GENOME

• Ritesh Ranjan Pal, PhD

Assistant Professor,
School Of Biological Sciences (SBS),
Indian Association For The Cultivation Of Science
(IACS),
Jadavpur, Kolkata-700032, INDIA
 GENOME

• The word “genome,” coined by German botanist

Hans Winkler in 1920, was derived simply by
combining gene and the final syllable of
chromosome.
• In the field of molecular biology and genetics, a
genome is the genetic material of an organism.
• It consists of DNA or RNA. In general, a genome
is simply the sum total of an organism’s DNA.
• The study of the genome is called genomics.
 Three types of Genome

1. Prokaryotic genomes: DNA genomes- Archaea and most bacteria have a

single circular chromosome. While, some bacterial species have linear
or multiple chromosomes. Most prokaryotes have very little repetitive
DNA in their genomes.
2. Eukaryotic genomes: Eukaryotic genomes are composed of one or more
linear DNA chromosomes. Eukaryotic Genomes Contain Non-
repetitive and Repetitive DNA Sequences.
 Two general types of genomic sequences –
 A. Non-repetitive DNA : There is only one copy in a haploid genome.

 B. Repetitive DNA consists of sequences that are present in more than one
copy in each haploid genome.
3. Viral genomes: Viral genomes can be composed of either RNA or DNA.
The genomes of RNA viruses can be either single-stranded RNA or double-
stranded RNA, and may contain one or more separate RNA molecules.
 Prokaryotic Genome

❖ Lacks a membrane bound nucleus.

❖ Circular DNA and supercoiled domain.
❖ Histones not present.
❖ Prokaryotic genomes generally contains one large circular
piece of DNA refered to as aCHROMOSOME.
❖ Some bacteria have linear chromosome.
❖ Many bacteria have small circular DNA str. Called PLASMIDS
which can be swapped between neighbours and across
bacterial species.
 Prokaryotic genomes

 Generally 1 circular chromosome (dsDNA)

 Usually without introns
 Relatively high gene density (~2500 genes per mm
of E. coli DNA)
 length of E.coli genome: 1.7 mm
 Often indigenous(natural) plasmids are present
 Plasmids -lactamase

ori

Extra chromosomal circular DNAs

 Found in bacteria, yeast and other fungi
foreign gene
 Size varies form ~ 3,000 bp to 100,000 bp.
 Replicate autonomously (origin of replication)
 May contain resistance genes
 May be transferred from one bacterium to another
 May be transferred across kingdoms
 Multicopy plasmids (~ up to 400 plasmids/per cell)
 Low copy plasmids (1 –2 copies per cell)
 Plasmids may be incompatible with each other
 Are used as vectors that could carry a foreign gene of
interest (e.g. insulin)
 PLASMID

o The term plasmid was first

introduced by the American
molecular biologist Joshua
Lederberg in 1952.
o A plasmid is separate form,
and can replicate
independently of, the
chromosomal DNA.
o Plasmid size varies from 1 to
over 1,000 (kbp).
 Types of PLASMIDs

•Plasmids can be broadly classified into

conjugative plasmids and non-conjugative
plasmids.
•In the complex process of conjugation, plasmid
may be transferred from one bacterium to
another via sex pili encoded by someof
the tra genes(transfer operon).
•Non-conjugative plasmids are incapable of
initiating conjugation, hence they can be
transferred only with the assistance ofconjugative
plasmids.
 Another way to classify plasmids isby
function. There are five main classes:
• Fertility F-plasmids, which contain tra genes. They are capable
of conjugation and result in the expression ofsex pili.

• Resistance (R) plasmids, which contain genes that provide

resistance against antibiotics or poisons.

• Col plasmids, which contain genes that code

for bacteriocins(p), proteins that can kill other bacteria.

• Degradative plasmids, which enable the digestion of unusual

substances, e.g. toluene(aromatic hydrocarbon) and salicylic
acid(aromatic acid)

• Virulence plasmids, which turn the bacterium intoa pathogen.

 Bacterial genes

 Most do not have introns

 Many are organized in operons: contiguous
genes, transcribed as a single polycistronic
mRNA(bac and chloroplast mrna), that encode
proteins with related functions

Polycistronic mRNA encodes several proteins

 Viral genomes
Viral genomes: ssRNA, dsRNA, ssDNA, dsDNA, linear or ciruclar

Viruses with RNA genomes:

•Almost all plant viruses and some bacterial and animal viruses
•Genomes are rather small (a few thousand nucleotides)
Viruses with DNA genomes (e.g. lambda = 48,502 bp):
•Often a circular genome.
Replicative form of viral genomes
•all ssRNA viruses produce dsRNA molecules
•many linear DNA molecules become circular
Molecular weight and contour length:
• duplex length per nucleotide = 3.4 Å
• Mol. Weight per base pair = ~ 660
 Mitochondrial genome (mtDNA)
 Multiple identical circular chromosomes
 Size ~15 Kb in animals
 Size ~ 200 kb to 2,500 kb in plants
 Over 95% of mitochondrial proteins are encoded in
the nuclear genome.
 Often A+T rich genomes.
 Mt DNA is replicated before or during mitosis
 Mitochondrial DNA contains 37 genes, all of which are
essential for normal mitochondrial function. Thirteen of
these genes provide instructions for making enzymes
involved in oxidative phosphorylation. Oxidative
phosphorylation is a process that uses oxygen and simple
sugars to create adenosine triphosphate (ATP), the cell's
main energy source.
 The remaining genes provide instructions for making
molecules called transfer RNA (tRNA) and ribosomal
RNA (rRNA), which are chemical cousins of DNA. These
types of RNA help assemble protein building blocks
(amino acids) into functioning proteins.
 Chloroplast genome (cpDNA)

 Multiple circular molecules

 Size ranges from 120 kb to 160 kb
 Similar to mtDNA
 Many chloroplast proteins are encoded in the
nucleus (separate signal sequence)
 “Cellular” Genomes
Viruses Prokaryotes Eukaryotes
Nucleus

Capsid
Plasmids

Viral genome Bacterial

Chromosomes Mitochondrial
chromosome
(Nuclear genome) genome

Chloroplast
genome
Genome: all of an organism’s genes plus intergenic DNA
Intergenic DNA = DNA between genes
 Size of genomes

Epstein-Barr virus 0.172 x 106

E. coli 4.6 x 106
S. cerevisiae 12.1 x 106
C. elegans 95.5 x 106
A. thaliana 117 x 106
D. melanogaster 180 x 106
H. sapiens 3200 x 106
 KARYOTYPE

o The study of chromosomes, their structure and

their inheritance is known as Cytogenetics.
o Each species has a characteristic number of
chromosomes and this is known as karyotype.
 GENES– GENETICINFORMATION
• One gene : one enzyme
hypothesis: summarizes
that a gene is a stretch of
DNA coding for one or
more isoforms of a single
enzyme.(Beadle 1941)
• One gene : one
polypeptide hypothesis: a
gene is responsible for the
production of a single
polypeptide.(Beadle 1945)
•Many genes: one protein:
e.g. Hemoglobin requires different globin genes.