Sadava MSC

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UNIT - I
LESSON-1 CELL
Contents
1.0 Aims and Objectives
1.1 Introduction
1.2 Structure of Prokaryotic and Eukaryotic Cell
1.3 Let Us Sum Up
1.4 Points for Discussion
1.5 Check your Progress
1.6 Lesson End Activities
1.7 References
To know about the cell and its types, etc.
1.1. Introduction
A cell is a microscopic, structural and functional unit of living organisms capable of
independent existence (e.g. Amoeba). All living things are composed of cells. Some
functioning cells come together to form a tissue and tissues collectively form organs. In
more complex living organisms, organs work together for the purpose of survival as
system. However, in all living organisms, the cell is a functional unit and all of biology
revolves around the activity of the cell.
The study of cell is impossible without the microscope. The first simple microscope was
prepared by Anton Van Leewenhoek (1632-1723) who studied the structure of bacteria,
protozoa, spermatozoa, red blood cells etc. The word cell was first coined by Robert
Hooke in 1665 to designate the empty honey-comb like structures viewed in a thin
section of bottle cork which he examined. He was impressed by the microscopic
compartments in the cork as they reminded him of rooms in a monastery which are
known as cells. He therefore referred to the units as cells. In 1838, the German botanist
Matthios Schleiden proposed that all the plants are made up of plant cells. Then in 1839,
his colleague, the anatomist Theodore Schwann studied and concluded that all animals
are also composed of animal cells. Schwann and Schleiden studied a wide variety of plant
and animal tissues and proposed the "cell theory" in 1839. It stated that "all organisms are
composed of cells." But still the real nature of a cell was in doubt. Cell theory was again
rewritten by Rudolf Virchow in 1858 and said that all living things are made up of cells
and that all cells arise from pre-existing cells. It was German biologist Schulze who
found in 1861 that the cells are not empty as were seen by Hooke but contain a stuff of
life called protoplasm. During the 1950s scientists developed the concept that all
organisms may be classified as prokaryotes or eukaryotes. For example, in prokaryotic
cells, there is no nucleus; eukaryotic cells have a nucleus. Another important difference
between prokaryotes and eukaryotes is that the prokaryotic cell does not have any
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intracellular components. Bacteria and blue- green algae come under the prokaryotic
group, and
1.2 Structure of Prokaryotic and Eukaryotic Cell
Cells in our world come in two basic types, prokaryotic and eukaryotic. "Karyose" comes
from a Greek word which means "kernel," as in a kernel of grain. In biology, we use this
word root to refer to the nucleus of a cell. "Pro" means "before," and "eu" means "true,"
or "good." So "Prokaryotic" means "before a nucleus," and "eukaryotic" means
"possessing a true nucleus." This is a big hint about one of the differences between these
two cell types. Prokaryotic cells have no nuclei, while eukaryotic cells do have true
Fig. 1. Prokaryotic and Eukaryotic Cell

Nuclei: Despite their apparent differences, these two cell types have a lot in common.
They perform most of the same kinds of functions, and in the same ways. Both are
enclosed by plasma membranes, filled with cytoplasm, and loaded with small structures
called ribosome. Both have DNA which carries the archived instructions for operating the
cell. And the similarities go far beyond the visibility; for example, the DNA in the two
cell types is precisely the same kind of DNA, and the genetic code for a prokaryotic cell
is exactly the same genetic code used in eukaryotic cells. The difference is that the
prokaryotic cell has a cell wall which is absent in animal cells. However, many kinds of
eukaryotic cells do have cell walls. The size and complexity do exist. Eukaryotic cells are
much larger and much more complex than prokaryotic cells. These two observations are
not unrelated to each other.
If we take a closer look at the comparison of these cells, we see the following differences:
1.
Eukaryotic cells have a true nucleus, bound by a double membrane. Prokaryotic cells
have no nucleus. The purpose of the nucleus is to sequester the DNA-related functions
of the big eukaryotic cell into a smaller chamber, for the purpose of increased
efficiency. This function is unnecessary for the prokaryotic cell, because its much
smaller size means that all materials within the cell are relatively close together. Of
course, prokaryotic cells do have DNA and DNA functions. Biologists describe the
central region of the cell as its "nucleoid" (-oid=similar or imitating), because it's
pretty much where the DNA is located. But note that the nucleoid is essentially an
imaginary "structure." There is no physical boundary enclosing the nucleoid.
2.
Eukaryotic DNA is linear complexed with proteins called "histones," and is

organized into chromosomes; prokaryotic DNA is "naked," meaning that it has no
histones associated with it, and it is not formed into chromosomes. Though many are
sloppy about it, the term "chromosome" does not technically apply to anything in a
prokaryotic cell. A eukaryotic cell contains a number of chromosomes; a prokaryotic
cell contains only one circular DNA molecule (has no ends) and a varied assortment of
much smaller circlets of DNA called "plasmids." The smaller, simpler prokaryotic cell
requires far fewer genes to operate than the eukaryotic cell.
3.
Both cell types have many ribosomes, but the ribosomes of the eukaryotic cells are
larger and more complex than those of the prokaryotic cell. Ribosomes are made out
of a special class of RNA molecules (ribosomal RNA, or rRNA) and a specific
collection of different proteins. A eukaryotic ribosome is composed of five kinds of
rRNA and about eighty kinds of proteins. Prokaryotic ribosomes are composed of only
three kinds of rRNA and about fifty kinds of protein.
4.
The cytoplasm of eukaryotic cells is filled with a large, complex collection of

organelles, many of them enclosed in their own membranes; the prokaryotic cell
contains no membrane-bound organelles which are independent of the plasma
membrane. This is a very significant difference, and the source of the vast majority of
the greater complexity of the eukaryotic cell.
5. There is much more space within a eukaryotic cell than within a prokaryotic cell,
and many of these structures, like the nucleus, increase the efficiency of functions by
confining them within smaller spaces within the huge cell, or with communication and
movement within the cell.
6. One aspect of that evolutionary connection is particularly interesting within
eukaryotic cells by the presence of fascinating organelle called mitochondria. And in
plant cells, an additional family of organelles called plastids, the most famous of
which is the renowned chloroplast. Mitochondria (the plural of mitochondrion) and
chloroplasts almost certainly have a similar evolutionary origin. Both are pretty clearly
the descendants of independent prokaryotic cells, which have taken up permanent
residence within other cells through a well-known and very common phenomenon
called endosymbiosis.
7. One structure not shown in our prokaryotic cell is called a mesosome, which is an
elaboration of the plasma membrane-a sort of rosette of ruffled membrane intruding
into the cell and not all prokaryotic cells have these.
Fig. 2. Prokaryotic cell and Mitochondrion

Fig. 2 shows a trimmed down prokaryotic cell, including only the plasma membrane and
a couple of mesosomes. A mitochondrion is included for comparison. The similarities in
appearance between these structures are pretty clear. The mitochondrion is a doublemembrane organelle, with a smooth outer membrane and an inner membrane which
protrudes into the interior of the mitochondrion in folds called cristae. This membrane is
very similar in appearance to the prokaryotic plasma membrane with its mesosomes,
however not more significant than appearance. Both the mesosomes and the cristae are
used for the same function: the aerobic part of aerobic cellular respiration. Cellular
respiration is the process by which a cell converts the raw, potential energy of food into
biologically useful energy, and there are two general types, anaerobic (not using oxygen)
and aerobic (requiring oxygen). In practical terms, the big difference between the two is
that aerobic cellular respiration has a much higher energy yield than anaerobic
respiration. Aerobic respiration is clearly the evolutionary offspring of anaerobic
respiration. (In anaerobic respiration with additional chemical sequences added on to the
end of the process to allow utilization of oxygen).
Fig. 3. Prokaryotic and Eukaryotic cells

Protozoa, fungi, animals, and plants come under the eukaryotic group
1.3 Let Us Sum Up
All living things are composed of cells.

The word cell was first coined by Robert Hooke in 1665.
Cell is basically of two types prokaryotic and eukaryotic.
Cell in the basic unit of life Comment.

Write down the main features of a eukaryotic cell
Note: a) Please dont proceed till you attempt the above question.
b) The space given below is for your answer
1.6 Lesson-end activities

1) Define cell.
2) Write down the main differences between prokaryotic and eukaryotic cells
1.7 References
1. Lehinger, A.L. 1984, Principles of Biochemistry, CBS Publishers and distributors,
New Delhi, India.
2. Horton, Moran, Ochs, Rawn, Scrimgeour Principles of Biochemistry, Prentice Hall
Publishers.
3. Shanmughavel, P. 2005, Principles of Bioinformatics, Pointer Publishers, Jaipur, India.
4. David, E. Sadava Cell Biology: Organelle structure and Fucntion Jones & Bartlett
Publishers.
LESSON 2: Cell Organelles and Their Functions

Contents
2.1 Mitochondria
2.2 Chloroplasts
2.3 Endoplasmic reticulum
2.4 Golgi apparatus
2.5 Ribosome
2.6 Lysosome
2.7 Nucleus
2.8 Nucleolus
2.9 Peroxisome
2.10 Let Us Sum Up
2.14 References

In this lesson weve learn about the cell organelles and their functions.
A living cell is a complex, multi- functional unit. Even the simplest of cells
performs a large array of different tasks and functions by the arrangement of the cell
organelles such as cell wall and plasma membrane and cytosolic substances such as
nucleus, Golgi bodies, endoplasmic reticulum, mitochondria etc.
2.1 Mitochondria
Fig. 4. Mitochondrial Components

Mitochondria are the cells' power sources. They are distinct organelles with two
membranes. Usually they are rod-shaped, however they can be round. The outer
membrane limits the organelle. The inner membrane is thrown into folds or shelves that
project inward are called "cristae mitochondriales". They contain two membranes,
separated by a space. Both are the typical "unit membrane" (railroad track) in structure.
Inside the space enclosed by the inner membrane is the matrix. Which contains dense
strands of DNA, ribosomes, or small granules and can code for part of their proteins with
these molecular tools.
The food we eat is oxidized to produce high-energy electrons that are converted to stored
energy. This energy is stored in high energy phosphate bonds in a molecule called
adenosine triphosphate, or (ATP). Which is converted from adenosine diphosphate by
adding the phosphate group with the high-energy bond. Various reactions in the cell can
either use energy (whereby the ATP is converted back to ADP, releasing the high energy
bond) or produce it (whereby the ATP is produced from ADP). Let us break down each
of the steps so you can see how food turns into ATP energy packets and water. The food
we eat must first be converted to basic chemicals that the cell can use. Some of the best
energy supplying foods contains sugars or carbohydrates. Using bread as an example, the
sugars are broken down by enzymes that split them into the simplest form of sugar which
is called glucose. Then, glucose enters the cell by special molecules in the membrane
called glucose transporters.
Once inside the cell, glucose is broken down to make ATP in two pathways. The first
pathway requires no oxygen and is called anaerobic metabolism. This pathway is called
glycolysis and it occurs in the cytoplasm outside the mitochondria. During glycolysis,
glucose is broken down into pyruvate. Other foods like fats can also be broken down for
use as fuel (see following cartoon). Each reaction is designed to produce some hydrogen
ions (electrons) that can be used to make energy packets (ATP). However, only 4 ATP
molecules can be made by one molecule of glucose run through this pathway. That is
why mitochondria and oxygen are so important. We need to continue the breakdown
process with the Krebs cycle inside the mitochondria in order to get enough ATP to run
all the cell functions.
Fig. 5. ATP Synthase

Pyruvate is carried into the mitochondria and there it is converted into Acetyl Co-A
which enters the Kreb's cycle. This first reaction produces carbon dioxide because it
involves the removal of one carbon from the pyruvate
Mitochondrial membrane morphology
The outer membrane of the mitochondria contains the protein "porin". This forms an
aqueous channel through which proteins up to 10,000 daltons can pass and go into the
intermembrane space. Indeed, the small molecules actually equilibrate between the outer
membrane and the cytosol. However, most proteins cannot get into the matrix unless they
pass through the inner membrane. This membrane contains cardiolipin which renders it
virtually impermeable and requires transport mechanisms across the membrane that are
more organized and regulated.
Fig. 6. Protein import by Mitochondria
Transport across the mitochondrial membranes requires the concerted action of a number
of translocation machineries. The machinery in the outer membrane is called the Tom
complex (Translocator outer membrane) and that for the inner membrane is called the
Tim complex (Translocator Inner Membrane). Proteins that have to go all the way to the
matrix have an NH2 cleavable signal sequence and become uncoiled or stretched out to
go through the translocators. This involves ATP binding and is monitored and stabilized
by a chaperone protein, including hsp70. Thus, before the protein can go through Tom
complex, it must become "translocation competent", and processed as follows:
1. First, as with many mitochondrial proteins, Tom40 requires cytosolic chaperones
t o p repare it for entry. In the case of this protein, becoming "translocation
competent" requires ATP and a partially folded state (the latter is mediated by the
cytosolic chaperone (hsp70).
2. Second, when it is "competent", it interacts with the surface receptor, Tom20.
There is no cleavable signal peptide however, the experiments showing the
requirement for partial folding suggests targeting information is found in
discontinuous sites brought together in the folded domain.
3. Final insertion is into preexisting Tom complexes and requires an intact N
terminus.
4. Dimerization occurs after entry into the membrane.
5. Tim54 carries a amino terminal, noncleaved translocation sequence that is
positively charged. However, it prefers to use Tom70 as its receptor instead of
Tom20. After moving through the GIP, it uses its positively charged amino
terminal sequence to enter the matrix. It required chaperones and ATP to get to
the matrix.
6. Tim22 is a hydrophobic protein that uses Tom20 for targeting to the OM. Then it
follows the Tim route for carrier proteins, like Tim23. and does not require hsp70
or ATP for entry.
7. Small Tims are normally found in the intermembrane space and are not membrane
proteins. They used Tom20 for their receptor and transfer to the GIP complex.
However, when Tom20 was destroyed by trypsin, leaving only Tom5, the small
Tims were able to enter.
2.2 Chloroplast
Chloroplasts are organelles found in plant cells and eukaryotic algae that conduct
photosynthesis. Chloroplasts absorb sunlight and use it in conjunction with water and
carbon dioxide to produce sugars, the raw material for energy and biomass production in
all green plants and the animals that depend on them, directly or indirectly, for food.
Chloroplasts capture light energy from the sun to conserve free energy in the form of
ATP and reduce NADP t o NADPH through a complex set of processes called
photosynthesis. It is derived from the Greek words chloros which means green and plast
which means form or entity. Chloroplasts are members of a class of organelles known as
plastids. They have their own genome, and may contain 60-100 genes.
Structure
Chloroplasts are observable morphologically as flat discs usually 2 to 10 micrometers in
diameter and 1 micrometer thick. The chloroplast is contained by an envelope that
consists of an inner and an outer phospholipid membrane. Between these two layers is the
intermembrane space. The material within the chloroplast is called the stroma,
corresponding to the cytosol of the original bacterium, and contains one or more
molecules of small circular DNA. It also contains ribosomes, although most of its
proteins are encoded by genes contained in the host cell nucleus, with the protein
products transported to the chloroplast.
Within the stroma are stacks of thylakoids, the sub-organelles which are the site of
photosynthesis. The thylakoids are arranged in stacks called grana (singular: granum). A
thylakoid has a flattened disk shape. Inside it is an empty area called the thylakoid space
or lumen. Photosynthesis takes place on the thylakoid membrane; as in mitochondrial
oxidative phosphorylation, it involves the coupling of cross- membrane fluxes with
biosynthesis via the dissipation of a proton electrochemical gradient. Embedded in the
thylakoid membrane is the antenna complex, which consists of proteins, and lightabsorbing pigments, including chlorophyll and carotenoids. This complex both increases
the surface area for light capture, and allows capture of photons with a wider range of
wavelengths. The energy of the incident photons is absorbed by the pigments and
funneled to the reaction centre of this complex through resonance energy transfer. Two
chlorophyll molecules are then ionised, producing an excited electron which then passes
onto the photochemical reaction centre.
Chloroplast membrane: Chloroplasts contain several important membranes, vital for
their function. Like mitochondria, chloroplasts have a doublemembrane envelope, called
the chloroplast envelope. Each membrane is a phospholipid bilayer, between 6 and 8 nm
thick, and the two are separated by a gap of 10-20nm, called the intermembrane space.
The outer membrane is permeable to most ions a n d metabolites, but the inner
membrane is highly specialised with transport proteins within the inner membrane, in the
region called the stroma, there is a system of interconnecting flattened membrane
compartments, called the lamellae, or thylakoids. These are the sites of light absorption
and ATP synthesis, and contain many proteins, including those involved in the electron
transport chain. Photosynthetic pigments such as chlorophyll and B, and some others
e.g. xanthophylls and carotenoids are also located within this space. The membranes of
the chloroplasts contain photosystems I and II which harvest solar energy in order to
excite electrons which travel down the electron transport chain. and along the way is
used to pump H+ ions from the stroma into the thylakoid space. A concentration
gradient is formed, which allows chemiosmosis to occur, where the protein ATP
synthase harvests the potential energy of the Hydrogen ions and uses it to combine ADP
and a phosphate group to form ATP.
Functions
Photosynthesis:
The heart of photosynthesis as it occurs in most autotrophs consists of two key
processes:
the removal of hydrogen (H) atoms from water molecules

the reduction of carbon dioxide (CO2 ) by these hydrogen atoms to form organic
molecules.
The second process involves a cyclic series of reactions named the Calvin Cycle (after its
discoverer). It is discussed in Photosynthesis: Pathway of Carbon Fixation. The detail of
the first process is our topic here.
The electrons (e- ) and protons (H+) that make up hydrogen atoms are stripped away
separately from water molecules.
2H2O -> 4e- + 4H+ + O2

The electrons serve two functions:
They reduce NADP+ to NADPH for use in the Calvin Cycle.

They set up an electrochemical charge that provides the energy for pumping
protons from the stroma of the chloroplast into the interior of the thylakoid.
The protons also serve two functions:
They participate in the reduction of NADP+ to NADPH.

As they flow back out from the interior of the thylakoid (by facilitated diffusion),
passing down their concentration gradient), the energy they give up is harnessed
to the conversion of ADP to ATP.
Because it is drive by light, this process is called photophosphorylation.
ADP + Pi -> ATP
The ATP provides the second essential ingredient for running the Calvin Cycle.
The removal of electrons from water molecules and their transfer to NADP+ requires
energy. The electrons are moving from a redox potential of about +0.82 volt in water to
- 0.32 volt in NADPH. Thus enough energy must be available to move them against a
total potential of 1.14 volts. Where does the needed energy come from? The answer:
Light.
Fig. 7. Calvin Cycle

The Thylakoid Membrane
Chloroplasts contain a system of thylakoid membranes surrounded by a fluid stroma.
Six different complexes of integral membrane proteins are embedded in the thylakoid
membrane. The exact structure of these complexes differs from group to group (e.g.,
plant vs. alga) and even within a group (e.g., illuminated in air or underwater). But, in
general, one finds:
1. Photosystem I
The structure of photosystem I in a cyanobacterium ("blue-green alga") has been
completely worked out. It probably closely resembles that of plants as well.
It is a homotrimer with each subunit in the trimer containing:
12 different protein molecules bound to

96 molecules of chlorophyll a
o 2 molecules of the reaction center chlorophyll P700
o 4 accessory molecules closely associated with them
o 90 molecules that serve as antenna pigments
22 carotenoid molecules
4 lipid molecules
3 clusters of Fe4 S4
2 phylloquinones
2. Photosystem II
Photosystem II is also a complex of
> 20 different protein molecules bound to

50 or more chlorophyll a molecules
o 2 molecules of the reaction center chlorophyll P680
o 2 accessory molecules close to them
++
o 2 molecules of pheophytin (chlorophyll without the Mg )
o the remaining molecules of chlorophyll a serve as antenna pigments.
some half dozen carotenoid molecules. These also serve as antenna pigments.
2 molecules of plastoquinone
2.3 Endoplasmic Reticulum

The endoplasmic reticulum or ER is an organelle found in all eukaryotic cells that is an
interconnected network of tubules, vesicles and cisternae that is responsible for several
specialized functions: Protein translation, folding, and transport of proteins to be used in
the cell membrane ( e . g . , transmembrane receptors and other integral membrane
proteins), or to be secreted ( exocytosed) from the cell (e.g., digestive enzymes);
sequestration of calcium; and production and storage of glycogen, steroids, and other
macromolecules. The endoplasmic reticulum is part of the endomembrane system. The
basic structure and composition of the ER membrane is similar to the plasma membrane.
Structure: The general structure of the endoplasmic reticulum is an extensive membrane
network of cisternae (sac- like structures) held together by the cytoskeleton. T h e
phospholipid membrane encloses a space, the cisternal space (or lumen), from the
cytosol. The functions of the endoplasmic reticulum vary greatly depending on the exact
type of endoplasmic reticulum and the type of cell in which it resides. The three varieties
are called rough endoplasmic reticulum, smooth endoplasmic reticulum, and
sarcoplasmic reticulum.
Rough endoplasmic reticulum: The surface of the rough endoplasmic reticulum is
studded with proteinmanufacturing ribosomes giving it a "rough" appearance (hence its
name). But it should be noted that these ribosomes are not resident of the endoplasmic
reticulum incessantly. The ribosomes only bind to the ER once it begins to synthesize a
protein destined for sorting. The membrane of the rough endoplasmic reticulum is
continuous with the outer layer of the nuclear envelope. Although there is no continuous
membrane between the rough ER and the Golgi apparatus, membrane bound vesicles
shuttle proteins between these two compartments. The rough endoplasmic reticulum
works in concert with the Golgi complex to target new proteins to their proper
destinations.
Smooth endoplasmic reticulum: Smooth endoplasmic reticulum is found in a variety of
cell types (both animal and plant) and it serves different functions in each. The Smooth
ER also contains the enzyme Glucose-6-phosphatase which converts Glucose-6phosphate to Glucose, a step in gluconeogenesis. The Smooth ER consists of tubules and
vesicles that branch forming a network. In some cells there are dilated areas like the sacs
of rough endoplasmic reticulum. The network of smooth endoplasmic reticulum allows
increased surface area for the action or storage of key enzymes and the products of these
enzymes. The smooth endoplasmic reticulum is known for its storage of calcium ions in
muscle cells. The smooth endoplasmic reticulum has functions in several metabolic
processes, including synthesis of lipids, metabolism of carbohydrates and calcium
concentration, drug detoxification, and attachment of receptors on cell membrane
proteins. It is connected to the nuclear envelope.
Fig. 8. Endoplasmic Reticulum

Sarcoplasmic reticulum: The sarcoplasmic reticulum is a special type of smooth ER
found in smooth a n d striated muscle. The only structural difference between this
organelle and the smooth endoplasmic reticulum is the medley of protein they have, both
bound to their membranes and drifting within the confines of their lumens. This
fundamental difference is indicative of their functions: the smooth ER is built to
synthesize molecules and the sarcoplasmic reticulum is built to store and pump calcium
ions. The sarcoplasmic reticulum contains large stores of calcium, which it sequesters and
then releases when the cell is depolarised. This has the effect of triggering muscle
contraction.
Functions
The endoplasmic reticulum serves many general functions, including the facilitation of
protein folding and the transport of synthesized proteins in sacs called cisternae. Correct
folding of newly- made proteins is made possible by several endoplasmic reticulum
chaperone proteins, including protein disulfide isomerase (PDI), ERp29, the Hsp70
family member Grp78, calnexin, calreticulin, and the peptidylpropyl isomerase family.
Only properly- folded proteins are transported from the rough ER to the Golgi complex.
Transport of proteins
Secretory proteins, mostly glycoproteins, are moved across the endoplasmic reticulum
membrane. Proteins that are transported by the endoplasmic reticulum and from there
throughout the cell are marked with an address tag called a signal sequence. The Nterminus (one end) of a polypeptide chain (i.e., a protein) contains a few amino acids
that work as an address tag, which are removed when the polypeptide reaches its
destination. Proteins that are destined for places outside the endoplasmic reticulum are
packed into transport vesicles and moved along the cytoskeleton toward their
destination.
The endoplasmic reticulum is also part of a protein sorting pathway. It is, in essence, the
transportation system of the eukaryotic cell. The majority of endoplasmic reticulum
resident proteins are retained in the endoplasmic reticulum through a retention motif.
This motif is composed of four amino acids at the end of the protein sequence. The most
common retention sequence is KDEL ( lys-asp-glu-leu). However, variation on KDEL
does occur and other sequences can also give rise to endoplasmic reticulum retention. It
is not known if such variation can lead to sub-endoplasmic reticulum localizations. There
are three KDEL receptors in mammalian cells, and they have a very high degree of
sequence identity. The functional differences between these receptors remain to be
established.
Other functions
Insertion of proteins into the endoplasmic reticulum membrane: Integral proteins

must be inserted into the endoplasmic reticulum membrane after they are
synthesized. Insertion into the endoplasmic reticulum membrane requires the
correct topogenic sequences.
Glycosylation: Glycosylation involves the attachment of oligosaccharides.
Disulfide bond formation and rearrangement: Disulfide bonds stabilize the tertiary
and quaternary structure of many proteins.
Drug Detoxification: The smooth ER is the site at which some drugs are
detoxified.
2.4 Golgi Apparatus

The Golgi apparatus (also called the Golgi body, Golgi complex, or dictyosome) is an
organelle found in typical eukaryotic cells. It was identified in 1898 by the Italian
physician Camillo Golgi and was named after him. The primary function of the Golgi
apparatus is to process and package macromolecules synthesised by the cell, primarily
proteins and lipids. The Golgi apparatus forms a part of the endomembrane system
present in eukaryotic cells.
Structure: The Golgi is composed of membrane-bound sacs known as cisternae.
Between five and eight are usually present, however as many as sixty have been
observed. Surrounding the main cisternae are a number of spherical vesicles which have
budded off from the cisternae. The cisternae stack has five functional regions: the cisGolgi network, cis-Golgi, medial- Golgi, trans-Golgi, and trans-Golgi network. Vesicles
from the endoplasmic reticulum (via the vesicular-tubular cluster) fuse with the cis-Golgi
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 are destined to
reside.
Fig. 9. The Golgi Apparatus

Function
1.Cells synthesise a large number of different macromolecules required for life. The Golgi
apparatus is integral in modifying, sorting, and packaging these substances for cell
secretion ( exocytosis) or for use within the cell. It primarily modifies proteins delivered
from the rough endoplasmic reticulum, but is also involved in the transport of lipids
around the cell, and the creation of lysosomes. In this respect it can be thought of as
similar to a post office; it packages and labels "items" and then sends them to different
parts of the cell.
2.
Enzymes within the cisternae are able to modify substances by the addition of
carbohydrates ( glycosylation) and phosphate ( phosphorylation) to them. In order to do
so the Golgi transports substances such as nucleotide sugars into the organelle from the
cytosol. Proteins are also labelled with a signal sequence of molecules which determine
their final destination. For example, the Golgi apparatus adds a mannose-6-phosphate
label to proteins destined for lysosomes. The Golgi also plays an important role in the
synthesis of proteoglycans, molecules present in the extracellular matrix of animals, and
it is a major site of carbohydrate synthesis.
3.
This includes the productions of glycosaminoglycans or GAGs, long unbranched
polysaccharides which the Golgi then attaches to a protein synthesized in the
endoplasmic
reticulum
to
form
the proteoglycan.
http://en.wikipedia.org/wiki/Golgi_apparatus - _ n o t e -0Enzymes in the Golgi will
polymerize several of these GAGs via a xylose link onto the core protein. Another task
of the Golgi involves the sulfation of certain molecules passing through its lumen via
sulphotranferases that gain their sulphur molecule from a donor called PAPs. This
process occurs on the GAGs of proteoglycans as well as on the core protein. The level of
sulfation is very important to the proteoglycans signalling abilities as well as giving the
proteoglycan its overall negative charge.
4. The Golgi is also capable of phosphorylating molecules. To do so it transports ATP
into the lumen. The Golgi itself contains resident kinases, such as casein kinases. One
molecule that is phosphorylated in the Golgi is Apolipoprotein, which forms a molecule
k n o w n a s VLDL that is a constitute of blood serum. It is thought that the
phosphorylation of these molecules is important to help aid in their sorting of secretion
into the blood serum.
5. The Golgi also has a putative role in apoptosis, with several Bcl-2 family members
localised there, as well as to the mitochondria. In addition a newly characterised antiapoptotic protein, GAAP (Golgi anti-apoptotic protein), which almost exclusively resides
in the Golgi, protects cells from apoptosis by an as-yet undefined mechanism (Gubser et
al., 2007).
Vesicular transport
Vesicles which leave the rough endoplasmic reticulum are transported to the cis face of
the Golgi apparatus, where they fuse with the Golgi membrane and empty their contents
into the lumen. Once inside they are modified, sorted, and shipped towards their final
destination. As such, the Golgi apparatus tends to be more prominent and numerous in
cells synthesising and secreting many substances: plasma B cells, the antibody-secreting
cells of the immune system, have prominent Golgi complexes.
Fig. 10. Inner view of Golgi Apparatus

Those proteins destined for areas of the cell other than either the endoplasmic reticulum
or Golgi apparatus are moved towards the trans face, to a complex network of
membranes and associated vesicles known as the trans-Golgi network (TGN). This area
of the Golgi is the point at which proteins are sorted and shipped to their intended
destinations by their placement into one of at least three different types of vesicles,
depending upon the molecular marker they carry.
Transport mechanism
The transport mechanism which proteins use to progress through the Golgi apparatus is
not yet clear; however a number of hypotheses currently exist. Until recently, the
vesicular transport mechanism was favoured but now more evidence is coming to light to
support cisternal maturation. The two proposed models may actually work in conjunction
with each other, rather than being mutually exclusive. This is sometimes referred to as the
combined model.
Cisternal maturation model: The cisternae of the Golgi apparatus move by

being built at the cis face and destroyed at the trans face. Vesicles from the
endoplasmic reticulum fuse with each other to form a cisterna at the cis face,
consequently this cisterna would appear to move through the Golgi stack when a
new cisterna is formed at the cis face. This model is supported by the fact that
structures larger than the transport vesicles, such as collagen rods, were observed
microscopically to progress through the Golgi apparatus. This was initially a
popular hypothesis, but lost favour in the 1980s. Recently it has made a
comeback, as laboratories at the University of Chicago and the University of
Tokyo have been able to use new technology to directly observe Golgi
compartments maturing. Additional evidence comes from the fact that COP1
vesicles move in the retrograde direction,. transporting ER proteins back to where
they belong by recognizing a signal peptide.
Vesicular transport model: Vesicular transport views the Golgi as a very stable
organelle, divided into compartments is the cis to trans direction. Membrane
bound carriers transported material between the ER and Golgi and the different
compartments of the Golgi. Experimental evidence inlcudes the abundance of
small vesicles (known technically as shuttle vesicles) in proximity to the Golgi
apparatus. Directionality is achieved by packaging proteins into either forwardmoving or backward- moving (retrograde) transport vesicles, or alternatively this
directionality may not be necessary as the constant input of proteins from the
endoplasmic reticulum on the cis face of the Golgi would ensure flow.
Irrespectively, it is likely that the transport vesicles are connected to a membrane
via actin filaments to ensure that they fuse with the correct compartment.
2.5 Ribosome
Ribosomes were first observed in the mid-1950s by Romanian cell biologist George
Palade in the electron microscope a s dense particles or granules for which he was
awarded the Nobel Prize. The term ribosome was proposed by scientist Richard B.
Roberts in 1958. A ribosome is a small, dense, functional structure found in all known
cells that assembles proteins. They are about 20nm in diameter and are composed of
65% ribosomal RNA and 35% ribosomal proteins (known as a Ribonucleoprotein or
RNP). It translates messenger RNA (mRNA) to build a polypeptide chain (e.g., a
protein) using amino acids delivered by Transfer RNA (tRNA). It can be thought of as a
giant enzyme but, although it contains proteins, its active site is made of RNA, so
ribosomes are now classified as " ribozymes".
Ribosomes build proteins from the genetic instructions held within a messenger RNA.
Free ribosomes are suspended in the cytosol (the semi- fluid portion of the cytoplasm) or
bound to the rough endoplasmic reticulum, or to the nuclear envelope. Since ribosomes
are ribozymes, it is thought that they might be remnants of the RNA world. While
catalysis of the peptide bond involves the C2' hydroxyl of tRNA's P-site adenosine in a
sort of proton shuttle mechanism, the full function (ie, translocation) of the ribosome is
reliant on changes in protein conformations.
Fig. 11. Structure of Ribosome

Ribosomes consist of two subunits that fit together and work as one to translate the
mRNA into a polypeptide chain during protein synthesis. Prokaryotic subunits consist of
one or two and eukaryotic of one or three very large RNA molecules (known as
ribosomal RNA or rRNA) and multiple smaller protein molecules. Prokaryotes have 70 S
ribosomes, each consisting of a small ( 30S) and a large ( 50S) subunit. Their large
subunit is composed of a 5S RNA subunit (consisting of 120 nucleotides), a 23S RNA
subunit (2900 nucleotides) and 34 proteins. The 30S subunit has a 1540 nucleotide RNA
subunit bound to 21 proteins. Eukaryotes have 80S ribosomes, each consisting of a small
( 40S) and large ( 60S) subunit. Their large subunit is composed of a 5S RNA (120
nucleotides), a 28S RNA (4700 nucleotides), a 5.8S subunit (160 nucleotides) and ~49
proteins. The 40S subunit has a 1900 nucleotide (18S) RNA and ~33 proteins.
Crystallographic work has shown that there are no ribosomal proteins close to the
reaction site for polypeptide synthesis. This suggests that the protein components of
ribosomes act as a scaffold that may enhance the ability of rRNA to synthesize protein
rather than directly participating in catalysis.Free ribosomes: Free ribosomes are "free" to
move about anywhere in the cytoplasm (within the cell membrane). Proteins made by
free ribosomes are used within the cell. Proteins containing disulfide bonds using
cysteine amino acids cannot be produced outside of the lumen of the endoplasmic
reticulum.
Membrane-bound ribosomes: When certain proteins are synthesized by a ribosome
they can become "membrane-bound". The newly produced polypeptide chains are
inserted directly into the endoplasmic reticulum by the ribosome and are then transported
to their destinations. Bound ribosomes usually produce proteins that are used within the
cell membrane or are expelled from the cell via exocytosis.
Function of Ribosomes
1. Ribosomes are the workhorses of protein biosynthesis, the process of translating
messenger RNA (mRNA) into protein. The mRNA comprises a series of codons
that dictate to the ribosome the sequence of the amino acids needed to make the
protein. Using the mRNA as a template, the ribosome traverses each codon of the
mRNA, pairing it with the appropriate amino acid. This is done using molecules
of transfer RNA (tRNA) containing a complementary anticodon on one end and
the appropriate amino acid on the other.
2. Protein synthesis begins at a start codon near the 5' end of the mRNA. The small
ribosomal subunit, typically bound to a tRNA containing the amino acid
methionine, binds to an AUG codon on the mRNA and recruits the large
ribosomal subunit. The large ribosomal subunit contains three tRNA binding sites,
designated A, P, and E. The A site binds an aminoacyl- tRNA (a tRNA bound to
an amino acid); the P site binds a peptidyl-tRNA (a tRNA bound to the peptide
being synthesized); and the E site binds a free tRNA before it exits the ribosome.
Both ribosomal subunits (small and large) assemble at the start codon (towards the 5'
end of the mRNA). The ribosome uses tRNA which matches the current codon
(triplet) on the mRNA to append an amino acid to the polypeptide chain. This is done
for each triplet on the mRNA, while the ribosome moves towards the 3' end of the
mRNA. Usually in bacterial cells, several ribosomes are working parallel on a single
mRNA, forming what we call a polyribosome or polysome
2.6 Lysosome
Lysosomes are organelles that contain digestive enzymes (acid hydrolases). They digest
excess or worn out organelles, food particles, and engulfed viruses o r bacteria. The
membrane surrounding a lysosome prevents the digestive enzymes inside from
destroying the cell. Lysosomes fuse with vacuoles and dispense their enzymes into the
vacuoles, digesting their contents. They are built in the Golgi apparatus. The name
lysosome derives from the Greek words lysis, which means dissolution or destruction, and
soma, which means body. They are frequently nicknamed "suicide-bags" or "suicidesacs" by cell biologists due to their role in autolysis. Lysosomes were discovered by the
Belgian cytologist Christian de Duve in 1949.
Acidic environment
At pH 4.8, the interior of the lysosomes is more acidic than the cytosol (pH 7.2). The
lysosome single membrane stabilizes the low pH by pumping in protons (H+) from the
cytosol via proton pumps and chloride ion channels. The membrane also protects the
cytosol, and therefore the rest of the cell, f rom the degradative enzymes within the
lysosome. For this reason, should a lysosome's acid hydrolases leak into the cytosol, their
potential to damage the cell will be reduced, because they will not be at their optimum
pH. The hydrolytic enzymes in lysosomes are produced in the endoplasmic reticulum
and transported and processed through the Golgi apparatus. The Golgi apparatus
produces lysosomes by budding. Each acid hydrolase is then targeted to a lysosome by
phosphorylation. The lysosome itself is likely to be safe from enzymatic action due to
having proteins in the inner membrane which has a three-dimensional molecular structure
that protects vulnerable bonds from enzymatic attack.
Fig. 13. Lysosome

Some important enzymes in lysosomes are:
Lipase, which digests lipids,

Carbohydrases, which digest carbohydrates (e.g., sugars),
Proteases, which digest proteins,
Nucleases, which digest nucleic acids.
Phosphatases, which digest 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.
Functions
The lysosomes are used for the digestion of macromolecules f r o m phagocytosis
(ingestion of other dying cells or larger extracellular material), endocytosis (where
receptor proteins are recycled from the cell surface), and autophagy (where old or
unneeded organelles or proteins, or microbes which have invaded the cytoplasm are
delivered to the lysosome). Autophagy may also lead to autophagic cell death, a form of
programmed self-destruction, o r 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. Lysosomes also do much of the cellular digestion required to digest
tails of tadpoles and to remove the web from the fingers of a 3-6 month old fetus. This
process of programmed cell death is called apoptosis.
2.7 Nucleus
In cell biology, the nucleus (pl. nuclei; from Latin nucleus o r nuculeus, kernel) is a
membrane-enclosed organelle found in most eukaryotic cells. It contains most of the
cell's genetic material, organized as multiple long linear DNA molecules in complex
with a large variety of proteins, such as histones, to form chromosomes. The genes
within these chromosomes make up the cell's nuclear genome. The function of the
nucleus is to maintain the integrity of these genes and to control the activities of the cell
by regulating gene expression.
Fig. 13. Nuclear

The main structural elements of the nucleus are the nuclear envelope, a double
membrane that encloses the entire organelle and keeps its contents separated from the
cellular cytoplasm, and the nuclear lamina, a meshwork within the nucleus that adds
mechanical support much like the cytoskeleton supports the cell as a whole. Because the
nuclear membrane is impermeable to most molecules, nuclear pores are required to allow
movement of molecules across the envelope. These pores cross both membranes of the
envelope, providing a channel that allows free movement of small molecules and ions.
The movement of larger molecules such as proteins is carefully controlled, and requires
active transport facilitated by carrier proteins. Nuclear transport is of paramount
importance to cell function, as movement through the pores is required for both gene
expression and chromosomal maintenance.
Although the interior of the nucleus does not contain any membrane-delineated bodies,
its contents are not uniform, and a number of subnuclear bodies exist, made up of unique
proteins, RNA molecules, and DNA conglomerates. The best known of these is the
nucleolus, which is mainly involved in assembly of ribosomes. After being produced in

the nucleolus, ribosomes are exported to the cytoplasm where they translate mRNA.
2.8 Nucleolus
The nucleolus is a discrete densely-stained structure found in the nucleus. It is not
surrounded by a membrane, and is sometimes called a suborganelle. It forms around
tandem repeats of rDNA, DNA coding for ribosomal RNA (rRNA). These regions are
called nucleolar organizer regions (NOR). The main roles of the nucleolus are to
synthesize rRNA and assemble ribosomes. The structural cohesion of the nucleolus
depends on its activity, as ribosomal assembly in the nucleolus results in the transient
association of nucleolar components, facilitating further ribosomal assembly, and hence
further association. This model is supported by observations that inactivation of rDNA
results in intermingling of nucleolar structures.
Fig. 14. Nucleolus

The first step in ribosomal assembly is transcription of the rDNA, by a protein called
RNA polymerase I, forming a large pre-rRNA precursor. This is cleaved into the
subunits 5.8S, 18S, and 28S rRNA. The transcription, post-transcriptional processing, and
assembly of rRNA occurs in the nucleolus, aided by small nucleolar RNA (snoRNA)
molecules, some of which are derived from spliced introns f r o m messenger RNAs
encoding genes related to ribosomal function. The assembled ribosomal subunits are the
largest structures passed through the nuclear pores.
When observed under the electron microscope, the nucleolus can be seen to consist of
three distinguishable regions: the innermost fibrillar centers (FCs), surrounded by the
dense fibrillar component (DFC), which in turn is bordered by the granular component
(GC). Transcription of the rDNA occurs either in the FC or at the FC-DFC boundary, and
therefore when rDNA transcription in the cell is increased more FCs are detected. Most
of the cleavage and modification of rRNAs occurs in the DFC, while the latter steps
involving protein assembly onto the ribosomal subunits occurs in the GC.
2.9 Peroxisome
Peroxisomes are ubiquitous organelles in eukaryotes that participate in the metabolism
of fatty acids and other metabolites. Peroxisomes have enzymes that rid the cell of toxic
peroxides. They have a single lipid bilayer membrane that separates their contents from
the cytosol (the internal fluid of the cell) and contain membrane proteins critical for
various functions, such as importing proteins into the organelles and aiding in
proliferation. Like lysosomes, peroxisomes are part of the secretory pathway of a cell,
but they are much more dynamic and can replicate by enlarging and then dividing.
Peroxisomes were identified as cellular organelles by the Belgian cytologist Christian de
Duve i n 1965 after they had been first described in a Swedish Ph.D. thesis a decade
earlier.
Fig. 15. Anatomy of the Peroxisome

Function of Peroxisomes
Peroxisomes contain oxidative enzymes, such as catalase, D-amino acid oxidase and
uric acid oxidase. 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 (H2 O2 , itself toxic):
. . . . . (1)
Catalase, another enzyme in the peroxisome, in turn uses this H2 O2 to oxidize
other substrates, including phenols, formic acid, formaldehyde and alcohol, by means
of the peroxidation reaction:
, . . . (2)
thus eliminating the poisonous hydrogen peroxide in the process.
This reaction is important in liver and kidney cells where the peroxisomes
detoxifiy various toxic substances that enter the blood. About 25% of the ethanol we
drink is oxidized to acetaldehyde in this way. In addition, when excess H2 O2 accumulates

in the cell, catalase converts it to H2 O through this reaction:
. . . (3)
A major function of the peroxisome is the breakdown of fatty acid molecules, in a
process called beta-oxidation. In this process, the fatty acids are broken down two
carbons at a time, converted to Acetyl-CoA, which is then transported back to the
cytosol for further use. In animal cells, beta-oxidation can also occur in the
mitochondria. In yeast and plant cells this process is exclusive for the peroxisome.The
first reactions in the formation of plasmalogen in animal cells also occurs 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 of the reasons that many peroxisomal disorders lead to neurological
disease.Peroxisomes also play a role in the production of bile acids.
Protein import
Proteins are selectively imported into peroxisomes. Since the organelles contain no DNA
or ribosomes and thus have no means of producing proteins, all of their proteins must be
imported across the membrane. It is believed that proteins do not transit through the
endoplasmic reticulum to get to the peroxisome.
A specific protein signal (PTS or peroxisomal targeting signal) of three amino acids at
the C-terminus of many peroxisomal proteins signals the membrane of the peroxisome to
import them into the organelle. Other peroxisomal proteins contain a signal at the Nterminus. There are at least 32 known peroxisomal proteins, called peroxins, which
participate in the process of importing proteins by means of ATP hydrolysis. Proteins do
not have to unfold to be imported into the peroxisome. The protein receptors, the
peroxins Pex5 a n d Pex7, accompany their cargoes (containing a PTS1 or a PTS2,
respectively) all the way into the peroxisome where they release the cargo and then return
to the cytosol - a step named "recycling". Overall, the import cycle is referred to as the
"extended shuttle mechanism". Evidence now indicates that ATP hydrolysis is required
for the recycling of receptors to the cytosol. Also, ubiquitination appears to be crucial for
the export of PEX5 from the peroxisome, to the cytosol. Little is known about the import
of PEX7, although it has helper proteins that have been shown to be ubiquitinated.
Deficiencies: Peroxisomal disorders are a class of conditions which lead to disorders of
lipid metabolism. One well known example is Zellweger syndrome.One of these is called
a tight junction or "occluding junction" (zonula occludens). This is shown as the top
junction in the above drawing. At this site, membrane glycoproteins and associated
"glue" bind the cells together like double-sided "strapping tape".
2.10 Let Us Sum Up

1. Mitochondria are the cells' power house of the cells
2. the high energy compound ATP is produced in the mitochondria
3. Glucose is breakdown by two pathways in mitochondria. Anaerobic
metabolism and aerobic metabolism.
4. Kreb cycle and oxidative phosphorylation takes place in mitochondria
5. The chloroplast consists of an inner and an outer phospholipid membrane
6. Main function is photosynthesis.
7. Endoplasmic reticulum is responsible for several specialized functions like
Protein translation, folding.
8. There are three varieties of endoplasmic reticulum they are rough endoplasmic
reticulum, smooth endoplasmic reticulum, and sarcoplasmic reticulum.
9. The surface of the rough endoplasmic reticulum is studded with proteinmanufacturing ribosomes giving it a "rough" appearance
10. Prokaryotes have 70S ribosomes, each consisting of a small (30S) and a large
(50S) subunit.
11. Lysosomes are organelles that contain digestive enzymes (acid hydrolases) to
digest excess or worn out organelles, food particles, and engulfed viruses or
bacteria.
12. The nucleolus consists of three distinguishable regions: the innermost
fibrillar centers, surrounded by the dense fibrillar component, which in turn
is bordered by the granular component.
13. Peroxisomes are ubiquitous organelles in eukaryotes that participate in the
metabolism of fatty acids and other metabolites.
14. Peroxisomes contain oxidative enzymes, such as catalase, D-amino acid
oxidase and uric acid oxidase.
Exploring cell organelles is as important as knowing the cell itself

Substantiate.
2.12 Self-Check Exercise

Discuss the structure of mitochondria and its importance as a power house
b) The space given below is for your answer.

1) What are the different types of endoplasmic reticulum?
2) Write about the main functions of endoplasmic reticulum
3) Define the terms Exocytotic vesicles, Secretory vesicles, Lysosomal vesicles
4) How the molecules are transported across the golgi complex?
5) What is zone of exclusion?
6) What are the subunits of ribosome?
7) Explain the role of ribosomes in protein synthesis.
8) What are the different enzymes present in Lysosomes?
9) Give short notes on the functions of Lysosome?
10) What is nucleolus?
11) Give short notes on the structure of nucleolus.
2.14 References
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LESSON - 3 Cell membrane structure and transport proteins

Contents
3.1. Membrane Structure
3.2 Let us sum up
3.4 Self check exercise
3.6 References

To know about cell membrane structure and transport proteins.
3.1. Membrane Structure

The cell is highly organized with many functional units or organelles. Most of these units
are limited by one or more membranes. To perform the function of the organelle, the
membrane is specialized in that it contains specific proteins and lipid components that
enable it to perform its unique roles for that cell or organelle. In essence membranes are
essential for the integrity and function of the cell. Membrane components may:
a) be protective
b) regulate transport in and out of cell or subcellular domain
c) allow selective receptivity and signal transduction by providing transmembrane
receptors that bind signaling molecules
d) allow cell recognition
e) Provide anchoring sites for cytoskeletal filaments or components of the
extracellular matrix. This allows the cell to maintain its shape and perhaps move
to distant sites.
f) help compartmentalize subcellular domains or microdomains
g) Provide a stable site for the binding and catalysis of enzymes.
h) regulate the fusion of the membrane with other membranes in the cell via
specialized junctions )
i) Provide a passageway across the membrane for certain molecules, such as in gap
junctions.
j) allow directed cell or organelle motility
Membrane theories: In the early 1930's-40's, Danielli and Davson studied triglyceride
lipid bilayers over a water surface. They found them to arrange themselves with the polar
heads facing outward. However, they always formed droplets (oil in water) and the
surface tension was much higher than that of cells. However, if proteins were added the
surface tension was reduced and the membranes flattened out.
Fig. 16 Cell Membrane

In the 1950's Robertson noted the structure of membranes seen in the above electron
micrographs. He saw no spaces for pores in the electron micrographs. He hypothesized
that the railroad track appearance came from the binding of osmium tetroxide to proteins
and polar groups of lipids.
Fig. 17. Inner View of Cell Membrane

Fluid-mosaic model:
Biological membranes are sheet- like structures composed mainly of lipids and proteins.
All biological membranes have a similar general structure. Membrane lipids are
organized in a bilayer (two sheets of lipids making up a single membrane) that is
approximately 60 to 100 thick. The proteins, on the other hand, are scattered
throughout the bilayer and perform most membrane functions. Membranes are twodimensional fluids: both lipids and proteins are constantly in motion. The fluid-mosaic
model encompasses our current understanding of membrane structure. It describes both
the "mosaic" arrangement of proteins embedded throughout the lipid bilayer as well as
the "fluid" movement of lipids and proteins alike.
Fig. 19. Reaction of Cell Membranes

Membrane Phospholipids: One of the principal types of lipid in the membrane include
the phospholipids . These have a polar head group and two hydrocarbon tails. An
example of a phospholipid is shown in this figure (right). The top region beginning with
the NH3 is the polar group. It is connected by glycerol to two fatty acid tails. One of the
tails is a straight chain fatty acid (saturated). The other has a link in the tail because of a
cis double bond (unsaturated).The lipid bilayer gives the membranes its fluid
characteristics. The following figure shows the effect of temperature on the packing of
the hydrocarbons. Note that a low temperatures, the bilayer is in a gel state and tightly
packed. At higher (body) temperatures, the bilayer actually "melts' and the interior is
fluid allowing the lipid molecules to move around, rotate, exchange places.
Fig. 20. Reaction of Cell Membranes

Membrane Cholesterol: Another type of lipid in the membrane is cholesterol. The
amount of cholesterol may vary with the type of membrane. Plasma membranes have
nearly one cholesterol per phospholipid molecule. Other membranes (like those around
bacteria) have no cholesterol. The cholesterol molecule inserts itself in the membrane
with the same orientation as the phospholipid molecules. The figures show phospholipid
molecules with a cholesterol molecule inbetween. Note that the polar head of the
cholesterol is aligned with the polar head of the phospholipids. Cholesterol molecules
have several functions in the membrane: a) They immobilize the first few hydrocarbon
groups of the phospholipid molecules. This makes the lipid bilayer less deformable and
decreases its permeability to small water-soluble molecules. Without cholesterol (such as
in a bacterium) a cell would need a cell wall b) Cholesterol prevents crystallization of
hydrocarbons and phase shifts in the membrane.
Membrane Glycolipids: Glycolipids are also a constituent of membranes which
projecting into the extracellular space and hereby serving as protective, insulators, and
sites of receptor binding. Among the molecules bound by glycososphingolipids include
cell poisons such as cholera and tetanus toxins.Formation of "Microdomains":
Sphingolipids and cholesterol work together to help cluster proteins in a region called a
"microdomain". They function as "rafts" or platforms for the attachment of proteins as
membranes are moved around the cell and also during signal transduction.
Membrane Proteins: Transmembrane proteins are amphipathic, in that they have
hydrophobic and hydrophilic regions that are oriented in the same regions in the lipid
bilayer. Another name for them is "integral proteins". Other types of proteins may be
linked only at the cytoplasmic surface (by attachment to a fatty acid chain), or at the
external cell surface, attached by a oligosaccharide. Or, these non-transmembrane
proteins may be bound to other membrane proteins. Collectively these are called
"peripheral membrane proteins". We will be studying specific membrane proteins in later
lectures (ion channels, proteins in endoplasmic reticulum, etc). Therefore, this
presentation will not spend much time on them. Proteins inserted once through the
membrane are called "single-pass transmembrane proteins." Those that pass through
several times are called "multipass transmembrane proteins" and form loops outside the
membrane
Fig. 20. Inner View of Cell Membrane
3.2 Let Us Sum Up

1. Membrane is specialized in that it contains specific proteins and lipid components
to perform the function of the organelle
2. various membrane theories have been proposed
3. Danielli and Davson, Robertson model, and Fluid mosaic model have been
proposed
4. Membrane transport like facilitated diffusion, active transport, channels and
pores, active transporters have been discussed.
5. Phagocytosis, pinocytosis, endocytosis are also discussed.

Do an analysis of the structure of the cell membrane and highlight the interesting teachers
of it.

Explain the models proposed for membrane strcuture?

1)
2)
3)
4)
Which component(s) of membranes give it its fluid characteristics?

What feature in a membrane helps to prevent freezing? Be specific.
Which part of a membrane helps it keep its shape (prevents deformation)?
How are proteins arranged in a membrane? What is the difference between a
transmembrane protein and a peripheral membrane protein?
5) What is a microdomain, and how is it formed?
6) If one type of membrane contains 76% proteins and another type contains only 18%
proteins, what might you conclude about functional differences? For example, see
Membrane Architecture
7) What experiments might you conduct to prove that proteins moved in the plane of the
membrane?
8) How do membranes support the polarity of a cell?
9) How would you detect receptors in the plasma membrane of a cell?
10) In a freeze- fracture/freeze etch specimen, what are the bumps seen in the plane of the
membrane?
11) How would you distinguish tight, or occluding junction between two cells, both
structurally and functionally.
12) What experiments would you use to prove cells were communicating via gap
junctions? Do you know how gap junctions are formed?
13) What does the presence of microvilli signify?
14) What experimental approach could you use to show that a protein is inserted in the
membrane?
3.6 References
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LESSON 4: Mechanisms of transport

Contents
4.1 Facilitated diffusion
4.2 Active transport
4.3 Let us sum up
4.7 References

To know about mechanisms of transports and its branches of transports.
4.1 Facilitated diffusion

A facilitated diffusion protein speeds the movement of a chemical through a membrane
in the absence of energy input; therefore, the transported chemical can only move down a
concentration gradient. This can be accomplished by the formation of a high-specificity
pore or channel that spans the membrane.
4.2 Active transport:

Transport proteins are also used in active transport, which by definition does require an
energy input. Chemiosmotic transport utilizes electrochemical gradients to drive
transport. As the creation and maintenance of chemiosmotic gradients require energy
input from the cell, this is a form of active transport. Prokaryotes typically use hydrogen
ions as the driving force for chemiosmotic transport, while eukaryotes typically use
sodium ions. A symporter/ coporter transports a chemical in the same direction as the
electrochemical gradient, while an antiporter moves the target chemical in a direction
opposite to the gradient.The uniporter is also often included as a category of
chemiosmotic transporter, although a uniporter can also be considered as a facilitated
diffusion protein on the basis of function.
Binding dependent active transport: Binding dependent active transport also moves the
targeted chemical against a concentration gradient, but uses stored chemical energy,
typically in the form of adenosine triphosphate, to power the transport. Generally
speaking, a binding dependent transport system consists of a membrane spanning
component with a high degree of specifity. The membrane spanning component changes
configuration with the aid of chemical energy input, thus translocating the chemical from
one side of the membrane to the other.
Channels/Pores
o
o
o
o
o
o
o
o
Voltage-gated ion channel like, including potassium channels KcsA and KvAP, and
inward-rectifier potassium ion channel Kirbac
Large-conductance mechanosensitive channel, MscL
Small-conductance mechanosensitive ion channel (MscS)
CorA metal ion transporters
Ligand-gated ion channel of neurotransmitter receptors ( acetylcholine receptor)
Aquaporins
Chloride channels
Outer membrane auxiliary proteins (polysaccharide transporter)
Electrochemical Potential-driven transporters

o
o
o
o
o
o
o
o
Mitochondrial carrier proteins

Major Facilitator Superfamily (Glycerol-3-hosphate transporter, Lactose permease,
and Multidrug transporter EmrD)
Resistance- nodulation-cell division (multidrug efflux transporter AcrB)
Dicarboxylate/amino acid:cation symporter (proton glutamate symporter)
Monovalent cation/proton antiporter (Sodium/proton antiporter 1 NhaA)
Neurotransmitter sodium symporter
Ammonia transporters
Drug/Metabolite Transporter (small multidrug resistance transporter EmrE)
Primary Active Transporters

Light absorption-driven transporters:
Bacteriorhodopsin- like proteins including rhodopsin (see also opsin)
Bacterial photosynthetic reaction centres and photosystems I and II
Light harvesting complexes from bacteria and chloroplasts
Oxidoreduction-driven transporters
Transmembrane cytochrome b-like proteins: coenzyme Q - cytochrome c
reductase (cytochrome bc1 ); cytochrome b6f complex; formate dehydrogenase,
respiratory nitrate reductase; succinate - coenzyme Q reductase (fumarate
reductase); and succinate dehydrogenase.
o
Cytochrome c oxidases from bacteria and mitochondria
Electrochemical potential-driven transporters

o
Proton or sodium translocating F-type and V-type ATPases
P-P-bond hydrolysis-driven transporters

o
P-type calcium ATPase (five different conformations)
o
Calcium ATPase regulators phospholamban and sarcolipin
o
ABC transporters: BtuCD, multidrug transporter, a n d molybdate uptake
transporter
o
General secretory pathway (Sec) translocon (preprotein translocase SecY)
o
o
o
Accessory Factors Involved in Transport

Endocytosis is a process whereby cells absorb material ( molecules such as proteins)
from the outside by engulfing it with their cell membrane. It is used by all cells of the
body because most substances important to them are large polar molecules, and thus
cannot pass through the hydrophobic plasma membrane. The function of endocytosis is
the opposite of exocytosis.
Fig. 21. Endocytosis

The absorption of material from the outside environment of the cell is commonly divided
into two processes: phagocytosis and pinocytosis.
Phagocytosis (literally, cell-eating) is the process by which cells ingest large objects,
such as cells which have undergone apoptosis, bacteria, or viruses. The membrane folds
around the object, and the object is sealed off into a large vacuole known as a
phagosome.
Fig. 22. Phagocytosis

Pinocytosis (literally, cell-drinking) is a synonym for endocytosis. This process is
concerned with the uptake of solutes and single molecules such as proteins.
Fig. 23. Pinocytosis

Receptor-mediated endocytosis is a more specific active event where the cytoplasm
membrane folds inward to form coated pits. These inward budding vesicles bud to form
cytoplasmic vesicles.
4.3 Let Us Sum Up

Mechanism of transport to produce facilitates diffusion.
Various transports are activated in this lesson.
Channels/pores are to help them transporters.

Comment on the various transport mechanisms in a cell.

Explain the models proposed for mechanism of transport?

1. What is meant by membrane transport protein?
2. Define Channels/pores.
3. What are the electrochemical potential-driven transporters?
4. Which are primary active transporters?
4.7 References
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UNIT - II
LESSON - 4: CARBOHYDRATES
Contents
5.1 Introduction to carbohydrates
5.2 Types of carbohydrates
Monosaccharides
Disaccharides
Polysaccharides
5.4 Importance of Carbohydrates
5.5 Let us sum up
5.9 References

To know about the significance of carbohydrates and its types.
5.1 Introduction to carbohydrates
The monosaccharides traditionally referred to a class of polyhydroxylcarbonyl
compounds that had the empirical formula CH2 O. This definition has been expanded to
include compounds that may contain certain oxidized, reduced, or heteroatom-substituted
groups. Carboydrates are built from these monosaccharide units. A sugar may refer to a
monosaccharide or to small compounds with more than one monosaccharide. A
polysaccharide contains many monosaccharide units.The suffix -ose indicates a sugar.
Hexoses are six-carbon sugars and pentoses are five-carbon sugars. Many
monosaccharides, such as glucose, may be in equilibrium between their acyclic and
cyclic form. From their acyclic form the terms aldose and ketose are derived. An aldose
will contain an aldeyde and a ketose contains a ketone. The monosaccharide may also be
referred to its cyclic form. If the ring has five carbons and one oxygen, it is a pyranose. If
it has four carbons and one oxygen, it is a furanose.Carbos = Sugars: C, H, and O in 1:2:1
ratio (roughly CH2 O).
5.2 Types of Carbohydrates:
Monosaccharides: simple sugars ( t h e building block of all larger sugars)

C6 H12O6 . Because of their six carbon atoms, each is a hexose. Examples of
Monosaccharides: Glucose - Form of simple sugar used by all cells. From grapes
& honey, Fructose - Fruit sugar, Galactose, a sugar in milk (and yogurt).
Fig 24. Monosaccharide

Although all three share the same molecular formula (C6 H12 O6 ), the arrangement of
atoms differs in each case. Substances such as these three, which have identical
molecular formulas but different structural formulas, are known as structural isomers
Disaccharides: double sugars, f ormed by dehydration synthesis (removal of

water as the 2 monosaccharides bond), Maltose = glucose + glucose, Sucrose =
glucose + fructose, Lactose = glucose + galactose.
Polysaccharides: starches, chains of sugars ,formed by dehydration synthesis,
examples: Amylose, Pectins, Glycogen, Cellulose, undigestible by most
organisms.
Fig 25. Polysaccharides

5.3 Importance of Carbohydrates
Glucose - key metabolic fuel (energy source) of all cells. Animal Starch (Glycogen)- long
term energy storage for animal cells (stores the glucose molecules in a form not easily
used).Plant Starch (Amylose) - long term energy storage for plant cells. Cellulose Structural polysaccharide of cell walls, Chitin - Structural polysaccharide of exoskeletons
of insects and crustaceans.
Ribose is the 5 carbon sugar found in RNA (ribonucleic acid).
5.4 Let Us Sum Up

Carboydrates are built from these monosaccharide units. There are three different types
carbohydrates such as Monosaccharides, Disaccharides, Polysaccharides. They play
important roles in organisms acting as energy sources for different activities.

Carbohydrates are essential metabolic fuel of all cells Express your views on
this.

Give an account on polysaccharides?
5.7 Lesson-End Activities

1) Notes on introduction to carbohydrate.
2) Explain the types of Carbohydrates.
3) What is the importance of Carbohydrates in living systems?
5.8 References
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LESSON - 6: PROTEINS
Contents
6.1 Introduction
6.2 Amino Acids
6.3 Different level of organization
Primary Structure
Secondary Structure
6.4 Let us sum up
6.8 References

To learn the importance of proteins and amino acids and their different levels of
organization.
6.1 Introduction
Proteins are large organic compounds made of amino acids arranged in a linear chain and
joined together by peptide bonds between the carboxyl and amino groups of adjacent
amino acid residues. The sequence of amino acids in a protein is defined by a gene and
encoded in the genetic code. Although this genetic code specifies 20 "standard" amino
acids, the residues in a protein are often chemically altered in post-translational
modification: either before the protein can function in the cell, or as part of control
mechanisms. Proteins can also work together to achieve a particular function, and they
often associate to form stable complexes. Like other biological macromolecules such as
polysaccharides and nucleic acids, proteins are essential parts of organisms and
participate in every process within cells. Many proteins are enzymes that catalyze
biochemical reactions, and are vital to metabolism. Proteins also have structural or
mechanical functions, such as actin and myosin in muscle, and the proteins in the
cytoskeleton, which forms a system of scaffolding that maintains cell shape. Other
proteins are important in cell signaling, immune responses, cell adhesion, and the cell
cycle. Protein is also a necessary part of animals' diets, since they cannot synthesise all
the amino acids and must obtain essential amino acids from food. Through the process of
digestion, animals break down ingested protein into free amino acids that can be used for
protein synthesis
6.2 Amino Acids

An amino acid is by definition an organic compound containing an amine group and a
carboxylic acid group in the same molecule. While there are many forms of amino acids,
all of the important amino acids found in living organisms are alpha-amino acids. Alpha
amino acids have the -COOH and -NH2 groups both attached to the same carbon atom.
The simplest amino acid, which is the molecule glycine, H2 NCH2 COOH, contains no
asymmetric carbon atoms (tetrahedral carbon atoms with four different groups attached).
All of the other amino acids do contain such a carbon atom and are therefore optically
active. The general structure of the alpha-amino acids is R-CHNH2 (alpha)-COOH, and
optical activity for the alpha-amino acids more complex than glycine is found at the alpha
carbon. Amino acids have both an acidic group, in the carboxylic acid, and a basic
group, in the amine. Under physiological aqueous conditions a proton transfer from the
acid to the base occurs, forming a dipolar ion or zwitterion, because the carboxylic acid is
a much stronger acid than is the ammonium ion. The actual structure of glycine in
solution, for example, is +H3 NCH2 COO- at pH 7 rather than H2 NCH2 COOH.At very low
pH the acid group can be protonated and at very high pH the ammonium group can be
deprotonated, but the forms of amino acids relevant to living organisms are the
zwitterions. Each asymmetric carbon gives rise to two optical isomers which are
traditionally distinguished by the letters D or L. Only those amino acids which are the L
forms (left-handed) at the alpha carbon are found in terrestrial life.
Fig 27. Amino acids with hydrophobic side groups
Fig 28. Amino acids with hydrophilic side groups
Fig 29. Amino acids for cysteine, proline, tyrosine and tryptophan
Amino acids are the "building Blocks" of the body. Besides building cells and repairing
tissue, they form antibodies to combat invading bacteria & viruses; they are part of the
enzyme & hormonal system; they build nucleoproteins (RNA & DNA); they carry
oxygen throughout the body and participate in muscle activity. When protein is broken
down by digestion the result is 22 known amino acids. Eight are essential (cannot be
manufactured by the body) the rest are non-essential ( can be manufactured by the body
with proper nutrition).
6.3 Different level of organization
A polypeptide chain consists of a linear sequence of peptide linkages with the remaining
R groups of the amino acids branching from the chain like leaves from a twig. Although
these R groups contain other organic functional groups within them, under physiological
conditions the different R groups do not generally react with each other to form covalent
bonds which link two polypeptide chains together or form cross- links from one part of a
polypeptide chain to another part of the same chain.
a) Primary Structure
The sequential order of the amino acids that make up its polypeptide chains, is the most
important factor in establishing the three-dimensional structure of the protein molecule.
One group on one of the common amino acids--the -SH sulfhydryl group of cysteine-reacts with itself to form disulfide bridges between polypeptide chains. The formation of
a cysteine bridge is a reduction reaction.
b) Secondary Structure
Proteins may consist of a single polypeptide chain, as myoglobin does, or of multiple
chains linked by disulfide bonds; the two chains of insulin are joined by two disulfide
bonds. More complex proteins may consist of multiple chains held together by
noncovalent forces. Some protein molecules contain organic structures which are not
polypeptide chains. Hemoglobin, for example, includes the additional iron-containing
heme group which is essential for its transport of oxygen. The four polypeptide chains of
hemoglobin (two of one kind and two of another) are held together by noncovalent
forces. The effect of the noncovalent forces, particularly hydrogen bonding, is often to
form local regions of ordered structures within the protein. One common type of local
order is the alpha helix structure discovered by the American chemist Linus Pauling.The
effects of local ordering, of disulfide bridge formation, and of additional organic
structures establish the secondary structure of a protein, which is its overall threedimensional configuration. The detailed three-dimensional structure of a protein
molecule, called its tertiary structure, can be established for many proteins by use of xray crystallography. Knowledge of the tertiary structure is often necessary to understand
the chemical and physiological actions of protein molecules, since their most significant
actions may involve only a single small active site on a very large molecule.
Properties of the -helix.

The structure repeats itself every 5.4 along the helix axis, i.e. we say that the -helix
has a pitch of 5.4 . -helices have 3.6 amino acid residues per turn, i.e. a helix 36
amino acids long would form 10 turns. The separation of residues along the helix axis is
5.4/3.6 or 1.5 , i.e. the -helix has a rise per residue of 1.5 . Every main chain C=O
and N-H group is hydrogen-bonded to a peptide bond 4 residues away (i.e. Oi to Ni+4).
This gives a very regular, stable arrangement. The peptide planes are roughly parallel
with the helix axis and the dipoles within the helix are aligned, i.e. all C=O groups point
in the same direction and all N-H groups point the other way. Side chains point outward
from helix axis and are generally oriented towards its amino-terminal end. All the amino
acids have negative phi and psi angles, typical values being -60 degrees and -50 degrees,
respectively.All the amino acids have negative phi and psi angles, typical values being 60 degrees and -50 degrees, respectively.
Helix
Fig 30. Structure of Amino acids
Helices.
Strictly, these form a distinct class of helix but they are always short and frequently
occur at the termini of regular -helices. The name 310 arises because there are three
residues per turn and ten atoms enclosed in a ring formed by each hydrogen bond (note
the hydrogen atom is included in this count). There are main chain hydrogen bonds
between residues separated by three residues along the chain (i.e. Oi to Ni+3). In this
nomenclature the Pauling-Corey -helix is a 3.613 -helix. The dipoles of the 310 -helix are
not so well aligned as in the -helix, i.e. it is a less stable structure and side chain
packing is less favourable.
-sheet structure. Pauling and Corey derived a model for the conformation of
fibrous proteins known as -keratins. In this conformation the polypeptide does not
form a coil. Instead, it zigzags in a more extended conformation than the -helix.
sheets are compact and stable structures. They are formed when two or more lengths
of a protein chain lie next to each other so as to form hydrogen bonds between their
respective backbones. In order for the backbones to be close enough for hydrogen
bonds to form, the side chains must not come between the backbones. Each length
that participates in a sheet is called a strand. There are two ways the strands can
orient themselves to form &beta sheets: parallel and anti-parallel.Anti-parallel
Sheets: Protein chains are synthesized starting at the amino terminus and ending at
the carboxyl terminus. Thus a protein chain has directionality. In an anti-parallel
sheet, the beta strands are aligned next to each other, running in opposite directions.
Reverse turns:
A reverse turn is region of the polypeptide having a hydrogen bond from one main
chain carbonyl oxygen to the main chain N-H group 3 residues along the chain (i.e. Oi
to N i+3). Helical regions are excluded from this definition and turns between strands form a special class of turn known as the -hairpin (see later). Reverse turns
are very abundant in globular proteins and generally occur at the surface of the
molecule. It has been suggested that turn regions act as nucleation centres during
protein folding. Reverse turns are divided into classes based on the and angles of
the residues at positions i+1 and i+2.
Fig. 31 Different level of organization
6.4 Let Us Sum Up

1. Proteins are large organic compounds made of amino acids arranged in a
linear chain and joined together by peptide bonds between the carboxyl and
amino groups of adjacent amino acid residues.
2. An amino acid is by definition an organic compound containing an amine
group and a carboxylic acid group in the same molecule.
3. A polypeptide chain consists of a linear sequence of peptide linkages with the
remaining R groups of the amino acids branching from the chain like leaves
from a twig.
4. Protein structure mainly has two types of organization such as primary
structure and secondary structure.
5. Primary structure is the linear arrangement of amino acids.
6. Secondary structure is again divided in to alpha helix and beeta sheets.
7. Reverse turns are another type of organization which are formed mainly due
to the hydrogen bonding occurring in the main chain protein structure.

Proteins and amino acids are the building blocks of organisms Justify.

Explain different level of organization of proteins?

1) What is amino acid and briefly discuss the different types.
2) Explain the different level of organization of protein structure
3) Define - helix and -sheet structure
6.8 References
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LESSON 7: LIPIDS
Contents
7.1 Introduction
7.2. Fatty acid
7.3 Triacylglycerol (TAG)
7.4 Sphingolipids
7.5 Steroid
7.6 Glycerophospholipid
7.7 Let us sum up
7.11 References

To know about the fatty acids and their functions.
7.1. Introduction
Lipids can be broadly defined as any fat-soluble (hydrophobic) naturally-occurring
molecules. The term is more-specifically used to refer to fatty-acids and their derivatives
(including tri-, di-, and monoglycerides and phospholipids) as well as other fat-soluble
sterol-containing metabolites such as cholesterol. Lipids serve many functions in living
organisms including nutrients, energy storage, structural components of cell membranes,
and important signaling molecules. Although the term lipid is sometimes used as a
synonym for fat, it is in fact a subgroup of lipids called triglycerides and should not be
confused with the term fatty acid.
3.2. Fatty acid
A fatty acid is a carboxylic acid often with a long unbranched aliphatic tail (chain), which
is either saturated or unsaturated. Carboxylic acids as short as butyric acid (4 carbon
atoms) are considered to be fatty acids, while fatty acids derived from natural fats and
oils may be assumed to have at least 8 carbon atoms, e.g. caprylic acid (octanoic acid).
Most of the natural fatty acids have an even number of carbon atoms, because their
biosynthesis involves acetyl-CoA, a coenzyme carrying a two-carbon-atom group (see
fatty acid synthesis).
Saturated fatty acids do not contain any double bonds or other functional groups along
the chain. The term "saturated" refers to hydrogen, in that all carbons (apart from the
carboxylic acid [-COOH] group) contain as many hydrogens as possible. In other words,
the omega () end contains 3 hydrogens (CH3-) and each carbon within the chain
contains 2 hydrogen
Unsaturated fatty acids are of similar form, except that one or more alkenyl functional
groups exist along the chain, with each alkene substituting a singly-bonded " -CH2-CH2" part of the chain with a doubly-bonded "-CH=CH- " portion (that is, a carbon double
bonded to another carbon).
Essential fatty acids are polyunsaturated fatty acids and are the parent compounds of the
omega-6 and omega-3 fatty acid series, respectively. They are essential in the human diet
because there is no synthetic mechanism for them. Humans can easily make saturated
fatty acids or monounsaturated fatty acids with a double bond at the omega-9 position,
but do not have the enzymes necessary to introduce a double bond at the omega-3 or
omega-6 position.
Free fatty acids: Fatty acids can be bound or attached to other molecules, such as in
triglycerides or phospholipids. When they are not attached to other molecules, they are
known as "free" fatty acids. The uncombined fatty acids or free fatty acids may come
from the breakdown of a triglyceride into its components (fatty acids and glycerol).Free
fatty acids are an important source of fuel for many tissues since they can yield relatively
large quantities of ATP. Many cell types can use either glucose or fatty acids for this
purpose. In particular, heart and skeletal muscle prefer fatty acids. The brain cannot use
fatty acids as a source of fuel; it relies on glucose, or on ketone bodies. Ketone bodies are
produced in the liver by fatty acid metabolism during starvation, or during periods of low
carbohydrate intake.
A trans fatty acid (commonly shortened to trans fat) is an unsaturated fatty acid molecule
that contains a trans double bond between carbon atoms, which makes the molecule less
'kinked' in comparison to fatty acids with cis double bonds. These bonds are
characteristically produced during industrial hydrogenation of plant oils. Research
suggests that amounts of trans fats correlate with circulatory diseases such as
atherosclerosis and coronary heart disease more than the same amount of non-trans fats,
for reasons that are not well understood
7.3 Triacylglycerol (TAG)
TAGs are storage lipids stored mostly in adipose (fat) cells and tissues, which are highly
concentrated stores of metabolic energy. As the term triacylglycerols implies the
molecules are composed of three FA attached to a glycerol skeleton. TAG are excellent
storage forms of energy because of the high number of reduced CH groups available for
oxidation dependent energy generation processes.The average male (65 kg) stores
approx. 420,000 kJ as TAG, and only 2500 kJ as glycogen. TAG is the preferred form for
energy storage because FA have greater potential chemical energy due to the reduced CH
groups than does glucose, which is already partly oxidised with plenty of OH groups.
Thus oxidation of FA yields 40 kJ/g whereas oxidation of glucose yield 18 kJ/g. Also
TAG provide a more efficient form of storage because they are almost completely
anhydrous with no bound water.
Glycogen is very polar and binds water molecules such that 1g of glycogen binds 2g
water. Thus 100g of glycogen stored in the liver is actually 33g glycogen and 66g water,
while 100g of TAG in adipose cells is 100g of TAG. If the average male were to store the
420,000 kJ as glycogen then in order to accommodate the water he would need to weigh
125 kg (21 stone).
TAG's are formed when ester bonds are formed between the three OH groups of glycerol
and the acid carboxyl groups of three FA. The three FA are normally different e.g.1palmitoyl-2-palmitoleol-3-s t e r o y l g lycerol contains palmitate, palmitoleate and
stearate.When bound in TAG, the FA lose the ionised carboxyl group so are not charged
thus TAG are also called neutral fats. The loss of the polar head makes the entire
molecule very hydrophobic, and almost completely insoluble in water so that TAG are
stored as oil droplets in adipose cells. Almost always find two saturated FA with one
unsaturated FA in TAG, because 3 saturated FA would provide TAG that was solid waxtype at room temperature. More than one unsaturated FA, and the TAG would be too
fluid for storage purposes inside cells.
7.4 Sphingolipids
These are a class of lipids derived from the aliphatic amino alcohol sphingosine.
Sphingolipids are often found in neural tissue, and play an important role in both signal
transmission and cell recognition.The sphingosine backbone is O-linked to a (usually)
charged head group such as ethanolamine, serine, or choline.The backbone is also amidelinked to an acyl group, such as a fatty acid.There are three main types of sphingolipids:
a. Ceramides. Ceramides are the simplest type of sphingolipid. They consist simply
of a fatty acid chain attached through an amide linkage to sphingosine.
b. Sphingomyelins.
Sphingomyelins
have
a
phosphorylcholine
or
phosphoroethanolamine molecule esterified to the 1-hydroxy group of a ceramide.
c. Glycosphingolipids, which differ in the substituents on their head group (see
image). Glycosphingolipids are ceramides with one or more sugar residues joined
in a -glycosidic linkage at the 1-hydroxyl position. Glycosphingolipids may be
further subdivided into cerebrosides and gangliosides.
Cerebrosides have a single glucose or galactose at the 1-hydroxy position.
Gangliosides have at least three sugars, one of which must be sialic acid.
Function
Sphingolipids are commonly believed to protect the cell surface against harmful
environmental factors by forming a mechanically stable and chemically resistant outer
leaflet of the plasma membrane lipid bilayer. Certain complex glycosphingolipids were
found to be involved in specific functions, such as cell recognition and signaling. The
first feature depends mainly on the physical properties of the sphingolipids, whereas
signaling involves specific interactions of the glycan structures of glycosphingolipids
with similar lipids present on neighboring cells or with proteins.
7.5 Steroid
Fig. 32 Steroid skeleton of lanosterol

The total number of carbons (30) reflects its triterpenoid origin. In some steroids some
carbons may be removed (such as carbon 18) or added (such as carbons 241 and 242) in
downstream biosynthetic reactions. A steroid is a terpenoid lipid characterized by a
carbon skeleton with four fused rings, generally arranged in a 6-6-6-5 fashion. Steroids
can vary by the functional groups attached to these rings and the oxidation state of the
rings. Hundreds of distinct steroids are found in plants, animals, and fungi. All steroids
are biosynthetically derived either from the sterol lanosterol (animals and fungi) or the
sterol cycloartenol (plants). Both sterols are derived from the cyclization of the triterpene
squalene.
Some of the common categories of steroids:
Animal steroids
Insect steroids Ecdysteroids such as ecdysterone
Vertebrate steroids Steroid hormones
Sex steroids -androgens, estrogens, and progestagens.
Corticosteroids - glucocorticoids and mineralocorticoids. Glucocorticoids
Anabolic steroids -Cholesterol
Plant steroids -Phytosterols ,Brassinosteroids
Fungus steroids Ergosterols
7.6 Glycerophospholipid
Fig. 33 Glycerol
Glycerophospholipids or phosphoglycerides are glycerol-based phospholipids. They are
the main component of biological membranes.The term glycerophospholipid signifies
any derivative of sn-glycero-3-phosphoric acid that contains at least one O-acyl, or Oalkyl or O-alk-1'-enyl residue attached to the glycerol moiety and a polar head made of a
nitrogenous base, a glycerol, or an inositol unit.It contains a glycerol core with fatty
acids. They can be the same or different subunits of fatty acids.
Carbon 1 (tail, apolar) contains a fatty acid, typically saturated
Carbon 2 (tail, apolar) contains a fatty acid, typically unsaturated and in the cis
conformation, thus appearing "bent"
Carbon 3 (head, polar) contains a phosphate group or an alcohol attached to a phosphate
group
Lecithin and cephalin are more common than the others in most human membranes, but
cardiolipin is quite common in the inner membranes of mitochondria. One of a
glycerophospholipid's functions is to serve as a structural component of cell membranes.
The cell membrane seen under the electron microscope consists of two identifiable
layers, or "leaflets", each of which is made up of an ordered row of glycerophospholipid
molecules. The composition of each layer can vary widely depending on the type of
cell.Glycerophospholipids can also act as an emulsifying agent to promote dispersal of
one substance into another. This is sometimes used in candy making.
7.7 Let Us Sum Up

1. Lipids are those macromolecules which has a wide variety of fatty acids and their
2.
3.
4.
5.
6.
7.
8.
9.
derivatives.
Lipids serve many functions in living organisms including nutrients, energy
storage, structural components of cell membranes, and important signaling
molecules.
A fatty acid is a carboxylic acid often with a long unbranched aliphatic tail
(chain), which is either saturated or unsaturated.
Saturated fatty acids do not contain any double bonds or other functional groups
along the chain.
Triacyl Glycerides are storage lipids stored mostly in adipose (fat) cells and
tissues, which are highly concentrated stores of metabolic energy.
TAG's are formed when ester bonds are formed between the three OH groups of
glycerol and the acid carboxyl groups of three fatty acids.
Sphingolipids are a class of lipids derived from the aliphatic amino alcohol
sphingosine.
A steroid is a terpenoid lipid characterized by a carbon skeleton with four fused
rings, generally arranged in a 6-6-6-5 fashion.
Glycerophospholipids or phosphoglycerides are glycerol-based phospholipids.
They are the main component of biological membranes.

Make a complete analysis of lipids as macromolecules.

Describe a few points on steroids?

1) Draw the chemical structures of Fatty acids
2) Define Steroid and Glycerophospholipid
3) What are Triacylglycerol (TAG) and Sphingolipids.
7.11 References
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LESSON 8: Nucleic Acids

Contents
8.1 Introduction
Purine
Pyrimidine
Nucleoside
Nucleotide:
8.2. Different forms of DNA
8.3. Let us sum up
8.4. Points for Discussion
8.5. Check your Progress
8.6. Lesson-end activities
8.7. References

To learnt he concepts like purine, pyrimidine and forms of DNA.
Also the denaturation and renaturation of proteins are discussed.
8.1. Introduction
Living organisms are complex systems. Hundreds of thousands of proteins exist inside
each one of us to help carry out our daily functions. These proteins are produced
locally, assembled piece-by-piece to exact specifications. An enormous amount of
information is required to manage this complex system correctly. This information,
detailing the specific structure of the proteins inside of our bodies, is stored in a set of
molecules called nucleic acids. The nucleic acids are very large molecules that have
two main parts. The backbone of a nucleic acid is made of alternating sugar and
phosphate molecules bonded together in a long chain, represented below.
Fig. 34 Purines
Purine: It is a heterocyclic aromatic organic compound,consisting of a

pyrimidine ring fused to an imidazole ring. Purines make up one of the two
groups of nitrogenous bases. Pyrimidines make up the other group. These
bases make up a crucial part of both deoxyribonucleotides and
ribonucleotides, and the basis for the universal genetic code
Pyrimidine: is a heterocyclic aromatic organic compound similar to
benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of
the six- member ring. [1] It is isomeric with two other forms of diazine
Fig. 35 Pyrimidine
Nucleoside: Purine or pyrimidine base linked glycosidically to ribose or

deoxyribose, but lacking the phosphate residues that would make it a
nucleotide.
Nucleotide: Phosphate esters of nucleosides. The metabolic precursors of

nucleic acids are monoesters with phosphate on carbon 5 of the pentose
(known as 5' to distinguish sugar from base numbering).DNA is basically a
long molecule that contains coded instructions for the cells. Everything the
cells do is coded somehow in DNA - which cells should grow and when,
which cells should die and when, which cells should make hair and what color
it should be. Our DNA is inherited from our parents. We resemble our parents
simply because our bodies were formed using DNA to guide the process - the
DNA we inherited from them.
DNA is a long molecule, like a chain, where the links of the chain are pieces called
nucleotides (sometimes also called 'bases'). There are four different types of nucleotides
in DNA which we'll call 'A', 'G', 'C' and 'T'. These four are all that's necessary to write a
code that describes our entire body plan.
The four nucleotides look a little bit alike. They all have a ring of carbons called, in
chemist's terminology, a 'sugar' (not the same as 'table sugar', however). Each nucleotide
also has another type of ring structure, and this is where the four types of nucleotide are
different. These rings are organic bases, much like the more familiar mineral acids and
bases like NaOH or HCl, except these bases are composed of carbon, nitrogen and
oxygen.
DNA chains are made by connecting those nucleotides together via chemical bonds. At
right is a diagram showing four nucleotides connected to form an oligonucleotide, in this
case an RNA oligo (note that it has '-OH' at the lower right corner of each nucleotide, as
opposed to the '-H' in DNA). I've left off the bases, for simplicity's sake. You can see the
sugar rings linked together with phosphate bridges. This is a "single-stranded" nucleic
acid. Below is the double-stranded form.Double-stranded DNA is simply two chains of
single- stranded DNA, positioned so their "bases" can interact with each other. At left is a
cartoon depiction of double-stranded DNA.
Importantly, the two strands travel in opposite directions; hence the structure is said to be
"anti-parallel".The bases in the middle "pair up" with bases on the opposite strand, so that
a type 'A' nucleotide is always opposite a type 'T', and 'G' is opposite 'C'. The attraction
between the paired nucleotides is fairly weak, but when there is a whole string of them, it
adds up to enough strength to hold the strands together.
8.2. Different forms of DNA
There are three natural forms of DNA (A, B and Z). The origin of these different forms
are related to the conformation of the sugar (C2'-endo/ C3'-endo) and the orientation of
the base relative to the sugar (syn/anti).Thus depending on base composition and physical
conditions (Hydration/Salt-Content), DNA can assume several different conformations
(A, B, Z).Each conformation possesses specific parameters: diameter of the helix,
number of bases per tour and distance between plan of bases.
The B- form is the common natural form, prevailing under physiological

conditions of low ionic strength and high degree of hydration. B-DNA arranges
10 nucleotides per helix tour, all of conformation C2'-endo/anti . The plane of the
bases is nearly perpendicular to the helix axis and the helix surface exhibits two
prominent grooves (major and minor).
The Z- form (Zigzag chain) is observed in DNA G-C rich local region. Z-DNA is
longer, thinner and possess an unusual left-handed helix (of 12 bases pairs/tour)
with a single narrow deep groove. These Zigzag form mainly results from the
alternation of purines (C3'-endo/syn) and pyrimidines (C2'-endo/anti).
The A-form is sometimes found in some parts of natural DNA in presence of high
concentration of cations or at a lower degree of hydration (<65%). A-DNA
possess 11 nucleotides per tour (all C3'-endo/anti) and two grooves (a narrow
deep major and a wide shallow minor).
The C- form and D-form are unusual subclasses of B-type. C-DNA is sometimes
observed under 45% of hydration while D-DNA is only found in artificial DNA.
The changes in the shape of DNA can affect its binding with proteins and may be
involved in some regulation process during replication or transcription.
8.3 Let Us Sum Up

Nucleic acids are large molecules which has the genetic code of organisms. The
backbone of a nucleic acid is made of alternating sugar and phosphate molecules bonded
together in a long chain. Nucleic acids contain nitrogenous bases, sugar, and a phosphate
residue. DNA is a long molecule, like a chain, where the links of the chain are pieces
called nucleotides. Dna contains the following nucleotides A,C,G, and T. DNA mainly
has three natural forms like A,B and Z. The conversion of double stranded DNA to single
stranded is known as denaturation. The conversion of single strands back to the doublestranded structure is called renaturation.

Do a closer analysis on the functions of purines and pyrimidines.

Explain the different forms of DNA?

1) Give the structures of purines and pyrimidines
2) Define nucleotide and Nucleoside
3) What are the different forms of DNA.
4) Explain the denaturation of Nucleic Acids & renaturation
8.7 References
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UNIT - III
LESSON 9: CELL ENERGETICS
Contents
9.1 Cell energetics
9.1.1 Glycolysis
9.1.2 Aerobic oxidation
9.1.3 Photosynthesis
9.2. Let us sum up
9.3. Points for Discussion
9.4. Check your Progress
9.5. Lesson-end activities
9.6. References

To know the steps in glycolysis and photosynthesis.
9.1. CELL ENERGETICS
The most important molecule for capturing and transferring free energy in biological
systems is adenosine triphosphate, or ATP. Under standard conditions, hydrolysis of the
terminal high-energy phosphoanhydride bond in ATP to yield adenosine diphosphate
(ADP) and inorganic phosphate (Pi) releases 7.3 kcal/mol of free energy. Cells can use
the energy released during this reaction to power many otherwise energetically
unfavorable processes, such as the transport of molecules against a concentration gradient
by ATP-powered pumps the movement (beating) of cilia, the contraction of muscle (and
the synthesis of proteins from amino acids and of nucleic acids from nucleotides).
Although other high-energy molecules occur in cells, ATP is the universal currency of
chemical energy; it is found in all types of organisms and must have occurred in the
earliest life- forms.
This chapter focuses on how cells generate the high-energy phosphoanhydride bond of
ATP from ADP and Pi. This endergonic reaction, which is the reverse of ATP hydrolysis
and requires an input of 7.3 kcal/mol to proceed, where Pi2- represents inorganic
phosphate (HPO42- ). The energy to drive this reaction is produced primarily by two
main processes aerobic oxidation, which occurs in nearly all cells, and photosynthesis,
which occurs only in leaf cells of plants and certain single-celled organisms.
9.1.1 Glycolysis
Pathway
The most common and well-known type of glycolysis is the Embden-Meyerhof pathway.
Glycolysis is a metabolic pathway by which a 6-carbon glucose (Glc) molecule is
oxidized to two molecules of pyruvic acid (Pyr). The word glycolysis is derived from
Greek (sweet) and (rupture). It is the initial process of most carbohydrate
catabolism, and it serves three principal functions:
Fig. 36. Pathway of Glycolysis
Fig. 37 Pathway of Glycolysis
The generation of high-energy molecules (ATP and NADH) as cellular energy sources
as part of anaerobic and aerobic respiration.
Production of pyruvate for the citric acid cycle as part of aerobic respiration.
The production of a variety of six- and three-carbon intermediate compounds, which
may be removed at various steps in the process for other cellular purposes.
As the foundation of both aerobic and anaerobic respiration, glycolysis is the archetype of
universal metabolic processes known and occurring (with variations) in many types of
cells in nearly all organisms. Glycolysis, through anaerobic respiration, is the main
energy source in many prokaryotes, eukaryotic cells devoid of mitochondria (e.g. mature
erythrocytes) and eukaryotic cells under low oxygen conditions (e.g. heavily exercising
muscle or fermenting yeast).In eukaryotes and prokaryotes, glycolysis takes place within
the cytosol of the cell. In plant cells some of the glycolytic reactions are also found in the
Calvin- Benson cycle which functions inside the chloroplasts. The wide conservation
includes the most phylogenetically deep rooted extant organisms and thus it is considered
to be one of the most ancient metabolic pathways.
Regulation of glycolysis
Key enzymes: Glucokinase, Phosphofructokinase-1 & Pyruvate kinase.

Insulin stimulates the synthesis of key enzymes responsible for glycolysis.
The hormones epinephrine & glucagon increase cAMP level to activate cAMPdependent protein kinase which phosphorylates & inactivates pyruvate kinase &
inhibit glycolysis.
Phosphofructo kinase is involved in feed back control.
Inhibitors: Iodoacetate, arsenite & fluoride.

9.1.2 Aerobic Oxidation
In aerobic oxidation, fatty acids and sugars, principally glucose, are metabolized to CO2
a n d H 2 O, and the released energy is converted to the chemical energy of
phosphoanhydride bonds in ATP. In animal cells and most other nonphotosynthetic cells,
ATP is generated mainly by this process. The initial steps in the oxidation of glucose,
called glycolysis, occur in the cytosol in both eukaryotes and prokaryotes and do not
require O2 . The final steps, which require O2 , generate most of the ATP. In eukaryotes,
the later stages of aerobic oxidation occur in mitochondria, whereas in prokaryotes,
which lack mitochondria, many of the final steps occur on the plasma membrane. The
final stages of fatty acid metabolism sometimes occur in mitochondria and generate ATP;
in most eukaryotic cells, however, fatty acids are metabolized in peroxisomes without
production of ATP.
9.1.3 Photosynthesis
In photosynthesis, light energy is converted to the chemical energy of phosphoanhydride
bonds in ATP and stored in the chemical bonds of carbohydrates (primarily sucrose and
starch). Oxygen also is formed during photosynthesis. In plants and eukaryotic singlecelled algae, photosynthesis occurs in chloroplasts. Although they lack chloroplasts,
several prokaryotes also carry out photosynthesis by a mechanism similar to that in
chloroplasts. The oxygen generated during photosynthesis is the source of virtually all the
oxygen in the air, and the carbohydrates produced are the ultimate source of energy for
virtually all nonphotosynthetic organisms.
At first glance, photosynthesis and aerobic oxidation appear to have little in common.
However, a revolutionary discovery in cell biology is that bacteria, mitochondria, and
chloroplasts all use the same (or very nearly the same) process, called chemiosmosis (or
chemiosmotic coupling), to generate ATP from ADP and Pi . The immediate energy
sources that power ATP synthesis are the transmembrane proton concentration gradient
and electric potential (voltage gradient), collectively termed the protonmotive force. The
protonmotive force is generated by the stepwise movement of electrons from higher to
lower energy states via membrane-bound electron carriers. In mitochondria and
nonphotosynthetic bacterial cells, electrons from NADH (produced during the
metabolism of sugars, fatty acids, and other substances) are transferred to O2 , the ultimate
electron acceptor. In the thylakoid membrane of chloroplasts, energy absorbed from light
strips electrons from water (forming O2 ) and powers their movement to other electron
carriers, particularly NADP+; eventually these electrons are donated to CO2 to synthesize
carbohydrates. All these systems, however, contain some similar carriers that couple
electron transport to the pumping of protons (always from the cytosolic face to the
exoplasmic face of the membrane), thereby generating the protonmotive force.
Moreover, all cells utilize essentially the same kind of membrane protein, the F0F1
complex, to synthesize ATP. The F0F1 complex, also called ATP synthase and F0F1
ATPase, is a member of the F class of ATP-powered proton pumps . In all cases, the
F0F1 complex is positioned with the globular F1 segment, which catalyzes ATP
synthesis, on the cytosolic face of the membrane, so ATP is always formed on the
cytosolic face of the membrane .(Protons always flow through the F0F1 complex from
the exoplasmic to the cytosolic face of the membrane, driven by a combination of the
proton concentration gradient (exoplasmic face > cytosolic face) and the membrane
electric potential (exoplasmic face positive with respect to the cytosolic face).
In addition to powering ATP synthesis, the protonmotive force can supply energy for the
transport of small molecules across a membrane against a concentration gradient
example, the uptake of lactose by certain bacteria is catalyzed by a H+/sugar symport
protein, and the accumulation of ions and sucrose by plant vacuoles is catalyzed by
proton-driven antiporters. The rotation of bacterial flagella is also powered by the protonmotive force; in contrast, the beating of eukaryotic cilia is powered by ATP hydrolysis.
Conversely, hydrolysis of ATP by V-class ATP-powered proton pumps, which are
similar in structure to P-class pumps ,provides the energy for transporting protons against
a concentration gradient. Chemiosmotic coupling thus illustrates an important principle
introduced in our discussion of active transport in: the membrane potential, the
concentration gradients of protons (and other ions) across a membrane, and the
phosphoanhydride bonds in ATP are equivalent and interconvertible forms of chemical
potential energy.
9.2 Let Us Sum Up

1. The most important molecule for capturing and transferring free energy in
biological systems is adenosine triphosphate, or ATP.
2. The energy to drive this reaction is produced primarily by aerobic oxidation, and
photosynthesis.
3. Glucokinase, Phosphofructokinase-1 & Pyruvate kinase are the key enzymes for
glycolysis.
4. Iodoacetate, arsenite & fluoride are the inhibitors for glycolysis.
9. 3 Points for Discussion

Glycolysis is the formulation for both aerobic and anaerobic respiration
Substantiate.

1. Describe the Cell energetics and Glycolysis.
2. What is photosynthesis?

Give an account of anaerobic respiration. Give an Example.
9.6 References
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LESSON 1 0 : UTILIZATION OF GLUCOSE, FAT AND

PROTEIN.
Contents
10.1 Introduction
10.2 Let us Sum Up
10.6 References

As already mentioned, metabolism refers to the chemical reactions carried out inside of
the cell. The major metabolic reactions which we will study are those involving
catabolism which is the breakdown of larger molecules to extract energy. We will focus
our discussion on the individual steps in the metabolic reactions where energy is
produced. Some attention will also be given to the synthesis of other biomolecules.
The overall reaction for the combustion of glucose is written:
C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + energy
10.1 Introduction
Although the above equation represents the overall metabolic reaction for
carbohydrates, there are actually over thirty individual reactions. Each reaction is
controlled by a different enzyme. The failure of an enzyme to function may have serious
and possibly fatal consequences. Slightly less than half of the 686 kcal/mole of the
energy produced by combustion is available for storage and use by the cell with the
remaining amount dissipated as heat.
Metabolism will be studied in various parts. Interrelationships will be pointed out
as they are encountered. Just as there are three basic biomolecules - carbohydrates, lipids,
and proteins, the metabolism of each of these will be studied individually. T h e
interrelationships of the major components in metabolism are diagramed in Figure 1. At
the end of the study of metabolism, you may be asked to diagram portions of it from
memory. A complete diet must supply the elements; carbon, hydrogen, oxygen, nitrogen,
phosphorus, sulfur, and at least 18 other inorganic elements. The major elements are
supplied in carbohydrates, lipids, and protein. In addition, at least 17 vitamins and water
are necessary. If an essential nutrient is omitted from the diet, certain deficiency
symptoms appear.
Carbohydrates: Foods supply carbohydrates in three forms: starch, sugar, and cellulose
(fiber). Starch and sugar are major and essential sources of energy for humans. A lack of
carbohydrates in the diet would probably result in an insufficient number of calories in

the diet. Cellulose furnishes bulk in the diet.
Since the tissues of the body need glucose at all times, the diet must contain substances
such as carbohydrates or substances which will yield glucose by digestion or metabolism.
For the majority of the people in the world, more than half of the diet consists of
carbohydrates from rice, wheat, bread, potatoes, macaroni.
Proteins: All life requires protein since it is the chief tissue builder and part of every cell
in the body. Among other functions, proteins help to: make hemoglobin in the blood that
carries oxygen to the cells; form anti-bodies that fight infection; supply nitrogen for DNA
and RNA genetic material; and supply energy.
Proteins are necessary for nutrition because they contain amino acids. Among the 20 or
more amino acids, the human body is unable to synthesize 8, therefore, these amino acids
are called essential amino acids. A food containing protein may be of poor biological
value if it is deficient in one or more of the 8 essential amino acids: lysine, tryptophan,
methionine, leucine, isoleucine, phenylalanine, valine, and threonine. Proteins of animal
origin have the highest biological value because they contain a greater amount of the
essential amino acids. Foods with the best quality protein are listed in diminishing quality
order: whole eggs, milk, soybeans, meats, vegetables, and grains.
Fats and Lipids: Fats are concentrated sources of energy because they give twice as
much energy as either carbohydrates or protein on a weight basis. The functions of fats
are to: make up part of the structure of cells, form a protective cushion and heat
insulation around vital organs, carry fat soluble vitamins, and provide a reserve storage
for energy. Three unsaturated fatty acids which are essential include: linoleic, linolinic,
and arachidonic and have 2, 3, and 4 double bonds respectively. Saturated fats, along
with cholesterol, have been implicated in arteriosclerosis, "hardening of the arteries". For
this reason, the diet should be decreased in saturated fats (animal) and increased in
unsaturated fat (vegetable).
a) MH + NAD+ ---> NADH + H+ + M + energy
b) ADP + P + energy ---> ATP + H2 O
The major metabolic reactions which we will study are those involving
catabolism which is the breakdown of larger molecules to extract energy. We will focus
our discussion on the individual steps in the metabolic reactions where energy is
produced. Some attention will also be given to the synthesis of other biomolecules. The
overall reaction for the combustion of glucose is written:
C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + energy
Although the above equation represents the overall metabolic reaction for carbohydrates,
there are actually over thirty individual reactions. Each reaction is controlled by a
different enzyme. The failure of an enzyme to function may have serious and possibly
fatal consequences.
10.2 LET US SUM UP
Foods supply carbohydrates in three forms: starch, sugar, and cellulose (fiber).
All life requires protein since it is the chief tissue builder and part of every cell in
the body.
Fats are concentrated sources of energy because they give twice as much energy
as either carbohydrates or protein on a weight basis.

How glucose, fat and protein are effectively used within our body? Do an analysis.

Give an account of anaerobic respiration. Give an Example.

1. How the lipid molecules are getting utilized in the body?
2. Define carbohydrate, proteins, fats and lipids.
10.6 References
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UNIT - IV
LESSON 11: ENZYMES
Contents
11.1 Enzymes -Unit of Activity
11.2 Coenzymes And Metal Cofactors
11.3 Factors affecting enzymatic activity
11.4 Let us sum up
11.8 References
To know and understand the different enzymes and factors affecting enzymatic activity.
11.1 Enzymes -Unit of Activity
An enzyme is a protein made up of a sequence of the twenty amino acids. Its chemical
properties are effectively limited to those available from that limited number of building
blocks. Enzymes are globular proteins - their molecules are round in shape. They have an
area - usually thought of as a pocket-shaped gap in the molecule - which is called the
active site. Some enzymes are found inside cells (intracellular enzymes), and some especially digestive enzymes - are released so they have their effects outside the cell
(extracellular enzymes). Error! Hyperlink reference not valid.Only the substrate (or
substrates) fits/fit into the active site. There are several types of enzyme which contribute
to different types of biochemical reaction.
Fig. Biochemical reactions
The enzyme speeds up the process of conversion of substrates (reactants) into products usually so much that the reaction does not take place in the absence of enzyme.
Although the enzyme obviously joins with the substrate for a short while, the enzyme and
substrate split apart afterwards, releasing the enzyme. Thus the enzyme is not used up in
the process (unlike the substrate(s)), so it can continue to react if more substrate is
provided.
11.2 Coenzymes and Metal Cofactors
Coenzymes are small organic non-protein molecules that carry chemical groups between
enzymes. Many enzymes require additional help in catalysing their reaction from a
coenzyme or cofactor. This is a small organic molecule, or a metallic ion, which carry out
some part of the catalytic process beyond the chemical abilities of the enzyme itself.
Coenzymes can fill any gaps in the chemical armory of proteins by introducing other
types of chemical structures.
The name "coenzyme" suggests that a molecule has catalytic properties used in
cooperation with the enzyme proper,speed up the reaction but was itself unchanged .This
is certainly true of some coenzymes but other compounds, frequently referred to as
coenzymes, certainly undergo change. Examples of these are ATP (adenosine
triphosphate) which is changed to ADP (adenosine diphosphate) in many reactions and
NAD (nicotinamide adenine dinucleotide) which is changed to NADH (the reduced form
of NAD). The rationale behind referring to these compounds (which are really substrates
of the enzymes which use them) as coenzymes is that they are recycled by other
metabolic reactions which convert them back to the original compound again. Although
these coenzymes are changed by an individual enzyme reaction, and so are not truly
catalytic, they are not permanently changed in metabolism. They can therefore be
regarded as metabolically catalytic. Many coenzymes are phosphorylated water-soluble
vitamins and are also commonly made from nucleotides such as adenosine triphosphate,
the biochemical carrier of phosphate groups, or coenzyme A, the coenzyme that carries
acyl groups; eg., Vitamin and nucleotide derivatives like Ascorbic acid (Vitamin C) ;
Coenzyme A - Contains pantothenic acid (Vitamin B5) and ATP ; Coenzyme B12 ;
Riboflavin (B2) - FAD and FMN ; Thiamine pyrophosphate (B1) ; NAD and NADP Contain both a nucleotide and a Niacin (vitaimin B3) moiety.
Cofactor
A cofactor is a non-protein chemical compound that is bound tightly to an enzyme and is
required for catalysis. They can be considered "helper molecules/ions" that assist in
biochemical transformations. Certain substances such as water and various abundant ions
may be bound tightly by enzymes, but are not considered to be cofactors since they are
ubiquitous and rarely limiting. An enzyme without a cofactor is referred to as an

apoenzyme, and the completely active enzyme (in addition to the cofactor) is called a
holoenzyme.
Apoenzyme + cofactor <=> Holoenzyme.
Metal ions are common cofactors. In nutrition, the list of essential trace elements reflects
their role as cofactors. This list includes manganese, iron, cobalt, nickel, copper, zinc, and
molybdenum. Other organisms require additional metals, such as vanadium and tungsten.
The study of these cofactors falls under the area of bioinorganic chemistry. Some
cofactors undergo chemical changes during the course of a reaction, undergoing
reduction or oxidation. Nonetheless, as a catalyst, cofactors return to their original state in
the course of the catalytic cycle. They are not consumed. In this respect, cofactors differ
from substrates or coenzymes. In many cases, the cofactor includes both an inorganic and
organic components. One diverse set of examples are the heme proteins, which consists
of a porphyrin ring coordinated to iron. Cofactors vary in their location and the tightness
of their binding to the host enzyme. When bound tightly to the enzyme, cofactors are
called prosthetic groups. Loosely-bound cofactors typically associate in a similar fashion
to enzyme substrates. These are better described as coenzymes, which are organic
substances that directly participate as substrates in an enzyme reaction. Vitamins can
serve as precursors to coenzymes (e.g. vitamins B1, B2, B6, B12, niacin, folic acid) or as
coenzymes themselves (e.g. vitamin C).
11.3 Factors affecting enzymatic activity
Within the normal range, changes in temperature, pH, and concentrations of substrate and
enzyme affect the rate of reaction in accordance with predictable interactions between
enzyme and substrate molecules.
Effect of temperature:- http://www.biotopics.co.uk/other/hienz.html The effects of
temperature may be explained on the basis of kinetic theory - increased temperature
increases the speed of molecular movement and thus the chances of molecular collisions,
so within a narrow range (often 0-45C), the rate of reaction is proportional to the
temperature. It is often said that an enzyme's rate of reaction doubles for every 10C rise
in temperature. However, the interaction between this positive effect of increased
temperature and the negative effect results in a different situation, so that enzymes may
be said to have an optimum temperature for their action. Like most chemical reactions,
the rate of an enzyme-catalyzed reaction increases as the temperature is raised. A 10C
rise in temperature will increase the activity of most enzymes by 50 to 100%. Variations
in reaction temperature as small as 1 or 2 degrees may introduce changes of 10 to 20% in
the results. In the case of enzymatic reactions, this is complicated by the fact that many
enzymes are adversely affected by high temperatures. As shown in figure, the reaction
rate increases with temperature to a maximum level, then abruptly declines with further
increase of temperature. Because most animal enzymes rapidly become denatured at
temperatures above 40C, most enzyme determinations are carried out somewhat below
that temperature. Over a period of time, enzymes will be deactivated at even moderate
temperatures. Storage of enzymes at 5C or below is generally the most suitable. Some
enzymes lose their activity when frozen.
Effects of pH:- Changes in the pH probably affect the attraction between the substrate
and enzyme, and thus the efficiency of the conversion process. Often, there is a n
optimum pH - near to pH 7 (neutral) in intracellular enzymes, and either in the acidic
range (perhaps pH 1- 6) or in the alkaline range (pH 8-14) for different digestive
enzymes. The most favorable pH value - the point where the enzyme is most active - is
known as the optimum pH. Extremely high or low pH values generally result in complete
loss of activity for most enzymes. pH is also a factor in the stability of enzymes. As with
activity, for each enzyme there is also a region of pH optimal stability.
Fig. 39 Graph depicting pH stability

Presence of other substances:- Some enzymes work better if other substances are also
present. Some enzymes (pepsin - from the stomach) work better if acid is present e.g.
lipases are more effective if emulsifying agents are present because they break up the
substrate into smaller droplets. Above normal temperatures (60 C), heat alters
irreversibly the enzyme molecule. This denaturation is due to molecular vibrations
(caused by heat) which change the shape of the protein, altering the folding and internal
cross- linkages in its polypeptide chains. These changes - especially in the region of the
active site - mean that the enzyme is inactivated, even when returned to normal
temperature.
The higher the temperature to which the enzyme is subjected and the longer the heating is
continued, the greater the proportion of damaged enzyme molecules and the result is that
the conversion process becomes less and less efficient. Below normal temperatures,
enzymes become less and less active, due to reductions in speed of molecular movement,
but this is reversible, so enzymes work effectively when returned to normal temperature.
Enzymes are sometimes adversely affected by other chemical substances which combine
with them, either at their active site or by altering the overall shape of their molecule.
http://www.biotopics.co.uk/other/aninac.html
Fig. 40 Enzyme Reactions
11.4 Let Us Sum Up

1. An enzyme is a protein made up of a sequence of the twenty protein amino acids.
2. They have an area - usually thought of as a pocket-shaped gap in the molecule which is called the active site.
3. Within the normal range, changes in temperature, pH, and concentrations of
substrate and enzyme affect the rate of reaction in accordance with predictable
interactions between enzyme and substrate molecules. There are approximately
3000 enzymes which have been characterised.
4. These are grouped into six main classes according to the type of reaction
catalysed. Such as Oxidoreductases ,Transferases, Hydrolases, Lyases,
Isomerases, Ligases.
5. The mechanism of enzyme action can be described in two ways. First one is using
Lock and Key hypothesis and the second one is Induced fit model.

The enzyme activity is affected more by the pH than temperature Comment.
11.6 Check Your Progress

Give the effect of pH and temperature on enzymes?

1. What are enzymes?
2. Explain the unit of activity of the enzymes?
3) What are the main factors which affect enzymatic activity?
3) Explain the Lock and key model of the active site.
4) Explain the Induced fit model of the active site.
11.7 References
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LESSON 12: MICHAELIS MENTON KINETICS

Contents
12.1 Deriving the Michaelis Menton Equation

12.2 Enzyme Inhibitions
12.3 Enzyme Activators
12.4 Let us Sum Up
12.7 Lesson-end Activities
12.8 References
To learn to derive Michaelis Menton equation and to understand the enzyme
inhibitors and activators.
12.1 Deriving the Michaelis-menten equation
Start with the generalised scheme for enzyme-catalysed production of a product (P) from
substrate (S). The enzyme (E) does not magically convert S into P, it must first come into
physical contact with it, i.e. E binds S to form an enzyme-substrate complex
(ES). Michaelis and Menten therefore set out the following scheme:
. . . . (1)
The terms k1 , k-1 and k2 are rate constants respectively corresponding to the association
of substrate and enzyme, the dissociation of unaltered substrate from the enzyme and the
dissociation of product (= altered substrate) from the enzyme. Note that there is the
theoretical possibility of a reverse reaction, with ES complex forming from E and P, but
this can be ignored because we are considering initial rates of reaction, i.e. when the
enzyme is first provided with substrate, so there should not be any product available to
combine with enzyme.
The overall rate of the reaction (v) is limited by the step ES to E + P, and this will depend
on two factors - the rate of that step (i.e. k2 ) and the concentration of enzyme that has
substrate bound, i.e. [ES]. This can be written as:
. . . (2)
At this point it is important to draw your attention to two assumptions that are
made in this scheme. The first is the availability of a vast excess of substrate, so that
[S]>>[E]. Secondly, it is assumed that the system is in steady-state, i.e. that the ES
complex is being formed and broken down at the same rate, so that overall [ES] is
constant. The formation of ES will depend on the rate constant K1 and the availability of
enzyme and substrate, i.e. [E] and [S]. The breakdown of [ES] can occur in two ways,
either the conversion of substrate to product or the non-reactive dissociation of substrate
from the complex. In both instances the [ES] will be significant. Thus, at steady state we
can write:
. . . (3)
The next couple of steps are rearrangements of this equation. First of all we can collect
together the rate constants on the right- hand side because they are both multiplied by
[ES], this gives us:
. . . (4)
Then dividing both sides by (k-1 + k2 ), this becomes:
. . . (5)
Note that the three rate constants are now on the same side of the equation. As the name
implies, these terms are constants, so we can actually combine them into one term. This
new constant is termed the Michaelis constant and is written KM.
. . . . (6)
Notice that the three rate constants in the definition of KM are actually inverted (the other
way up) compared with our previous equation. This is a 'trick' that makes for easier
calculation at a later stage. Substituting this definition of KM into our previous equation
now gives us:
. . . . (7)
The total amount of enzyme in the system must be the same throughout the experiment,
but it can either be free (unbound) E or in complex with substrate, ES. If we term the
total enzyme E0 , this relationship can be written out:
. . . (8)
This can be rearranged (by subtracting [ES] from each side) to give:
. . . . (9)
So, the [E] free in solution is equal to the total amount of enzyme minus the amount that
has substrate bound. Substituting this definition of [E] back into equation 2 gives us:
. . . (10)
This can now be rearranged in several steps. First of all, open the bracket so that the
terms [E0 ] and [ES] are separately multiplied by [S]
. . . (11)
Next, multiply each side by KM, this gives us:
. . . (12)
Then collect the two [ES] terms together on the same side (you can either think of this as
adding [ES][S] to both sides or as carry over and change the sign your preference will
probably be an indication of how long ago you went to school). This gives:
. . . (13)
Then because both terms on the right- hand side are multiplied by [ES] we can collect
them together into a bracket:
. . . (14)
Dividing both sides by (KM + [S]) now gives us:
. . . (15)
Substituting this left-hand side into in place of [ES] results in:
. . . . (16)
The maximum rate, which we can call Vmax, would be achieved when all of the enzyme
molecules have substrate bound. Under conditions when [S] is much greater than [E], it
is fair to assume that all E will be in the form ES. Therefore [E0 ] = [ES]. Thinking again
about Equation 1, we could substitute the term Vmax for v and [E0 ] for [ES]. This would
give us:
. . . (17)
Notice that k2 [E0 ] was present in our previous equation, so we can replace this with
Vmax, giving a final equation:
. . . (18)
This final equation is actually called the Michaelis-Menten equation.
Perhaps this derivation still leaves you puzzled about the importance of the MichaelisMenten equation. The significance becomes clearer when you consider the case when the
rate of reaction (v) is exactly half of the maximal reaction rate (Vmax). Under those
circumstances, the Michaelis-Menten equation could be written:
. . . (19)
On dividing both sides by Vmax this becomes:
. . . (20)
Multiplying both sides by (KM + [S]) gives:
. . . (21)
And then multiplying both sides by 2 further resolves the equation to:
. . . (22)
2[S] on the right-hand side is the same as [S] + [S], so we can take away one [S] from
each side. Thus when the rate of the reaction is half of the maximum rate:
. . . (23)
The KM of an enzyme is therefore the substrate concentration at which the reaction occurs
at half of the maximum rate.
Fig. 41 Graph showing the Km status of an enzyme

12.2 Enzyme inhibitors
Reversible inhibitors bind to enzymes with non-covalent interactions such as hydrogen
bonds, hydrophobic interactions and ionic bonds. Multiple weak bonds between the
inhibitor and the active site combine to produce strong and specific binding. In contrast to
substrates and irreversible inhibitors, reversible inhibitors generally do not undergo
chemical reactions when bound to the enzyme and can be easily removed by dilution or
dialysis.There are three kinds of reversible enzyme inhibitors. They are classified
according to the effect of varying the concentration of the enzyme's substrate on the
inhibitor.
a) A competitive inhibition, where the substrate and inhibitor cannot bind to the
enzyme at the same time. This usually results from the inhibitor having an affinity
for the active site of an enzyme where the substrate also binds; the substrate and
inhibitor compete for access to the enzyme's active site. This type of inhibition
can be overcome by sufficiently high concentrations of substrate, i.e., by outcompeting the inhibitor. Competitive inhibitors are often similar in structure to the
real substrate.
b) Mixed inhibition, where the inhibitor can bind to the enzyme at the same time as
the enzyme's substrate. However, the binding of the inhibitor affects the binding
of the substrate, and vice versa. This type of inhibition can be reduced, but not
overcome by increasing concentrations of substrate. Although it is possible for
mixed-type inhibitors to bind in the active site, this type of inhibition generally
results from an allosteric effect where the inhibitor binds to a different site on an
enzyme. Inhibitor binding to this allosteric site changes the conformation (i.e.,
tertiary structure or three-dimensional shape) of the enzyme so that the affinity of
the substrate for the active site is reduced.
c) Non-competitive inhibition is a form of mixed inhibition where the binding of the
inhibitor to the enzyme reduces its activity but does not affect the binding of
substrate. As a result, the extent of inhibition depends only on the concentration
of the inhibitor.
12.3 Enzyme activator:

A substance, other than the catalyst or one of the substrates, that increases the rate of a
catalysed reaction without itself being consumed; the process is called activation. An
activator of an enzyme-catalysed reaction may be called enzyme activator, if it acts by
binding to the enzyme eg., fructose 2,6-bisphosphate, which activates
phosphofructokinase 1 and increases the rate of glycolysis in response to the hormone
glucagon.
12.4 Let Us Sum Up

1. Michaelis-Menten kinetics describes the kinetics of many enzymes.
2. To determine the maximum rate of an enzyme mediated reaction, the substrate
concentration ([S]) is increased until a constant rate of product formation is
achieved.
3. This is the maximum velocity (Vmax) of the enzyme. This equation can be
derived from the basic substate-product enzyme reaction.
4. Enzyme inhibitors are molecules that bind to enzymes and decrease their activity.
The binding of an inhibitor can stop a substrate from entering the enzyme's active
site and/or hinder the enzyme from catalysing its reaction.
5. Many drug molecules are enzyme inhibitors, so their discovery and improvement
is an active area of research in biochemistry and pharmacology.
6. Reversible inhibitors bind to enzymes with non-covalent interactions such as
hydrogen bonds, hydrophobic interactions and ionic bonds.

Do a critical analysis of Michaelis Menton kinetics and the equations involved.

Describe about enzyme inhibitors and enzyme activators?

1. Explain the Michaelis menton equation.
2. What are enzyme inhibitors? Explain the types of enzyme inhibitors.
12.8 References
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LESSON 13: MECHANISM OF ENZYME ACTION

Contents
13.1 Lack and Key model of the active site
13.2 Induced fit model of the active site
13.3 Let us Sum Up
13.7 References

To learn the types of the active site and their significance.
13.1 Lock and key model of the active site:

In the picture below, the active site of the enzyme and the substrate have complementary
shapes. This is so illustrated to indicate that the enzyme can recognize the substrate
based, at least in part, on its shape. Secondly, it is meant to illustrate that the enzyme and
substrate form a very close interaction. Thirdly, it shows that the substrate will
preferentially bind to the active site and not to other sites on the enzyme.
Fig. 42 Lack and key model
13.2 Induced fit model of the active site:

In the induced fit model of enzyme-substrate binding, the shape of the active site of the
unbound enzyme is not the exact complement of the shape of the substrate. However, the
enzyme does bind to the substrate. After binding of the enzyme to the substrate is
initiated, a conformational change in the shape of the active site which results in a new
shape of the active site that is complementary to the shape of the substrate.
Fig. 43 Induced fit model of the active site

Isozymes
Isozymes were first described by Hunter and Markert (1957) who defined them as
different variants of the same enzyme having identical functions and present in the same
individual. This definition encompasses (1) enzyme variants that are the product of
different genes and thus represent different loci (described as isozymes) and (2) enzymes
that are the product of different alleles of the same gene (described as allozymes).
Isozymes are usually the result of gene duplication, but can also arise from
polyploidisation or nucleic acid hybridization. Over evolutionary time, if the function of
the new variant remains identical to the original, then it is likely that one or the other will
be lost as mutations accumulate, resulting in a pseudogene. However, if the mutations do
not immediately prevent the enzyme from functioning, but instead modify either its
function, or its pattern of gene expression, then the two variants may both be favoured by
natural selection and become specialised to different functions. For example, they may be
expressed at different stages of development or in different tissues. Glucokinase, a variant
of hexokinase which is not inhibited by glucose 6-phosphate. Its different regulatory
features and lower affinity for glucose (compared to other hexokinases), allows it to serve
different functions in cells of specific organs, such as control of insulin release by the
beta cells of the pancreas, or initiation of glycogen synthesis by liver cells. Both of these
processes must only occur when glucose is abundant, or problems occur.
Allozymes may result from point mutations or from insertion-deletion (indel) events that
affect the DNA coding sequence of the gene. As with any other new mutation, there are
three things that may happen to a new allozyme:
a) It is most likely that the new allele will be non-functional in which case it will
probably result in low fitness and be removed from the population by natural
selection.
b) Alternatively, if the amino acid residue that is changed is in a relatively
unimportant part of the enzyme, for example a long way from the active site then
the mutation may be selectively neutral and subject to genetic drift.
c) In rare cases the mutation may result in an enzyme that is more efficient, or one
that can catalyse a slightly different chemical reaction, in which case the mutation
may cause an increase in fitness, and be favoured by natural selection.
Allosteric Enzymes
Enzymes which contain regions to which small, regulatory molecules (cf. effector) may
bind in addition to and separate from substrate binding sites. On binding the effector, the
catalytic activity of the enzyme towards the substrate may be enhanced, in which case the
effector is an activator, or reduced, in which case it is an inhibitor. In addition to simple
enzymes that interact only with substrates and inhibitors,there is a class of enzymes that
bind substrate and small, physiologically important molecules in ways other than those
described above. These are known as allosteric enzymes; the small regulatory molecules
to which they bind are known as effectors. If you examine the Michaelis-Menten
equation you will find that an increase in V from 0.1 to 0.9 Vmax requires an 81- fold
change in substrate concentration. In other words the velocity is rather insensitive to
substrate concentration. Allosteric enzymes are "co-operative" systems,in which a small
change in one parameter, e.g. substrate, inhibitor, activator concentration, brings about a
large change in velocity. A consequence of a cooperative system is that the V vs. S plot is
no longer hyperbolic.To understand allosterism one must understand that it is based on
ligand interactions and conformational changes.
Allosteric effectors bring about catalytic modification by binding to the enzyme at
distinct allosteric sites, well removed from the catalytic site, and causing conformational
changes that are transmitted through the bulk of the protein to the catalytically active
site(s). The hallmark of effectors is that when they bind to enzymes, they alter the
catalytic properties of an enzyme's active site. Those that increase catalytic activity are
known as positive effectors. Effectors that reduce or inhibit catalytic activity are negative
effectors.
Most allosteric enzymes are oligomeric (consisting of multiple subunits); generally they
are located at or near branch points in metabolic pathways, where they are influential in
directing substrates along one or another of the available metabolic paths. The effectors
that modulate the activity of these allosteric enzymes are of two types. Those activating
and inhibiting effectors that bind at allosteric sites are called heterotropic effectors. These
effectors can assume a vast diversity of chemical forms, ranging from simple inorganic
molecules to complex nucleotides such as cyclic adenosine monophosphate (cAMP).
Their single defining feature is that they are not identical to the substrate.The substrate
itself induces distant allosteric effects when it binds to the catalytic site. Substrates acting
as effectors are said to be homotropic effectors. When the substrate is the effector, it can
act as such, either by binding to the substrate-binding site, or to an allosteric effector site.
When the substrate binds to the catalytic site it transmits an activity- modulating effect to
other subunits of the molecule. Often used as the model of a homotropic effector is
haemoglobin, although it is not a branch-point enzyme and thus does not fit the definition
on all counts.
13.3 Let Us Sum Up

1. Coenzymes are small organic non-protein molecules that carry chemical groups
between enzymes. Examples of these are ATP (adenosine triphosphate) which is
changed to ADP (adenosine diphosphate) in many reactions and NAD
(nicotinamide adenine dinucleotide) which is changed to NADH (the reduced
form of NAD).
2. A cofactor is a non-protein chemical compound that is bound tightly to an enzyme
and is required for catalysis.
3. Isozymes are usually the result of gene duplication, but can also arise from
polyploidisation or nucleic acid hybridization.
4. They are different variants of the same enzyme having identical functions and
present in the same individual.
5. Allozymes may result from point mutations or from insertion-deletion (indel)
events that affect the DNA coding sequence of the gene.
6. Allosteric enzymes are "co-operative" systems,in which a small change in one
parameter.

Do a comparative study on isozymes and allozymes.

Explain Isoenzymes and allosteric enzyme?

1. Explain coenzymes and metal cofactors?
2. Describe isoenzymes with example.
3. Explain allosteric enzymes in detail.
4. How enzymes are used as molecular markers?
13.7 References
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UNIT - V
Lesson -14: CELL CYCLE
Contents
14.1 Mitosis
14.2 Phases of Mitosis
14.2.1 Metaphase
14.2.2 Anaphase
14.2.3 Telophase
14.2.4 Cytokinesis
14.2.5 G1 phase
14.2.6 S phase
14.2.7 G2 phase
14.2.8 G0 phase
14.2.9 Regulation of cell cycle
14.2.10 Role of Cyclins and CDKs
14.2.11 General mechanism of cyclin-CDK interaction
14.2.12 Specific action of cyclin-CDK complexes
14.2.13 Cell cycle inhibitors
14.3 Let us Sum Up

14.7 References

To know the stages of Mitosis elaborately.
The cell cycle, or cell-division cycle, is the series of events that take place in a eukaryotic
cell leading to its replication. These events can be divided in two broad periods:
interphaseduring which the cell grows, accumulating nutrients needed for mitosis and
duplicating its DNAand the mitotic (M) phase, during which the cell splits itself into
two distinct cells, often called "daughter cells". The cell-division cycle is an essential
process by which a single-celled fertilized egg develops into a mature organism, as well
as the process by which hair, skin, blood cells, and some internal organs are renewed.The
cell cycle consists of four distinct phases: G1 phase, S phase, G2 phase (collectively
known as interphase) and M phase. M phase is itself composed of two tightly coupled
processes: mitosis, in which the cell's chromosomes are divided between the two
daughter cells, and cytokinesis, in which the cell's cytoplasm divides forming distinct
cells. Activation of each phase is dependent on the proper progression and completion of
the previous one. Cells that have temporarily or reversibly stopped dividing are said to
have entered a state of quiescence called G0 phase
14.1 Mitosis:
Mitosis is the process in which a cell duplicates its chromosomes to generate two
identical cells. It is generally followed by cytokinesis which divides the cytoplasm and
cell membrane. This results in two identical cells with an equal distribution of organelles
and other cellular components. Mitosis and cytokinesis jointly define the mitotic (M)
phase of the cell cycle, the division of the mother cell into two sister cells, each with the
genetic equivalent of the parent cell. Mitosis occurs most often in eukaryotic cells. In
multicellular organisms, the somatic cells undergo mitosis, while germ cells cells
destined to become sperm in males or ova in females divide by a related process called
meiosis.
Cytokinesis usually occurs in conjunction with mitosis, However, there are many cells
whose mitosis and cytokinesis occur separately, forming single cells with multiple nuclei.
This occurs most notably among the fungi and slime moulds, but is found in various
different groups. Even in animals, cytokinesis and mitosis may occur independently, for
instance during certain stages of fruit fly embryonic development.Errors in mitosis can
either kill a cell through apoptosis or cause mutations that may lead to cancer or cell
death. The process of Mitosis can be divided into seven stages: Preprophase, Prophase,
Prometaphase, Metaphase, Anaphase, Telophase and Cytokinesis.
Interphase: The mitotic phase is a relatively short period of the cell cycle. It alternates
with the much longer interphase, where the cell prepares itself for cell division.
Interphase is divided into three phases, G1 (first gap), S (synthesis), and G2 (second gap).
During all three phases, the cell grows by producing proteins and cytoplasmic organelles.
However, chromosomes are replicated only during the S phase. Thus, a cell grows (G1),
grows as it duplicates its chromosomes (S), grows more and prepares for mitosis (G2),
and divides (M).
After M phase, the daughter cells each begin interphase of a new cycle. Although the
various stages of interphase are not usually morphologically distinguishable, each phase
of the cell cycle has a distinct set of specialized biochemical processes that prepare the
cell for initiation of cell division.
Preprophase: In plant cells only, prophase is preceded by a pre-prophase stage and
followed by a post-prophase stage. In plant cells that are highly vacuolated and somewhat
amorphoric, the nucleus has to migrate into the center of the cell before mitosis can
begin. This is achieved through the formation of a phragmosome, a transverse sheet of
cytoplasm that bisects the cell along the future plane of cell division. In addition to
phragmosome formation, preprophase is characterized by the formation of a ring of
microtubules and actin filaments (called preprophase band) underneath the
plasmamembrane around the equatorial plane of the future mitotic spindle and predicting
the position of cell plate fusion during telophase. The cells of higher plants (such as the
flowering plants) lack centrioles. Instead, spindle microtubules aggregate on the surface
of the nuclear envelope during prophase. The preprophase band disappears during nuclear
envelope disassembly and spindle formation in prometaphase.
Prophase: Normally, the genetic material in the nucleus is in a loosely bundled coil
called chromatin. At the onset of prophase, chromatin condenses together into a highly
ordered structure called a chromosome. Since the genetic material has already been
duplicated earlier in S phase, the replicated chromosomes have two sister chromatids,
bound together at the centromere by the cohesion complex. Chromosomes are visible at
high magnification through a light microscope. Close to the nucleus are two centrosomes.
Each centrosome, which was replicated earlier independent of mitosis, acts as a
coordinating center for the cell's microtubules. The two centrosomes nucleate
microtubules (or microfibrils) (which may be thought of as cellular ropes) by
polymerizing soluble tubulin present in the cytoplasm. Molecular motor proteins create
repulsive forces that will push the centrosomes to opposite side of the nucleus. The
centrosomes are only present in animals. In plants the microtubules form independently.
Some centrosomials contain a pair of centrioles that may help organize microtubule
assembly, but they are not essential to formation of the mitotic spindle.
Prometaphase: The nuclear envelope disassembles and microtubules invade the nuclear
space. This is called open mitosis, and it occurs in most multicellular organisms. Fungi
and some protists, such as algae or trichomonads, undergo a variation called closed
mitosis where the spindle forms inside the nucleus or its microtubules are able to
penetrate an intact nuclear envelope. Each chromosome forms two kinetochores at the
centromere, one attached at each chromatid. A kinetochore is a complex protein structure
that is analogous to a ring for the microtubule hook; it is the point where microtubules
attach themselves to the chromosome. Although the kinetochore structure and function
are not fully understood, it is known that it contains some form of molecular motor.
When a microtubule connects with the kinetochore, the motor activates, using energy
from ATP to "crawl" up the tube toward the originating centrosome. This motor activity,
coupled with polymerisation and depolymerisation of microtubules, provides the pulling
force necessary to later separate the chromosome's two chromatids.
Fig. 44 Mitosis - Phases

When the spindle grows to sufficient length, usually at least 7 nanometers, kinetochore
microtubules begin searching for kinetochores to attach to. A number of nonkinetochore
microtubules find and interact with corresponding nonkinetochore microtubules from the
opposite centrosome to form the mitotic spindle. Prometaphase is sometimes considered
part of prophase.
14.2 Phases of Mitosis

14.2.1 Metaphase:
As microtubules find and attach to kinetochores in prometaphase, the centromeres of the
chromosomes convene along the metaphase plate or equatorial plane, an imaginary line
that is equidistant from the two centrosome poles.[9] This even alignment is due to the
counterbalance of the pulling powers generated by the opposing kinetochores, analogous
to a tug-of-war between equally strong people. In certain types of cells, chromosomes do
not line up at the metaphase plate and instead move back and forth between the poles
randomly, only roughly lining up along the midline. Metaphase comes from the Greek
word for "metanosis" meaning "after." Because proper chromosome separation
requires that every kinetochore be attached to a bundle of microtubules (spindle fibers) ,
it is thought that unattached kinetochores generate a signal to prevent premature
progression to anaphasewithout all chromosomes being aligned. The signal creates the
mitotic spindle checkpoint.
14.2.2. Anaphase:
When every kinetochore is attached to a cluster of microtubules and the chromosomes
have lined up along the metaphase plate, the cell proceeds to anaphase (from the Greek
meaning up, against, back, or re- ).
Two events then occur; first, the proteins that bind sister chromatids together are cleaved,
allowing them to separate. These sister chromatids are hereafter independent sister
chromosomes. They are pulled apart by shortening kinetochore microtubules and toward
the respective centrosomes to which they are attached. This is followed by the elongation
of the nonkinetochore microtubules, which pushes the centrosomes (and the set of
chromosomes to which they are attached) apart to opposite ends of the cell. These three
stages are sometimes called early, mid and late anaphase. Early anaphase is usually
defined as the separation of the sister chromatids. Mid anaphase occurs with the
reunification of certain metastic chromatids. Late anaphase is the elongation of the
microtubules and the microtubules being pulled further apart. At the end of anaphase, the
cell has succeeded in separating identical copies of the genetic material into two distinct
populations.
14.2.3. Telophase:
Telophase (from the Greek meaning "end") is a reversal of prophase and
prometaphase events. It "cleans up" the after effects of mitosis. At telophase, the
nonkinetochore microtubules continue to lengthen, elongating the cell even more.
Corresponding sister chromosomes attach at opposite ends of the cell. A new nuclear
envelope, using fragments of the parent cell's nuclear membrane, forms around each set
of separated sister chromosomes. Both sets of chromosomes, now surrounded by new
nuclei, unfold back into chromatin. Mitosis is complete, but cell division is not yet
complete.
14.2.4. Cytokinesis:
Cytokinesis is often mistakenly thought to be the final part of telophase; however
cytokinesis is a separate process that begins after telophase. Cytokinesis is technically not
even a phase of mitosis, but rather a separate process, necessary for completing cell
division. In animal cells, a cleavage furrow (pinch) containing a contractile ring develops
where the metaphase plate used to be, pinching off the separated nuclei. In both animal
and plant cells, cell division is also driven by vesicles derived from the Golgi apparatus,
which move along microtubules to the middle of the cell. In plants this structure
coalesces into a cell plate at the center of the phragmoplast and develops into a cell wall,
separating the two nuclei. The phragmoplast is a microtubule structure typical for higher
plants, whereas some green algae use a phycoplast microtubule array during cytokinesis.
Each daughter cell has a complete copy of the genome of its parent cell. The end of
cytokinesis marks the end of the M-phase.
14.2.5. G1 phase:
The first phase within interphase, from the end of the previous M phase till the beginning
of DNA synthesis is called G1 (G indicating gap or growth). During this phase the
biosynthetic activities of the cell, which had been considerably slowed down during M
phase, resume at a high rate. This phase is marked by synthesis of various enzymes that
are required in S phase, mainly those needed for DNA replication. Duration of G1 is
highly variable, even among different cells of the same species.
14.2.6. S phase:
The ensuing S phase starts when DNA synthesis commences; when it is complete, all of
the chromosomes have been replicated, i.e., each chromosome has two (sister)
chromatids. Thus, during this phase, the amount of DNA in the cell has effectively
doubled, though the ploidy of the cell remains the same. Rates of RNA transcription and
protein synthesis are very low during this phase. An exception to this is histone
production, most of which occurs during the S phase. The duration of S phase is
relatively constant among cells of the same species.
14.2.7. G2 phase:
The cell then enters the G2 phase, which lasts until the cell enters the next round of
mitosis. Again, significant protein synthesis occurs during this phase, mainly involving
the production of microtubules, which are required during the process of mitosis.
Inhibition of protein synthesis during G2 phase prevents the cell from undergoing mitosis.
14.2.8. G0 phase:
The term "post- mitotic" is sometimes used to refer to both quiescent and senescent cells.
Nonproliferative cells in multicellular eukaryotes generally enter the quiescent G0 state
from G1 and may remain quiescent for long periods of time, possibly indefinitely (as is
often the case for neurons). This is very common for cells that are fully differentiated.
Cellular senescence is a state that occurs in response to DNA damage or degradation that
would make a cell's progeny nonviable; it is often a biochemical alternative to the selfdestruction of such a damaged cell by apoptosis. Some cell types in mature organisms,
such as parenchymal cells of the liver and kidney, enter the G0 phase semi-permanently
and can only be induced to begin dividing again under very specific circumstances; other
types, such as epithelial cells, continue to divide throughout an organism's life.
14.2.9. Regulation of cell cycle
Regulation of the cell cycle involves steps crucial to the cell, including detecting and
repairing genetic damage, and provision of various checks to prevent uncontrolled cell
division. The molecular events that control the cell cycle are ordered and directional; that
is, each process occurs in a sequential fashion and it is impossible to "reverse" the cycle.
14.2.10. Role of Cyclins and CDKs

Two key classes of regulatory molecules, cyclins and cyclin-dependent kinases (CDKs),
determine a cell's progress through the cell cycle. Leland H. Hartwell, R. Timothy Hunt,
and Paul M. Nurse won the 2001 Nobel Prize in Physiology or Medicine for their
discovery of these central molecules. Many of the genes encoding cyclins and CDKs are
conserved among all eukaryotes, but in general more complex organisms have more
elaborate cell cycle control systems that incorporate more individual components. Many
of the relevant genes were first identified by studying yeast, especially Saccharomyces
cerevisiae; genetic nomenclature in yeast dubs many of these genes cdc (for "cell division
cycle") followed by an identifying number, e.g., cdc25.
Cyclins form the regulatory subunits and CDKs the catalytic subunits of an activated
heterodimer; cyclins have no catalytic activity and CDKs are inactive in the absence of a
partner cyclin. When activated by a bound cyclin, CDKs perform a common biochemical
reaction called phosphorylation that activates or inactivates target proteins to orchestrate
coordinated entry into the next phase of the cell cycle. Different cyclin-CDK
combinations determine the downstream proteins targeted. CDKs are constitutively
expressed in cells whereas cyclins are synthesised at specific stages of the cell cycle, in
response to various molecular signals.
14.2.11. General mechanism of cyclin-CDK interaction
Upon receiving a pro- mitotic extracellular signal, G1 cyclin-CDK complexes become
active to prepare the cell for S phase, promoting the expression of transcription factors
that in turn promote the expression of S cyclins and of enzymes required for DNA
replication. The G1 cyclin-CDK complexes also promote the degradation of molecules
that function as S phase inhibitors by targeting them for ubiquitination. Once a protein
has been ubiquitinated, it is targeted for proteolytic degradation by the proteasome.
Active S cyclin-CDK complexes phosphorylate proteins that make up the pre-replication
complexes assembled during G1 phase on DNA replication origins. The phosphorylation
serves two purposes: to activate each already-assembled pre-replication complex, and to
prevent new complexes from forming. This ensures that every portion of the cell's
genome will be replicated once and only once. The reason for prevention of gaps in
replication is fairly clear, because daughter cells that are missing all or part of crucial
genes will die. However, for reasons related to gene copy number effects, possession of
extra copies of certain genes would also prove deleterious to the daughter cells.
Mitotic cyclin-CDK complexes, which are synthesized but inactivated during S and G2
phases, promote the initiation of mitosis by stimulating downstream proteins involved in
chromosome condensation and mitotic spindle assembly. A critical complex activated
during this process is a ubiquitin ligase known as the anaphase-promoting complex
(APC), which promotes degradation of structural proteins associated with the
chromosomal kinetochore. APC also targets the mitotic cyclins for degradation, ensuring
that telophase and cytokinesis can proceed.
14.2.12. Specific action of cyclin-CDK complexes

Cyclin D is the first cyclin produced in the cell cycle, in response to extracellular signals
(eg. growth factors). Cyclin D binds to existing CDK4, forming the active cyclin DCDK4 complex. Cyclin D-CDK4 complex in turn phosphorylates the retinoblastoma
susceptibility protein (RB). The hyperphosphorylated RB dissociates from the
E2F/DP1/RB complex (which was bound to the E2F responsive genes, effectively
"blocking" them from transcription), activating E2F. Activation of E2F results in
transcription of various genes like cyclin E, cyclin A, DNA polymerase, thymidine
kinase, etc. Cyclin E thus produced binds to CDK2, forming the cyclin E-CDK2
complex, which pushes the cell from G1 to S phase (G1/S transition). Cyclin A along
with CDK2 forms the cyclin A-CDK2 complex, which initiates the G2/M transition.
Cyclin B-CDK1 complex activation causes breakdown of nuclear envelope and initiation
of prophase, and subsequently, it's deactivation causes the cell to exit mitosis.
14.2.13. Cell cycle inhibitors
Two families of genes, the cip/kip family and the INK4a/ARF (Inhibitor of Kinase
4/Alternative Reading Frame) prevent the progression of the cell cycle. Because these
genes are instrumental in prevention of tumor formation, they are known as tumor
suppressors.The cip/kip family includes the genes p21, p27 and p57. They halt cell cycle
in G1 phase, by binding to, and inactivating, cyclin-CDK complexes. p21 is activated by
p53 (which, in turn, is triggered by DNA damage eg. due to radiation). p27 is activated
by Transforming Growth Factor (TGF ), a growth inhibitor.The INK4a/ARF family
includes p16INK4a, which binds to CDK4 and arrests the cell cycle in G1 phase, and
p14arf which prevents p53 degradation.
14.3 Let Us Sum Up

1) The cell cycle, or cell-division cycle, is the series of events that take place in a
eukaryotic cell leading to its replication.
2) Mitosis is the process in which a cell duplicates its chromosomes to generate two
identical cells.
3) Mitosis occurs most often in eukaryotic cells.
4) Mitosis contains Interphase, pre-prophase, prophase, Prometaphase, metaphase,
Anaphase, Telophase, and Cytokinesis.
5) Interphase is divided into three phases, G1 (first gap), S (synthesis), and G2
(second gap).
6) Regulation of the cell cycle involves detecting and repairing genetic damage, and
provision of various checks to prevent uncontrolled cell division.
7) Two families of genes, the cip/kip family and the INK4a/ARF (Inhibitor of
Kinase 4/Alternative Reading Frame) prevent the progression of the cell cycle.
8) Because these genes are instrumental in prevention of tumor formation, they are
known as tumor suppressors.

Mitosis is an essential part of the regulations of cell cycle Express your views.

Explain the prophase and prometaphase of mitosis.

1)
2)
3)
4)
Define cell cycle

What does it mean by the term interphase in cell division?
Describe the different steps involved in mitosis
Write notes on the regulation of cell cycle
14.7 References
New Delhi, India.
Publishers.
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Lesson 15: MEIOSIS

Contents
15.1 Meiosis I
15.1.1 Prophase I
15.2 Meiosis II
15.3 Let us Sum Up
15.7 References

To learn and understand the stages of meisosi.
In biology, meiosis is the process by which one diploid eukaryotic cell divides to
generate four haploid cells often called gametes. The word "meiosis" comes from the
Greek meioun, meaning "to make smaller," since it results in a reduction in chromosome
number in the gamete cell. During meiosis, the genome of a diploid germ cell, which is
composed of long segments of DNA packaged into chromosomes, undergoes DNA
replication followed by two rounds of division, resulting in haploid cells called gametes.
Each gamete contains one complete set of chromosomes, or half of the genetic content of
the original cell. These resultant haploid cells can fuse with other haploid cells of the
opposite sex or mating type during fertilization to create a new diploid cell, or zygote.
Thus, the division mechanism of meiosis is a reciprocal process to the joining of two
genomes that occurs at fertilization. Because the chromosomes of each parent undergo
genetic recombination during meiosis, each gamete, and thus each zygote, will have a
unique genetic blueprint encoded in its DNA. In other words, meiosis and sexual
reproduction produce genetic variation.
Growth 1 (G1) phase: Immediately follows cytogenesis. This is a very active period,
where cell synthesizes its vast array of proteins, including the enzymes and structural
proteins it will need for growth. In G1 stage each of the 46 human chromosomes consists
of a single (very long) molecule of DNA
Synthesis (S) phase: The genetic material is replicated: each of its chromosomes
duplicates. The cell is still diploid, however, because it still contains the same number of
centromeres. However, the identical sister chromatids are in the chromatin form because
spiralisation and condensation into denser chromosomes have not taken place yet. It will
take place in prophase I in meiosis.
Growth 2 (G2) phase: The cell continues to grow making the cell larger. Interphase is
immediately followed by meiosis I and meiosis II. Meiosis I consists of segregating the
homologous chromosomes from each other, then dividing the diploid cell into two
haploid cells each containing one of the segregates. Meiosis II consists of decoupling
each chromosome's sister strands (chromatids), segregating the DNA into two sets of
strands (each set containing one of each homolog), and dividing both haploid, duplicated
cells to produce four haploid, unduplicated cells. Meiosis I and II are both divided into
prophase, metaphase, anaphase, and telophase subphases, similar in purpose to their
analogous subphases in the mitotic cell cycle. Therefore, meiosis encompasses the
interphase (G1, S, G2), meiosis I (prophase I, metaphase I, anaphase I, telophase I), and
meiosis II (prophase II, metaphase II, anaphase II, telophase II).
15.1 Meiosis I
15.1.1 Prophase I
Leptotene: The first stage of prophase I is the leptotene stage, also known as leptonema,
from Greek words meaning "thin threads." During this stage, individual chromosomes
begin to condense into long strands within the nucleus. However the two sister
chromatids are still so tightly bound that they are indistinguishable from one another.
Zygotene: The zygotene stage, also known as zygonema, from Greek words meaning
"paired threads," occurs as the chromosomes approximately line up with each other into
homologous chromosomes. The combined homologous chromosomes are said to be
bivalent. They may also be referred to as a tetrad, a reference to the four sister
chromatids. The two chromatids become "zipped" together, forming the synaptonemal
complex, in a process known as synapsis.
Pachytene: The pachytene stage, also known as pachynema, from Greek words meaning
"thick threads, contains the chromosomal crossover. Nonsister chromatids of homologous
chromosomes randomly exchange segments of genetic information over regions of
homology. (Sex chromosomes, however, are not identical, and only exchange
information over a small region of homology.) Exchange takes place at sites where
recombination nodules have formed. The exchange of information between the non-sister
chromatids results in a recombination of information; each chromosome has the complete
set of information it had before, and there are no gaps formed as a result of the process.
Because the chromosomes cannot be distinguished in the synaptonemal complex, the
actual act of crossing over is not perceivable through the microscope.
Diplotene: During the diplotene stage, also known as diplonema, from Greek words
meaning "two threads," the synaptonemal complex degrades and homologous
chromosomes separate from one another a little. The chromosomes themselves uncoil a
bit, allowing some transcription of DNA. However, the homologous chromosomes of
each bivalent remain tightly bound at chiasmata, the regions where crossing over
occurred.
Diakinesis: Chromosomes condense further during the diakinesis stage, from Greek
words meaning "moving through."[1] This is the first point in meiosis where the four
parts of the tetrads are actually visible. Sites of crossing over entangle together,
effectively overlapping, making chiasmata clearly visible. Other than this observation,
the rest of the stage closely resembles prometaphase of mitosis; the nucleoli disappears,
the nuclear membrane disintegrates into vesicles, and the meiotic spindle begins to form.
Synchronous processes
During these stages, centrioles are migrating to the two poles of the cell. These centrioles,
which were duplicated during interphase, function as microtubule coordinating centers.
Centrioles sprout microtubules, essentially cellular ropes and poles, during crossing over.
They invade the nuclear membrane after it disintegrates, attaching to the chromosomes at
the kinetochore. The kinetochore functions as a motor, pulling the chromosome along the
attached microtubule toward the originating centriole, like a train on a track. There are
two kinetochores on each tetrad, one for each centrosome.
Prophase I is the longest phase in meiosis.Microtubules that attach to the kinetochores
are known as kinetochore microtubules. Other microtubules will interact with
microtubules from the opposite centriole. These are called nonkinetochore microtubules.
Metaphase I: Homologous pairs move together along the phase plate: as kinetochore
microtubules from both centrioles attach to their respective kinetochores, the homologous
chromosomes align along an equatorial plane that bisects the spindle, due to continuous
counterbalancing forces exerted on the bivalents by the microtubules emanating from the
two kinetochores. The physical basis of the independent assortment of chromosomes is
the random orientation of each bivalent along the metaphase plate.
Anaphase I: Kinetochore microtubules shorten, severing the recombination nodules and
pulling homologous chromosomes apart. Since each chromosome only has one
kinetochore, whole chromosomes are pulled toward opposing poles, forming two diploid
sets. Each chromosome still contains a pair of sister chromatids. Nonkinetochore
microtubules lengthen, pushing the centrioles further apart. The cell elongates in
preparation for division down the middle. In prophase 1 the DNA coils tightly and
individual chromosomes become visible under the light microscope. Homologous
chromosomes closely associated in synapsis and they exchange segments by crossing
over.
Telophase I: The first meiotic division effectively ends when the centromeres arrive at
the poles. Each daughter cell now has half the number of chromosomes but each
chromosome consists of a pair of chromatids. This effect produces a variety of responses
from the neuro-synrchromatic enzyme, also known as NSE. The microtubules that make
up the spindle network disappear, and a new nuclear membrane surrounds each haploid
set. The chromosomes uncoil back into chromatin. Cytokinesis, the pinching of the cell
membrane in animal cells or the formation of the cell wall in plant cells, occurs,
completing the creation of two daughter cells. Cells enter a period of rest known as
interkinesis or interphase II. No DNA replication occurs during this stage. Note that
many plants skip telophase I and interphase II, going immediately into prophase II.
15.2 Meiosis II
Prophase II takes an inversely proportional time compared to telophase I. In this
prophase we see the disappearance of the nucleoli and the nuclear envelope again as well
as the shortening and thickening of the chromatids. Centrioles move to the polar regions
and are arranged by spindle fibres. The new equatorial plane is rotated by 90 degrees
when compared to meiosis I, perpendicular to the previous plane.
In metaphase II, the centromeres contain three kinetochores, organizing fibers from the
centrosomes on each side. This is followed by anaphase II, where the centromeres are
cleaved, allowing the kinetochores to pull the sister chromatids apart. The sister
chromatids by convention are now called sister chromosomes, and they are pulled toward
opposing poles. The process ends with telophase II, which is similar to telophase I,
marked by uncoiling, lengthening, and disappearance of the chromosomes occur as the
disappearance of the microtubules. Nuclear envelopes reform; cleavage or cell wall
formation eventually produces a total of four daughter cells, each with a haploid set of
chromosomes. Meiosis is now complete.
Significance of meiosis
Meiosis facilitates stable sexual reproduction without the halving of ploidy, or
chromosome count, fertilization would result in zygotes that have twice the number of
chromosomes than the zygotes from the previous generation. Successive generations
would have an exponential increase in chromosome count, resulting in an unwieldy
genome that would cripple the reproductive fitness of the species. Polyploidy, the state of
having three or more sets of chromosomes, also results in developmental abnormalities or
lethality. Polyploidy is poorly tolerated in animal species. Plants, however, regularly
produce fertile, viable polyploids. Polyploidy has been implicated as an important
mechanism in plant speciation. Most importantly, however, meiosis produces genetic
variety in gametes that propagate to offspring. Recombination and independent
assortment allow for a greater diversity of genotypes in the population. As a system of
creating diversity, meiosis allows a species to maintain stability under environmental
changes.
15.3 Let Us Sum Up

1) Meiosis is the process by which one diploid eukaryotic cell divides to generate
four haploid cells often called gametes.
2) Meiosis encompasses the interphase (G1, S, G2), meiosis I (prophase I,
metaphase I, anaphase I, telophase I), and meiosis II (prophase II, metaphase II,
anaphase II, telophase II).
3) Meiosis facilitates stable sexual reproduction.
4) The normal separation of chromosomes in Meiosis I or sister chromatids in
meiosis II is termed disjunction.

Do a comparative study between mitosis and meiosis.

Give an account on meiosis I and the steps involved in it.

1.
2.
3.
4.
5.
Define meiosis
What is Diakinesis?
Write the mechanism of meiosis
What is the significance of meiosis in organisms?
What are Down's syndrome, Patau syndrome, Edward syndrome, Klinefelter
syndrome, Turner syndrome?
15.7 References
New Delhi, India.
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Lesson 16: DNA REPLICATION

Contents
16.1 DNA structure
16.2 Lagging strand synthesis
16.3 Leading strand synthesis
16.4 Dynamics at the replication fork
16.5 Mechanism of replication
16.6 DNA replication in enbacteria initiation of replication and the
bacterial origin.
16.7 Termination of replication
16.8 Regulation of replication
16.9 Rolling circle replication
16.10 Plasmid replication
16.11 Let us Sum Up
16.15 References
To study the DNA structure and its replication.
16.1 DNA Structure
A DNA strand is a long polymer built from nucleotides; two complementary DNA
strands form a double helix. The two strands in the DNA backbone run anti-parallel to
each other: One of the DNA strands is built in the 5' 3' direction, while the
complementary strand is built in the 3' 5' direction (5' and 3' each mark one end of a
strand). Each nucleotide consists of a phosphate and a deoxyribose sugar - forming the
backbone of the DNA double helix and a base. When a nucleotide base forms hydrogen
bonds with a complementary base on the other strand,they form a base pair: Adenine
pairs with thymine and cytosine pairs with guanine. These pairings are often expressed
with C:::G and A::T where the dots indicate hydrogen bonds. A strand running in the 5'
3' direction that has adenine will pair with base thymine on the complementary strand
running in 3' 5' direction.
The replication fork: Many enzymes are involved in the DNA replication fork.The
replication fork is a structure which forms when DNA is being replicated. It is created
through the action of helicase, which breaks the hydrogen bonds holding the two DNA
strands together. The resulting structure has two branching "prongs", each one made up
of a single strand of DNA.
Fig. 45 DNA replication

16.2 Lagging Strand Synthesis:
In DNA replication, the lagging strand is the DNA strand at the opposite side of the
replication fork from the leading strand. It goes from 3' to 5' (these numbers indicate the
position of the molecule in respect to the carbon atoms it contains). When the enzyme
helicase unwinds DNA, two single stranded regions of DNA (the "replication fork")
form. DNA polymerase cannot build a strand in the 3' 5' direction. Thus, the strand
complementary to the 5' 3' template strand (known as the lagging strand) is
synthesized in short segments known as Okazaki fragments. On the lagging strand,
primase builds an RNA primer in short bursts. DNA polymerase is then able to use the
free 3' OH group on the RNA primer to synthesize DNA in the 5' 3' direction. The
RNA fragments are then removed (different mechanisms are used in eukaryotes and
prokaryotes) and new deoxyribonucleotides are added to fill the gaps where the RNA was
present. DNA ligase is then able to ligate the deoxyribonucleotides together, completing
the synthesis of the lagging strand.
16.3 Leading Strand Synthesis:
The leading strand is defined as the DNA strand that is synthesized in the 5' 3'
direction in a continuous manner. On this strand, DNA polymerase III is able to
synthesize DNA using the free 3'-OH group donated by a single RNA primer (multiple
RNA primers are not used) and continuous synthesis occurs in the direction in which the
replication fork is moving.
16.4 Dynamics at the Replication Fork:
The sliding clamp in all domains of life share a similar structure, and are able to interact
with the various processive and non-processive DNA polymerases found in cells. In
addition, the sliding clamp serves as a processivity factor. The C-terminal end of the
clamps forms loops which are able to interact with other proteins involved in DNA
replication (such as DNA polymerase and the clamp loader). The inner face of the clamp
allows DNA to be threaded through it. The sliding clamp forms no specific interactions
with DNA. There is a large 35A0 hole in the middle of the clamp. This allows DNA to fit
through it, and water to take up the rest of the space allowing the clamp to slide along the
DNA. Once the polymerase reaches the end of the template or detects double stranded
DNA, the sliding clamp undergoes a conformational change which releases the DNA
polymerase.
The clamp loader, a multisubunit protein, is able to bind to the sliding clamp and DNA
polymerase. When ATP is hydrolyzed, it loses affinity for the sliding clamp allowing
DNA polymerase to bind to it. Furthermore, the sliding clamp can only be bound to a
polymerase as long as single stranded DNA is being synthesized. Once the single
stranded DNA runs out, the polymerase is able to bind to the subunit on the clamp loader
and move to a new position on the lagging strand. On the leading strand, DNA
polymerase III associates with the clamp loader and is bound to the sliding clamp.Recent
evidence suggests that the enzymes and proteins involved in DNA replication remain
stationary at the replication forks while DNA is looped out to maintain bidirectionality in
observed in replication. This is a result of an interaction between DNA polymerase, the
sliding clamp, and the clamp loader. DNA replicationDNA replication differs somewhat
between eukaryotic and prokaryotic cells. Much of our knowledge of the process DNA
replication was derived from the study of E. coli, while yeast has been used as a model
organism for understanding eukaryotic DNA replication.
16.5 Mechanism of Replication:
Once priming of DNA is complete, DNA polymerase is loaded into the DNA and
replication begins. The catalytic mechanism of DNA polymerase involves the use of two
metal ions in the active site and a region in the active site that can discriminate between
deoxynucleotides and ribonucleotides. The metal ions are general divalent cations that
help the 3'-OH to initiate a nucleophilic attack onto the alpha-phosphate of the
deoxyribonucleotide and orient and stabilize the negatively-charged triphosphate on the
deoxyribonucleotide. Nucleophillic attack by the 3'-OH on the alpha phosphate releases
pyrophosphate, which is then subsequently hydrolyzed by inorganic pyrophosphatase into
two phosphates. Subsequently driving DNA synthesis to completion.
Furthermore, DNA polymerase must be able to distinguish between correctly paired
bases and incorrectly paired bases. This is accomplished by distinguishing Watson-Crick
base pairs through the use of an active site pocket that is complementary in shape to the
structure of correctly paired nucleotides. This pocket has a tyrosine residue that is able to
form van der Waals interactions with the correctly paired nucleotide. In addition, double
stranded DNA in the active site has a wider and shallower minor groove that permits the
formation of hydrogen bonds with the third nitrogen of purine bases and the second
oxygen of pyrimidine bases. Finally, the active site makes extensive hydrogen bonds with
the DNA backbone. These interactions result in the DNA polymerase III closing around a
correctly paired base. If a base is inserted and incorrectly paired, these interactions could
not occur due to disruptions in hydrogen bonding and van der Waals interactions. The
mechanism of replication is similar in eukaryotes and prokaryotes.
DNA is read in the 3' 5' direction, relative to the parent strand, therefore, nucleotides
are synthesized (or attached to the template strand) in the 5' 3' direction, relative to the
daughter strand. However, one of the parent strands of DNA is 3' 5' and the other is 5'
3'. To solve this, replication must proceed in opposite directions. The leading strand
runs towards the replication fork and is thus synthesized in a continuous fashion, only
requiring one primer. On the other hand, the lagging strand runs in the opposite direction,
heading away from the replication fork, and is synthesized in a series of short fragments
known as Okazaki fragments, consequently requiring many primers. The RNA primers of
Okazaki fragments are subsequently degraded by RNase H and DNA polymerase I
(exonuclease), and the gap (or nick's) are filled with deoxyribonucleotides and sealed by
the enzyme ligase.
16.6 DNA Replication in Eubacteria Initiation of Replication and the Bacterial
Origin:
DNA replication in E. coli is bi-directional and originates at a single origin of replication
(OriC). The initiation of replication is mediated by DnaA, a protein that binds to a region
of the origin known as the DnaA box. In E. coli, there are 5 DnaA boxes, each of which
contains a highly conserved 9-base pair consensus sequence 5' - TTATCCACA - 3'.
Binding of DnaA to this region causes it to become negatively supercoiled. Following
this, a region of OriC upstream of the DNA A boxes (known as DNA B boxes) melts.
There are three of these regions. Each are 13 base pairs long and rich in A-T base pairs.
This facilitates melting because less energy is required to break the two hydrogen bonds
that form between A and T nucleotides. This region has the consensus sequence 5' GATCTNTTNTTTT - 3. Melting of the DnaB boxes requires ATP (which is hydrolyzed
by DnaA). Following melting, DNA A recruits a hexameric helicase (six DNA B
proteins) to opposite ends of the melted DNA. This is where the replication fork will
form. Recruitment of helicase requires six DnaC proteins, each of which is attached to
one subunit of helicase. Once this complex is formed, an additional five DnaA proteins
bind to the original five DnaA proteins to form five DnaA dimers. DnaC is then released,
and the prepriming complex is complete. In order for DNA replication to continue,
single-strand binding proteins (SSBs) are needed to prevent the single strands of DNA
from forming any secondary structures and to prevent them from reannealing, and DNA
gyrase is needed to relieves the stress (by creating negative supercoils) created by the
action of DNA B helicase. The unwinding of DNA by DNA B helicase allows for
primase (DNA G) and RNA polymerase to prime each DNA template so that DNA
synthesis can begin.
16.7 Termination of Replication:
Termination of DNA replication in E. coli is completed through the use of termination
sequences and the Tus protein. These sequences allow the two replication forks to pass
through in only one direction, but not the other. In order to slow down and stop the
movement of the replication fork in the termination region of the E. coli chromosome, the
Tus protein is required. This protein binds to the termination sites, and prevents DnaB
from displacing DNA strands. However, these sequences are not required for termination
of replication.
16.8 Regulation of Replication:
Regulation of DNA replication is achieved through several mechanisms. Mechanisms of
regulation involve the ratio of ATP to ADP, the ratio of DnaA protein to DnaA boxes and
the hemimethylation and sequestering of OriC. The ratio of ATP to ADP indicates that
the cell has reached a specific size and is ready to divide. This "signal" occurs because in
a rich medium, the cell will grow quickly and will have a lot of excess ATP.
Furthermore, DnaA binds equally well to ATP or ADP, but only the DnaA-ATP complex
is able to initiate replication. Thus, in a fast growing cell, there will be more DnaA-ATP
than DnaA-ADP.Another mode of regulation involves the levels of DnaA in the cell. 5
DnaA-DnaA dimers are needed to initiate replication. Thus, the ratio of DnaA to the
number of DnaA boxes in the cell is important. After DNA replication is complete, this
number is halved and replication cannot occur until the levels of DnaA protein increase.
Finally, upon completion of DNA replication, DNA is sequestered to a membranebinding protein called SeqA. This protein binds to hemimethylated GATC DNA
sequences. This 4-base pair sequence occurs 11 times in OriC. Only the parent strand is
methylated upon completion of DNA synthesis. DAM methyltransferase methylates the
adenine residues in the newly synthesized strand of DNA only if it is not bound to SeqA.
The importance of this form of regulation is twofold: 1) OriC becomes inaccessible to
DnaA and 2) DnaA binds better to fully methylated DNA than hemimethylated DNA.
16.9 Rolling Circle Replication:
Replication of the bacterial chromosome is known as theta () replication. However,
another method of replication exists in bacterial cells, known as rolling circle
replication.Rolling circle replication describes a process of DNA replication that can
rapidly synthesize multiple copies of circular molecules of DNA, such as plasmids and
the genomes of bacteriophages.Rolling circle replication is initiated by an initiator protein
encoded by the plasmid or bacteriophage DNA. This protein is able to nick one strand of
the double-stranded, circular DNA molecule at a site called the double-strand origin
(DSO) and remains bound to the 5'-PO4 end of the nicked strand. The free 3'-OH end is
released and can serve as a primer for DNA synthesis by DNA polymerase III. Using the
unnicked strand as a template, replication proceeds around the circular DNA molecule,
displacing the nicked strand as single-stranded DNA.
Continued DNA synthesis can produce multiple single-stranded linear copies of the
original DNA in a continuous head-to-tail series. These linear copies can be converted to
double-stranded circular molecules through the following process: First, the initiator
protein makes another nick to terminate synthesis of the first (leading) strand. RNA
polymerase and DNA polymerase III then replicate the single-stranded origin (SSO)
DNA to make another double-stranded circle. DNA polymerase I removes the primer,
replacing it with DNA, and DNA ligase joins the ends to make another molecule of
double-stranded circular DNA.
A striking feature of rolling circle replication is the uncoupling of the replication of the
two strands of the DNA molecule. In contrast to common modes of DNA replication
where both the parental DNA strands are replicated simultaneously, in rolling circle
replication one strand is replicated first (which protrudes after being displaced, giving the
characteristic appearance) and the second strand is replicated after completion of the first
one.Rolling circle replication has found wide uses in academic research and
biotechnology, and has been successfully used for amplification of DNA from very small
amounts of starting material.
16.10 Plasmid replication:
Origin and regulation:-The regulation of plasmids differs considerably from the
regulation of chromosomal replication. However, the machinery involved in the
replication of plasmids is similar to that of chromosomal replication. The plasmid origin
is commonly termed OriV, and at this site DNA replication is initiated. The ori region of
plasmids, unlike that found on the host chromosome, contain the genes required for its
replication. In addition, the ori region determines the host range. Plasmids carrying the
ColE1 origin have a narrow host range and are restricted to the relatives of E. coli.
Plasmids of utilizing the RK2 ori and ones that replicate using rolling circle replication
have a broad host range and are compatible with gram positive and gram negative
bacteria. Another important characteristic of the ori region is the regulation of plasmid
copy number. Generally, high copy number plasmids have mechanisms that inhibit the
initiation of replication. Regulation of plasmids based on the ColE1 origin, a high copy
number origin, require an antisense RNA. A gene close to the origin, RNAII is
transcribed and the 3'-OH of the transcript primes the origin only if it is cleaved by
RNase H. Transcription of RNAI, the antisense RNA, inhibits the RNAII from priming
the DNA because it prevents the formation of the RNA-DNA hybrid recognized by
RNase H.
16.11 Let Us Sum Up

1) DNA replication is the process of copying a double-stranded DNA molecule
resulting in identical double-stranded DNA molecules.
2) The replication tales place in three steps. They are initiation, elongation and
termination.
3) The lagging strand is the DNA strand at the opposite side of the replication fork
from the leading strand.
4) The leading strand is defined as the DNA strand that is synthesized in the 5' 3'
direction in a continuous manner.

DNA replication is by for the most important aspect in any organism Give your
opinions on this statement.

Explain the leading and lagging strand synthesis in DNA replication

1) What is leading and lagging strand synthesis
2) Give short notes on steps involved in DNA replication.
16.15 References
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Lesson 17: DNA TRANSCRIPTION

Contents
17.1 Initiation
17.2 Elongation
17.3 Termination
17.4 Prokaryotic Vs. Eukaryotic transcription
17.5 Measuring and Defecting Transcription
17.6 Transcription factories
17.7 Transcription initiation and complex
17.8 Terminology
17.9 Reverse transcription
17.10 Let us Sum Up
17.14 References

To learn and understand DNA transcription.
17.1 Initiation:
In transcription, one strand of DNA, the non-coding strand, is used as a template for RNA
synthesis. As transcription proceeds in the 5' 3' direction, and uses base pairing
complimentarity with the DNA template to specify the correct copying, the DNA
template strand is that oriented in the 3' 5' direction. The strand that is not used as the
template is called the coding strand, and has the DNA sequence that reflects that of the
RNA produced.
Transcription begins with the binding of RNA polymerase to the promoter in DNA. In
prokaryotes, the RNA polymerase is a core enzyme consisting of five subunits: 2
subunits, 1 subunit, 1 ' subunit, and 1 subunit. At the start of initiation, the core
enzyme is associated with a sigma factor (number 70) that aids in finding the appropriate
-35 and -10 basepairs downstream of promoter sequences. Transcription initiation is far
more complex in eukaryotes, the main difference being that eukaryotic polymerases do
not recognize directly their core promoter sequences. Unlike DNA replication,
transcription does not need a primer to start. The DNA unwinds and produces a small
open complex and synthesis begins on only the template strand.
17.2 Elongation:
Unlike DNA replication, mRNA transcription can involve multiple RNA polymerases; so
many mRNA molecules can be produced from a single copy of the gene. This step also
involves a proofreading mechanism that can replace an incorrectly added RNA molecule.
17.3 Termination:
Bacteria use two different strategies for transcription termination: in Rho-independent
transcription termination, RNA transcription stops when the newly synthesized RNA
molecule forms a hairpin loop, followed by a run of Us, which makes it detach from the
DNA template. In the "Rho-dependent" type of termination, a protein factor called "Rho"
destabilizes the interaction between the template and the mRNA, thus releasing the newly
synthesized mRNA from the elongation complex. Transcription termination in eukaryotes
is less well understood. It involves cleavage of the nascent transcript, followed by
template- independent addition of As at its new 3' end, in a process called
polyadenylation.
17.4 Prokaryotic vs. eukaryotic transcription:

Prokaryotic transcription occurs in the cytoplasm alongside translation. Eukaryotic
transcription is primarily localized to the nucleus, where it is separated from the
cytoplasm (where translation occurs) by the nuclear membrane.
17.5 Measuring and detecting transcription:Transcription can be measured and detected in a variety of ways:
Northern blot
RNase protection assay
RT-PCR
In vitro transcription
In situ hybridization
DNA microarrays
17.6 Transcription factories:

Active transcription units are clustered in the nucleus, in discrete sites called
transcription factories. Such sites could be visualized after allowing engaged
polymerases to extend their transcripts in tagged precursors (Br-UTP or Br-U), and
immuno- labeling the tagged nascent RNA. Transcription factories can also be localized
using fluorescence in situ hybridization, or marked by antibodies directed against
polymerases. There are ~10,000 factories in the nucleoplasm of a HeLa cell, among
which are ~8,000 polymerase II factories and ~2,000 polymerase III factories. Each
polymerase II factory contains ~8 polymerases. As most active transcription units are
associated with only one polymerase, each factory will be associated with ~8 different
transcription units. These units might be associated through promoters and/or enhancers,
with loops forming a cloud around the factory.
17.7 Transcription initiation complex:

Transcription factors mediate the binding of RNA polymerase and the initiation of
transcription. The RNA polymerase only binds to the promoter after certain transcription
factors are assembled. The completed assembly of transcription factors and RNA
polymerase bound to the promoter is called the transcription initiation complex.
History: A molecule which allows the genetic material to be realized as a protein was
first hypothesized by Jacob and Monod. RNA synthesis by RNA polymerase was
established in vitro by several laboratories by 1965; however, the RNA synthesized by
these enzymes had properties that suggested the existence of an additional factor needed
to terminate transcription correctly. Recently, Roger D. Kornberg won the 2006 Nobel
Prize in Chemistry "for his studies of the molecular basis of eukaryotic transcription".
17.8 Terminology:
Activator is a DNA-binding protein that regulates one or more genes by increasing the
rate of transcription. Repressor is a DNA-binding protein that regulates one or more GEVIL alpha & beta gene by decreasing the rate of transcription. Upstream, denotes the
region to the left of the +1 (or towards the 5' end) transcription initiation site.
Downstream, denotes the region to the right (or towards the 3') of the termination site.
Thus, transcription of a single gene follows this pattern: 5'- promoter - +1 transcription
initiation site - RNA-coding sequence - terminator - transcription termination site - 3'<-upstream downstream -->
17.9 Reverse transcription

Some viruses (such as HIV, the cause of AIDS), have the ability to transcribe RNA into
DNA in order to see a cell's genome. The main enzyme responsible for this type of
transcription is called reverse transcriptase. In the case of HIV, reverse transcriptase is
responsible for synthesising a complementary DNA strand (cDNA) to the viral RNA
genome. An associated enzyme, ribonuclease H, digests the RNA strand and reverse
transcriptase synthesises a complementary strand of DNA to form a double helix DNA
structure. This cDNA is integrated into the host cell's genome via another enzyme
(integrase) causing the host cell to generate viral proteins which reassemble into new
viral particles. Subsequently, the host cell undergoes programmed cell death (apoptosis).
17.10 Let Us Sum Up

1) Transcription is the process through which a DNA sequence is enzymatically
copied by an RNA polymerase to produce a complementary RNA.
2) The stretch of DNA that is transcribed into an RNA molecule is called a
transcription unit.
3) It contains three stages initiation, elongation and termination.
4) Transcription may be measured and detected by northern blot, RNase protection
assay, RT-PCR, In situ hybridization, and DNA microarrays.

Elaborate the role and significance of transcription.

Describe the initiation and elongation of DNA transcription

1) What is DNA Transcription
2) Define the terms initiation, elongation and termination.
17.14 References
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Lesson 18: TRANSLATION

Contents
18.1 Initiation
18.2 Elongation
18.3 Termination
18.4 Let us Sum up
18.8 References

To learn and understand the process of translation
Translation occurs in the cytoplasm where the ribosomes are located. Ribosomes are
made of a small and large subunits which surround the mRNA.Transfer RNA (tRNA)
molecules are 75 - 95 nucleotides long and have four arms and three loops. True to its
name, tRNA transfers amino acids to the site of the growing protein chain (polypeptide).
Each tRNA molecule recognises a specific, three base-pair mRNA code or codon (the
DNA form of a codon is called a triplet and the sequence on the tRNA is called an
anticodon). Since there are three bases and four possible nucleotides, there can be up to
64 (4x4x4) possible tRNA molecules. Three of these tRNA molecules recognise "stop" or
termination codons which have been named amber (UAG), opal (UGA) and ochre
(UAA).
The codon indicates which amino acid is to be added and the amino acid is attached to
the tRNA molecule at the acceptor arm. As we can see from the table below, most amino
acids are represented by more than one codon. This means that the expected protein can
still be synthesised, even when a degree of mutation occurs in the DNA or mRNA. There
are 20 essential amino acids; however they can be combined in any order, just like the
four nucleotides. This permits the production of the many different proteins which let
organisms grow and function.
18.1 Initiation:
When the large ribosmal subunit, small ribosomal subunit, mRNA and the tRNA carrying
a methionine come together in the cytoplasm, the ribosome becomes active and the
synthesis of a polypeptide, or "translation", is initiated. The AUG codon binds at the
protein binding site (P) of the ribosome and AUG is always the first codon of an mRNA
the next complementary tRNA will bind at the attachment binding site (A) of the
ribosome. The adjacent amino acids are then joined by a peptide bond via a peptidase
enzyme. Thus the polypeptide chain begins to grow and as it does, it is passed to the next
tRNA currently occupying the A site.
18.2 Elongation:
The ribosome then moves 1 codon down the mRNA in a 5' to 3' direction. This is
achieved by a translocase enzyme. As the process of ribosome translocation continues,
the "old" tRNA is released to bind another amino acid and go in search of a new codon.
The binding of a new aminoacid is mediated by an enzyme called amino-acyl-tRNA
synthase.
Fig. 46 Translation
18.3
Termination:
The process continues along the mRNA until a stop codon is reached. While there is no
tRNA for a stop codon, there is an enzyme called release factor which cleaves the
polypeptide chain resulting in a new protein.
Finally, the entire complex is disrupted, the ribosome separates and the mRNA is
released to be used again or degraded. Translation occurs at multiple sites along an
mRNA so that many ribosomes can be seen by electron microscopy bound to a single
mRNA strand with many polypeptide chains forming from each. Not only do different
sequences make different proteins, but slight sequence changes can radically change the
shape of a protein. The shape or structure of the protein is essential for its correct
function e.g. as an enzyme or an ion channel embedded in a cell membrane
18.4 Let Us Sum Up

1)
2)
3)
4)
5)
Translation is a process of synthesis a protein.

Translation occurs in the cytoplasm where the ribosomes are located.
It contains three stages, initiation. elongation and termination.
Elongation is achieved by the translocase enzyme.
The process of elongation continues along the mRNA until a stop codon is
reached and this is called as termination.

Translation is a process of synthesis of a protein Elaborate and justify.

What are the enzymes involved in elongation and termination of DNA translation?

1) Describe the mechanism of DNA translation.
18.8 References
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Fig. 1. Prokaryotic and Eukaryotic Cell

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Eukaryotic DNA is linear complexed with proteins called "histones," and is

The cytoplasm of eukaryotic cells is filled with a large, complex collection of

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Fig. 2. Prokaryotic cell and Mitochondrion

Fig. 3. Prokaryotic and Eukaryotic cells

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1.3 Let Us Sum Up

All living things are composed of cells.

1.4 Points for Discussion

Cell in the basic unit of life Comment.

1.5 Check your Progress

1.6 Lesson-end activities

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LESSON 2: Cell Organelles and Their Functions

2.0 Aims and Objectives

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Fig. 4. Mitochondrial Components

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Fig. 5. ATP Synthase

Fig. 6. Protein import by Mitochondria

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the removal of hydrogen (H) atoms from water molecules

2H2O -> 4e- + 4H+ + O2

They reduce NADP+ to NADPH for use in the Calvin Cycle.

The protons also serve two functions:

They participate in the reduction of NADP+ to NADPH.

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Fig. 7. Calvin Cycle

12 different protein molecules bound to

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> 20 different protein molecules bound to

2.3 Endoplasmic Reticulum

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Fig. 8. Endoplasmic Reticulum

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Insertion of proteins into the endoplasmic reticulum membrane: Integral proteins

2.4 Golgi Apparatus

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Fig. 9. The Golgi Apparatus

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Fig. 10. Inner view of Golgi Apparatus

Cisternal maturation model: The cisternae of the Golgi apparatus move by

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Fig. 11. Structure of Ribosome

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Fig. 13. Lysosome

Lipase, which digests lipids,

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Fig. 13. Nuclear

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nucleolus, which is mainly involved in assembly of ribosomes. After being produced in

Fig. 14. Nucleolus

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