What is Genome ?

A genome is an organism’s complete set of DNA, comprising of nuclear and mitochondrial

DNA. A total hereditary material present in an organism. Genome is a totality of
chromosome, unique to a particular organism or any cell within the organism. Each genome
contains all of the information needed to build and maintain that organism.

How genome and genotype differs?

Genome is a total hereditary material.

Genotype is the information contained within the chromosomes.

Types of Genome

There are four categories of genome according to different kinds of organisms.

Genetic Organization

In the cell, each DNA molecule associated with proteins, and each DNA molecule and its
associated protein is called as chromsome. This organization holds true for prokaryotic and
eukaryotic cells.
Packaging of DNA into chromosome

● Packaging of DNA into the chromosome serves several important functions.

1. Chromosome is compact form of DNA that readily fits inside the cell.
2. Protect the DNA from the damage.
3. Only packaged DNA can be transmitted efficiently to both daughter cells, when a cell
divides.

Genome organization in prokaryotes

● They have small bodies and small extra-chromosomal DNA called

genomes. plasmids.
● Do not contain a nucleus or any other
membrane-bound organelle.
● small, circular (sometimes linear)
DNA present in the nucleoid region.
● They have a single chromosome that
floats in the cytoplasm.
● The genome size ranges in between
104 to 107bp with a high gene
density.
● Apart from this single
chromosome, some bacteria have

Plasmids

• Prokaryotes also frequently carry one or more smaller independent extra-chromosomal

DNA called plasmids.
• Plasmids are not genomic DNA. They are accessory DNA molecules.
• Small circular DNA molecules that have the ability to self-replicate.
• Unlike the larger chromosomal DNA, plasmids typically are not essential for
bacterial growth.

Importance of Plasmid

• Plasmids provide advantages to bacteria such as antibiotic resistance, herbicide

resistance, etc.
• In addition, unlike chromosomal DNA, plasmids are often present in many complete
copies per cell.

BACTERIAL GENOME
 Bacterial chromosomal DNA is usually a circular molecule that is a few million
nucleotides in length.
Escherichia coli :: 4.6 million base pairs
Haemophilus influenzae :: 1.8 million base pairs
 A typical bacterial chromosome contains a few thousand different genes
● Structural gene sequences (encoding proteins) account for the majority of bacterial DNA
 ● The no transcribed DNA between adjacent genes are termed intergenic regions

Packaging of DNA

● Prokaryotic cells typically have smaller genomes, the need to compact their DNA is still
substantial.
● Escherichia coli must pack its 1 mm chromosome into a cell that is only 1 µm in
length.
● It is less clear how prokaryotic DNA compacted.

Nucleoid
• A prokaryotic chromosome is
circular and resides in a cell region
called the nucleoid.
• Prokaryotic cells typically have only
one complete copy of their
chromosome that is package into a
nucleoid.
• The bacterial nucleoid is -80% DNA
by mass and can be unfolded by
agents that act on RNA or protein.
• The proteins that are responsible for
condensing and maintain the
supercoiled structure of the DNA
have not been identified.
● The types of proteins found in
prokaryotic chromosomes, known as
the nucleoid-associated proteins,
differ from the histone proteins that
appear in eukaryotic chromosomes
and cause the prokaryotic
chromosomes to form looped
structures.
• The function of nucleoids is DNA
determines what proteins and
enzymes an organism can synthesize
and, therefore, what chemical
reactions it is able to carry out.
Key features

● Most, but not all bacterial species

contain circular chromosomal DNA.
● A typical chromosomes is a few
million base pairs in length.
● Most bacterial species contain a
single type of chromosome, but it
may be present in multiple copies.
● Several thousand different genes are
interspersed throughout the
chromosome.
● One origin of replication is required
to initiate DNA replication.
● Short repetitive sequences may be
interspersed throughout the
chromosome.

● The chromosomal DNA must be compacted about a 1000-folds.

● The formation of loop domains.
● Number of loops varies according to the size of the bacterial chromosome and the
species.
● E. coli has 50-100 with 40,000 to 80,000 bp of DNA in each.

● DNA super coiling is a second important way to compact the bacterial chromosome.
• DNA super coiling refers to the over or under winding of a DNA strand, and is an
expression of the strain on that strand.
• A super coiled form of DNA is the one in which the double helix is further twisted about
itself, forming a tightly coiled structure.
• There is 2 structure formed :2 structures-toroid and plectoneme
In prokaryotes, plectonemic super coils are predominant because of circular DNA and small
amount of genetic material.

● DNA super coiling is a second important way to compact the bacterial chromosome.
• DNA super coiling refers to the over or under winding of a DNA strand, and is an
expression of the strain on that strand.
• A super coiled form of DNA is the one in which the double helix is further twisted about
itself, forming a tightly coiled structure.
• There is 2 structure formed :2 structures-toroid and plectoneme
In prokaryotes, plectonemic super coils are predominant because of circular DNA and small
amount of genetic material.

Enzyme

DNA topoisomerases are essential in the unwinding, replication, and rewinding of the
circular, supercoiled bacterial DNA
● A topoisomerase called DNA gyrase catalyzes the negative supercoiling of the circular
DNA found in bacteria
on the other hand, is involved in the relaxation of the supercoiled circular DNA, enabling the
separation of the interlinked daughter chromosomes at the end of bacterial DNA replication.

E.coli
● The E.coli chromosome is compact, one fifth of cell volume
● The determinants of nucleoid folding
 Negative supercoiling by topoisomerases
 Condensation by the attachment of nucleoid structure proteins
 The nucleoid is highly condensed during rapid growth,
● RNAP (RNA polymerase) concentrates in transcriptional loci
● RNAP is distributed throughout the chromosome
Genome organization in eukaryotes

● Eukaryotic genome is linear and

conforms the Watson-Crick Double
Helix structural model.
● Embedded in Nucleosome-complex
DNA & Protein (Histone) structure
that pack together to form
chromosomes.
● Eukaryotic genome have unique
features of Exon - Intron
organization of protein coding genes,
representing coding sequence and
intervening sequence that represents
the functionality of RNA part inside
the genome.
● A human haploid cell, consist of 23
nuclear chromosome and one
mitochondrial chromosome, contains
more than 3.2 billion DNA base
pairs.
● Eukaryotic chromosomes are usually linear.
● A typical chromosome is tens of millions to hundreds of millions of base pairs in length.
● Eukaryotic chromosomes occurs in sets. Many species are diploid. Which means that
somatic cells contains 2 sets of chromosomes.
● Each chromosome contains a centromere that forms a recognition site for the kinetochore
proteins.
● Telomere contains specialized sequences located at both ends of the linear chromosomes.
● Repetitive sequences are commonly found near centromeric and telomeric regions.
Chemical composition of chromatin
● DNA (20-40%)
○ most important chemical constituent of chromatin
● RNA (05-10%)
○ associated with chromatin as; rRNA, mRNA, tRNA
● Proteins (55-60%)
○ Histones: very basic proteins, constitute about 60% of total protein, almost 1:1
ratio with DNA.
● Five Types: H1, H2a, H2b, H3 and H4
○ Non-Histones: They are 20% of total chromatin protein:
● Nucleosomal Assembly Proteins (NAP), Other Histone chaperones
Chromosome remodeling complexes 3
● Structural (actin, L & B tubulin & myosin) contractile proteins, function
during chromosome condensation & in movement of chromosomes.
● all enzymes and co factors– involved in replication, transcription and its
regulation

Nucleosome model

Three type of model used to understand DNA packaginf in eukaryotes

 Multi-strand model
 Folded fiber model
 Nucleosome model
Nucleosome model is widely accepted.

● Most compaction in eukaryotic cells is the result of the regular association of DNA with
histones to form structures called nucleosomes.
● DNA is tightly bound to histone proteins which serve to form a repeating array of DNA-
Protein particles.
● The DNA is wrapped around the histone core of eight protein subunits, forming the
nucleosome.
● The nucleosome is clamped by histone H1.
● About 200 base pairs (bp) of DNA coil around one histone. The coil "untwists" so as to
generate one negative superturn per nucleosome.
 ● Histone tails-
○ Protein modification
○ Protein production
● When histone tails are dissociated-
○ DNA is released for the process of transcription and translation

Levels of DNA Packaging

Three levels of organization:

• DNA wrapping around “Nucleosomes”- The string on beads structure.
• The solenoid structure.
• Scaffold structure.
DNA diameter is 2nm or 20
angstrom. This DNA wrapped around
nucleosome and form bead like structure.
At that time the size of string will be 11 nm.
Bead like structure get closer to each other
and form 30 nm fiber of chromatin. This is
known as The solenoid structure. Further
in this chromatin, loop formation occurs.
And loop domains are formed. The size of
fiber will be 300 nm at that time. This type
of structure known as SCAPFOLD structure.
These looped domains produce the
characteristics of metaphase chromosome of
700 nm. After the formation of entire
chromosome the size will be 1400 nm.
Prokaryotic Genome v/s Eukaryotic Genome

Prokaryotic Genome Eukaryotic Genome

Small genome, no specialization Larger genome, cell specialization

Genome = DNA + few proteins in simple Genome = DNA with many proteins in
arrangement complex arrangement
Contain single set of chromosome contain one or more sets of Chromosomes

Amount of DNA is smaller typically greater than that in bacterial cells

They are polyistronic They are monocistronic

Most of their DNA codes for protein or Most of the DNA does not code for protein or
RNA’s, very little “junk” RNA’s
RNA processing not an option for controlling RNA processing allows for several
gene expression opportunities to regulate genes
mRNA has a short life span (minutes) mRNA is long lived (days to months)