Module 1: Cell and Molecular Biology

Cell Structure

Objectives:

• Describe and interpret drawings and electron micrographs of the

structure of membrane systems and organelles of typical plant and
animal cells
• Make drawings of typical plant and animal cells as seen under the light
microscope (differences between electron and light microscopes as
well as differences between resolution and magnification to be
included.)
• Outline the functions of membrane systems and organelles
• Compare the structures of typical plant and animal cells
• Describe the structure of a prokaryotic cell
• Compare the structure of prokaryotic cells with that of eukaryotic cells
• Explain the concepts of tissue and organs using as an example the
dicotyledonous root.
• Make plan drawings to show the distribution of tissues within an organ
such as the dicot root.

Electron Microscopy

What are Electron Microscopes?

Electron Microscopes are scientific instruments that use a beam of
highly energetic electrons to examine objects on a very fine scale. This
examination can yield the following information:
• Topography: the surface features of an object or "how it looks", its
texture
• Morphology: the shape and size of the particles making up the object
• Composition: the elements and compounds that the object is
composed of and the relative amounts of them
• Crystallographic Information: how the atoms are arranged in the object

Where did Electron Microscopes come From?

Electron Microscopes were developed due to the limitations of Light
Microscopes which are limited by the physics of light to 500x or 1000x
 magnification and a resolution of 0.2 micrometers. In the early 1930's
there was a scientific desire to see the fine details of the interior
structures of organic cells (nucleus, mitochondria...etc.) and this
required 10,000x plus magnification which was just not possible using
light microscopes.
The Transmission Electron Microscope (TEM) was the first type of
Electron Microscope to be developed and is patterned exactly on the
Light Transmission Microscope except that a focused beam of
electrons is used instead of light to "see through" the specimen.

How do Electron Microscopes Work?

Electron Microscopes (EMs) function exactly as their optical counterparts

(light microscopes) except that they use a focused beam of electrons
instead of light to "image" the specimen and gain information as to its
structure and composition.

Light Microscopy

The light microscope, so called because it employs visible light to detect

small objects, is probably the most well-known and well-used research tool in
biology.
Fig 1: Light microscope.

Magnification and Resolution

Magnification is how much bigger a sample appears to be under the

microscope than it is in real life.

Overall magnification = Objective lens x

Eyepiece lens

Resolution is the ability to distinguish between two points on an image i.e.

the amount of detail

Resolution consists of the capacity to show minute details of an object

distinctly, and is determined by the aperture of the beam of light that enters
the objective (the eyepiece in general has little effect on the resolution of the
microscope).

Cell Structure
 M- Mitochondrion
V-vacuole
ER-Endoplasmic reticulum
C- Chloroplast
Go-Golgi body
CW-Cell wall
N- Nucleus

Fig 2: electron micrograph of a plant cell

A B C

Fig 3: A- Mitochondrion, note the highly folded inner membrane into cristae.
External to the mitochondrion are the rough endoplasmic reticulum studded
with ribosomes, the sites of protein synthesis; B-chloroplast, G indicates the
presence of granules, which are the sites of starch storage. Non-
membranous regions indicate the sites of the dark reactions of
photosynthesis. Stacks of photosynthetic membranes are the sites of the
light reactions of photosynthesis and also where chlorophyll resides; C- Golgi
body, site of packaging and modification of synthesized proteins from the
ribosomes.
Fig 4: Electron micrograph of animal cell

Membrane Systems

The membrane system of a cell performs many important functions. This

system controls the entrance and exit of substances into and out of the cell,
and also provides for the manufacture and packaging of substances within
the cell. The membrane system of the cell consists of the plasma membrane,
which encloses the cell contents; the endoplasmic reticulum, which
manufactures lipids and proteins; the Golgi body, which packages
substances manufactured within the cell; and various vesicles, which
perform different functions.

The Plasma Membrane

The plasma membrane of the cell is often described as "selectively

permeable;" that is, the plasma membrane is designed so that only certain
substances are allowed to pass through. The plasma membrane is composed
of two layers of molecules called phospholipids. Each phospholipid molecule
consists of a phosphate "head" and two fatty acid chains tails.

The orientation of these two sections of the phospholipid molecule is crucial

to the functioning of the plasma membrane. The phosphate region is
hydrophilic (literally, "water-loving") and attracts water. The fatty acid region
is hydrophobic (literally, "water-hating") and repels water. In the
phospholipid bilayer of the plasma membrane, the phospholipid layers are
arranged so that the two phosphate hydrophilic regions face outward,
towards the watery extracellular environment, and inward, towards the
cellular cytoplasm, which also contains water. The two hydrophobic fatty acid
portions of the chains face each other, forming a water-tight shield. The
plasma membrane, then, is both water-proof and water-attracting. It
functions both as a boundary between the cell's contents and the external
cellular environment, yet also allows the transport of water-containing and
other substances across its boundaries.

Endoplasmic Reticulum

The endoplasmic reticulum (meaning "within the cytoplasm" and "net")

consists of flattened sheets, sacs, and tubes of membrane that cover the
entire expanse of a eukaryotic cell's cytoplasm. This internal system of
membrane is continuous with the double membrane that surrounds the cell's
nucleus. Therefore, the encoded instructions that the nucleus sends out for
the synthesis of proteins flow directly into the endoplasmic reticulum. Within
the cell, the endoplasmic reticulum synthesizes lipids and proteins. The
proteins that the endoplasmic reticulum synthesizes, such as enzymes, are
exported from the cell to perform various functions in the body. Proteins that
are made in the cell for use by the cell-for instance, as channels in the
plasma membrane-are made by the free ribosomes that are situated within
the cytoplasm.

Two types of endoplasmic reticulum are found in the eukaryotic cell. Rough
endoplasmic reticulum is studded with ribosomes on its outer face. These
ribosomes are the sites of protein synthesis. Once a protein is synthesized on
a ribosome, it is enclosed within a vesicle, a small, membrane-bound
"bubble." The vesicle travels to another organelle, the Golgi body. Within the
Golgi body, the proteins within the vesicle are further modified before they
are exported from the cell. Cells that specialize in protein secretion contain
large amounts of rough endoplasmic reticulum. For instance, beta cells of
the pancreas that produce the protein insulin, have abundant rough
endoplasmic reticulum.

The other type of endoplasmic reticulum is smooth endoplasmic reticulum.

Smooth endoplasmic reticulum does not have ribosomes and is the site of
lipid metabolism. Here, macromolecules containing lipids are broken down
into their constituent parts. In addition, smooth endoplasmic reticulum
functions in the synthesis of lipid-containing macromolecules. Smooth
endoplasmic reticulum is not as common in cells as rough endoplasmic
reticulum. Large amounts of smooth endoplasmic reticulum are found in cells
that specialize in lipid metabolism. For instance, liver cells remove alcohol
and drugs from the bloodstream. Liver cells have an impressive network of
smooth endoplasmic reticulum. Similarly, cells of the ovaries and testes,
which produce the lipid-containing hormones estrogen and testosterone,
contain large amounts of smooth endoplasmic reticulum.

The Golgi Body

The Golgi body is one of the most unusually shaped organelles. The Golgi
body consists of stacked, membrane-bounded, flattened sacs. Surrounding
the Golgi body are numerous, small, membrane-bounded vesicles. The Golgi
body and its vesicles function in the sorting, modifying, and packaging of
macro-molecules,such as lipids or proteins, that are secreted by the cell or
used within the cell for various functions.

The Golgi body can be compared to the shipping and receiving department
of a large company. Each Golgi body within a cell has a cis face, which is
analogous to the receiving division of the department. Here, the Golgi body
receives macromolecules synthesized in the endoplasmic reticulum encased
within vesicles. The trans face of the Golgi body is analogous to the shipping
division of the department, and is the site from which modified and
packaged macromolecules are transported to their destinations.

Within the Golgi body, various chemical groups are added to the
macromolecules so ensure that they reach their proper destination. In this
way, the Golgi body attaches an "address" to each macromolecule it
receives. For example, cells called goblet cells in the lining of the intestine
secrete mucous. The protein component of mucous, called mucin, is modified
in the Golgi body by the addition of carbohydrate groups. From the Golgi
body, the modified mucin is packaged within a vesicle. The vesicle
containing its mucous cargo fuses with the plasma membrane of the goblet
cell, and is released into the extracellular environment.

Vesicles

Vesicles are small, membrane-bounded spheres that contain various

macromolecules. Some vesicles are used to transport macromolecules from
the endoplasmic reticulum to the Golgi body and from the Golgi body to
various destinations. Special kinds of vesicles perform other functions as
well.
Lysosomes are vesicles that contain enzymes involved in cellular digestion.
Some protists, for instance, engulf other cells for food. In a process called
phagocytosis, the protist surrounds a food particle and engulfs it within a
vesicle. This food containing vesicle is transported within the protist's
cytoplasm until it comes into contact with a lysosome. The food vesicle and
lysosome merge, and the enzymes within the lysosome are released into the
food vesicle. The enzymes break the food down into smaller parts for use by
the protist.

Lysosomes, however, are found in all kinds of cells. In all cells, lysosomes
digest old, worn-out organelles. They also play a role in cell death, known as
apoptosis. Cell death is a component of normal developmental processes.
For instance, a human fetus has web-like hands and feet. As the fetus
develops, the cells that compose these webs slowly self-destruct, freeing the
fingers.

Peroxisomes contain hydrogen peroxide. Peroxisomes function in the

oxidation of many materials, including fats. In oxidation, oxygen is added to
a molecule. When oxygen is added to fats, hydrogen peroxide is formed. The
oxidation of fats takes place within the membranes of peroxisomes so that
the harmful chemical does not leak out into the cell's cytoplasm.

The Nucleus

The nucleus is the control center of the cell. Under a microscope, the nucleus
looks like a dark blob, with a darker region, called the nucleolus, centered
within it. The nucleolus is the site where the subunits of ribosomes(70s and
80s subunits) are manufactured. Surrounding the nucleus is a double
membrane called the nuclear envelope. The nuclear envelope is studded all
over with tiny openings called nuclear pores.

The nucleus directs all cellular activities by controlling the synthesis of

proteins. The nucleus contains encoded instructions for the synthesis of
proteins in a helical molecule called deoxyribonucleic acid (DNA). The cell's
DNA is packaged within the nucleus in a structural form called chromatin.
Chromatin consists of DNA wound tightly around spherical proteins called
histones. When the cell prepares to divide, the DNA unwinds from the
histones and assumes the shape of chromosomes, the X-shaped structures
visible within the nucleus prior to cell division. Chromatin packaging of DNA
allows the cell’s entire complement of DNA to fit into the combined space of
the nucleus. If DNA was not packaged into chromatin, it would spill out over
a space about 100 times as large as the cell itself.

Chloroplasts
Plant chloroplasts are large organelles (5 to 10 μm long) that, like
mitochondria, are bounded by a double membrane called the chloroplast
envelope. In addition to the inner and outer membranes of the envelope,
chloroplasts have a third internal membrane system, called the thylakoid
membrane. The thylakoid membrane forms a network of flattened discs
called thylakoids, which are frequently arranged in stacks called grana.
Because of this three-membrane structure, the internal organization of
chloroplasts is more complex than that of mitochondria. In particular, their
three membranes divide chloroplasts into three distinct internal
compartments:
(1) The intermembrane space between the two membranes of the
chloroplast envelope;
(2) The stroma, which lies inside the envelope but outside the thylakoid
membrane; and
(3) The thylakoid lumen.
The major difference between chloroplasts and mitochondria, in terms of
both structure and function, is the thylakoid membrane. This membrane is of
central importance in chloroplasts.
The inner membrane of the chloroplast envelope (which is not folded into
cristae) does not function in photosynthesis.

Comparing plant and animal cells

Similarities

Plant cells Animals cells

1. Nucleus present Nucleus present
2. Cell membrane present Cell membrane present
3. Mitochondria present Mitochondria present
4. Cytoplasm Cytoplasm
5.
6.

Differences

Plant cells Animal cells

1. Chloroplasts present No chloroplasts present
2. Cell wall present No cell wall present
3. Large cell vacuoles Smaller vacuoles
4.
5.
6.

Prokaryotes
The Basic Structure of a Prokaryote

Prokaryotes are the single-celled organisms, such as bacteria, and are

roughly one micrometer in diameter. Unlike Eukaryotes, prokaryotes do not
have a nucleus that houses its genetic material. Rather, the genetic material
of a prokaryote cell consists of a large DNA molecule compacted in an area
of cytoplasm called the nucleoid region. The nucleoid region is protected
and encased by the cell wall, or cell membrane, the outer layering of the cell
(similar to human's skin). Finally, a flagellum (flagetta - plural), a rudder-like
device, affords the prokaryote the luxury of mobility.

Fig 5: Prokaryotic Structure

Pili: are hollow, hairlike structures made of protein allow bacteria to attach to
other cells. A specialized pilus, the sex pilus, allows the transfer from one
bacterial cell to another. Pili (sing., pilus) are also called fimbriae (sing.,
fimbria.

Flagella: The purpose of flagella (sing., flagellum) is motility. Flagella are

long appendages which rotate by means of a "motor" located just under the
cytoplasmic membrane. Bacteria may have one, a few, or many flagella in
different positions on the cell.

Cell Wall: Composed of peptidoglycan (polysaccharides + protein), the cell

wall maintains the overall shape of a bacterial cell. The three primary shapes
in bacteria are coccus (spherical), bacillus (rod-shaped) and spirillum (spiral).
Mycoplasma are bacteria that have no cell wall and therefore have no
definite shape.

Capsule: This layer of polysaccharide (sometimes proteins) protects the

bacterial cell and is often associated with pathogenic bacteria because it
serves as a barrier against phagocytosis by white blood cells.

Inclusions: Nutrient reserves for the bacterial cell, present to afford

additional, specialised functions. These may take many diverse forms such
as carbohydrates, proteins as well as other forms.

The major similarities between the two types of cells (prokaryote and
eukaryote) are:

1. They both have DNA as their genetic material.

2. They are both membrane bound.
3. They both have ribosomes .
4. They have similar basic metabolism .
5. They both exist in diverse forms.

The major and extremely significant difference between prokaryotes and

eukaryotes is that eukaryotes have a nucleus and membrane-bound
organelles , while prokaryotes do not. The DNA of prokaryotes floats freely
around the cell; the DNA of eukaryotes is held within its nucleus. The
organelles of eukaryotes allow them to exhibit much higher levels of
intracellular division of labour than is possible in prokaryotic cells.
Additional obvious differences between prokaryotes and eukaryotes include:

Size
Eukaryotic cells are, on average, ten times the size of prokaryotic cells.
Genomic composition and length
The DNA of eukaryotes is much more complex and therefore much
more extnsive than the DNA of prokaryotes.
Cell Wall
Prokaryotes have a cell wall composed of peptidoglycan, a single large
polymer of amino acids and sugar. Many types of eukaryotic cells, such
as plant cells, also have cell walls, made of cellulose instead of
peptidoglycan.

The Endosymbiotic Development of Eukaryotic cells, the

Endosymbiotic theory

The Endosymbiotic Theory concerns the origins of mitochondria and

chloroplasts, which are organelles of eukaryotic cells. According to this
theory, these organelles originated as prokaryotic endosymbionts, which
came to live inside eukaryotic cells. The theory postulates that the
mitochondria evolved from aerobic bacteria, that is, prokaryotes which use
oxygen, and that the chloroplast evolved from endosymbiotic cyanobacteria
(autotrophic prokaryotes). The evidence for this theory is compelling as a
whole, and it is now generally accepted. Evidence of this is provided through
observations that:

• Both mitochondria and chloroplasts can arise only from pre-existing

mitochondria and chloroplasts. They cannot be formed in a cell that
lacks them because nuclear genes encode only some of the proteins of
which they are made.
• Both mitochondria and chloroplasts have their own genome and it
resembles that of bacteria not that of the nuclear genome.
o Both genomes consist of a single circular molecule of DNA.
o There are no histones associated with the DNA.
• Both mitochondria and chloroplasts have their own protein-
synthesizing machinery, and it more closely resembles that of bacteria
than that found in the cytoplasm of eukaryotes.

Tissues and Organ Systems

Cells group together to form tissues. Tissues are essentially collections of

cells having specialised functions.

Organs are the next level of organisation. An organ is a structure consisting

of at least two types of tissues functioning together for a common purpose.

Plants are made up of two organ systems: the shoot system and the root
system. For terrestrial plants the shoot system is above ground and consists
of a number of organs. These include stems, leaves, and flowers. On the
other hand, the root system is most often underground and consists of
organs such as roots, underground stems (tubers), and rhizomes.

Each of these organs performs a different function. Stems are support

structures and mediate the growth of the plant. Shoot tips contain actively
dividing regions called meristems, which produce auxin, a hormone that
regulates the growth and shape of the plant. Leaves are the primary sites of
photosynthesis, so they are the food production centers of the plant. Flowers
are reproductive structures, where eggs and sperm (pollen) are produced
and where pollination and fertilization occur. Roots, tubers, and rhizomes are
the main system for nutrient and water acquisition and storage. All of these
organs are made up of cells that can be categorized into three major tissue
types: dermal, ground, and vascular tissue.

Dermal Tissue

Dermal tissue makes up the outer layers of the plant and contains epidermal
cells that secrete and are coated with a waxy layer. This waxy coating, the
cuticle, prevents excessive water loss from the plant. While the dermal tissue
primarily serves a protective role, it also has a variety of other specialized
functions depending on the particular organ where it is located.

In leaves, dermal tissue contains specialized cells called guard cells that
make up structures called stomata . Stomata facilitate the exchange of
gases in the leaf. Carbon dioxide (CO 2 ) diffuses into the leaf through the
stomata for use in photosynthesis, and oxygen (O 2 ), the waste product of
photosynthesis, diffuses out of the leaf through stomata. Stomata are also
crucial for water transport through the xylem . Stomatal opening results in
the evaporation of water from the air spaces of the leaf. This creates
negative water pressure that pulls on the column of water in the xylem. The
evaporation of water from the stomata is the main driving force for water
transport through the water. In roots, epidermal cells have a specialized
structure that facilitates water and nutrient absorption, the main function of
the root. Some of the root epidermal cells have long membranous extensions
called root hairs that increase the absorptive surface area of the root. Root
epidermis also interacts with symbiotic fungi that form mycorrhizae , which
increase nutrient absorption.

Ground Tissue

Many different functions are performed by ground tissue including

photosynthesis, storage, and support. Ground tissue makes up the majority
of the plant structure and is composed of three cell types: parenchyma,
collenchyma, and sclerenchyma cells.

Parenchyma cells are the least specialized cells in a plant. These cells are
responsible for the production and storage of nutrients. Photosynthesis
occurs in the chloroplasts of parenchyma cells in leaves. Parenchyma cells in
stems, roots, and fruits have structures that store starch. Most developing
plant cells are structurally similar to parenchyma cells. During their
differentiation, they become specialized in form and function and lose the
potential to divide. Mature parenchyma cells do not usually divide, but they
retain the ability to divide and differentiate into different cell and tissue
types in the event of an injury to the plant.

Collenchyma and sclerenchyma cells provide structural support for the plant.
Collenchyma cells have thick, yet pliable, cell walls. These cells give
structural support to newly formed portions of a plant without restricting
growth. Collenchyma cells are stacked end on end and are oriented in
strands just beneath the epidermis of the young structure. The relatively soft
cell wall allows the collenchyma cells to elongate as the structure grows.

Sclerenchyma cells provide support to mature plant structures. Like

collenchyma cells, they have very thick cell walls. However, the cell walls of
sclerenchyma cells contain lignin , a molecule that makes the cell wall hard.
This provides strength to the cell wall, but restricts the ability of the cells to
elongate and grow. Since a sclerenchyma cell functions solely to provide
structural support, many sclerenchyma cells are actually dead at functional
maturity. The cell membrane, protoplasm (cytoplasm) and organelles are
gone, leaving only the rigid cell wall that serves as a scaffolding system for
that structure.

Vascular Tissue
Vascular tissues make up the organs that transport water, minerals , and
food throughout the plant. Vascular tissue can be divided into two functional
units. Xylem transports water and minerals from root to shoot. phloem
transports nutrients (such as sugar and amino acids ) from leaves and other
production sites to roots, flowers, stems, and other tissues that need them.
The cells that make up vascular tissue are unique in their structure. Their
specialized characteristics allow them to transport material through the plant
efficiently while providing structural support to the plant.

Xylem tissue contains two types of cells: tracheids and vessel elements. Like
sclerenchyma, both of these cell types are dead at functional maturity and
therefore lack protoplasm. Tracheids are long, thin cells that have tapered
ends. They overlap on another, and water passes from tracheid to tracheid
via small pores. Vessel elements are shorter and are stacked end to end,
forming more of a tube structure. Water flows in the tube by passing through
perforated end walls between cells.

Phloem tissue is made up of two different types of cells: sieve tube members
and companion cells. Sieve tube members are the main conducting cells,
and are named for the sievelike areas along their cell walls through which
the phloem sap moves from cell to cell. Unlike cells of the xylem, sieve tube
members are alive at functional maturity, but do not have nuclei. For this
reason, companion cells are closely associated with sieve tube members.
These cells do have nuclei and serve to support the sieve tube members.
The cytoplasm of sieve tube members and companion cells is connected
through numerous pores called plasmodesmata. These pores allow the
companion cells to regulate the content and activity of the sieve tube
member's cytoplasm. Moreover, the companion cells help to load the sieve
tube members with sugar and the other metabolic products that they
transport throughout the plant.
Fig 6:Cross Section through dicotyledonous root

Fig 7: TS through dicot root.