• In animal cells, it is present around the
nucleus while in plant cell it is scattered
throughout the cell.
• These cell organelles pack and sort the
proteins before they are sent to their
destinations.
• Functions:-
–The proteins that enter it from RER is
modified, processed, sorted and transported in
the form of vesicles to the cell membrane and
other destinations.
–Glycolipids, sphingomyelin are synthesised
within it.
–In plant cells, it help in the synthesis of
polysaccharides needed by the cell wall.
–It has a role in the synthesis of
carbohydrates like galactose.
–Primary lysosomes develop from mature
Golgi bodies.
–It plays an important role in lipid trafficking.
• They are spherical shaped organelles
seen either free in the cytoplasm or
attached to RER.
• They are found in eukaryotes and
prokaryotes.
• They are synthesised by the
nucleolus.
• The ribosomes link the amino acids
together in the order that is specified by
the messengers RNA.
• They are made up of two subunits - a
small sub unit and a large sub unit.
• The small sub unit reads the mRNA
while the large subunit assembles the
amino acids to form large polypeptide.
• The ribosomal sub units are made up
of one or more eRNA and proteins.

• Function:-
–It is the site for protein synthesis.
• They are tiny sac like organelles of size
0.5 to 1.5 µm, which are membrane
bound and found in hundreds in a
single cell.
• They are formed from the Golgi
bodies as small vesicles which bud
off from them.
• Within the sac there are several
hydrolytic enzymes that breakdown
macromolecules like nucleic acid,
proteins and polysaccharides.
• They are also called as “suicidal bags”
as enzymes contained in them can
digest the cell's own material when
damaged or dead.
• The important enzymes in it are DNA-
ase, RNA-ase, protease, lipase,
glycosidase, phosphatase, sulfatase
which are synthesized in the
endoplasmic reticulum and then
transported to the Golgi bodies.
• Functions:-
–It helps in the digestion of food
releasing enzymes.
–They digest worn out organelles
–It helps in the defense, by digesting
germs
–It helps sperm cells in entering the egg by
breaking through the egg membrane
–It provides energy during cell starvation by
the digestion of its own cell parts.
• It is a type of microbody which is small,
spherical shaped, with single membrane
and of size 0.5-1.5 µm.
• They are found in both animal and plant
cells.
• Just like lysosomes they contain many
enzymes which help in biological
reactions.
• They are formed from the endoplasmic
reticulum unlike lysosomes which are
formed from the Golgi bodies.
• Functions:-
–The enzymes found in peroxisomes are
usually used for different metabolic reactions
and for digesting different materials in the
cell.
–They help in the oxidation of many
substances resulting in the formation of
hydrogen peroxide as a by product.
–But, it contains enzyme peroxidase or
catalase which decomposes this harmful
hydrogen peroxide into water and oxygen or
uses it to oxidize other organic compounds
like phenol, alcohol, formaldehyde, etc.
–They are also involved in the catabolism of
fatty acids (beta oxidation), D- aminoacids and
polyamines.
–They are needed in the synthesis of
plasmalogens (type of ether phospholipid
needed for functioning of brain and lungs.)
–They participate in the synthesis of
cholesterol, bile acids and myelin.
–In plants, it helps in the photorespiration
and symbiotic nitrogen fixation.
• They are long, hollow cylinders of size
24 nm in diameter and can grow up to a
length of 50 µm.
• They are found in eukaryotic cells.
• They are made up of
two globular
proteins namely
α-tubulin and
β-tubulin.
• Along the
microtubule axis
tubulins are joined
end to end to
form
protofilaments.
• The cytoskeleton is a structure
that helps cells maintain their
shape and internal organization,
and it also provides mechanical
support that enables cells to
carry out essential functions like
division and movement.
• They are organized by
microtubule organizing
structures, primarily the
centrioles.
• Functions:-
–They are part of the cytoskeleton and it
provides mechanical support to the cell
–It helps in the organization of cytoplasm
–They help in the segregation of
chromosomes during mitosis
–They are used for locomotion
(movement from one place to another)
when present)
• These are small rod like structures of
size 4-7nm in diameter found in the
cytoplasm of all eukaryotic cells,
forming a part of the cytoskeleton.
• They are made up of protein, Actin
(contractile protein)
• Functions:-
–It provides support and shape to
cell
–Along with myosin, it helps in
contraction
–It helps in cytokinesis (a physical process
of cell division)
• They are part of the cytoskeleton in the
cytoplasm, also surrounding the
nucleus and extending to the cell
membrane.
• They are made up of different types of
fibrous proteins unlike microtubules
which are made up of actin.
• They are of size 8-12 nm in diameter.
• They are found in hair, nails, scales and
skin since they have high tensile
strength.
• Due to their rope like structure they
provide mechanical strength to the
cells and help cells to withstand stress
like stretching and changing shape.
• e.g. Keratin filaments in skin and
epithelial cells.
• It is cylindrical in shape and of length
0.5 micrometer.
• it is present in all animal cells just
outside the nucleus.
• It does not have a membrane.
• All centrioles are made up of protein
strands called tubulin.
• Each centriole has 9 sets of inter
connected peripheral tubules and each
set has 3 micro tubules arranged at
definite angles making the shape of a
cylinder.
• It has its own DNA and RNA and
therefore, self duplicating.
• Two centrioles when oriented at a right
angle, forms the centrosome.

❖Functions:-
▪ It is involved in cell division. They are seen
in the process of both meiosis and mitosis.
▪ It helps in the formation of cilia and
flagella.
▪ It helps in the organization and
alignment of microtubules within the
cell.
• It is a membrane enclosed fluid filled
sac present in animal and plant
cells including fungi.
• It contains organic and inorganic
molecules within it.
• They do not have particular size or
shape but adjust themselves according
to the need of the cell.
❖Functions:-
▪ It helps in removing waste products from
the cell
▪ It isolates substances that are harmful to
the cell
▪ It holds water and waste products within
it
▪ It helps in maintaining the internal pH of
cell
▪ It helps to maintain hydrostatic pressure
within the cell
▪ It plays a major role in autophagy by
maintaining a balance between biogenesis
and degradation.
NUCLEUS
• It is a specialized double membrane-
bound protoplasmic body present
at the center of the cell.
• It is known as the cell's information
center as it houses the chromosomes.
• The double membrane around the
nucleus is called nuclear membrane or
nuclear envelope.
• It is made of proteins and lipids,
• It enclose the nucleus to keep it
separate from surrounding materials off
the cell.
• The outer membrane is continuous with
endoplasmic reticulum and it has
ribosomes attached on the outer
surface.
• It has several large nuclear pores
through which nuclear transport of
large molecules, small molecules and
ions occur.
• The space between the nuclear
membranes is called perinuclear space
and it is continuous with the lumen of
rough endoplamic reticulum.
• Within the nuclear membrane is a jelly
like substance called karyolymph or
nucleoplasm.
• Within it, there is a network of
chromatin fibrils which condense to
form chromosomes during cell division
• The nucleolus is present within the
nucleus.
• It does not have a membrane
around it.
• It synthesizes rRNA and
assembles it.
• It regulates the synthetic activity of
❖Functions:-
▪ It controls the hereditary charateristics of an
organism
▪ Protein synthesis, cell division, growth and
dfferentiation occurs in it
▪ Stores heredity materials in the form of DNA
▪ It is the site for transcription in protein
synthesis
▪ Nucleolus helps in the synthesis of
ribosomes
▪ It regulates the integrity of genes and gene
expression
• A prokaryote is a single-celled organism
that does not have a 'true nucleus'.
e.g. Bacteria, Archaea.
• It does not contain any membrane
bound organelles like mitochndria,
nucleus, endoplasmic reticulum etc.
• They have many ribosomes scattered
throughout their cytoplasm and
nucleoid which contains the DNA.
 Parts of Prokaryotic Cell:

o Flagellum:
–It is long whip like structure
that helps in locomotion
o Pili:

–Small hair like structure present

on the surface which helps in
attaching to the surface of
other bacteria.
o Cell membrane:
–It surrounds the cytoplasm and
regulates the flow of substance in and
out of the cell
o Capsule:

–It is a polysaccharide layer that is

outside the cell envelope.
–It enhances the ability of bacteria
to cause disease
o Cell wall:
–It is the outer most covering of the cell
and it gives shape to the cell

o Cytoplasm:

–It is gel like substance present within

the cell.
–It contains enzymes, ions, organic
molecules, ribosomes, nucleoid
o Ribosome:
–It is the organelle which helps in
protein synthesis.

o Nucleoid:

–It contains the genetic material

o Plasmid:
• A small DNA molecule within the
cell that can replicate itself.
• It is a small, double stranded and
circular in shape organelle.
• These are usually found in
bacteria.
 MICROSCOPY

• It is the technical field of using

microscopes to view samples and
objects that cannot be seen with the
unaided eye.

• It is the science of investing small

objects using microscopes.
 MICROSCOPE

• Microscope is an instrument used to

see objects that are too small for
the naked eye.

• Identification of minute organisms are

necessary for diagnosis and
treatment.
 TYPES OF MICROSCOPE

❖Optical / Light microscope

❖Electron microscope
❖Darkfield or Ultra microscope
❖Phase Contrast and Differential
Interference Contrast microscope
❖Fluorescent microscope
❖Ultraviolet microscope
1.OPTICAL/LIGHT MICROSCOPE
❖It a type of microscope which uses
visible light and a system of lenses to
magnify images of small samples.

❖It was invented by Hans and

Zacharias Janssen in 1590.
❖The eyepiece, objective lenses,
reflector, condenser and stage is first
cleaned by a lens paper.
❖The specimen slide is then placed on
the stage with help of clips at the
center.
❖Observe through the eyepiece and
focus the object with the help of
coarse or fine adjustment.
❖The reflector can be adjusted to get
proper light.
❖The light shining through the
specimen is focused by the lens so
that a magnified image can be seen
through the eyepiece.
 2. ELECTRON MICROSCOPE
❖It was designed by Ernst Ruska
and Max Knoll in 1931 in Germany.
❖It is a type of microscope that uses
a beam of electrons to illuminate a
specimen and produces a magnified
image.
❖The wavelength of lens as when compared
to light is smaller and so they help magnify
even very small objects.
❖It has high magnifying power when
compared to light microscope as electrons
have shorter wavelength than visible light.
❖It uses electrostatic and electro magnetic
lenses to control electron beam and
focuses in to form an image.
❖It is used to see microorganisms, cell
organelles, large molecules, biopsy
samples, etc.
 TYPES OF ELECTRON MICROSCOPE

❖Transmission Electron microscope

❖Scanning Electron microscope
❖Reflection Electron microscope
❖Scanning Transmission
Electron microsope
❖Low Voltage Electron
microscope
❖Transmission Electron Microscope:-
▪ It uses high voltage electron beam to
create an image.
▪ The beam of electron is sent
through the specimen.
▪ Some electrons are reflected while
others pass through it creating an image
of the specimen.
❖Scanning Electron Microscope:-
▪ It does not produce a complete image
of the specimen.
▪ It scans the surface of the specimen
and forms an image by detecting
electron that are reflected or absorbed.

❖Reflection Electron Microscope:-

▪ Similar to the TEM, the reflected
electrons are detected to get the
information about the surface of the
specimen.
❖Scanning Transmission Electron
Microscope:-
▪ It combines high magnification of TEM
with surface details of SEM. It helps to
perform a complex analysis of the
specimen.

❖Low Voltage Electron Microscope:-

▪ It operates at accelerating voltage of a
few kilo electrovolts or less.
 3. DARKFIELD MICROSCOPE
❖A dark field microscope is arranged so that
the light source is blocked off, causing light
to scatter as it hits the specimen.
❖Here reflected light is used in place of
transmitted light.
❖The oblique beams of refracted and
diffracted light are coming from the sides
and passes into and over the specimen to
illuminate it.
❖The object looks bright on a dark
background.
❖It is useful in observing small living objects
and small organelles like nucleus,
mitochodria, vacuole, etc.
❖It is usually used to see unstained objects.
4. PHASE CONTRAST MICROSCOPE
❖It is a microscope which helps to see
unstained micro organisms.
❖It is the technique that converts
phase shifts in light passing through
a transparent specimen to
brighness changes in the image.
❖The light passing through two
different materials with different
refractive index will undergo a change
in the phase of light.
❖These phase differences are converted to
difference in intensity of light, making
image appear dark against a light
background.
❖Phase contrast microscopy improves the
contrast and make the structures
visible.
 5. FLUORESCENT MICROSCOPE
❖It is an optical microscope that uses
fluorescence and phosphorescence to
study the properties of organic and
inorganic substances.
❖Special dyes like fluorescein, rhodamine
and auramine are used.
 6. ULTRAVIOLET MICROSCOPE
❖It is a microscope that has quartz lens and
slides that uses ultra violet light as
illumination instead of the common light.
❖Uses the shorter wavelength (180-400 nm)
of ultraviolet rays compared to common
light, which brings about higher resolution
of objects.
 CELL FRACTIONATION
• It is the technique of rupturing the cell to
separate various cell components while
preserving their individual functions in
order to study their structure and chemistry.
• Cells can be broken down by many ways
like subjecting it to osmotic shock or
ultrasonic vibration or ground in a small
blender.
• Albert Claude (1899-1983) pioneered
techniques of cell fractionation by
differential centrifugation.
• These procedures break up the cell in
to fragments and its nuclei,
mitochondria, Golgi body, lysosomes,
peroxysomes, etc. can be separated.
• The cells are first suspended in 0.25
molar sucrose solution at 0-4℃.
• Cells are then grounded well to form
an isotonic slurry called
homogenate.
• The homogenate is then subjected to
different values of centrifugal force.
• This helps in seperating the cell
components by size and density.
• At a relatively low speed, the large
components like nuclei sediments
form a pellet at the bottom of the
centrifuge tube, at slightly higher
speed, a pellet of mitochondria is
formed, and at even higher speeds
and with longer period of
centrifugation, first the small closed
vesicles and then the ribosomes can
be collected.
 GEL ELECTROPHORESIS
• It is a method of separating
macromolecules like DNA,RNA and
proteins based on their size and
charge, by passing it through a gel
medium namely agarose and by
applying an electric field.
• The smaller molecules move faster
than the larger ones through the
pores of the gel and the molecules in
the gel can be stained to make them
visible.
• Ethidium bromide is the most commonly
used stain to make DNA or RNA strands
visible.
 CHROMATOGRAPHY
• It is the technique used for separation
of a mixture by dissolving it in a
solution or suspension and allowing
it to pass through a medium in which
the components move at different
rates.
• In this technique there is a stationary
phase and mobile phase.
• The various constituents of the
mixture travel at different speeds,
causing them to separate.
 TYPES OF CHROMATOGRAPHY
❖Column chromatography
❖Paper chromatography
❖Thin layer chromatography
❖Gel filtration chromatography
❖Ion exchange chromatography
❖Affinity chromatography