Biology book (written by Umesh kumar
CELL AND CELLULAR PROCESSES
(Written by UMESH KUMAR, B.Sc.(H) Chemistry) )
Unit 1st Techniques in Biology
Principle of microscopy
Microscope is the instrument that is used to see objects not visible to the naked
(unaided) eye. The study of fine structure of an object under a microscope is
called microscopy, and the person who studies it is termed microscopist. The
microscope magnifies as well as resolves the objects seen through it.
1. Magnification: Magnification (M) brought about by a microscope may be
defined as the ratio of the visible size of an object to its actual size.
𝑀=
𝑆𝑖𝑧𝑒 𝑜𝑓 𝑖𝑚𝑎𝑔𝑒 𝑠𝑒𝑒𝑛 𝑤𝑖𝑡ℎ 𝑚𝑖𝑐𝑟𝑜𝑠𝑐𝑜𝑝𝑒
𝑆𝑖𝑧𝑒 𝑜𝑓 𝑖𝑚𝑎𝑔𝑒 𝑠𝑒𝑒𝑛 𝑤𝑖𝑡ℎ 𝑛𝑜𝑟𝑚𝑎𝑙 𝑛𝑎𝑘𝑒𝑑 𝑒𝑦𝑒
2. Resolving Power: It refers to the ability of a magnifying instrument to
separate details of two closely placed points.
Human eye is unable to see objects smaller than 100µm.
This means that two points less than 100µm apart appear as one point to
our eyes. Thus, the resolving power of the human eye is 100µm or 0.1mm.
The optical theory underlying the designing of microscope
was largely developed by a German physicist Ernst Abbe in 1876. The
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Biology book (written by Umesh kumar
resolving power of a microscope is given by the Abbe Equation named in his
honour.
Accordingly, the minimum distance between the objects that reveals them
as separate entities is given by Abbe equation:
𝐿𝑚 =
0.61𝜆
𝑁𝐴
Where Lm=limit of resolution
0.61 values is derived from the computation of a number of complex
trigonometric ratios
NA=Numerical aperture=n sinα
Where n is the refractive index of the medium, sin ∞ is the sine from the
specimen.
λ = wavelength of light used to illuminate the objects.
LIGHT OR COMPOUND MICROSCOPE
The first compound microscope was assembled by Zacharias Janssen and J.
Janssen, the Dutch spectacles makers, in 1590.
The light microscope is a strong, heavy metal instrument. It comprise a Ushaped horizontal base on which are two vertical pillars to which is movably
joined a curved arm or limb to hold the inclination joint to suit the viewer.
The upper part of the arm holds the movable body tube. The other parts of
the microscopes are—
(1) Reflector: It illuminates the object with visible light. An electric
illuminator may also be used for this purpose.
(2) Condenser Lens: It concentrates the rays of light to a point on the
object. It is mounted under the stage. It can be moved up and down
with a screw. It is also provided with a diaphragm to control the amount
of light falling on the condenser lens.
(3) Stage: It provided space for the object mounted on a glass slide in fluid
medium and often covered with a thin glass cover slip. It has at its
centre a circular hole in the middle of which the object mounted on a
slide is set.
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Biology book (written by Umesh kumar
(4) Objective Lens: It is at the lower end of the body tube fitted into a
circular, revolving nose piece.
(5) Ocular Lens: It is fitted into the upper end of the body tube. It further
magnifies the observer s eye. Ocular lenses of 5X, 10X, 15X, or 20X
power are generally used.
(6) Adjustment Screws: These are present on the sides of the upper part of
the arm. They move the body tube up and down to focus the object.
Phase contrast Microscope: It was invented by the Dutchman Frederick
Zernicke in 1935. It is used to study living cells and tissues without staining.
In the phase contrast microscope, the source of illumination is the ordinary visible
light. Therefore, its resolving power is the same as that of the light microscope.
However, it makes the highly transparent objects much better visible than is done
by the light microscope. It has an annular diaphragm before the condenser and a
phase plate within the objective lens. This plate is a glass disc having an annular
groove in it.
The phase contrast microscope is based on the principle that the light transmitted
by a region of higher refractive index is retarded in velocity with respect to the
light transmitted by a region of lower refractive index, and emerges as out of
phase relative to that emerging from a region of lower refractive index. Thus, a
phase contrast is produced by deviated and undeviated light rays.
Use:
1) The study of organelles in living cells. Movement of chromosomes, cell
division, streaming of cytoplasm, motion of mitochondria and vacuoles,
endocytosis, and secretion by gland cells can be seen with this microscope.
2) Noting the effect of fixatives and stains on the cell components, including
artifacts.
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Biology book (written by Umesh kumar
Fluorescence Microscope: It was invented by Coon in 1945. Certain
compounds are fluorescent, i.e. absorb light of short wavelength (UV light) and
then re-emit light of longer wavelength (Visible). This phenomenon is called
fluorescence and is used in microscopy. The fluorescence microscope is
essentially an ordinary microscope having two special filters. UV light is obtained
by a high intensity lamp. This light is passed through an ‘exciter’ filter that allows
only the required wavelength to pass. This light cause fluorescence in the
specimen. A long wavelength filter placed beyond the objective lens allows only
the light of longer wavelength to pass and form an image.
Since the image is formed entirely by the light emanating from the specimen,
fluorescent objects appear as very bright images in a uniformly dark background.
The fluorescent compounds which occur in tissue and cells include collagen,
chlorophyll, riboflavin and vitamin A. The fluorescence microscope is used to
identify these compounds in the tissue and cells.
Use:
1) To locate fluorescence compound sin cells and tissues.
2) To identify strains of bacteria in infected tissues by straining them with
fluorochromes.
Preparation of Materials for microscope
The preparation of biological material for examination with either the light
microscope involves a series of physical and chemical manipulations that
1) Fixation: One notable advantage of the light microscope is the capability to
observe whole, living cells. It is also possible to employ “vital stains” which
improve contrast but do not interference with normal cell activity. More
frequently, however, the cells are first killed and fixed. The fixation step is
intended to preserve the structure of the material by preventing the
growth of bacteria in the sample and by precluding postmortem change.
Formaldehyde and osmium tetraoxide (Os𝑂4 ) are examples of fixation
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most often employed for light microscopy. OsO₄ has a very high electron
density, and because this gives contrast to the resulting image, OsO₄ has
also found widespread use as a fixative in electron microscopy. Other
popular fixatives including potassium permanganate and gultaraldehyde.
After fixation for the required length of time, the samples are dehydrated
by successive exposures to increasing concentrations of alcohol or acetone.
2) Embedding: embedding is aimed at making the material firm and fit for
section cutting such as hydroid colonies. The dehydrated material is kept in
melted paraffin wax taken in a crucible. The latter is placed in an
embedding oven with temperature maintained at the melting point of wax.
The wax enters the tissue spaces, and on solidifying provides mechanical
support during sectioning. Wax is an idea embedding medium as it can be
easily dissolved out from the tissue in organic solvents.
3) Sectioning: After embedding, the crucible is taken out from the embedding
oven, and its wax allowed solidifying. A block of wax of suitable size and
containing the tissue in it is cut out. The tissue held in the block of wax is
cut into very thin section with a machine called microtome. A section or a
few sections are fastened on to a glass slide with the help of Meyer’s
albumen. Meyer’s albumen is prepared by mixing 50 ml each of white of an
egg and glycerine. A gram of sodium salicylate is added as a preservative.
Mixture is thoroughly shaken and filtered.
4) Mounting: A drop of mounting medium is put on the section and a cover
ship is placed on it. The section is ready for microscope examination. The
mounting medium dries up in due to course of time and the slide becomes
a permanent preparation. The mounting medium commonly used is Canada
balsam.
Scanning Electron Microscope (SEM): SEM was invented by knoll I
1935. It is used for detailed study of the surface of the specimens. It is
so because the image is produced due to reflection of electrons from
the surface of the specimen. Therefore, properly dried specimens are
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Biology book (written by Umesh kumar
coated with metals such as gold, platinum etc. to create a reflected
surface, Deflected electrons from the specimen are subsequently
sensed by sophisticated detector and the image is produced which is
displayed on the computer screen. It gives 3-dimensional image. SEM
has a magnification range upto 2, 00, 00.
Scanning Transmission Electron Microscope (STEM): It is used for the
study of ultra structure of cell organelles. It requires ultra thin sections (0.1µm) of
the specimens for proper penetration of electrons. Such sections are obtained
with ultra microtome, using a cut glass or diamond knife. The ultra thin sections
of the specimens are then stained with the stains having the salts of heavy metals
such as lead, tungsten, uranium to enhance the contrast. The coating also
facilitates the material to withstand the electron bombardment. STEM
magnification is 1, 00,000 to 3, 00,000.
Difference between Light Microscope and Electron Microscope
Light Microscope
1) Source of illumination is visible
light.
2) It has glass lenses.
3) Its body tube has air.
4) Image results from differential
absorption of light by various
regions of the object.
5) Image is seen directly with the
eye.
6) Its resolving power is about
0.3µm.
7) It can magnify objects up to
1,000 times.
Electron Microscope
1) Source of illumination is a beam
of electrons.
2) It has electromagnetic lenses.
3) Its body tube has vacuum.
4) Image results from differential
scattering of electrons by various
molecular components of the
object.
5) Image is recorded on fluorescent
screen or photographic plate.
6) Its resolving power is about
0.03Å actually.
7) It can magnify objects up to
300,000 times.
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Sample Preparation for Electron Microscopy: A tissue is fixed, dehydrated,
embedded, sectioned and stained for observation with the electron microscope
as with the light microscope. For electron microscopy, the most commonly used
fixatives are glutaraldehyde and osmium tetroxide, the most widely used
embedding material is an epoxy plastic called epon, and the commonly employed
stains are uranyl acetate and lead citrate. Sections as thin as 0.05-0.1µm are with
ultramicrotome having extremely sharp cutting edge made of the cut glass or a
finely polished diamond face.
Disadvantage of Microscopy
Living cells and tissues can not be studied under the light and electron
microscope. These are killed, fixed in certain chemical solutions, sectioned, and
stained to provide contrast. Hence, the structure observed with these
microscopes may be not always being fully real.
X- ray Microscope
The X-rays are used as a source of illumination in this microscope. These rays
have very short wavelength but a great power of penetrating the thick living
tissue. The X-rays beam is focused by electromagnetic lenses or curved reflecting
mirror and the image is photographed on a film.
Use:
a) To determine the three-dimensional structure of macromolecules, such as
lysozyme, haemoglobin and nucleic acid of the cell.
b) In X-ray crystallography.
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Unit 2nd Cell as a unit of life
The cell is the functional basic unit of life. It was discovered by Robert Hooke and
is the functional unit of all known living organisms. It is the smallest unit of life
that is classified as a living thing, and is often called the building block of life.
Some organisms, such as most bacteria, are unicellular (consist of a single cell).
Other organisms, such as humans, are multicellular. Humans have about 100
trillion or 1014 cells; a typical cell size is 10 µm and a typical cell mass is
1 nanogram. The largest cells are about 135 µm in the anterior horn in the spinal
cord while granule cells in the cerebellum, the smallest, can be some 4 µm and the
longest cell can reach from the toe to the lower brain stem (Pseudounipolar cells).
The largest known cells are unfertilised ostrich egg cells which weigh 3.3 pounds.
In 1835, before the final cell theory was developed, Jan Evangelista Purkyně
observed small "granules" while looking at the plant tissue through a microscope.
The cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor
Schwann, states that all organisms are composed of one or more cells, that all cells
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Biology book (written by Umesh kumar
come from preexisting cells, that vital functions of an organism occur within cells,
and that all cells contain the hereditary information necessary for regulating cell
functions and for transmitting information to the next generation of cells .
Statement of Cell Theory
The cell theory states thata) All living things are composed of minutes units, the cells, which are the
smallest entities that can be called “living”.
b) A cell is a mass of protoplasm containing a nucleus and bounded by a cell
membrane, and in many cases by cell wall also.
c) All cells are basically alike in structure and metabolic activities.
d) The function of an organism as a whole is the result of the activities and
interactions of the constituents’ cells.
Short coming of Cell theory
Although the cell theory is substantially correct, it does not apply to all organisms.
Important exceptions are given
a) Protozoans are not cellular. They are acellular, i.e. their body is not divisible
into cells.
b) Bacteria and blue-green algae do not have an organism nucleus. Their
genetic material (DNA0 is not enclosed by a nucleus envelope and lies
directly in the cytoplasm. They also lack most of the cell organelles.
c) Certain fungi, such as Rhizopus, have hyphae composed of a multinucleate
mass of cytoplasm without division into cells.
d) Some tissues, e.g. connective tissues, have a good deal of nonliving material,
the matrix, between the cells. There is a no mention of intercellular material
in the cell theory.
e) Certain cells, e.g. red blood corpuscles, lose nuclei and many organelles but
still keep living.
f) Surface cells of the skin replace the protoplasm with a nonliving material,
keratin or horn.
g) Cell theory did not mention the mode of new cell formation.
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Statement of Cell Principle (Modern Cell Theory)
It state thata) Life exists only in cells.
b) Living object is composed of cells and cell products or are multinucleate
mass of protoplasm, or are a single free cell.
c) A cell is a small mass of protoplasm usually containing a nucleus or nuclear
material and some other organelles, and is bounded by a cell membrane.
d) Cell is also a unit of function, reproduction, heredity and disease, besides
being a unit of structure.
e) All cells having had fundamental similarity in physical structure, chemical
composition and basic metabolic reactions.
f) A cell, though an integral part of an organism, can act independently of the
other cells around it.
g) Cells may die and still remain functional such as horny cells in animals and
xylem vessels in plants.
h) Structure and working of a cell is controlled by DNA.
i) A cell is the smallest organization of matter that is capable of all the
processes collectively referred to as “life’.
There are two types of cells: eukaryotic and prokaryotic. Prokaryotic cells are
usually independent, while eukaryotic cells are often found in multicellular
organisms.
Prokaryotic cells
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The prokaryote cell is simpler, and therefore smaller, than a eukaryote cell, lacking
a nucleus and most of the other organelles of eukaryotes. There are two kinds of
prokaryotes: bacteria and archaea; these shares a similar structure.
Nuclear material of prokaryotic cell consist of a single chromosome which is in
direct contact with cytoplasm. Here the undefined nuclear region in the cytoplasm
is called nucleoid.
A prokaryotic cell has three architectural regions:



On the outside, flagella and pili project from the cell's surface. These are
structures (not present in all prokaryotes) made of proteins that facilitate
movement and communication between cells;
Enclosing the cell is the cell envelope – generally consisting of a cell wall
covering a plasma membrane though some bacteria also have a further
covering layer called a capsule. The envelope gives rigidity to the cell and
separates the interior of the cell from its environment, serving as a protective
filter. Though most prokaryotes have a cell wall, there are exceptions such
as Mycoplasma (bacteria) and Thermoplasma (archaea). The cell wall
consists of peptidoglycan in bacteria, and acts as an additional barrier
against exterior forces. It also prevents the cell from expanding and finally
bursting (cytolysis) from osmotic pressure against a hypotonic environment.
Inside the cell is the cytoplasmic region that contains the cell genome
(DNA) and ribosomes and various sorts of inclusions. A prokaryotic
chromosome is usually a circular molecule. Though not forming a nucleus,
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the DNA is condensed in a nucleoid. Prokaryotes can carry
extrachromosomal DNA elements called plasmids, which are usually
circular. Plasmids enable additional functions, such as antibiotic resistance.
Eukaryotic cells
Diagram of a typical animal (eukaryotic) cell, showing subcellular components.
Organelles:
(1) nucleolus (2) nucleus (3) ribosome (4) vesicle (5) rough endoplasmic
reticulum (ER)
(6) Golgi apparatus (7) Cytoskeleton (8) smooth
endoplasmic reticulum (9) mitochondria
(10) vacuole (11) cytoplasm (12) lysosome (13) centrioles within centrosome
Eukaryotic cells are about 15 times wider than a typical prokaryote and can be as
much as 1000 times greater in volume. The major difference between prokaryotes
and eukaryotes is that eukaryotic cells contain membrane-bound compartments in
which specific metabolic activities take place. Most important among these is a cell
nucleus, a membrane-delineated compartment that houses the eukaryotic cell's
DNA. This nucleus gives the eukaryote its name, which means "true nucleus."
Other differences include:



The plasma membrane resembles that of prokaryotes in function, with minor
differences in the setup. Cell walls may or may not be present.
The eukaryotic DNA is organized in one or more linear molecules, called
chromosomes, which are associated with histone proteins. All chromosomal
DNA is stored in the cell nucleus, separated from the cytoplasm by a
membrane. Some eukaryotic organelles such as mitochondria also contain
some DNA.
Many eukaryotic cells are ciliated with primary cilia. Primary cilia play
important roles in chemosensation, mechanosensation, and thermosensation.
Cilia may thus be "viewed as sensory cellular antennae that coordinate a
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
large number of cellular signaling pathways, sometimes coupling the
signaling to ciliary motility or alternatively to cell division and
differentiation."
Eukaryotes can move using motile cilia or flagella. The flagella are more
complex than those of prokaryotes.
Table 1: Comparison of features of prokaryotic and eukaryotic cells
Prokaryotes
Eukaryotes
protists, fungi, plants, animals
Typical organisms bacteria, archaea
~ 10–100 µm (sperm cells, apart from the tail, are
~ 1–10 µm
Typical size
smaller)
nucleoid region; no
real nucleus with double membrane
Type of nucleus
real nucleus
linear molecules (chromosomes) with histone
circular (usually)
DNA
proteins
RNA-synthesis inside the nucleus
RNA-/proteincoupled in cytoplasm
protein synthesis in cytoplasm
synthesis
50S+30S
60S+40S
Ribosomes
highly structured by endomembranes and a
Cytoplasmatic
very few structures
cytoskeleton
structure
flagella made of
flagella and cilia containing microtubules;
Cell movement
flagellin
lamellipodia and filopodia containing actin
one to several thousand (though some lack
Mitochondria none
mitochondria)
none
in algae and plants
Chloroplasts
single cells, colonies, higher multicellular organisms
Organization usually single cells
with specialized cells
Binary fission (simple Mitosis (fission or budding)
Cell division
division)
Meiosis
Subcellular components
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All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the
cell, separates its interior from its environment, regulates what moves in and out
(selectively permeable), and maintains the electric potential of the cell. Inside the
membrane, a salty cytoplasm takes up most of the cell volume. All cells possess
DNA, the hereditary material of genes, and RNA, containing the information
necessary to build various proteins such as enzymes, the cell's primary machinery.
Membrane
The cytoplasm of a cell is surrounded by a cell membrane or plasma membrane.
The plasma membrane in plants and prokaryotes is usually covered by a cell wall.
This membrane serves to separate and protect a cell from its surrounding
environment and is made mostly from a double layer of lipids (hydrophobic fatlike molecules) and hydrophilic phosphorus molecules. Hence, the layer is called a
phospholipid bilayer. It may also be called a fluid mosaic membrane. Embedded
within this membrane is a variety of protein molecules that act as channels and
pumps that move different molecules into and out of the cell. The membrane is
said to be 'semi-permeable', in that it can either let a substance (molecule or ion)
pass through freely, pass through to a limited extent or not pass through at all. Cell
surface membranes also contain receptor proteins that allow cells to detect external
signaling molecules such as hormones.
Cytoskeleton
The cytoskeleton acts to organize and maintain the cell's shape; anchors organelles
in place; helps during endocytosis, the uptake of external materials by a cell, and
cytokinesis, the separation of daughter cells after cell division; and moves parts of
the cell in processes of growth and mobility. The eukaryotic cytoskeleton is
composed of microfilaments, intermediate filaments and microtubules. There is a
great number of proteins associated with them, each controlling a cell's structure by
directing, bundling, and aligning filaments. The prokaryotic cytoskeleton is less
well-studied but is involved in the maintenance of cell shape, polarity and
cytokinesis.
Genetic material
Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA). Most organisms use DNA for their long-term information
storage, but some viruses (e.g., retroviruses) have RNA as their genetic material.
The biological information contained in an organism is encoded in its DNA or
RNA sequence. RNA is also used for information transport (e.g., mRNA) and
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enzymatic functions (e.g., ribosomal RNA) in organisms that use DNA for the
genetic code itself. Transfer RNA (tRNA) molecules are used to add amino acids
during protein translation.
Prokaryotic genetic material is organized in a simple circular DNA molecule (the
bacterial chromosome) in the nucleoid region of the cytoplasm. Eukaryotic genetic
material is divided into different, linear molecules called chromosomes inside a
discrete nucleus, usually with additional genetic material in some organelles like
mitochondria a chloroplasts.
A human cell has genetic material contained in the cell nucleus (the nuclear
genome) and in the mitochondria (the mitochondrial genome). In humans the
nuclear genome is divided into 23 pairs of linear DNA molecules called
chromosomes. The mitochondrial genome is a circular DNA molecule distinct
from the nuclear DNA. Although the mitochondrial DNA is very small compared
to nuclear chromosomes, it codes for 13 proteins involved in mitochondrial energy
production and specific tRNAs.
Organelles
The human body contains many different organs, such as the heart, lung, and
kidney, with each organ performing a different function. Cells also have a set of
"little organs," called organelles, that are adapted and/or specialized for carrying
out one or more vital functions. Both eukaryotic and prokaryotic cells have
organelles but organelles in eukaryotes are generally more complex and may be
membrane bound.
There are several types of organelles in a cell. Some (such as the nucleus and golgi
apparatus) are typically solitary, while others (such as mitochondria, peroxisomes
and lysosomes) can be numerous (hundreds to thousands). The cytosol is the
gelatinous fluid that fills the cell and surrounds the organelles.
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Cell nucleus – eukaryotes only - a cell's
information center
The cell nucleus is the most
conspicuous organelle found in a
eukaryotic cell. It houses the cell's
chromosomes, and is the place where
almost all DNA replication and RNA
synthesis (transcription) occur. The
nucleus is spherical and separated from
the cytoplasm by a double membrane
called the nuclear envelope. The
nuclear envelope isolates and protects a
cell's DNA from various molecules that
could accidentally damage its structure
or interfere with its processing. During
processing, DNA is transcribed, or
copied into a special RNA, called
messenger RNA (mRNA). This mRNA Diagram of a cell nucleus
is then transported out of the nucleus,
where it is translated into a specific
protein molecule. The nucleolus is a
specialized region within the nucleus
where ribosome subunits are assembled.
In prokaryotes, DNA processing takes
place in the cytoplasm.
Mitochondria and Chloroplasts – eukaryotes
only - the power generators
Mitochondria are self-replicating organelles
that occur in various numbers, shapes, and
sizes in the cytoplasm of all eukaryotic cells.
Mitochondria play a critical role in generating
energy in the eukaryotic cell. Mitochondria
generate the cell's energy by oxidative
phosphorylation, using oxygen to release
energy stored in cellular nutrients (typically
pertaining to glucose) to generate ATP.
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Mitochondria multiply by splitting in two.
Respiration occurs in the cell mitochondria.
Organelles that are modified chloroplasts are
broadly called plastids, and are involved in
energy storage through photosynthesis,
which uses solar energy to generate
carbohydrates and oxygen from carbon
dioxide and water.
Mitochondria and chloroplasts each contain
their own genome, which is separate and
distinct from the nuclear genome of a cell.
Both organelles contain this DNA in circular
plasmids, much like prokaryotic cells, strongly
supporting the evolutionary theory of
endosymbiosis; since these organelles
contain their own genomes and have other
similarities to prokaryotes, they are thought
to have developed through a symbiotic
relationship after being engulfed by a
primitive cell.
Endoplasmic reticulum – eukaryotes only
The endoplasmic reticulum (ER) is the
transport network for molecules
targeted for certain modifications and
specific destinations, as compared to
molecules that will float freely in the
cytoplasm. The ER has two forms: the
rough ER, which has ribosomes on its
surface and secretes proteins into the
cytoplasm, and the smooth ER, which
lacks them. Smooth ER plays a role in
calcium sequestration and release.
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Golgi apparatus – eukaryotes only
The primary function of the Golgi
apparatus is to process and package the
macromolecules such as proteins and
lipids that are synthesized by the cell. It
is particularly important in the
processing of proteins for secretion.
The Golgi apparatus forms a part of the
endomembrane system of eukaryotic
cells. Vesicles that enter the Golgi
apparatus are processed in a cis to trans
direction, meaning they coalesce on the
cis side of the apparatus and after
processing pinch off on the opposite
Diagram of an endomembrane
(trans) side to form a new vesicle in the system
animal cell.
Ribosomes
The ribosome is a large complex of
RNA and protein molecules. They each
consist of two subunits, and act as an
assembly line where RNA from the
nucleus is used to synthesise proteins
from amino acids. Ribosomes can be
found either floating freely or bound to
a membrane (the rough endoplasmatic
reticulum in eukaryotes, or the cell
membrane in prokaryotes).
Lysosomes and Peroxisomes – eukaryotes only
Lysosomes contain digestive enzymes (acid hydrolases). They digest excess
or worn-out organelles, food particles, and engulfed viruses or bacteria.
Peroxisomes have enzymes that rid the cell of toxic peroxides. The cell
could not house these destructive enzymes if they were not contained in a
membrane-bound system. These organelles are often called a "suicide bag"
because of their ability to detonate and destroy the cell.
Centrosome – the cytoskeleton organiser
The centrosome produces the microtubules of a cell – a key component of
the cytoskeleton. It directs the transport through the ER and the Golgi
apparatus. Centrosomes are composed of two centrioles, which separate
during cell division and help in the formation of the mitotic spindle. A single
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centrosome is present in the animal cells. They are also found in some fungi
and algae cells.
Vacuoles
Vacuoles store food and waste. Some vacuoles store extra water. They are
often described as liquid filled space and are surrounded by a membrane.
Some cells, most notably Amoeba, have contractile vacuoles, which can
pump water out of the cell if there is too much water. The vacuoles of
eukaryotic cells are usually larger in those of plants than animals.
Structures outside the cell wall
Capsule
A gelatinous capsule is present in some bacteria outside the cell wall. The capsule
may be polysaccharide as in pneumococci, meningococci or polypeptide as
Bacillus anthracis or hyaluronic acid as in streptococci. Capsules are not marked
by ordinary stain and can be detected by special stain. The capsule is antigenic.
The capsule has antiphagocytic function so it determines the virulence of many
bacteria. It also plays a role in attachment of the organism to mucous membranes.
Flagella
Flagella are the organelles of cellular mobility. They arise from cytoplasm and
extrude through the cell wall. They are long and thick thread-like appendages,
protein in nature. Are most commonly found in bacteria cells but are found in
animal cells as well.
Fimbriae (pili)
They are short and thin hair like filaments, formed of protein called pilin
(antigenic). Fimbriae are responsible for attachment of bacteria to specific
receptors of human cell. There are special types of pili called (sex pili) involved in
conjunction.
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Difference between Cilia and Flagella
1)
2)
3)
4)
5)
6)
7)
Cilia
Cilia are short, hair –like
organelles, 2-20µm in average
length.
They occur in relatively large
numbers per cell.
They often cover the entire cell
or the entire exposed surface of a
cell.
They beat coordinately in groups
or rows.
They show sweeping or rowing
motion.
Cilia fuse in some protozoans to
form undulating membranes,
membranelles or cirri.
Cilia lacks filmmer filaments
Flagella
1) Flagella are long, whip-like
organelles that may be 10-200µm
long.
2) They are usually fewer per cell.
3) They are often at one end of a
cell.
4) They usually beat independently.
5) They show adulatory motion.
6) Flagella do not fuse.
7) Flagella may bear stiff hair, the
filmmer filaments, on the side.
Prokaryotic DNA versus Eukaryotic DNA
Prokaryotic DNA
1) Occurs in the cytoplasm.
2) Much less in amount than in
eukaryotic cells
3) Circular in form.
4) Has little protein associated with
it.
5) Can code for fewer proteins.
6) Denatures into a tangled mass.
7) There is little non function DNA.
8) No non coding introns exist.
9) No organeller DNA.
10)Exists as a single
Eukaryotic
1) Occurs in the nucleus,
mitochondria and plastids.
2) Much more in amount than in
prokaryotic cells.
3) Linear in form in the nucleus,
circular in mitochondria and
plastids.
4) Nuclear DNA has proteins
associated with it, extra nuclear
DNA is without proteins.
5) Can code for far more proteins.
6) Nuclear DNA denature into two
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Biology book (written by Umesh kumar
molecule(chromosomes).
distinct strands, extra nuclear
DNA denatures into a tangled
mass.
7) Greater part of DNA is
nonfunctional.
8) Noncoding introns occur
between coding exons.
9) Organeller DNA present in
mitochondria and plastids.
10)Exists as 2 to many molecule
(chromosomes)
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Biology book (written by Umesh kumar
Unit 3 Cell Organelles
Mitochondria
Two mitochondria from mammalian lung tissue displaying their matrix and membranes as
shown by electron microscopy
The mitochondria were first seen in 1880 by Kolliker, who isolated them from
insect muscle cells. They were named mitochondria by Benda in 1898.
The mitochondria are found in all aerobic eukaryotic cells. They are lacking in
certain unusual anaerobic protozoans. The mitochondria are often concentrated in
the more active regions of the cells where energy-requiring processes occur.
Structure
(a) Form: The mitochondria are usually sausage-shaped, but may be spherical,
oval, cylindrical, filamentous or even branched.
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Biology book (written by Umesh kumar
(b) Size: The spherical mitochondria are 1-5micrometer in diameter. The
cylindericalmitochondria are usually 1-4 micrometer long and 0.2-1
micrometer thick.
(c) Outer membrane: The outer membrane is smooth, freely permeable to
most small molecules, contains fewer enzymes and is poor in proteins. It has
porin proteins which form channels for the passage of molecules through it.
It allows uptake of substrate and release of ATP.
(d) Inner membrane: The inner membranes is semipermeable and regulates the
passage of materials into and out of the mitochondrion. It is rich in enzymes
and carrier proteins are usually produced into numerous infolds called
cristae.
(e) Cristae: The inner mitochondrial membrane is compartmentalized into
numerous cristae, which expand the surface area of the inner
mitochondrial membrane, enhancing its ability to produce ATP. For typical
liver mitochondria the area of the inner membrane is about five times
greater than the outer membrane. This ratio is variable and mitochondria
from cells that have a greater demand for ATP, such as muscle cells, contain
even more cristae. These folds are studded with small round bodies known
as F1 particles or oxysomes.
(f) Oxisomes: The inner mitochondrial membranes bears minute regularly
spaced lollipop shaped about 8.5nm wide particles known as the inner
membranes subunits or elementary particles (EP), or oxisomess. An
oxysomes consists of three parts –a rounded head piece
joined by a short stalk to base pieces, or Fo subunit, located in the inner
membrane. There may be 100,000 to 1,000,000 oxysomes in a single
mitochondrion. The oxysomes, also called Foadenosine triphosphatase, or ARPase or ATP synthetase, enzymes and is
thus concerned with ATP formation. The rest of the inner mitochondrial
membrane contains the electron carrier molecules of the electron transport
chain.
(g) Matrix: The matrix is the space enclosed by the inner membrane. It
contains about 2/3 of the total protein in a mitochondrion. The matrix is
important in the production of ATP with the aid of the ATP synthase
contained in the inner membrane. The matrix contains a highlyconcentrated mixture of hundreds of enzymes, special mitochondrial
ribosomes, tRNA, and several copies of the mitochondrial DNA genomes.
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Origin: Mitochondria are self-duplicating organelles. New mitochondria arise by
the division of existing ones. This is another prokaryotic feature. Cells cannot form
them from raw materials. Mitochondria are continually renewed.
Marker enzymes: Marker enzymes indicate or mark the presence of substrate
of particular cell organelles. For example mitochondria and chloroplast enzymes.
Whenever provided that appropriate substrate then particular product will be form
and that product will indicate that in the process of isolation of some fraction of a
cell organelle, we have isolated the right one.
Autonomy (Semiautonomous organelles): Mitochondria are semiautonomous
organelles. They are capable of self-duplication (replication). For replication, they
have
(1) genetic information (DNA),
(2) selftranscried RNAs(rRNA, tRNA and mRNA),
(3) protein-making machinery(ribosomes),
(4) energy-producing mechanism(respiratory enzymes),
(5) synthesize membrane material and also structural proteins and enzymes for
their use.
However, they can manufacture only some of their proteins. They gat other
proteins from cytoplasm formed under the directions of nuclear DNA. During cell
division, each daughter cell receives some mitochondria from the mother cell.
These mitochondria later replicate to restore the normal number in the cell.
Function:
1.
2.
3.
4.
It is site of ATP production.
Oxidation of food (protein, fat and carbohydrate).
Oxidative decarboxilaton of pyruvate into Acetyle Co-enzyme.
Tricarboxlic acid (TCA) cycle take in the matrix of mitochondira, this cycle
is known as kreb’s cycle.
5. Oxidative phosphorylation take place in this organelles.
6. Electron transport chain is located in the inner membrane of mitochondria
where NADH₂ and FADH₂ molecules are oxidized and ATP molecules are
formed.
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Biology book (written by Umesh kumar
Production of ATP:
The most prominent roles of mitochondria are to produce ATP (i.e.,
phosphorylation of ADP) through respiration, and to regulate cellular metabolism.
The central set of reactions involved in ATP production are collectively known as
the citric acid cycle, or the Krebs Cycle. However, the mitochondrion has many
other functions in addition to the production of ATP.
Pyruvate and the citric acid cycle (Krebs cycle or TCA cycle)
Each pyruvate molecule produced by glycolysis is actively transported across the
inner mitochondrial membrane, and into the matrix where it is oxidized and
combined with coenzyme A to form CO2, acetyl-CoA, and NADH.
The acetyl-CoA is the primary substrate to enter the citric acid cycle, also known
as the tricarboxylic acid (TCA) cycle or Krebs cycle. Krebs cycle consists of 8
steps, producing an equal number of organic acids. Each step is catalyzed by a
specific enzyme. In Krebs cycle, the entrant molecule is 2- carbon acetyle CoA and
the receptor molecule is 4-carbon oxaloacetate.
(1) Condensation: Acetyle: Aetyle coenzyme A reacts in the presence of water
with the oxaloacetate normally present in a cell, forming 6-carbon citrate
and freeing coenzyme A for reuse in pyruvate oxidation. The high- energy
bond of acetyl coenzyme A provides the energy for this reaction. The
reaction is catalyzed by the citrate synthetase enzyme.
𝑂𝑥𝑎𝑙𝑜𝑎𝑐𝑒𝑡𝑎𝑡𝑒 + 𝐴𝑐𝑒𝑡𝑦𝑙𝑒 𝐶𝑜𝐴 + 𝐻2 𝑂
+ 𝐶𝑜𝐴(𝑅𝑒𝑢𝑠𝑒𝑑)
𝐶𝑖𝑡𝑟𝑎𝑡𝑒 𝑠𝑦𝑛𝑡ℎ𝑒𝑡𝑎𝑠𝑒
→
𝐶𝑖𝑡𝑟𝑎𝑡𝑒
(2) Reorganization(Dehydration): Citrate undergoes reorganization in the
presence of an enzyme, aconitase, forming 6-carbon cisaconitateand
releasing water.
𝐴𝑐𝑜𝑛𝑖𝑡𝑎𝑠𝑒
𝐶𝑖𝑡𝑟𝑎𝑡𝑒 →
𝐶𝑖𝑠𝑎𝑐𝑜𝑛𝑖𝑡𝑎𝑡𝑒 + 𝐻₂𝑂
(3) Reorganization (Hydration): Cisaconitate is further reorganized into 6carbon isocitrate by the enzyme, aconitase, with the addition of water.
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Biology book (written by Umesh kumar
𝐴𝑐𝑜𝑛𝑖𝑡𝑎𝑠𝑒
𝐶𝑖𝑠𝑎𝑐𝑜𝑛𝑖𝑡𝑎𝑡𝑒 + 𝐻₂𝑂 →
𝐼𝑠𝑜𝑐𝑖𝑡𝑟𝑎𝑡𝑒
(4) Oxidative Decarboxylation: Isocitrate gives off a pair of hydrogen atoms
(oxidation) and a molecule of CO₂ (decarboxylation) and becomes 5-carbon
α-ketogluttarate. The pair of hydrogen atoms give two electrons and one 𝐻 +
to 𝑁𝐴𝐷+ forming NADH + 𝐻 + .The enzyme isocitrate dehyrogenase
catalyses the reaction in the presence of 𝑀𝑛2+ . NADH generates ATP by
transferring its electrons over the ETS.
𝐼𝑠𝑜𝑐𝑖𝑡𝑟𝑎𝑡𝑒 + 𝑁𝐴𝐷+
𝑖𝑠𝑜𝑐𝑖𝑡𝑟𝑎𝑡𝑒 𝑑𝑒ℎ𝑦𝑑𝑟𝑜𝑔𝑒𝑛𝑎𝑠𝑒,𝑀𝑛+
→
𝛼 − 𝑘𝑒𝑡𝑜𝑔𝑙𝑢𝑡𝑎𝑟𝑎𝑡𝑒 + 𝑁𝐴𝐷𝐻 + 𝐶𝑂2 (↑) + 𝐻 +
(5) Oxidative Decarboxilation: This is a 2-stage process(a) Coenzyme A reacts with α-ketoglutarate, forming 4-carbon succinylcoenzyme A and releasing CO₂ and a pair of hydrogen atoms. The reaction
is catalysed by α-ketoglutarate dehydrogenase complex enzyme. The pair of
hydrogen atoms pass two electrons and one 𝐻+ to 𝑁𝐴𝐷+ , forming NADH +
𝐻+ .
𝛼−𝑘𝑒𝑡𝑜𝑔𝑙𝑢𝑡𝑎𝑟𝑎𝑡𝑒 𝑑𝑒ℎ𝑦𝑑𝑟𝑜𝑔𝑒𝑛𝑎𝑠𝑒
𝛼 − 𝑘𝑒𝑡𝑜𝑔𝑙𝑢𝑡𝑎𝑟𝑎𝑡𝑒 + 𝐶𝑜𝐴 + 𝑁𝐴𝐷 + →
𝑆𝑢𝑐𝑐𝑖𝑛𝑦𝑙 − 𝐶𝑜𝐴 + 𝐶𝑂₂
+ 𝑁𝐴𝐷𝐻 + 𝐻 +
(b) Succinyl-coenzyme A splits into 4-carbon succinate and coenzyme A with
the addition of water. The coenzyme A transfers its high GDP ( guanosine
diphosphate), formingGTP (guanosine triphosphate). The latter is an energy
carrier like ATP. This is the only high-energy phosphate produced in the
Krebs cycle.
𝑆𝑢𝑐𝑐𝑖𝑛𝑦𝑙−𝐶𝑂𝐴 𝑠𝑦𝑛𝑡ℎ𝑒𝑡𝑎𝑠𝑒
𝑆𝑢𝑐𝑐𝑖𝑛𝑦𝑙 − 𝐶𝑜𝐴 + 𝐻2 𝑂 + 𝐺𝐷𝑃/𝐴𝐷𝑃 →
𝐺𝑇𝑃/𝐴𝑇𝑃
𝑆𝑢𝑐𝑐𝑖𝑛𝑎𝑡𝑒 + 𝐶𝑜𝐴 +
In a plant cell, this reaction produced ATP from ADP.
(6) Dehydrogenation: This process converts succinate ionto 4-carbon fumarate
with the aid of an enzyme, succinate dehydrogenase, and liberates a pair of
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Biology book (written by Umesh kumar
hydrogen atoms. The latter pass to FAD (Flavin adenine diunucleotide),
forming FADH₂.
𝑆𝑢𝑐𝑐𝑖𝑛𝑎𝑡𝑒 𝑑𝑒ℎ𝑦𝑑𝑟𝑜𝑔𝑒𝑛𝑎𝑠𝑒
𝑆𝑢𝑐𝑐𝑖𝑛𝑎𝑡𝑒 + 𝐹𝐴𝐷 →
𝐹𝑢𝑚𝑎𝑟𝑎𝑡𝑒 + 𝐹𝐴𝐷𝐻₂
(7) Hydration: This process changes fumarate into 4-carbon maltate in the
presence of water and an enzyme, fumarase.
𝐹𝑢𝑚𝑎𝑟𝑎𝑠𝑒
𝐹𝑢𝑚𝑎𝑟𝑎𝑡𝑒 + 𝐻₂𝑂 →
𝑀𝑎𝑙𝑡𝑎𝑡𝑒
(8) Dehydrogenation: This process restores oxaloacetate by removing a pair of
hydrogen atoms from maltate with the help of an enzyme maltate
dehydrogenase. The pair of hydrogen atoms pass two electrons and
𝐻+ to𝑁𝐴𝐷+ , forming NADH + 𝐻+ .
𝑀𝑎𝑙𝑡𝑎𝑡𝑒 𝑑𝑒ℎ𝑦𝑑𝑟𝑜𝑔𝑒𝑛𝑎𝑠𝑒
𝑀𝑎𝑙𝑡𝑎𝑡𝑒 + 𝑁𝐴𝐷+ →
𝑂𝑥𝑎𝑙𝑜𝑎𝑐𝑒𝑡𝑎𝑡𝑒 + 𝑁𝐴𝐷𝐻 + 𝐻+
Oxaloacetate combine with acetyl coenzyme A to form citrate and so the cycle
continues.
The electron transport chain or system
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Biology book (written by Umesh kumar
Diagram of the electron transport chain in the mitochondrial intermembrane space
The various components of electron transport system include-4 type of
cytochrome b, 2 type of cytochrome c, ubiquinone, flavopratein (FMN or FAD),
iron sulphur protein (Fe-S) and enzyme cytochrome oxidase which is intimately
associated with cytochrome a and a₃. These components are arranged in a
sequence in the inner mitochondrial membrane. Reduced coenzymes transfer
their electrons and proton through the electron transport system in the following
manner :
(1) First step involves transfer of hydrogen from NADH +𝐻+ (formed in the
matrix by Krebs cycle) to a metalloflavoprotein –FMN (Flavin
mononucleotide). The FMN gets reduced to FMNH₂ and the coenzyme
NADH + 𝐻+ gets reduced to NA𝐷+ .
(2) Reduced FMN (i.e.FMN𝐻2 ) then transport its electrons to Fe-S protein and
2 𝐻+ into the inter membrane space.
(3) The reduced Fe-s protein then transfers its electrons to ubiquinone (UQ).
The UQ takes two electrons from the matrix to become UQ𝐻2 .
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Biology book (written by Umesh kumar
(4) Reduced ubiquinone (UQ𝐻2 ) then transfers its electrons transport system
at this stage by transferring its 2 H ton UQ. The UQ is reduced to UQ𝐻2 .
Evidences suggest that NADH +𝐻+ , reduced in the glycolsis (EMP pathway),
also enters into electron transport system at this step. The NADH reduced a
flavoprotein containing NADH –dehydrogence located on the outer surface
of inner mitochondrial membrane. The reduced flavoprotein (FP𝐻2 ) then
enters into main pathway by transferring 2 H to UQ. The reduced UQ (i.e.,
UQ𝐻2 ) then transfer its electrons to cytochrome b and 2 𝐻 + to the outer
side.
(5) Reduced cytochrome b then transfer its electrons to Fe-S protein. The
𝐹𝑒 3+ −S is converted to Fe₂-S. This protein then transfer electrons to UQ
which also takes 2𝐻+ from inner matrix to become UQ𝐻2 .
(6) The reducedUQ (i.e. UQH₂) transfer its electron to cytochrome c . At this
stage a third pair of 𝐻 + is transported outwardly.
(7) Reduced cytochrome c then reduced Cyt c by transferring its electron.
(8) Finally the electrons from cytochrome c are transferred via. Cyt 𝑎3 and
Cyt𝑎3 to 𝑂2 .
This step, also known as terminal oxidation, is catalysed by enzyme
cytochrome oxidase. The enzyme catalyses reducation of 𝑂2 to 𝐻2 O by
transferring electrons from Cyts 𝑎3 and 2𝐻+ from the medium in the
following manner:
2Cyt (F𝑒 2 +) +1/2 𝑂2 + 2𝐻+ →
H₂O +2 Cyt (𝐹𝑒 3+ )
Glycolsis :
Glycolysis is a metabolic pathway that is found in the cytosol of cells in all living
organisms. The process converts one molecule of glucose into two molecules of
pyruvate(pyruvic acid), it makes energy in the form of two net molecules of ATP.
Four molecules of ATP per glucose are actually produced; however, two are
consumed for the preparatory phase. The initial phosphorylation of glucose is
required to destabilize the molecule for cleavage into two pyruvate. During the
pay-off phase of glycolysis, four phosphate groups are transferred to ADP by
substrate-level phosphorylation to make four ATP, and two NADH are produced
when the pyruvate are oxidized. The overall reaction can be expressed this way:
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Biology book (written by Umesh kumar
Glucose + 2 NAD+ + 2 Pi + 2 ADP → 2 pyruvate + 2 NADH + 2 ATP + 2 H+ + 2
H2O
Cellular respiration
Respiration is one of the key ways a cell gains useful energy to fuel cellular
reformations. Nutrients commonly used by animal and plant cells in respiration
include sugar, amino acids and fatty acids, and a common oxidizing agent (electron
acceptor) is molecular oxygen (O2). The energy released in respiration is used to
synthesize ATP to store this energy. The energy stored in ATP can then be used to
drive processes requiring energy, including biosynthesis, locomotion or
transportation of molecules across cell membranes.
Aerobic respiration:
Aerobic respiraton is the main means by which both plants and animals utilize
energy in the form of organic compounds that was previously created through
photosynthesis.
Aerobic respiration requires oxygen in order to generate energies (ATP). Although
carbohydrates, fats, and proteins can all be processed and consumed as reactant, it
is the preferred method of pyruvate breakdown in glycolysis and requires that
pyruvate enter the mitochondrion in order to be fully oxidized by the Krebs cycle.
The product of this process is energy in the form of ATP (Adenosine triphosphate),
by substrate-level phosphorylation, NADH and FADH2Simplified reaction:
C6H12O6 (aq) + 6 O2 (g) → 6 CO2 (g) + 6 H2O (l)
The reducing potential of NADH and FADH2 is converted to more ATP through
an electron transport chain with oxygen as the "terminal electron acceptor". Most
of the ATP produced by aerobic cellular respiration is made by oxidative
phosphorylation. This works by the energy released in the consumption of
pyruvate being used to create a chemiosmotic potential by pumping protons across
a membrane. This potential is then used to drive ATP synthase and produce ATP
from ADP and a phosphate group.
Anaerobic respiration (fermentation):
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Oxidation of respiratory substrates in absence of atmospheric oxygen is termed as
anaerobic respiraton. It involves incomplete break down of respiratory substrate in
which the end products, such as ethanol or lactic acid are produced and CO₂ is
released. Anaerobic respiration is common among certain microorganisms.
𝐶₆𝐻 ₂𝑂₆ →
2𝐶₂𝐻₅𝑂𝐻 + 2𝐶𝑂₂
Anaerobic respiration carried out by some fungi (e.g. yeast) and bacteria is some
times termed as fermentation.
The difference between Aerobic respiration and Anaeribic respiration.
Sr.N.
Aerobic respiration
Anaerobic respiration
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Biology book (written by Umesh kumar
1.
It is common in all higher plants.
2.
It occurs inside the living cells.
It is uncommon in higher plants, but
common in certain micro-organisms.
It occurs inside the living cells.
Living cells are not essential in some
fermentation.
3.
It is a permanent process and goes
on throughout the life of plants.
It occurs for a temporary phase under
anaerobic conditions in higher plants.
4.
Energy released in larger amount
in the form ATP (36 ATP0.
Energy released in lesser amount in
the form of 2 mol of ATP. Heat is
generated in fermentation.
5.
Not toxic to plants.
6.
Occurs in presence of 𝑂2 .
7.
End products are CO₂ and H₂O.
Toxic to higher plants.
Occurs in absence of O₂.
End products are ethanol and CO₂.
Chloroplasts
A typical plant cell (e.g., in the palisade layer of a leaf) might contain as many as
50 chloroplasts. . 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.
Structure:
The chloroplast is made up of 3 types of membrane:
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Biology book (written by Umesh kumar
1. A smooth outer membrane which is freely permeable to molecules.
2. A smooth inner membrane which contains many transporters: integral
membrane proteins that regulate the passage in an out of the chloroplast of
o small molecules like sugars
o proteins synthesized in the cytoplasm of the cell but used within the
chloroplast
3. A system of thylakoid membranes
Thylakoids



The thylakoid membranes enclose a lumen: a system of vesicles (that may
all be interconnected).
At various places within the chloroplast these are stacked in arrays called
grana (resembling a stack of coins).
Four types of protein assemblies are embedded in
the thylakoid membranes:
1. Photosystem I which includes chlorophyll
and carotenoid molecules
2. Photosystem II which also contains
chlorophyll and carotenoid molecules
3. Cytochromes b and f
4. ATP synthase
These carry out the so-called light reactions of
photosynthesis.

The thylakoid membranes are surrounded by a
fluid stroma.
The stroma contains:
o all the enzymes, e.g., RUBISCO, needed to carry out the "dark"
reactions of photosynthesis; that is, the conversion of CO2 into
organic molecules like glucose.
o A number of identical molecules of DNA, each of which carries the
complete chloroplast genome. The genes encode some — but not all
— of the molecules needed for chloroplast function. The others are
 transcribed from genes in the nucleus of the cell
 translated in the cytoplasm and
 transported into the chloroplast.
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Chloroplast ultrastructure:
1. outer membrane
2. Intermembrane space
3. inner membrane (1+2+3: envelope)
4. stroma (aqueous fluid)
5. thylakoid lumen (inside of thylakoid)
6. thylakoid membrane
7. granum (stack of thylakoids)
8. thylakoid (lamella)
9. starch
10. ribosome
11. plastidial DNA
12. plastoglobule (drop of lipids)
Origin: Chloroplasts are self-duplicating organelles. They grow by expansion and
then fission. They also arise by division of their precursors, the proplastids.
Functions
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Biology book (written by Umesh kumar
(1) Photosynthesis: The chloroplasts trap the radiant energy of
sunlight and transition it into the chemical energy of glucose
formed from water and carbon dioxide.
(2) Oxygen Supply: Chloroplast provide oxygen, the byproduct of
photosynthesis, to all aerobic organisms for respiration.
(3) Starch Storage: chloroplasts temporarily store starch grains
during the day-time in the pyrenoid, the starch-forming
organelles. At night, the starch is transferred to regions of
growth and storage.
(4) Utilise Carbon dioxide: Chloroplast fix carbon dioxide, thereby
keeping its concentration in the air normal.
(5) Food supply: Chloroplasts provide food and chemical energy to
practically all organisms.
Photosynthesis
Photosynthesis is a process that converts carbon dioxide into organic compounds,
especially sugars, using the energy from sunlight. Photosynthesis occurs in plants,
algae, and many species of bacteria, but not in archaea. In plants, algae, and
cyanobacteria, photosynthesis uses carbon dioxide and water, releasing
oxygen as a waste product. Photosynthesis is vital for all aerobic life on Earth.
Two pigment System (Photosystem I and Photosytem II)
Photosystem I
Photosystem I (PS I) (or plastocyanin: ferredoxin oxidoreductase) is the second
photosystem in the photosynthetic light reactions of algae, plants, and some
bacteria. Photosystem I is so named because it was discovered before photosystem
II.
Photon
Photons of light photoexcite pigment molecules in the antenna complex. Energy
from each photon is transferred to an electron, causing an excited state.
Antenna Complex
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The antenna complex is composed of molecules of chlorophyll and carotenoids
mounted on two proteins. These pigment molecules transmit the resonance energy
from photons when they become photoexcited. Antenna molecules can absorb all
wavelengths of light within the visible spectrum. The number of these pigment
molecules varies from organism to organism. For instance, the cyanobacterium
Synechococcus elongatus (Thermosynechococcus elongatus) has about 100
chlorophylls and 20 carotenoids, whereas spinach chloroplasts have around 200
chlorophylls and 50 carotenoids. Located within the antenna complex of PS I are
molecules of chlorophyll called P700 reaction centers. The energy passed around
by antenna molecules is directed to the reaction center. There may be as many as
120 or as few as 25 chlorophyll molecules per P700.
P700 Reaction Center
The P700 reaction center is composed of modified chlorophyll a that best absorbs
light at a wavelength of 700nm, with higher wavelengths causing bleaching. P700
receives energy from antenna molecules and uses the energy from each photon to
raise an electron to a higher energy level. These electrons are moved in pairs in an
oxidation/reduction process from P700 to electron acceptors. P700 has an electric
potential of about -1.2 volts. The reaction center is made of two chlorophyll
molecules and is therefore referred to as a dimer. The dimer is thought to be
composed of one chlorophyll a molecule and one chlorophyll a' molecule.
However, if P700 forms a complex with other antenna molecules, it can no longer
be a dimer.
Modified Chlorophyll A0
Modified chlorophyll A0 is an early electron acceptor in PS I. Chlorophyll A0
accepts electrons from P700 before passing them along to another early electron
acceptor.
Phylloquinone A1
Phylloquinone A1 is the next early electron acceptor in PS I. Phylloquinone is a
polypeptide made up of vitamin K1.Phylloquinone A1 oxidizes A0 in order to
receive the electron and in turn reduces Fx in order to pass the electron to Fb and Fa.
A1 transfers electrons from A0 to the iron-sulfur complex, yet it seems that this
molecule is not required for electron transport from chlorophyll A0 to the ironsulfur centers Fx, Fb, and Fa (A2). However, A1 may function in non-cyclic transfer.
The Iron-sulfur Complex
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Biology book (written by Umesh kumar
Three proteinaceous iron-sulfur reaction centers exist in this complex. The
structure of iron-sulfur proteins is cube-like with four iron atoms and four sulfur
atoms making eight points of the cube. The reaction centers in this complex are
secondary electron acceptors. The three centers named Fx, Fa, and Fb direct
electrons to ferredoxin. Fa and Fb are bound to protein subunits of the PS I
complex and Fx is tied to the PS I complex by cysteines. Various experiments have
shown some disparity between theories of iron-sulfur co-factor orientation and
operation order. However, most of the results of these experiments point to three
conclusions. First, the placement of Fx, Fa, and Fb form a triangle with Fa placed
closer to Fx than Fb. Second, the order of electron transport within the iron-sulfur
complex is from Fx to Fa to Fb wherein Fa and Fb form a terminal for electron
receipt from Fx. Finally, Fb is the component that reduces ferredoxin in order to
pass on the electron.
Ferredoxin
Ferredoxin (Fd) is a soluble protein that facilitates reduction of NADP+ to
NADPH. Fd moves to carry an electron either to a lone thylakoid or to an enzyme
that reduces NADP+. Thylakoid membranes have one binding site for each function
of Fd. The main function of Fd is to carry an electron from the iron-sulfur complex
to the enzyme ferredoxin-NADP+ reductase.
Ferredoxin-NADP+ Reductase (FNR)
This enzyme transfers the electron from reduced ferredoxin to NADP+ to complete
the reduction to NADPH. FNR may also accept an electron from NADPH by
binding to it.
Plastocyanin
Plastocyanin is a metallic protein containing a copper atom and with patches of
negative charge. After an electron is carried to a cytochrome complex, it is passed
on to plastocyanin. Plastocyanin binds to cytochrome though little is known about
the mechanism of this binding. Plastocyanin then transfers the electron directly to
the P700 reaction center in the PS I antenna complex.
Photosystem II
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Photosystem II (or water-plastoquinone oxidoreductase) is the first protein
complex in the Light-dependent reactions. It is located in the thylakoid membrane
of plants, algae, and cyanobacteria. The enzyme uses photons of light to energize
electrons that are then transferred through a variety of coenzymes and cofactors to
reduce plastoquinone to plastoquinol. The energized electrons are replaced by
oxidizing water to form hydrogen ions and molecular oxygen. By obtaining these
electrons from water, photosystem II provides the electrons for all of
photosynthesis to occur. The hydrogen ions (protons) generated by the oxidation of
water help to create a proton gradient that is used by ATP synthase to generate
ATP. The energized electrons transferred to plastoquinone are ultimately used to
reduce NADP+ to NADPH or are used in Cyclic Photophosphorylation.
Oxygen-Evolving Complex (OEC)
The oxygen-evolving complex is the site of water oxidation. It is a metallo-oxo
cluster comprising four manganese ions (in oxidation states ranging from +3 to +5)
and one divalent calcium ion. When it oxidizes water, producing dioxygen gas and
protons, it sequentially delivers the four electrons from water to a tyrosine (D1Y161) sidechain and then to P680 itself. The structure of the oxygen-evolving
complex is still contentious. The structures obtained by X-ray crystallography are
particularly controversial, since there is evidence that the manganese atoms are
reduced by the high-intensity X-rays used, altering the observed OEC structure.
However, crystallography in combination with a variety of other (less damaging)
spectroscopic methods such as EXAFS and electron paramagnetic resonance have
given a fairly clear idea of the structure of the cluster. One possibility is the
cubane-like structure.
Water splitting
Photosynthetic water splitting (or oxygen evolution) is one of the most important
reactions on the planet, since it is the source of nearly all the atmosphere's oxygen.
Moreover, artificial photosynthetic water-splitting may contribute to the effective
use of sunlight as an alternative energy-source.
The mechanism of water oxidation is still not fully elucidated, but we know many
details about this process. The oxidation of water to molecular oxygen requires
extraction of four electrons and four protons from two molecules of water. The
experimental evidence that oxygen is released through cyclic reaction of oxygen
evolving complex (OEC) within one PSII was provided by Pierre Joliot et al. They
have shown that, if dark-adapted photosynthetic material (higher plants, algae, and
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cyanobacteria) is exposed to a series of single turnover flashes, oxygen evolution is
detected with typical period-four damped oscillation with maxima on the third and
the seventh flash and with minima on the first and the fifth flash . Based on this
experiment, Bessel Kok and co-workers introduced a cycle of five flash-induced
transitions of the so-called S-states, describing the four redox states of OEC: When
four oxidizing equivalents have been stored (at the S4-state), OEC returns to its
basic and in the dark stable S0-state.
MECHANISM OF PHOTOSYNTHESIS
The process of photosynthesis complete in two steps- light reaction and dark
reaction. Light reaction is also called photochemical phase and occure in thykoids
whereas dark reaction is called thermochemical phase and occurs inside the stroma
of chloroplasts.
LIGHT REACTION: Light reaction begins as soon as light quanta fall on PSI
and PSII located in thylakoids. Pigment molecules pass their absorbed energy
finally to their reaction centre which take part in photochemical act. The two
photosystems are connected in series with each other by the components of
electron transport chain. The reaction centres become so excited that they escape
high energy electron which move to nearby electron acceptor molecules. The
electrons move through two pathways –noncyclic and cyclic. The noncyclic
electron transport involves participation of both PSII and PSI whereas cyclic
electron transport involves only PSI.
Noncyclic electron transport pathway
a) The light energy of specific wavelengths is absorbed by chlorophylls and
accessory pigments of PSII. These pigments transfer their absorbed
energy to PSII reaction centre-𝑃680 . The reaction centre-𝑃680 becomes
photoexcited and exudes an electron with a gain of energy. The electron
is immediately accepted by the primary acceptor quinine. The reaction
centre comes to ground state by getting an electron from photooxidaton
of water.
b) The PSII reaction centre-𝑃680 , by transferring electron to primary
acceptor, becomes oxidized. This oxidized chlorophyll molecule takes
replacement electron from water, which splits, releasing oxygen.
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Biology book (written by Umesh kumar
2𝐻₂𝑂 ⇌ 4𝐻+ + 4𝑒 − + 𝑂₂
The overall process is called photooxidation of water. It required the
presence of manganese ions, chloride ions, a water oxidizing enzyme and
an unknown substance Z. It is believed that oxygen evolves as oxygen
gas, electrons are accepted by PSII reaction centre through unknown
substance and hydrogen ions temporarily stay in the thylakoid space.
c) The high energy electrons that leave PSII are captured by quinine, which
sends them to an electron transport system consisting of plastoquinone
(PQ). Every time electron passes from donor to acceptor is reduced. For
example, reduced quinine gets oxidized by transferring its electron to
plastoquinone and the later gets reduced. The reduced plastoquinone
transfers its to electron to cytochrome complex which finally transfers to
plastocyanin. The electrons of plastocyanin are picked by PSI.
d) Simultaneously, the pigment molecules of PSI complex absorb solar
radiation and transfer their absorbed electronic excitation (energy) to PSI
reaction centre-𝑃700 . 𝑃700 gets excited and exudes an electron, which
goes to reduce an electron acceptor (A). The oxidizes reaction centre of
PSI takes electron from plastocyanin and comes to ground state.
e) The electron emitted from the 𝑃700 is accepted by an unknown acceptor
(A) which transferres its electron to ferredoxin an iron containing protein
positioned at the outer surface of thylakoid membrane. The reduced
ferredoxin donates its electron to 𝑁𝐴𝐷𝑃+ (nicotinamide adenine
dinucleotide phosphate). The 𝑁𝐴𝐷𝑃+ takes electronsfrom ferredoxin,
protons from the medium and gets reduced to NADPH in presence of
enzyme Ferredoxin-NADP-reductase.
𝐹𝑒𝑟𝑟𝑒𝑑𝑜𝑥𝑖𝑛(𝑟𝑒𝑑. ) + 𝑁𝐴𝐷𝑃 + + 𝐻+ →
𝑁𝐴𝐷𝑃𝐻 + 𝐹𝑒𝑟𝑟𝑒𝑑𝑜𝑥𝑖𝑛(𝑜𝑥𝑖. )
Cyclic electron transport pathway: Cyclic electron transport occurs only
occasionally when synthesis if carbohydrates are curtailed due to limited supply of
CO₂ and NADPH starts accumulating. At this, there would be no need for
additional NADPH. Moreover, the cyclic electron transport serves the purpose of
more production of ATP when need by the chloroplast.
a) The cyclic electron transport pathway begins after the PSI pigment complex
absorbs solar energy. They transfer their energy to PSI reaction centre-𝑃700 .
The outer valance electron of excited 𝑃700 is raised to higher energy level
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Biology book (written by Umesh kumar
which is captured by the primary acceptor of PSI. The primary acceptor then
transfers electron to ferredoxin.
b) Reduced ferredoxin, unable to reduce𝑁𝐴𝐷𝑃 + , returns the electron to PSI via
cytochrome𝑏6 , plastoquinone (PQ), cytochrome f and plastocyanin.
c) The electron transport is called cyclic because the electron emitted from PSI
returns back to PSI passing through several intermediate carriers.
Differences between Non-cyclic electron transports.
DARK REACTION: Dark reaction or thermochemical reaction occurs in the
stroma of chloroplasts where the products of light reaction are used to incorporate
carbon from CO₂ to carbohydrate. Although the reaction itself does not require
light but the process usually occurs the light and continues for a very brief period
after a plant is kept in dark as long as NADPH and ATP are available.
ATP and NADPH provide the energy and electrons to reduce carbon dioxide
(CO2) to organic molecules.
The Steps







CO2 combines with the phosphorylated 5-carbon sugar ribulose
bisphosphate.
This reaction is catalyzed by the enzyme ribulose bisphosphate
carboxylase oxygenase (RUBISCO)(an enzyme which can fairly claim to
be the most abundant protein on earth).
The resulting 6-carbon compound breaks down into two molecules of 3phosphoglyceric acid (PGA).
The PGA molecules are further phosphorylated (by ATP) and are reduced
(by NADPH) to form phosphoglyceraldehyde (PGAL).
Phosphoglyceraldehyde serves as the starting material for the synthesis of
glucose and fructose.
Glucose and fructose make the disaccharide sucrose, which travels in
solution to other parts of the plant (e.g., fruit, roots).
Glucose is also the monomer used in the synthesis of the polysaccharides
starch and cellulose.
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The Calvin cycle and carbon fixation
Cyclic Photophosphorylation
In cyclic photophosphorylation,




the electrons expelled by the energy of light absorbed by photosystem I
pass, as normal, to ferredoxin (Fd).
But instead of going on to make NADPH,
they pass to plastoquinone (PQ) and on back into the cytochrome b6/f
complex.
Here the energy each electron liberates pumps 2 protons (H+) into the
interior of the thylakoid — enough to make up the deficit left by noncyclic
photophosphorylation.
This process is truly cyclic because no outside source of electrons is required. Like
the photocell in a light meter, photosystem I is simply using light to create a flow
of current. The only difference is that instead of using the current to move the
needle on a light meter, the chloroplast uses the current to help synthesize ATP.
Carbon dioxide levels and photorespiration
As carbon dioxide concentrations rise, the rate at which sugars are made by the
light-independent reactions increases until limited by other factors. RuBisCO, the
enzyme that captures carbon dioxide in the light-independent reactions, has a
binding affinity for both carbon dioxide and oxygen. When the concentration of
carbon dioxide is high, RuBisCO will fix carbon dioxide. However, if the carbon
dioxide concentration is low, RuBisCO will bind oxygen instead of carbon dioxide.
This process, called photorespiration, uses energy, but does not produce sugars.
RuBisCO oxygenase activity is disadvantageous to plants for several reasons:
1. One product of oxygenase activity is phosphoglycolate (2 carbon) instead of
3-phosphoglycerate (3 carbon). Phosphoglycolate cannot be metabolized
by the Calvin-Benson cycle and represents carbon lost from the cycle. A
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Biology book (written by Umesh kumar
high oxygenase activity, therefore, drains the sugars that are required to
recycle ribulose 5-bisphosphate and for the continuation of the CalvinBenson cycle.
2. Phosphoglycolate is quickly metabolized to glycolate that is toxic to a plant
at a high concentration; it inhibits photosynthesis.
3. Salvaging glycolate is an energetically expensive process that uses the
glycolate pathway, and only 75% of the carbon is returned to the CalvinBenson cycle as 3-phosphoglycerate. The reactions also produce ammonia
(NH3), which is able to diffuse out of the plant, leading to a loss of nitrogen.
A highly simplified summary is:
2 glycolate + ATP → 3-phosphoglycerate + carbon dioxide + ADP +NH3
The salvaging pathway for the products of RuBisCO oxygenase activity is more
commonly known as photorespiration, since it is characterized by light-dependent
oxygen consumption and the release of carbon dioxide.
Difference between Mitochondria and chloroplasts
Mitochondria
1. Cristae remain attached to inner
membrane.
2. Cristae produce ATP by break –down of
glucose.
3. Lack pigments.
4. Occur in practically all eukaruotic cells.
5. Consume organic compounds in their
activity,
Leading to decrease in weight.
6. Produce CO₂ and H₂O by break down of
organic
compounds.
7. Use oxygen.
8. Function all the time.
9. Present in gametes.
10. Do not trap light energy.
Chloroplasts
1. Thylakoids separate from inner
membrane.
2. Thylakoids produce ATP by action of
light.
3. Have pigments.
4. Occur only in green eukaryotic cells
exposed
To sun light.
5.Produce organic compounds, leading
to
increase in weight.
6. Use CO₂ and H₂O as row materials to
synthesize organic compounds.
7. Release oxygen.
8. Function only in sun light.
9. Gametes have proplastids.
10.Trap light energy in the chemical
bonds of
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Biology book (written by Umesh kumar
organic compounds.
Difference between photorespiration, photosynthesis and true respiration
Photorespiration
Photosynthesis
True Respiration
1) Occurs in green
1) Occurs in green plants in
1) Occurs in all living
plants in light.
light.
organisms in light
2) The primary substrate
and dark.
2) Substrate is CO₂ and H₂O.
is glycolate formed
2) Substrates are
from RuBP.
carbohydrates, fat
3) Occurs in most of the
and proteins.
3)
Occurs
in
all
green
plants.
3) Occurs in all living
C₃ plants.
4)
Occurs
in
chloroplasts.
organisms.
4) Intracellularaly, the
4) Occurs in cytosol
process occurs in
and mitochondria.
peroxisomes in
5) The process
association with
chloroplasts and
saturates at 2-3%
mitochondria.
5) The process is inhibited
O₂ in the
5) The process increase
with increasing
with increasing
concentration of O₂.
atmosphere and
concentration of O₂
beyond this conc.
and decreasing
concentration of CO₂.
Virtuallyno
6) Hydrogen peroxide is
6) H₂O is not formed.
increase occurs.
formed during this
process.
6) H₂O ₂ is not
7) Phosphorylation does
7) Photophosphorylation
formed.
not occur.
occurs.
7) Oxidative
phosphorylation
occurs.
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The Endoplasmic Reticulum
The endoplasmic reticulum (ER) is a system of membrane-enclosed sacs and
tubules in the cell. Their lumens are probably all interconnected, and their
membranes are continuous with the outer membrane of the nuclear envelope. All
the materials within the system are separated from the cytosol by a membrane. The
ER discovered by first Porter, Cluade and Fullman in 1945 as network. It was
named by Porter in 1953.
Physical Structure:
1. Cisternae: These are flattened, unbranched, sac-like elements. They lie in
stacks (piles) parallel to one another. The sacs in the stack are interconnected
with one another. They bear ribosomes on the surface that, therefore,
appears rough. The cisternae contain glycoproteins named ribophorin-I and
ribophorin-II that bind the ribosomes. There are cytosolic spaces between
the cisternae.
2. Tubules: These are irregular branching elements which form a network
along with other elements. They are often free of ribosomes.
3. Vesicles: These are oval or rounded, vacuole-like elements. They often
occur isolated in tee cytoplasmic matrix. They are also free of ribosomes.
Molecular Structure:
The endoplasmic reticulum is of two types:
The Rough Endoplasmic Reticulum (RER)
The RER is typically arranged as interconnecting stacks of
disc-like sacs. The cytosolic surface of the RER is studded
with ribosomes engaged in protein synthesis.
As the messenger RNA is translated by the ribosome, the
growing polypeptide chain is inserted into the membrane of
the RER.

Proteins destined to be secreted by the cell or shipped
into the lumen of certain other organelles like the
Golgi apparatus and lysosomes pass all the way
through into the lumen of the RER.
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Biology book (written by Umesh kumar

Transmembrane proteins destined for the plasma membrane or the
membrane of those organelles are retained within the membrane of the RER.
In either case, the portion of the protein within the lumen of the RER is subject to
extensive glycosylation (primarily N-linked).
This electron micrograph (courtesy of Keith Porter) shows the RER in a bat
pancreas cell. The clearer areas are the lumens.
The RER takes up a large proportion of the cytoplasm of cells specialized for
protein synthesis such as


cells secreting digestive enzymes (e.g. the pancreas cell above);
antibody-secreting plasma cells.
The Smooth Endoplasmic Reticulum (SER)
The SER differs from the RER in lacking attached ribosomes and usually being
tubular rather than disc-like.
A major function of the SER is the synthesis of lipids


from which various cell membranes are made or which,
like steroids, are secreted from the cell.
The SER represents only a small portion of the ER is most cells, e.g. serving as
transport vesicles for the transport of protein to the Golgi apparatus.
However, it is a prominent constituent of some cells. Examples:



the cells of the adrenal cortex (which secrete steroid hormones);
the cells of the liver (hepatocytes) where it synthesis lipids for secretion of
lipoproteins.
The sarcoplasmic reticulum of muscle cells is SER.
Origin:
The ER appears to arise from the outer membrane of the nuclear envelope by
outfolding or from the plasma membrane by infolding or from the preexisting ER.
The smooth ER seems to arise from the rough ER by detachment of ribosomes.
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Biology book (written by Umesh kumar
Functions:
(a) Common Functions of SER and RER
(1) Transport of Materials: The Facilitates transport of materials from one
part of the cell to another, thus forming the cell’s circulatory system.
(2) Formation of Desmotubules: Tabular ER extensions, called
desmotubues, extend through the plasmodesmata to make ER continuous
in the two adjacent plant cells.
(3) Support: The ER acts as an intracellular supporting framework, the
cytoskeleton that also maintains the form of the cells.
(4) Localization of Organelles: It keeps the cell organelles properly
stationed and distributed in relation to one another.
(5) Surface for Synthesis: The ER offer extensive surface for synthesis of a
variety of materials.
(6) Location of Enzymes: The ER membranes contain a variety of enzymes
(ATPase, dehydrogenases, phosphatases, etc) to catalyse synthetic
activites.
(7) Storage of Materials: The ER provides space for temporary storage of
synthetic products such as glycogen.
(8) Exchange of Materials: The ER helps in the exchange of materials
between the cytoplasm and the nucleus.
(9) Muscle Contraction: Sarcoplasmic reticulum helps in muscle
contraction by regulating Ca++ ions concentration in the sarcoplasm.
(b) Functions of RER
(1) Surface for Ribosomes: The RER provides space and ribophorins for
the attachment of ribosomes to itself.
(2) Surface for Protein Synthesis: The RER offers extensive surface on
which protein synthesis can be conventiently carried by ribosomes.
(3) Packaging: The proteins formed on ribosomes pass into the ER lumen
where they are modified. For example, they may be phosphorylated or
converted into glycoproteins. Then the modified proteins move on into
the transitional area, where the buds off membranous sacs, the transport
vesicles, carrying the proteins to the golgi apparatus. Here, they are
further processed and packaged into secretory vesicles for export by
exocytosis at the plasma membrane.
(4) SER formation: The RER gives rise to the smooth ER by loss of
ribosomes.
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Biology book (written by Umesh kumar
(5) Formation of Glycoproteins: Linking of sugars to proteins to form
glycoproteins starts in the RER and is completed in Golgi complex.
(6) Synthesis of Enzyme Precursors: The RER produces enzyme
precursors for the formation of lysosomes by Golgi complex .
(7) Membrane Formation: Enzymes of ER use substrates from cytosol to
form new phospholiplds. The latter may be inserted into the ER
membrane for its growth. Parts of ER can pinch off as vesicles which
may fuse with the membranes of other organelles, such as golgi
apparatus.
(c) Function of SER
(1) Surface for Synthesis: The SER provides surface for the synthesis of
lipids, including phospholipids, cholesterol, steroid hormones etc.
(2) Glycogen Metabolism: The SER carries enzyme bodies, the
glycosomes, for glycogen metabolism in the liver cells.
(3) Detoxification: The SER bring about detoxification in the liver, i.e.
converts harmful materials into harmless ones for excretion by the cell.
(4) Formation of Organelles: The SER produces Golgi apparatus,
lysosomes and vacuoles.
(5) Transport Route: Proteins shift from RER through SER to Golgi
complex for further processing.
Difference between RER and SER
Sr.
no.
RER
SER
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Biology book (written by Umesh kumar
1.
Consists mainly of cisternae.
2.
Bear ribosomes on its cytoplasmic
surface.
Free of ribosomes.
Usually lies deep in the cytoplasm.
Usually lies near the cell membrane.
Takes part in the synthesis of
proteins.
Takes part in the synthesis of lipids,
steroids, glycogen.
Arises from the RER by detachment of
ribosomes.
Give rise to golgi apparatus, lysosomes
and vacuoles.
Ribophorins are lacking.
Consists of mainly of tubules and
vesicles.
3.
4.
5.
6.
7.
Arises form the nuclear envelope by
outfolding.
Give rise to SER.
Contains Ribophorins for binding
ribosomes
Golgi apparatus
Micrograph of Golgi apparatus, visible as a stack of semicircular black rings near
the bottom. Numerous circular vesicles can be seen in proximity to the organelle
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Biology book (written by Umesh kumar
Diagram of secretory process from endoplasmic reticulum (orange) to Golgi
apparatus (pink).
1. Nuclear membrane; 2. Nuclear pore; 3. Rough endoplasmic reticulum
(RER); 4. Smooth endoplasmic reticulum (SER); 5. Ribosome attached to
RER; 6. Macromolecules; 7. Transport vesicles; 8. Golgi apparatus; 9. Cis
face of Golgi apparatus; 10. Trans face of Golgi apparatus; 11. Cisternae of
lipids
The (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,
after whom the Golgi apparatus is named.
Structure
Found in both plant and animal cells, the Golgi is composed of stacks of
membrane-bound structures known as cisternae (singular: cisterna). An individual
stack is sometimes called a dictyosome 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 flat, membrane enclosed disc that includes special Golgi
enzymes which modify or help to modify cargo proteins that travel through it.
The cisternae stack has four functional regions: the cis-Golgi network, medialGolgi, endo-Golgi, and trans-Golgi network. Vesicles from the endoplasmic
reticulum (via the vesicular-tubular 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.
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The Golgi apparatus is a cell structure
mainly devoted to processing the proteins
synthesized in the endoplasmic
reticulum (ER).







Some of these will eventually end
up as integral membrane proteins
embedded in the plasma
membrane.
Other proteins moving through the
Golgi will end up in lysosomes
or be secreted by exocytosis (e.g.,
digestive enzymes).
The major processing activity is
In this cell (from a bat), the Golgi apparatus
glycosylation: the adding of sugar (boxed in red) is used for the final stages in the
molecules to form glycoproteins. synthesis of proteins that are to be secreted
In some cells, e.g., mucus-secreting from the cell. (Courtesy of Keith R. Porter.)
cells in epithelia, the amount of carbohydrate so far exceeds that of the
protein that the product is called a mucopolysaccharide (also known as a
proteoglycan).
In plant cells, the Golgi secretes the cell plate and cell wall.
Small peptides, e.g., some hormones and neurotransmitters, are too small
to be synthesized directly by ribosomes. Instead, the ribosomes on the ER
synthesize a large precursor protein that is later cut up into small peptide
fragments as it traverses the Golgi.
Example: proopiomelanocortin (POMC) — a polypeptide of 265 amino
acids from which is cut
o
o
o
o
ACTH
alpha and beta MSH
beta-endorphin
and others.
The Golgi consists of a stack of membrane-bounded cisternae located between the
endoplasmic reticulum and the cell surface.
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Many different enzymes (proteins) are
present in the Golgi to perform its
various synthetic activities. So there must
be mechanisms


to sort out the processed proteins
and send them on to their
destinations while
reclaiming processing proteins
(e.g., glycosylases) for reuse.
The Outbound Path








Transition vesicles pinch off from
the surface of the endoplasmic
reticulum carrying
o integral membrane proteins
o soluble proteins awaiting
processing
o processing enzymes
Pinching off requires that the vesicle be coated with COPII (Coat Protein
II)
The transition vesicles move toward the cis Golgi on microtubules.
As they do so, their COPII coat is removed and they may fuse together
forming larger vesicles.
These fuse with the cis Golgi
Sugars are added to proteins in small packets so many glycoproteins have to
undergo a large number of sequential steps of glycosylation, each requiring
its own enzymes.
These steps take place as shuttle vesicles carry the proteins from cis to
medial to the trans Golgi compartments.
At the outer face of the trans Golgi, vesicles pinch off and carry their
completed products to their various destinations.
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The Inbound Path
The movement of cisternal contents through the stack means that essential
processing enzymes are also moving away from their proper site of action.
Using a variety of signals, the Golgi separates the products from the processing
enzymes that made them and returns the enzymes back to the endoplasmic
reticulum.
This transport is also done by pinching off vesicles, but the inbound vesicles are
coated with COPI (coat protein I)
How does a vesicle recognize its correct target?
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Biology book (written by Umesh kumar
This involves pairs of complementary integral
membrane proteins


v-SNAREs = "vesicle SNAREs" — on
the vesicle surface;
t-SNAREs = "target SNAREs" — on the
surface of the target membrane.
V-SNAREs and t-SNAREs bind specifically to
each other to the complementary structure of
their surface domains.
Binding is followed by fusion of the two membranes.
Other mechanisms of Golgi traffic?
There is evidence (in yeast) that in addition to the pinching off and fusing of
shuttle vesicles, the cisternae of the Golgi actually migrate themselves; that is, the
cis Golgi gradually migrates up the stack becoming a medial and finally a trans
Golgi
In mammalian cells, there is evidence that all the cisternae are interconnected so
that cargo to be processed can flow easily through the system without the need to
pinch of migrating vesicles.
Function of cisternea in more view
Type
Description
Example
Vesicle contains proteins destined for
extracellular release. After packaging the
Antibody release by
Exocytotic vesicles bud off and immediately move
towards the plasma membrane, where they
activated plasma B
vesicles
cells
(continuous) fuse and release the contents into the
extracellular space in a process known as
constitutive secretion.
Vesicle contains proteins destined for
Neurotransmitter
Secretory extracellular release. After packaging, the
vesicles bud off and are stored in the cell until release from
vesicles
(regulated) a signal is given for their release. When the neurons
appropriate signal is received they move
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Lysosomal
vesicles
towards the membrane and fuse 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
proteins include both digestive enzymes and destined for the
membrane proteins. The vesicle first fuses
lysosome
with the late endosome, and the contents are
then transferred to the lysosome via unknown
mechanisms.
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Lysosome
Lysosomes are cellular organelles that contain acid hydrolase enzymes to break
up waste materials and cellular debris. They are found in animal cells, while in
yeast and plants the same roles are performed by lytic vacuoles. Lysosomes digest
excess or worn-out organelles, food particles, and engulfed viruses or bacteria.
The membrane around a lysosome allows the digestive enzymes to work at the
4.5 pH they require. Lysosomes fuse with vacuoles and dispense their enzymes
into the vacuoles, digesting their contents. They are created by the addition
of hydrolytic enzymes to early endosomes from the Golgi apparatus. Lysosomes
were discovered by the Belgian cytologist Christian de Duve in the 1950s.
The size of lysosomes varies from 0.1–1.2 μm. At pH 4.8, the interior of the
lysosomes is acidic compared to the slightly alkaline cytosol (pH 7.2). The
lysosome maintains this pH differential by pumping protons (H+ ions) from the
cytosol across the membrane via proton pumps and chloride ion channels. The
lysosomal membrane protects the cytosol, and therefore the rest of the cell, from
the degradative enzymes within the lysosome. The cell is additionally protected
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from any lysosomal acid hydrolases that leak into the cytosol, as these enzymes are
pH-sensitive and do not function as well in the alkaline environment of the cytosol.
Enzymes
Some important enzymes found within lysosomes include:





Lipase, which digests lipids
Amylase, which digests amylose, starch, and maltodextrins
Proteases, which digest proteins
Nucleases, which digest nucleic acids
Phosphoric acid monoesters.
Lysosomal enzymes are synthesized in the cytosol and the endoplasmic reticulum,
where they receive a mannose-6-phosphate tag that targets them for the lysosome .
Aberrant lysosomal targeting causes inclusion-cell disease, whereby enzymes do
not properly reach the lysosome, resulting in accumulation of waste within these
organelles.
Types of lysosomes
(1)
Primary Lysosomes: A newly formed lysosomes contained enzymes
only. It is called the primary lysosomes. Its enzymes are probably in an inactive state.
(2)
Secondary Lysosomes: When some material to be digested enters a
primary lysosomes, the latter is named the secondary lysosomes,or phagolysosomes or
digestive vacuole, or heterophagosomes. This commonly occurs by fusion of a primary
lysosomes with a vacuole or a secretory granule.
(3)
Residual Bodies: In a secondary lysosomes, the enzymes digest the
incoming materials. The products of digestion pass through the lysosomes membranes
into the cytoplasmic matrix for use as a source of nutrition or energy. Indigestible matter
remains in the secondary lysosomes. A secondary lysosomes containing indigestible
matter is known as the residual bodies or tertiary lysosomes.
(4)
Autophagic Vacuoles: A cell may digest its own organelles, such a
mitochondria and ER. This process is called autophagy, or autolysis.Primary lysosomes
fuse together about the damaged or unwanted organelles, forming a large sac known as
autolyphagic vacuole or autophagosomes or autolysosomes.
Origin: Lysosomes arise from the Golgi complex. Their membrane and
hydrolytic enzymes are synthesized on the rough ER and are transported in
transport vesicles to the Golgi complex for modification and packaging. Secretory
vesicles filled with lysosomal enzymes bud off from the trans face of the Golgi
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complex as primary lysosomes. Proteins of the inner surface of the lysosomes
membrane escape enzymatic breakdown probably by having three- dimension
conformations that protect the vulnerable bonds from enzyme attack.
Adverse role of lysosomes: Lysosomes may prove harmful too. Retention of
residual bodies can cause diseases and ageing. The lysosomes, by releasing
nucleases, may cause mutations and breakage of chromosomes. This may lead to
blood cancer.
Functions
Lysosomes are the cell's waste disposal system and can break up anything. They
digest almost everything. They are used for the digestion of macromolecules from
phagocytosis (ingestion of other dying cells or larger extracellular material, like
foreign invading microbes), endocytosis (where receptor proteins are recycled
from the cell surface), and autophagy (where in old or unneeded organelles or
proteins, or microbes that have invaded the cytoplasm are delivered to the
lysosome). Autophagy may also lead to autophagic cell death, a form of
programmed self-destruction, or autolysis, of the cell, which means that the cell is
digesting itself.
Other functions include digesting foreign bacteria (or other forms of waste) that
invade a cell and helping repair damage to the plasma membrane by serving as a
membrane patch, sealing the wound.
Glyoxysome
Glyoxysomes are specialized peroxisomes found in plants (particularly in the fat
storage tissues of germinating seeds) and also in filamentous fungi. As in all
peroxisomes, in glyoxysomes the fatty acids are hydrolyzed to acetyl-CoA by
peroxisomal β-oxidation enzymes. Besides peroxisomal functions, glyoxysomes
possess additionally the key enzymes of glyoxylate cycle (isocitrate lyase and
malate synthase) which accomplish the glyoxylate cycle bypass.
Thus, glyoxysomes (as all peroxisomes) contain enzymes that initiate the
breakdown of fatty acids and additionally possess the enzymes to produce
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intermediate products for the synthesis of sugars by gluconeogenesis. The seedling
uses these sugars synthesized from fats until it is mature enough to produce them
by photosynthesis.
Peroxisome
Peroxisomes (also called microbodies) are organelles found in virtually all
eukaryotic cells. They are involved in the catabolism of very long chain fatty acids,
branched chain fatty acids, D-amino acids, polyamines, and biosynthesis of
plasmalogens, etherphospholipids critical for the normal function of mammalian
brains and lungs. They also contain approximately 10% of the total activity of two
enzymes in the pentose phosphate pathway, which is important for energy
metabolism. It is rigorously debated if peroxisomes are involved in isoprenoid and
cholesterol synthesis in animals. Other known peroxisomal functions include the
glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves,
glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation
and assimilation in some yeasts.
Metabolic functions
A major function of the peroxisome is the breakdown of very long chain fatty acids
through beta-oxidation. In animal cells, the very long fatty acids are converted to
medium chain fatty acids, which are subsequently shuttled to mitochondria where
they are eventually broken down to carbon dioxide and water. In yeast and plant
cells, this process is exclusive for the peroxisome.
The first reactions in the formation of plasmalogen in animal cells also occur in
peroxisomes. Plasmalogen is the most abundant phospholipid in myelin.
Deficiency of plasmalogens causes profound abnormalities in the myelination of
nerve cells, which is one reason why many peroxisomal disorders affect the
nervous system. Peroxisomes also play a role in the production of bile acids
important for the absorption of fats and fat-soluble vitamins, such as vitamin K.
Peroxisomes contain oxidative enzymes, such as catalase, D-amino acid oxidase,
and uric acid oxidase. However the last enzyme is absent in humans, explaining
the disease known as gout, caused by the accumulation of uric acid. Certain
enzymes within the peroxisome, by using molecular oxygen, remove hydrogen
atoms from specific organic substrates (labeled as R), in an oxidative reaction,
producing hydrogen peroxide (H2O2, itself toxic):
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Catalase, another peroxisomal enzyme, uses this H2O2 to oxidize other substrates,
including phenols, formic acid, formaldehyde, and alcohol, by means of the
peroxidation reaction:
, thus eliminating the poisonous hydrogen peroxide
in the process.
This reaction is important in liver and kidney cells, where the peroxisomes
detoxify various toxic substances that enter the blood. About 25% of the ethanol
humans drink is oxidized to acetaldehyde in this way. In addition, when excess
H2O2 accumulates in the cell, catalase converts it to H2O through this reaction:
In higher plants, peroxisomes contain also a complex battery of antioxidative
enzymes such as superoxide dismutase, the components of the ascorbateglutathione cycle, and the NADP-dehydrogenases of the pentose-phosphate
pathway. It has been demonstrated the generation of superoxide (O2•-) and nitric
oxide (•NO) radicals.
The peroxisome of plant cells is polarised when fighting fungal penetration.
Infection causes a glucosinolate molecule to play an antifungal role to be made and
delivered to the outside of the cell through the action of the peroxisomal proteins
(PEN2 and PEN3).
The Nucle
The Nuclear Envelope
The nucleus is enveloped by a pair of membranes enclosing a lumen that is
continuous with that of the endoplasmic reticulum. The inner membrane is
stabilized by a intermediate filament proteins called lamins.
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The nuclear envelope is perforated by thousands of nuclear pore complexes
(NPCs) that control the passage of molecules in and out of the nucleus.
Chromatin
The nucleus contains the chromosomes of the cell. Each chromosome consists of a
single molecule of DNA complexed with an equal mass of proteins. Collectively,
the DNA of the nucleus with its associated proteins is called chromatin.
Most of the protein consists of multiple copies of 5 kinds of histones. These are
basic proteins, bristling with positively charged arginine and lysine residues. (Both
Arg and Lys have a free amino group on their R group, which attracts protons (H+)
giving them a positive charge.) Just the choice of amino acids you would make to
bind tightly to the negatively-charged phosphate groups of DNA.
Chromatin also contains small amounts of a wide variety of nonhistone proteins.
Most of these are transcription factors (e.g., the steroid receptors) and their
association with the DNA is more transient.
The image running down on the left shows the 5 histones separated by
electrophoresis. These 5 proteins vary little from one cell type to another or even
from one species to another. However, the many nonhistone proteins in chromatin
(shown on the right) do vary from one cell type to another and from one species to
another.
Nucleosomes
Two copies of each of four
kinds of histones




H2A
H2B
H3 and
H4
form a core of protein, the nucleosome core. Around this is wrapped about 147
base pairs of DNA.
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From 20–60 bp of DNA link one nucleosome to the next. Each linker region is
occupied by a single molecule of histone 1 (H1). This region is longer (50–150 bp)
adjacent to the promoters of genes which presumably makes more room for the
binding of transcription factors.
The binding of histones to DNA does not depend on particular nucleotide
sequences in the DNA but does depend critically on the amino acid sequence of the
histone. Histones are some of the most conserved molecules during the course of
evolution. Histone H4 in the calf differs from H4 in the pea plant at only 2 amino
acids residues in the chain of 102.
This electron micrograph shows
chromatin from the nucleus of a
chicken red blood cell (birds, unlike
most mammals, retain the nucleus in
their mature red blood cells). The
arrows point to the nucleosomes. You
can see why the arrangement of
nucleosomes has been likened to "beads
on a string".
The formation of nucleosomes helps
somewhat, but not nearly enough, to
make the DNA sufficiently compact to
fit in the nucleus. In order to fit 46 DNA molecules (in humans), totaling over 2
meters in length, into a nucleus that may be only 10 µm across requires more
extensive folding and compaction.


Interactions between the exposed "tails" of the core histones causes
nucleosomes to associate into a compact fiber 30 nm in diameter.
These fibers are then folded into more complex structures whose precise
configuration is uncertain and which probably changes with the level of
activity of the genes in the region.
Histone Modifications
Although their amino acid sequence (primary structure) is unvarying, individual
histone molecules do vary in structure as a result of chemical modifications that
occur later to individual amino acids.
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These include adding:



acetyl groups (CH3CO−) to lysines
phosphate groups to serines and threonines
methyl groups to lysines and arginines
Although 75–80% of the histone molecule is incorporated in the core, the
remainder — at the N-terminal — dangles out from the core as a "tail".
The chemical modifications occur on these tails, especially of H3 and H4. Most of
theses changes are reversible. For example, acetyl groups are


added by enzymes called histone acetyltransferases (HATs)(not to be
confused with the "HAT" medium used to make monoclonal antibodies!)
and
Removed by histone deacetylases (HDACs).
More often than not, acetylation of histone tails occurs in regions of chromatin
that become active in gene transcription. This makes a kind of intuitive sense as
adding acetyl groups neutralizes the positive charges on Lys thus reducing the
strength of the association between the highly-negative DNA and the highlypositive histones.
Histone Variants

We have genes for 8 different varieties of histone 1 (H1). Which variety is
found at a particular linker depends on such factors as
o the type of cell,
o where it is in the cell cycle, and
o its stage of differentiation.
In some cases, at least, a particular variant of H1 associates with certain
transcription factors to bind to the enhancer of specific genes turning off
expression of those genes.

Some other examples of histone variants:
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o
o
o
H3 is replaced by CENP-A ("centromere protein A") at the
nucleosomes near centromeres. Failure to substitute CENP-A for H3
in this regions blocks centromere structure and function.
H2A is replaced by the variant H2A.Z at gene promoters.
All the "standard" histones are replaced by variants as sperm
develop.
In general, the "standard" histones are incorporated into the nucleosomes as new
DNA is synthesized during S phase of the cell cycle. Later, some are replaced by
variant histones as conditions in the cell dictate.
Chromosome Territories
During interphase, little can be seen of chromatin structure (except for special
cases like the polytene chromosomes of Drosophila and some other flies).
Although each chromosome is greatly elongated, it tends to occupy a discrete
region within the nucleus called its territory. This can be demonstrated by:


directing a tiny laser beam at a small portion of the nucleus. If all the
chromosomes were intertwined, one would expect that all would receive
some damage. That does not occur — only one or two chromosomes are
damaged.
Fluorescent stains specific for a particular chromosome stain only two
regions in the nucleus — revealing the territory of the two homologs.
"Kissing" Chromosomes
Portions of one chromosome can loop out of its territory and interact with part of a
different chromosome looping out from its territory. These are "kissing"
chromosomes.
The examples that have been found so far indicate that these interactions are
another way of coordinating the activity of genes residing on different
chromosomes.
Example:
The human genome contains many genes — scattered along different
chromosomes — that are turned on by the arrival of a single signal. Among the
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many genes activated by estrogen, are TIFF1 on chromosome 21 and GREB1 on
chromosome 2. Using FISH analysis, researchers at the University of California in
San Diego showed that within a little as 2 minutes after exposing cells to estrogen,
the TIFF1 and GREB1 loci move from their respective chromosome territories and
"kiss".
Another example:
In the head region of the Drosophila larva, expression of the homeobox (HOX)
genes Antp and Abd-B is shut down. FISH analysis shows that these two loci —
10,000,000 base pairs apart on chromosome III — are brought together in the
nucleus bound by proteins that prevent their transcription.
And still another example:
In the mouse, naive helper T cells — awaiting a signal to direct them to become
either Th1 cells or Th2 cells — have


the part of chromosome 10 carrying the gene for interferon-gamma (a Th1
cytokine) kissing
the part of chromosome 11 carrying the genes for IL-4 and IL-5 (Th2
cytokines).
When the cell receives the signals committing it to one path or the other, the two
regions separate, the appropriate one going to a region of active transcription; the
other to a region of heterochromatin.
Euchromatin versus Heterochromatin
The density of the chromatin that makes up each chromosome (that is, how tightly
it is packed) varies along the length of the chromosome.


dense regions are called heterochromatin
less dense regions are called euchromatin.
Heterochromatin

is found in parts of the chromosome where there are few or no genes, such
as
o centromeres and
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telomeres
is densely-packed;
is greatly enriched with transposons and other "junk" DNA;
is replicated late in S phase of the cell cycle;
has reduced crossing over in meiosis.
Those genes present in heterochromatin are generally inactive; that is, not
transcribed and show increased methylation of the cytosines in CpG islands
of the gene's promoter(s) [Link];
The histones in the nucleosomes of heterochromatin show characteristic
modifications:
o decreased acetylation;
o increased methylation of lysine-9 in histone H3 (H3K9), which now
provides a binding site for heterochromatin protein 1 (HP1), which
blocks access by the transcription factors needed for gene
transcription.
o increased methylation of lysine-27 in histone H3 (H3K27).
o






Euchromatin





is found in parts of the chromosome that
contain many genes;
is loosely-packed in loops of 30-nm fibers.
These are separated from adjacent
heterochromatin by insulators.
In yeast, the loops are often found near
the nuclear pore complexes. However, in
animal cells, active gene transcription
occurs near the center of the nucleus and appears to be repressed
(heterochromatin) near the inner surface of the nuclear envelope.
The genes in euchromatin are active and show
o decreased methylation of the cytosines in CpG islands of the gene's
promoter(s) [Link];
o increased acetylation of nearby histones and
o decreased methylation of lysine-9 and lysine-27 in histone H3.
The diagram represents a hypothetical model of how euchromatin and
heterochromatin may be organized during interphase in a yeast cell (but not in an
animal cell).
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Nucleosomes and Transcription
Transcription factors cannot bind to their promoter if the promoter is blocked by a
nucleosome. One of the first functions of the assembling transcription factors is to
either expel the nucleosome from the site where transcription begins or at least to
slide the nucleosomes along the DNA molecule. Either action exposes the gene's
promoter so that the transcription factors can then bind to it.
The actual transcription of protein-coding genes is done by RNA polymerase II
(RNAP II). In order for it to travel along the DNA to be transcribed, a complex of
proteins removes the nucleosomes in front of it and then replaces them after RNAP
II has transcribed that portion of DNA and moved on.
The Nucleolus
During the period between cell divisions, when the chromosomes are in their
extended state, one or more of them (10 in human cells) have loops extending into
a spherical mass called the nucleolus. Here are synthesized three (of the four) kinds
of RNA molecules (28S, 18S, 5.8S) used in the assembly of the large and small
subunits of ribosomes.
28S, 18S, and 5.8S ribosomal RNA is transcribed (by RNA polymerase I) from
hundreds to thousands of tandemly-arranged rDNA genes distributed (in humans)
on 10 different chromosomes. The rDNA-containing regions of these 10
chromosomes cluster together in the nucleolus.
(In yeast, the 5S rRNA molecules — as well as transfer RNA molecules — are also
synthesized (by RNA polymerase III) in the nucleolus.)
Once formed, rRNA molecules associate with the dozens of different ribosomal
proteins used in the assembly of the large and small subunits of the ribosome.
But proteins are synthesized in the cytosol — and all the ribosomes are needed in
the cytosol to do their work — so there must be a mechanism for the transport of
these large structures in and out of the nucleus. This is one of the functions of the
nuclear pore complexes.
Nuclear Pore Complexes (NPCs)
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The nuclear envelope is perforated with thousands of
pores.
Each is constructed from a number (30 in yeast;
probably around 50 in vertebrates) different proteins
called nucleoporins.
The entire assembly forms an aqueous channel
connecting the cytosol with the interior of the nucleus
("nucleoplasm"). When materials are to be transported through the pore, it opens
up to form a channel some 25 nm wide — large enough to get such large
assemblies as ribosomal subunits through.
Transport through the nuclear pore complexes is active; that is, it requires



energy
many different carrier molecules each specialized to transport a particular
cargo
docking molecules in the NPC (represented here as colored rods and disks).
Import into the nucleus
Proteins are synthesized in the cytosol and those needed by the nucleus must be
imported into it through the NPCs.
They include:




all the histones needed to make the nucleosomes
all the ribosomal proteins needed for the assembly of ribosomes
all the transcription factors (e.g., the steroid receptors) needed to turn
genes on (and off)
all the splicing factors needed to process pre-mRNA into mature mRNA
molecules; that is, to cut out intron regions and splice the exon regions.
Probably all of these proteins has a characteristic sequence of amino acids —
called a nuclear localization sequence (NLS) — that target them for entry.
Export from the nucleus
Molecules and macromolecular assemblies exported from the nucleus include:
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Biology book (written by Umesh kumar




the ribosomal subunits containing both rRNA and proteins
messenger RNA (mRNA) molecules (accompanied by proteins)
transfer RNA (tRNA) molecules (also accompanied by proteins)
transcription factors that are returned to the cytosol to await reuse
Both the RNA and protein molecules contain a characteristic nuclear export
sequence (NES) needed to ensure their association with the right carrier molecules
to take them out to the cytosol.
"Nucleoplasm"
The term "nucleoplasm" is still used to describe the contents of the nucleus.
However, the term disguises the structural complexity and order that we have
seen here exist within the nucleus.
Difference between Euchromatin and Heterochromatin
Euchromatin
1.It consists of thin, uncoiled, extended,
scattered
Chromatin fibres.
2. It forms the bulk of chromatin.
3. It occupies most of the nucleus.
4. It stains lightly.
5. Its genes are active.
6. It is transcribed.
7. It replicates early in S phase.
8. It permits crossing over.
Heterochromatin
1. It consists of thick, coiled,
compacted, localized
Chromatin fibres.
2. It forms a fraction of chromatin.
3. It lies close to the nuclear lamina.
4. It stains deeply.
5. Its genes are inactive.
6. It is not transcribed.
7. It replicates late in S phase.
8. It inhibits crossing over.
Difference between Chromatin and Chromosomes
Chromatin
Chromosomes
1. It is visible in the inter phase nucleus. 1. These are visible in the M phase.
2. It is extended, uncondensed form
2. They are coiled, condensed form of
RNA
deoxychain.
ribonucleoprotein chains.
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3. It appears as fine filaments lying
crisscross,
forming chromatin reticulum.
4. It controls metabolism.
5. Replication of DNA occurs in the
chromatin
phase.
3. thjese appear as short, thick, rod-like
organelles.
4. Chromosomes distribute genetic
information to the daughter cells.
5. Replication of DNA is suspended in
chromosomes phase.
Unit 4th Cell membrane and Cell wall
Cell membrane
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Illustration of a Eukaryotic cell membrane
The cell membrane is a biological membrane that separates the interior of all cells
from the outside environment.The cell membrane is selectively-permeable to ions
and organic molecules and controls the movement of substances in and out of cells.
It consists of the phospholipid bilayer with embedded proteins. Cell membranes
are involved in a variety of cellular processes such as cell adhesion, ion
conductivity and cell signaling and serve as the attachment surface for the
extracellular glycocalyx and cell wall and intracellular cytoskeleton.
Function
The cell membrane surrounds the protoplasm of a cell and, in animal cells,
physically separates the intracellular components from the extracellular
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environment. Fungi, bacteria and plants also have the cell wall which provides a
mechanical support for the cell and precludes passage of the larger molecules. The
cell membrane also plays a role in anchoring the cytoskeleton to provide shape to
the cell, and in attaching to the extracellular matrix and other cells to help group
cells together to form tissues.
.
Structure
Fluid mosaic model
According to the fluid mosaic model of S. J. Singer and Garth Nicolson 1972, the
biological membranes can be considered as a two-dimensional liquid where all
lipid and protein molecules diffuse more or less easily.This picture may be valid in
the space scale of 10 nm. However, the plasma membranes contain different
structures or domains that can be classified as: (a) protein-protein complexes; (b)
lipid rafts, and (c) pickets and fences formed by the actin-based cytoskeleton.
Danielli-Davson membrane modal(Lipid bilayer)
Diagram of the arrangement of amphipathic lipid molecules to form a lipid bilayer.
The yellow polar head groups separate the grey hydrophobic tails from the aqueous
cytosolic and extracellular environments.
Lipid bilayers go through a self assembly process in the formation of membranes.
The cell membrane consists primarily of a thin layer of amphipathic phospholipids
which spontaneously arrange so that the hydrophobic "tail" regions are shielded
from the surrounding polar fluid, causing the more hydrophilic "head" regions to
associate with the cytosolic and extracellular faces of the resulting bilayer. This
forms a continuous, spherical lipid bilayer. Forces such as Van der Waal,
electrostatic, hyrdogen bonds, and noncovalent interactions, are all forces that
contribute to the formation of the lipid bilayer. Overall, hydrophobic interactions
are the major driving force in the formation of lipid bilayers.
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Lipid bilayers have very low permeability for ions and most polar molecules.The
arrangement of hydrophilic heads and hydrophobic tails of the lipid bilayer prevent
polar solutes (e.g. amino acids, nucleic acids, carbohydrates, proteins, and ions)
from diffusing across the membrane, but generally allows for the passive diffusion
of hydrophobic molecules. This affords the cell the ability to control the movement
of these substances via transmembrane protein complexes such as pores and gates.
Flippases and Scramblases concentrate phosphatidyl serine, which carries a
negative charge, on the inner membrane. Along with NANA, this creates an extra
barrier to charged moieties moving through the membrane.
Membranes serve diverse functions in eukaryotic and prokaryotic cells. One
important role is to regulate the movement of materials into and out of cells. The
phospholipid bilayer structure (fluid mosaic model) with specific membrane
proteins accounts for the selective permeability of the membrane and passive and
active transport mechanisms. In addition, membranes in prokaryotes and in the
mitochondria and chloroplasts of eukaryotes facilitate the synthesis of ATP
through chemiosmosis.
Membrane polarity
Alpha intercalated cell
The apical membrane of a polarized cell is the surface of the plasma membrane
that faces the lumen. This is particularly evident in epithelial and endothelial cells,
but also describes other polarized cells, such as neurons.
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The basolateral membrane of a polarized cell is the surface of the plasma
membrane that forms its basal and lateral surfaces. It faces towards the
interstitium, and away from the lumen.
"Basolateral membrane" is a compound phrase referring to the terms basal (base)
membrane and lateral (side) membrane, which, especially in epithelial cells, are
identical in composition and activity. Proteins (such as ion channels and pumps)
are free to move from the basal to the lateral surface of the cell or vice versa in
accordance with the fluid mosaic model.
Tight junctions that join epithelial cells near their apical surface prevent the
migration of proteins from the basolateral membrane to the apical membrane. The
basal and lateral surfaces thus remain roughly equivalent to one another, yet
distinct from the apical surface.
Membrane proteins
Peripheral membrane proteins
Peripheral proteins are proteins that are bounded to the membrane by electrostatic
interactions and hydrogen bonding with the hydrophilic phospholipid heads. Many
of these proteins can be found bounded to the surfaces of integral proteins on either
the cytoplasimic side of the cell or the extracellular side of the membrane. Some
are anchored to the bilayer through covalent bond with a fatty acid.
Integral membrane proteins
The cell membrane contains many integral membrane proteins, which pepper the
entire surface. These structures, which can be visualized by electron microscopy or
fluorescence microscopy, can be found on the inside of the membrane, the outside,
or membrane spanning. These may include integrins, cadherins, desmosomes,
clathrin-coated pits, caveolaes, and different structures involved in cell adhesion.
Integral proteins are the most abundant type of protein to span the lipid bilayer.
They interact widely with hydrocarbon chains of membrane lipids and can be
released by agents that compete for same nonpolar interactions.
Composition
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Cell membranes contain a variety of biological molecules, notably lipids and
proteins. Material is incorporated into the membrane, or deleted from it, by a
variety of mechanisms:



Fusion of intracellular vesicles with the membrane (exocytosis) not only
excretes the contents of the vesicle but also incorporates the vesicle
membrane's components into the cell membrane. The membrane may form
blebs around extracellular material that pinch off to become vesicles
(endocytosis).
If a membrane is continuous with a tubular structure made of membrane
material, then material from the tube can be drawn into the membrane
continuously.
Although the concentration of membrane components in the aqueous phase
is low (stable membrane components have low solubility in water), there is
an exchange of molecules between the lipid and aqueous phases.
Lipids
Examples of the major membrane phospholipids and glycolipids:
phosphatidylcholine (PtdCho), phosphatidylethanolamine (PtdEtn),
phosphatidylinositol (PtdIns), phosphatidylserine (PtdSer).
The cell membrane consists of three classes of amphipathic lipids: phospholipids,
glycolipids, and cholesterols. The amount of each depends upon the type of cell,
but in the majority of cases phospholipids are the most abundant. In RBC studies,
30% of the plasma membrane is lipid.
The fatty chains in phospholipids and glycolipids usually contain an even number
of carbon atoms, typically between 16 and 20. The 16- and 18-carbon fatty acids
are the most common. Fatty acids may be saturated or unsaturated, with the
configuration of the double bonds nearly always cis. The length and the degree of
unsaturation of fatty acid chains have a profound effect on membrane fluidity as
unsaturated lipids create a kink, preventing the fatty acids from packing together as
tightly, thus decreasing the melting temperature (increasing the fluidity) of the
membrane. The ability of some organisms to regulate the fluidity of their cell
membranes by altering lipid composition is called homeoviscous adaptation.
The entire membrane is held together via non-covalent interaction of hydrophobic
tails, however the structure is quite fluid and not fixed rigidly in place. Under
physiological conditions phospholipid molecules in the cell membrane are in the
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liquid crystalline state. It means the lipid molecules are free to diffuse and exhibit
rapid lateral diffusion along the layer in which they are present. However, the
exchange of phospholipid molecules between intracellular and extracellular leaflets
of the bilayer is a very slow process. Lipid rafts and caveolae are examples of
cholesterol-enriched microdomains in the cell membrane.
In animal cells cholesterol is normally found dispersed in varying degrees
throughout cell membranes, in the irregular spaces between the hydrophobic tails
of the membrane lipids, where it confers a stiffening and strengthening effect on
the membrane.
Phospholipids forming lipid vesicles
Lipid vesicles or liposomes are circular pockets that are enclosed by a lipid bilayer.
These structures are used in laboratories to study the effects of chemicals in cells
by delivering these chemicals directly to the cell, as well as getting more insight
into cell membrane permeability. Lipid vesicles and liposomes are formed by first
suspending a lipid in an aqueous solution then agitating the mixture through
sonication, resulting in a uniformly circular vesicle. By measuring the rate of
efflux from that of the insideof the vesicle to the ambient solution, allows
researcher to better understand membrane permeability. Vesicles can be formed
with molecules and ions inside the vesicle by forming the vesicle with the desired
molecule or ion present in the solution. Proteins can also be embedded into the
membrane through solubilizing the desired proteins in the presence of detergents
and attaching them to the phospholipids in which the liposome is formed. These
provide researchers with a tool to examine various membrane protein functions.
Carbohydrates
Plasma membranes also contain carbohydrates, predominantly glycoproteins, but
with some glycolipids (cerebrosides and gangliosides). For the most part, no
glycosylation occurs on membranes within the cell; rather generally glycosylation
occurs on the extracellular surface of the plasma membrane.
The glycocalyx is an important feature in all cells, especially epithelia with
microvilli. Recent data suggest the glycocalyx participates in cell adhesion,
lymphocyte homing, and many others.
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The penultimate sugar is galactose and the terminal sugar is sialic acid, as the sugar
backbone is modified in the golgi apparatus. Sialic acid carries a negative charge,
providing an external barrier to charged particles.
Proteins
Proteins within the membrane are key to the functioning of the overall membrane.
These proteins mainly transport chemicals and information across the membrane.
Every membrane has a varying degree of protein content. Proteins can be in the
form of peripheral or integral.
Type
Description
Span the membrane and have a
hydrophilic cytosolic domain,
which interacts with internal
molecules, a hydrophobic
membrane-spanning domain that
Integral
anchors it within the cell
proteins
membrane, and a hydrophilic
or
extracellular domain that
transmembrane
interacts with external
proteins
molecules. The hydrophobic
domain consists of one,
multiple, or a combination of αhelices and β sheet protein
motifs.
Covalently-bound to single or
multiple lipid molecules;
Lipid anchored hydrophobically insert into the
proteins
cell membrane and anchor the
protein. The protein itself is not
in contact with the membrane.
Attached to integral membrane
proteins, or associated with
peripheral regions of the lipid
bilayer. These proteins tend to
Peripheral
have only temporary interactions
proteins
with biological membranes, and,
once reacted the molecule,
dissociates to carry on its work
in the cytoplasm.
Examples
Ion
channels,
proton
pumps, G
proteincoupled
receptor
G proteins
Some
enzymes,
some
hormones
The cell membrane plays host to a large amount of protein that is responsible for
its various activities. The amount of protein differs between species and according
to function, however the typical amount in a cell membrane is 50%.These proteins
are undoubtedly important to a cell: Approximately a third of the genes in yeast
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code specifically for them, and this number is even higher in multicellular
organisms.
The cell membrane, being exposed to the outside environment, is an important site
of cell-cell communication. As such, a large variety of protein receptors and
identification proteins, such as antigens, are present on the surface of the
membrane. Functions of membrane proteins can also include cell-cell contact,
surface recognition, cytoskeleton contact, signaling, enzymatic activity, or
transporting substances across the membrane.
Most membrane proteins must be inserted in some way into the membrane. For
this to occur, an N-terminus "signal sequence" of amino acids directs proteins to
the endoplasmic reticulum, which inserts the proteins into a lipid bilayer. Once
inserted, the proteins are then transported to their final destination in vesicles,
where the vesicle fuses with the target membrane.
Permeability
The permeability of a membrane is the ease of molecules to pass through it.
Permeability depends mainly on the electric charge of the molecule and to a lesser
extent the molar mass of the molecule. Electrically neutral and small molecules
pass the membrane easier than charged, large ones.
The inability of charged molecules to pass through the cell membrane results in pH
parturition of substances throughout the fluid compartments of the body.
Cell wall
The cell wall is the tough, usually flexible but sometimes fairly rigid layer that
surrounds some types of cells. It is located outside the cell membrane and provides
these cells with structural support and protection, and also acts as a filtering
mechanism. A major function of the cell wall is to act as a pressure vessel,
preventing over-expansion when water enters the cell. They are found in plants,
bacteria, fungi, algae, and some archaea. Animals and protozoa do not have cell
walls.
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The materials in a cell wall vary between species, and in plants and fungi also
differ between cell types and developmental stages. In plants, the strongest
component of the complex cell wall is a carbohydrate called cellulose, which is a
polymer of glucose. In bacteria, peptidoglycan forms the cell wall. Archaean cell
walls have various compositions, and may be formed of glycoprotein S-layers,
pseudopeptidoglycan, or polysaccharides. Fungi possess cell walls made of the
glucosamine polymer chitin, and algae typically possess walls made of
glycoproteins and polysaccharides. Unusually, diatoms have a cell wall composed
of silicic acid. Often, other accessory molecules are found anchored to the cell
wall.
Properties
The cell wall serves a similar purpose in those organisms that possess them. The
wall gives cells rigidity and strength, offering protection against mechanical stress.
In multicellular organisms, it permits the organism to build and hold its shape
(morphogenesis). The cell wall also limits the entry of large molecules that may be
toxic to the cell. It further permits the creation of a stable osmotic environment by
preventing osmotic lysis and helping to retain water. The composition, properties,
and form of the cell wall may change during the cell cycle and depend on growth
conditions.
Diagram of the plant cell, with the cell wall in green.
Rigidity of cell walls
The rigidity of the cell walls is often over-estimated. In most cells, the cell wall is
flexible, meaning that it will bend rather than holding a fixed shape, but has
considerable tensile strength. The apparent rigidity of primary plant tissues is
enabled by cell walls, but not due to the walls' strength. Hydraulic turgor pressure
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creates this rigidity, along with the wall structure. The flexibility of the cell walls is
seen when plants wilt, so that the stems and leaves begin to droop, or in seaweeds
that bend in water currents. As John Howland states it:
Think of the cell wall as a wicker basket in which a balloon has been inflated so
that it exerts pressure from the inside. Such a basket is very rigid and resistant to
mechanical damage. Thus does the prokaryote cell (and eukaryotic cell that
possesses a cell wall) gain strength from a flexible plasma membrane pressing
against a rigid cell wall.
The rigidity of the cell wall thus results in part from inflation of the cell contained.
This inflation is a result of the passive uptake of water.
In plants, a secondary cell wall is a thicker additional layer of cellulose which
increases wall rigidity. Additional layers may be formed containing lignin in xylem
cell walls, or containing suberin in cork cell walls. These compounds are rigid and
waterproof, making the secondary wall stiff. Both wood and bark cells of trees
have secondary walls. Other parts of plants such as the leaf stalk may acquire
similar reinforcement to resist the strain of physical forces.
Certain single-cell protists and algae also produce a rigid wall. Diatoms build a
frustule from silica extracted from the surrounding water; radiolarians also
produce a test from minerals. Many green algae, such as the Dasycladales encase
their cells in a secreted skeleton of calcium carbonate. In each case, the wall is
rigid and essentially inorganic.
Permeability
The primary cell wall of most plant cells is semi-permeable and permit the passage
of small molecules and small proteins, with size exclusion estimated to be 30-60
kDa. Key nutrients, especially water and carbon dioxide, are distributed throughout
the plant from cell wall to cell wall in apoplastic flow. The pH is an important
factor governing the transport of molecules through cell walls.
Plant cell walls
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Many plant cells have walls that are strong enough to withstand the osmotic
pressure from the difference in solute concentration between the cell interior and
distilled water.
Layers
Up to three strata or layers may be found in plant cell walls:



The middle lamella, a layer rich in pectins. This outermost layer forming
the interface between adjacent plant cells and glues them together.
The primary cell wall, generally a thin, flexible and extensible layer formed
while the cell is growing.
The secondary cell wall, a thick layer formed inside the primary cell wall
after the cell is fully grown. It is not found in all cell types. In some cells,
such as found xylem, the secondary wall contains lignin, which strengthens
and waterproofs the wall.
Composition
In the primary (growing) plant cell wall, the major carbohydrates 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. In grass cell walls, xyloglucan and pectin are reduced in abundance
and partially replaced by glucuronarabinoxylan, a hemicellulose. Primary cell
walls characteristically extend (grow) by a mechanism called acid growth, which
involves turgor-driven movement of the strong cellulose microfibrils within the
weaker hemicellulose/pectin matrix, catalyzed by expansin proteins. The outer part
of the primary cell wall of the plant epidermis is usually impregnated with cutin
and wax, forming a permeability barrier known as the plant cuticle.
Secondary cell walls contain a wide range of additional compounds that modify
their mechanical properties and permeability. The major polymers that make up
wood (largely secondary cell walls) include:



cellulose, 35-50%
xylan, 20-35%, a type of hemicellulose
lignin, 10-25%, a complex phenolic polymer that penetrates the spaces in the
cell wall between cellulose, hemicellulose and pectin components, driving
out water and strengthening the wall.
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Additionally, structural proteins (1-5%) are found in most plant cell walls; they are
classified as hydroxyproline-rich glycoproteins (HRGP), arabinogalactan proteins
(AGP), glycine-rich proteins (GRPs), and proline-rich proteins (PRPs). Each class
of glycoprotein is defined by a characteristic, highly repetitive protein sequence.
Most are glycosylated, contain hydroxyproline (Hyp) and become cross-linked in
the cell wall. These proteins are often concentrated in specialized cells and in cell
corners. Cell walls of the epidermis and endodermis may also contain suberin or
cutin, two polyester-like polymers that protect the cell from herbivores. The
relative composition of carbohydrates, secondary compounds and protein varies
between plants and between the cell type and age.
Plant cells walls also contain numerous enzymes, such as hydrolases, esterases,
peroxidases, and transglycosylases, that cut, trim and cross-link wall polymers.
The walls of cork cells in the bark of trees are impregnated with suberin, and
suberin also forms the permeability barrier in primary roots known as the
Casparian strip. Secondary walls - especially in grasses - may also contain
microscopic silica crystals, which may strengthen the wall and protect it from
herbivores.
Cell walls in some plant tissues also function as storage depots for carbohydrates
that can be broken down and resorbed to supply the metabolic and growth needs of
the plant. For example, endosperm cell walls in the seeds of cereal grasses,
nasturtium, and other species, are rich in glucans and other polysaccharides that are
readily digested by enzymes during seed germination to form simple sugars that
nourish the growing embryo. Cellulose microfibrils are not readily digested by
plants, however.
Formation
The middle lamella is laid down first, formed from the cell plate during
cytokinesis, and the primary cell wall is then deposited inside the middle lamella.
The actual structure of the cell wall is not clearly defined and several models exist
- the covalently linked cross model, the tether model, the diffuse layer model and
the stratified layer model. However, the primary cell wall, can be defined as
composed of cellulose microfibrils aligned at all angles. Microfibrils are held
together by hydrogen bonds to provide a high tensile strength. The cells are held
together and share the gelatinous membrane called the middle lamella, which
contains magnesium and calcium pectates (salts of pectic acid). Cells interact
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though plasmodesma(ta), which are inter-connecting channels of cytoplasm that
connect to the protoplasts of adjacent cells across the cell wall.
In some plants and cell types, after a maximum size or point in development has
been reached, a secondary wall is constructed between the plant cell and primary
wall. Unlike the primary wall, the microfibrils are aligned mostly in the same
direction, and with each additional layer the orientation changes slightly. Cells
with secondary cell walls are rigid. Cell to cell communication is possible through
pits in the secondary cell wall that allow plasmodesma to connect cells through the
secondary cell walls.
Fungal cell walls
There are several groups of organisms that may be called "fungi". Some of these
groups have been transferred out of the Kingdom Fungi, in part because of
fundamental biochemical differences in the composition of the cell wall. Most true
fungi have a cell wall consisting largely of chitin and other polysaccharides. True
fungi do not have cellulose in their cell walls, but some fungus-like organisms do.
True fungi
Not all species of fungi have cell walls but in those that do, the plasma membrane
is followed by three layers of cell wall material. From inside out these are:



a chitin layer (polymer consisting mainly of unbranched chains of N-acetylD-glucosamine)
a layer of β-1,3-glucan (zymosan)
a layer of mannoproteins (mannose-containing glycoproteins) which are
heavily glycosylated at the outside of the cell.
Fungus-like protists
The group Oomycetes, also known as water molds, are saprotrophic plant
pathogens like fungi. Until recently they were widely believed to be fungi, but
structural and molecular evidence has led to their reclassification as heterokonts,
related to autotrophic brown algae and diatoms. Unlike fungi, oomycetes typically
possess cell walls of cellulose and glucans rather than chitin, although some genera
(such as Achlya and Saprolegnia) do have chitin in their walls.The fraction of
cellulose in the walls is no more than 4 to 20%, far less than the fraction comprised
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by glucans.Oomycete cell walls also contain the amino acid hydroxyproline, which
is not found in fungal cell walls.
The dictyostelids are another group formerly classified among the fungi. They are
slime molds that feed as unicellular amoebae, but aggregate into a reproductive
stalk and sporangium under certain conditions. Cells of the reproductive stalk, as
well as the spores formed at the apex, possess a cellulose wall. The spore wall has
been shown to possess three layers, the middle of which is composed primarily of
cellulose, and the innermost is sensitive to cellulase and pronase.
Prokaryotic cell walls
Bacterial cell walls
Around the outside of the cell membrane is the bacterial cell wall. Bacterial cell
walls are made of peptidoglycan (also called murein), which is made from
polysaccharide chains cross-linked by unusual peptides containing D-amino acids.
Bacterial cell walls are different from the cell walls of plants and fungi which are
made of cellulose and chitin, respectively.Thecell wall of bacteria is also distinct
from that of Archaea, which do not contain peptidoglycan. The cell wall is
essential to the survival of many bacteria, although L-form bacteria can be
produced in the laboratory that lack a cell wall. The antibiotic penicillin is able to
kill bacteria by preventing the cross-linking of peptidoglycan and this causes the
cell wall to weaken and lyse.The lysozyme enzyme can also damage bacterial cell
walls.
There are broadly speaking two different types of cell wall in bacteria, called
Gram-positive and Gram-negative. The names originate from the reaction of cells
to the Gram stain, a test long-employed for the classification of bacterial species.
Gram-positive bacteria possess a thick cell wall containing many layers of
peptidoglycan and teichoic acids. In contrast, Gram-negative bacteria have a
relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a
second lipid membrane containing lipopolysaccharides and lipoproteins. Most
bacteria have the Gram-negative cell wall and only the Firmicutes and
Actinobacteria (previously known as the low G+C and high G+C Gram-positive
bacteria, respectively) have the alternative Gram-positive arrangement. These
differences in structure can produce differences in antibiotic susceptibility, for
instance vancomycin can kill only Gram-positive bacteria and is ineffective against
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Gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas
aeruginosa.
Diagram of a typical gram-negative bacterium, with the thin cell wall sandwiched
between the red outer membrane and the thin green plasma membrane
Schematic of typical gram-positive cell wall showing arrangement of NAcetylglucosamine and N-Acetlymuramic acid
Further information: Cell envelope
Archaeal cell walls
Although not truly unique, the cell walls of Archaea are unusual. Whereas
peptidoglycan is a standard component of all bacterial cell walls, all archaeal cell
walls lack peptidoglycan,[19] with the exception of one group of methanogens. In
that group, the peptidoglycan is a modified form very different from the kind found
in bacteria. There are four types of cell wall currently known among the Archaea.
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One type of archaeal cell wall is that composed of pseudopeptidoglycan (also
called pseudomurein). This type of wall is found in some methanogens, such as
Methanobacterium and Methanothermus. While the overall structure of archaeal
pseudopeptidoglycan superficially resembles that of bacterial peptidoglycan, there
are a number of significant chemical differences. Like the peptidoglycan found in
bacterial cell walls, pseudopeptidoglycan consists of polymer chains of glycan
cross-linked by short peptide connections. However, unlike peptidoglycan, the
sugar N-acetylmuramic acid is replaced by N-acetyltalosaminuronic acid, and the
two sugars are bonded with a β,1-3 glycosidic linkage instead of β,1-4.
Additionally, the cross-linking peptides are L-amino acids rather than D-amino
acids as they are in bacteria.
A second type of archaeal cell wall is found in Methanosarcina and Halococcus.
This type of cell wall is composed entirely of a thick layer of polysaccharides,
which may be sulfated in the case of Halococcus. Structure in this type of wall is
complex and as yet is not fully investigated.
A third type of wall among the Archaea consists of glycoprotein, and occurs in the
hyperthermophiles, Halobacterium, and some methanogens. In Halobacterium, the
proteins in the wall have a high content of acidic amino acids, giving the wall an
overall negative charge. The result is an unstable structure that is stabilized by the
presence of large quantities of positive sodium ions that neutralize the charge.
Consequently, Halobacterium thrives only under conditions with high salinity.
In other Archaea, such as Methanomicrobium and Desulfurococcus, the wall may
be composed only of surface-layer proteins, known as an S-layer. S-layers are
common in bacteria, where they serve as either the sole cell-wall component or an
outer layer in conjunction with polysaccharides. Most Archaea are Gram-negative,
though at least one Gram-positive member is known.
Difference between Primary and Secondary Cell Wall
1.
2.
3.
4.
5.
6.
Primary Cell Wall
It is formed in a growing cell.
It is lies internal to the middle lamella.
It is present in all plant cells.
It is elastic and capable of expansion in a
growing cell.
It grows in thickness by intussusceptions.
It consists of a single layer of wall
1.
2.
3.
4.
5.
6.
Secondary Cell Wall
It is formed in a mature cell.
It lies internal to the primary wall.
It is present in certain cells only.
It is rigid and incapable of
expansion.
It grows in thickness by accretion.
It consists of ir more layers of wall
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material.
7. It is 1-3 µm thick.
8. Its cellulose macrofibrills are short, wavy
loosely arranged.
9. It lacks pits.
10.It lacks additional materials.
11.It water content is about 60%.
12.It has relatively high hemicelluloses,
protein and lipid contents.
material.
7. It consists 5-10 µm thick.
8. It cellulose macrofibrills are long,
straight, compactly arranged.
9. It has pits at certain places.
10.It has additional materials such as
lignin, suberin.
11.Its water content is about 30-40%.
12.It has relatively low
hemicelluloses, protein and lipid
contents.
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