Chapter 1: Cell structure

Cell definition

 The cell (from Latin cella, meaning "small room is the basic
structural, functional, and biological unit of all known living
organism. A cell is the smallest unit of life. Cells are often called
the "building blocks of life". The study of cells is called cell biology.

 Cells consist of cytoplasm enclosed within a membrane, which

contains many biomolecules such as proteins andnucleic acids.
Organisms can be classified as unicellular (consisting of a single
cell; including bacteria)
or multicellular (including plants and animals). While the number
of cells in plants and animals varies from species to
species, humans contain more than 10 trillion (1013) cells. Most
plant and animal cells are visible only under a microscope, with
dimensions between 1 and 100 micrometers.

 Cells were discovered by Robert Hooke in 1665

Levels of Organization
Cells are the basic unit of Structure and Function!
 Cell biology and microscopy

 Cells can now be studied by many different methods, but

scientists began simply by looking at them, using various types of
microscope.

 There are two fundamentally different types of microscope now in

use: The light microscope and the electron microscope. Both use
a form of radiation in order to create an image of the specimen
being examined. The light microscope uses light as a source of
radiation, while the electron microscope uses electrons.

Light microscope
 Light Microscopes, or Optical Microscopes, as they are more
correctly termed, use light and several lenses in order to magnify
a sample. Light from the Condenser Lens, and then through
the Specimen where certain wavelengths are filtered to produce
an image. The light then passes through the Objective Lens, which
focuses it and can be changed in order to alter the magnification.
Finally, the light passes through the Eyepiece Lens, which can also
be changed to alter the magnification, and into the eye.

 The maximum magnification of light microscopes is

usually ×1500, and their maximum resolution is 200nm, due to
the wavelength of light. An advantage of the light microscope is
that it can be used to view a variety of samples, including whole
living organisms or sections of larger plants and animals. It is
also relatively inexpensive.

 They have two eyepieces to produce a 3D stereoscopic view.

Many specimens require preparation before being viewed by a
light microscope, as some may not be colored or might distort
when cut. Samples are Stained with colored stains that bind to
certain chemicals or cell structures

Electron microscope

 The electron microscope is a type of microscope that uses a beam

of electrons to create an image of the specimen. Electrons have a
much lower wavelength than light (100000 times shorter in fact,
at 0.004nm) which means that they can be used to produce an
image with resolution as great as 0.5nm. Electron Microscopes
can have magnifications of ×500000.
 There are different types of Electron Microscope. A Transmission
Electron Microscope (TEM) produces a 2D image of a thin
sample, and has a maximum magnification of ×500000.

 A Scanning Electron Microscope (SEM) produces a 3D image of a

sample by ‘bouncing’ electrons off and detecting them at multiple
detectors. It has a maximum magnification of about ×100000.

 The preparation of a sample for electron microscopy is a complex

process. It may involve

 Chemical Fixation: Stabilising an organism/sample’s mobile

macrostructure

 Cryofixation: Freezing the sample very rapidly to preserve

its state

 Dehydration: Removing the water from a specimen, for

example, by replacing it with ethanol

 Sectioning: Cutting the sample into thin strips that are

semitransparent to electrons, for example with a diamond
knife

 Staining: Using heavy metals to scatter electrons and

produce contrast

 Freeze Fracturing: Freezing the sample rapidly, and then

fracturing it, for example, when viewing cell membranes

 It is advantageous to use an Electron Microscope in many

situations because they offer a much higher resolution than Light
Microscopes, so they can be used to image very small objects in
detail, and also because of the 3D images that SEMs offer.
However, samples must be placed in a vacuum as electrons are
deflected by particles in the air, they are very expensive to buy
and maintain, and preparing the samples requires a lot of skill to
do. It Requires extremely stable high voltage supplies
 Electron vs. Light

Magnification and resolution

 Magnification is the number of times larger an image is, than the

real size of the object.

 Resolution is the amount of information that can be seen in the

image - defined as the smallest distance below which two
discrete objects will be seen as one.

 Where M is the magnification, I is the observed size of the image

(that is what you can measure with a ruler. A is the actual size.

 Resolution equal half the wavelength of the radiation used.

 Graticule calibration

 Eyepiece graticules allow the size of a specimen to be measured.

 The eyepiece graticule is a glass disc fitted into the eyepiece of the
microscope. These can be fitted to existing eyepieces or eyepieces
can be purchased with graticules already fitted. The disc is marked
with a scale from 0 to 100. The absolute size of the scale is not
important as this is what will be calibrated.

Stage micrometer

 The stage micrometer is used to calibrate the eyepiece graticule.

A stage micrometer consists of a microscope slide on which is
engraved a small and accurate scale. Because the scale has to be
 accurately produced to give reference dimensions, stage
micrometers are much more expensive than eyepiece graticule.

Method

 The scale on the stage micrometer is aligned with the scale of the
eyepiece graticule and then a reading is taken from the scales.
These readings are then used to calculate the calibration factor
for the objective lens in use. The following example shows how to
calibrate the graticule for the x40 objective lens:

 Reading from the two scales we find 100 divisions on the eyepiece
graticule equals 25.9 divisions on the stage micrometer.

 For the particular stage micrometer we are using 100 divisions =

1mm (this information is marked on the stage micrometer).

 Each division is 1/100 mm = 10µm

 100 eyepiece div = 25.9*10 µm

 1 eyepiece div = 259/100 µm =2.59 µm

 Cells

Two fundamental types: Prokaryotic no Nucleus very few

organelles Small 100nm-5um

Eukaryotic True Nucleus Membrane bound organelles

10-100um some are larger
 Comparison table between Prokaryotic and Eukaryotic cells
Cell Characteristics
Featured in organisms
Origin
Size of the cell
Cell number
Nucleus of the cell
Nuclear membrane or Nucleolus
The genetic material-
Deoxyribonucleic acid(DNA)
Plasma Membrane or
Cytoplasmic Membrane or Outer
Membrane (phospholipid bilayer)
Chromosomes
Reproduction
Cell wall
organelle membrane
Prokaryotic Cells Eukaryotic Cells
Domain Bacteria and plants, animals, fungi, algae.
Archae
3.5 billion years ago 1.5 billion years ago
0.5-5 micrometer in 5 micrometer in diameter or
diameter or may be less more
Single-celled Multicellular
Absent Present
Absent Nucleus enclosed within the
Nuclear membrane
DNA is freely floating , DNA is linear and bound by
circular and is naked nuclear membrane
Lacks steroid Consists of steroid and
carbohydrates
Contain Histone-like Contain Histone proteins
proteins
By binary fission Mitotic and meioitic division
seen
Contains peptidoglycan (a Animal cells lack cell wall.
polysaccharide combine Others have either cellulose or
with amino acids) chitin
- Some organelles are bounded
 by a single membrane
( lysosomes, golgi body,
vacuoles)
Some are bounded by two
membranes( mitochondria,
chloroplast and nucleus)
Some have no membrane
(ribosome, centrioles,
microtubules)
Capsules-slimy coverings Present in bacterial cells Absent
Ribosomes 70S type( 20 nm) 80S type (25nm). Though
mitochondria and chloroplast
have 70S type
Mitochondria Absent Present
Chloroplast Absent Present in plants
Endoplasmic Reticulum Absent Present
Golgi apparatus Absent Present
Gas vacuoles May be present Present
Membrane vacuoles Absent Present
Centrioles Absent Present
Lysosymes Absent Present

Cell Organelles

What are cell organelles?

 Cell organelles are the internal organs of a cell responsible for

carrying out specific jobs to keep the cell alive. In fact, the
word organelle is just a big word which means small organ.
These organelles are responsible for providing all the needs of
the cell. They work to bring in food supplies, get rid of waste,
protect the cell, repair the cell, and help it grow or reproduce.

Structures and functions of organelles

Nucleus:

The nucleus is the largest cell organelle that you can see under a
microscope. It often has a spherical or oval shape and is located in
 the middle of the cell. It is surrounded by a double membrane
called the nuclear envelope. The outer membrane is continuous
with the endoplasmic reticulum. The nuclear envelope separates
the contents of the nucleus from the cytoplasm. There are several
tiny pores in the nuclear envelope through which substances pass
between the nucleus and the cytoplasm. Examples of substance
leaving the nucleus are mRNA and ribosome for protein synthesis.
Examples of substances entering are proteins to help make
ribosomes, nucleotides, and ATP.

 Within the nucleus, the chromosomes are in a loosely coiled state

known as chromatin (except during nuclear division).
Chromosomes contain DNA, which is organised into functional
units called genes. Genes control the activities of the cell and
inheritance; thus the nucleus controls the cell’s activities. When a
cell is about to divide, the nucleus divide first so that each new
cell will have its own nucleus.

 Also within the nucleus, the nucleolus makes ribosomes, using

the information in its own DNA.
 Endoplasmic reticulum

 The ER functions as a manufacturing and packaging system. It

works closely with the Golgi apparatus, ribososmes, mRNA, and
tRNA.

Structurally, the endoplasmic reticulum is a network of

membranes found throughout the cell and connected to the
nucleus. The membranes are slightly different from cell to cell and
a cell’s function determines the size and structure of the ER. For
example, some cells, such as prokaryotes or red blood cells, do
not have an ER of any kind. Cells that synthesize and release a lot
of proteins would need a large amount of ER. You might look at a
 cell from the pancreas or liver for good examples of cells with
large ER structures.

 Rough and Smooth

 There are two basic types of ER. Rough and smooth ER. Both
rough ER and smooth ER have the same types of membranes but
they have different shapes. Rough ER looks like sheets or disks of
bumpy membranes while smooth ER looks more like tubes. Rough
ER is called rough because it has ribosomes attached to its
surface.

 Smooth ER (SER) acts as a storage organelle. It is important in the

creation, and the storage of lipids and steroids such as
cholesterol and the reproductive hormones oestrogen and
testosterone. Cells in your body that release oils also have more
SER than most cells.

 Rough ER (RER) was also mentioned in the section on ribosomes

and is very important in the synthesis and packaging of proteins.
Ribosomes are attached to the membrane of the ER, making it
“rough.” The RER is also attached to the nuclear envelope that
surrounds the nucleus. This direct connection between the
perinuclear space and the lumen of the ER allows for the
movement of molecules through both membranes.

 The process of protein synthesis starts when mRNA moves from

the nucleus to a ribosome on the surface of the RER. Then
the proteins folded into correct shapes, collected and pinches off
a vesicle. That vesicle, a small membrane bubble, can move to
the cell membrane or the Golgi apparatus. Some of the proteins
will be used in the cell and some will be sent out into intercellular
space.
 Golgi body or (Golgi apparatus)

 The Golgi complex is referred to as the manufacturing and the

shipping center of the eukaryotic cell. The Golgi apparatus or the
Golgi body or Golgi complex or Golgi is a cellular organelle present
in most of the cells of the eukaryotic organisms.

Golgi apparatus Function

 The cell synthesizes a huge amount of variety of macromolecules.

The main function of the Golgi apparatus is to modify, sort
 and package the macromolecules that are synthesized by the cells
for secretion purposes or for use within the cell.

 It mainly modifies the proteins that are prepared by the rough

endoplasmic reticulum by the addition of carbohydrates and
phosphate by the process of glycosylation and phoshphorylation
respectively..

 They are also involved in the transport of lipid molecules around

the cell.

 They also create lysosomes.

 The Golgi complex is thus referred as post office where the

molecules are packaged, labelled and sent to different parts of the
cell. In order to modify the proteins the golgi
complex imports substances like nucleotides from the cytosol of
the cell and by the removal of the first amino acid, methionine.

 The Golgi complex also plays an important role in the production

of proteoglycans. The proteoglycans are molecules that are
present in the extracellular matrix of the animal cells.

 The Golgi involves in the sulfation process of certain molecules.

 The process of phosphorylation of molecules by the Golgi requires

the import of ATP into the lumen of the Golgi.
 Lysosome

Lysosome structure

 Lysosomes are spherical sacs, surrounded by a single membrane

and having no internal structure. They are commonly 0.1-0.5
in diameter. They contain digestive (hydrolytic) enzymes which
must be kept separate from the rest of the cell to prevent damage
from being done.

Lysosome function

 Lysosomes are responsible for the breakdown of unwanted

structures such as old organelles or even whole cells as in
mammary glands after lactation (breast feeding). In white blood
cells, lysosomes are used to digest bacteria. Enzymes are
sometimes released outside the cell. The heads of the sperm
contain a special lysosome, the acrosome for digesting a path to
the egg.
 Mitochondria

 Mitochondria are known as the powerhouses of the cell. They

are organelles that act like a digestive system which takes in
nutrients, breaks them down, and creates energy for the cell. The
biochemical processes of the cell are known as cellular
respiration. Many of the reactions involved in cellular respiration
happen in the mitochondria. Mitochondria are the working
organelles that keep the cell full of energy. Some cells have
several thousand mitochondria while others have none. Muscle
cells need a lot of energy so they have loads of mitochondria
 Structure of Mitochondria

 Mitochondria are shaped perfectly to maximize their productivity.

They are made of two membranes. The outer membrane covers
the organelle and contains it like a skin. The inner
membrane folds over many times and creates layered structures
called cristae. The fluid contained in the mitochondria is called
the matrix. The space between the two membranes is called the
intermembrane space

 The folding of the inner membrane increases the surface area

inside the organelle. Since many of the chemical reactions happen
on the inner membrane, the increased surface area creates more
space for reactions to occur. If you have more space to work, you
can get more work done. Similar surface area strategies are used
by microvilli in your intestines.

What’s in the matrix? Mitochondria are special because they have

their own ribosomes and DNA floating in the matrix. There are
also structures called granules which may control concentrations
of ions. Cell biologists are still exploring the activity of granules.

Function of mitochondria

 As we have seen the main function of mitochondria is to carry out

aerobic respiration, although they do have other functions, such
as the synthesis of lipids. During respiration, a series of reactions
takes place in which energy is released from energy-rich
molecules such as sugars and fats. Most of this energy is
transferred to molecules of ATP. ATP (adenosine triphosphate) is
 the energy carrying molecule found in all living cells. It is known as
the universal energy carrier.

 The reactions of respiration take place in solution in the matrix

and the inner membrane (cristae). Once made, ATP leaves the
mitochondrion and as it is soluble molecule, it can spread rapidly
to all parts of the cell where energy is needed. Its energy is
released by breaking the molecule down to ADP (adenosine
diphosphate). This reaction is called hydrolysis reaction. The ADP
can then be recycled into a mitochondrion for conversion back to
ATP during aerobic respiration.

The endosymbiont theory

 How did the eukaryotes become so complicated? And where did

these battery-like organelles come from?

 We think we know part of the answer. Eukaryotic cells may have

evolved when multiple cells joined together into one. They began
to live in what we call symbiotic relationships. The theory that
explains how this could have happened is called endosymbiotic
theory. An endosymbiont is one organism that lives inside of
another one.

 In the 1960s, it was discovered that mitochondria and

chloroplasts contain ribosomes which are slightly smaller than
those in the cytoplasm and are the same size as those found in
bacteria. The size of ribososmes is measured in (Svedberg) S unit
which are a measure of how fast they sediment in a centrifuge.
Cytoplasmic ribosomes are 80S while those of bacteria,
mitochondria and chloroplast are 70S.
 It was also discovered that mitochondria and chloroplast contain
small, circular DNA molecules also like those found in bacteria.

 It was later proved that mitochondria and chloroplasts are, in

effect, ancient bacteria which now live inside the larger cells
typical of animals and plants.

Cell surface membrane

 The cell membrane (also known as the plasma

membrane or cytoplasmic membrane) is a biological membrane
that separates the interior of all cells from the outside
environment (the extracellular space). It consists of a lipid
bilayer with embedded proteins. The basic function of the cell
membrane is to protect the cell from its surroundings. The cell
membrane controls the movement of substances in and out of
cells and organelles
 Microvilli

 Microvilli (singular: microvillus) are microscopic cellular

membrane protrusions that increase the surface area for diffusion
and minimize any increase in volume, and are involved in a wide
variety of functions, including absorption, secretion, and cellular
adhesion.

Microtubules

 Microtubules are long, rigid, hollow tubes found in the cytoplasm.

They are very small, about 25nm in diameter. Together with actin
filament and intermediate filament they make up the
cytoskeleton an essential structural component that helps to
determine cell shape.
 Microtubules are made of a protein called tubulin. Tubulin has
two forms, α- tubulin and β –tubulin. Alpha and beta tubulin
molecules combine to form dimers (double molecules).

 These dimers are then joined end to end to form long

protofilaments. This is an example of polymerisation. Thirteen
protofilaments line up alongside each other in a ring to form a
cylinder with a hollow center.

Function of Microtubules

1. The main function is to help support and give shape to the cell.
They also serve a transportation function, as they are the routes
upon which organelles move through the cell. Microtubules have
many more jobs than just giving support to the cell. The
microtubules also play a very important role during cell division.
Their primary cell division function is to connect to the
chromosomes, help those chromosomes complete their first split,
and then move the new chromosomes to their places in the new
daughter cells.

2. This job is carried out by microtubules that make up the

centrioles, organelles that have been given the specific job of
helping cells divide. After cell division has finished, those same
microtubules return to their functions in other parts of the cell.

3. Other than support, organelle movement, and cell division,

microtubules also play a part in forming large structures on the
outside of the cells. Microtubules can combine in very specific
bundles to form cilia and flagella for cell movement.
 Centrioles and centrosomes

 In cell biology, the centrosome is an organelle that serves as the

main microtubule organizing center (MTOC) of the animal cell as
well as a regulator of cell-cycle progression. Centrosomes are
composed of two centrioles arranged at right-angles to each
other. Centrioles and centrosomes are absent from most plant
cells.

 A centriole is a hollow cylinder about 500 nm long, formed from a

ring of short microtubules. Each centriole contains nine triplets of
microtubules.
 In higher animal cells the centrioles form the mitotic poles.

 The centrioles function as the microtubule organizing center, it is

an important event in major cellular process, that is cell division
and flagella formation.

 In the prophase stage the centriole pairs start moving towards the
opposite poles of the cell, and also forming the spindle
simultaneously.

 The spindle fibers are responsible for the segregation

of chromosomes into the daughter cells..

 At end of each cell cycle, the cell has two centrioles - one the
mother centriole and the other newly formed centriole which is
the daughter centriole.

 After segregation, the centrioles determine the position of the

nucleus and also influence the cellular organization in the new
formed daughter cells.

 The centrioles may produce flagella or cilia.

 The fiber of the tail of sperms also arises from the centriole.

 The dysfunctioning of the centrosome is also responsible for the

development of certain cancers.
 Chloroplast

 Chloroplasts are the food producers of the cell. The organelles are
only found in plant cells and some protists such as algae. Animal
cells do not have chloroplasts. Chloroplasts work to convert light
energy of the Sun into sugars that can be used by cells. The entire
process is called photosynthesis and it all depends on the little
green chlorophyll molecules in each chloroplast.

Structure of Chloroplast

 Choloroplasts tend to have an elongated shape and a diameter of

about (compare diameter for mitochondria); they are
surrounded by two membranes forming the chloroplast envelope.
 Also like mitochondria replicate independently of cell division by
dividing into two.

Parts of chloroplast

 Outer membrane – It is a semi-porous membrane and is

permeable to small molecules and ions, which diffuses easily. The
outer membrane is not permeable to larger proteins.

 Intermembrane Space – It is usually a thin intermembrane space

about 10-20 nanometers and it is present between the outer and
the inner membrane of the chloroplast.

 Inner membrane – The inner membrane of the chloroplast forms

a border to the stroma. It regulates passage of materials in and
out of the chloroplast. In addition of regulation activity, the fatty
acids, lipids and carotenoids are synthesized in the inner
chloroplast membrane.

 Stroma- Stroma is an alkaline, aqueous fluid which is protein rich

and is present within the inner membrane of the chloroplast. The
space outside the thylakoid space is called the stroma. The
chloroplast DNA chlroplast ribosomes and the thylakoid sytem,
starch granules and many proteins are found floating around the
stroma.

 Thylakoid System- The thylakoid system is suspended in the

stroma. The thylakoid system is a collection of membranous sacks
called thylakoids. The chlorophyll is found in the thylakoids and is
the sight for the process of light reactions of photosynthesis to
happen. The thylakoids are arranged in stacks known as grana.
Each granum contains around 10-20 thylakoids.
 Function of chloroplast

 Photosynthesis has two stages. In the first stage, the light-

dependent reactions occur. These reactions capture sunlight
through chlorophyll and carotenoids to form adenosine
triphosphate (ATP, the energy currency of the cell) and
nicotinamide adenine dinucleotide phosphate (NADPH), which
carries electrons. The second stage consists of the light-
independent reactions, also known as the Calvin cycle. In the
Calvin cycle, the electrons carried by NADPH convert inorganic
carbon dioxide and to an organic molecule in the form of a
carbohydrate, a process known as CO2 fixation. Carbohydrates
and other organic molecules can be stored and used at a later
time for energy.

Animal and plant cell

How do plant cells differ from animal cells?

 Plant cells have different structures

 Contains:

◦ Cell wall

◦ Chloroplast

 Site of photosynthesis

◦ Vacuole (large central, takes up most part of cell)

Animal cell
 Cell walls and plasmodesmata

 With a light microscope, individual plant cells are more easily seen
than animal cells, because they are usually larger and, unlike
animal cells, surrounded by a cell wall outside the cell membrane.
This is relatively rigid because it contains fibers of cellulose, a
polysaccharide which strength the wall. The cell wall gives the cell
a definite shape.

 It prevents the cell from bursting when water enters by osmosis,

allowing large pressure to develop inside the cell. Cell walls may
also reinforced by extra cellulose or hard material called lignin for
extra strength.

 Cell walls are freely permeable, allowing free movement of

molecules, ions to cell surface membrane.

 Plant cells are linked to neighboring cells by fine strands of

cytoplasm called plasmodesmata (singular: plasmodesma).
 Vacuoles

 Vacuoles are storage bubbles found in cells. They are found in

both animal and plant cells but are much larger in plant cells.
Vacuoles might store food or any variety of nutrients a cell might
need to survive. They can even store waste products so the rest of
the cell is protected from contamination. Eventually, those waste
products would be sent out of the cell.

 The structure of vacuoles is fairly simple. There is

a membrane that surrounds a mass of fluid is called tonoplast. In
that fluid are nutrients or waste products. Plants may also use
vacuoles to store water. Those tiny water bags help to support the
plant and may contain pigments which colour the petals of certain
flowers.

 In plant cells, the vacuoles are much larger than in animal cells.
When a plant cell has stopped growing, there is usually one very
large vacuole. Sometimes that vacuole can take up more than half
of the cell's volume.
 Virus

 Virus, an infectious agent of small size 20-300 nm (about 50 times

smaller than bacteria).

 In fact, viruses should not even be considered organisms, in the

strictest sense, because they are not free-living; i.e., they cannot
reproduce and carry on metabolic processes without a host cell
(animal, plant and bacteria).

 All true viruses contain nucleic acid—

either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid)—
and protein.
 In virtually all viruses, at least one of these proteins forms a shell
(called a capsid) around the nucleic acid.

 The capsomere is a subunit of the capsid,