The genome of prokaryotes and eukaryotes- nuclear and

extranuclear genetic organization

Genomics, Genetics and Biochemistry

• Genetics: study of inherited phenotypes. • Genomics: study of genomes.

• Biochemistry: study of the chemistry of living organisms and/or cells.

Genomes and Genomics

• The word “genome,” coined by German botanist Hans Winkler in 1920, was derived simply by combining gene and chromos-ome.

•    If not specified, “genome” usually refers to the nuclear genome!

• An organism’s genome is defined as the complete haploid genetic complement of a typical cell.

•   The genetic content of the organelles in the cell, is not considered part of the nuclear genome.

•   In diploid organisms, sequence variations exist between the two copies of each chromosome present in a cell.

•    The genome is the ultimate source of information about an organism.

"Genes" are units of genetic information present on the DNA in the chromosomes and chromatin.

" Genome" is all the DNA contained in an organism or a cell, which includes the chromosomes plus the DNA in mitochondria (and DNA in the chloroplasts of plant cells).

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• The number of genomes sequenced in their entirety is now in the thousands and includes organisms ranging from bacteria to mammals.

• The first complete genome to be sequenced was that of the bacterium Haemophilus influenzae, in 1995.

• The first eukaryotic genome sequence, that of the yeast Saccharomyces cerevisiae, followed in 1996.

• The genome sequence for the bacterium Escherichia coli became available in 1997 .

• The much larger effort directed at the human genome was also accelerating.

Prokaryotes and Eukaryotes genome

Prokaryotic and Eukaryotic Cells Chromosomal differences

Prokaryotes

ØThe genome of E.coli contains amount of 4X106 base pairs

Ø> 90% of DNA encode protein ØLacks a membrane-bound nucleus.

§Circular DNA and supercoiled domain

ØHistones not present

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o Prokaryotic genomes generally contain one large circular piece of DNA referred to as a "chromosome" (not a true chromosome in the eukaryotic sense).

o Some bacteria have linear "chromosomes".

o Many bacteria have small circular DNA structures called plasmids which can be swapped between neighbors and across bacterial species.

Plasmid

o The term plasmid was first introduced by the American                     molecular                     biologist        Joshua Lederberg in 1952.

o A plasmid is separate from, and can replicate independently of, the chromosomal DNA.

o Plasmid size varies from 1 to over 1,000 (kbp).

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Eukaryotes

ØThe genome of yeast cells contains 1.35x107 base pairs

ØA small fraction of the total DNA encodes protein. • Many repeats of non-coding sequences

ØAll chromosomes are contained in a membrane bound nucleus

• DNA is divided between two or more chromosomes

ØA set of five histones

• DNA packaging and gene expression regulation

Karyotype

oThe study of chromosomes, their structure and their inheritance is known as Cytogenetics.

oEach    species    has    a    characteristic             number   of chromosomes and this is known as karyotype.

• Bacteria                         1 • Fruit fly       8 • Garden Pea                14 • Yeast                       16 • Frog     26

• Cat                                   38

• Fox                                   34 • Mouse                            40 • Rat                                  42 • Rabbit                            44 • Human                          46

• Chicken                           78

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o Prior to 1950's it was believed that humans had 48 chromosomes but in 1956 it was confirmed that each human cell has 46

chromosomes (Tjio and Levan, 1956).

o On the chromosomes the genes are situated in a linear order.

o Each gene has a precise position or locus.

o The size of bacterial chromosomes ranges from 0.6 -10 Mbp, and the size of Archael range from 0.5 - 5.8 Mbp, whereas Eukaryotic

chromosomes range from 2.9 - 4,000 Mbp.

Eukaryotic Genome

• Nuclear

• Mitochondrial

• Plasmids (in yeast and plant chloroplasts)

Mitochondrial DNA

• Mitochondrial DNA is a single double stranded circular molecule.

• There are several copies in each mitochondrion and there are many mitochondria in each of your cells.

• Mitochondrial DNA is similar to prokaryotic DNA. There are no histones or any other protein associated with mt DNA.

• The genes contain no introns. Maternal inheritance.

• Because it is in a highly oxidizing environment it has a much higher rate of mutations than nuclear DNA.

• The genes in mt DNA code for mitochondrial ribosomes and transfer RNAs.

• Some genes code for polypeptide subunits of the electron transport chain common to all mitochondria.