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SEMESTER -II
CORE PAPER III: CELL BIOLOGY
UNIT – I
Ultrastructure of Eubacteria-Cell wall – Cell membrane- Extra mural layer - Slime –
Capsule – Cytoplasmic inclusions – Mesosomes – Nuclear material – Reserve materials Pigment – Cell appendages – Flagella – Pili.
UNIT – II
Ultrasturcute and functions of Eukaryotic cell organelles – Cell wall – Cell membrane Mitochondria – Chloroplast – Endoplasmic reticulum – Golgiconplex – Nucleus –
Ribosomes – Other cell inclusions and Flagella.
UNIT III
Cell division in Bacteria – Binary fission - Cell division of Eukaryotes – Mitosis and
Meiosis.
UNIT IV
Transport mechanisms – Diffusion - Facilitated diffusion – Active transport – Group
translocation – Phagocytosis – Pinocytosis.
UNIT V
Archaebacterial cell wall and cell membranes of Methanogens - Halophiles Thermoacdiphiles.
Write about the ultrastructure of eubacteria:
Cell biology (formerly cytology, from the Greek kytos, "container") is an academic discipline
that studies cells – their physiological properties, their structure, the organelles they contain,
interactions with their environment, their life cycle, division and death. This is done both on a
microscopic and molecular level. Cell biology research encompasses both the great diversity of
single-celled organisms like bacteria and protozoa, as well as the many specialized cells in
multicellular organisms such as humans.
Prokaryotes are single-celled organisms that are the earliest and most primitive forms of life on
earth. As organized in the Three Domain System, prokaryotes include bacteria and archaeans.
Prokaryotes are able to live and thrive in various types of environments including extreme
habitats such as hydrothermal vents, hot springs, swamps, wetlands, and the guts of animals.
Explain about the Prokaryotic Cell Structure.
Prokaryotic cells are not as complex as eukaryotic cells. They have no true nucleus as the DNA
is not contained within a membrane or separated from the rest of the cell, but is coiled up in a
region of the cytoplasm called the nucleoid. Using bacteria as our sample prokaryote, the
following structures can be found in bacterial cells:

Capsule - Found in some bacterial cells, this additional outer covering protects the cell
when it is engulfed by other organisms, assists in retaining moisture, and helps the cell
adhere to surfaces and nutrients.

Cell Wall - Outer covering of most cells that protects the bacterial cell and gives it shape.

Cytoplasm - A gel-like substance composed mainly of water that also contains enzymes,
salts, cell components, and various organic molecules.

Cell Membrane or Plasma Membrane - Surrounds the cell's cytoplasm and regulates
the flow of substances in and out of the cell.

Pili - Hair-like structures on the surface of the cell that attach to other bacterial cells.
Shorter pili called fimbriae help bacteria attach to surfaces.

Flagella - Long, whip-like protrusion that aids in cellular locomotion.

Ribosomes - Cell structures responsible for protein production.

Plasmids - Gene carrying, circular DNA structures that are not involved in reproduction.

Nucleiod Region - Area of the cytoplasm that contains the single bacterial DNA
molecule
Prokaryotic Cell Membranes
Membranes are an absolute requirement for all living organisms.Cells must interact in a selective
fashion with their environment,whether it is the internal environment of a multicellular organism
or a less protected and more variable external environment. Cells must not only be able to
acquire nutrients and eliminate wastes, but they also have to maintain their interior in a constant,
highly organized state in the face of external changes. The plasma membrane encompasses the
cytoplasm of both procaryotic and eucaryotic cells. This membrane is the chief point of contact
with the cell’s environment and thus is responsible for much of its relationship with the outside
world. To understand membrane function, it is necessary to become familiar with membrane
structure, and particularly with plasma membrane structure.
Give detail account on the Plasma Membrane.
Membranes contain both proteins and lipids, although the exact proportions of protein and lipid
vary widely. Bacterial plasma membranes usually have a higher proportion of protein than do
eucaryotic membranes, presumably because they fulfill so many different functions that are
carried out by other organelle membranes in eucaryotes. Most membrane-associated lipids are
structurally asymmetric with polar and nonpolar ends and are called amphipathic. The polar ends
interact with water and are hydrophilic; the nonpolar hydrophobic ends are insoluble in
water and tend to associate with one another. This property of lipids enables them to form a
bilayer in membranes. The outer surfaces are hydrophilic, whereas hydrophobic ends are buried
in the interior away from the surrounding water. Many of these am-phipathic lipids are
phospholipids .Bacterial membranes usually differ from eucaryotic membranes in lacking
sterols such as cholesterol . However, many bacterial membranes do contain pentacyclic sterollike molecules called hopanoids and huge quantities of hopanoids are present in our ecosystem
Hopanoids are synthesized from the same precursors as steroids. Like steroids in eucaryotes,
they probably stabilize the bacterial membrane. The membrane lipid is organized in two layers,
or sheets, of molecules arranged end-to-end .Many archaeal membranes differ from other
bacterial membranes in having a monolayer with lipid molecules spanning the whole membrane.
Cell membranes are very thin structures, about 5 to 10 nm thick, and can only be seen
with the electron microscope. The freeze-etching technique has been used to cleave membranes
down the center of the lipid bilayer, splitting them in half and exposing the interior. In this way it
has been discovered that many membranes, including the plasma membrane, have a complex
internal structure. The small globular particles seen in these membranes are thought to be
membrane proteins that lie within the membrane lipid bilayer .The most widely accepted current
model for membrane structure is the fluid mosaic model of S. Jonathan Singer and
Garth Nicholson ,They distinguish between two types of membrane proteins. Peripheral
proteins are loosely connected to the membrane and can be easily removed. They are soluble
in aqueous solutions and make up about 20 to 30% of total membrane protein. About 70 to 80%
of membrane proteins are integral proteins. These are not easily extracted from membranes
and are insoluble in aqueous solutions when freed of lipids. Integral proteins, like membrane
lipids, are amphipathic; their hydrophobic regions are buried in the lipid while the hydrophilic
portions project from the membrane surface .Some of these proteins even extend all the way
through the lipid layer. Integral proteins can diffuse laterally around the surface to new locations,
but do not flip-flop or rotate through the lipid layer. Often carbohydrates are attached to the outer
surface of plasma membrane proteins and seem to have important functions.The emerging
picture of the cell membrane is one of a highly organized and asymmetric system, which also is
flexible and dynamic.Although membranes apparently have a common basic design, there are
wide variations in both their structure and functional capacities. The differences are so large and
characteristic that membrane chemistry can be used in bacterial identification. The plasma
membranes of procaryotic cells must fill an incredible variety of roles successfully. cytoplasm,
particularly in cells without cell walls, and separates it from the surroundings. The plasma
membrane also serves as a selectively permeable barrier: it allows particular ions and molecules
to pass, either into or out of the cell, while preventing the movement of others. Thus the
membrane prevents the loss of essential components through leakage while allowing the
movement of other molecules. Because many substances cannot cross the plasma membrane
without assistance, it must aid such movement when necessary. Transport systems can be used
for such tasks as nutrient uptake, waste excretion, and protein secretion. The procaryotic
plasma membrane also is the location of a variety of crucial metabolic processes: respiration,
photosynthesis, the synthesis of lipids and cell wall constituents, and probably chromosome
segregation.Finally, the membrane contains special receptor molecules that help procaryotes
detect and respond to chemicals in their surroundings.Clearly the plasma membrane is essential
to the survival of microorganisms.
What is Internal Membrane Systems?
Although procaryotic cytoplasm does not contain complex membranous organelles like
mitochondria or chloroplasts, membranous structures of several kinds can be observed. A
commonly observed structure is the mesosome. Mesosomes are invaginations of the plasma
membrane in the shape of vesicles, tubules, or lamellae .They are seen in both grampositive
and gram-negative bacteria, although they are generally more prominent in the former.
Mesosomes often are found next to septa or cross-walls in dividing bacteria and sometimes seem
attached to the bacterial chromosome. Thus they may be involved in cell wall formation during
division or play a role in chromosome replication and distribution to daughter cells.Currently
many bacteriologists believe that mesosomes are artifacts generated during the chemical fixation
of bacteria for electron microscopy. Possibly they represent parts of the plasma membrane
that are chemically different and more disrupted by fixatives.Many bacteria have internal
membrane systems quite different from the mesosome .Plasma membrane infoldings
can become extensive and complex in photosynthetic bacteria such as the cyanobacteria and
purple bacteria or in bacteria with very high respiratory activity like the nitrifying bacteria
They may be aggregates of spherical vesicles, flattened vesicles, or tubular membranes. Their
function may be to provide a larger membrane surface for greater metabolic
activity. 1. Describe with a labeled diagram and in words the fluid mosaic model for cell
membranes.
2. List the functions of the plasma membrane.
3. Discuss the nature, structure, and possible functions of the mesosome.
Define the Cytoplasmic Matrix.
Procaryotic cytoplasm, unlike that of eucaryotes, lacks unit membrane-bound organelles.
The cytoplasmic matrix is the substance lying between the plasma membrane and the nucleoid.
The matrix is largely water (about 70% of bacterial mass is water). It is featureless in electron
micrographs but often is packed with ribosomes and highly organized .Specific proteins are
positioned at particular sites such as the cell pole and the place where the bacterial cell will
divide. Thus although bacteria may lack a true cytoskeleton, they do have a cytoskeletonlike
system of proteins in their cytoplasmic matrix. The plasma membrane and everything within is
called the protoplast; thus the cytoplasmic matrix is a major part of the protoplast.
What are the Inclusion Bodies in prokaryotes.
A variety of inclusion bodies, granules of organic or inorganic material that often are clearly
visible in a light microscope, is present in the cytoplasmic matrix. These bodies usually are used
for storage (e.g., carbon compounds, inorganic substances, and energy), and also reduce osmotic
pressure by tying up molecules in particulate form. Some inclusion bodies are not bounded by a
membrane and lie free in the cytoplasm—for example, polyphosphate granules, cyanophycin
granules, and some glycogen granules. Other inclusion bodies are enclosed by a membrane about
2.0 to 4.0 nm thick, which is single-layered and not a typical bilayer membrane. Examples of
membrane-enclosed inclusion bodies are poly-_-hydroxybutyrate granules, some glycogen and
sulfur granules, carboxysomes, and gas vacuoles. Inclusion body membranes vary in
composition. Some are protein in nature, whereas others contain lipid. Because inclusion bodies
are used for storage, their quantity will vary with the nutritional status of the cell. For example,
polyphosphate granules will be depleted in freshwater habitats that are phosphate limited. A brief
description of several important inclusion bodies follows. Organic inclusion bodies usually
contain either glycogen or poly-_-hydroxybutyrate. Glycogen is a polymer of glucose units
composed of long chains formed by _(1→4) glycosidic bonds and branching chains connected to
them by _(1→6) glycosidic bonds .Poly-_-hydroxybutyrate (PHB) contains _-hydroxybutyrate
molecu les joined by ester bonds between the carboxyl and hydroxyl groups of adjacent
molecules. Usually only one of these polymers is found in a species, but purple photosynthetic
bacteria have both. Poly-_-hydroxybutyrate accumulates in distinct bodies, around 0.2 to 0.7 _m
in diameter, that are readily stained with Sudan black for light microscopy and 3.3 The
Cytoplasmic Matrix are clearly visible in the electron microscope . Glycogen is dispersed more
evenly throughout the matrix as small granules (about 20 to 100 nm in diameter) and often can
be seen only with the electron microscope. If cells contain a large amount of glycogen, staining
with an iodine solution will turn them reddish-brown. Glycogen and PHB inclusion bodies are
carbon storage reservoirs providing material for energy and biosynthesis. Many bacteria also
store carbon as lipid droplets. Cyanobacteria have two distinctive organic inclusion bodies.
Cyanophycin granules are composed of large polypeptides containing approximately
equal amounts of the amino acids arginine and aspartic acid. The granules often are large enough
to be visible in the light microscope and store extra nitrogen for the bacteria. Carboxysomes are
present in many cyanobacteria, nitrifying bacteria, and thiobacilli. They are polyhedral,
about 100 nm in diameter, and contain the enzyme ribulose- 1,5-bisphosphate carboxylase in a
paracrystalline arrangement. They serve as a reserve of this enzyme and may be a site of CO2
fixation.
A most remarkable organic inclusion body, the gas vacuole, is present in many
cyanobacteria ,purple and green photosynthetic bacteria, and a few other aquatic forms such
as Halobacterium and Thiothrix. These bacteria float at or near the surface, because gas vacuoles
give them buoyancy. This is vividly demonstrated by a simple but dramatic experiment.
Cyanobacteria held in a full, tightly stoppered bottle will float, but if the stopper is struck with a
hammer, the bacteria sink to the bottom. Examination of the bacteria at the beginning and end of
the experiment shows that the sudden pressure increase has collapsed the gas vacuoles and
destroyed the microorganisms’ buoyancy.Gas vacuoles are aggregates of enormous numbers of
small, hollow, cylindrical structures called gas vesicles . Gas vesicle walls do not contain lipid
and are composed entirely of a single small protein. These protein subunits assemble to form
a rigid enclosed cylinder that is hollow and impermeable to water but freely permeable to
atmospheric gases. Bacteria with gas vacuoles can regulate their buoyancy to float at the depth
necessary for proper light intensity, oxygen concentration, and nutrient levels.They descend by
simply collapsing vesicles and float upward when new ones are constructed. Two major types of
inorganic inclusion bodies are seen. Many bacteria store phosphate as polyphosphate granules
or volutin granules .Polyphosphate is a linear polymer of orthophosphates joined by ester
bonds. Thus volutin granules function as storage reservoirs for phosphate, an important
component of cell constituents such as nucleic acids. In some cells they act as an energy reserve,
and polyphosphate can serve as an energy source in reactions. These granules are sometimes
called metachromatic granules because they show the metachromatic effect; that is, they
appear red or a different shade of blue when stained with the blue dyes methylene blue or
toluidine blue. Some bacteria also store sulfur temporarily as sulfur granules, a second type of
inorganic inclusion body .
Inorganic inclusion bodies can be used for purposes other than storage. An excellent
example is the magnetosome, which is used by some bacteria to orient in the earth’s magnetic
field. These inclusion bodies contain iron in the form of magnetite .
Explain about the The Procaryotic Cell Wall
The cell wall is the layer, usually fairly rigid, that lies just outside the plasma membrane. It is
one of the most important parts of a procaryotic cell for several reasons. Except for the
mycoplasmas and some Archaea ,most bacteria have strong walls that give them shape and
protect them from osmotic lysis ,wall shape and strength is primarily due to peptidoglycan, as we
will see shortly. The cell walls of many pathogens have components that contribute to their
pathogenicity.The wall can protect a cell from toxic substances and is the site of action of several
antibiotics. After Christian Gram developed the Gram stain in 1884, it soon became evident that
bacteria could be divided into two major groups based on their response to the Gram-stain
procedure .Gram-positive bacteria stained purple, whereas gram-negative bacteria were colored
pink or red by the technique. The true structural difference between these two groups became
clear with the advent of the transmission electron microscope. The gram-positive cell wall
consists of a single 20 to 80 nm thick homogeneous peptidoglycan or murein layer lying
outside the plasma membrane .In contrast, the gram-negative cell wall is quite complex. It has a
2 to 7 nm peptidoglycan layer surrounded by a 7 to 8 nm thick outer membrane. Because of the
thicker peptidoglycan layer, the walls of gram-positive cells are stronger than those of gramnegative bacteria. Microbiologists often call all the structures from the plasma membrane
outward the envelope or cell envelope. This includes the wall and structures like capsules .when
present. Frequently a space is seen between the plasma membrane and the outer membrane in
electron micrographs of gramnegative bacteria, and sometimes a similar but smaller gap may be
observed between the plasma membrane and wall in grampositive bacteria. This space is called
the periplasmic space. Recent evidence indicates that the periplasmic space may be filled with a
loose network of peptidoglycan. Possibly it is more a gel than a fluid-filled space. The substance
that occupies the periplasmic space is the periplasm. Gram-positive cells may have periplasm
even if they lack a discrete, obvious periplasmic space. Size estimates of the periplasmic space in
gram-negative bacteria range from 1 nm to as great as 71 nm. Some recent studies indicate that it
may constitute about 20 to 40% of the total cell volume (around 30 to 70 nm), but more research
is required to establish an accurate value. When cell walls are disrupted carefully or removed
without disturbing the underlying plasma membrane, periplasmic enzymes and other proteins are
released and may be easily studied. The periplasmic space of gram-negative bacteria contains
many proteins that participate in nutrient acquisition for example, hydrolytic enzymes attacking
nucleic acids and phosphorylated molecules, and binding proteins involved in transport of
materials into the cell. Denitrifying and chemolithoautotrophic bacteria often have electron
transport proteins in their periplasm. The periplasmic space also contains enzymes involved in
peptidoglycan synthesis and the modification of toxic compounds that could harm the cell.
Grampositive bacteria may not have a visible periplasmic space and do not appear to have as
many periplasmic proteins; rather, they secrete several enzymes that ordinarily would be
periplasmic in gram-negative bacteria. Such secreted enzymes are often called exoenzymes.
Some enzymes remain in the periplasm and are attached to the plasma membrane.
Although they may be either gram positive or gram negative, their cell walls are
distinctive in structure and chemical composition. The walls lack peptidoglycan and are
composed of proteins, glycoproteins, or polysaccharides.Following this overview of the
envelope, peptidoglycan structure and the organization of gram-positive and gram-negative cell
walls are discussed in more detail.
Peptidoglycan Structure
Peptidoglycan or murein is an enormous polymer composed of many identical subunits. The
polymer contains two sugar derivatives, N-acetylglucosamine and N-acetylmuramic acid (the
lactyl ether of N-acetylglucosamine), and several different amino acids, three of which—Dglutamic acid, D-alanine, and meso-diaminopimelic acid—are not found in proteins. The
presence of D-amino acids protects against attack by most peptidases. The peptidoglycan subunit
present in most gram-negative bacteria and many gram-positive .The backbone of this polymer is
composed of alternating N-acetylglucosamine and N-acetylmuramic acid residues. A peptide
chain of four alternating D- and L-amino acids is connected to the carboxyl group of Nacetylmuramic acid. Many bacteria substitute another diaminoacid, usually L-lysine, in the third
position for meso-diaminopimelic acid .
Chains of linked peptidoglycan subunits are joined by crosslinks between the peptides. Often the
carboxyl group of the terminal D-alanine is connected directly to the amino group of
diaminopimelic acid, but a peptide interbridge may be used instead . Most gram-negative cell
wall peptidoglycan lacks the peptide interbridge. This cross-linking results in an enormous
peptidoglycan sac that is actually one dense, interconnected network .These sacs have been
isolated from gram-positive bacteria and are strong enough to retain their shape and integrity yet
they are elastic and somewhat stretchable, unlike cellulose. They also must be porous, as
molecules can penetrate them.
Explain the Gram-Positive Cell Walls.
Normally the thick, homogeneous cell wall of gram-positive bacteria is composed primarily of
peptidoglycan, which often contains a peptide interbridge .However gram-positive cell walls
usually also contain large amounts of teichoic acids, polymers of glycerol or ribitol joined by
phosphate groups .Amino acids such as D-alanine or sugars like glucose are attached to the
glycerol and ribitol groups. The teichoic acids are connected to either the peptidoglycan itself
by a covalent bond with the six hydroxyl of N-acetylmuramic acid or to plasma membrane lipids;
in the latter case they are called lipoteichoic acids. Teichoic acids appear to extend to the
surface of the peptidoglycan, and, because they are negatively charged, help give the grampositive cell wall its negative charge. The functions of these molecules are still unclear, but they
may be important in maintaining the structure of the wall. Teichoic acids are not present in gramnegative bacteria.
Explain the Gram-Negative Cell Walls
Gram-negative cell walls are much more complex than gram-positive walls. The thin
peptidoglycan layer next to the plasma membrane may constitute not more than 5 to 10% of the
wall weight. In E. coli it is about 2 nm thick and contains only one or two layers or sheets of
peptidoglycan. The outer membrane lies outside the thin peptidoglycan layer . The most
abundant membrane protein is Braun’s lipoprotein, a small lipoprotein covalently joined
to the underlying peptidoglycan and embedded in the outer membrane by its hydrophobic end.
The outer membrane and peptidoglycan are so firmly linked by this lipoprotein that they can be
isolated as one unit. Another structure that may strengthen the gram-negative wall and hold the
outer membrane in place is the adhesion site. The outer membrane and plasma membrane appear
to be in direct contact at many locations in the gram-negative wall. In E. coli 20 to 100 nm are as
of contact between the two membranes are seen in plasmolyzed cells. Adhesion sites may be
regions of direct contact or possibly true membrane fusions. It has been proposed that substances
can move into the cell through these adhesion sites rather than traveling through the periplasm.
Possibly the most unusual constituents of th e outer membrane are its lipopolysaccharides
(LPSs). These large, complex molecules contain both lipid and carbohydrate, and consist
of three parts: (1) lipid A, (2) the core polysaccharide, and (3) the O side chain. The LPS from
Salmonella typhimurium has been studied most, and its general structure is described here
The lipid A region contains two glucosamine sugar derivatives, each with three fatty acids and
phosphate or pyrophosphate attached. It is buried in the outer membrane and the remainder of the
LPS molecule projects from the surface. The core polysaccharide is joined to lipid A. In
Salmonella it is constructed of 10 sugars, many of them unusual in structure. The O side chain
or O antigen is a polysaccharide chain extending outward from the core. It has several peculiar
sugars and varies in composition between bacterial strains. Although O side chains are readily
recognized by host antibodies, gramnegative bacteria may thwart host defenses by rapidly
changing the nature of their O side chains to avoid detection. Antibody interaction
with the L PS before reaching the outer membrane proper may also protect the cell wall from
direct The LPS is important for several reasons ot her than the avoidance of host defenses. Since
the core polysaccharide usually contains charged sugars and phosphate ,LPS contributes to the
negative charge on the bacterial surface. Lipid A is a major constituent of the outer membrane,
and the LPS helps stabilize membrane structure. Furthermore, lipid A often is toxic; as a result
the LPS can act as an endotoxin and cause some of the symptoms that arise in gram-negative
bacterial infections.
A most important outer membrane function is to serve as a protective barrier. It prevents
or slows the entry of bile salts, antibiotics, and other toxic substances that might kill or injure the
bacterium. Even so, the outer membrane is more permeable than the plasma membrane and
permits the passage of small molecules like glucose and other monosaccharides. This is due to
the presence of special porin proteins .Three porin molecules cluster together and span the outer
membrane to form a narrow channel through which molecules smaller than about 600 to 700
daltons can pass. Larger molecules such as vitamin B12 must be transported across the outer
membrane by specific carriers. The outer membrane also prevents the loss of constituents like
periplasmic enzymes.
What is Capsules, Slime Layers, and S-Layers?
Some bacteria have a layer of material lying outside the cell wall. When the layer is well
organized and not easily washed off, it is called a capsule. A slime layer is a zone of diffuse,
unorganized material that is removed easily. A glycocalyx is a network of polysaccharides
extending from the surface of bacteria and other cells (in this sense it could encompass both
capsules and slime layers). Capsules and slime layers usually are composed of polysaccharides,
but they may be constructed of other materials. For example, Bacillus anthracis has a capsule of
poly- D-glutamic acid. Capsules are clearly visible in the light microscope when negative stains
or special capsule stains are employed ,they also can be studied with the electron microscope
Although capsules are not required for bacterial growth and reproduction in laboratory
cultures, they do confer several advantages when bacteria grow in their normal habitats. They
help bacteria resist phagocytosis by host phagocytic cells. Streptococcus pneumoniae provides a
classic example. When it lacks a capsule, it is destroyed easily and does not cause disease,
whereas the capsulated variant quickly kills mice. Capsules contain a great deal of water and can
protect bacteria against desiccation. They exclude bacterial viruses and most hydrophobic toxic
materials such as detergents. The glycocalyx also aids bacterial attachment to surfaces of solid
objects in aquatic environments or to tissue surfaces in plant and animal hosts .Gliding bacteria
often produce slime, which presumably aids in their motility .
Many gram-positive and gram-negative bacteria have a regularly structured layer called
an S-layer on their surface. Slayers also are very common among Archaea, where they may be
the only wall structure outside the plasma membrane. The Slayer has a pattern something like
floor tiles and is composed of protein or glycoprotein . In gram-negative bacteria the S-layer
adheres directly to the outer membrane; it is associated with the peptidoglycan surface in grampositive bacteria. It may protect the cell against ion and pH fluctuations, osmotic stress, enzymes,
or the predacious bacterium Bdellovibrio. The S-layer also helps maintain the shape and
envelope rigidity of at least some bacterial cells. It can promote cell adhesion to surfaces.
Finally, the layer seems to protect some pathogens against complement attack and phagocytosis,
thus contributing to their virulence.
Explain the Pili and Fimbriae.
Many gram-negative bacteria have short, fine, hairlike appendages that are thinner than
flagella and not involved in motility. These are usually called fimbriae (s., fimbria). Although a
cell may be covered with up to 1,000 fimbriae, they are only visible in an electron microscope
due to their small size . They seem to be slender tubes composed of helically arranged protein
subunits and are about 3 to 10 nm in diameter and up to several micrometers long. At least some
types of fimbriae attach bacteria to solid surfaces such as rocks in streams and host tissues. Sex
pili (s., pilus) are similar appendages, about 1 to 10 per cell, that differ from fimbriae in the
following ways. Pili often arelarger than fimbriae (around 9 to 10 nm in diameter). They are
genetically determined by sex factors or conjugative plasmids and are required for bacterial
mating .Some bacterial viruses attach specifically to receptors on sex pili at the start
of their reproductive cycle.
Explain about the Flagellum.
flagellum (in plural form: flagella) is a tail-like projection that protrudes from the cell body of
certain prokaryotic and eukaryotic cells, and functions in locomotionThere are some notable
differences between prokaryotic and eukaryotic flagella, such as protein composition, structure,
and mechanism of propulsion. An example of a flagellated bacterium is the ulcer-causing
Helicobacter pylori, which uses multiple flagella to propel itself through the mucus lining to
reach the stomach epithelium. An example of a eukaryotic flagellated cell is the sperm cell,
which uses its flagellum to propel itself through the female reproductive tract. Eukaryotic
flagella are structurally identical to eukaryotic cilia, although distinctions are sometimes made
according to function and/or length. The word flagellum is the Latin word for whip.
Types
Three types of flagella have so far been distinguished; bacterial, archaeal and eukaryotic.
The main differences among these three types are summarized below:
 Bacterial flagella are helical filaments that rotate like screws. They provide two of several
kinds of bacterial motility.

Archaeal flagella are superficially similar to bacterial flagella, but are different in many
details and considered non-homologous.
 Eukaryotic flagella - those of animal, plant, and protist cells - are complex cellular
projections that lash back and forth.
Sometimes eukaryotic flagella are called cilia or undulipodia to emphasize their distinctiveness.
Bacterial
Flagellum of Gram-negative Bacteria
Examples of bacterial flagella arrangement schemes. A-Monotrichous; B-Lophotrichous; CAmphitrichous; D-Peritrichous.
Physical model of a bacterial flagellum
The bacterial flagellum is made up of the protein flagellin. Its shape is a 20 nanometer-thick
hollow tube. It is helical and has a sharp bend just outside the outer membrane; this "hook"
allows the helix to point directly away from the cell. A shaft runs between the hook and the basal
body, passing through protein rings in the cell's membrane that act as bearings. Gram-positive
organisms have 2 of these basal body rings, one in the peptidoglycan layer and one in the plasma
membrane. Gram-negative organisms have 4 such rings: the L ring associates with the
lipopolysaccharides, the P ring associates with peptidoglycan layer, the M ring is embedded in
the plasma membrane, and the S ring is directly attached to the plasma membrane. The filament
ends with a capping protein.
The bacterial flagellum is driven by a rotary engine (the Mot complex) made up of protein,
located at the flagellum's anchor point on the inner cell membrane. The engine is powered by
proton motive force, i.e., by the flow of protons (hydrogen ions) across the bacterial cell
membrane due to a concentration gradient set up by the cell's metabolism (in Vibrio species there
are two kinds of flagella, lateral and polar, and some are driven by a sodium ion pump rather
than a proton pump). The rotor transports protons across the membrane, and is turned in the
process. The rotor alone can operate at 6,000 to 17,000 rpm, but with the flagellar filament
attached usually only reaches 200 to 1000 rpm. The direction of rotation can be switched almost
instantaneously, caused by a slight change in the position of a protein, FliG, in the rotor.
The cylindrical shape of flagella is suited to locomotion of microscopic organisms; these
organisms operate at a low Reynolds number, where the viscosity of the surrounding water is
much more important than its mass or inertia.
Flagella do not rotate at a constant speed but instead can increase or decrease their rotational
speed in relation to the strength of the proton motive force. Flagellar rotation can move bacteria
through liquid media at speeds of up to 60 cell lengths/second (sec). Although this is only about
0.00017 km/h (0.00011 mph), when comparing this speed with that of higher organisms in terms
of number of lengths moved per second, it is extremely fast. By comparison, the cheetah, the
fastest land animal, can sprint at 110 km/h (68 mph), which is approximately 25 body
lengths/sec.
During flagellar assembly, components of the flagellum pass through the hollow cores of the
basal body and the nascent filament. During assembly, protein components are added at the
flagellar tip rather than at the base In vitro, flagellar filaments assemble spontaneously in a
solution containing purified flagellin as the sole protein.
The flagellar filament is the long helical screw that propels the bacterium when rotated by the
motor, through the hook. In most bacteria that have been studied, including the Gram negative
Escherichia coli, Salmonella typhimurium, Caulobacter crescentus, and Vibrio alginolyticus, the
filament is made up of eleven protofilaments approximately parallel to the filament axis. Each
protofilament is a series of tandem protein chains. However in Campylobacter jejuni, there are
seven protofilaments.
The basal body has several traits in common with some types of secretory pores, such as the
hollow rod-like "plug" in their centers extending out through the plasma membrane. Given the
structural similarities between bacterial flagella and bacterial secretory systems, it is thought that
bacterial flagella may have evolved from the type three secretion system; however, it is not
known for certain whether these pores are derived from the bacterial flagella or the bacterial
secretory system.
Through use of their flagella, E. coli are able to move rapidly towards attractants and away from
repellents. They do this by means of a biased random walk, with 'runs' and 'tumbles' brought
about by rotating the flagellum counter-clockwise and clockwise respectively.
Flagella arrangement schemes
Different species of bacteria have different numbers and arrangements of flagella. Monotrichous
bacteria have a single flagellum (e.g., Vibrio cholerae). Lophotrichous bacteria have multiple
flagella located at the same spot on the bacteria's surfaces which act in concert to drive the
bacteria in a single direction. In many cases, the bases of multiple flagella are surrounded by a
specialized region of the cell membrane, the so-called polar membrane.
Amphitrichous bacteria have a single flagellum on each of two opposite ends (only one flagellum
operates at a time, allowing the bacteria to reverse course rapidly by switching which flagellum
is active). Peritrichous bacteria have flagella projecting in all directions (e.g., E. coli).
In some bacteria, such as the larger forms of Selenomonas, the individual flagella are organized
outside the cell body, helically twining about each other to form a thick structure called a
"fascicle". Other bacteria, such as Spirochetes, have a specialized type of flagellum called an
"axial filament" that is located in the periplasmic space, the rotation of which causes the entire
bacterium to move forward in a corkscrew-like motion.
Counterclockwise rotation of monotrichous polar flagella pushes the cell forward with the
flagella trailing behind, much like a corkscrew moving inside cork. Indeed water in the
microscopic scale is highly viscous, very different from our daily experience of water. The
flagella are left-handed helices, and bundle and rotate together only when rotating
counterclockwise. When some of the rotors reverse direction, the flagella unwind and the cell
starts "tumbling". It has also been suggested that even if all flagella would rotate clockwise, they
will not form a bundle, due to geometrical as well as hydrodynamical reasons. Such "tumbling"
may happen occasionally, leading to the cell seemingly thrashing about in place, resulting in the
reorientation of the cell. The clockwise rotation of a flagellum is suppressed by chemical
compounds favorable to the cell (e.g. food), but the motor is highly adaptive to this. Therefore,
when moving in a favorable direction, the concentration of the chemical attractant increases and
"tumbles" are continually suppressed; however, when the cell's direction of motion is
unfavorable (e.g., away from a chemical attractant), tumbles are no longer suppressed and occur
much more often, with the chance that the cell will be thus reoriented in the correct direction.
In some Vibrio spp. (particularly Vibrio parahemolyticus) and related proteobacteria such as
Aeromonas, two flagellar systems co-exist, using different sets of genes and different ion
gradients for energy. The polar flagella are constitutively expressed and provide motility in bulk
fluid, while the lateral flagella are expressed when the polar flagella meet too much resistance to
turn. These provide swarming motility on surfaces or in viscous fluids.
How does Archaeal cell wall diferrentiate from the prokaryote?
The archaeal flagellum is superficially similar to the bacterial (or eubacterial) flagellum; in the
1980s they were thought to be homologous on the basis of gross morphology and behavior. Both
flagella consist of filaments extending outside of the cell, and rotate to propel the cell. Archaeal
flagella have a unique structure which lacks a central channel. Similar to bacterial type IV pilins,
the component flagellins are made with class 3 signal peptides and they are processed by a type
IV prepilin peptidase-like enzyme. The archaeal flagellins are typically modified by the addition
of N-linked glycans which are necessary for proper assembly and/or function.
Discoveries in the 1990s revealed numerous detailed differences between the archaeal and
bacterial flagella; these include:

Bacterial flagella are motorized by a flow of H+ ions (or occasionally Na+ ions); archaeal
flagella are almost certainly powered by ATP. The torque-generating motor that powers
rotation of the archaeal flagellum has not been identified.

While bacterial cells often have many flagellar filaments, each of which rotates
independently, the archaeal flagellum is composed of a bundle of many filaments that
rotate as a single assembly.

Bacterial flagella grow by the addition of flagellin subunits at the tip; archaeal flagella
grow by the addition of subunits to the base.

Bacterial flagella are thicker than archaeal flagella, and the bacterial filament has a large
enough hollow "tube" inside that the flagellin subunits can flow up the inside of the
filament and get added at the tip; the archaeal flagellum is too thin to allow this.

Many components of bacterial flagella share sequence similarity to components of the
type III secretion systems, but the components of bacterial and archaeal flagella share no
sequence similarity. Instead, some components of archaeal flagella share sequence and
morphological similarity with components of type IV pili, which are assembled through
the action of type II secretion systems (the nomenclature of pili and protein secretion
systems is not consistent).[

These differences could mean that the bacterial and archaeal flagella could be a classic
case of biological analogy, or convergent evolution, rather than homology. However, in
comparison to the decades of well-publicized study of bacterial flagella (e.g. by Berg),
archaeal flagella have only recently begun to get serious scientific attention. Therefore,
many assume erroneously that there is only one basic kind of prokaryotic flagellum, and
that archaeal flagella are homologous to it. For example, Cavalier-Smith (2002)is aware
of the differences between archaeal and bacterial flagellins, but retains the misconception
that the basal bodies are homologous.[ Eukaryotic
Eukaryotic flagella. 1-axoneme, 2-cell membrane, 3-IFT (IntraFlagellar Transport), 4-Basal
body, 5-Cross section of flagella, 6-Triplets of microtubules of basal body
Cross section of an axoneme
Longitudinal section through the flagella area in Chlamydomonas reinhardtii. In the cell apex is
the basal body that is the anchoring site for a flagella. Basal bodies originate from and have a
substructure similar to that of centrioles, with nine peripheral microtubule triplets (see structure
at bottom center of image)
Along with cilia, flagella make up a group of organelles known as undulipodia.
Structure
A eukaryotic flagellum is a bundle of nine fused pairs of microtubule doublets surrounding two
central single microtubules. The so-called "9+2" structure is characteristic of the core of the
eukaryotic flagellum called an axoneme. At the base of a eukaryotic flagellum is a basal body,
"blepharoplast" or kinetosome, which is the microtubule organizing center (MTOC) for flagellar
microtubules and is about 500 nanometers long. Basal bodies are structurally identical to
centrioles. The flagellum is encased within the cell's plasma membrane, so that the interior of the
flagellum is accessible to the cell's cytoplasm.
Give detail an account on the Mechanism of fagellum.
Each of the outer 9 doublet microtubules extends a pair of dynein arms (an "inner" and an
"outer" arm) to the adjacent microtubule; these dynein arms are responsible for flagellar beating,
as the force produced by the arms causes the microtubule doublets to slide against each other and
the flagellum as a whole to bend. These dynein arms produce force through ATP hydrolysis. The
flagellar axoneme also contains radial spokes, polypeptide complexes extending from each of the
outer 9 microtubule doublets towards the central pair, with the "head" of the spoke facing
inwards. The radial spoke is thought to be involved in the regulation of flagellar motion,
although its exact function and method of action are not yet understood.
Flagella vs Cilia
Difference of beating pattern of flagellum and cilia
Though eukaryotic flagella and motile cilia are ultrastructurally identical, the beating pattern of
the two organelles can be different. In the case of flagella (e.g. the tail of a sperm) the motion is
propeller-like. In contrast, beating of motile cilia consists of coordinated back-and-forth cycling
of many cilia on the cell surface.[citation needed] Thus, flagella serve for the propulsion of single cells
(e.g. swimming of protozoa and spermatozoa), and motile cilia for the transport of fluids (e.g.
transport of mucus by stationary ciliated cells in the trachea). However, cilia are also used for
locomotion (through liquids) in organisms such as Paramecium.[citation needed]
UNIT – II
Explain the Eukaryote structure.
A eukaryote (pronounced /juːˈkæri.oʊt/ ew-KARR-ee-oht or /juːˈkæriət/) is an organism whose
cells contain complex structures enclosed within membranes. The defining membrane-bound
structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear
envelope, within which the genetic material is carried.[1][2][3] The presence of a nucleus gives
eukaryotes their name, which comes from the Greek ευ (eu, "good") and κάρυον (karyon, "nut"
or "kernel"). Most eukaryotic cells also contain other membrane-bound organelles such as
mitochondria, chloroplasts and the Golgi apparatus. All species of large complex organisms are
eukaryotes, including animals, plants and fungi, although most species of eukaryotic protists are
microorganisms.
Cell division in eukaryotes is different from that in organisms without a nucleus (prokaryotes). It
involves separating the duplicated chromosomes, through movements directed by microtubules.
There are two types of division processes. In mitosis, one cell divides to produce two genetically
identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two
instances of each chromosome, one from each parent) undergoes recombination of each pair of
parental chromosomes, and then two stages of cell division, resulting in four haploid cells
(gametes). Each gamete has just one complement of chromosomes, each a unique mix of the
corresponding pair of parental chromosomes.
Eukaryotes appear to be monophyletic, and so make up one of the three domains of life. The two
other domains, Bacteria and Archaea, are prokaryotes and have none of the above features.
Eukaryotes represent a tiny minority of all living things; even in a human body there are 10 times
more microbes than human cells.[4]

Cell features
Eukaryotic cells are typically much larger than prokaryotes. They have a variety of internal
membranes and structures, called organelles, and a cytoskeleton composed of microtubules,
microfilaments, and intermediate filaments, which play an important role in defining the cell's
organization and shape. Eukaryotic DNA is divided into several linear bundles called
chromosomes, which are separated by a microtubular spindle during nuclear division.
Detail of the endomembrane system and its components
Internal membrane
Eukaryotic cells include a variety of membrane-bound structures, collectively referred to as the
endomembrane system. Simple compartments, called vesicles or vacuoles, can form by budding
off other membranes. Many cells ingest food and other materials through a process of
endocytosis, where the outer membrane invaginates and then pinches off to form a vesicle. It is
probable that most other membrane-bound organelles are ultimately derived from such vesicles.
The nucleus is surrounded by a double membrane (commonly referred to as a nuclear envelope),
with pores that allow material to move in and out. Various tube- and sheet-like extensions of the
nuclear membrane form what is called the endoplasmic reticulum or ER, which is involved in
protein transport and maturation. It includes the rough ER where ribosomes are attached, and the
proteins they synthesize enter the interior space or lumen. Subsequently, they generally enter
vesicles, which bud off from the smooth ER. In most eukaryotes, these protein-carrying vesicles
are released and further modified in stacks of flattened vesicles, called Golgi bodies or
dictyosomes.
Vesicles may be specialized for various purposes. For instance, lysosomes contain enzymes that
break down the contents of food vacuoles, and peroxisomes are used to break down peroxide,
which is toxic otherwise. Many protozoa have contractile vacuoles, which collect and expel
excess water, and extrusomes, which expel material used to deflect predators or capture prey. In
multicellular organisms, hormones are often produced in vesicles. In higher plants, most of a
cell's volume is taken up by a central vacuole, which primarily maintains its osmotic pressure.
Mitochondria structure:
1) Inner membrane
2) Outer membrane
3) Crista
4) Matrix
What is Mitochondria and plastids?
Mitochondria are organelles found in nearly all eukaryotes. They are surrounded by double
membranes (known as the phospholipid bi-layer), the inner of which is folded into invaginations
called cristae, where aerobic respiration takes place. Mitochondria contain their own DNA. They
are now generally held to have developed from endosymbiotic prokaryotes, probably
proteobacteria. The few protozoa that lack mitochondria have been found to contain
mitochondrion-derived organelles, such as hydrogenosomes and mitosomes.
Plants and various groups of algae also have plastids. Again, these have their own DNA and
developed from endosymbiotes, in this case cyanobacteria. They usually take the form of
chloroplasts, which like cyanobacteria contain chlorophyll and produce organic compounds
(such as glucose) through photosynthesis. Others are involved in storing food. Although plastids
likely had a single origin, not all plastid-containing groups are closely related. Instead, some
eukaryotes have obtained them from others through secondary endosymbiosis or ingestion.
Endosymbiotic origins have also been proposed for the nucleus, for which see below, and for
eukaryotic flagella, supposed to have developed from spirochaetes. This is not generally
accepted, both from a lack of cytological evidence and difficulty in reconciling this with cellular
reproduction.
Cytoskeletal structures
Longitudinal section through the flagellum of Chlamydomonas reinhardtii
Many eukaryotes have long slender motile cytoplasmic projections, called flagella, or similar,
but shorter[citation needed] structures called cilia. Flagella and cilia are sometimes referred to as
undulipodia,[citation needed] and are variously involved in movement, feeding, and sensation. They
are composed mainly of tubulin. These are entirely distinct from prokaryotic flagella. They are
supported by a bundle of microtubules arising from a basal body, also called a kinetosome or
centriole, characteristically arranged as nine doublets surrounding two singlets. Flagella also may
have hairs, or mastigonemes, and scales connecting membranes and internal rods. Their interior
is continuous with the cell's cytoplasm.
Microfilamental structures composed by actin and actin binding proteins, e.g., α-actinin, fimbrin,
filamin are present in submembraneous cortical layers and bundles, as well. Motor proteins of
microtubules, e.g., dynein or kinesin and actin, e.g., myosins provide dynamic character of the
network.
Centrioles are often present even in cells and groups that do not have flagella. They generally
occur in groups of one or two, called kinetids, that give rise to various microtubular roots. These
form a primary component of the cytoskeletal structure, and are often assembled over the course
of several cell divisions, with one flagellum retained from the parent and the other derived from
it. Centrioles may also be associated in the formation of a spindle during nuclear division.
Significance of cytoskeletal structures is underlined in determination of shape of the cells, as
well as their being essential components of migratory responses like chemotaxis and
chemokinesis. Some protists have various other microtubule-supported organelles. These include
the radiolaria and heliozoa, which produce axopodia used in flotation or to capture prey, and the
haptophytes, which have a peculiar flagellum-like organelle called the haptonema.
Plant cell wall
Plant cells have a cell wall, a fairly rigid layer outside the cell membrane, providing the cell with
structural support, protection, and a filtering mechanism. The cell wall also prevents overexpansion when water enters the cell. The major carbohydrates making up the primary cell wall
of land plants are cellulose, hemicellulose, and pectin. The cellulose microfibrils are linked via
hemicellulosic tethers to form the cellulose-hemicellulose network, which is embedded in the
pectin matrix. The most common hemicellulose in the primary cell wall is xyloglucan.
Differences between eukaryotic cells.
There are many different types of eukaryotic cells, though animals and plants are the most
familiar eukaryotes, and thus provide an excellent starting point for understanding eukaryotic
structure. Fungi and many protists have some substantial differences, however.
Animal cell
Structure of a typical animal cell
Structure of a typical plant cell
An animal cell is a form of eukaryotic cell that makes up many tissues in animals. The animal
cell is distinct from other eukaryotes, most notably plant cells, as they lack cell walls and
chloroplasts, and they have smaller vacuoles. Due to the lack of a rigid cell wall, animal cells can
adopt a variety of shapes, and a phagocytic cell can even engulf other structures.
There are many different cell types. For instance, there are approximately 210 distinct cell types
in the adult human body.
Plant cell
Plant cells are quite different from the cells of the other eukaryotic organisms. Their distinctive
features are:

A large central vacuole (enclosed by a membrane, the tonoplast), which maintains the
cell's turgor and controls movement of molecules between the cytosol and sap

A primary cell wall containing cellulose, hemicellulose and pectin, deposited by the
protoplast on the outside of the cell membrane; this contrasts with the cell walls of fungi,
which contain chitin, and the cell envelopes of prokaryotes, in which peptidoglycans are
the main structural molecules

The plasmodesmata, linking pores in the cell wall that allow each plant cell to
communicate with other adjacent cells; this is different from the functionally analogous
system of gap junctions between animal cells.

Plastids, especially chloroplasts that contain chlorophyll, the pigment that gives plants
their green color and allows them to perform photosynthesis

Higher plants, including conifers and flowering plants (Angiospermae) lack the flagellae
and centrioles that are present in animal cells.
Fungal cell
Fungal cells are most similar to animal cells, with the following exceptions:

A cell wall that contains chitin

Less definition between cells; the hyphae of higher fungi have porous partitions called
septa, which allow the passage of cytoplasm, organelles, and, sometimes, nuclei.
Primitive fungi have few or no septa, so each organism is essentially a giant
multinucleate supercell; these fungi are described as coenocytic.

Only the most primitive fungi, chytrids, have flagella.
Other eukaryotic cells
Eukaryotes are a very diverse group, and their cell structures are equally diverse. Many have cell
walls; many do not. Many have chloroplasts, derived from primary, secondary, or even tertiary
endosymbiosis; and many do not. Some groups have unique structures, such as the cyanelles of
the glaucophytes, the haptonema of the haptophytes, or the ejectisomes of the cryptomonads.
Other structures, such as pseudopods, are found in various eukaryote groups in different forms,
such as the lobose amoebozoans or the reticulose foraminiferans.
Reproduction
Nuclear division is often coordinated with cell division. This generally takes place by mitosis, a
process that allows each daughter nucleus to receive one copy of each chromosome. In most
eukaryotes, there is also a process of sexual reproduction, typically involving an alternation
between haploid generations, wherein only one copy of each chromosome is present, and diploid
generations, wherein two are present, occurring through nuclear fusion (syngamy) and meiosis.
There is considerable variation in this pattern, however.
Eukaryotes have a smaller surface area to volume ratio than prokaryotes, and thus have lower
metabolic rates and longer generation times. In some multicellular organisms, cells specialized
for metabolism will have enlarged surface areas, such as intestinal vili.
Give the details of Chloroplast stucture and funtion.
The simplified internal structure of a chloroplast
Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct
photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and
reduce NADP to NADPH through a complex set of processes called photosynthesis.

The word chloroplast is derived from the Greek words chloros, which means green, and
plast, which means form or entity. Chloroplasts are members of a class of organelles
known as plastids.
Evolutionary origin
Chloroplasts visible in the cells of Plagiomnium affine — Many-fruited Thyme-moss
A model chloroplast
Chloroplasts are one of the many different types of organelles in the plant cell. In general, they
are considered to have originated from cyanobacteria through endosymbiosis. This was first
suggested by Mereschkowsky in 1905 after an observation by Schimper in 1883 that chloroplasts
closely resemble cyanobacteria. All chloroplasts are thought to derive directly or indirectly from
a single endosymbiotic event (in the Archaeplastida), except for Paulinella chromatophora,
which has recently acquired a photosynthetic cyanobacterial endosymbiont which is not closely
related to chloroplasts of other eukaryotes. In that they derive from an endosymbiotic event,
chloroplasts are similar to mitochondria, but chloroplasts are found only in plants and protista.
The chloroplast is surrounded by a double-layered composite membrane with an intermembrane
space; further, it has reticulations, or many infoldings, filling the inner spaces. The chloroplast
has its own DNA, which codes for redox proteins involved in electron transport in
photosynthesis; this is termed the plastome.
In green plants, chloroplasts are surrounded by two lipid-bilayer membranes. They are
believed to correspond to the outer and inner membranes of the ancestral cyanobacterium.
Chloroplasts have their own genome, which is considerably reduced compared to that of freeliving cyanobacteria, but the parts that are still present show clear similarities with the
cyanobacterial genome. Plastids may contain 60-100 genes whereas cyanobacteria often contain
more than 1500 genes. Many of the missing genes are encoded in the nuclear genome of the host.
The transfer of nuclear information has been estimated in tobacco plants at one gene for every
16000 pollen grains.
In some algae (such as the heterokonts and other protists such as Euglenozoa and Cercozoa),
chloroplasts seem to have evolved through a secondary event of endosymbiosis, in which a
eukaryotic cell engulfed a second eukaryotic cell containing chloroplasts, forming chloroplasts
with three or four membrane layers. In some cases, such secondary endosymbionts may have
themselves been engulfed by still other eukaryotes, thus forming tertiary endosymbionts. In the
alga Chlorella, there is only one chloroplast, which is bell-shaped.
Structure
Chloroplasts are observable as flat discs usually 2 to 10 micrometers in diameter and 1
micrometer thick. In land plants, they are, in general, 5 μm in diameter and 2.3 μm thick. They
are 200-400 nm (nano-meters). The chloroplast is contained by an envelope that consists of an
inner and an outer phospholipid membrane. Between these two layers is the intermembrane
space. A typical parenchyma cell contains about 10 to 100 chloroplasts.
The material within the chloroplast is called the stroma, corresponding to the cytosol of the
original bacterium, and contains one or more molecules of small circular DNA. It also contains
ribosomes; however most of its proteins are encoded by genes contained in the host cell nucleus,
with the protein products transported to the chloroplast.
Within the stroma are stacks of thylakoids, the sub-organelles, which are the site of
photosynthesis. The thylakoids are arranged in stacks called grana (singular: granum). A
thylakoid has a flattened disk shape. Inside it is an empty area called the thylakoid space or
lumen. Photosynthesis takes place on the thylakoid membrane; as in mitochondrial oxidative
phosphorylation, it involves the coupling of cross-membrane fluxes with biosynthesis via the
dissipation of a proton electrochemical gradient.
In the electron microscope, thylakoid membranes appear as alternating light-and-dark
bands, each 0.01 μm thick. Embedded in the thylakoid membrane are antenna complexes, each
of which consists of the light-absorbing pigments, including chlorophyll and carotenoids, as well
as proteins that bind the pigments. This complex both increases the surface area for light capture,
and allows capture of photons with a wider range of wavelengths. The energy of the incident
photons is absorbed by the pigments and funneled to the reaction centre of this complex through
resonance energy transfer. Two chlorophyll molecules are then ionised, producing an excited
electron, which then passes onto the photochemical reaction centre.
Give the details of Endoplasmic reticulum stucture and function .
Endoplasmic reticulum (ER) is an eukaryotic organelle that forms an interconnected
network of tubules, vesicles, and cisternae within cells. Rough endoplasmic reticulua
synthesize proteins, while smooth endoplasmic reticulua synthesize lipids and steroids,
metabolize carbohydrates and steroids, and regulate calcium concentration, drug detoxification,
and attachment of receptors on cell membrane proteins. Sarcoplasmic reticulua solely regulate
calcium levels.

The lacey membranes of the endoplasmic reticulum were first seen by Keith R. Porter,
Albert Claude, and Ernest F. Fullam in 1945.
Structure
1 Nucleus 2 Nuclear pore 3 Rough endoplasmic reticulum (RER)
4 Smooth endoplasmic
reticulum (SER) 5 Ribosome on the rough ER 6 Proteins that are transported 7 Transport
vesicle 8 Golgi apparatus 9 Cis face of the Golgi apparatus
10 Trans face of the Golgi
apparatus 11 Cisternae of the Golgi apparatus
The general structure of the endoplasmic reticulum is an extensive membrane network of
cisternae (sac-like structures) held together by the cytoskeleton. The phospholipid membrane
encloses a space, the cisternal space (or lumen), from the cytosol, which is continuous with the
perinuclear space. The functions of the endoplasmic reticulum vary greatly depending on the
exact type of endoplasmic reticulum and the type of cell in which it resides. The three varieties
are called rough endoplasmic reticulum, smooth endoplasmic reticulum and sarcoplasmic
reticulum.
The quantity of RER and SER in a cell can quickly interchange from one type to the other,
depending on changing metabolic needs: one type will undergo numerous changes including new
proteins embedded in the membranes in order to transform. Also, massive changes in the protein
content can occur without any noticeable structural changes, depending on the enzymatic needs
of the cell (as per the functions listed below).
Rough endoplasmic reticulum
The surface of the rough endoplasmic reticulum (RER) is studded with protein-manufacturing
ribosomes giving it a "rough" appearance (hence its name). However, the ribosomes bound to the
RER at any one time are not a stable part of this organelle's structure as ribosomes are constantly
being bound and released from the membrane. A ribosome only binds to the ER once it begins to
synthesize a protein destined for the secretory pathway. Here, a ribosome in the cytosol begins
synthesizing a protein until a signal recognition particle recognizes the pre-piece of 5-15
hydrophobic amino acids preceded by a positively charged amino acid. This signal sequence
allows the recognition particle to bind to the ribosome, causing the ribosome to bind to the RER
and pass the new protein through the ER membrane. The pre-piece is then cleaved off within the
lumen of the ER and the ribosome released back into the cytosol.
The membrane of the RER is continuous with the outer layer of the nuclear envelope. Although
there is no continuous membrane between the RER and the Golgi apparatus, membrane-bound
vesicles shuttle proteins between these two compartments. Vesicles are surrounded by coating
proteins called COPI and COPII. COPII targets vesicles to the golgi and COPI marks them to be
brought back to the RER. The RER works in concert with the Golgi complex to target new
proteins to their proper destinations. A second method of transport out of the ER are areas called
membrane contact sites, where the membranes of the ER and other organelles are held closely
together, allowing the transfer of lipids and other small molecules.
The RER is key in multiple functions:

lysosomal enzymes with a mannose-6-phosphate marker added in the cis-Golgi network

Secreted proteins, either secreted constitutively with no tag, or regulated secretion
involving clathrin and paired basic amino acids in the signal peptide.

integral membrane proteins that stay imbedded in the membrane as vesicles exit and bind
to new membranes. Rab proteins are key in targeting the membrane, SNAP and SNARE
proteins are key in the fusion event.

initial glycosylation as assembly continues. This is either N-linked (O-linking occur in
the golgi).
o
N-linked glycosylation: if the protein is properly folded, glycosyltransferase
recognizes the AA sequence NXS or NXT (with the S/T residue phosphorylated)
and adds a 14 sugar backbone (2 N-acetylglucosamine, 9 branching mannose, and
3 glucose at the end) to the side chain nitrogen of Asn.
Give the details of Smooth endoplasmic reticulum.
The smooth endoplasmic reticulum (SER) has functions in several metabolic processes,
including synthesis of lipids and steroids, metabolism of carbohydrates, regulation of calcium
concentration, drug detoxification, attachment of receptors on cell membrane proteins, and
steroid metabolism. It is connected to the nuclear envelope. Smooth endoplasmic reticulum is
found in a variety of cell types (both animal and plant) and it serves different functions in each.
The Smooth ER also contains the enzyme glucose-6-phosphatase which converts glucose-6phosphate to glucose, a step in gluconeogenesis. The SER consists of tubules and vesicles that
branch forming a network. In some cells there are dilated areas like the sacs of RER. The
network of SER allows increased surface area for the action or storage of key enzymes and the
products of these enzymes.
Functions
The endoplasmic reticulum serves many general functions, including the facilitation of protein
folding and the transport of synthesized proteins in sacs called cisternae.
Correct folding of newly-made proteins is made possible by several endoplasmic reticulum
chaperone proteins, including protein disulfide isomerase (PDI), ERp29, the Hsp70 family
member Grp78, calnexin, calreticulin, and the peptidylpropyl isomerase family. Only properlyfolded proteins are transported from the rough ER to the Golgi complex.
Transport of proteins
Secretory proteins, mostly glycoproteins, are moved across the endoplasmic reticulum
membrane. Proteins that are transported by the endoplasmic reticulum and from there throughout
the cell are marked with an address tag called a signal sequence. The N-terminus (one end) of a
polypeptide chain (i.e., a protein) contains a few amino acids that work as an address tag, which
are removed when the polypeptide reaches its destination. Proteins that are destined for places
outside the endoplasmic reticulum are packed into transport vesicles and moved along the
cytoskeleton toward their destination.
The endoplasmic reticulum is also part of a protein sorting pathway. It is, in essence, the
transportation system of the eukaryotic cell. The majority of endoplasmic reticulum resident
proteins are retained in the endoplasmic reticulum through a retention motif. This motif is
composed of four amino acids at the end of the protein sequence. The most common retention
sequence is KDEL (lys-asp-glu-leu). However, variation on KDEL does occur and other
sequences can also give rise to endoplasmic reticulum retention. It is not known if such variation
can lead to sub-endoplasmic reticulum localizations. There are three KDEL receptors in
mammalian cells, and they have a very high degree of sequence identity. The functional
differences between these receptors remain to be established.
Other functions

Insertion of proteins into the endoplasmic reticulum membrane: Integral membrane
proteins are inserted into the endoplasmic reticulum membrane as they are being
synthesized (co-translational translocation). Insertion into the endoplasmic reticulum
membrane requires the correct topogenic signal sequences in the protein.

Glycosylation: Glycosylation involves the attachment of oligosaccharides.

Disulfide bond formation and rearrangement: Disulfide bonds stabilize the tertiary
and quaternary structure of many proteins.

Drug Metabolism: The smooth ER is the site at which some drugs are modified by
microsomal enzymes which include the cytochrome P450 enzymes.
Draw the diagrame of Golgi apparatus.
he Golgi apparatus (also Golgi body or the Golgi complex) is an organelle found in most
eukaryotic cells. It was identified in 1897 by the Italian physician Camillo Golgi and named after
him.

The primary function of the Golgi apparatus is to process and package macromolecules,
such as proteins and lipids, after their synthesis and before they make their way to their
destination; it is particularly important in the processing of proteins for secretion. The
Golgi apparatus forms a part of the cellular endomembrane system.
Discovery
Due to its fairly large size, the Golgi apparatus was one of the first organelles to be discovered
and observed in detail. The apparatus was discovered in 1897 by Italian physician Camillo Golgi
during an investigation of the nervous system.After first observing it under his microscope, he
termed the structure the internal reticular apparatus. The structure was then renamed after Golgi
not long after the announcement of his discovery in 1898. However, some doubted the discovery
at first, arguing that the appearance of the structure was merely an optical illusion created by the
observation technique used by Golgi. With the development of modern microscopes in the 20th
century, the discovery was confirmed.
Structure
The Golgi is composed of stacks of membrane-bound structures known as cisternae (singular:
cisterna). An individual stack is sometimes called a dictyosome (from Greek dictyon, net +
soma, body), especially in plant cells.A mammalian cell typically contains 40 to 100 stacks.
Between four and eight cisternae are usually present in a stack; however, in some protists as
many as sixty have been observed. Each cisterna comprises a flattened membrane disk, and
carries Golgi enzymes to help or to modify cargo proteins that travel through them. They are
found in both plant and animal cells.
The cisternae stack has four functional regions: the cis-Golgi network, medial-Golgi, endoGolgi, and trans-Golgi network. Vesicles from the endoplasmic reticulum (via the vesiculartubular clusters) fuse with the network and subsequently progress through the stack to the trans
Golgi network, where they are packaged and sent to the required destination. Each region
contains different enzymes which selectively modify the contents depending on where they
reside. The cisternae also carry structural proteins important for their maintenance as flattened
membranes which stack upon each other.
Function
Cells synthesize a large number of different macromolecules. The Golgi apparatus is integral in
modifying, sorting, and packaging these macromolecules for cell secretion (exocytosis) or use
within the cell. It primarily modifies proteins delivered from the rough endoplasmic reticulum
but is also involved in the transport of lipids around the cell, and the creation of lysosomes. In
this respect it can be thought of as similar to a post office; it packages and labels items which it
then sends to different parts of the cell.
Enzymes within the cisternae are able to modify substances by the addition of carbohydrates
(glycosylation) and phosphates (phosphorylation). In order to do so, the Golgi imports
substances such as nucleotide sugars from the cytosol. These modifications may also form a
signal sequence which determines their final destination. For example, the Golgi apparatus adds
a mannose-6-phosphate label to proteins destined for lysosomes.
The Golgi plays an important role in the synthesis of proteoglycans, which are molecules present
in the extracellular matrix of animals. It is also a major site of carbohydrate synthesis.This
includes the productions of glycosaminoglycans (GAGs), long unbranched polysaccharides
which the Golgi then attaches to a protein synthesised in the endoplasmic reticulum to form
proteoglycans. Enzymes in the Golgi polymerize several of these GAGs via a xylose link onto
the core protein. Another task of the Golgi involves the sulfation of certain molecules passing
through its lumen via sulphotranferases that gain their sulphur molecule from a donor called
PAPs. This process occurs on the GAGs of proteoglycans as well as on the core protein. The
level of sulfation is very important to the proteoglycans' signalling abilities as well as giving the
proteoglycan its overall negative charge.
The phosphorylation of molecules requires that ATP is imported into the lumen of the Golgi and
then utilised by resident kinases such as casein kinase 1 and casein kinase 2. One molecule that is
phosphorylated in the Golgi is Apolipoprotein, which forms a molecule known as VLDL that is a
constitute of blood serum. It is thought that the phosphorylation of these molecules is important
to help aid in their sorting for secretion into the blood serum.
The Golgi has a putative role in apoptosis, with several Bcl-2 family members localised there, as
well as to the mitochondria. A newly characterized protein, GAAP (Golgi anti-apoptotic
protein), almost exclusively resides in the Golgi and protects cells from apoptosis by an as-yet
undefined mechanism.
Vesicular transport
The vesicles that leave the rough endoplasmic reticulum are transported to the cis face of the
Golgi apparatus, where they fuse with the Golgi membrane and empty their contents into the
lumen. Once inside they are modified, sorted and shipped towards their final destination. As
such, the Golgi apparatus tends to be more prominent and numerous in cells synthesising and
secreting many substances: plasma B cells, the antibody-secreting cells of the immune system,
have prominent Golgi complexes.
Those proteins destined for areas of the cell other than either the endoplasmic reticulum or Golgi
apparatus are moved towards the trans face, to a complex network of membranes and associated
vesicles known as the trans-Golgi network (TGN). This area of the Golgi is the point at which
proteins are sorted and shipped to their intended destinations by their placement into one of at
least three different types of vesicles, depending upon the molecular marker they carry:
Type
Description
Example
Vesicle contains proteins destined for
extracellular release. After packaging the
vesicles bud off and immediately move Antibody
Exocytotic vesicles (continuous) towards the plasma membrane, where they by
release
activated
fuse and release the contents into the plasma B cells
extracellular space in a process known as
constitutive secretion.
Vesicle contains proteins destined for
extracellular release. After packaging the
vesicles bud off and are stored in the cell
Secretory vesicles (regulated)
until a signal is given for their release.
When the appropriate signal is received
they move towards the membrane and fuse
Neurotransmitter
release
from
neurons
to release their contents. This process is
known as regulated secretion.
Vesicle contains proteins destined for the
lysosome, an organelle of degradation
containing many acid hydrolases, or to
lysosome-like storage organelles. These Digestive proteases
Lysosomal vesicles
proteins include both digestive enzymes destined
for
the
and membrane proteins. The vesicle first lysosome
fuses with the late endosome, and the
contents are then transferred to the
lysosome via unknown mechanisms.
Transport mechanism
The transport mechanism which proteins use to progress through the Golgi apparatus is not yet
clear; however a number of hypotheses currently exist. Until recently, the vesicular transport
mechanism was favoured but now more evidence is coming to light to support cisternal
maturation. The two proposed models may actually work in conjunction with each other, rather
than being mutually exclusive. This is sometimes referred to as the combined model.

Cisternal maturation model: the cisternae of the Golgi apparatus move by being built at
the cis face and destroyed at the trans face. Vesicles from the endoplasmic reticulum fuse
with each other to form a cisterna at the cis face, consequently this cisterna would appear
to move through the Golgi stack when a new cisterna is formed at the cis face. This
model is supported by the fact that structures larger than the transport vesicles, such as
collagen rods, were observed microscopically to progress through the Golgi apparatus.
This was initially a popular hypothesis, but lost favour in the 1980s. Recently it has made
a comeback, as laboratories at the University of Chicago and the University of Tokyo
have been able to use new technology to directly observe Golgi compartments maturing.
Additional evidence comes from the fact that COPI vesicles move in the retrograde
direction, transporting Endoplasmic Reticulum proteins back to where they belong by
recognizing a signal peptide.

Vesicular transport model: Vesicular transport views the Golgi as a very stable
organelle, divided into compartments in the cis to trans direction. Membrane bound
carriers transport material between the ER and the different compartments of the Golgi.
Experimental evidence includes the abundance of small vesicles (known technically as
shuttle vesicles) in proximity to the Golgi apparatus. To direct the vesicles, actin
filaments connect packaging proteins to the membrane to ensure that they fuse with the
correct compartment.
Golgi apparatus during mitosis
The Golgi apparatus will break up and disappear following the onset of mitosis, or cellular
division. During the telophase of mitosis, the Golgi apparatus reappears; however, it is still
uncertain how this occurs.
Explain about the Ribosome stucture and funtion.
Ribosomes are the components of cells that make proteins from all amino acids. One of the
central tenets of biology, often referred to as the "central dogma," is that DNA is used to make
RNA, which, in turn, is used to make protein. The DNA sequence in genes is copied into a
messenger RNA (mRNA). Ribosomes then read the information in this RNA and use it to create
proteins. This process is known as translation; i.e., the ribosome "translates" the genetic
information from RNA into proteins. Ribosomes do this by binding to an mRNA and using it as
a template for the correct sequence of amino acids in a particular protein. The amino acids are
attached to transfer RNA (tRNA) molecules, which enter one part of the ribosome and bind to
the messenger RNA sequence. The attached amino acids are then joined together by another part
of the ribosome. The ribosome moves along the mRNA, "reading" its sequence and producing a
chain of amino acids.
Ribosomes are made from complexes of RNAs and proteins. Ribosomes are divided into two
subunits, one larger than the other. The smaller subunit binds to the mRNA, while the larger
subunit binds to the tRNA and the amino acids. When a ribosome finishes reading a mRNA,
these two subunits split apart. Ribosomes have been classified as ribozymes, since the ribosomal
RNA seems to be most important for the peptidyl transferase activity that links amino acids
together.
Ribosomes from bacteria, archaea and eukaryotes (the three domains of life on Earth), have
significantly different structures and RNA sequences. These differences in structure allow some
antibiotics to kill bacteria by inhibiting their ribosomes, while leaving human ribosomes
unaffected. The ribosomes in the mitochondria of eukaryotic cells resemble those in bacteria,
reflecting the likely evolutionary origin of this organelle.he word ribosome comes from
ribonucleic acid and the Greek: soma (meaning body).
Description
Archaeal, eubacterial and eukaryotic ribosomes differ in their size, composition and the ratio of
protein to RNA. Because they are formed from two subunits of non-equal size, they are slightly
longer in the axis than in diameter. Prokaryotic ribosomes are around 20 nm (200 ångströms) in
diameter and are composed of 65% ribosomal RNA and 35% ribosomal proteins (known as a
ribonucleoprotein or RNP). Eukaryotic ribosomes are between 25 and 30 nm (250-300
ångströms) in diameter and the ratio of rRNA to protein is close to 1. Ribosomes translate
messenger RNA (mRNA) and build polypeptide chains (e.g., proteins) using amino acids
delivered by transfer RNA (tRNA). Their active sites are made of RNA, so ribosomes are now
classified as "ribozymes".
Ribosomes build proteins from the genetic instructions held within messenger RNA. Free
ribosomes are suspended in the cytosol (the semi-fluid portion of the cytoplasm); others are
bound to the rough endoplasmic reticulum, giving it the appearance of roughness and thus its
name, or to the nuclear envelope. As ribozymes are partly constituted from RNA, it is thought
that they might be remnants of the RNA world. Although catalysis of the peptide bond involves
the C2 hydroxyl of RNA's P-site (see Function section below) adenosine in a protein shuttle
mechanism, other steps in protein synthesis (such as translocation) are caused by changes in
protein conformations.
Ribosomes are sometimes referred to as organelles, but the use of the term organelle is often
restricted to describing sub-cellular components that include a phospholipid membrane, which
ribosomes, being entirely particulate, do not. For this reason, ribosomes may sometimes be
described as "non-membranous organelles".
Ribosomes were first observed in the mid-1950s by Romanian cell biologist George Palade using
an electron microscope as dense particles or granules for which he would win the Nobel Prize.
The term "ribosome" was proposed by scientist Richard B. Roberts in 1958:
During the course of the symposium a semantic difficulty became apparent. To some of the
participants, "microsomes" mean the ribonucleoprotein particles of the microsome fraction
contaminated by other protein and lipid material; to others, the microsomes consist of protein
and lipid contaminated by particles. The phrase “microsomal particles” does not seem adequate,
and “ribonucleoprotein particles of the microsome fraction” is much too awkward. During the
meeting, the word "ribosome" was suggested, which has a very satisfactory name and a pleasant
sound. The present confusion would be eliminated if “ribosome” were adopted to designate
ribonucleoprotein particles in sizes ranging from 35 to 100S.
The structure and function of the ribosomes and associated molecules, known as the
translational apparatus, has been of research interest since the mid-twentieth century and is a
very active field of study today.
Figure 2 : Large (red) and small (blue) subunit fit together
Ribosomes consist of two subunits (Figure 1) that fit together (Figure 2) and work as one to
translate the mRNA into a polypeptide chain during protein synthesis (Figure 3). Bacterial
subunits consist of one or two and eukaryotic of one or three very large RNA molecules (known
as ribosomal RNA or rRNA) and multiple smaller protein molecules. Crystallographic work has
shown that there are no ribosomal proteins close to the reaction site for polypeptide synthesis.
This suggests that the protein components of ribosomes act as a scaffold that may enhance the
ability of rRNA to synthesize protein rather than directly participating in catalysis (See:
Ribozyme).
Biogenesis
In bacterial cells, ribosomes are synthesized in the cytoplasm through the transcription of
multiple ribosome gene operons. In eukaryotes, the process takes place both in the cell cytoplasm
and in the nucleolus, which is a region within the cell nucleus. The assembly process involves
the coordinated function of over 200 proteins in the synthesis and processing of the four rRNAs,
as well as assembly of those rRNAs with the ribosomal proteins.
Ribosome locations
Ribosomes are classified as being either "free" or "membrane-bound".
A ribosome translating a protein that is secreted into the endoplasmic reticulum.
Free and membrane-bound ribosomes differ only in their spatial distribution; they are identical in
structure. Whether the ribosome exists in a free or membrane-bound state depends on the
presence of an ER-targeting signal sequence on the protein being synthesized, so an individual
ribosome might be membrane-bound when it is making one protein, but free in the cytosol when
it makes another protein.
Free ribosomes
Free ribosomes can move about anywhere in the cytosol, but are excluded from the cell nucleus
and other organelles. Proteins that are formed from free ribosomes are released into the cytosol
and used within the cell. Since the cytosol contains high concentrations of glutathione and is,
therefore, a reducing environment, proteins containing disulfide bonds, which are formed from
oxidized cysteine residues, cannot be produced in this compartment.
Membrane-bound ribosomes
When a ribosome begins to synthesize proteins that are needed in some organelles, the ribosome
making this protein can become "membrane-bound". In eukaryotic cells this happens in a region
of the endoplasmic reticulum (ER) called the "rough ER". The newly produced polypeptide
chains are inserted directly into the ER by the ribosome and are then transported to their
destinations, through the secretory pathway. Bound ribosomes usually produce proteins that are
used within the plasma membrane or are expelled from the cell via exocytosis.
structure
Atomic structure of the 30S Subunit from Thermus thermophilus. Proteins are shown in blue and
the single RNA strand in orange.
The ribosomal subunits of prokaryotes and eukaryotes are quite similar.
The unit of measurement is the Svedberg unit, a measure of the rate of sedimentation in
centrifugation rather than size and accounts for why fragment names do not add up (70S is made
of 50S and 30S).
Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large (50S) subunit.
Their large subunit is composed of a 5S RNA subunit (consisting of 120 nucleotides), a 23S
RNA subunit (2900 nucleotides) and 34 proteins. The 30S subunit has a 1540 nucleotide RNA
subunit (16S) bound to 21 proteins.
Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their
large subunit is composed of a 5S RNA (120 nucleotides), a 28S RNA (4700 nucleotides), a 5.8S
subunit (160 nucleotides) and ~49 proteins. The 40S subunit has a 1900 nucleotide (18S) RNA
and ~33 proteins.
The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and
small subunits bound together with proteins into one 70S particle.These organelles are believed
to be descendants of bacteria (see Endosymbiotic theory) and as such their ribosomes are similar
to those of bacteria.
The various ribosomes share a core structure, which is quite similar despite the large differences
in size. Much of the RNA is highly organized into various tertiary structural motifs, for example
pseudoknots that exhibit coaxial stacking. The extra RNA in the larger ribosomes is in several
long continuous insertions, such that they form loops out of the core structure without disrupting
or changing it. All of the catalytic activity of the ribosome is carried out by the RNA; the
proteins reside on the surface and seem to stabilize the structure.
The differences between the bacterial and eukaryotic ribosomes are exploited by pharmaceutical
chemists to create antibiotics that can destroy a bacterial infection without harming the cells of
the infected person. Due to the differences in their structures, the bacterial 70S ribosomes are
vulnerable to these antibiotics while the eukaryotic 80S ribosomes are not. Even though
mitochondria possess ribosomes similar to the bacterial ones, mitochondria are not affected by
these antibiotics because they are surrounded by a double membrane that does not easily admit
these antibiotics into the organelle.
High-resolution structure
Atomic structure of the 50S Subunit from Haloarcula marismortui. Proteins are shown in blue
and the two RNA strands in orange and yellow. The small patch of green in the center of the
subunit is the active site.
The general molecular structure of the ribosome has been known since the early 1970s. In the
early 2000s the structure has been achieved at high resolutions, on the order of a few ångströms.
The first papers giving the structure of the ribosome at atomic resolution were published in rapid
succession in late 2000. First, the 50S (large prokaryotic) subunit from the archaeon Haloarcula
marismortui was published. Soon after, the structure of the 30S subunit from Thermus
thermophilus was published. Shortly thereafter, a more detailed structure was published. These
structural studies were awarded the Nobel Prize in Chemistry in 2009. Early the next year (May
2001) these coordinates were used to reconstruct the entire T. thermophilus 70S particle at 5.5
ångström resolution.[Two papers were published in November 2005 with structures of the
Escherichia coli 70S ribosome. The structures of a vacant ribosome were determined at 3.5ångström resolution using x-ray crystallography. Then, two weeks later, a structure based on
cryo-electron microscopy was published, which depicts the ribosome at 11-15 ångström
resolution in the act of passing a newly synthesized protein strand into the protein-conducting
channel.
First atomic structures of the ribosome complexed with tRNA and mRNA molecules were solved
by using X-ray crystallography by two groups independently, at 2.8 angstrom and at 3.7
ångström.[hese structures allow one to see the details of interactions of the Thermus thermophilus
ribosome with mRNA and with tRNAs bound at classical ribosomal sites. Interactions of the
ribosome with long mRNAs containing Shine-Dalgarno sequences were visualized soon after
that at 4.5- to 5.5-ångström resolution.
Function
Ribosomes are the workhorses of protein biosynthesis, the process of translating mRNA
into protein. The mRNA comprises a series of codons that dictate to the ribosome the sequence
of the amino acids needed to make the protein. Using the mRNA as a template, the ribosome
traverses each codon (3 nucleotides) of the mRNA, pairing it with the appropriate amino acid
provided by a tRNA. Molecules of transfer RNA (tRNA) contain a complementary anticodon on
one end and the appropriate amino acid on the other. The small ribosomal subunit, typically
bound to a tRNA containing the amino acid methionine, binds to an AUG codon on the mRNA
and recruits the large ribosomal subunit. The ribosome then contains three RNA binding sites,
designated A, P and E. The A site binds an aminoacyl-tRNA (a tRNA bound to an amino acid);
the P site binds a peptidyl-tRNA (a tRNA bound to the peptide being synthesized); and the E site
binds a free tRNA before it exits the ribosome. Protein synthesis begins at a start codon AUG
near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome is
able to identify the start codon by use of the Shine-Dalgarno sequence of the mRNA in
prokaryotes and Kozak box in eukaryotes.
Figure 3 : Translation of mRNA (1) by a ribosome (2)(shown as small and large subunits) into a
polypeptide chain (3). The ribosome begins at the start codon of mRNA (AUG) and ends at the
stop codon (UAG).
In Figure 3, both ribosomal subunits (small and large) assemble at the start codon (towards the 5'
end of the mRNA). The ribosome uses tRNA that matches the current codon (triplet) on the
mRNA to append an amino acid to the polypeptide chain. This is done for each triplet on the
mRNA, while the ribosome moves towards the 3' end of the mRNA. Usually in bacterial cells,
several ribosomes are working parallel on a single mRNA, forming what is called a
polyribosome or polysome.
Give the details of Cell nucleus.
In cell biology, the nucleus (pl. nuclei; from Latin nucleus or nuculeus, meaning kernel) is a
membrane enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic
material, organized as multiple long linear DNA molecules in complex with a large variety of
proteins, such as histones, to form chromosomes. The genes within these chromosomes are the
cell's nuclear genome. The function of the nucleus is to maintain the integrity of these genes and
to control the activities of the cell by regulating gene expression — the nucleus is therefore the
control center of the cell. The main structures making up the nucleus are the nuclear envelope, a
double membrane that encloses the entire organelle and separates its contents from the cellular
cytoplasm, and the nuclear lamina, a meshwork within the nucleus that adds mechanical support,
much like the cytoskeleton supports the cell as a whole. Because the nuclear membrane is
impermeable to most molecules, nuclear pores are required to allow movement of molecules
across the envelope. These pores cross both of the membranes, providing a channel that allows
free movement of small molecules and ions. The movement of larger molecules such as proteins
is carefully controlled, and requires active transport regulated by carrier proteins. Nuclear
transport is crucial to cell function, as movement through the pores is required for both gene
expression and chromosomal maintenance.
Although the interior of the nucleus does not contain any membrane-bound subcompartments, its
contents are not uniform, and a number of subnuclear bodies exist, made up of unique proteins,
RNA molecules, and particular parts of the chromosomes. The best known of these is the
nucleolus, which is mainly involved in the assembly of ribosomes. After being produced in the
nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA.
The nucleus was the first organelle to be discovered. The probably oldest preserved
drawing dates back to the early microscopist Antonie van Leeuwenhoek (1632 – 1723). He
observed a "Lumen", the nucleus, in the red blood cells of salmon.[1] Unlike mammalian red
blood cells, those of other vertebrates still possess nuclei. The nucleus was also described by
Franz Bauer in 1804[2] and in more detail in 1831 by Scottish botanist Robert Brown in a talk at
the Linnean Society of London. Brown was studying orchids microscopically when he observed
an opaque area, which he called the areola or nucleus, in the cells of the flower's outer layer.[3]
He did not suggest a potential function. In 1838 Matthias Schleiden proposed that the nucleus
plays a role in generating cells, thus he introduced the name "Cytoblast" (cell builder). He
believed that he had observed new cells assembling around "cytoblasts". Franz Meyen was a
strong opponent of this view having already described cells multiplying by division and
believing that many cells would have no nuclei. The idea that cells can be generated de novo, by
the "cytoblast" or otherwise, contradicted work by Robert Remak (1852) and Rudolf Virchow
(1855) who decisively propagated the new paradigm that cells are generated solely by cells
("Omnis cellula e cellula"). The function of the nucleus remained unclear.[4]
Between 1876 and 1878 Oscar Hertwig published several studies on the fertilization of sea
urchin eggs, showing that the nucleus of the sperm enters the oocyte and fuses with its nucleus.
This was the first time it was suggested that an individual develops from a (single) nucleated
cell. This was in contradiction to Ernst Haeckel's theory that the complete phylogeny of a species
would be repeated during embryonic development, including generation of the first nucleated
cell from a "Monerula", a structureless mass of primordial mucus ("Urschleim"). Therefore, the
necessity of the sperm nucleus for fertilization was discussed for quite some time. However,
Hertwig confirmed his observation in other animal groups, e.g. amphibians and molluscs. Eduard
Strasburger produced the same results for plants (1884). This paved the way to assign the
nucleus an important role in heredity. In 1873 August Weismann postulated the equivalence of
the maternal and paternal germ cells for heredity. The function of the nucleus as carrier of
genetic information became clear only later, after mitosis was discovered and the Mendelian
rules were rediscovered at the beginning of the 20th century; the chromosome theory of heredity
was developed.
Structures
The nucleus is the largest cellular organelle in animals.[5] In mammalian cells, the average
diameter of the nucleus is approximately 6 micrometers (μm), which occupies about 10% of the
total cell volume.[6] The viscous liquid within it is called nucleoplasm, and is similar in
composition to the cytosol found outside the nucleus.[7] It appears as a dense, roughly spherical
organelle.
The eukaryotic cell nucleus. Visible in this diagram
are the ribosome-studded double membranes of the A cross section of a nuclear pore on the
nuclear
envelope,
the
DNA
(complexed
as surface of the nuclear envelope (1). Other
chromatin), and the nucleolus. Within the cell diagram labels show (2) the outer ring, (3)
nucleus is a viscous liquid called nucleoplasm, spokes, (4) basket, and (5) filaments.
similar to the cytoplasm found outside the nucleus.
What is role of Nuclear envelope and pores in transport?
The nuclear envelope otherwise known as nuclear membrane consists of two cellular
membranes, an inner and an outer membrane, arranged parallel to one another and separated by
10 to 50 nanometers (nm). The nuclear envelope completely encloses the nucleus and separates
the cell's genetic material from the surrounding cytoplasm, serving as a barrier to prevent
macromolecules from diffusing freely between the nucleoplasm and the cytoplasm.[8] The outer
nuclear membrane is continuous with the membrane of the rough endoplasmic reticulum (RER),
and is similarly studded with ribosomes. The space between the membranes is called the
perinuclear space and is continuous with the RER lumen.
Nuclear pores, which provide aqueous channels through the envelope, are composed of multiple
proteins, collectively referred to as nucleoporins. The pores are about 125 million daltons in
molecular weight and consist of around 50 (in yeast) to 100 proteins (in vertebrates). The pores
are 100 nm in total diameter; however, the gap through which molecules freely diffuse is only
about 9 nm wide, due to the presence of regulatory systems within the center of the pore. This
size allows the free passage of small water-soluble molecules while preventing larger molecules,
such as nucleic acids and larger proteins, from inappropriately entering or exiting the nucleus.
These large molecules must be actively transported into the nucleus instead. The nucleus of a
typical mammalian cell will have about 3000 to 4000 pores throughout its envelope, each of
which contains a donut-shaped, eightfold-symmetric ring-shaped structure at a position where
the inner and outer membranes fuse. Attached to the ring is a structure called the nuclear basket
that extends into the nucleoplasm, and a series of filamentous extensions that reach into the
cytoplasm. Both structures serve to mediate binding to nuclear transport proteins.
Most proteins, ribosomal subunits, and some RNAs are transported through the pore complexes
in a process mediated by a family of transport factors known as karyopherins. Those
karyopherins that mediate movement into the nucleus are also called importins, while those that
mediate movement out of the nucleus are called exportins. Most karyopherins interact directly
with their cargo, although some use adaptor proteins. Steroid hormones such as cortisol and
aldosterone, as well as other small lipid-soluble molecules involved in intercellular signaling can
diffuse through the cell membrane and into the cytoplasm, where they bind nuclear receptor
proteins that are trafficked into the nucleus. There they serve as transcription factors when bound
to their ligand; in the absence of ligand many such receptors function as histone deacetylases that
repress gene expression.
Chromosomes
The cell nucleus contains the majority of the cell's genetic material, in the form of
multiple linear DNA molecules organized into structures called chromosomes. During most of
the cell cycle these are organized in a DNA-protein complex known as chromatin, and during
cell division the chromatin can be seen to form the well defined chromosomes familiar from a
karyotype. A small fraction of the cell's genes are located instead in the mitochondria.
There are two types of chromatin. Euchromatin is the less compact DNA form, and contains
genes that are frequently expressed by the cell. The other type, heterochromatin, is the more
compact form, and contains DNA that are infrequently transcribed. This structure is further
categorized into facultative heterochromatin, consisting of genes that are organized as
heterochromatin only in certain cell types or at certain stages of development, and constitutive
heterochromatin that consists of chromosome structural components such as telomeres and
centromeres. During interphase the chromatin organizes itself into discrete individual patches,
called chromosome territories. Active genes, which are generally found in the euchromatic
region of the chromosome, tend to be located towards the chromosome's territory boundary.
Antibodies to certain types of chromatin organization, particularly nucleosomes, have been
associated with a number of autoimmune diseases, such as systemic lupus erythematosus. These
are known as anti-nuclear antibodies (ANA) and have also been observed in concert with
UNIT III
Write about the reproduction of Bacteria.
Binary fission
Binary fission, or prokaryotic fission, is form of asexual reproduction and cell division used by
all prokaryotes, some protozoa, and some organelles within eukaryotic organisms. This process
results in the reproduction of a living prokaryotic cell by division into two parts which each have
the potential to grow to the size of the original cell.
Mitosis and cytokinesis are not the same as binary fission; specifically, binary fission cannot be
divided into prophase, metaphase, anaphase, and telophase because prokaryotes have no nucleus
and no centromeres. The ability of some multicellular animals, such as echinoderms and
flatworms, to regenerate two whole organisms after having been cut in half, is also not the same
as binary fission. Neither is vegetative reproduction of plants.
Process
Binary fission begins with DNA replication. DNA replication starts from an origin of replication,
which opens up into a replication bubble (note: prokaryotic DNA replication usually has only 1
origin of replication, whereas eukaryotes have multiple origins of replication). The replication
bubble separates the DNA double strand, each strand acts as template for synthesis of a daughter
strand by semiconservative replication, until the entire prokaryotic DNA is duplicated.
Each circular DNA strand then attaches to the cell membrane. The cell elongates, causing the
DNA to separate.
Cell division in bacteria is controlled by the FtsZ, a collection of about a dozen proteins that
collect around the site of division. There, they direct assembly of the division septum. The cell
wall and plasma membrane starts growing transversely from near the middle of the dividing cell.
This separates the parent cell into two nearly equal daughter cells, each having a nuclear body.[1]
The cell membrane then invaginates (grows inwards) and splits the cell into two daughter cells,
separated by a newly grown cell plate.
Explain the eukaryotes reproduction .
Meiosis
Meiosis (pronounced maɪˈoʊsɨs (help·info)) is a special type of cell division necessary
for sexual reproduction. In animals, meiosis produces gametes like sperm and egg cells, while in
other organisms like fungi it generates spores. In many organisms, including humans, meiosis
begins with one cell containing two copies of each chromosome—one from the organism's
mother and one from its father—and produces four gamete cells containing one copy of each
chromosome. Each of the resulting chromosomes in the gamete cells is a unique mixture of
maternal and paternal DNA, ensuring that offspring are genetically distinct from either parent.
This gives rise to genetic diversity in sexually reproducing populations, which enables them to
adapt during the course of evolution.
Meiosis begins when a cell's chromosomes are duplicated by a round of DNA replication. This
leaves the maternal and paternal versions of each chromosome, called homologs, with an exact
copy known as a sister chromatid attached at the center of the new chromosome pair. The
maternal and paternal chromosome pairs then become interwoven by homologous
recombination, which often leads to crossovers of DNA from the maternal version of the
chromosome to the paternal version and vice versa. A spindle fiber binds to the center of each
pair of homologs, and pulls the recombined maternal and paternal homolog pairs to different
poles of the cell.
The cell then divides into two daughter cells as the chromosomes move away from the center.
After the recombined maternal and paternal homologs have separated into the two daughter cells,
a second round of cell division occurs. There, meiosis ends as the two sister chromatids making
up each homolog are separated and move into one of the four resulting gamete cells. Upon
fertilization, for example when a sperm enters an egg cell, two gamete cells produced by meiosis
fuse. The gamete from the mother and the gamete from the father each contribute half to the set
of chromosomes that make up the new offsping's genome.
Meiosis uses many of the same mechanisms as mitosis, a type of cell division used by eukaryotes
like plants and animals to split one cell into two identical daughter cells. In all plants, and in
many protists, meiosis results in the formation of spores, haploid cells that can divide
vegetatively without undergoing fertilization. Some eukaryotes, like Bdelloid rotifers, have lost
the ability to carry out meiosis and have acquired the ability to reproduce by parthenogenesis.
Meiosis does not occur in archaea or bacteria, which reproduce via asexual processes such as
binary fission.

History
Meiosis was discovered and described for the first time in sea urchin eggs in 1876 by the
German biologist Oscar Hertwig. It was described again in 1883, at the level of chromosomes,
by the Belgian zoologist Edouard Van Beneden, in Ascaris worms' eggs. The significance of
meiosis for reproduction and inheritance, however, was described only in 1890 by German
biologist August Weismann, who noted that two cell divisions were necessary to transform one
diploid cell into four haploid cells if the number of chromosomes had to be maintained. In 1911,
the American geneticist Thomas Hunt Morgan observed crossover in Drosophila melanogaster
meiosis and provided the first genetic evidence that genes are transmitted on chromosomes.
Occurrence of meiosis in eukaryotic life cycles
Gametic life cycle.
Zygotic life cycle.
Sporic life cycle.
Meiosis occurs in eukaryotic life cycles involving sexual reproduction, comprising of the
constant cyclical process of meiosis and fertilization. This takes place alongside normal mitotic
cell division. In multicellular organisms, there is an intermediary step between the diploid and
haploid transition where the organism grows. The organism will then produce the germ cells that
continue in the life cycle. The rest of the cells, called somatic cells, function within the organism
and will die with it.
Cycling meiosis and fertilization events produces a series of transitions back and forth between
alternating haploid and diploid states. The organism phase of the life cycle can occur either
during the diploid state (gametic or diploid life cycle), during the haploid state (zygotic or
haploid life cycle), or both (sporic or haplodiploid life cycle, in which there two distinct
organism phases, one during the haploid state and the other during the diploid state). In this
sense, there are three types of life cycles that utilize sexual reproduction, differentiated by the
location of the organisms phase(s).
In the gametic life cycle, of which humans are a part, the species is diploid, grown from a diploid
cell called the zygote. The organism's diploid germ-line stem cells undergo meiosis to create
haploid gametes (the spermatozoa for males and ova for females), which fertilize to form the
zygote. The diploid zygote undergoes repeated cellular division by mitosis to grow into the
organism. Mitosis is a related process to meiosis that creates two cells that are genetically
identical to the parent cell. The general principle is that mitosis creates somatic cells and meiosis
creates germ cells.
In the zygotic life cycle the species is haploid instead, spawned by the proliferation and
differentiation of a single haploid cell called the gamete. Two organisms of opposing gender
contribute their haploid germ cells to form a diploid zygote. The zygote undergoes meiosis
immediately, creating four haploid cells. These cells undergo mitosis to create the organism.
Many fungi and many protozoa are members of the zygotic life cycle.
Finally, in the sporic life cycle, the living organism alternates between haploid and diploid states.
Consequently, this cycle is also known as the alternation of generations. The diploid organism's
germ-line cells undergo meiosis to produce spores. The spores proliferate by mitosis, growing
into a haploid organism. The haploid organism's germ cells then combine with another haploid
organism's cells, creating the zygote. The zygote undergoes repeated mitosis and differentiation
to become the diploid organism again. The sporic life cycle can be considered a fusion of the
gametic and zygotic life cycles.
Process
Because meiosis is a "one-way" process, it cannot be said to engage in a cell cycle as mitosis
does. However, the preparatory steps that lead up to meiosis are identical in pattern and name to
the interphase of the mitotic cell cycle.
Interphase is divided into three phases:

Growth 1 (G1) phase: This is a very active period, where the cell synthesizes its vast
array of proteins, including the enzymes and structural proteins it will need for growth. In
G1 stage each of the chromosomes consists of a single (very long) molecule of DNA. In
humans, at this point cells are 46 chromosomes, 2N, identical to somatic cells.

Synthesis (S) phase: The genetic material is replicated: each of its chromosomes
duplicates, so that each of the 46 chromosomes forms a second identical sister chromatid.
The cell is still considered diploid because it still contains the same number of
centromeres. The identical sister chromatids have not yet condensed into the densely
packaged chromosomes visible with the light microscope. This will take place during
prophase I in meiosis.

Growth 2 (G2) phase: G2 phase is absent in Meiosis
Interphase is followed by meiosis I and then meiosis II. Meiosis I consists of separating the pairs
of homologous chromosome, each made up of two sister chromatids, into two cells. One entire
haploid content of chromosomes is contained in each of the resulting daughter cells; the first
meiotic division therefore reduces the ploidy of the original cell by a factor of 2.
Meiosis II consists of decoupling each chromosome's sister strands (chromatids), and segregating
the individual chromatids into haploid daughter cells. The two cells resulting from meiosis I
divide during meiosis II, creating 4 haploid daughter cells. Meiosis I and II are each divided into
prophase, metaphase, anaphase, and telophase stages, similar in purpose to their analogous
subphases in the mitotic cell cycle. Therefore, meiosis includes the stages of meiosis I (prophase
I, metaphase I, anaphase I, telophase I), and meiosis II (prophase II, metaphase II, anaphase II,
telophase II).
Meiosis generates genetic diversity in two ways: (1) independent alignment and subsequent
separation of homologous chromosome pairs during the first meiotic division allows a random
and independent selection of each chromosome segregates into each gamete; and (2) physical
exchange of homologous chromosomal regions by homologous recombination during prophase I
results in new combinations of DNA within chromosomes.
A diagram of the meiotic phases
Phases
Meiosis takes place in several stages.
Meiosis I
Meiosis I separates homologous chromosomes, producing two haploid cells (N chromosomes,
23 in humans), so meiosis I is referred to as a reductional division. A regular diploid human cell
contains 46 chromosomes and is considered 2N because it contains 23 pairs of homologous
chromosomes. However, after meiosis I, although the cell contains 46 chromatids, it is only
considered as being N, with 23 chromosomes. This is because later, in Anaphase I, the sister
chromatids will remain together as the spindle fibres pulls the pair toward the pole of the new
cell. In meiosis II, an equational division similar to mitosis will occur whereby the sister
chromatids are finally split, creating a total of 4 haploid cells (23 chromosomes, N) per daughter
cell from the first division.
Prophase I
During prophase I, DNA is exchanged between homologous chromosomes in a process called
homologous recombination. This often results in chromosomal crossover. The new combinations
of DNA created during crossover are a significant source of genetic variation, and may result in
beneficial new combinations of alleles. The paired and replicated chromosomes are called
bivalents or tetrads, which have two chromosomes and four chromatids, with one chromosome
coming from each parent. At this stage, non-sister chromatids may cross-over at points called
chiasmata (plural; singular chiasma).
Leptotene
The first stage of prophase I is the leptotene stage, also known as leptonema, from Greek words
meaning "thin threads".[1]:27In this stage of prophase I, individual chromosomes—each consisting
of two sister chromatids—change from the diffuse state they exist in during the cell's period of
growth and gene expression, and condense into visible strands within the nucleus.[1]:27[2]:353
However the two sister chromatids are still so tightly bound that they are indistinguishable from
one another.
Zygotene
The zygotene stage, also known as zygonema, from Greek words meaning "paired threads",[1]:27
occurs as the chromosomes approximately line up with each other into homologous chromosome
pairs. This is called the bouquet stage because of the way the telomeres cluster at one end of the
nucleus. At this stage, the synapsis (pairing/coming together) of homologous chromosomes takes
place.
Pachytene
The pachytene stage, also known as pachynema, from Greek words meaning "thick threads",[1]:27
contains the following chromosomal crossover. Nonsister chromatids of homologous
chromosomes randomly exchange segments of genetic information over regions of homology.
Sex chromosomes, however, are not wholly identical, and only exchange information over a
small region of homology. Exchange takes place at sites where recombination nodules (the
chiasmata) have formed. The exchange of information between the non-sister chromatids results
in a recombination of information; each chromosome has the complete set of information it had
before, and there are no gaps formed as a result of the process. Because the chromosomes cannot
be distinguished in the synaptonemal complex, the actual act of crossing over is not perceivable
through the microscope.
Diplotene
During the diplotene stage, also known as diplonema, from Greek words meaning "two
threads",the synaptonemal complex degrades and homologous chromosomes separate from one
another a little. The chromosomes themselves uncoil a bit, allowing some transcription of DNA.
However, the homologous chromosomes of each bivalent remain tightly bound at chiasmata, the
regions where crossing-over occurred. The chiasmata remain on the chromosomes until they are
severed in anaphase I.
In human fetal oogenesis all developing oocytes develop to this stage and stop before birth. This
suspended state is referred to as the dictyotene stage and remains so until puberty. In males, only
spermatogonia (spermatogenesis) exist until meiosis begins at puberty.
Diakinesis
Chromosomes condense further during the diakinesis stage, from Greek words meaning "moving
through".This is the first point in meiosis where the four parts of the tetrads are actually visible.
Sites of crossing over entangle together, effectively overlapping, making chiasmata clearly
visible. Other than this observation, the rest of the stage closely resembles prometaphase of
mitosis; the nucleoli disappear, the nuclear membrane disintegrates into vesicles, and the meiotic
spindle begins to form.
Synchronous processes
During these stages, two centrosomes, containing a pair of centrioles in animal cells, migrate to
the two poles of the cell. These centrosomes, which were duplicated during S-phase, function as
microtubule organizing centers nucleating microtubules, which are essentially cellular ropes and
poles. The microtubules invade the nuclear region after the nuclear envelope disintegrates,
attaching to the chromosomes at the kinetochore. The kinetochore functions as a motor, pulling
the chromosome along the attached microtubule toward the originating centriole, like a train on a
track. There are four kinetochores on each tetrad, but the pair of kinetochores on each sister
chromatid fuses and functions as a unit during meiosis I.
Microtubules that attach to the kinetochores are known as kinetochore microtubules. Other
microtubules will interact with microtubules from the opposite centriole: these are called
nonkinetochore microtubules or polar microtubules. A third type of microtubules, the aster
microtubules, radiates from the centrosome into the cytoplasm or contacts components of the
membrane skeleton.
Metaphase I
Homologous pairs move together along the metaphase plate: As kinetochore microtubules from
both centrioles attach to their respective kinetochores, the homologous chromosomes align along
an equatorial plane that bisects the spindle, due to continuous counterbalancing forces exerted on
the bivalents by the microtubules emanating from the two kinetochores of homologous
chromosomes. The physical basis of the independent assortment of chromosomes is the random
orientation of each bivalent along the metaphase plate, with respect to the orientation of the other
bivalents along the same equatorial line.
Anaphase I
Kinetochore (bipolar spindles) microtubules shorten, severing the recombination nodules and
pulling homologous chromosomes apart. Since each chromosome has only one functional unit of
a pair of kinetochores[4], whole chromosomes are pulled toward opposing poles, forming two
haploid sets. Each chromosome still contains a pair of sister chromatids. Nonkinetochore
microtubules lengthen, pushing the centrioles farther apart. The cell elongates in preparation for
division down the center.
Telophase I
The last meiotic division effectively ends when the chromosomes arrive at the poles. Each
daughter cell now has half the number of chromosomes but each chromosome consists of a pair
of chromatids. The microtubules that make up the spindle network disappear, and a new nuclear
membrane surrounds each haploid set. The chromosomes uncoil back into chromatin.
Cytokinesis, the pinching of the cell membrane in animal cells or the formation of the cell wall in
plant cells, occurs, completing the creation of two daughter cells. Sister chromatids remain
attached during telophase I.
Cells may enter a period of rest known as interkinesis or interphase II. No DNA replication
occurs during this stage.
Meiosis II
Meiosis II is the second part of the meiotic process. Much of the process is similar to mitosis.
The end result is production of four haploid cells (23 chromosomes, 1N in humans) from the
two haploid cells (23 chromosomes, 1N * each of the chromosomes consisting of two sister
chromatids) produced in meiosis I. The four main steps of Meiosis II are: Prophase II, Metaphase
II, Anaphase II, and Telophase II.
In prophase II we see the disappearance of the nucleoli and the nuclear envelope again as well
as the shortening and thickening of the chromatids. Centrioles move to the polar regions and
arrange spindle fibers for the second meiotic division.
In metaphase II, the centromeres contain two kinetochores that attach to spindle fibers from the
centrosomes (centrioles) at each pole. The new equatorial metaphase plate is rotated by 90
degrees when compared to meiosis I, perpendicular to the previous plate[citation needed].
This is followed by anaphase II, where the centromeres are cleaved, allowing microtubules
attached to the kinetochores to pull the sister chromatids apart. The sister chromatids by
convention are now called sister chromosomes as they move toward opposing poles.
The process ends with telophase II, which is similar to telophase I, and is marked by uncoiling
and lengthening of the chromosomes and the disappearance of the spindle. Nuclear envelopes
reform and cleavage or cell wall formation eventually produces a total of four daughter cells,
each with a haploid set of chromosomes. Meiosis is now complete and ends up with four new
daughter cells.
Significance
Meiosis facilitates stable sexual reproduction. Without the halving of ploidy, or chromosome
count, fertilization would result in zygotes that have twice the number of chromosomes as the
zygotes from the previous generation. Successive generations would have an exponential
increase in chromosome count. In organisms that are normally diploid, polyploidy, the state of
having three or more sets of chromosomes, results in extreme developmental abnormalities or
lethality[5]. Polyploidy is poorly tolerated in most animal species. Plants, however, regularly
produce fertile, viable polyploids. Polyploidy has been implicated as an important mechanism in
plant speciation.
Most importantly, recombination and independent assortment of homologous chromosomes
allow for a greater diversity of genotypes in the population. This produces genetic variation in
gametes that promote genetic and phenotypic variation in a population of offspring.
Nondisjunction
The normal separation of chromosomes in meiosis I or sister chromatids in meiosis II is termed
disjunction. When the separation is not normal, it is called nondisjunction. This results in the
production of gametes which have either too many or too few of a particular chromosome, and is
a common mechanism for trisomy or monosomy. Nondisjunction can occur in the meiosis I or
meiosis II, phases of cellular reproduction, or during mitosis.
This is a cause of several medical conditions in humans (such as):

Down Syndrome - trisomy of chromosome 21

Patau Syndrome - trisomy of chromosome 13

Edward Syndrome - trisomy of chromosome 18

Klinefelter Syndrome - extra X chromosomes in males - i.e. XXY, XXXY, XXXXY

Turner Syndrome - lacking of one X chromosome in females - i.e. XO

Triple X syndrome - an extra X chromosome in females

XYY Syndrome - an extra Y chromosome in males
Meiosis in mammals
In females, meiosis occurs in cells known as oogonia (singular: oogonium). Each oogonium that
initiates meiosis will divide twice to form a single oocyte and two polar bodies.[6] However,
before these divisions occur, these cells stop at the diplotene stage of meiosis I and lie dormant
within a protective shell of somatic cells called the follicle. Follicles begin growth at a steady
pace in a process known as folliculogenesis, and a small number enter the menstrual cycle.
Menstruated oocytes continue meiosis I and arrest at meiosis II until fertilization. The process of
meiosis in females occurs during oogenesis, and differs from the typical meiosis in that it
features a long period of meiotic arrest known as the Dictyate stage and lacks the assistance of
centrosomes.
In males, meiosis occurs in precursor cells known as spermatogonia that divide twice to become
sperm. These cells continuously divide without arrest in the seminiferous tubules of the testicles.
Sperm is produced at a steady pace. The process of meiosis in males occurs during
spermatogenesis.
In female mammals, meiosis begins immediately after primordial germ cells migrate to the ovary
in the embryo, but in the males, meiosis begins years later at the time of puberty. It is retinoic
acid, derived from the primitive kidney (mesonephros) that stimulates meiosis in ovarian
oogonia. Tissues of the male testis suppress meiosis by degrading retinoic acid, a stimulator of
meiosis. This is overcome at puberty when cells within seminiferous tubules called Sertoli cells
start making their own retinoic acid. Sensitivity to retinoic acid is also adjusted by proteins called
nanos and DAZL.[7][8] Meiosis involves Spermatocytes.
Mitosis
Mitosis is the process by which a eukaryotic cell separates the chromosomes in its cell
nucleus into two identical sets in two nuclei. It is generally followed immediately by cytokinesis,
which divides the nuclei, cytoplasm, organelles and cell membrane into two cells containing
roughly equal shares of these cellular components. Mitosis and cytokinesis together define the
mitotic (M) phase of the cell cycle—the division of the mother cell into two daughter cells,
genetically identical to each other and to their parent cell. This accounts for approximately 10%
of the cell cycle.
Mitosis occurs exclusively in eukaryotic cells, but the process varies in different species. For
example, animals undergo an "open" mitosis, where the nuclear envelope breaks down before the
chromosomes separate, while fungi such as Aspergillus nidulans and Saccharomyces cerevisiae
(yeast) undergo a "closed" mitosis, where chromosomes divide within an intact cell nucleus.[1]
Prokaryotic cells, which lack a nucleus, divide by a process called binary fission.
The process of mitosis is complex and highly regulated. The sequence of events is divided into
phases, corresponding to the completion of one set of activities and the start of the next. These
stages are interphase, prophase, prometaphase, metaphase, anaphase and telophase. During
mitosis the pairs of chromosomes condense and attach to fibers that pull the sister chromatids to
opposite sides of the cell. The cell then divides in cytokinesis, to produce two identical daughter
cells.
Because cytokinesis usually occurs in conjunction with mitosis, "mitosis" is often used
interchangeably with "mitotic phase". However, there are many cells where mitosis and
cytokinesis occur separately, forming single cells with multiple nuclei. This occurs most notably
among the fungi and slime moulds, but is found in various different groups. Even in animals,
cytokinesis and mitosis may occur independently, for instance during certain stages of fruit fly
embryonic development. Errors in mitosis can either kill a cell through apoptosis or cause
mutations that may lead to cancer.

Overview
The primary result of mitosis is the transferring of the parent cell's genome into two daughter
cells. The genome is composed of a number of chromosomes—complexes of tightly-coiled DNA
that contain genetic information vital for proper cell function. Because each resultant daughter
cell should be genetically identical to the parent cell, the parent cell must make a copy of each
chromosome before mitosis. This occurs during the S phase of interphase, the period that
precedes the mitotic phase in the cell cycle where preparation for mitosis occurs.[4]
Each new chromosome now contains two identical copies of itself, called sister chromatids,
attached together in a specialized region of the chromosome known as the centromere. Each
sister chromatid is not considered a chromosome in itself, and a chromosome always contains
two sister chromatids.
In most eukaryotes, the nuclear envelope that combines the DNA from the cytoplasm
disassembles. The chromosomes align themselves in a line spanning the cell. Microtubules,
essentially miniature strings, splay out from opposite ends of the cell and shorten, pulling apart
the sister chromatids of each chromosome.[5] As a matter of convention, each sister chromatid is
now considered a chromosome, so they are renamed to sister chromosomes. As the cell
elongates, corresponding sister chromosomes are pulled toward opposite ends. A new nuclear
envelope forms around the separated sister chromosomes.
As mitosis completes cytokinesis is well underway. In animal cells, the cell pinches inward
where the imaginary line used to be (the area of the cell membrane that pinches to form the two
daughter cells is called the cleavage furrow), separating the two developing nuclei. In plant cells,
the daughter cells will construct a new dividing cell wall between each other. Eventually, the
mother cell will be split in half, giving rise to two daughter cells, each with an equivalent and
complete copy of the original genome.
Prokaryotic cells undergo a process similar to mitosis called binary fission. However,
prokaryotes cannot be properly said to undergo cytokinesis because they lack a nucleus and only
have a single chromosome with no mitochondria.[6]
Phases of cell cycle and mitosis
Interphase
The cell cycle
The mitotic phase is a relatively short period of the cell cycle. It alternates with the much longer
interphase, where the cell prepares itself for cell division. Interphase is therefore not part of
mitosis. Interphase is divided into three phases, G1 (first gap), S (synthesis), and G2 (second gap).
During all three phases, the cell grows by producing proteins and cytoplasmic organelles.
However, chromosomes are replicated only during the S phase. Thus, a cell grows (G1),
continues to grow as it duplicates its chromosomes (S), grows more and prepares for mitosis
(G2), and finally it divides (M) before restarting the cycle.
Preprophase
In plant cells only, prophase is preceded by a pre-prophase stage. In highly vacuolated plant
cells, the nucleus has to migrate into the center of the cell before mitosis can begin. This is
achieved through the formation of a phragmosome, a transverse sheet of cytoplasm that bisects
the cell along the future plane of cell division. In addition to phragmosome formation,
preprophase is characterized by the formation of a ring of microtubules and actin filaments
(called preprophase band) underneath the plasma membrane around the equatorial plane of the
future mitotic spindle. This band marks the position where the cell will eventually divide. The
cells of higher plants (such as the flowering plants) lack centrioles; instead, microtubules form a
spindle on the surface of the nucleus and are then being organized into a spindle by the
chromosomes themselves, after the nuclear membrane breaks down.[7] The preprophase band
disappears during nuclear envelope disassembly and spindle formation in prometaphase.
Prophase: The two round objects
above
the
centrosomes.
nucleus
The
are
chromatin
the
has
condensed.
Prometaphase:
The
membrane
degraded,
has
nuclear
and
microtubules have invaded the nuclear
space. These microtubules can attach
to kinetochores or they can interact
with opposing microtubules.
Metaphase: The chromosomes have
aligned at the metaphase plate.
Early anaphase: The kinetochore
microtubules shorten.
Telophase:
The
chromosomes
are
decondensing
surrounded
by
nuclear membranes. Cytokinesis has
already begun; the pinched area is
known as the cleavage furrow.
Prophase
Micrograph showing condensed chromosomes in blue and the mitotic spindle in green during
prometaphase of mitosis
ormally, the genetic material in the nucleus is in a loosely bundled coil called chromatin. At the
onset of prophase, chromatin condenses together into a highly ordered structure called a
chromosome. Since the genetic material has already been duplicated earlier in S phase, the
replicated chromosomes have two brother chromatids, bound together at the centromere by the
cohesion complex. Chromosomes are typically visible at high magnification through a light
microscope.
Close to the nucleus are structures called centrosomes, which are made of a pair of centrioles.
The centrosome is the coordinating center for the cell's microtubules. A cell inherits a single
centrosome at cell division, which replicates before a new mitosis begins, giving a pair of
centrosomes. The two centrosomes nucleate microtubules (which may be thought of as cellular
ropes or poles) to form the spindle by polymerizing soluble tubulin. Molecular motor proteins
then push the centrosomes along these microtubules to opposite sides of the cell. Although
centrioles help organize microtubule assembly, they are not essential for the formation of the
spindle, since they are absent from plants,[7] and centrosomes are not always used in meiosis.[9]
Prometaphase
The nuclear envelope disassembles and microtubules invade the nuclear space. This is called
open mitosis, and it occurs in most multicellular organisms. Fungi and some protists, such as
algae or trichomonads, undergo a variation called closed mitosis where the spindle forms inside
the nucleus, or its microtubules are able to penetrate an intact nuclear envelope.[10][11]
Each chromosome forms two kinetochores at the centromere, one attached at each chromatid. A
kinetochore is a complex protein structure that is analogous to a ring for the microtubule hook; it
is the point where microtubules attach themselves to the chromosome.[12] Although the
kinetochore structure and function are not fully understood, it is known that it contains some
form of molecular motor.[13] When a microtubule connects with the kinetochore, the motor
activates, using energy from ATP to "crawl" up the tube toward the originating centrosome. This
motor activity, coupled with polymerisation and depolymerisation of microtubules, provides the
pulling force necessary to later separate the chromosome's two chromatids.[13]
When the spindle grows to sufficient length, kinetochore microtubules begin searching for
kinetochores to attach to. A number of nonkinetochore microtubules find and interact with
corresponding nonkinetochore microtubules from the opposite centrosome to form the mitotic
spindle. Prometaphase is sometimes considered part of prophase.
In the fishing pole analogy, the kinetochore would be the "hook" that catches a brother chromatid
or "fish". The centrosome acts as the "reel" that draws in the spindle fibers or "fishing line".
Metaphase
A cell in late metaphase. All chromosomes (blue) but one have arrived at the metaphase plate.
As microtubules find and attach to kinetochores in prometaphase, the centromeres of the
chromosomes convene along the metaphase plate or equatorial plane, an imaginary line that is
equidistant from the two centrosome poles.[14] This even alignment is due to the counterbalance
of the pulling powers generated by the opposing kinetochores, analogous to a tug-of-war
between people of equal strength. In certain types of cells, chromosomes do not line up at the
metaphase plate and instead move back and forth between the poles randomly, only roughly
lining up along the midline. Metaphase comes from the Greek μετα meaning "after."
Because proper chromosome separation requires that every kinetochore be attached to a bundle
of microtubules (spindle fibres), it is thought that unattached kinetochores generate a signal to
prevent premature progression to anaphase without all chromosomes being aligned. The signal
creates the mitotic spindle checkpoint.[15]
Anaphase
When every kinetochore is attached to a cluster of microtubules and the chromosomes have lined
up along the metaphase plate, the cell proceeds to anaphase (from the Greek ανα meaning “up,”
“against,” “back,” or “re-”).
Two events then occur: first, the proteins that bind sister chromatids together are cleaved,
allowing them to separate. These sister chromatids, which have now become distinct sister
chromosomes, are pulled apart by shortening kinetochore microtubules and move toward the
respective centrosomes to which they are attached. Next, the nonkinetochore microtubules
elongate, pulling the centrosomes (and the set of chromosomes to which they are attached) apart
to opposite ends of the cell. The force that causes the centrosomes to move towards the ends of
the cell is still unknown, although there is a theory that suggests that the rapid assembly and
breakdown of microtubules may cause this movement.[16]
These two stages are sometimes called early and late anaphase. Early anaphase is usually defined
as the separation of the sister chromatids, while late anaphase is the elongation of the
microtubules and the chromosomes being pulled farther apart. At the end of anaphase, the cell
has succeeded in separating identical copies of the genetic material into two distinct populations.
Telophase
Telophase (from the Greek τελος meaning "end") is a reversal of prophase and prometaphase
events. It "cleans up" the after effects of mitosis. At telophase, the nonkinetochore microtubules
continue to lengthen, elongating the cell even more. Corresponding sister chromosomes attach at
opposite ends of the cell. A new nuclear envelope, using fragments of the parent cell's nuclear
membrane, forms around each set of separated sister chromosomes. Both sets of chromosomes,
now surrounded by new nuclei, unfold back into chromatin. Mitosis is complete, but cell division
is not yet complete.
Cytokinesis
Cytokinesis is often mistakenly thought to be the final part of telophase; however, cytokinesis is
a separate process that begins at the same time as telophase. Cytokinesis is technically not even a
phase of mitosis, but rather a separate process, necessary for completing cell division. In animal
cells, a cleavage furrow (pinch) containing a contractile ring develops where the metaphase plate
used to be, pinching off the separated nuclei. In both animal and plant cells, cell division is also
driven by vesicles derived from the Golgi apparatus, which move along microtubules to the
middle of the cell.[18] In plants this structure coalesces into a cell plate at the center of the
phragmoplast and develops into a cell wall, separating the two nuclei. The phragmoplast is a
microtubule structure typical for higher plants, whereas some green algae use a phycoplast
microtubule array during cytokinesis.[19] Each daughter cell has a complete copy of the genome
of its parent cell. The end of cytokinesis marks the end of the M-phase.
Significance
Mitosis is important for the maintenance of the chromosomal set; each cell formed receives
chromosomes that are alike in composition and equal in number to the chromosomes of the
parent cell. Transcription is generally believed to cease during mitosis, but epigenetic
mechanisms such as bookmarking function during this stage of the cell cycle to ensure that the
"memory" of which genes were active prior to entry into mitosis are transmitted to the daughter
cells.[20]
Consequences of errors
This
section
needs
additional
citations
for
verification.
Please help improve this article by adding reliable references. Unsourced material may be
challenged and removed. (May 2009)
An abnormal (tripolar) mitoses (12 o'clock position) in a precancerous lesion of the stomach.
H&E stain
Although errors in mitosis are rare, the process may go wrong, especially during early cellular
divisions in the zygote. Mitotic errors can be especially dangerous to the organism because
future offspring from this parent cell will carry the same disorder.
In non-disjunction, a chromosome may fail to separate during anaphase. One daughter cell will
receive both sister chromosomes and the other will receive none. This results in the former cell
having three chromosomes containing the same genes (two sisters and a homologue), a condition
known as trisomy, and the latter cell having only one chromosome (the homologous
chromosome), a condition known as monosomy. These cells are considered aneuploid, a
condition often associated with cancer.[21]
Mitosis is a demanding process for the cell, which goes through dramatic changes in
ultrastructure, its organelles disintegrate and reform in a matter of hours, and chromosomes are
jostled constantly by probing microtubules. Occasionally, chromosomes may become damaged.
An arm of the chromosome may be broken and the fragment lost, causing deletion. The fragment
may incorrectly reattach to another, non-homologous chromosome, causing translocation. It may
reattach to the original chromosome, but in reverse orientation, causing inversion. Or, it may be
treated erroneously as a separate chromosome, causing chromosomal duplication. The effect of
these genetic abnormalities depends on the specific nature of the error. It may range from no
noticeable effect to cancer induction or organism death.
Endomitosis
Endomitosis is a variant of mitosis without nuclear or cellular division, resulting in cells with
many copies of the same chromosome occupying a single nucleus. This process may also be
referred to as endoreduplication and the cells as endoploid.[3] An example of a cell that goes
through endomitosis is the megakaryocyte.
UNIT-IV
Explain the Transport mechanisms of bacteria.
There are two ways in which substances can enter or leave a cell:
1) Passive
a) Simple Diffusion
b) Facilitated Diffusion
c) Osmosis (water only)
2) Active
a) Molecules
b) Particles
Diffusion
Diffusion is the net passive movement of particles (atoms, ions or molecules) from a region in which
they are in higher concentration to regions of lower concentration. It continues until the concentration
of substances is uniform throughout. Some major examples of diffusion in biology:
• Gas exchange at the alveoli — oxygen from air to blood, carbon dioxide from blood to air.
• Gas exchange for photosynthesis — carbon dioxide from air to leaf, oxygen from leaf to air.
• Gas exchange for respiration — oxygen from blood to tissue cells, carbon dioxide in opposite
direction.
• Transfer of transmitter substance — acetylcholine from presynaptic to postsynaptic membrane
at a synapse.
• Osmosis — diffusion of water through a semipermeable membrane.
High Diffusion Rate: short distance, large surface area, big concentration difference (Fick’s Law).
High temperatures increase diffusion; large molecules slow diffusion.
Facilitated Diffusion
This is the movement of specific molecules down a concentration gradient, passing through the
membrane via a specific carrier protein. Thus, rather like enzymes, each carrier has its own shape
and only allows one molecule (or one group of closely related molecules) to pass through.
Selection is by size; shape; charge.
Common molecules entering/leaving cells this way include glucose and amino-acids.
It is passive and requires no energy from the cell. If the molecule is changed on entering the cell
(glucose + ATP → glucose phosphate + ADP), then the concentration gradient of glucose will be
kept high, and there will a steady one-way traffic.
Active Transport
Active transport is the energy-demanding transfer of a substance across a cell membrane against its
concentration gradient, i.e., from lower concentration to higher concentration.
Special proteins within the cell membrane act as specific protein ‘carriers’. The energy for active
transport comes from ATP generated by respiration (in mitochondria).
Major examples of Active Transport Re-absorption of glucose, amino acids and salts by the
proximal convoluted tubule of the nephron in the kidney.
Sodium/potassium pump in cell membranes (especially nerve cells)
PEP group translocation
PEP group translocation, also known as the phosphotransferase system or PTS, is a distinct
method used by bacteria for sugar uptake where the source of energy is from
phosphoenolpyruvate (PEP). It is known as multicomponent system that always involves
enzymes of the plasma membrane and those in the cytoplasm. An example of this transport is
found in E. coli cells. The system was discovered by Saul Roseman in 1964.
The phosphotransferase system is involved in transporting many sugars into bacteria, including
glucose, mannose, fructose and cellobiose. PTS sugars can differ between bacterial groups,
mirroring the most suitable carbon sources available in the environment every group evolved.
The phosphoryl group on PEP is eventually transferred to the imported sugar via several
proteins. The phosphoryl group is transferred to the Enzyme E I (EI), Histidine Protein (HPr,
Heat-stable Protein) and Enzyme E II (EII) to a conserved histidine residue, whereas in the
Enzyme E II B (EIIB) the phosphoryl group is usually transferred to a cysteine residue and
rarely to a histidine.[
In the process of glucose PTS transport specific of enteric bacteria, PEP transfers its phosphoryl
to a histidine residue on EI. EI in turn transfers the phosphate to HPr. From HPr the phosphoryl
is transferred to EIIA. EIIA is specific for glucose and it further transfers the phosphoryl group
to a juxtamembrane EIIB. Finally, EIIB phosphorylates glucose as it crosses the plasma
membrane through the transmembrane Enzyme II C (EIIC), forming glucose-6-phosphate.The
benefit of transforming glucose into glucose-6-phosphate is that it will not leak out of the cell,
therefore providing a one-way concentration gradient of glucose. The HPr is common to the
phosphotransferase systems of the other substrates mentioned earlier, as is the upstream EI.
Proteins downstream of HPr tend to vary between the different sugars. The transfer of a
phosphate group to the substrate once it has been imported through the membrane transporter
prevents the transporter from recognizing the substrate again, thus maintaining a concentration
gradient that favours further import of the substrate through the transporter.
With the glucose phosphotransferase system, the phosphorylation status of EIIA can have
regulatory functions. For example, at low glucose concentrations phosphorylated EIIA
accumulates and this activates membrane-bound adenylate cyclase. Intracellular cyclic AMP
levels rise and this then activate CAP (catabolite activator protein), which is involved in the
catabolite repression system, also known as glucose effect. When the glucose concentration is
high, EIIA is mostly dephosphorylated and this allows it to inhibit adenylate cyclase, glycerol
kinase, lactose permease, and maltose permease. Thus, as well as the PEP group translocation
system being an efficient way to import substrates into the bacterium, it also links this transport
to regulation of other relevant proteins.
It is an active transport. After the translocation, the metabolites transported are modified.
Endo/exocytosis
This is the movement of very large molecules (or particles, bacteria or other organisms) across the
cell membrane. It involves the fusion of vesicles (containing the target/victim) with the cell
membrane e.g. bacteria entering macrophages. Substances destined for secretion are packaged in the
Golgi body first.
Pinocytosis (‘cell drinking’)
This is the uptake of large molecules (DNA, protein) from solution, by a form of endocytosis – the
vesicles formed are minute and short-lived.
Phagocytosis (‘cell eating’)
This is the uptake of solid particles by a cell e.g. Amoeba feeding, phagocytes engulfing bacteria.
UNIT V
Explain About The Archaea physiology.
The Archaea (/ɑrˈkiːə/ (
listen) ar-KEE-ə) are a group of single-celled microorganisms. A
single individual or species from this domain is called an archaeon (sometimes spelled
"archeon"). They have no cell nucleus or any other membrane-bound organelles within their
cells. In the past they were viewed as an unusual group of bacteria and named archaebacteria,
but since the Archaea have an independent evolutionary history and show many differences in
their biochemistry from other forms of life, they are now classified as a separate domain in the
three-domain system. In this system the phylogenetically distinct branches of evolutionary
descent are the Archaea, Bacteria and Eukarya. Archaea are further divided into four recognized
phyla, but many more phyla may exist. Of these groups the Crenarchaeota and the Euryarchaeota
are most intensively studied. Classification is still difficult, since the vast majority have never
been studied in the laboratory and have only been detected by analysis of their nucleic acids in
samples from the environment. Although archaea have, in the past, been classed with bacteria as
prokaryotes (or Kingdom Monera), this classification is outdated.[1]
Archaea and bacteria are quite similar in size and shape, although a few archaea have very
unusual shapes, such as the flat and square-shaped cells of Haloquadra walsbyi. Despite this
visual similarity to bacteria, archaea possess genes and several metabolic pathways that are more
closely related to those of eukaryotes: notably the enzymes involved in transcription and
translation. Other aspects of archaean biochemistry are unique, such as their reliance on ether
lipids in their cell membranes. The archaea exploit a much greater variety of sources of energy
than eukaryotes: ranging from familiar organic compounds such as sugars, to using ammonia,
metal ions or even hydrogen gas as nutrients. Salt-tolerant archaea (the Halobacteria) use
sunlight as an energy source and other species of archaea fix carbon; however, unlike plants and
cyanobacteria, no species of archaea is known to do both. Archaea reproduce asexually and
divide by binary fission, fragmentation, or budding; in contrast to bacteria and eukaryotes, no
known species form spores.
Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot
springs and salt lakes, but they have since been found in a broad range of habitats, including
soils, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea
in plankton may be one of the most abundant groups of organisms on the planet. Archaea are
now recognized as a major part of Earth's life and may play roles in both the carbon cycle and
nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are
often mutualists or commensals. One example are the methanogens that inhabit the gut of
humans and ruminants, where their vast numbers aid digestion. Methanogens are used in biogas
production and sewage treatment, and enzymes from extremophile archaea that can endure high
temperatures and organic solvents are exploited in biotechnology.
Classification
A new domain
Early in the 20th century, prokaryotes were regarded as a single group of organisms and
classified based on their biochemistry, morphology and metabolism. For example,
microbiologists tried to classify microorganisms based on the structures of their cell walls, their
shapes, and the substances they consume.[2] However, a new approach was proposed in 1965,[3]
using the sequences of the genes in these organisms to work out which prokaryotes are genuinely
related to each other. This approach, known as phylogenetics, is the main method used today.
Archaea were first detected in extreme environments, such as volcanic hot springs.
Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and
George E. Fox in phylogenetic trees based on the sequences of ribosomal RNA (rRNA) genes.[4]
These two groups were originally named the Archaebacteria and Eubacteria and treated as
kingdoms or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that this
group of prokaryotes is a fundamentally different sort of life. To emphasize this difference, these
two domains were later renamed Archaea and Bacteria.[5] The word archaea comes from the
Ancient Greek ἀρχαῖα, meaning "ancient things".[6]
At first, only the methanogens were placed in this new domain, and the archaea were seen as
extremophiles that exist only in habitats such as hot springs and salt lakes. By the end of the 20th
century, microbiologists realized that archaea is a large and diverse group of organisms that are
widely distributed in nature and are common in much less extreme habitats, such as soils and
oceans.[7] This new appreciation of the importance and ubiquity of archaea came from using the
polymerase chain reaction to detect prokaryotes in samples of water or soil from their nucleic
acids alone. This allows the detection and identification of organisms that cannot be cultured in
the laboratory, which generally remains difficult.[8][9]
Current classification
The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious
field. Current classification systems aim to organize archaea into groups of organisms that share
structural features and common ancestors.[10] These classifications rely heavily on the use of the
sequence of ribosomal RNA genes to reveal relationships between organisms (molecular
phylogenetics).[11] Most of the culturable and well-investigated species of archaea are members
of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively
created. For example, the peculiar species Nanoarchaeum equitans, which was discovered in
2003, has been given its own phylum, the Nanoarchaeota.[12] A new phylum Korarchaeota has
also been proposed. It contains a small group of unusual thermophilic species that shares features
of both of the main phyla, but is most closely related to the Crenarchaeota.[13][14] Other recently
detected species of archaea are only distantly related to any of these groups, such as the Archaeal
Richmond Mine Acidophilic Nanoorganisms (ARMAN), which were discovered in 2006[15] and
are some of the smallest organisms known.[16]
The ARMAN are a new group of archaea recently discovered in acid mine drainage.
Species
The classification of archaea into species is also controversial. Biology defines a species as a
group of related organisms. The familiar exclusive breeding criterion (organisms that can breed
with each other but not with others), is of no help because archaea reproduce asexually.[17]
Archaea show high levels of horizontal gene transfer between lineages. Some researchers
suggest that individuals can be grouped into species-like populations given highly similar
genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus
Ferroplasma On the other hand, studies in Halorubrum found significant genetic transfer to/from
less-related populations, limiting the criteria's applicability. A second concern is to what extent
such species designations have practical meaning.
Current knowledge on genetic diversity is fragmentary and the total number of archaean species
cannot be estimated with any accuracy.[11] Estimates of the number of phyla range from 18 to 23,
of which only 8 have representatives that have been cultured and studied directly. Many of these
hypothesized groups are known from a single rRNA sequence, indicating that the diversity
among these organisms remains obscure.[21] The Bacteria also contain many uncultured microbes
with similar implications for characterization.[22]
Origin and evolution
Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes
do not have distinctive morphologies and fossil shapes cannot be used to identify them as
Archaea.[23] Instead, chemical fossils of unique lipids are more informative because such
compounds do not occur in other organisms. Some publications suggest that archaean or
eukaryotic lipid remains are present in shales dating from 2.7 billion years ago; such data have
since been questioned.= Such lipids have also been detected in Precambrian formations. The
oldest such traces come from the Isua district of west Greenland, which include Earth's oldest
sediments, formed 3.8 billion years ago. The archaeal lineage may be the most ancient that exists
on earth.
Phylogenetic tree showing the relationship between the archaea and other forms of life.
Eukaryotes are colored red, archaea green and bacteria blue. Adapted from Ciccarelli et al.[29]
Woese argued that the bacteria, archaea, and eukaryotes represent separate lines of descent that
diverged early on from an ancestral colony of organisms.[30][31] A few biologists, however, argue
that the Archaea and Eukaryota arose from a group of bacteria.[32] In any case it is thought that
viruses and archaea began relationships approximately two billion years ago, and that coevolution may have been occurring between members of these groups.[33] It is possible that the
last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility
that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in
cooler environments appeared only later.[34] Since the Archaea and Bacteria are no more related
to each other than they are to eukaryotes, the term prokaryote's only surviving meaning is "not a
eukaryote", limiting its value.[35]
Archaea and eukaryotes
The relationship between archaea and eukaryotes remains problematic. Aside from the
similarities in cell structure and function that are discussed below, many genetic trees group the
two.
Complicating factors include claims that the relationship between eukaryotes and the archaeal
phylum Euryarchaeota is closer than the relationship between the Euryarchaeota and the phylum
Crenarchaeota[36] and the presence of archaean-like genes in certain bacteria, such as
Thermotoga maritima, from horizontal gene transfer.[37] The leading hypothesis is that the
ancestor of the eukaryotes diverged early from the Archaea,[38][39] and that eukaryotes arose
through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this
accounts for various genetic similarities but runs into difficulties explaining cell structure.[40]
Morphology
The sizes of prokaryotic cells relative to other cells and biomolecules (logarithmic scale).
Individual archaea range from 0.1 micrometers (μm) to over 15 μm in diameter, and occur in
various shapes, commonly as spheres, rods, spirals or plates.[41] Other morphologies in the
Crenarchaeota include irregularly shaped lobed cells in Sulfolobus, needle-like filaments that are
less than half a micrometer in diameter in Thermofilum, and almost perfectly rectangular rods in
Thermoproteus and Pyrobaculum.[42] Haloquadra walsbyi are flat, square archaea that live in
hypersaline pools. These unusual shapes are probably maintained both by their cell walls and a
prokaryotic cytoskeleton. Proteins related to the cytoskeleton components of other organisms
exist in archaea, and filaments form within their cells,[45] but in contrast to other organisms, these
cellular structures are poorly understood.[46] In Thermoplasma and Ferroplasma the lack of a cell
wall means that the cells have irregular shapes, and can resemble amoebae.
Some species form aggregates or filaments of cells up to 200 μm long.[41] These organisms can
be prominent in biofilms. Notably, aggregates of Thermococcus coalescens cells fuse together in
culture, forming single giant cells. Archaea in the genus Pyrodictium produce an elaborate
multicell colony involving arrays of long, thin hollow tubes called cannulae that stick out from
the cells' surfaces and connect them into a dense bush-like agglomeration.[50] The function of
these cannulae is not settled, but they may allow communication or nutrient exchange with
neighbors.[51] Multi-species colonies exist, such as the "string-of-pearls" community that was
discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota
species are spaced along thin filaments that can range up to 15 centimetres (5.9 in) long; these
filaments are made of a particular bacteria species.
Structure, composition development, operation
Archaea and bacteria have generally similar cell structure, but cell composition and organization
set the archaea apart. Like bacteria, archaea lack interior membranes and organelles.[35] Like
bacteria, archaea cell membranes are usually bounded by a cell wall and they swim using one or
more flagella. Structurally, archaea are most similar to gram-positive bacteria. Most have a
single plasma membrane and cell wall, and lack a periplasmic space; the exception to this
general rule is Ignicoccus, which possess a particularly large periplasm that contains membranebound vesicles and is enclosed by an outer membrane.
Membranes
Membrane structures. Top: an archaeal phospholipid, 1 isoprene sidechain, 2 ether linkage, 3 Lglycerol, 4 phosphate moieties. Middle: a bacterial and eukaryotic phospholipid: 5 fatty acid, 6
ester linkage, 7 D-glycerol, 8 phosphate moieties. Bottom: 9 lipid bilayer of bacteria and
eukaryotes, 10 lipid monolayer of some archaea.
Archaeal membranes are made of molecules that differ strongly from those in other life forms,
showing that archaea are related only distantly to bacteria and eukaryotes.[55] In all organisms
cell membranes are made of molecules known as phospholipids. These molecules possess both a
polar part that dissolves in water (the phosphate "head"), and a "greasy" non-polar part that does
not (the lipid tail). These dissimilar parts are connected by a glycerol group. In water,
phospholipids cluster, with the heads facing the water and the tails facing away from it. The
major structure in cell membranes is a double layer of these phospholipids, which is called a
lipid bilayer.
These phospholipids are unusual in four ways:

Bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids,
whereas archaea have membranes composed of glycerol-ether lipids.[56] The difference is
the type of bond that joins the lipids to the glycerol group; the two types are shown in
yellow in the Figure at the right. In ester lipids this is an ester bond, whereas in ether
lipids this is an ether bond. Ether bonds are chemically more resistant than ester bonds.
This stability might help archaea to survive extreme temperatures and very acidic or
alkaline environments.[57] Bacteria and eukaryotes do contain some ether lipids, but in
contrast to archaea these lipids are not a major part of their membranes.

The stereochemistry of the glycerol group is the reverse of that found in other organisms.
The glycerol group can occur in two forms that are mirror images of one another, called
the right-handed and left-handed forms; in chemistry these are called enantiomers. Just as
a right hand does not fit easily into a left-handed glove, a right-handed glycerol molecule
generally cannot be used or made by enzymes adapted for the left-handed form. This
suggests that archaea use entirely different enzymes for synthesizing phospholipids than
do bacteria and eukaryotes. Such enzymes developed very early in life's history,
suggesting an early split from the other two domains.[55]

Archeal lipid tails are chemically different from other organisms. Archaeal lipids are
based upon the isoprenoid sidechain and are long chains with multiple side-branches and
sometimes even cyclopropane or cyclohexane rings.[58] This is in contrast to the fatty
acids found in other organisms' membranes, which have straight chains with no branches
or rings. Although isoprenoids play an important role in the biochemistry of many
organisms, only the archaea use them to make phospholipids. These branched chains may
help prevent archaean membranes from leaking at high temperatures.[59]

In some archaea the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse
the tails of two independent phospholipid molecules into a single molecule with two
polar heads; this fusion may make their membranes more rigid and better able to resist
harsh environments.[60] For example, the lipids in Ferroplasma are of this type, which is
thought to aid this organism's survival in its highly acidic habitat.[61]
Wall and flagella
Most archaea (not Thermoplasma and Ferroplasma) possess a cell wall. n most archaea
the wall is assembled from surface-layer proteins, which form an S-layer. An S-layer is a rigid
array of protein molecules that cover the outside of the cell (like chain mail). This layer provides
both chemical and physical protection, and can prevent macromolecules from contacting the cell
membrane.[64] Unlike bacteria, most archaea lack peptidoglycan in their cell walls. he exception
is pseudopeptidoglycan, which is found in Methanobacteriales, but pseudopeptidoglycan lacks
D-amino acids and N-acetylmuramic acid.
Archaea flagella operate like bacterial flagella—their long stalks are driven by rotatory motors at
the base. These motors are powered by the proton gradient across the membrane. However,
archaeal flagella are notably different in composition and development. The two types of flagella
evolved from different ancestors. The bacterial flagellum shares a common ancestor with the
type III secretion system, while archaeal flagella appear to have evolved from bacterial type IV
pili. In contrast to the bacterial flagellum, which is hollow and is assembled by subunits moving
up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits
at the base.
Metabolism
Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources
of energy. These reactions are classified into nutritional groups, depending on energy and carbon
sources. Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they
are lithotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. In these
reactions one compound passes electrons to another (in a redox reaction), releasing energy to
fuel the cell's activities. One compound acts as an electron donor and one as an electron acceptor.
The energy released generates adenosine triphosphate (ATP) through chemiosmosis, in the same
basic process that happens in the mitochondrion of eukaryotic cells.
Other groups of archaea use sunlight as a source of energy (they are phototrophs). However,
oxygen–generating photosynthesis does not occur in any of these organisms. Many basic
metabolic pathways are shared between all forms of life; for example, archaea use a modified
form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid
cycle.[72] These similarities to other organisms probably reflect both early origins in the history
of life and their high level of efficiency.
Nutritional types in archaeal metabolism
Nutritional
Source
type
energy
Phototrophs
Lithotrophs
Organotrophs
of
Source of carbon
Examples
Sunlight
Organic compounds
Halobacteria
Inorganic
Organic
compounds
carbon fixation
Organic
Organic
compounds
carbon fixation
compounds
compounds
or Ferroglobus, Methanobacteria or
Pyrolobus
or Pyrococcus,
Sulfolobus
or
Methanosarcinales
Some Euryarchaeota are methanogens living in anaerobic environments such as swamps. This
form of metabolism evolved early, and it is even possible that the first free-living organism was a
methanogen.[74] A common reaction involves the use of carbon dioxide as an electron acceptor to
oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these
archaea, such as coenzyme M and methanofuran. Other organic compounds such as alcohols,
acetic acid or formic acid are used as alternative electron acceptors by methanogens. These
reactions are common in gut-dwelling archaea. Acetic acid is also broken down into methane and
carbon dioxide directly, by acetotrophic archaea. These acetotrophs are archaea in the order
Methanosarcinales, and are a major part of the communities of microorganisms that produce
biogas.
Bacteriorhodopsin from Halobacterium salinarum. The retinol cofactor and residues involved in
proton transfer are shown as ball-and-stick models.
Other archaea use CO2 in the atmosphere as a source of carbon, in a process called carbon
fixation (they are autotrophs). This process involves either a highly modified form of the Calvin
cycler
a
recently discovered
metabolic
pathway called
the
3-hydroxypropionate/4-
hydroxybutyrate cycle. The Crenarchaeota also use the reverse Krebs cycle while the
Euryarchaeota also use the reductive acetyl-CoA pathway. Carbon–fixation is powered by
inorganic energy sources. No known archaea carry out photosynthesis.[81] Archaeal energy
sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales
to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either
oxygen or metal ions as electron acceptors.
Phototrophic archaea use light to produce chemical energy in the form of ATP. In the
Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion
gradients by pumping ions out of the cell across the plasma membrane. The energy stored in
these electrochemical gradients is then converted into ATP by ATP synthase.[41] This process is a
form of photophosphorylation. The ability of these light-driven pumps to move ions across
membranes depends on light-driven changes in the structure of a retinol cofactor buried in the
center of the protein.
Genetics
Archaea usually have a single circular chromosome, the size of which may be as great as
5,751,492 base pairs in Methanosarcina acetivorans,[86] the largest known archaean genome.
One-tenth of this size is the tiny 490,885 base-pair genome of Nanoarchaeum equitans, the
smallest archaean genome known; it is estimated to contain only 537 protein-encoding genes.[87]
Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be
transferred between cells by physical contact, in a process that may be similar to bacterial
conjugation.
Archaea can be infected by double-stranded DNA viruses that are unrelated to any other form of
virus and have a variety of unusual shapes, including bottles, hooked rods, or teardrops. These
viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and
Thermoproteales. A single-stranded DNA virus that infects halophilics was identified in 2009.
Defenses against these viruses may involve RNA interference from repetitive DNA sequences
that are related to the genes of the viruses.
Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins
encoded by any one archaeal genome being unique to the domain, although most of these unique
genes have no known function. f the remainder of the unique proteins that have an identified
function, most are involved in methanogenesis. The proteins that archaea, bacteria and
eukaryotes share form a common core of cell function, relating mostly to transcription,
translation, and nucleotide metabolism. Other characteristic archaean features are the
organization of genes of related function—such as enzymes that catalyze steps in the same
metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl
tRNA synthetases.
Transcription and translation in archaea resemble these processes in eukaryotes more than in
bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents
in eukaryotes.[85] Although archaea only have one type of RNA polymerase, its structure and
function in transcription seems to be close to that of the eukaryotic RNA polymerase II, with
similar protein assemblies (the general transcription factors) directing the binding of the RNA
polymerase to a gene's promoter. However, other archaean transcription factors are closer to
those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since
most archaean genes lack introns, although there are many introns in their transfer RNA and
ribosomal RNA genes, and introns may occur in a few protein-encoding genes.
Reproduction
Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; meiosis
does not occur, so if a species of archaea exists in more than one form, all have the same genetic
material.[41] Cell division is controlled in a cell cycle; after the cell's chromosome is replicated
and the two daughter chromosomes separate, the cell divides.[103] Details have only been
investigated in the genus Sulfolobus, but here that cycle has characteristics that are similar to
both bacterial and eukaryotic systems. The chromosomes replicate from multiple starting-points
(origins of replication) using DNA polymerases that resemble the equivalent eukaryotic
enzymes.[104] However, the proteins that direct cell division, such as the protein FtsZ, which
forms a contracting ring around the cell, and the components of the septum that is constructed
across the center of the cell, are similar to their bacterial equivalents.[103]
Both bacteria and eukaryotes, but not archaea, make spores.[105] Some species of Haloarchaea
undergo phenotypic switching and grow as several different cell types, including thick-walled
structures that are resistant to osmotic shock and allow the archaea to survive in water at low salt
concentrations, but these are not reproductive structures and may instead help them reach new
habitats.
Habitats
Archaea exist in a broad range of habitats, and as a major part of global ecosystems, may
contribute up to 20% of earth's biomass. The first-discovered archaeans were extremophiles.
ndeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in
geysers, black smokers, and oil wells. Other common habitats include very cold habitats and
highly saline, acidic, or alkaline water. However, archaea include mesophiles that grow in mild
conditions, in marshland, sewage, the oceans, and soils.
Image of plankton (light green) in the oceans; archaea form a major part of oceanic life.
Extremophile archaea are members of four main physiological groups. These are the halophiles,
thermophiles, alkaliphiles, and acidophiles.[108] These groups are not comprehensive or phylumspecific, nor are they mutually exclusive, since some archaea belong to several groups.
Nonetheless, they are a useful starting point for classification.
Halophiles, including the genus Halobacterium, live in extremely saline environments such as
salt lakes and outnumber their bacterial counterparts at salinities greater than 20–25%.[70]
Thermophiles grow best at temperatures above 45 °C (113 °F), in places such as hot springs;
hyperthermophilic archaea grow optimally at temperatures greater than 80 °C (176 °F).[109] The
archaeal Methanopyrus kandleri Strain 116 grows at 122 °C (252 °F), the highest recorded
temperature of any organism.
Other archaea exist in very acidic or alkaline conditions.[108] For example, one of the most
extreme archaean acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent
to thriving in 1.2 Molar sulfuric acid.
This resistance to extreme environments has made archaea the focus of speculation about the
possible properties of extraterrestrial life.[112] Extremophile habitats are not dissimilar to those on
Mars, leading to the suggestion that viable microbes could be transferred between planets in
meteorites.
Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic
environments but are also present, sometimes in high numbers, at low temperatures as well. For
example, archaea are common in cold oceanic environments such as polar seas.[115] Even more
significant are the large numbers of archaea found throughout the world's oceans in non-extreme
habitats among the plankton community (as part of the picoplankton).[116] Although these
archaea can be present in extremely high numbers (up to 40% of the microbial biomass), almost
none of these species have been isolated and studied in pure culture.[117] Consequently, our
understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on
global biogeochemical cycles remains largely unexplored.[118] Some marine Crenarchaeota are
capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle,[119]
although these oceanic Crenarchaeota may also use other sources of energy.[120] Vast numbers of
archaea are also found in the sediments that cover the sea floor, with these organisms making up
the majority of living cells at depths over 1 meter into this sediment.
Role in chemical cycling
Archaea recycle elements such as carbon, nitrogen and sulfur through their various
habitats. Although these activities are vital for normal ecosystem function, archaea can also
contribute to human-made changes, and even cause pollution.
Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove
nitrogen from ecosystems, such as nitrate-based respiration and denitrification, as well as
processes that introduce nitrogen, such as nitrate assimilation and nitrogen fixation.[123][124]
Archaean involvement in ammonia oxidation reactions was recently discovered. These reactions
are particularly important in the oceans. The archaea also appear to be crucial for ammonia
oxidation in soils. The produce nitrite, which other microbes then oxidize to nitrate. Plants and
other organisms consume the latter.
In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from
rocks, making it available to other organisms. However, the archaea that do this, such as
Sulfolobus, produce sulfuric acid as a waste product, and the growth of these organisms in
abandoned mines can contribute to acid mine drainage and other environmental damage.
In the carbon cycle, methanogen archaea remove hydrogen and are important in the decay of
organic matter by the populations of microorganisms that act as decomposers in anaerobic
ecosystems, such as sediments, marshes and sewage treatment works. However, methane is one
of the most abundant greenhouse gases in Earth's atmosphere, constituting 18% of the global
total. It is 25 times more potent as a greenhouse gas than carbon dioxide. Methanogens are the
primary source of atmospheric methane, and are responsible for most of the world's yearly
methane emissions. As a consequence, these archaea contribute to global greenhouse gas
emissions and global warming.
Methanogenic archaea form a symbiosis with termites.
Significance in technology and industry
Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and
alkalinity, are a source of enzymes that function under these harsh conditions. These enzymes
have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA
polymerase from Pyrococcus furiosus, revolutionized molecular biology by allowing the
polymerase chain reaction to be used in research as a simple and rapid technique for cloning
DNA. In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that
function at over 100 °C (212 °F) allow food processing at high temperatures, such as the
production of low lactose milk and whey. Enzymes from these thermophilic archaea also tend to
be very stable in organic solvents, allowing their use in environmentally friendly processes in
green chemistry that synthesize organic compounds.This stability makes them easier to use in
structural biology. Consequently the counterparts of bacterial or eukaryotic enzymes from
extremophile archaea are often used in structural studies.
In contrast to the range of applications of archaean enzymes, the use of the organisms themselves
in biotechnology is less developed. Methanogenic archaea are a vital part of sewage treatment,
since they are part of the community of microorganisms that carry out anaerobic digestion and
produce biogas. In mineral processing, acidophilic archaea display promise for the extraction of
metals from ores, including gold, cobalt and copper.
Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been
characterized, but hundreds more are believed to exist, especially within Haloarchaea and
Sulfolobus. These compounds have different structure than bacterial antibiotics, so they may
have novel modes of action. In addition, they may allow the creation of new selectable markers
for use in archaeal molecular biology.
Write about the Halophile.
Halophiles are extremophile organisms that thrive in environments with very high
concentrations of salt. The name comes from the Greek for "salt-loving". While the term is
perhaps most often applied to some halophiles classified into the Archaea domain, there are also
bacterial halophiles and some eukaryota, such as the alga Dunaliella salina. Some well-known
species give off a red color from carotenoid compounds. Such species contain the photosynthetic
pigment bacteriorhodopsin. Halophiles are categorized slight, moderate or extreme, by the extent
of their halotolerance. Halophiles can be found anywhere with a concentration of salt five times
greater than the salt concentration of the ocean, such as the Great Salt Lake in Utah, Owens Lake
in California, the Dead Sea, and in evaporation ponds.

Halophiles: where they work and what they do
High salinity represents an extreme environment that relatively few organisms have been able to
adapt to and occupy. Most halophilic and all halotolerant organisms expend energy to exclude
salt from their cytoplasm to avoid protein aggregation (‘salting out’). In order to survive the high
salinities, halophiles employ two differing strategies to prevent desiccation through osmotic
movement of water out of their cytoplasm. Both strategies work by increasing the internal
osmolarity of the cell. In the first (that is employed by the majority of bacteria, some archaea,
yeasts, algae and fungi), organic compounds are accumulated in the cytoplasm – these
osmoprotectants are known as compatible solutes. These can be synthesised or accumulated from
the environment.The most common compatible solutes are neutral or zwitterionic and include
amino acids, sugars, polyols, betaines and ectoines, as well as derivatives of some of these
compounds.
The second, more radical, adaptation involves the selective influx of potassium (K+) ions into the
cytoplasm. This adaptation is restricted to the moderately halophilic bacterial Order
Halanerobiales, the extremely halophilic archaeal Family Halobacteriaceae and the extremely
halophilic bacterium Salinibacter ruber. The presence of this adaptation in three distinct
evolutionary lineages suggests convergent evolution of this strategy, it being unlikely to be an
ancient characteristic retained in only scattered groups or through massive lateral gene transfer.
The primary reason for this is that the entire intracellular machinery (enzymes, structural
proteins, etc.) must be adapted to high salt levels, whereas in the compatible solute adaptation
little or no adjustment is required to intracellular macromolecules – in fact, the compatible
solutes often act as more general stress protectants as well as just osmoprotectants.
Of particular note are the extreme halophiles or haloarchaea (often known as halobacteria), a
group of archaea, which require at least a 2 M salt concentration and are usually found in
saturated solutions (about 36% w/v salts). These are the primary inhabitants of salt lakes, inland
seas, and evaporating ponds of seawater, such as the Dead Sea and solar salterns, where they tint
the water column and sediments bright colors. In other words, they will most likely perish if they
are exposed to anything other than a very high concentration salt-conditioned environment.
These prokaryotes require salt for growth. The high concentration of NaCl in their environment
limits the availability of oxygen for respiration. Their cellular machinery is adapted to high salt
concentrations by having charged amino acids on their surfaces, allowing the retention of water
molecules around these components. They are heterotrophs that normally respire by aerobic
means. Most halophiles are unable to survive outside their high-salt native environment. Indeed,
many cells are so fragile that when placed in distilled water they immediately lyse from the
change in osmotic conditions.
Haloarchaea, and particularly, the family Halobacteriaceae are members of the domain Archaea,
and comprise the majority of the prokaryotic population in hypersaline environments. There are
currently 15 recognised genera in the family. The domain Bacteria (mainly Salinibacter ruber)
can comprise up to 25% of the prokaryotic community, but is more commonly a much lower
percentage of the overall population At times, the alga Dunaliella salina can also proliferate in
this environment.
A comparatively wide range of taxa have been isolated from saltern crystalliser ponds, including
members of the following genera: Haloferax, Halogeometricum, Halococcus, Haloterrigena,
Halorubrum, Haloarcula and Halobacterium families (Oren 2002). However, the viable counts
in these cultivation studies have been small when compared to total counts, and the numerical
significance of these isolates has been unclear. Only recently has it become possible to determine
the identities and relative abundances of organisms in natural populations, typically using PCRbased strategies that target 16S small subunit ribosomal ribonucleic acid (16S rRNA) genes.
While comparatively few studies of this type have been performed, results from these suggest
that some of the most readily isolated and studied genera may not in fact be significant in the insitu community. This is seen in cases such as the genus Haloarcula, which is estimated to make
up less than 0.1% of the in situ community but commonly appears in isolation studies.
Genomic and proteomic signature of halophiles
The comparative genomic and proteomic analysis showed that there is a distinct molecular
signatures for environmental adaptation of halophiles. At the protein level, the halophilic species
are
characterized
by
low
hydrophobicity,
overrepresentation
of
acidic
residues,
underrepresentation of Cys, lower propensities for helix formation and higher propensities for
coil structure. It is also evident that the core of these proteins is less hydrophobic, such as DHFR,
that was found to have narrower β-strands At the DNA level, the halophiles exhibit distinct
dinucleotide and codon usage.
Examples
Halobacterium is a group of Archaea that have a high tolerance for elevated levels of salinity.
Some species of halobacteria have acidic proteins that resist the denaturing effects of salts.
Halococcus is a specific genus of the family Halobacterium.
Some hypersaline lakes are a habitat to numerous families of halophiles. For example, the
Makgadikgadi Pans in Botswana is a vast seasonal high salinity water body that manifests
halophilic species within the diatom genus Nitzschia in the family Bacillariaceae as well as
species within the genus Lovenula in the family Diaptomidae. Owens lake in California also
contains a large population of the halophilic bacteria Halobacterium halobium.
The fermentation of salty foods (such as soy sauce, Chinese fermented beans, salted cod, etc.)
often involves halobacteria, as either essential ingredients or accidental contaminants. One
example is Chromohalobacter beijerinckii, found in salted beans preserved in brine and in salted
herring.
What is habitat of Thermoacidophile?
A thermoacidophile (combination of thermophile and acidophile) is an extreme archeon which
thrives in acidous, sulfur rich, high temperature environments.
Thermoacidophiles prefer temperatures of 70 - 80 °C and pH between 2 and 3. They live mostly
in hot springs and/or within deep ocean vent communities. Classified as an Archaebacteria and
an extremeophile, Thermoacidophiles are found in places where most organisims would not
survive.
Taxonomy
Thermoacidophiles belong to the Kingdom Archaebacteria, in the Domain Archaea.
There are many unique characteristics that make up these prokaryotes. They are specially
resistant to high temperatures and high acid concentrations. They have a plasma membrane
which contains high amounts of saturated fats, and its enzymes are able to withstand extreme
conditions without denaturation.
Possibly the progenitor of cellular life
The similarities between DNA sequences of thermoacidophiles, and other Archaebacteria, and
complex eukaryotes provides support to Archae being the progenitor species for the first cellular
life on Earth. They were able to thrive on the early, warmer Earth with an atmosphere that lacked
oxygen.
Comparisons to Eukaryotes and Eubacteria
Archaeobacteria constitute the third domain of living organisms, one distinct from that
represented by the eubacteria and the eukaryotes.
Archaeobacteria are prokaryotes, like eubacteria, however, and therefore are most facilely
compared to eubacteria (i.e., archaeobacteria represent a monophyletic taxon of bacteria-like
things).
Nevertheless, some aspects of archaeobacteria are more eukaryote-like than eubacteria. Most
fascinating about archaeobacteria are the often bizarre environments which they inhabit,
including water whose temperature exceeds that of hot springs.
Identification
Archaeobacteria nevertheless often may be differentiated in terms of Gram staining.
This is because the Gram stain is a measure of physical aspects of cell walls that are shared
between the eubacteria and the archaeobacteria (though gram-negative archaeobacteria lack outer
membranes).
There exist cell-wall less archaeobacteria which live in the high temperature (55 to 59°C) and
acidic piles of coal tailings.
Physical Characteristics
The following is quoted from Prescott et al., 1996 (p. 478):
As a group the archaeobacteria [Greek archaios, ancient, and bakterion, a small rod] are quite
diverse, both in morphology and physiologically. They can stain either gram positive or gram
negative and may be spherical, rod-shaped, spiral, lobed, plate-shaped, irregularly shaped, or
pleomorphic. Some are single cells, whereas others form filaments or aggregates. They range in
diameter from 0.1 to over 15 µm, and some filaments can grow up to 200 µm in length.
Multiplication may be by binary fission, budding, fragmentation, or other mechanisms.
Archaeobacteria are just as diverse physiologically. They can be aerobic, facultatively anaerobic,
or strictly anaerobic. Nutritionally they range from chemolithoautotrophs to organotrophs. Some
are mesophiles; others are hyperthermophiles that can grow above 100°C. Archaeobacteria
usually prefer restricted or extreme aquatic and terrestrial habitats. They are often present in
anaerobic, hypersaline, or high-temperature environments. Recently archaeobacteria have been
discovered in cold environments. It appears that they constitute up to 34% of the procaryotic
biomass in coastal Antarctic surface waters. A few are symbionts in animal digestive systems.
Cell wall
The archaeobacteria cell wall differs chemically from that of the eubacteria cell wall.
Specifically, they lack in peptidoglycan.
Membranes
Branched chain hydrocarbons
Archaeobacteria lipid bilayers consist of branched chain hydrocarbons linked by ether (as
opposed to ester) linkages to glycerol.
Typical structure of eubacteria monoglyceride:
H
H-C-OH O
|
||H H H H H H H
H-C -O- C-C-C-C-C-C-C-C-H
|
HHHHHHH
H-C-OH
H
Typical structure of archaeobacteria monoglyceride:
H
H
H
H-C-OH H-C-H H-C-H
|
HH|HHH|H
H-C -O- C-C-C-C-C-C-C-C-H
|
HHHHHHHH
H-C-OH
H
Membrane-spanning lipids
Archaeobacteria lipid bilayers also contain lipids consisting of ether-linked hydrocarbons
stretched between glycerol moieties, linked at both ends (think of two fats joined at the end of
their fatty acid chains and you'll get an idea: |==| where | is glycerol, = are two parallel fatty
acids, and |= is a eubacterium diglyceride).
For these linked lipids each glycerol is found in the opposite membrane leaflet, at the
hydrophilic-hydrophobic interface.
An archaeobacteria membrane spanning, glycerol-based lipid (only one of expected two
spanning hydrocarbon chains shown):
H
H
H
H
H
H-C-OH H-C-H H-C-H H-C-H
H-C-H
| HH|HHH|HHH|HHHH|H H
H-C-O-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-O-C-H
| HHHHHHHHHHHHHHHHH |
H-C-OH
H-C-OH
H
|
H-C-OH
H
One obvious explanation for the existence of such lipids is that they may make the
archaeobacteria membrane sufficiently stable, at least in part, to allow growth and survival in the
extreme environments in which many archaeobacteria may be found.
Types
Chloroflexus
Bacteria
Deinococcus
radiodurans · Deinococcus-Thermus · Snottite ·
Thermus aquaticus · Thermus thermophilus ·
Spirochaeta americana
Notable
extremophiles
aurantiacus ·
Archaea
Animalia
Pyrococcus furiosus · Strain 121 · Pyrolobus
fumarii
Paralvinella
sulfincola ·
Pompeii
worm ·
Tardigrada
Abiogenic
petroleum
origin ·
Acidithiobacillales ·
Acidobacteria · Acidophiles in acid mine drainage ·
Archaeoglobaceae ·
Berkeley
Pit ·
Grylloblattidae ·
Blood
Falls ·
Related
Crenarchaeota ·
Halobacteria ·
articles
Halobacterium · Helaeomyia petrolei · Hydrothermal
vent · Methanopyrus · Movile Cave · Radioresistance ·
Radiotrophic fungus · Rio Tinto · Taq polymerase ·
Thermostability · Thermotogae
All the best
The
radioresistant
bacterium
Deinococcus
radiodurans