1. Organization of prokaryotic, eukaryotic and viral genomes

2. DNA Chromosomal Extrachromosomal
Mitochondrial and Chloroplast DNA (eukaryotic cells)
Plasmids (prokaryotic cells)
Chromosomes (eukaryotic cells)
Nucleoid (prokaryotic cells)

3. Chromosomes (eukaryotic cells)
A chromosome is formed from chromatin. Chromatin
DNA
Proteins
Structural
Regulatory
Histones
Nonhistone proteins Н1
Н2А
Н2В Н3 Н4

4. Levels of DNA packing (eukaryotic cells)
Chain of nucleosomes (10-11 nm)
Chromatin fiber or solenoid (30 nm)
Looped domains ( nm)
Metaphase chromosome ( nm)

5. Nucleosomes

6. Levels of DNA packing DNA A nucleosome chain A solenoid Looped domains
A metaphase chromosome

7. Chromatin Euchromatin Heterochromatin Constitutive heterochromatin
Less condensed regions of chromosomes
Transcriptionally active
Tightly compacted regions of chromosomes
Transcriptionally inactive (in general)
Constitutive heterochromatin
Facultative heterochromatin
Regions that are always heterochromatic
Permanently inactive with regard to transcription
Regions that can interconvert between euchromatin and heterochromatin

8. The human nuclear genome
The human nuclear genome is 3.1 Gb (3×109 bp) in size.
More than 30,000 genes.
24 different types of linear double-stranded DNA molecule.
There are multiple replicons per chromosome (several ori-sites per chromosome).
No operons. Eukaryotic genes are individually transcribed.
There are introns and exons in genes.
Large numbers of regulatory sequences.
Supergene families and pseudogenes.
Single-copy (60%) and repetitive sequences (40%).

9. Classifications of Repetitive sequences
Based on number of copies:
moderately repeated DNA (10 – 1,000 copies) (30%)
highly repeated DNA (more than 1,000 copies) (10%)
Based on location:
Interspersed repeats (SINE, LINE)
Tandem repeats (macrosatellites, minisatellites and microsatellites)
Based on direction of the repeats:
Direct repeats
Inverted repeats

10. The human mitochondrial genome
A circular double-stranded DNA.
The size is 16,569 bp.
37 genes: 2 rRNA genes, 13 protein coding genes, 22 tRNA genes.
There are overlapping genes
1 ori-site (one replicon).
2 promoters
Polycistronic RNAs
No introns
mtDNA is maternally inherited
Genetic code is different:
AUA specifies methionine not isoleucine
UGA encodes tryptophan not stop-codon
AGA and AGG are stop-codons (they specify arginine in the nuclear genetic code)

11. Nucleoid (prokaryotic cells)
Double-stranded supercoiled circular DNA molecule
The length is 2 - 5×106 bp.
1 ori-site (one replicon).
Attached to plasma membrane in the ori-site region.
Associated with only a few protein molecules.
Structural gene sequences (encoding proteins and RNAs) account for the majority of bacterial DNA (70%). The nontranscribed DNA between genes are called intergenic regions (30%).
A typical bacterial chromosome contains a few thousand different genes (about 4 000)
Genes are often clustered into operons.
No introns.

12. Plasmids
Plasmids are double stranded, extrachromosomal genetic elements that replicate independently of the host cell chromosome. Plasmids vary in size ( bp) Plasmids that can replicate free in the cytoplasm or can be inserted into the nucleoid and replicate with the chromosome are called episome.

13. Plasmid Classifications
Based on the structure of DNA:
Circular
Linear
Based on their function (marker genes):
R-plasmids (plasmids that carry one or more antibiotic resistance genes)
Col-plasmids (plasmids which encode the genes to synthesize colicins)
Cryptic plasmids (plasmids that have no known function)
Based on their ability to transfer to other bacteria:
Conjugative plasmids
Non-conjugative plasmids (incapable of initiating conjugation)
Based on their ability to coexist in a single cell
Compatible
Incompatible

14. Mobile (transposable) DNA
Mobile elements are segments of DNA that can move around to different positions in the genome of a single cell. prokaryotic mobile elements IS-elements Transposons Simple Composite

15. IS-elements (insertion sequences)
The length is bp.
The coding region in an insertion sequence is usually flanked by inverted repeats (22-41 bp)
Most of the sequence is taken by one or two genes for transposase – enzyme that catalyzes transposition.
Cut-and-paste or copy-and-paste transposition.

16. Composite transposons
The length is bp
Composite transposons are basically the pair of IS elements flanking a segment of DNA usually containing one or more genes, often coding for antibiotic resistance.

17. Simple transposons The length is 2000 - 5000 bp.
are flanked by inverted repeats (IR)
contain multiple protein-coding genes (transposase gene and additional genes) between the IRs.

18. Eukaryotic mobile elements
DNA transposons (the Ac/Ds elements of maize, P elements of Drosophila etc.) are flanked by IRs. Cut-paste transposition.
Polintons (the length is 15,000 – 20,000 bp) encode more than 10 proteins, including a protein-primed DNA polymerase B). They are flanked by IRs (several hundred bp). Copy-paste transposition.

19. Eukaryotic mobile elements
Helitrons don’t have terminal inverted repeats. Copy-paste transposition. They are replicated by a "rolling-circle" mechanism.
Retrotransposons are transposable elements that move within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA. To insert it must be converted back to DNA by reverse transcriptase.
Types of retrotransposons:
LTR retrotransposons
Non-LTR retrotransposons (L1, Alu).

20. Significance of mobile elements
Mutagens
May alter control of gene expression
Are a possible tool for inserting therapeutic genes into patients (gene-therapy).

21. Viral Genomes DNA RNA single-stranded linear DNA (parvovirus)
single-stranded circular DNA (M13 bacteriophage)
double-stranded linear DNA (adenoviruses, herpes viruses )
double-stranded circular DNA (papillomaviruses)
double-stranded with regions of single-strandedness (Hepatitis B virus)
double-stranded linear RNA (reoviruses)
single-stranded linear RNA
negative-sense («-» strand) (Influenza virus, Measles virus, mumps virus, Ebola virus)
positive-sense («+» strand) (Tick-borne encephalitis virus, retroviruses, including HIV)

22. Viral Genomes
Viral genomes vary in size from a few thousand to more than a hundred thousand nucleotides;
Compact genomes with little spacer DNA or RNA
May have overlapping genes and genes-within-genes;
May have exons (eukaryotic viruses).