TEXTBOOK CELL BIOLOGY

NURUL MARFU’AH

PHARMACY DEPARTMENT
FACULTY OF SCIENCE
UNIVERSITY OF DARUSSALAM GONTOR
2018

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CHAPTER 1 : CELL
What is a cell?

It could easily be said that a cell is the fundamental unit of life, the smallest unit
capable of life or the structural and functional unit necessary for life. But whatever it
is, a cell is necessary for life. The Cell Biology chapter will discuss some of the
fundamental properties of the cell, with lessons that include the cell structure,
transport in and out of the cell, energy metabolism, and cell division and
reproduction.

PROKARYOTIC DAN EUKARYOTIC CELL

How many different types of cells are there?

There are many different types of cells. For example, in you there are blood cells and
skin cells and bone cells and even bacteria. Here we have drawings of bacteria and
human cells. Can you tell which depicts various types of bacteria? However, all cells
- whether from bacteria, human, or any other organism - will be one of two general
types. In fact, all cells other than bacteria will be one type, and bacterial cells will be
the other. And it all depends on how the cell stores its DNA.

Two Types of Cells

There is another basic cell structure that is present in many but not all living cells:
the nucleus. The nucleus of a cell is a structure in the cytoplasm that is surrounded
by a membrane (the nuclear membrane) and contains, and protects, most of the
cell's DNA. Based on whether they have a nucleus, there are two basic types of
cells: prokaryotic cells and eukaryotic cells. You can watch animations of both types
of cells at the link below.

Prokaryotic Cells
Prokaryotic cells are cells without a nucleus. The DNA in prokaryotic cells is in the
cytoplasm rather than enclosed within a nuclear membrane. Prokaryotic cells are
found in single-celled organisms, such as bacteria, like the one shown
in Figure below. Organisms with prokaryotic cells are called prokaryotes. They
were the first type of organisms to evolve and are still the most common organisms
today.

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[Figure 1]
Prokaryotic Cell. This diagram shows the structure of a typical prokaryotic cell, a bacterium. Like other prokaryotic cells,
this bacterial cell lacks a nucleus but has other cell parts, including a plasma membrane, cytoplasm, ribosomes, and DNA.
Identify each of these parts in the diagram.

Eukaryotic Cells
Eukaryotic cells are cells that contain a nucleus. A typical eukaryotic cell is shown
in Figure below. Eukaryotic cells are usually larger than prokaryotic cells, and they
are found mainly in multicellular organisms. Organisms with eukaryotic cells are
called eukaryotes, and they range from fungi to people.

Eukaryotic cells also contain other organelles besides the nucleus. An organelle is a
structure within the cytoplasm that performs a specific job in the
cell. Organelles called mitochondria, for example, provide energy to the cell, and
organelles called vacuoles store substances in the cell. Organelles allow eukaryotic
cells to carry out more functions than prokaryotic cells can. This allows eukaryotic
cells to have greater cell specificity than prokaryotic cells. Ribosomes, the organelle
where proteinsare made, are the only organelles in prokaryotic cells.

[Figure 2]
Eukaryotic Cell. Compare and contrast the eukaryotic cell shown here with the prokaryotic cell. What similarities and
differences do you see?

In some ways, a cell resembles a plastic bag full of Jell-O. Its basic structure is
a plasma membrane filled with cytoplasm. Like Jell-O containing mixed fruit, the
cytoplasm of the cell also contains various structures, such as a nucleus and
other organelles.

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CHAPTER 2 : ANIMAL AND PLANT CELL STRUCTURE
PLANT CELL STRUCTURE
Special Structures in Plant Cells
Most organelles are common to both animal and plant cells. However, plant cells
also have features that animal cells do not have: a cell wall, a large central vacuole,
and plastids such as chloroplasts.

Plants have very different lifestyles from animals, and these differences are apparent
when you examine the structure of the plant cell. Plants make their own food in a
process called photosynthesis. They take in carbon dioxide (CO2) and water (H2O)
and convert them into sugars. The features unique to plant cells can be seen
in Figure below.

[Figure 1]
In addition to containing most of the organelles found in animal cells, plant cells also have a cell wall, a large central
vacuole, and plastids. These three features are not found in animal cells.

The Cell Wall

A cell wall is a rigid layer that is found outside the cell membrane and surrounds the
cell. The cell wall contains not only cellulose and protein, but
other polysaccharides as well. The cell wall provides structural support and
protection. Pores in the cell wall allow water and nutrients to move into and out of the
cell. The cell wall also prevents the plant cell from bursting when water enters the
cell.

Microtubules guide the formation of the plant cell wall. Cellulose is laid down
by enzymes to form the primary cell wall. Some plants also have a secondary cell
wall. The secondary wall contains a lignin, a secondary cell component in plant cells
that have completed cell growth/expansion.

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The Central Vacuole
Most mature plant cells have a central vacuole that occupies more than 30% of the
cell's volume. The central vacuole can occupy as much as 90% of the volume of
certain cells. The central vacuole is surrounded by a membrane called
the tonoplast. The central vacuole has many functions. Aside from storage, the
main role of the vacuole is to maintain turgor pressure against the cell
wall. Proteins found in the tonoplast control the flow of water into and out of the
vacuole. The central vacuole also stores the pigments that color flowers.

The central vacuole contains large amounts of a liquid called cell sap, which differs
in composition to the cell cytosol. Cell sap is a mixture of water, enzymes, ions, salts,
and other substances. Cell sap may also contain toxic byproducts that have been
removed from the cytosol. Toxins in the vacuole may help to protect some plants
from being eaten.

Plastids
Plant plastids are a group of closely related membrane-bound organellesthat carry
out many functions. They are responsible for photosynthesis, for storage of products
such as starch, and for the synthesis of many types of molecules that are needed as
cellular building blocks. Plastids have the ability to change their function between
these and other forms. Plastids contain their own DNA and some ribosomes, and
scientists think that plastids are descended from photosynthetic bacteria that allowed
the first eukaryotes to make oxygen. The main types of plastids and their functions
are:

 Chloroplasts are the organelle of photosynthesis. They capture light energy from
the sun and use it with water and carbon dioxide to make food (sugar) for the plant.
The arrangement of chloroplasts in a plant’s cells can be seen in Figure below.
 Chromoplasts make and store pigments that give petals and fruit their orange and
yellow colors.
 Leucoplasts do not contain pigments and are located in roots and non-
photosynthetic tissues of plants. They may become specialized for bulk storage of
starch, lipid, or protein. However, in many cells, leucoplasts do not have a major
storage function. Instead, they make molecules such as fatty acids and many amino
acids.

Chloroplasts
Chloroplasts capture light energy from the sun and use it with water and carbon
dioxide to produce sugars for food. Chloroplasts look like flat discs and are usually 2
to 10 micrometers in diameter and 1 micrometer thick. A model of a chloroplast is
shown in Figure below. The chloroplast is enclosed by an inner and an outer
phospholipid membrane. Between these two layers is the intermembrane space. The
fluid within the chloroplast is called the stroma, and it contains one or more
molecules of small, circular DNA. The stroma also has ribosomes. Within the stroma
are stacks of thylakoids, sub-organelles that are the site of photosynthesis. The
thylakoids are arranged in stacks called grana (singular: granum). A thylakoid has a

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flattened disk shape. Inside it is an empty area called the thylakoid space or lumen.
Photosynthesis takes place on the thylakoid membrane.

Within the thylakoid membrane is the complex of proteins and light-absorbing

pigments, such as chlorophyll and carotenoids. This complex allows capture of
light energy from many wavelengths because chlorophyll and carotenoids both
absorb different wavelengths of light. These will be further discussed in the
"Photosynthesis" concept.

[Figure 3]
The internal structure of a chloroplast, with a granal stack of thylakoids circled.

ANIMAL CELL STRUCTURE

Animal cells are typical of the eukaryotic cell, enclosed by a plasma membrane and containing a
membrane-bound nucleus and organelles. Unlike the eukaryotic cells of plants and fungi, animal
cells do not have a cell wall. This feature was lost in the distant past by the single-celled
organisms that gave rise to the kingdom Animalia. Most cells, both animal and plant, range in
size between 1 and 100 micrometers and are thus visible only with the aid of a microscope.

The lack of a rigid cell wall allowed animals to develop a greater diversity of cell types, tissues,
and organs. Specialized cells that formed nerves and muscles—tissues impossible for plants to
evolve—gave these organisms mobility. The ability to move about by the use of specialized
muscle tissues is a hallmark of the animal world, though a few animals, primarily sponges, do not
possess differentiated tissues. Notably, protozoans locomote, but it is only via nonmuscular
means, in effect, using cilia, flagella, and pseudopodia.

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The animal kingdom is unique among eukaryotic organisms because most animal tissues are
bound together in an extracellular matrix by a triple helix of protein known as collagen. Plant
and fungal cells are bound together in tissues or aggregations by other molecules, such
as pectin. The fact that no other organisms utilize collagen in this manner is one of the
indications that all animals arose from a common unicellular ancestor. Bones, shells, spicules,
and other hardened structures are formed when the collagen-containing extracellular matrix
between animal cells becomes calcified.

Animals are a large and incredibly diverse group of organisms. Making up about three-quarters
of the species on Earth, they run the gamut from corals and jellyfish to ants, whales, elephants,
and, of course, humans. Being mobile has given animals, which are capable of sensing and
responding to their environment, the flexibility to adopt many different modes of feeding, defense,
and reproduction. Unlike plants, however, animals are unable to manufacture their own food, and
therefore, are always directly or indirectly dependent on plant life.

Most animal cells are diploid, meaning that their chromosomes exist in homologous pairs.
Different chromosomal ploidies are also, however, known to occasionally occur. The proliferation
of animal cells occurs in a variety of ways. In instances of sexual reproduction, the cellular
process of meiosis is first necessary so that haploid daughter cells, or gametes, can be
produced. Two haploid cells then fuse to form a diploid zygote, which develops into a new
organism as its cells divide and multiply.

The earliest fossil evidence of animals dates from the Vendian Period (650 to 544 million years
ago), with coelenterate-type creatures that left traces of their soft bodies in shallow-water
sediments. The first mass extinction ended that period, but during the Cambrian Period which
followed, an explosion of new forms began the evolutionary radiation that produced most of the
major groups, or phyla, known today. Vertebrates (animals with backbones) are not known to
have occurred until the early Ordovician Period (505 to 438 million years ago).

Cells were discovered in 1665 by British scientist Robert Hooke who first observed them in his
crude (by today's standards) seventeenth century optical microscope. In fact, Hooke coined the
term "cell", in a biological context, when he described the microscopic structure of cork like a tiny,
bare room or monk's cell. Illustrated in Figure 2 are a pair of fibroblast deer skin cells that have
been labeled with fluorescent probes and photographed in the microscope to reveal their internal
structure. The nuclei are stained with a red probe, while the Golgi apparatus and microfilament
actin network are stained green and blue, respectively. The microscope has been a fundamental
tool in the field of cell biology and is often used to observe living cells in culture. Use the links
below to obtain more detailed information about the various components that are found in animal
cells.

 Centrioles - Centrioles are self-replicating organelles made up of nine bundles of

microtubules and are found only in animal cells. They appear to help in organizing cell
division, but aren't essential to the process.
 Cilia and Flagella - For single-celled eukaryotes, cilia and flagella are essential for the
locomotion of individual organisms. In multicellular organisms, cilia function to move fluid
or materials past an immobile cell as well as moving a cell or group of cells.

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  Endoplasmic Reticulum - The endoplasmic reticulum is a network of sacs that
manufactures, processes, and transports chemical compounds for use inside and outside
of the cell. It is connected to the double-layered nuclear envelope, providing a pipeline
between the nucleus and the cytoplasm.
 Endosomes and Endocytosis - Endosomes are membrane-bound vesicles, formed via
a complex family of processes collectively known as endocytosis, and found in the
cytoplasm of virtually every animal cell. The basic mechanism of endocytosis is the
reverse of what occurs during exocytosis or cellular secretion. It involves the invagination
(folding inward) of a cell's plasma membrane to surround macromolecules or other matter
diffusing through the extracellular fluid.
 Golgi Apparatus - The Golgi apparatus is the distribution and shipping department for
the cell's chemical products. It modifies proteins and fats built in the endoplasmic
reticulum and prepares them for export to the outside of the cell.
 Intermediate Filaments - Intermediate filaments are a very broad class of fibrous
proteins that play an important role as both structural and functional elements of the
cytoskeleton. Ranging in size from 8 to 12 nanometers, intermediate filaments function
as tension-bearing elements to help maintain cell shape and rigidity.
 Lysosomes - The main function of these microbodies is digestion. Lysosomes break
down cellular waste products and debris from outside the cell into simple compounds,
which are transferred to the cytoplasm as new cell-building materials.
 Microfilaments - Microfilaments are solid rods made of globular proteins called actin.
These filaments are primarily structural in function and are an important component of
the cytoskeleton.
 Microtubules - These straight, hollow cylinders are found throughout the cytoplasm of all
eukaryotic cells (prokaryotes don't have them) and carry out a variety of functions,
ranging from transport to structural support.
 Mitochondria - Mitochondria are oblong shaped organelles that are found in the
cytoplasm of every eukaryotic cell. In the animal cell, they are the main power
generators, converting oxygen and nutrients into energy.
 Nucleus - The nucleus is a highly specialized organelle that serves as the information
processing and administrative center of the cell. This organelle has two major functions: it
stores the cell's hereditary material, or DNA, and it coordinates the cell's activities, which
include growth, intermediary metabolism, protein synthesis, and reproduction (cell
division).
 Peroxisomes - Microbodies are a diverse group of organelles that are found in the
cytoplasm, roughly spherical and bound by a single membrane. There are several types
of microbodies but peroxisomes are the most common.
 Plasma Membrane - All living cells have a plasma membrane that encloses their
contents. In prokaryotes, the membrane is the inner layer of protection surrounded by a
rigid cell wall. Eukaryotic animal cells have only the membrane to contain and protect
their contents. These membranes also regulate the passage of molecules in and out of
the cells.
 Ribosomes - All living cells contain ribosomes, tiny organelles composed of
approximately 60 percent RNA and 40 percent protein. In eukaryotes, ribosomes are
made of four strands of RNA. In prokaryotes, they consist of three strands of RNA.

In addition the optical and electron microscope, scientists are able to use a number of other
techniques to probe the mysteries of the animal cell. Cells can be disassembled by chemical
methods and their individual organelles and macromolecules isolated for study. The process
of cell fractionation enables the scientist to prepare specific components, the mitochondria for
example, in large quantities for investigations of their composition and functions. Using this
approach, cell biologists have been able to assign various functions to specific locations within
the cell. However, the era of fluorescent proteins has brought microscopy to the forefront of
biology by enabling scientists to target living cells with highly localized probes for studies that
don't interfere with the delicate balance of life processes.

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CHAPTER 3 : PART OF CELL
1. Plasma Membrane
The plasma membrane (also known as the cell membrane) forms a barrier
between the cytoplasm inside the cell and the environment outside the cell. It
protects and supports the cell and also controls everything that enters and leaves the
cell. It allows only certain substances to pass through, while keeping others in or out.
The ability to allow only certain molecules in or out of the cell is referred to as
selective permeability or semipermeability. To understand how the plasma
membrane controls what crosses into or out of the cell, you need to know
its composition.

A Phospholipid Bilayer
The plasma membrane is composed mainly of phospholipids, which consist of fatty
acids and alcohol. The phospholipids in the plasma membrane are arranged in two
layers, called a phospholipid bilayer. As shown in Figure below, each phospholipid
molecule has a head and two tails. The head “loves” water (hydrophilic) and the
tails “hate” water(hydrophobic). The water-hating tails are on the interior of the
membrane, whereas the water-loving heads point outwards, toward either the
cytoplasm or the fluid that surrounds the cell.

Molecules that are hydrophobic can easily pass through the plasma membrane, if
they are small enough, because they are water-hating like the interior of the
membrane. Molecules that are hydrophilic, on the other hand, cannot pass through
the plasma membrane—at least not without help—because they are water-loving like
the exterior of the membrane, and are therefore excluded from the interior of the
membrane.

[Figure 1]
Phospholipid Bilayer. The phospholipid bilayer consists of two layers of phospholipids, with a hydrophobic, or water-hating,
interior and a hydrophilic, or water-loving, exterior. The hydrophilic (polar) head group and hydrophobic tails (fatty acid
chains) are depicted in the single phospholipid molecule. The polar head group and fatty acid chains are attached by a 3-
carbon glycerol unit.

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Cell Signaling
In order to respond to changes in their immediate environment, cells must be able to receive and
process signals that originate outside their borders. Individual cells often receive many signals
simultaneously, and they then integrate the information they receive into a unified action plan. But
cells aren't just targets. They also send out messages to other cells both near and far.

What Kind of Signals Do Cells Receive?

Most cell signals are chemical in nature. For example, prokaryotic organisms have sensors
that detect nutrients and help them navigate toward food sources. In multicellular organisms,
growth factors, hormones, neurotransmitters, and extracellular matrix components are some
of the many types of chemical signals cells use. These substances can exert their effects
locally, or they might travel over long distances. For instance, neurotransmitters are a class
of short-range signaling molecules that travel across the tiny spaces between adjacent
neurons or between neurons and muscle cells. Other signaling molecules must move much
farther to reach their targets. One example is follicle-stimulating hormone, which travels from
the mammalian brain to the ovary, where it triggers egg release. Some cells also respond to
mechanical stimuli. For example, sensory cells in the skin respond to the pressure of touch,
whereas similar cells in the ear react to the movement of sound waves. In addition,
specialized cells in the human vascular system detect changes in blood pressure —
information that the body uses to maintain a consistent cardiac load.
How Do Cells Recognize Signals?
Cells have proteins called receptors that bind to signaling molecules and initiate a
physiological response. Different receptors are specific for different molecules. Dopamine
receptors bind dopamine, insulin receptors bind insulin, nerve growth factor receptors bind
nerve growth factor, and so on. In fact, there are hundreds of receptor types found in cells,
and varying cell types have different populations of receptors. Receptors can also respond
directly to light or pressure, which makes cells sensitive to events in the atmosphere.
Receptors are generally transmembrane proteins, which bind to signaling molecules outside
the cell and subsequently transmit the signal through a sequence of molecular switches to
internal signaling pathways. Membrane receptors fall into three major classes: G-protein-
coupled receptors, ion channel receptors, and enzyme-linked receptors. The names of these
receptor classes refer to the mechanism by which the receptors transform external signals
into internal ones — via protein action, ion channel opening, or enzyme activation,
respectively. Because membrane receptors interact with both extracellular signals and
molecules within the cell, they permit signaling molecules to affect cell function without
actually entering the cell. This is important because most signaling molecules are either too
big or too charged to cross a cell's plasma membrane (Figure 1).

Not all receptors exist on the exterior of the cell. Some exist deep inside the cell, or even in
the nucleus. These receptors typically bind to molecules that can pass through the plasma
membrane, such as gases like nitrous oxide and steroid hormones like estrogen.

Figure 1: An example of ion channel activation

An acetylcholine receptor (green) forms a gated ion channel in the plasma membrane. This receptor is a membrane protein
with an aqueous pore, meaning it allows soluble materials to travel across the plasma membrane when open. When no external
signal is present, the pore is closed (center). When acetylcholine molecules (blue) bind to the receptor, this triggers a
conformational change that opens the aqueous pore and allows ions (red) to flow into the cell.

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© 2010 Nature Education All rights reserved.

How Do Cells Respond to Signals?

Once a receptor protein receives a signal, it undergoes a conformational change, which in
turn launches a series of biochemical reactions within the cell. These intracellular signaling
pathways, also called signal transduction cascades, typically amplify the message,
producing multiple intracellular signals for every one receptor that is bound.
Activation of receptors can trigger the synthesis of small molecules called second
messengers, which initiate and coordinate intracellular signaling pathways. For
example, cyclic AMP (cAMP) is a common second messenger involved in signal
transduction cascades. (In fact, it was the first second messenger ever discovered.) cAMP is
synthesized from ATP by the enzyme adenylyl cyclase, which resides in the cell
membrane. The activation of adenylyl cyclase can result in the manufacture of hundreds or
even thousands of cAMP molecules. These cAMP molecules activate the enzyme protein
kinase A (PKA), which then phosphorylates multiple protein substrates by attaching
phosphate groups to them. Each step in the cascade further amplifies the initial signal, and
the phosphorylation reactions mediate both short- and long-term responses in the cell
(Figure 2). How does cAMP stop signaling? It is degraded by the enzyme
phosphodiesterase.
Other examples of second messengers include diacylglycerol (DAG) and inositol 1,4,5-
triphosphate (IP3), which are both produced by the enzyme phospholipase, also a
membrane protein. IP3 causes the release of Ca2+ — yet another second messenger —
from intracellular stores. Together, DAG and Ca2+ activate another enzyme called protein
kinase C (PKC).

Figure 2: An example of a signal transduction cascade involving cyclic AMP

The binding of adrenaline to an adrenergic receptor initiates a cascade of reactions inside the cell. The signal transduction
cascade begins when adenylyl cyclase, a membrane- bound enzyme, is activated by G-protein molecules associated with the
adrenergic receptor. Adenylyl cyclase creates multiple cyclic AMP molecules, which fan out and activate protein kinases (PKA,
in this example). Protein kinases can enter the nucleus and affect transcription.

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© 2010 Nature Education All rights reserved.

How Do Signals Affect Cell Function?

Protein kinases such as PKA and PKC catalyze the transfer of phosphate groups from ATP
molecules to protein molecules. Within proteins, the amino acids serine, threonine, and
tyrosine are especially common sites for phosphorylation. These phosphorylation reactions
control the activity of many enzymes involved in intracellular signaling pathways.
Specifically, the addition of phosphate groups causes a conformational change in the
enzymes, which can either activate or inhibit the enzyme activity. Then, when appropriate,
protein phosphatases remove the phosphate groups from the enzymes, thereby reversing
the effect on enzymatic activity.

Phosphorylation allows for intricate control of protein function. Phosphate groups can be
added to multiple sites in a single protein, and a single protein may in turn be the substrate
for multiple kinases and phosphatases.

At any one time, a cell is receiving and responding to numerous signals, and multiple signal
transduction pathways are operating in its cytoplasm. Many points of intersection exist
among these pathways. For instance, a single second messenger or protein kinase might
play a role in more than one pathway. Through this network of signaling pathways, the cell is
constantly integrating all the information it receives from its external environment.

2. Cytoplasm and Cytoskeleton

Does a cell have, or even need, a "skeleton"?
What do you get if you take some tubing, and make the tubes smaller and smaller and
smaller? You get very small tubes, or microtubes. Very small tubes, or microtubules,
together with microfilaments, form the basis of the "skeleton" inside the cell.

The Cytoplasm and Cytoskeleton

The cytoplasm consists of everything inside the plasma membrane of the cell, excluding
the nucleus in a eukaryotic cell. It includes the watery, gel-like material called cytosol, as
well as various structures. The water in the cytoplasm makes up about two thirds of the
cell’s weight and gives the cell many of its properties.
Functions of the Cytoplasm
The cytoplasm has several important functions, including:
1. suspending cell organelles.
2. pushing against the plasma membrane to help the cell keep its shape.
3. providing a site for many of the biochemical reactions of the cell.

The Cytoskeleton
The cytoskeleton is a cellular "scaffolding" or "skeleton" that crisscrosses the cytoplasm. All
eukaryotic cells have a cytoskeleton, and recent research has shown that prokaryotic cells
also have a cytoskeleton. The eukaryotic cytoskeleton is made up of a network of long,
thin proteinfibers and has many functions. It helps to maintain cell shape. It
holds organelles in place, and for some cells, it enables cell movement. The cytoskeleton
also plays important roles in both the intracellular movement of substances and in cell
division. Certain proteins act like a path that vesicles and organelles move along within the
cell. The threadlike proteins that make up the cytoskeleton continually rebuild to adapt to the

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cell's constantly changing needs. Three main kinds of cytoskeleton fibers are microtubules,
intermediate filaments, and microfilaments.
 Microtubules, shown in Figure below (a), are hollow cylinders and are the thickest
of the cytoskeleton structures. They are most commonly made of filaments which are
polymers of alpha and beta tubulin, and radiate outwards from an area near
the nucleus called the centrosome. Tubulin is the protein that forms microtubules.
Two forms of tubulin, alpha and beta, form dimers (pairs) which come together to
form the hollow cylinders. The cylinders are twisted around each other to form the
microtubules. Microtubules help the cell keep its shape. They hold organelles in
place and allow them to move around the cell, and they form the mitotic spindle
during cell division. Microtubules also make up parts of cilia and flagella, the
organelles that help a cell move.
 Microfilaments, shown in Figure below (b), are made of two thin actinchains that
are twisted around one another. Microfilaments are mostly concentrated just beneath
the cell membrane, where they support the cell and help the cell keep its shape.
Microfilaments form cytoplasmatic extensions, such as pseudopodia and microvilli,
which allow certain cells to move. The actin of the microfilaments interacts with
the proteinmyosin to cause contraction in muscle cells. Microfilaments are found in
almost every cell, and are numerous in muscle cells and in cells that move by
changing shape, such as phagocytes (white blood cells that search the body
for bacteria and other invaders).
 Intermediate filaments differ in make-up from one cell type to another. Intermediate
filaments organize the inside structure of the cell by holding organelles and providing
strength. They are also structural components of the nuclear envelope. Intermediate
filaments made of the protein keratin are found in skin, hair, and nails cells.

[Figure 1]
(a) The eukaryotic cytoskeleton. Microfilaments are shown in red, microtubules in green, and the nuclei are in blue. By
linking regions of the cell together, the cytoskeleton helps support the shape of the cell. (b) Microscopy of microfilaments
(actin filaments), shown in green, inside cells. The nucleus is shown in blue.

Cytoskeleton Structure

Intermediate
Microtubules Microfilaments
Filaments

Fiber Diameter About 25 nm 8 to 11 nm Around 7 nm

Protein Compositi Tubulin, with two One of different types

Actin
on subunits, alpha and of proteinssuch as

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Cytoskeleton Structure

Intermediate
Microtubules Microfilaments
Filaments

beta tubulin lamin, vimentin, and

keratin

Hollow cylinders
Protein fiber coils Two actin chains
made of two protein
Shape twisted into each twisted around one
chains twisted around
other another
each other

Keep cellular shape;

Organize cell shape;
allows movement of
Organelle and vesicle positions organelles
certain cells by
movement; form in cytoplasm
forming cytoplasmatic
mitotic spindles structural support of
extensions or
Main Functions during the nuclear envelope
contraction of actin
cell reproduction; cell and sarcomeres;
fibers; involved in
motility (in cilia and involved in cell-to-cell
some cell-to-cell or
flagella) and cell-to-matrix
cell-to-matrix
junctions
junctions

Representation

3. Ribosome
Ribosomes are small organelles and are the sites of protein synthesis (or assembly). They
are made of ribosomal protein and ribosomal RNA, and are found in both eukaryotic and
prokaryotic cells. Unlike other organelles, ribosomes are not surrounded by a membrane.
Each ribosomehas two parts, a large and a small subunit, as shown in Figure below. The
subunits are attached to one another. Ribosomes can be found alone or in groups within the
cytoplasm. Some ribosomes are attached to the endoplasmic reticulum (ER), and others are
attached to the nuclear envelope.

[Figure 1]
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The two subunits that make up a ribosome, small organelles that are intercellular protein factories.

Ribozymes are RNA molecules that catalyze chemical reactions, such

as translation. Translation is the process of ordering the amino acids in the assembly of
a protein, and translation will be discussed more in another concept. Briefly, the ribosomes
interact with other RNA molecules to make chains of amino acids called polypeptide chains,
due to the peptide bond that forms between individual amino acids. Polypeptide chains are
built from the genetic instructions held within a messenger RNA (mRNA) molecule.
Polypeptide chains that are made on the rough ER are inserted directly into the ER and then
are transported to their various cellular destinations. Ribosomes on the rough ER usually
produce proteins that are destined for the cell membrane.

Ribosomes are found in both eukaryotic and prokaryotic cells. Ribosomes are not
surrounded by a membrane. The other organelles found in eukaryotic cells are surrounded
by a membrane.

Protein biosynthesis
Protein synthesis is the process whereby biological cells generate new proteins; it is balanced
by the loss of cellular proteins via degradation or export. Translation, the assembly of amino
acids by ribosomes, is an essential part of the biosynthetic pathway, along with generation
of messenger RNA (mRNA), aminoacylation of transfer RNA (tRNA), co-translational transport,
and post-translational modification. Protein biosynthesis is strictly regulated at multiple
steps.[1] They are principally during transcription (phenomena of RNA synthesis from DNA
template) and translation (phenomena of amino acid assembly from RNA).
The cistron DNA is transcribed into the first of a series of RNAintermediates. The last version is
used as a template in synthesis of a polypeptide chain. Protein will often be synthesized directly
from genes by translating mRNA. However, when a protein must be available on short notice or
in large quantities, a protein precursor is produced. A proprotein is an inactive protein containing
one or more inhibitory peptides that can be activated when the inhibitory sequence is removed
by proteolysis during posttranslational modification. A preprotein is a form that contains a signal
sequence (an N-terminal signal peptide) that specifies its insertion into or through membranes,
i.e., targets them for secretion.[2]The signal peptide is cleaved off in the endoplasmic
reticulum.[2] Preproproteins have both sequences (inhibitory and signal) still present.
In protein synthesis, a succession of tRNA molecules charged with appropriate amino acids are
brought together with an mRNA molecule and matched up by base-pairing through the anti-
codons of the tRNA with successive codons of the mRNA. The amino acids are then linked
together to extend the growing protein chain, and the tRNAs, no longer carrying amino acids, are
released. This whole complex of processes is carried out by the ribosome, formed of two main
chains of RNA, called ribosomal RNA (rRNA), and more than 50 different proteins. The ribosome
latches onto the end of an mRNA molecule and moves along it, capturing loaded tRNA
molecules and joining together their amino acids to form a new protein chain.[3]
Protein biosynthesis, although very similar, is different for prokaryotes and eukaryotes.

Transcription

In transcription an mRNA chain is generated, with one strand of the DNA double helix in
the genomeas a template. This strand is called the template strand. Transcription can be divided
into 3 stages: initiation, elongation, and termination, each regulated by a large number of proteins
such as transcription factors and coactivators that ensure that the correct gene is transcribed.
Transcription occurs in the cell nucleus, where the DNA is held and is never able to leave. The
DNA structure of the cell is made up of two helixes made up of sugar and phosphate held
together by hydrogen bonds between the bases of opposite strands. The sugar and the
phosphate in each strand are joined together by stronger phosphodiester covalent bonds. The

15
DNA is "unzipped" (disruption of hydrogen bonds between different single strands) by the
enzyme helicase, leaving the single nucleotide chain open to be copied. RNA polymerase reads
the DNA strand from the 3-prime (3') end to the 5-prime (5') end, while it synthesizes a single
strand of messenger RNA in the 5'-to-3' direction. The general RNA structure is very similar to
the DNA structure, but in RNA the nucleotide uracil takes the place that thymine occupies in
DNA. The single strand of mRNA leaves the nucleus through nuclear pores, and migrates into
the cytoplasm.
The first product of transcription differs in prokaryotic cells from that of eukaryotic cells, as in
prokaryotic cells the product is mRNA, which needs no post-transcriptional modification,
whereas, in eukaryotic cells, the first product is called primary transcript, that needs post-
transcriptional modification (capping with 7-methyl-guanosine, tailing with a poly A tail) to give
hnRNA (heterogeneous nuclear RNA). hnRNA then undergoes splicing of introns (noncoding
parts of the gene) via spliceosomes to produce the final mRNA.

16
Translation
Phenomena of amino acid assembly from RNA. The synthesis of proteins from RNA is known as
translation. In eukaryotes, translation occurs in the cytoplasm, where the ribosomes are located.
Ribosomes are made of a small and large subunit that surround the mRNA. In
translation, messenger RNA (mRNA) is decoded to produce a specific polypeptide according to
the rules specified by the trinucleotide genetic code. This uses an mRNA sequence as a
template to guide the synthesis of a chain of amino acids that form a protein. Translation
proceeds in four phases: activation, initiation, elongation, and termination (all describing the
growth of the amino acid chain, or polypeptide that is the product of translation).

Diagram showing the process of translation

17
Diagram showing the translation of mRNA and the synthesis of proteins by a ribosome

In activation, the correct amino acid (AA) is joined to the correct transfer RNA (tRNA). While this
is not, in the technical sense, a step in translation, it is required for translation to proceed. The
AA is joined by its carboxyl group to the 3' OH of the tRNA by an ester bond. When the tRNA has
an amino acid linked to it, it is termed "charged". Initiation involves the small subunit of the
ribosome binding to 5' end of mRNA with the help of initiation factors (IF), other proteins that
assist the process. Elongation occurs when the next aminoacyl-tRNA (charged tRNA) in line
binds to the ribosome along with GTPand an elongation factor. Termination of the polypeptide
happens when the A site of the ribosome faces a stop codon (UAA, UAG, or UGA). When this
happens, no tRNA can recognize it, but releasing factor can recognize nonsense codons and
causes the release of the polypeptide chain. The capacity of disabling or inhibiting translation in
protein biosynthesis is used by some antibiotics such
as anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, purom
ycin, etc.

Events during or following protein translation

Events that occur during or following biosynthesis include proteolysis, post-translational
modification and protein folding.Proteolysis may remove N-terminal, C-terminal or internal amino-
acid residues or peptides from the polypeptide. The termini and side-chains of the polypeptide
may be subjected to post-translational modification. These modifications may be required for
correct cellular localisation or the natural function of the protein. During and after synthesis,
polypeptide chains often fold to assume, so called, native secondary and tertiary structures. This
is known as protein folding and is typically required for the natural function of the protein.

4. Mitochondria
A mitochondrion (mitochondria, plural), is a membrane-enclosed organelle that is
found in most eukaryotic cells. Mitochondria are called the "power plants" of the cell
because they are the sites of cellular respiration, where they
use energy from organic compounds to make ATP (adenosine triphosphate). ATP is
the cell's energy source that is used for such things such as movement and cell
division. Some ATP is made in the cytosol of the cell, but most of it is made inside
mitochondria. The number of mitochondria in a cell depends on the cell’s energy
needs. For example, active human muscle cells may have thousands of
mitochondria, while less active red blood cells do not have any.

18
[Figure 2]
(a): Electron micrograph of a single mitochondrion, within which you can see many cristae. Mitochondria range from 1 to
10 μm in size. (b): This model of a mitochondrion shows the organized arrangement of the inner and outer membranes, the
protein matrix, and the folded inner mitochondrial membranes.

As Figure above (a) and (b) show, a mitochondrion has two phospholipid
membranes. The smooth outer membrane separates the mitochondrion from the
cytosol. The inner membrane has many folds, called cristae. The fluid-filled inside of
the mitochondrion, called matrix, is where most of the cell’s ATP is made.

Although most of a cell's DNA is contained in the cell nucleus, mitochondria have
their own DNA. Mitochondria are able to reproduce asexually, and scientists think
that they are descended from prokaryotes. According to the endosymbiotic theory,
mitochondria were once free-living prokaryotes that infected or were engulfed by
ancient eukaryotic cells. The invading prokaryotes were protected inside the
eukaryotic host cell, and in turn the prokaryote supplied extra ATP to its host.

5. Endoplasmic Reticulum
The endoplasmic reticulum (ER) (plural, reticuli) is a network of phospholipid
membranes that form hollow tubes, flattened sheets, and round sacs. These
flattened, hollow folds and sacs are called cisternae. The ER has two major
functions:

 Transport: Molecules, such as proteins, can move from place to place inside the ER,
much like on an intracellular highway.
 Synthesis: Ribosomes that are attached to ER, similar to unattached ribosomes,
make proteins. Lipids are also produced in the ER.
There are two types of endoplasmic reticulum, rough endoplasmic reticulum (RER)
and smooth endoplasmic reticulum (SER).

 Rough endoplasmic reticulum is studded with ribosomes, which gives it a "rough"

appearance. These ribosomes make proteins that are then transported from the ER
in small sacs called transport vesicles. The transport vesicles pinch off the ends of
the ER. The rough endoplasmic reticulum works with the Golgi apparatus to move
new proteins to their proper destinations in the cell. The membrane of the RER is
continuous with the outer layer of the nuclear envelope.
 Smooth endoplasmic reticulum does not have any ribosomes attached to it, and
so it has a smooth appearance. SER has many different functions, some of which

19
 include lipid synthesis, calcium ionstorage, and drug detoxification. Smooth
endoplasmic reticulum is found in both animal and plant cells and it serves different
functions in each. The SER is made up of tubules and vesicles that branch out to
form a network. In some cells there are dilated areas like the sacs of RER. Smooth
endoplasmic reticulum and RER form an interconnected network.

[Figure 1]
Image of nucleus, endoplasmic reticulum and Golgi apparatus, and how they work together. The process of secretion from
endoplasmic reticuli to Golgi apparatus is shown.

6. Golgi Apparatus
The Golgi apparatus is a large organelle that is usually made up of five to eight cup-
shaped, membrane-covered discs called cisternae, as shown in Figure above. The
cisternae look a bit like a stack of deflated balloons. The Golgi apparatus modifies,
sorts, and packages different substances for secretion out of the cell, or for use
within the cell. The Golgi apparatus is found close to the nucleus of the cell, where it
modifies proteins that have been delivered in transport vesicles from the RER. It is
also involved in the transport of lipids around the cell. Pieces of the Golgi membrane
pinch off to form vesicles that transport molecules around the cell. The Golgi
apparatus can be thought of as similar to a post office; it packages and labels "items"
and then sends them to different parts of the cell. Both plant and animal cells have a
Golgi apparatus. Plant cells can have up to several hundred Golgi stacks scattered
throughout the cytoplasm. In plants, the Golgi apparatus contains enzymes that
synthesize some of the cell wall polysaccharides.

7. Vesicles
A vesicle is a small, spherical compartment that is separated from the cytosol by at
least one lipid bilayer. Many vesicles are made in the Golgi apparatus and the
endoplasmic reticulum, or are made from parts of the cell membrane. Vesicles from
the Golgi apparatus can be seen in Figureabove. Because it is separated from the
cytosol, the space inside the vesicle can be made to be chemically different from the
cytosol. Vesicles are basic tools of the cell for organizing metabolism, transport, and
storage of molecules. Vesicles are also used as chemical reactionchambers. They
can be classified by their contents and function.

20
  Transport vesicles are able to move molecules between locations inside the cell.
For example, transport vesicles move proteins from the rough endoplasmic reticulum
to the Golgi apparatus.
 Lysosomes are vesicles that are formed by the Golgi apparatus. They contain
powerful enzymes that could break down (digest) the cell. Lysosomes break down
harmful cell products, waste materials, and cellular debris and then force them out of
the cell. They also digest invading organisms such as bacteria. Lysosomes also
break down cells that are ready to die, a process called autolysis.
 Peroxisomes are vesicles that use oxygen to break down toxic substances in the
cell. Unlike lysosomes, which are formed by the Golgi apparatus, peroxisomes self-
replicate by growing bigger and then dividing. They are common in liver and kidney
cells that break down harmful substances. Peroxisomes are named for the hydrogen
peroxide (H2O2) that is produced when they break down organic compounds.
Hydrogen peroxide is toxic, and in turn is broken down into water (H2O) and oxygen
(O2) molecules.

8. Vacuoles
Vacuoles are membrane-bound organelles that can have secretory, excretory, and
storage functions. Many organisms will use vacuoles as storage areas and some
plant cells have very large vacuoles. Vesicles are much smaller than vacuoles and
function in transporting materials both within and to the outside of the cell.

9. Centrioles
Centrioles are rod-like structures made of short microtubules. Nine groups of three
microtubules make up each centriole. Two perpendicular centrioles make up
the centrosome. Centrioles are very important in cellular division, where they
arrange the mitotic spindles that pull the chromosome apart during mitosis.

10. Chloroplast

Chloroplasts: Theaters for Photosynthesis

Photosynthesis, the process of turning the energy of sunlight into ‘‘food,’’ is divided
into two basic sets of reactions, known as the light reactions and the Calvin cycle,
which uses carbon dioxide. As you study the details in other concepts, refer
frequently to the chemical equation of photosynthesis: 6CO2 + 6H2O + Light Energy
→ C6H12O6 + 6O2. Photosynthesis occurs in the chloroplast, an organelle specific to
plant cells.

If you examine a single leaf of a Winter Jasmine leaf, shown in Figure below, under
a microscope, you will see within each cell dozens of small green ovals. These
are chloroplasts, the organelles which conduct photosynthesis in plants and algae.
Chloroplasts closely resemble some types of bacteria and even contain their own
circular DNA and ribosomes. In fact, the endosymbiotic theory holds that
chloroplasts were once independently living bacteria (prokaryotes). So when we say
that photosynthesis occurs within chloroplasts, we speak not only of
the organelles within plants and algae, but also of some bacteria – in other words,
virtually all photosynthetic autotrophs.

21
Before you read about these two stages of photosynthesis in greater detail, you need
to know more about the chloroplast, where the two stages take place.

[Figure 2]
High power microscopic photo of the upper part of a Winter Jasmine leaf. Viewed under a microscope, many green
chloroplasts are visible.

Each chloroplast contains neat stacks called grana (singular, granum). The grana
consist of sac-like membranes, known as thylakoid membranes. These membranes
contain photosystems, which are groups of molecules that include chlorophyll, a
green pigment. The light reactions of photosynthesis occur in the thylakoid
membranes. The stroma is the space outside the thylakoid membranes, as shown
in Figure below. This is where the reactions of the Calvin cycle take place. In
addition to enzymes, two basic types of molecules - pigments
and electron carriers – are key players in this process and are also found in the
thylakoid membranes.

[Figure 3]
A chloroplast consists of thylakoid membranes surrounded by stroma. The thylakoid membranes contain molecules of the
green pigment chlorophyll.

22
11. Nucleus

The nucleus consists of the following main parts:

(1) Nucleolemma or nuclear membrane (karyotheca) (2) Nuclear sap or karyolymph or

nucleoplasm (3) Chromatin network or fibres (4) Nucleolus (5) Endosomes.

A. Nuclear membrane (karyotheca):

The nucleus is separated from the cytoplasm by a limiting membrane called as karyotheca or
nuclear membrane.

This membrane plays an important role for the transport of the material between the nucleus
and the cytoplasm. Nuclear envelope regulates nucleocytoplasmic exchanges and coordinates
gene action with cytoplasmic activity.

Image Courtesy : upload.wikimedia.org/wikipedia/Blausen_0212_CellNucleus.png

It has direct connections with the endoplasmic reticulum and during cell division, this
nuclear envelope (nuclear membrane) develops as an extension of the endoplasmic
reticulum applied to the nucleus and subsequently modified. In the end of mitosis, i.e, in
telophase, the cisternae of the endoplasmic reticulum gather around the chromosomes and
by fusing together they form the nuclear membrane.

Structure:
The nuclear membrane appears to be a double membrane having interruptions or pores at
intervals. The outer one is called ectokaryotheca and inner one is termed endokaryotheca.
Each of the membranes is about 75 to 90 A thick and both the membranes enclose an
intervening space of about 100-150 A (Robertis et al., 1970), or 100 to 300 A (Cohn, 1970) or
400 to 700 A (Burke, 1970), called as perinuclear space or cisterna.

Outer nuclear membrane is comparatively thicker than the inner membrane and has a rough
outline due to the presence of attached RNA particles which may form spirals, parallel lines
or crescents. The inner membrane is smooth having no ribosomes. The nuclear membrane is
followed by a supporting membrane, the fibrous lamina, of uniform thickness (300 A thick).

23
Nuclear pores:
The nuclear membrane possesses a number of nuclear pores or annuli, which vary from 40
to 145 per square micro-meter in nuclei of various plants and animals. Watson (1959) stated
the number of pores in mammalian cells as 10 percent of the total surface of the nucleus. In
amphibian oocytes, certain plant cells and protozoa the surface occupied by the pores may be
as high as 20 to 36 percent.

The nuclear pores are octagonal in shape, their diameter varies from 400-1000 A, and they
are separated from each other by a space of 1500 A. The nuclear pores are enclosed by
circular annuli. At the annulus the inner and outer membranes of the nuclear envelope fuse.

The pores and annuli collectively form the pore complex. Eaqh annulus consists of eight
granules of about 15 nm, which are present on both the nuclear and cytoplasmic surfaces.
Inside the pore is a central granule. Fine fibrils (about 30 A in diameter) extend from central
granule to the peripheral granules, forming a cartwheel structure.

A less defined amorphous annular material is present in the opening itself. This material is
digested by trypsin and remains unaffected when exposed to ribonuclease and
deoxyribonuclease. It means that annular material is protein in nature. The pore complex is
a rigid structure present in a fixed number according to cell type. In certain physiological
stages, however, they may change in number.

For example, they are reduced in number in maturing erythroblasts and spermatids and it is
due to low transcriptional activity of these cells. In some cases, the pore complex is covered
by a thin membrane. It has been suggested that the annulus may serve as a sphincter,
alternately decreasing and increasing the size of the pore with varying conditions.

Some evidence suggests the presence of myosin in the annulus area (Du Praw, 1970).
Annulus is supposed to be a hollow cylinder fitting into the nuclear pore (Witschnitzer,
1958). The lumen of the cylinder is 500 A in diameters representing the nuclear pore.

The wall of the cylinder consists of eight evenly placed microtubules or microcylinders. Each
microtubule is about 200 A in diameters. According to Viviers, a central microtubule of 150
to 180 A diameters is present with in the lumen of annulus and is attached to its inner wall
by fibrous struts.

24
Amorphous annular material extends beyond the pore margins (Franke and co-workers,
1966-74). The materials exchanged between nucleus and cytoplasm must traverse the
nuclear pore complexes. Thus, annuli or pores control the passage of some molecules and
particles, even some ribosome components, between nucleus and cytoplasm. This exchange
is very selective and allows passage of only certain molecules of either low or very high
molecular weight. The nuclear envelope is a diffusion barrier for ions as small as K +, Na+ or
Сl–.
On the other hand, very large structures such as ribosomal subunits, which are assembled in
the nucleolus, are able to leave the nucleus through the nuclear pore complexes. The unit
membranes of karyotheca are composed of protein and lipid, like plasma membrane.

At the margins of these pores, the two unit membranes are continuous and at certain places
this nuclear membrane joins the membrane of endoplasmic reticulum. In the apothecial
(reproductive) cells of Mollisia (an ascomycetes fungus), the nuclear membrane makes direct
contact with the plasma membrane of cell.

B. Nuclear sap (karyolymph or nucleoplasm):

The nucleus contains a transparent, semi-solid, granular and homogeneous matrix during
interphase called as nuclear sap or karyolymph (enchylema). This karyolymph is a fluid
substance containing many particles and network. Primarily it is composed of proteinous
material and is the main site for enzyme activity. This nuclear sap also shows variable
appearance during different stages of cell division. There is some evidence that karyolymph
contributes to the formation of the spindle apparatus in plants.

Recently, Bernhard (1968) has described the localization of RNP (ribonucleoprotein) in the
nucleus, being mainly fibrillar and granular types. Besides, in nucleoplasm, there are (i)
interchromatic RNP fibrils located near the chromatin, (ii) interchromatic RNP granules
measuring about 250A in diameter and present around chromatin, (iii) Perichromatic RNP
granules of about 450A diameter, and (iv) large RNP coiled bodies and RNA granules of 300-
400A in diameter. In nuclei of Amoeba, there are present helices of about 700|i length and
300-800A in diameter.

Nuclear constituents:
The nucleus contains RNA, DNA, proteins of two kinds, histone and nonhistone; some lipids;
various organic phosphorus compounds; and various inorganic compounds, mostly salts
(Davidson, 1976).

DNA:
In Salmon sperm heads, which are mostly occupied by nucleus, may constitute 48.5 % of the
dry, fat-free substance. Generally less than half the dry weight is DNA but the amount varies
from species to species. DNA remains constant and do not vary with nutrition or during
starvation, while proteins in nuclei vary, presistent (ultra-structure,)

25
RNAs:
Three kinds of RNA are present in cells: ribosomal (rRNA), transfer (tRNA) and messenger
(mRNA). RNA contains nucleotides of the purines, adenine and guanine and pyrimidines,
cytosine and uracil. In any of these RNAs the ratio of the bases to one another is constant for
a species. However, rRNA, tRNA and mRNA separated from one another disclose different
base ratio, indicating difference^ in their chemical composition.

The tRNAs have low molecular weight of about 25,000, the rRNAs have molecular weights
running to several million, and mRNAs are from half a million to several million. Differences
also exist in the affinities of the various RNAs for other molecules (Lehninger, 1975). The
rRNA is synthesized and assembled in the nucleolus, tRNAs and mRNAs are synthesized on
the chromosomes, and all the RNAs enter the cytoplasm through the nuclear pores.

Enzymes:
The nucleus contains a number of enzymes and performs metabolism, including synthesis of
DNA and various RNAs. Nucleus lacks the enzymes for aerobic metabolism that are found in
mitochondria, but it contains enzymes for anaerobic metabolism and for formation of high-
energy phosphates. It also contains enzymes for coenzyme synthesis (nicotinamide adenine
dinucleotide or NAD).

Proteins:
A variety of proteins is present in the nucleus: nucleoproteins, enzymes and structural
proteins. The nucleoproteins form two classes, deoxyribonucleoproteins and
ribonucleoproteins.

Deoxyribonucleoproteins:
These largely form the chromosomes; consist primarily of histories and DNA in about equal
amounts. However, chromosomes also contain non-histone proteins in smaller amounts.

Unlike histones, most of the nonhistone proteins are acidic, and they vary qualitatively in
different cell types of the same organism.

Non-histone proteins are complexed to areas of DNA whose information is being expressed.
Hence it has been suggested that nonhistone proteins, along with chromosomal RNA which
also binds to certain active portions of DNA, may somehow be involved in the specific
control of gene expression. However, if nonhistone proteins do regulate gene expression, we
do not know how this occurs.

Nonhistone proteins contain the aromatic amino acid tryptophan. A considerable amount of
the contractile proteins actin, myosin, tropomyosin and tubulin are said to be present.
Nonhistone proteins have a more rapid turnover than histones do.

Both histones and nonhistone proteins are synthesized in the cytoplasm and enter the
nucleus through the nuclear envelope. Histones are synthesized only when DNA is
replicated, whereas nonhistone proteins are synthesized continuously. Histones induce a
compact structure in the chromosome.

Histones are also considered as stabilizers against heat damage (Tashiro and Kurakawa,
1976) and against nucleases (Toczko et al., 1975). Activation and repression of genic
expression are thought to be carried out by nonhistone proteins. However, the mechanism by
which this is done in eukaryotic cells is less clear than it is in prokaryotic cells. All the
proteins are synthesized in the cytoplasm and then transported into the nucleus.

26
C. Chromatin: DNA plus histones:
DNA is the main genetic constituent of cells, carrying information in a coded form from cell
to cell and from organism to organism. Within cells, DNA is not free but is complexed with
proteins in a structure called chromatin.

Chromatin:
It appears as a viscous, gelatinous substance which contains DNA, RNA, basic proteins called
histones, and nonhistone (more acidic) proteins. The content of RNA and non-histone
protein is variable between different chromatin preparations, but histone and DNA are
always present in a fixed ratio about one to one by weight. The nonhistone proteins are very
heterogeneous; they vary in different tissues and include RNA and DNA polymerase.

Histones:
These are small proteins which are basic because they have a high content (10 to 20 percent)
of the basic amino acids arginine and lysine. Being basic, histones bind tightly to DNA which
is acid. The four main histones, H2A, H2B and H4 are very similar in different species.

These four histones are present in equimolar amounts, two of each being present every 200
pairs of DNA. Histone HI is not conserved between species and has tissue-specific forms. It
is present only once per 200 base pairs of DNA and is rather loosely associated with
chromatin (it can be eluted from DNA by adding low concentrations of salt).

It is not a component of the DNA-histone structural unit called the nucleosome core, but it is
bound to the linker segments of DNA that join neighbouring neucleosome. All histones
consist of a single polypeptide chain and have molecular weights between 11,000 and
21,000.

Functions of histones:
It is quite likely that they aid in the packing of DNA within the nucleus, and the binding of
histone to DNA serves to prevent the expression of hereditary information. All the hereditary
information present in any one cell is not expressed at all times. At any one moment, only a
very small proportion of the total information is expressed, i.e., only during a short period of
embryonic life. Prokaryotes do not have histones but a basic protein that might serve the
same function.

Chromatin has a repeating structure of beads about 10 nm in diameter connected by a string

of DNA. The 10 nm fibre represents the first level of organization of chromatin within cells.

The chromatin appears as thread-like, coiled and elongated structure which can be stained
with basic stains (e.g., basic fuchsin, orcein or Giemsa). These structures are termed
chromatin fibres or chromatin substance (Gr., chrome, colour). These are visible during
interphase stage.

In interphase, chromatin of the chromosomes spreads out as a fine threads of linin, but at
certain regions, the chromatin remains condensed in the form of darkly stained chromatin
mass. These condensed regions are heterochromatic regions or heterochromatin, and the
dispersed regions are euchromatin. Both regions are formed of DNA.

During cell division, chromatin fibres become thick ribbon-like structure known as
chromosomes. The chromatin fibres remain twisted or form a network in the nucleoplasm.
The chromatin material is of two types:

1. Heterochromatin:

27
Certain regions of chromosomes containing chromatin mass become more darkly stained
than other regions. These particular darkly-stained parts are called as heterochromatic
regions or simply heterochromatin. The darkly staining regions show numerous bead-like
bodies along the chromosomes, called as chromomeres.

There are evidences that heterochromatic regions have a higher ribonucleic acid content
than the euchromatic regions. The heterochromatin is supposed to be metabolically and
genetically inert since it possesses small amount of DNA and large amount of RNA.

2. Euchromatin:
The light stained region of chromatin is called the euchromatic part or euchromatin. It
contains relatively more DNA.

D. Nucleolus:
Embedded in the matrix of nucleus there is a dense rounded, oval and acidophilic body
called as nucleolus, first described by Fontana in 1781 (nucleolus meaning ‘small nucluns’).
Nucleolus has no membrane of its own and is more dense than the surrounding nucleoplasm
and hence is distinctly visible.

Size:
The size of the nucleolus is related with the synthetic activity of the cell. Cells with little or no
synthetic activity (e.g., muscle cells, blastomeres, sperm cells, etc.) are found to contain
smaller or no nucleoli. On the other side, the secretory cells, neurons and oocytes which
synthesize proteins or other substances possess relatively large nucleoli. In the living cell,
nucleoli are highly refringent bodies due to large concentration of solid material.

Number:
The number of nucleoli in nucleus depends upon the number of chromosomes and species.
There may be only one nucleolus in many plants and animal cells for each haploid set of
chromosomes. In others, there may be two or more nucleoli for each haploid set of
chromosomes. In man, there are two pairs of nucleoli in each diploid nucleus.

The nucleolus stains with pyronine and other stains and absorbs ultraviolet light at 260 nm.
Treatment with ribonuclease shows that the capacity to absorb this basophilic stain and
ultravoilet radiation depends on the presence of RNA.

Position:
There are certain heterochromatic regions of specific chromosomes found in association with
the nucleolus, constituting nucleolar organizing regions of chromosomes. This indicates that
although all of the chromosomes contribute to the formation of nucleolar material but these
certain organizing regions are responsible for its constitution. The nucleolar organizers are
now known to contain the genes coding for 18S, 28S and 5.8S and RNAs.

The 18S, 5.8S and 28S RNAs are synthesized in the nucleolus, where as 5S RNA is
synthesized on the chromosomes outside the nucleolus and the 70 ribosomal proteins are
synthesized in the cytoplasm.

All these components migrate to the nucleolus, where they are assembled into ribosomes and
transported to the cytoplasm. The nucleolar organizer is usually located in a secondary
constriction on the chromosome, i. e., in a chromosomal site that becomes less condensed
during mitosis.

There may be more than one nucleolar organizer region among the chromatin strands in a
nucleus, and hence more than one nucleolus may be present in a single cell.

28
The nucleolus is known to be the cellular site for the synthesis of ribosomal RNA, the RNA
component of the ribosomes.

1. Chemical composition of nucleolus:

Maggio, Palade (1963) and Vincent (1952) have described the chemical composition of
nucleolus. In liver cells, nucleoli contain RNA as 3-5%, whereas in pea embryo, RNA
contents are 10% or 20% of total nuclear RNA. The protein components include mainly
phosphoproteins.

Histones have not been reported in the isolated nucleoli but Tandler (1962) has described a
high concentration of orthophosphates, which may serve as a precursor of the RNA
phosphorus. Besides, Sirlin, Jacob and Tandler (1963) have verified the presence of acid
phosphatase, nucleoside, phosphorylase, DPN synthetase and RNA methylase enzymes,
although some of them may be lacking in different nucleoli.

2. Types of nucleoli:
According to E.B. Wilson, there are two or three categories of nucleoli, namely plasmosomes
or true nucleoli and karyosomes (Ogata) or chromatin-nucleoli, etc.

(a) Plasmosomes:
The plasmosomes are of oxyphilic nature, i.e., get staind with acidic stains. Their outer part
is transparent, called as halo, and inner one is dense.

(b) Karyosomes (Ogata):

These are basophilic in nature, i.e., get stained with basic dyes. Montgomery calls them as
chromatin nucleoli. They are associated with the chromosomes formation during cell
division. The karyosomes are of 3 kinds: Firstly, they may be net-knot type (i.e., in the form
of nodes composing spireme threads).

Secondly, they include chromosome nucleoli which occur only in gametocytes and are
spheroidal bodies. They represent a group of chromosomes in a condensed form during
resting phase. The third category includes karyospheres which are called nucleolus—noyanx
by Carnoy. They are also spheroidal bodies having basic chromatin.

(c) Amphinucleoli:
Sometimes plasmosomes and karyosomes are closely associated to form a double nucleolus
or amphinucleolus. These are very common in the eggs of molluscs, annelids, etc.

3. Components of nucleolus:
During cell division the nucleolus generally disappears during the first stage or prophase
stage, but it reappears in the daughter cells. Morphologically, two components may be
defined in a nucleolus:

(a) Pars amorpha:

This is a component of nucleolus which first disappears but reappears at the end of division.
This is the amorphous part which begins to disappear just prior to the breakdown of nuclear
membrane during cell division and reappears in daughter nuclei as division completes.

(b) Nucleolonema:
This is the second and permanent component which does not disappear but remains
persistent throughout the cell cycle. It is a filamentous structure having 80A fibrils with
which 150A particles of ribonucleoprotein are attached.

29
4. Ultra-structure of nucleolus:
Recently, as a result of high resolution studies (ultra-structure), it has been demonstrated
that there exists a definite submicroscopic organization within the nucleolus. The various
elements as described by De Robertis et al., (1971) are as follows:

(a) Granular portion being made up of dense granules arranged peripherally and measuring
about 150-200 A in diameter. This granular zone occupies the peripheral region of the
nucleolus, which is surrounded by the associated chromatin.

It consists of ribonucleic proteins. Granular zone contains ribosome precursor particles at

various stages of assembly and processing. Once the ribosomal subunits are mature, they are
released from the nucleolus and exit into the cytoplasm through the nuclear pores.

(b) Fibrillar portion having the fibrils of 50-80A length and composed of ribonucleoprotein.
This region is also known as nucleolonema. It generally occupies the central region of the
nucleolus. Both the granular and fibrillar zones are digested by ribonuclease. Fibrillar zone
contains rRNA genes that uncoil from the chromosome and penetrate the nucleolus, together
with nascent RNA molecules attached to it.

(c) Amorphous region having low electron density (dielectronic) and formed of certain
proteins which can be hydrolysed easily by the pepsin enzyme.

(d) Nucleolus associated chromatin present around the nucleolus which sometimes extends
into the nucleolus. The nucleolus has no limiting membrane and the calcium ions are
believed to maintain the intact organization of the nucleolus.

The nucleolus also contains vacuoles having no limiting membrane and it possesses certain
proteins. The chromatin of the nucleolar organizer becomes associated with fibrillar and
granular material to form the nucleolus.

During cellular reproduction, when the chromatin is condensed into discrete chromosomes,
nucleoli usually disappear, but they re-form later in the interphase nuclei of the new
daughter cells.

5. Functions of nucleolus:
It serves the following functions:

(a) Role in mitosis:

The nucleolus plays a significant part in mitosis. In grasshopper neuroblasts, there are two
nucleoli in each nucleus. If any one of these nucleoli is injured by ultra-violet radiation or by

30
other source, the mitosis is permanently stopped. It gives a clear evidence that both nucleoli
must be present for the initiation of mitosis.

(b) Help in protein synthesis:

The nucleoli help in protein synthesis by the formation of ribonucleic acid. This ribonucleic
acid (RNA) plays an important role in the formation of proteins. The cells with a high rate of
protein synthesis have large nucleoli with a high RNA content, whereas the cells with a low
rate of protein synthesis have small undeveloped nucleoli.

The nucleolus is a factory for ribosomes. The nucleolus is formed at the nucleolar organizer,
which is a chromosomal site that contains tandem (one behind another) repeats of the genes
coding for 18S and 28S rRNA.

This DNA becomes uncoiled and penetrates the nucleolus, where it is actively transcribed. In
addition, other ribosomal components such as 5S RNA and the ribosomal proteins, which
are synthesized in other parts of the cell, converge on the nucleolus, where the assembly of
ribosomal subunits starts.

(c) As intermediator in the transmission of genetic information:

The nucleolus serves as an intermediary for carrying the genetic information from
generation to generation. Evidences for this function are given by the structure of the
salivary gland cell of Bradysia mycorum (Sciaridae).

These gland cells contain large multiple nucleoli which arise from the primary nucleoli
associated with the chromosomes. These primary nucleoli become detached from
chromosomes and become congregated to form multiple nucleoli which are considered to be
the main site of genetic information.

6. Biogenesis of nucleolus cycle:

During mitosis the nucleoli undergo cyclic changes. Nucleoli are formed around the DNA
loop that extends from the nucleolar organizer. Thus, nucleoli are tormed from loops of one
or more chromosomes combining with specific proteins. There may be several nucleoli per
cell, but frequently they tend to fuse into one or a few nucleoli at this stage.

During late prophase the DNA loop containing rRNA genes gradually retracts and coils into
the nucleolar organizer of the corresponding chromosome. Since this DNA is highly extended
as a result of intense RNA synthesis, the nucleolar organizer region is one of the last to
undergo condensation, thus producing a secondary constriction on the chromosome.

The fibrillar and granular regions are gradually dispersed into the nucleoplasm. After the cell
divides, during telophase, the nucleolar organizer DNA uncoils and the nucleolus is
reassembled.

The chromatin material of the nucleolar organizer carries the information that directs the
formation of the nucleolus and of the ribosomal RNA. In the nucleolus, the newly
synthesized ribosomal RNA (probably the fibrillar material of nucleolus) combines with
proteins, which are apparently synthesized in the cytoplasm and transported to the
nucleolus, to form particles (nucleolar granules) that are precursors to cytoplasmic
ribosomes.

E. Endosomes:
These are rather smaller chromatin bodies present in the nucleoplasm of nucleus. They are
like nucleolus but smaller in size, showing changeable structure.

31
CHAPTER 4 : TRANSPORT IN THE PLASM MEMBRANE

1. Active Transport
In contrast to facilitated diffusion, which does not require energy and carries
molecules or ions down a concentration gradient, active transport pumps
molecules and ions against a concentration gradient. Sometimes an organism needs
to transport something against a concentration gradient. The only way this can be
done is through active transport, which uses energy that is produced by respiration
(ATP). In active transport, the particles move across a cell membrane from a lower
concentration to a higher concentration. Active transport is the energy-requiring
process of pumping molecules and ions across membranes "uphill" - against a
concentration gradient.

 The active transport of small molecules or ions across a cell membraneis generally
carried out by transport proteins that are found in the membrane.
 Larger molecules such as starch can also be actively transported across the cell
membrane by processes called endocytosis and exocytosis.

Endocytosis and Exocytosis

Some molecules or particles are just too large to pass through the plasma
membrane or to move through a transport protein. So cells use two other active
transport processes to move these macromolecules (large molecules) into or out of
the cell. Vesicles or other bodies in the cytoplasm move macromolecules or large
particles across the plasma membrane. There are two types of vesicle transport,
endocytosis and exocytosis (illustrated in Figure below). Both processes are active
transport processes, requiring energy.

[Figure 1]
Illustration of the two types of vesicle transport, exocytosis and endocytosis.

32
Endocytosis is the process of capturing a substance or particle from outside the cell
by engulfing it with the cell membrane. The membrane folds over the substance and
it becomes completely enclosed by the membrane. At this point a membrane-bound
sac, or vesicle, pinches off and moves the substance into the cytosol. There are two
main kinds of endocytosis:

 Phagocytosis, or cellular eating, occurs when the dissolved materials enter the cell.
The plasma membrane engulfs the solid material, forming a phagocytic vesicle.
 Pinocytosis, or cellular drinking, occurs when the plasma membranefolds inward to
form a channel allowing dissolved substances to enter the cell, as shown
in Figure below. When the channel is closed, the liquid is encircled within a pinocytic
vesicle.

[Figure 2]
Transmission electron microscope image of brain tissue that shows pinocytotic vesicles. Pinocytosis is a type of endocytosis.

Exocytosis describes the process of vesicles fusing with the plasma membrane and
releasing their contents to the outside of the cell, as shown in Figure below.
Exocytosis occurs when a cell produces substances for export, such as a protein, or
when the cell is getting rid of a waste product or a toxin. Newly made membrane
proteins and membrane lipids are moved on top the plasma membrane by
exocytosis.

[Figure 3]
Illustration of an axon releasing dopamine by exocytosis.

33
 2. Pasive Transport
Probably the most important feature of a cell’s phospholipid membranes is that they
are selectively permeable or semipermeable. A membrane that is selectively
permeable has control over what molecules or ions can enter or leave the cell, as
shown in Figure below. The permeability of a membrane is dependent on the
organization and characteristics of the membrane lipids and proteins. In this way, cell
membranes help maintain a state of homeostasis within cells (and tissues, organs,
and organ systems) so that an organism can stay alive and healthy.

[Figure 1]
A selectively permeable membrane allows certain molecules through, but not others.

Transport Across Membranes

The molecular make-up of the phospholipid bilayer limits the types of molecules that
can pass through it. For example, hydrophobic (water-hating) molecules, such as
carbon dioxide (CO2) and oxygen (O2), can easily pass through the lipid bilayer, but
ions such as calcium (Ca2+) and polar molecules such as water (H2O) cannot. The
hydrophobic interior of the phospholipid bilayer does not allow ions or polar
molecules through because these molecules are hydrophilic, or water loving. In
addition, large molecules such as sugars and proteins are too big to pass through
the bilayer. Transport proteins within the membrane allow these molecules to pass
through the membrane, and into or out of the cell. This way, polar molecules avoid
contact with the nonpolar interior of the membrane, and large molecules are moved
through large pores.

Every cell is contained within a membrane punctuated with transport proteins that act
as channels or pumps to let in or force out certain molecules. The purpose of the
transport proteins is to protect the cell's internal environment and to keep its balance
of salts, nutrients, and proteins within a range that keeps the cell and the organism
alive.

There are three main ways that molecules can pass through a phospholipid
membrane. The first way requires no energy input by the cell and is called passive
transport. The second way requires that the cell uses energy to pull in or pump out
certain molecules and ions and is called active transport. The third way is through
vesicle transport, in which large molecules are moved across the membrane in
bubble-like sacks that are made from pieces of the membrane.

34
Passive transport is a way that small molecules or ions move across the cell
membrane without input of energy by the cell. The three main kinds of passive
transport are diffusion, osmosis, and facilitated diffusion.

Diffusion
Diffusion is the movement of molecules from an area of high concentration of the
molecules to an area with a lower concentration. The difference in the concentrations
of the molecules in the two areas is called the concentration gradient. Diffusion will
continue until this gradient has been eliminated. Since diffusion moves materials
from an area of higher concentration to the lower, it is described as moving solutes
"down the concentration gradient." The end result of diffusion is an equal
concentration, or equilibrium, of molecules on both sides of the membrane.

If a molecule can pass freely through a cell membrane, it will cross the membrane by
diffusion (Figure below).

[Figure 2]
Molecules move from an area of high concentration to an area of lower concentration until an equilibrium is met. The
molecules continue to cross the membrane at equilibrium, but at equal rates in both directions.

Facilitated Diffusion
What happens if a substance needs assistance to move across or through
the plasma membrane? Facilitated diffusion is the diffusion of solutes through
transport proteins in the plasma membrane. Facilitated diffusion is a type of passive
transport. Even though facilitated diffusion involves transport proteins, it is still
passive transport because the solute is moving down the concentration gradient.

35
Small nonpolar molecules can easily diffuse across the cell membrane. However,
due to the hydrophobic nature of the lipids that make up cell membranes, polar
molecules (such as water) and ions cannot do so. Instead, they diffuse across the
membrane through transport proteins. A transport protein completely spans the
membrane, and allows certain molecules or ions to diffuse across the membrane.
Channel proteins, gated channel proteins, and carrier proteins are three types of
transport proteins that are involved in facilitated diffusion.

A channel protein, a type of transport protein, acts like a pore in the membrane that
lets water molecules or small ions through quickly. Water channel proteins
(aquaporins) allow water to diffuse across the membrane at a very fast
rate. Ion channel proteins allow ions to diffuse across the membrane.

A gated channel protein is a transport protein that opens a "gate," allowing a

molecule to pass through the membrane. Gated channels have a binding site that is
specific for a given molecule or ion. A stimulus causes the "gate" to open or shut.
The stimulus may be chemical or electrical signals, temperature, or mechanical
force, depending on the type of gated channel. For example, the sodium gated
channels of a nerve cell are stimulated by a chemical signal which causes them to
open and allow sodium ions into the cell. Glucose molecules are too big to diffuse
through the plasma membrane easily, so they are moved across the membrane
through gated channels. In this way glucose diffuses very quickly across a cell
membrane, which is important because many cellsdepend on glucose for energy.

A carrier protein is a transport protein that is specific for an ion, molecule, or group
of substances. Carrier proteins "carry" the ion or molecule across the membrane by
changing shape after the binding of the ion or molecule. Carrier proteins are involved
in passive and active transport. A model of a channel protein and carrier proteins is
shown in Figure below.

[Figure 1]
Facilitated diffusion through the cell membrane. Channel proteins and carrier proteins are shown (but not a gated-channel
protein). Water molecules and ions move through channel proteins. Other ions or molecules are also carried across the cell
membrane by carrier proteins. The ion or molecule binds to the active site of a carrier protein. The carrier protein changes
shape, and releases the ion or molecule on the other side of the membrane. The carrier protein then returns to its original
shape.

36
Ion Channels
Ions such as sodium (Na+), potassium (K+), calcium (Ca2+), and chloride (Cl-), are
important for many cell functions. Because they are charged (polar), these ions do
not diffuse through the membrane. Instead they move through ion channel proteins
where they are protected from the hydrophobic interior of the membrane. Ion
channels allow the formation of a concentration gradient between the extracellular
fluid and the cytosol. Ion channels are very specific, as they allow only certain ions
through the cell membrane. Some ion channels are always open, others are "gated"
and can be opened or closed. Gated ion channels can open or close in response to
different types of stimuli, such as electrical or chemical signals.

Osmosis
Imagine you have a cup that has 100ml water, and you add 15g of table sugar to the
water. The sugar dissolves and the mixture that is now in the cup is made up of
a solute (the sugar) that is dissolved in the solvent (the water). The mixture of a
solute in a solvent is called a solution.

Imagine now that you have a second cup with 100ml of water, and you add 45 grams
of table sugar to the water. Just like the first cup, the sugar is the solute, and the
water is the solvent. But now you have two mixtures of different solute
concentrations. In comparing two solutions of unequal solute concentration,
the solution with the higher solute concentration is hypertonic, and the solution with
the lower solute concentration is hypotonic. Solutions of equal solute concentration
are isotonic. The first sugar solution is hypotonic to the second solution. The second
sugar solution is hypertonic to the first.

You now add the two solutions to a beaker that has been divided by a selectively
permeable membrane, with pores that are too small for the sugar molecules to pass
through, but are big enough for the water molecules to pass through. The hypertonic
solution is on one side of the membrane and the hypotonic solution on the other. The
hypertonic solution has a lower water concentration than the hypotonic solution, so a
concentration gradient of water now exists across the membrane. Water molecules
will move from the side of higher water concentration to the side of lower
concentration until both solutions are isotonic. At this point, equilibrium is reached.

Osmosis is the diffusion of water molecules across a selectively permeable

membrane from an area of higher concentration to an area of lower concentration.
Water moves into and out of cells by osmosis. If a cell is in a hypertonic solution, the
solution has a lower water concentration than the cell cytosol, and water moves out
of the cell until both solutions are isotonic. Cells placed in a hypotonic solution will
take in water across their membrane until both the external solution and the cytosol
are isotonic.

A cell that does not have a rigid cell wall, such as a red blood cell, will swell and lyse
(burst) when placed in a hypotonic solution. Cells with a cell wall will swell when
placed in a hypotonic solution, but once the cell is turgid (firm), the tough cell wall
prevents any more water from entering the cell. When placed in a hypertonic

37
solution, a cell without a cell wall will lose water to the environment, shrivel, and
probably die. In a hypertonic solution, a cell with a cell wall will lose water too.
The plasma membranepulls away from the cell wall as it shrivels, a process
called plasmolysis. Animal cells tend to do best in an isotonic environment, plant
cells tend to do best in a hypotonic environment. This is demonstrated
in Figure below.

[Figure 1]
Unless an animal cell (such as the red blood cell in the top panel) has an adaptation that allows it to alter the osmotic uptake
of water, it will lose too much water and shrivel up in a hypertonic environment. If placed in a hypotonic solution, water
molecules will enter the cell, causing it to swell and burst. Plant cells (bottom panel) become plasmolyzed in a hypertonic
solution, but tend to do best in a hypotonic environment. Water is stored in the central vacuole of the plant cell.

Osmotic Pressure
When water moves into a cell by osmosis, osmotic pressure may build up inside the
cell. If a cell has a cell wall, the wall helps maintain the cell’s water
balance. Osmotic pressure is the main cause of support in many plants. When
a plant cell is in a hypotonic environment, the osmotic entry of water raises the turgor
pressure exerted against the cell wall until the pressure prevents more water from
coming into the cell. At this point the plant cell is turgid (Figure below). The effects of
osmotic pressures on plant cells are shown in Figure below.

38
[Figure 2]
The central vacuoles of the plant cells in this image are full of water, so the cells are turgid.

The action of osmosis can be very harmful to organisms, especially ones without cell
walls. For example, if a saltwater fish (whose cells are isotonic with seawater), is
placed in fresh water, its cells will take on excess water, lyse, and the fish will die.
Another example of a harmful osmotic effect is the use of table salt to kill slugs and
snails.

Controlling Osmosis
Organisms that live in a hypotonic environment such as freshwater, need a way to
prevent their cells from taking in too much water by osmosis. A contractile
vacuole is a type of vacuole that removes excess water from a cell.
Freshwater protists, such as the paramecium shown in Figure below, have a
contractile vacuole. The vacuole is surrounded by several canals, which absorb
water by osmosis from the cytoplasm. After the canals fill with water, the water is
pumped into the vacuole. When the vacuole is full, it pushes the water out of the cell
through a pore.

[Figure 3]
The contractile vacuole is the star-like structure within the paramecia

39
CHAPTER 5 : CELL-CELL INTERACTION

Cell–cell interaction refers to the direct interactions between cell surfaces that play a crucial
role in the developmentand function of multicellular organisms. These interactions allow cells
to communicate with each other in response to changes in their microenvironment. This ability to
send and receive signals is essential for the survival of the cell. Interactions between cells can be
stable such as those made through cell junctions. These junctions are involved in the
communication and organization of cells within a particular tissue. Others are transient or
temporary such as those between cells of the immune system or the interactions involved in
tissue inflammation. These types of intercellular interactions are distinguished from other types
such as those between cells and the extracellular matrix. The loss of communication between
cells can result in uncontrollable cell growth and cancer.

Stable interactions

Various types of cell junctions. In this diagram, the interface between neighboring cells or the basolateral
membrane is depicted as "sheets"; the space between these sheets being the extracellular environment
and the location of adhesion protein interaction.

Stable cell-cell interactions are required for cell adhesion within a tissue and controlling the
shape and function of cells. These stable interactions involve cell junctions which are multiprotein
complexes that provide contact between neighboring cells. Cell junctions allow for the
preservation and proper functioning of epithelial cell sheets. These junctions are also important in
the organization of tissues where cells of one type can only adhere to cells of the same tissue
rather than to a different tissue.
Tight junctions
Tight junctions are multi-protein complexes that hold cells of a same tissue together and prevent
movement of water and water-soluble molecules between cells. In epithelial cells, they function
also to separate the extracellular fluid surrounding their apical and basolateral
membranes. These junctions exist as a continuous band located just below the apical surface
between the membranes of neighboring epithelial cells. The tight junctions on adjacent cells line
up so as to produce a seal between different tissues and body cavities. For example, the apical
surface of gastrointestinal epithelial cells serve as a selective permeable barrier that separates
the external environment from the body.[3] The permeability of these junctions is dependent on a
variety of factors including protein makeup of that junction, tissue type and signaling from the
cells.
Tight junctions are made up of many different proteins. The four main transmembrane proteins
are occludin, claudin, junctional adhesion molecules (JAMs) and tricellulins. The extracellular
domains of these proteins form the tight junction barrier by making homophilic (between proteins
of the same kind) and heterophilic interactions (between different types of proteins) with the
protein domains on adjacent cells. Their cytoplasmic domains interact with the cell cytoskeleton
to anchor them.

40
Anchoring junctions
Of the three types of anchoring junctions, only two are involved in cell-cell interactions: adherens
junctions and desmosomes. Both are found in many types of cells. Adjacent epithelial cells are
connected by adherens junctions on their lateral membranes. They are located just below tight
junctions. Their function is to give shape and tension to cells and tissues and they are also the
site of cell-cell signaling. Adherens junctions are made of cell adhesion molecules from
the cadherin family. There are over 100 types of cadherins, corresponding to the many different
types of cells and tissues with varying anchoring needs. The most common are E-, N- and P-
cadherins. In the adherens junctions of epithelial cells, E-cadherin is the most abundant.
Desmosomes also provide strength and durability to cells and tissues and are located just below
adherens junctions. They are sites of adhesion and do not encircle the cell. They are made of
two specialized cadherins, desmoglein and desmocollin. These proteins have extracellular
domains that interact with each other on adjacent cells. On the cytoplasmic side, plakins form
plaques which anchor the desmosomes to intermediate filaments composed of keratin proteins.
Desmosomes also play a role in cell-cell signaling.
Gap junctions
Gap junctions are the main site of cell-cell signaling or communication that allow small molecules
to diffuse between adjacent cells. In vertebrates, gap junctions are composed of transmembrane
proteins called connexins. They form hexagonal pores or channels through which ions, sugars,
and other small molecules can pass. Each pore is made of 12 connexin molecules; 6 form a
hemichannel on one cell membrane and interact with a hemichannel on an adjacent cell
membrane. The permeability of these junctions is regulated by many factors including pH and
Ca2+ concentration.
Receptor proteins in direct-contact signaling
Receptor proteins on the cell surface have the ability to bind specific signaling molecules
secreted by other cells. Cell signaling allows cells to communicate with adjacent cells, nearby
cells (paracrine) and even distant cells (endocrine). This binding induces a conformational
change in the receptor which, in turn, elicits a response in the corresponding cell. These
responses include changes in gene expression and alterations in cytoskeleton structure. The
extracellular face of the plasma membrane has a variety of proteins, carbohydrates,
and lipids which project outward and act as signals. Direct contact between cells allows the
receptors on one cell to bind the small molecules attached to the plasma membrane of different
cell. In eukaryotes, many of the cells during early development communicate through direct
contact.
Synaptic signaling, an integral part of nervous system activity, occurs between neurons and
target cells. These target cells can also be neurons or other cell types
(i.e. muscle or gland cells). Protocadherins, a member of the cadherin family, mediate the
adhesion of neurons to their target cells at synapses otherwise known as synaptic junctions. In
order to for communication to occur between a neuron and its target cell, a wave of
depolarization travels the length of the neuron and causes neurotransmitters to be released into
the synaptic junction. These neurotransmitters bind and activate receptors on the post-synaptic
neuron thereby transmitting the signal to the target cell. Thus, a post-synaptic membranebelongs
to the membrane receiving the signal, while a pre-synaptic membrane is the source of the
neurotransmitter. In a neuromuscular junction, a synapse is formed between a motor
neuron and muscle fibers. In vertebrates, acetylcholinereleased from the motor neuron acts as a
neurotransmitter which depolarizes the muscle fiber and causes muscle contraction. A neuron’s
ability to receive and integrate simultaneous signals from the environment and other neurons
allows for complex animal behavior.
Plant cell-cell interactions
Plant cells are surrounded by cell walls which are barriers for cell-cell communication. This
barrier is overcome by specialized junctions called plasmodesmata. They are similar to gap
junctions, connecting the cytosol of adjacent cells. Small molecules (<1000 Da), such as ions,

41
amino acids, and sugars, can diffuse freely through plasmodesmata. These small molecules
include signaling molecule and transcription factors. The size of the channel is also regulated to
allow molecules up to 10,000 Da in size. The permeability of these channels is dependent on
many factors, including Ca2+ concentration. An increase in cytosolic Ca2+ concentration will
reversibly limit passage through the plasmodesmata. Unlike gap junctions, the cell membranes of
adjacent cells merge to form a continuous channel called an annulus. Additionally, within the
channel, there is an extension of the endoplasmic reticulum, called a desmotubule, which spans
between the cells. The cell-cell interactions facilitated by plasmodesmata play an important role
in development of plant cells and tissues and defense against viral infection.

Transient interactions
Immune system
Leukocytes or white blood cells destroy abnormal cells and also provide protection against
bacteria and other foreign matter. These interactions are transitory in nature but are crucial as an
immediate immune response. To fight infection, leukocytes must move from the blood into the
affected tissues. This movement into tissues is called extravasation. It requires successive
forming and breaking of cell-cell interactions between the leukocytes and the endothelial cells
that line blood vessels. These cell-cell interactions are mediated mainly by a group of Cell
Adhesion Molecules (CAMs) called selectins.
T helper cells, central to the immune system, interact with other leukocytes by releasing signals
known as cytokineswhich activate and stimulate the proliferation of B cells and killer T cells.T
helper cells also directly interact with macrophages, cells that engulf foreign matter and
display antigens on its surface. T-helper cells that possess the appropriate receptors can bind to
these antigens and proliferate resulting in T-helper cells that have the ability to identify the same
antigens.
Coagulation
Coagulation or blood clotting relies on, in addition to the production of fibrin, interactions
between platelets. When the endothelium or the lining of a blood vessel is damaged, connective
tissue including collagen fibers is locally exposed. Initially, platelets stick to the exposed
connective tissue through specific cell-surface receptors. This is followed by platelet activation
and aggregation in which platelets become firmly attached and release chemicals that recruit
neighboring platelets to the site of vascular injury. A meshwork of fibrin then forms around this
aggregation of platelets to increase the strength of the clot.
Cell interactions between bacteria
Bacterial populations interact in a similar manner to cells in tissue. They communicate through
physical interactions and signaling molecules such as homoserine lactones and peptides as a
means to control metabolism and regulate growth . A common example and one of the most
studied forms of bacterial cell interactions is biofilm. Biofilm is a cell aggregate that can be
attached to biological or abiotic surfaces. Bacteria form biofilms to adapt to various environments
such as changes in substrate availability. For example, the formation of biofilm increases a
bacterial cell's resistance to antibiotics compared to cells which are not part of the aggregate.

Pathological implications
Cancer
Cancer can result from the loss of cell-cell interaction. In normal cells, growth is controlled
by contact inhibition in which contact with neighboring cells causes a stunt in cell growth. Contact
inhibition is thought to be mediated by cadherins, proteins that play an important role in cell
adhesion. This inhibition prevents cells from piling up on top of one another and forming mounds.
However, in cancerous cells where expression of E-cadherin is lost, contact inhibition is lost and
results in uncontrolled growth or proliferation, tumor formation, and metastasis.
Bacterial pathogen
42
In order for pathogenic bacteria to invade a cell, communication with the host cell is required.
The first step for invading bacteria is usually adhesion to host cells. Strong anchoring, a
characteristic that determines virulence, prevents the bacteria from being washed away
before infection occurs. Bacterial cells can bind to many host cell surface structures such as
glycolipids and glycoproteins which serve as attachment receptors. Once attached, the bacteria
begin to interact with the host to disrupt its normal functioning and disrupt or rearrange its
cytoskeleton. Proteins on the bacteria surface can interact with protein receptors on the host
thereby affecting signal transduction within the cell. Alterations to signaling are favorable to
bacteria because these alterations provide conditions under which the pathogen can invade.
Many pathogens have Type III secretion systems which can directly inject protein toxins into the
host cells. These toxins ultimately lead to rearrangement of the cytoskeleton and entry of the
bacteria.
Disease
Cell–cell interactions are highly specific and are tightly regulated. Genetic defects and
dysregulation of these interactions can cause many different diseases. Dysregulation that leads
to leukocyte migration into healthy tissues can cause conditions such as acute respiratory
distress syndrome and some types of arthritis.[12] The autoimmune disease pemphigus
vulgaris results from autoantibodies to desmoglein and other normal body proteins. The
autoantibodies disrupt the adhesion between epithelial cells. This causes blisters of the skin and
mucous membranes. Mutations in the connexin genes cause 8 human diseases including heart
malformations and neurosensory deafness.[

43
CHAPTER 6 : METABOLISM
Metabolism is a term that is used to describe all chemical reactions involved in
maintaining the living state of the cells and the organism. Metabolism can be
conveniently divided into two categories:

 Catabolism - the breakdown of molecules to obtain energy (respiration and

fermentation)
 Anabolism - the synthesis of all compounds needed by the cells
(photosynthesis and chemosynthesis)

Aerobic Respiration
Why oxygen?
Oxygen is the final electron acceptor at the end of the electron transport chain of
aerobic respiration. In the absence of oxygen, only a few ATP are produced from
glucose. In the presence of oxygen, many more ATP are made.

Aerobic respiration, which takes place in the presence of oxygen, evolved after
oxygen was added to Earth’s atmosphere. This type of respiration is useful today
because the atmosphere is now 21% oxygen. However, some anaerobic organisms
that evolved before the atmosphere contained oxygen have survived to the present.
Therefore, anaerobic respiration, which takes place without oxygen, must also
have advantages.

Advantages of Aerobic Respiration

A major advantage of aerobic respiration is the amount of energy it releases. Without
oxygen, organisms can split glucose into just two molecules of pyruvate. This
releases only enough energy to make two ATP molecules. With oxygen, organisms
can break down glucose all the way to carbon dioxide. This releases enough energy
to produce up to 38 ATP molecules. Thus, aerobic respiration releases much more
energy than anaerobic respiration.

The amount of energy produced by aerobic respiration may explain why aerobic
organisms came to dominate life on Earth. It may also explain how organisms were
able to become multicellular and increase in size.

Advantages of Anaerobic Respiration

One advantage of anaerobic respiration is obvious. It lets organisms live in places
where there is little or no oxygen. Such places include deep water, soil, and the
digestive tracts of animals such as humans (see Figure below).

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[Figure 1]
E. coli bacteria are anaerobic bacteria that live in the human digestive tract.

Another advantage of anaerobic respiration is its speed. It produces ATP very

quickly. For example, it lets your muscles get the energy they need for short bursts
of intense activity (see Figure below). Aerobic respiration, on the other hand,
produces ATP more slowly.

Anaerobic Respiration: Fermentation

Today, most living things use oxygen to make ATP from glucose. However, many
living things can also make ATP without oxygen. This is true of some plants
and fungi and also of many bacteria. These organisms use aerobic respiration when
oxygen is present, but when oxygen is in short supply, they use anaerobic
respiration instead. Certain bacteria can only use anaerobic respiration. In fact, they
may not be able to survive at all in the presence of oxygen.

An important way of making ATP without oxygen is called fermentation. It

involves glycolysis, but not the other two stages of aerobic respiration.
Many bacteria and yeasts carry out fermentation. People use these organisms to
make yogurt, bread, wine, and biofuels. Human muscle cellsalso use fermentation.
This occurs when muscle cells cannot get oxygen fast enough to meet
their energy needs through aerobic respiration.

There are two types of fermentation: lactic acid fermentation and alcoholic
fermentation. Both types of fermentation are described below.

Lactic Acid Fermentation

In lactic acid fermentation, pyruvic acid from glycolysis changes to lactic acid. This
is shown in Figure below. In the process, NAD+ forms from NADH. NAD+, in turn,
lets glycolysis continue. This results in additional molecules of ATP. This type of
fermentation is carried out by the bacteria in yogurt. It is also used by your own
muscle cells when you work them hard and fast.

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[Figure 1]
Lactic acid fermentation produces lactic acid and NAD+. The NAD+ cycles back to allow glycolysis to continue so more ATP
is made. Each circle represents a carbon atom.

Did you ever run a race and notice that your muscles feel tired and sore afterward?
This is because your muscle cells used lactic acid fermentation for energy. This
causes lactic acid to build up in the muscles. It is the buildup of lactic acid that
makes the muscles feel tired and sore.

Alcoholic Fermentation
In alcoholic fermentation, pyruvic acid changes to alcohol and carbon dioxide. This
is shown in Figure below. NAD+ also forms from NADH, allowing glycolysis to
continue making ATP. This type of fermentation is carried out by yeasts and some
bacteria. It is used to make bread, wine, and biofuels.

[Figure 2]
Alcoholic fermentation produces ethanol and NAD+. The NAD+ allows glycolysis to continue making ATP.

Have your parents ever put corn in the gas tank of their car? They did if they used
gas containing ethanol. Ethanol is produced by alcoholic fermentation of the glucose
in corn or other plants. This type of fermentation also explains why bread dough
rises. Yeasts in bread dough use alcoholic fermentation and produce carbon dioxide
gas. The gas forms bubbles in the dough, which cause the dough to expand. The
bubbles also leave small holes in the bread after it bakes, making the bread light and
fluffy. Do you see the small holes in the slice of bread in Figure below?

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[Figure 3]
The small holes in bread are formed by bubbles of carbon dioxide gas. The gas was produced by alcoholic fermentation
carried out by yeast.

Gut Fermentation
Behind every fart is an army of gut bacteria undergoing some crazy biochemistry.
These bacteria break down the remains of digested food through fermentation,
creating gas in the process.

Photosynthesis
Photosynthesis occurs in two stages, which are shown in Figure below.

1. Stage I is called the light reactions. This stage uses water and changes
light energyfrom the sun into chemical energy stored in ATP and NADPH (another
energy-carrying molecule). This stage also releases oxygen as a waste product.
2. Stage II is called the Calvin cycle. This stage combines carbon from carbon dioxide
in the air and uses the chemical energy in ATP and NADPH to make glucose.

[Figure 1]
The two stages of photosynthesis are the light reactions and the Calvin cycle. Do you see how the two stages are related?

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Stage I: The Light Reactions
Chloroplasts Capture Sunlight
Every second, the sun fuses over 600 million tons of hydrogen into 596 tons of
helium, converting over 4 tons of helium (4.3 billion kg) into light and heat energy.
Countless tiny packets of that light energy travel 93 million miles (150 million km)
through space, and about 1% of the light which reaches the Earth’s surface
participates in photosynthesis. Light is the source of energy for photosynthesis, and
the first set of reactions which begin the process requires light – thus the name, light
reactions, or light-dependent reactions.

When light strikes chlorophyll (or an accessory pigment) within the chloroplast, it
energizes electrons within that molecule. These electrons jump up to
higher energy levels; they have absorbed or captured, and now carry, that energy.
High-energy electrons are “excited.” Who wouldn’t be excited to hold the energy for
life?

The excited electrons leave chlorophyll to participate in further reactions, leaving the
chlorophyll “at a loss”; eventually they must be replaced. That replacement process
also requires light, working with an enzyme complex to split water molecules. In this
process of photolysis (“splitting by light”), H2O molecules are broken into hydrogen
ions, electrons, and oxygen atoms. The electrons replace those originally lost from
chlorophyll. Hydrogen ions and the high-energy electrons from chlorophyll will carry
on the energy transformation drama after the light reactions are over.

The oxygen atoms, however, form oxygen gas, which is a waste product of
photosynthesis. The oxygen given off supplies most of the oxygen in our
atmosphere. Before photosynthesis evolved, Earth’s atmosphere lacked oxygen
altogether, and this highly reactive gas was toxic to the many organisms living at the
time. Something had to change! Most contemporary organisms rely on oxygen for
efficient respiration. So plants don’t just “restore” the air, they also had a major role
in creating it!

To summarize, chloroplasts “capture” sunlight energy in two ways. Light ‘‘excites’’

electrons in pigment molecules, and light provides the energy to
split water molecules, providing more electrons as well as hydrogen ions.

Light Energy to Chemical Energy

Excited electrons that have absorbed light energy are unstable. However, the highly
organized electron carrier molecules embedded in chloroplastmembranes order the
flow of these electrons, directing them through electron transport chains (ETCs).
At each transfer, small amounts of energy released by the electrons are captured
and put to work or stored. Some is also lost as heat with each transfer, but overall
the light reactions are extremely efficient at capturing light energy and transforming it
into chemical energy.

Two sequential transport chains harvest the energy of excited electrons, as shown
in Figure below.

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(1) First, they pass down an ETC, which captures their energy and uses it to pump
hydrogen ions by active transport into the thylakoids. These concentrated ions
store potential energy by forming a chemiosmotic or electrochemical gradient – a
higher concentration of both positive charge and hydrogen inside the thylakoid than
outside. (The gradient formed by the H+ ions is known as a chemiosmotic
gradient.) Picture this energy buildup of H+ as a dam holding back a waterfall.
Like water flowing through a hole in the dam, hydrogen ions “slide down”
their concentrationgradient through a membrane protein which acts as
both ion channel and enzyme. As they flow, the ion channel/enzyme ATP
synthase uses their energy to chemically bond a phosphate group to ADP, making
ATP.

(2) Light re-energizes the electrons, and they travel down a second electron
transport chain (ETC), eventually bonding hydrogen ions to NADP + to form a more
stable energy storage molecule, NADPH. NADPH is sometimes called “hot
hydrogen,” and its energy and hydrogen atoms will be used to help build sugar in the
second stage of photosynthesis.

[Figure 1]
Membrane architecture: The large colored carrier molecules form electron transport chains which capture small amounts of
energy from excited electrons in order to store it in ATP and NADPH. Follow the energy pathways: light → electrons →
NADPH (blue line) and light → electrons → concentrated H+ → ATP (red line). Note the intricate organization of the
chloroplast.

NADPH and ATP molecules now store the energy from excited electrons – energy
which was originally sunlight – in chemical bonds. Thus chloroplasts, with their
orderly arrangement of pigments, enzymes, and electron transport chains, transform
light energy into chemical energy. The first stage of photosynthesis – light-dependent
reactions or simply light reactions – is complete.

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Chemosynthesis
Why do bacteria that live deep below the ocean’s surface rely on chemical
compounds instead of sunlight for energy to make food?

Most autotrophs make food by photosynthesis, but this isn’t the only way that
autotrophs produce food. Some bacteria make food by another process, which uses
chemical energy instead of light energy. This process is called chemosynthesis. In
chemosynthesis, one or more carbon molecules (usually carbon dioxide or methane,
CH4) and nutrients is converted into organic matter, using the oxidation of inorganic
molecules (such as hydrogen gas, hydrogen sulfide (H2S) or ammonia (NH3)) or
methane as a source of energy, rather than sunlight. In hydrogen sulfide
chemosynthesis, in the presence of carbon dioxide and
oxygen, carbohydrates (CH2O) can be produced:

CO2 + O2 + 4H2S → CH2O + 4S + 3H2O

Many organisms that use chemosynthesis are extremophiles, living in harsh

conditions, such as in the absence of sunlight and a wide range
of water temperatures, some approaching the boiling point. Some chemosynthetic
bacteria live around deep-ocean vents known as “black smokers.” Compounds such
as hydrogen sulfide, which flow out of the vents from Earth’s interior, are used by the
bacteria for energy to make food. Consumers that depend on these bacteria to
produce food for them include giant tubeworms, like those pictured in Figure below.
These organisms are known as chemoautotrophs. Many chemosynthetic
microorganisms are consumed by other organisms in the ocean, and symbiotic
associations between these organisms and respiring heterotrophs are quite
common.

[Figure 1]
Tubeworms deep in the Galapagos Rift get their energy from chemosynthetic bacteria. Tubeworms have no mouth, eyes or
stomach. Their survival depends on a symbiotic relationship with the billions of bacteria that live inside them. These bacteria
convert the chemicals that shoot out of the hydrothermal vents into food for the worm.

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