Introduction to Cells

All living things are made of cells:

small, membrane-enclosed units filled
with a concentrated aqueous solution
of chemicals and endowed with the
extraordinary ability to create copies of
themselves by growing and dividing in
two.
The simplest forms of life are solitary
cells. Higher organisms, including
ourselves, are communities of cells
derived by growth and division from a
single founder cell. Cells, therefore, are
the fundamental units of life.

Unity and diversity of Cells

Cells are not all alike; in fact, they can be
widely different. A bacterial cellsay a
Lactobacillus in a piece of cheeseis a few
micrometers, or mm, in length. Thats about 25
times smaller than the width of a human hair.
Cells vary no less widely in their shapes and
functions. A typical nerve cell in your brain is
enormously extended; it sends out its electrical
signals along a fine protrusion that is 10,000
times longer than it is thick, and it receives
signals from other cells through a mass of
shorter processes that sprout from its body like
the branches of a tree.

Figure: A: Ba bacterial cell; B: a nerve cell

from the
cerebellum (a part of the brain that
controls
movement)

 Cells are also enormously diverse in their

chemical requirements and activities. Some
require oxygen to live; for others it is deadly.
Some appear to be specialized factories for the
production of particular substances, such as
hormones, starch, fat, latex, or pigments. Some
are engines, like muscle, burning fuel to do
mechanical work.
Some modifications specialize a cell so much that
they spoil its chances of leaving any
descendants. Such specialization would be
senseless for a cell that lived a solitary life. In a
multicellular organism, however, there is a
division of labour among cells, allowing some
cells to become specialized to an extreme degree
for particular tasks____the egg and the sperm.

Living Cells all have a similar Basic

Chemistry
Although they are infinitely varied when
viewed from the outside, all living things
are fundamentally similar inside. In every
cell, the instructions in the DNA are read
out, or transcribed, into a chemically
related set of polymers called RNA. RNA
molecules have a variety of functions,
but the major class serve as messenger
RNA: the messages carried by these
molecules are in turn translated into yet
another type of polymer called a protein.

Figure: In all living cells, genetic information flows

from DNA to RNA (transcription) and from RNA to
protein (translation). together these processes are
known as gene expression.

All present-day Cells have

apparently evolved from the same
ancestor
A cell reproduces by duplicating its DNA
and then dividing in two, passing a copy
of the genetic instructions encoded in its
DNA to each of its daughter cells.
Mutations can create offspring that are
changed for the worse, changed for the
better, or changed neutrally. The struggle
for survival eliminates the first, favours
the second, and tolerates the third.

 These simple principles of genetic change

and selection, applied repeatedly over
billions of cell generations, are the basis of
evolutionthe process by which living
species become gradually modified and
adapted to their environment in more and
more sophisticated ways. Evolution offers
a startling but compelling explanation of
why present-day cells are so similar in
their fundamentals: they have all inherited
their genetic instructions from the same
common ancestor. It is estimated that this
ancestral cell existed between 3.5 billion
and 3.8 billion years ago.

Cells Under the Microscope

Cells, in general, are very smalltoo small to
be seen with the naked eye. They were not
made visible until the seventeenth century,
when the microscope was invented.
Light microscopes, which use visible light
to illuminate specimens.
Electron microscopes, invented in the
1930s, go beyond this limit by using beams
of electrons instead of beams of light as the
source of illumination, greatly extending our
ability to see the fine details of cells.

The invention of the light Microscope

led to the discovery of Cells
By the seventeenth century, lenses were refined to the
point that they could be used to make simple
microscopes. Using such an instrument, Robert Hooke
examined a piece of cork and in 1665 reported that the
cork was composed of a mass of minute chambers,
which he called cells. Schleiden in 1838 and Schwann
in 1839 documented the results of a systematic
investigation of plant and animal tissues with the light
microscope, showing that cells were the universal
building blocks of all living tissues. Their work, and that
of other nineteenth-century microscopists, slowly led to
the realization that all living cells are formed by the
division of existing cellsa principle sometimes
referred to as the cell theory confirmed by

Cells, organelles, and even Molecules

Can Be seen Under the Microscope
THE LIGHT MICROSCOPE
The light microscopemagnify cells up to 1000 timesresolve
details as small as 0.2 mm
Three things are required:
A bright light must be focused onto the specimen by lenses in the
condenser.
Second, the specimen must be carefully prepared to allow light to
pass through it.
Third, an appropriate set of lenses (objective and eyepiece) must
be arranged to focus an image of the specimen in the eye.
FIXED SAMPLES:
Most tissuesneither small nor transparent enoughchemically
fixed and cut into very thin slices, or sectionsmounted on a
glass microscope slide and stained.

A
B
Figure: A. a light microscope; B. A
stained section of a plant root tip is
shown here

FLUORESCENCE
MICROSCOPY
Fluorescent dyes used for staining cells are detected
with the aid of a fluorescence microscope.
Similar to an ordinary light microscope except that
the illuminating light is passed through two sets of
filters.
(1): Filters the light before it reaches the specimen,
passing only those wavelengths that excite the
particular fluorescent dye.
(2): blocks out this light and passes only those
wavelengths emitted when the dye fluoresces. Dyed
objects show up in bright colour on a dark
background.

A
B

Figure: A. fluorescence microscopy; B. stain for

DNA (green ) microtubule protein in the mitotic
spindle is stained red with a fluorescent antibody.

CONFOCAL MICROSCOPY
A specialized type of fluorescence microscope
builds up an image by scanning the
specimen with a laser beam. The beam is
focused onto a single point at a specific depth
in the specimen, and a pinhole aperture in
the detector allows only fluorescence emitted
from this same point to be included in the
image. Scanning the beam across the
specimen generates a sharp image of the
plane of focusan optical section. A series of
optical sections at different depths allows a
three-dimensional image to be constructed.

A
B

Figure: A. Conventional fluorescence microscopy

gives a blurry Image; B. Confocal microscopy
provides an optical section showing the
individual cells clearly.

 The type of electron microscope used to

look at thin sections of tissue is known as
a Transmission electron microscope
(TEM). This is, in principle, similar to a
light microscope, except that it transmits
a beam of electrons rather than a beam
of light through the sample. Another type
of electron microscopethe
Scanning electron microscope (SEM)
scatters electrons off the surface of the
sample and so is used to look at the
surface detail of cells and other
structures.

The Procaryotic Cell

Organisms whose cells do not have a

nucleus are called procaryotes (from pro,
meaning before) e.g., bacteria.
Procaryotes are typically smalljust a few
micrometers long. They often have a tough
protective coat, called a cell wall,
surrounding the plasma membrane, which
encloses a single compartment containing
the cytoplasm and the DNA. The cells
reproduce quickly by dividing in two. Under
optimum conditions, when food is plentiful,
a procaryotic cell can duplicate itself in as
little as 20 minutes.

Procaryotes are the Most diverse of

Cells

In shape and structure, procaryotes may seem

simple and limited, but in terms of chemistry,
they are the most diverse and inventive class of
cells. These creatures exploit an enormous range
of habitats. Some are aerobic, using oxygen to
oxidize food molecules; some are strictly
anaerobic. Eucaryotic cellsare thought to have
evolved from aerobic bacteria. Virtually any
organic material can be used as food by one sort
of bacterium or another. Even more remarkably,
some procaryotes can live entirely on inorganic
substances. Some of these procaryotic cells, like
plant cells, perform photosynthesis, getting
energy from sunlight. Plants unaided by bacteria
cannot capture nitrogen from the atmosphere.

The World of procaryotes is divided into

two domains: Bacteria and archaea
Traditionally, all procaryotes have been
classified together in one large group. But
molecular studies reveal that there is a
gulf within the class of procaryotes,
dividing it into two distinct domains called
the bacteria (or sometimes eubacteria)
and the archaea. Remarkably, at a
molecular level, the members of these two
domains differ as much from one another
as either does from the eucaryotes.

The Eucaryotic Cell

Organisms whose cells have a nucleus are
called eucaryotes (from the Greek words eu,
meaning well or truly, and karyon, a
kernel or nucleus).
Eucaryotic cells, in general, are bigger,
some live independent lives as single-celled
organisms, such as amoebae and yeasts ,
others live in multicellular assemblies. All of
the more complex multicellular organisms
including plants, animals, and fungiare
formed from eucaryotic cells.

Basic structure

Plasma membrane separates inside

from outside of cell
Cell wall often present in prokaryotes,
plants, fungi an extra, tough layer outside
of the plasma membrane that provides
structural rigidity
The inside is called the cytoplasm, except
for the nucleus
Outside is the extracellular matrix, a
dense region connecting cells in tissues
made of strong protein fibers and a sugar
(polysaccharide) gel

The nucleus is the information store

of the Cell
The nucleus is usually the most prominent
organelle in a eucaryotic cell. It is enclosed
within two concentric membranes that
form the nuclear envelope, and it contains
molecules of DNA. In the light microscope,
these giant DNA molecules become visible
as individual chromosomes when they
become more compact as a cell prepares
to divide into two daughter cells

Figure: Nucleus

Mitochondria generate Usable

energy from food to power the Cell
Mitochondria are present in essentially all eucaryotic
cells. Each mitochondrion appears sausage- or
wormshaped, from one to many micrometers long;
Enclosed by two membranes; the inner one folds back
and forth inside. Have their own DNA and divide,
replicate separately from the rest of the cell The
source of the huge energy needs for the cell __
produce ATP from food molecules (e.g., sugars),
consume oxygen, and release CO2. the entire process
is called cellular respirationessentially, breathing on
a cellular level. Evidence that early prokaryotes
swallowed small bacterial cells that eventually
became mitochondria___ symbiotic relationship

Figure: Mitochondria

Chloroplasts Capture energy from

sunlight
Chloroplasts are large green organelles that are
found only in the cells of plants and algae, not in
the cells of animals or fungi. In addition to their
two surrounding membranes, chloroplasts
possess internal stacks of membranes containing
the green pigment chlorophyll. In plant cells,
capture sunlight to build energy-rich sugars.
Sugars then exported to mitochondria to provide
energy. Like mitochondria, contain their own DNA
and reproduce on their own suggests these two
used to be early eukaryotes that swallowed small
photosynthetic bacteria.

Figure: Chloroplast

Internal Membranes Create intracellular

Compartments with different functions
The endoplasmic reticulum (ER)an irregular maze
of interconnected spaces enclosed by a
membrane__Location of the synthesis of lipids and
many proteins. The membrane of the ER forms the
outer part of the nuclear envelope, such that the ER is
always in close contact with the nucleus. This is
important because the ER gets its synthesis
instructions from the genetic information
Stacks of flattened membrane-enclosed sacs next to the
ER constitute the Golgi apparatus, which receives
and often chemically modifies the molecules made in
the endoplasmic and then directs them to the exterior
of the cell or to various locations inside the cell.

A
B

Figure: A: Endoplasmic Reticulum; B: Golgi

apparatus

 Lysosomes are small, irregularly shaped organelles in

which intracellular digestion occurs, releasing
nutrients from food particles and breaking down
unwanted molecules for recycling or excretion. And
peroxisomes are small, membrane-enclosed vesicles
that provide a contained environment for reactions in
which hydrogen peroxide, a dangerously reactive
chemical, is generated and degraded. Membranes also
form many different types of small vesicles involved in
the transport of materials between one membraneenclosed organelle and another.
Animal cells can engulf very large particles, or even
entire foreign cells, by this process of endocytosis.
The reverse process, exocytosis, whereby vesicles
from inside the cell fuse with the plasma membrane
and release their contents into the external medium, is
also a common cellular activity.

The Cytosol is a Concentrated aqueous

gel of large and small Molecules
The cytosol is the part of the cytoplasm that is not
partitioned off within intracellular membranes. In most
cells, the cytosol is the largest single compartment. It
contains a host of large and small molecules, crowded
together so closely that it behaves more like a waterbased gel than a liquid solution. The cytosol is the site
of many chemical reactions that are fundamental to
the cells existence. The early steps in the breakdown
of nutrient molecules take place in the cytosol, for
example, and it is here that the cell performs one of its
key synthetic processesthe manufacture of proteins.
Ribosomes, the molecular machines that make the
protein molecules, are visible with the electron
microscope as small particles in the cytosol, often

The Cytoskeleton is responsible for

directed Cell Movements
In eucaryotic cells the cytosol is criss-crossed by long,
fine filaments of protein. Frequently the filaments are
seen to be anchored at one end to the plasma
membrane or to radiate out from a central site
adjacent to the nucleus. This system of filaments is
called the cytoskeleton. The thinnest of the filaments
are actin filaments, which are present in all
eucaryotic cells but occur in especially large numbers
inside muscle cells. The thickest filaments are called
microtubules, because they have the form of minute
hollow tubes. In dividing cells they become
reorganized into a spectacular array that helps pull the
duplicated chromosomes in opposite directions and

 Intermediate in thickness between

actin filaments and microtubules are
the intermediate filaments, which
serve to strengthen the cell
mechanically. These three types of
filaments, together with other
proteins that attach to them, form a
system of girders, ropes, and motors
that gives the cell its mechanical
strength, controls its shape, and
drives and guides its movements.

Plastids
Theplastidis a majororganellefound in thecellsof
plants andalgae.Plastids are the site of
manufacture and storage of important chemical
compounds used by the cell. All plastids are derived
fromproplastids. Undifferentiated plastids
(proplastids) may develop into any of the following
variants:
Chloroplastsgreen plastids: forphotosynthesis
Chromoplastscoloured plastids: for pigment
synthesis and storage.
Leucoplasts colourless plastids are organelles
where starch, oil and protein are stored.

Figure: A eukaryotic
animal cell

Figure: A eukaryotic
animal cell

Applications
Hemocytometer (or
haemocytometer or counting
chamber)a specimen slide
which is used to determine the
concentration of cells in a liquid
samplefrequently used to
determine the concentration of
blood cellsbut also the
concentration of sperm cells in a
samplea grid (an arrangement
of squares of different sizes) is
etched into the glass of the
hemocytometerallows for an
easy counting of cells.

Loading the
hemocytometer
Both the hemocytometer
and its coverslip (specially
made to be thicker) should
be clean.
Then place the pipette tip
with your sample into one
of the V-shaped wells and
gently expel the sample.
The area under the
coverslip fills by capillary
action.
You can load two samples
on one hemocytometer

Counting the cells

Cells that are on the
line of a grid require
special attention. Cells
that touch the top and
right lines of a square
should not be
counted, cells on the
bottom and left side
should be counted
using a microscope.

To distinguish between dead

and viable cells
The sample is often diluted
with a particular stain, such as
Trypan blue. This staining
method, also known as dye
exclusion staining, uses a diazo
dye that selectively penetrates
cell membranes of dead cells,
coloring them blue, whereas it
is not absorbed by membranes
of live cells, thus excluding live
cells from staining. When
viewed under a microscope,
dead cells would appear as
dark blue.

Flow cytometry
Itis alaser-based, biophysical technology
employed incell counting,cell
sorting,biomarkerdetection andprotein
engineering, by suspendingcellsin a stream of
fluid and passing them by an electronic detection
apparatus. It performs this ananlysis by passing
thousands of cells per second through a laser
beam & capturing the light that emerges from
each cell as it passes through.
Gathered data is statistically analyzed to report
cellular characteristics such as size, complexity,
phenotype and health

Working:
The sample is transported through the interrogation point. The particles
or cells are passed one by one through the laser beam.
A number of detectorsone in line with the light beam (Forward
Scatteror FSC) and several perpendicular to it (Side Scatter or SSC)
and one or morefluorescence detectors.
Each suspended particle from 0.2 to 150 micrometers passing through
the beam scatters the ray, and fluorescent chemicals found in the
particle or attached to the particle may beexcitedinto emitting light at
a longer wavelength than the light source. This combination
ofscatteredandfluorescentlight is picked up by the detectors, and, by
analysing fluctuations in brightness at each detector (one for
eachfluorescent emission peak), it is then possible to derive various
types of information about the physical and chemical structure of each
individual particle. FSC correlates with thecellvolume and SSC
depends on the inner complexity of the particle (i.e., shape of
thenucleus, the amount and type of cytoplasmicgranules or
themembraneroughness). This is because the light is scattered off of
the internal components of the cell.

Cell fractionation
It is the separation of homogeneous sets from
a larger population of cells.
Homogenization
Tissue is typically homogenized in
anisotonicbuffer solution, as well as a pH
buffer by use of a variety of mechanisms such
as grinding, chopping, pressure changes,
osmotic shock, freeze-thawing, and ultra-sound
homogenization. This is done to stop osmotic
damage. The samples are then kept cold to
prevent enzymatic damage .

 Filtration
This step may not be necessary
depending on the source of the cells.
Animal tissue however is likely to yield
connective tissue which must be
removed. Commonly, filtration is
achieved either by pouring through
gauze or with a suction filter.
Purification
Invariably achieved byDifferential
centrifugation- the sequential increase
in gravitational force results in the
sequential separation of organelles
according to their density.

Microfluidic cell culture

Cell culture is a key step in cell
biology, tissue engineering,
biomedical engineering, and
pharmacokinetics for drug
development. Microfluidic systems
can provide an in vivo-like
environment for a cell culture as well
as a reaction environment for a cellbased assay.