Organization of Genetic

Material
(Prokaryotic and
Eukaryotic chromosome)
DNA is a working molecule; it must be replicated when a cell is ready to
divide, and it must be “read” to produce the molecules, such as proteins, to
carry out the functions of the cell.
For this reason, the DNA is protected and packaged in very specific ways. In
addition, DNA molecules can be very long. Stretched end- to- end, the DNA
molecules in a single human cell would come to a length of about 2 meters.
Thus, the DNA for a cell must be packaged in a very ordered way to fit and
function within a structure (the cell) that is not visible to the naked eye.

The vast majority of an organism’s genome is organized into the cell’s

chromosomes, which are discrete DNA structures within cells that control
cellular activity. Eukaryotic chromosomes are housed in the membrane-
bound nucleus, The nucleus of a eukaryotic cell, it is surrounded by a
nuclear membrane.

Most prokaryotes contain a single, circular chromosome that is found in an

area in the cytoplasm called the nucleoid.
The nucleoid :(meaning nucleus- like) is an irregularly- shaped region within
the cell of a prokaryote that contains all or most of the genetic material. The
The term chromosome comes from the Greek words for color (chroma) and body
(soma) because they are cell structures, or bodies, that are strongly stained by
some colorful dyes used in research. Each chromosome is made of protein and a
single molecule of deoxyribonucleic acid (DNA).
Organization of Prokaryotic Chromosomes
The size of the genome in one of the most well- studied prokaryotes, Escherichia
coli, is 4.6 million base pairs, which would extend a distance of about 1.6 mm if
stretched out. The DNA is twisted beyond the double helix in what is known as
supercoiling. Some proteins are known to be involved in the supercoiling; other
proteins and enzymes help in maintaining the supercoiled structure.
Topoisomerases are involved in supercoiling DNA. DNA gyrase is a type of
topoisomerase, found in bacteria and some archaea, that helps prevent the over-
winding of DNA. Some antibiotics kill bacteria by targeting DNA gyrase. In addition,
histone- like proteins bind DNA and aid in DNA packaging. O ther proteins bind to the
origin of replication, the location in the chromosome where DNA replication initiates.
Chromosomes in bacteria and archaea are usually circular and typically contains
only a single chromosome within the nucleoid. Because the chromosome contains
only one copy of each gene, prokaryotes are haploid.
Because different regions of DNA are packaged differently, some regions of
chromosomal DNA are more accessible to enzymes and thus may be used more
readily as templates for gene expression. Interestingly, several bacteria, including
Helicobacter pylori and Shigella flexneri, have been shown to induce epigenetic
changes in their hosts upon infection, leading to chromatin remodeling that may
cause long- term effects on host immunity
The nucleoid is composed of DNA in association with a number of DNA- binding
proteins (histone- like proteins) that help it maintain its structure. The isolated
nucleoid contains 80% DNA, 10% protein, and 10% RNA by weight.

There are four major families of bacterial histone- like proteins:

1 Histone- like nucleoid structuring protein (H- NS): It belongs to a family of bacterial
proteins that play a role in the formation of nucleoid structure, it is believed that H- NS
achieves this by forming complexes with itself and binding to different sections of
DNA, bringing them together. Another major role of H- NS is to halt the expression of
genes. It regulates gene expression by binding to AT- rich DNA, which is a common
feature of promoters.
2 Heat unstable protein (HU): This protein binds non- specifically to DNA and bends
it, the DNA apparently wrapping around the HU protein.
3 Factor for inversion stimulation (FIS): It binds to a loose 15 nucleotide consensus
sequence in DNA. It stimulates DNA- related processes, such as DNA inversion and
excision; it activates transcription of tRNA and rRNA genes and regulates its own
synthesis.
4 Integration host factor(IHF): It facilitates bending of DNA by binding to specific DNA
 Proteins or nucleoid proteins or nucleoid- associated proteins (NAPs) and
are distinct from histones of eukaryotic nuclei.
In contrast to histones, the DNA- binding proteins of the nucleoid do not
form nucleosomes, in which DNA is wrapped around a protein core. Instead,
these proteins often use other mechanisms to promote compaction such as
DNA looping. The most studied NAPs are HU, H- NS, FIS, and IHF that
organize the genome by driving events such as DNA bending, bridging, and
- These proteins can form clusters and they seem to be involved also in
aggregation.
coordinating transcription events, spatially sequestering specific genes and
participating in their regulation.

Structure of bacterial chromosome

The chromosome is further folded into 50 or `10 0 loops (domains) of about 10 0
kbp. These domains supercoiled independently and indeed, even small sections
within the same loop can transiently have different degrees of supercoiling. the
specific supercoiling of a region can affect the ability of the cell to express genes
in that region.

A model of the overall structure of the bacterial chromosome.

(A) The unfolded, circular chromosome of E. coli depicted as a single line for
simplicity, though of course it is a double- stranded helix.

(B) The DNA folded into chromosomal domains by protein- DNA associations.
The proteins are depicted as the black circles, interacting with both the DNA and
with each other. Six domains are shown, but the actual number for E. coli is about
50.
A. An illustration of an open conformation of the circular genome of Escherichia coli.
Arrows represent bi- directional DNA replication. The genetic position of the origin of
bi- directional DNA replication (oriC) and the site of chromosome decatenation (dif)
in the replication termination region (ter) are marked. Colors represent specific
segments of DNA as discussed in C. B. An illustration of a random coil form adopted
by the pure circular DNA of Escherichia coli at thermal equilibrium without
supercoils and additional stabilizing factors. C. A cartoon of the chromosome of a
newly born Escherichia coli cell.
PLASMIDS

A plasmid is a small, circular, extrachromosomal double

stranded DNA that has the capacity to replicate
independently.
Discovered by Laderberg in 1952.
It naturally occur in bacteria, however sometimes
present in archaea and eukaryotes.
The genes carried in plasmid benefit the survival of the
organism by providing them with genetic advantages
like antibiotic resistance etc. under certain situation or
particular conditions.
They provide mechanism for horizontal gene transfer
within a population of microbes and thus provide a
selective advantage under a given environmental state.
Non Integrative Replication
In this type of replication the plasmid DNA once introduced into the cell grows
as per the copy number and the multiplication of the cells

Integrative Plasmid
Episome
Under certain conditions some plasmids may integrate into the bacterial
chromosome. They are called episome or integrative plasmids. At this stage
they replicate along with the bacterial chromosome.
The plasmids in this way are classified into 2 types

Relaxed plasmids
They are the ones which are normally maintained at multiple copies per cell.
Stringent plasmids
They are the ones which have a limited number of copies per cell.
In this case of plasmid replication, the plasmid DNA is integrated in the bacterial
chromosome and grows along with the cell. It uses the bacterial machinery for
division. A good example of this type of replication is Ti Plasmid, often used in
agricultural genetic engineering experiments. It completely uses the cell genetic
mechanism to grow.
Types of plasmid

Fertility plasmid :

That contains the tra genes required for conjugation else known as F plasmids. For
example F plasmids of E coli.

Resistance Plasmid or R plasmids

Carry genes of resistance to one or more antibacterial agents such as ampicilin, etc

Col plasmid :
It contains genes for production of bacteriocins, proteins that kill other bacteria example
col E1.

Virulent plasmids:
Which in turn convert bacteria into a pathogen. For example, the Ti plasmid of
agrobacterium tumefaciens induces crown gal disease on dicot of the palnts

Degradative plasmid
they enable the digestion of unusual substances like toluene, salicylic acid etc.

SUICIDE PLASMID
gets transferred to another bacterial cell but don’t replicate further.
Organization of Eukaryotic Chromosome

Eukaryotic chromosomes are typically linear, and eukaryotic cells contain

multiple distinct chromosomes. Many eukaryotic cells contain two copies of
each chromosome and, therefore, are diploid.

During DNA packaging, DNA- binding proteins called histones perform

various levels of DNA wrapping and attachment to scaffolding proteins. The
combination of DNA with these attached proteins is referred to as chromatin.

In eukaryotes, the packaging of DNA by histones may be influenced by

environmental factors that affect the presence of methyl groups on certain
cytosine nucleotides of DNA. The influence of environmental factors on
DNA packaging is called epigenetics.

Each species of plants and animals has a set number of chromosomes. for
example, Humans have 46 chromosomes while a rice plant has 12 and a
dog 39.
B a sic info r ma t io n a b o u
t chromatin

C hr o ma t in is t he c o mp l
e x combination of DNA and
proteins that makes up
chromosomes. It is found inside
the nuclei of eukaryotic cells.

The functions of chromatin are:

To package DNA into a smaller
volume to fit in the cell.
To strengthen the DNA to allow
mitosis and meiosis.

The primary protein components of

chromatin are histones, which bind
histones are highly basic proteins found in eukaryotic cell nuclei that pack
and order the DNA into structural units called nucleosomes. Five major
families of histones exist: H1/H5, H2A, H2B, H3, and H4.

Histones H2A, H2B, H3 and H4 are known as the core histones, while
histones H1/H5 are known as the linker histones.

All four of the core histones contain between 20 and 25% of lysine and
arginine.

Molecular size for the core protein ranges between 11.4 KD and 15.4 KD
making them relatively small yet highly positively charged proteins
allowing them to closely associate with negatively charged DNA, for H1
Histone it is relatively larger (MW:21KD)and percentage of basic amino
acid is 30.5%
Out side the nucleosome structure there are other type of proteins called non
histone protein. A variety of non- histone proteins also bind to DNA to affect
chromatin structure and exert epigenetic control on gene expression. The
best established of these are the Polycomb (PcG) proteins and Trithorax
group (TrxG) proteins which promote transcriptional repression and activation
respectively, and both of which act stably through cell division.

The two systems interact closely with one another and with other epigenetic
systems and have been implicated in the regulation of genes in early
development and stem cell renewal.

Usually they are acidic rather than basic protein. They don't play roles in DNA
packing, but they are the only protein that remain after removing histone
during division and clear during metaphase. Much larger in molecular weight
(more than 30 KD) and irregular heterochromatin rather regular.
the basic structural unit of DNA packaging in eukaryotes are called
nucleosomes. Each nucleosome is made of DNA wrapped around eight
histone proteins that function like a spool and are called a histone octamer .
Histones are a family of basic proteins that associate with DNA in the
nucleus and help condense it into chromatin. Nuclear DNA does not appear
in free linear strands; it is highly condensed and wrapped around histones in
order to fit inside of the nucleus and take part in the formation of
chromosomes.
Histones are basic proteins, and their positive charges allow them to
associate with DNA, which is negatively charged. Some histones function as
spools for the DNA to wrap around.
Each histone octamer is composed of two copies each of the histone
proteins H2A, H2B, H3, and H4. The chain of nucleosomes is then wrapped
into a 30 nm spiral called a solenoid, where additional H1 histone proteins
are associated with each nucleosome to maintain the chromosome
structure.
Each nucleosome attached with followed one by linker DNA ( 20 - 60 BP)
thus total DNA warp around it which will be protected from digestion with
 First level twisting or super
coiling of DNA molecules

Second level warping of DNA

around histons

Formation of folds or zig zag by

HI histone and the linker (other
benefits of linker create elasticity
and flexibility to chromatin beside
binding two adjacent nucleosome )

Formation of (30 nm) fibers and

salenoid model by collecting each
6 nucleosome together
Telomeres are repetitive stretches of DNA located at the ends of
linear chromosomes. They protect the ends of chromosomes.
In many types of cells, telomeres lose a bit of their DNA every time
a cell divides. Eventually, when all of the telomere DNA is gone, the
cell cannot replicate and dies.
Cells with the capacity to divide very frequently have a special
enzyme that prevents their chromosomes from losing their
telomeres because they retain their telomeres, such cells generally
live longer than other cells.
Telomeres also play a role in cancer. The chromosomes of
malignant cells usually do not lose their telomeres, helping to fuel

the uncontrolled growth that makes cancer so devastating.