Download Chromosomes

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.
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•
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.
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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).