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Organization of prokaryotic, eukaryotic and viral genomes DNA Chromosomal Extrachromosomal • Chromosomes (eukaryotic cells) •Mitochondrial and Chloroplast DNA (eukaryotic cells) • Nucleoid (prokaryotic cells) • Plasmids (prokaryotic cells) Chromosomes (eukaryotic cells) A chromosome is formed from chromatin. Chromatin DNA Proteins Structural Histones • Н1 • Н2А • Н2В • Н3 • Н4 Regulatory Nonhistone proteins Levels of DNA packing (eukaryotic cells) 1. 2. 3. 4. Chain of nucleosomes (10-11 nm) Chromatin fiber or solenoid (30 nm) Looped domains (200-300 nm) Metaphase chromosome (600-700 nm) Nucleosomes Levels of DNA packing DNA A nucleosome chain A solenoid Looped domains A metaphase chromosome Chromatin Heterochromatin Euchromatin • Less condensed regions of chromosomes • Tightly compacted regions of chromosomes • Transcriptionally active • Transcriptionally inactive (in general) Constitutive heterochromatin • Regions that are always heterochromatic • Permanently inactive with regard to transcription Facultative heterochromatin Regions that can interconvert between euchromatin and heterochromatin The human nuclear genome 1. 2. 3. 4. 5. 6. 7. 8. 9. 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 orisites 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%). Classifications of Repetitive sequences 1. • • 2. • • 3. • • 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 The human mitochondrial genome 1. 2. 3. A circular double-stranded DNA. The size is 16,569 bp. 37 genes: 2 rRNA genes, 13 protein coding genes, 22 tRNA genes. 4. There are overlapping genes 5. 1 ori-site (one replicon). 6. 2 promoters 7. Polycistronic RNAs 8. No introns 9. mtDNA is maternally inherited 10. 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) Nucleoid (prokaryotic cells) 1. 2. 3. 4. 5. 6. 7. 8. 9. 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. Plasmids Plasmids are double stranded, extrachromosomal genetic elements that replicate independently of the host cell chromosome. Plasmids vary in size (1 000 - 200 000 bp) Plasmids that can replicate free in the cytoplasm or can be inserted into the nucleoid and replicate with the chromosome are called episome. Plasmid Classifications 1. • • 2. • • • 3. • • 4. • • 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 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 IS-elements (insertion sequences) 1. The length is 700 - 1500 bp. 2. The coding region in an insertion sequence is usually flanked by inverted repeats (22-41 bp) 3. Most of the sequence is taken by one or two genes for transposase – enzyme that catalyzes transposition. 4. Cut-and-paste or copy-and-paste transposition. Composite transposons 1. The length is 2000 - 10 000 bp 2. 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. Simple transposons 1. The length is 2000 - 5000 bp. 2. are flanked by inverted repeats (IR) 3. contain multiple protein-coding genes (transposase gene and additional genes) between the IRs. Eukaryotic mobile elements 1. DNA transposons (the Ac/Ds elements of maize, P elements of Drosophila etc.) are flanked by IRs. Cutpaste transposition. 2. 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. Eukaryotic mobile elements 3. Helitrons don’t have terminal inverted repeats. Copy-paste transposition. They are replicated by a "rolling-circle" mechanism. 4. 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). Significance of mobile elements 1. Mutagens 2. May alter control of gene expression 3. Are a possible tool for inserting therapeutic genes into patients (gene-therapy). Viral Genomes DNA RNA • single-stranded linear DNA (parvovirus) • double-stranded linear RNA (reoviruses) • single-stranded circular DNA (M13 bacteriophage) • single-stranded linear RNA • double-stranded linear DNA (adenoviruses, herpes viruses ) • double-stranded circular DNA (papillomaviruses) • double-stranded with regions of single-strandedness (Hepatitis B virus) negative-sense («-» strand) (Influenza virus, Measles virus, mumps virus, Ebola virus) positive-sense («+» strand) (Tick-borne encephalitis virus, retroviruses, including HIV) 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-withingenes; • May have exons (eukaryotic viruses).