ORGANIZATION OF GENOME IN

PROKARYOTES AND EUKARYOTES

 The processes that enable information to be
copied from genes and then used to synthesize
proteins must be regulated if an organism is to
survive.
Different cells within an organism share the same
set of chromosomes.
In each cell some genes are active while others
are not.
For example, in humans only red blood cells
manufacture the protein hemoglobin and only
pancreas cells make the digestive enzyme known
as trypsin, even though both types of cells contain
the genes to produce both hemoglobin and
trypsin.
 Each cell produces different proteins according
to its needs so that it does not waste energy by
producing proteins that will not be used.
A variety of mechanisms regulate gene activity
in cells.
One method involves turning on or off gene
transcription, sometimes by blocking the
action of RNA polymerase, an enzyme that
initiates transcription.
 Gene regulation may also involve mechanisms
that slow or speed the rate of transcription,
using specialized regulatory proteins that bind
to DNA.
Depending on an organisms particular needs,
one regulatory protein may spur transcription
for a particular protein, and later, another
regulatory protein may slow or halt
transcription.
 Gene Structure
Transcription proceeds from left to right, regardless of
the orientation of the gene in the chromosome.
This means that the promoter lies to the left of the
coded region.
Taking the gene DNA organization first:
Transcription starts at the transcription initiation site,
and stops when it encounters the polyA attachment site.
Transcription produces mRNA as a copy of the
DNA, from the initiation site to the polyA attachment
site.

 A set of enzymes then attaches a series of a hundred

or more As to the mRNA called the polyA tail.
This tail appears to protect the mRNA from
degradation by enzymes.
So mRNA is simply a single strand of bases,
copied from the genomic DNA, from the initiation
site and ending with a polyA tail.
The start codon, for translation, is always AUG,
which encodes methionine and at the end is a stop
codon UGA.
 Genes in development
Gene regulation helps individual cells within an organism
function in a specialized way.
Other regulatory mechanisms coordinate the genes that
determine how cells develop.
All of the specialized cells in an organism, including those of
the skin, muscle, bone, liver, and brain, derive from identical
copies of a single fertilized egg cell.
Each of these cells has the exact same DNA as the original
cell, even though they have vastly different appearances and
functions.
Genes dictate how these cells specialize.
 Early in an organisms embryonic development the overall
body plan forms.
Individual cells commit to a particular layer and region of the
embryo, often migrating from one location to another to do so.
As the organism grows, cells become part of a particular body
organ or tissue, such as skin or muscle.
Ultimately, most cells become highly specializednot only to
develop into a neuron rather than a muscle cell,
for example, but to become a sensory neuron instead of a
motor neuron.
This process of specialization is called differentiation.
 At each stage of the differentiation process, specific
genes known as developmental control genes actively
turn on and switch off the genes that differentiate
cells.
One class of developmental control genes, known as
homeotic genes, directs the formation of particular
body parts.
Activating one set of homeotic genes instructs part of
an embryo to develop into a leg, while another set
initiates the formation of the head.
If a homeotic gene becomes altered or damaged, an
organisms body development can be dramatically
disrupted.
 A change in a single gene in some insects, for
instance, can cause a leg to grow where an antenna
belongs.
Homeotic genes work by regulating the activity of
other genes.
Homeotic genes code for the production of a
regulatory protein that can bind to DNA and thus
affect the transcription of one or more genes.
This enables homeotic genes to initiate or halt the
development and specialization of characteristics in
an organism
 Nearly identical homeotic genes have been identified
in varied organisms, such as insects, worms, mice,
birds, and humans, where they serve similar
embryonic development functions.
Scientists view that homeotic genes first appeared in
a single ancestor common to all these organisms.
Sometime in evolutionary history, these organisms
diverged from their common ancestor, but the
homeotic genes continued to be passed down through
generations virtually unchanged during the evolution
of these new organisms.
 The information present in the gene is not
always used.
Many genes remain silent and are expressed
only when the gene product is needed.
However, there are certain genes whose
products are constantly needed for cellular
activity.
These are known as housekeeping genes.
 Gene Expression in Prokaryotes
An average bacterium, contains one thousands the
DNA content of a typical eukaryotic cell.
The bacterial chromosome contains a single circular
DNA molecule associated with a few proteins and is
not enclosed within a limiting membrane unlike that
in the eukaryotic cell.
Bacteria can divide very rapidly. The doubling time is
also referred to as generation time and in some
bacteria, this can be as low as 20 minutes from a
single origin of replication and can proceed
bidirectionally.
 The bacterium Escherichia coli has about 2,500 genes.
The expression of these genes is usually controlled to
achieve maximum cellular economy.
This means that genes will be turned on or off as per the
requirement.
A set of genes will be switched on when there is necessity to
handle and metabolise a new substrate.
When these genes are turned on, enzymes are produced,
which metabolise the new substrate.
The phenomenon is known as induction and the small
molecules eliciting this induction are referred to as
inducers.
When a metabolite needed by the bacterium is provided in
excess from outside, the bacterium stops making it and thus
conserves its reserves.
 This is achieved by the added metabolite turning off a set of
genes involved in producing that metabolite in the bacterial
cell. This phenomenon is known as feed back repression.
As against the processes of induction and repression as
already indicated a set of genes are constantly expressed to
take care of house keeping functions such as glycolysis.
These genes which are constantly expressed are referred to
as constitutive.
In 1961, Francois Jacob and Jacques Monod, at the
Pasteur Institute in Paris, proposed that metabolic path ways
are regulated as a unit.
For example, when the sugar lactose is added to the cultures
of E. coli, it induces three enzymes necessary to break down
the lactose into glucose and galactose.
 Bacterial operons
Lac operon :
This operon consists of 3 genes, lac Z, Y and A coding for -
galactosidase, permease and transacetylase catalyzing a
catabolic pathway.
The genes for these three enzymes occur adjacent to each other
and thus are linked.
These are referred to as structural genes, since they have the
information to code for the amino acid sequence and thus
directly decide the structure and function of the individual
proteins of the pathway.
These 3 genes are regulated as a unit by a single switch
operator O.
This entire unit is referred to as an operon.
 RNA polymerase binds to the promoters region P and
initiates transcription.
Under normal conditions transcription cannot proceed, since a
repressor protein coded by the i gene binds to the operator
and blocks RNA polymerase movement.
In the presence of the inducer lactose, the repressor protein
structure is modified such that the repressor cannot bind to the
operator any more.
This leads to the transcription of the operon and induction of
-galactosidase and the other two enzymes..
When the switch is on, the three genes are transcribed by
RNA polymerase into a single stretch of mRNA covering all
the three genes.
Each gene segment is referred to as a cistron and the long
messenger RNA covering all the cistrons is known as
polycistronic.
 Gene Expression in Eukaryotes
Gene regulation in eukaryotes is more complex than in
bacteria and other prokaryotes.
Higher eukaryotes have several thousand genes.
Unlike the unicellular bacterium, these are multicellular
organisms which can also undergo differentiation.
Thus, the cells in the undifferentiated stage not only grow and
divide, but are also destined to become part of specialized
tissues such as the liver, spleen or heart in an animal and the
leaf, root, stem or flower in an angiosperm.
Thus regulation of gene expression in the eukaryotic cell is
very complex.
 Most multicellular organisms contain different types
of cells that serve specialized functions.
The cells of an animals heart, blood, skin, liver, and
muscles all contain the same genes.
But in order to carry out their specific functions
within the body, each cell must produce different
proteins and respond to changing environmental
stimuli, such as glucose levels in the blood or body
temperature.
Such specialization is possible only with
sophisticated gene regulation
 The information on the eukaryotic gene for assembling a
protein is not continuous, but split.
However, when messenger RNA is formed from such genes,
the unwanted RNA regions are removed and the regions
coding for amino acids are joined together. This process is
referred as SPLICING.
Bases in the messenger RNA and amino acids in proteins are
collinear even in eukaryotic cells, although the genes are split.
The regions of a gene, which become part of a mRNA and
code for different regions of the protein, are referred to as
exons.
The regions which do not form part of RNA processing before
mRNA formation are referred to as introns.
 In eukaryotes, genes involved in coding for the enzymes of a
particular metabolic pathway need not to be linked.
Sometimes they are present even on different chromosomes.
However, such genes are regulated together just as in bacterial
operons.
The basic processes of induction and repression is constantly
regulated by the changing environment in the cell.
Thus during growth and development, small molecules such
as hormones, vitamins, metal ions, chemicals and invading
pathogens can induce or repress certain genes and this would
result in the production or absence of certain proteins.
 Eukaryotes use a variety of mechanisms to ensure that each
cell uses the exact proteins it needs at any given moment.
In one method, eukaryotic cells use DNA sequences called
enhancers to stimulate the transcription of genes located far
away from the point on the chromosome where transcription
occurs.
If a specific protein binds to an enhancer site on the DNA, it
causes the DNA to fold so that the enhancer site is brought
closer to the site where transcription occurs.
This action can activate or speed up transcription in the
genes surrounding the enhancer site, thereby affecting the
type and quantity of proteins the cell will produce.
 Enhancers often exert their effects on large groups of
related genes, such as the genes that produce the set of
proteins that form a muscle cell.

Gene regulation can also take place after transcription has

occurred by interfering with the steps that modify mRNA
before it leaves the nucleus to take part in translation.

This process typically involves removing exons (segments

that code for specific proteins) and introns.

These sections of the mRNA can be modified in more than

one way, enabling a cell to synthesize different proteins
depending on its needs.
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