DNA or RNA in different viruses

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Organization of DNA in Viruses

• DNA or RNA in different viruses
• Single-stranded or double-stranded in different
  viruses
• Circular or linear in different viruses
• Usually one DNA molecule/viral particle
• DNA is packaged into the heads in a very
  compact manner
• DNA is not associated with proteins

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Organization of DNA in Bacteria

• DNA is in center of cell in a nucleoid
• Bacterial chromosome is circular
• Double-stranded
• Usually one DNA molecule per cell, may also
  have plasmids
• DNA is not associated with histones or in
  nucleosomes
• Supercoiling

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DNA Supercoiling
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Organization of DNA in Eukaryotes

• More DNA per chromosome per cell than
  bacteria
• -E. coli has 1200 micrometers of DNA /cell
• -Humans have 14,000 to 73,000 mm of DNA per
  chromosome
• -46 chromosomes total 2 m of DNA contained
  in 5 mm nucleus
• Nucleosomes
• .Repetitive DNA
• -Only about 5 of the DNA in a human is
  transcribed
• -Certain DNA sequences are present in
  multiple copies
• -Certain sequences are present thousands of
  times

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Description of Nucleosomes

• 2 copies each of H2a, H2b, H3, and H4 to form
  of an octamer with 200 bp of DNA wrapped twice
  around the core
• H1 particles are on the DNA between each
  nucleosome
• DNA associated with nucleosomes forms 11 nm
  fibers
• These coil further into solenoids 30 nm in
  diameter
• The solenoids coil into 300 nm chromatin fibers

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Discovery of Nucleosomes

• If chromatin is treated with detergents and
  examined with an electron microscope, you see 100
  angstrom beads on a string (Olins and Olins 1973)
• If you treat chromatin with certain
  endonucleases (micrococcal nuclease), you get
  DNA pieces that are 200 base pairs long or
  multiples of 200 bases
• Thus, the digestion is not random, but the DNA
  is protected from enzymatic digestion in regions
  200 bases long

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Chromatin Structure is Based on Successive Levels
of DNA Packaging

• Histones
• -Proteins that bind DNA (high positive charge)
• -5 types H1, H2A, H2B, H3, H4 (conserved)
• Nucleosomes
• -DNA wound around histone complex
• -200 nucleotides of DNA wrapped around
• -2 molecules each of H2A, H2B, H3 and H4
• -(core particle) plus one H1 on the outside of
  the bead
• Chromosomes
• -Highly packed arrangement of nucleosomes- Only
  ONE continuous double stranded helix per
  chromosome

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Heterochromatin vs Euchromatin
Heterochromatin vs Euchromatin

• Heterochromatin describes areas of DNA that
  are genetically inactive. It is involved in
  physical maintenance of chromosome structure.
• Euchromatin describes areas of chromatin
  available for transcription. It is involved in
  gene expression.

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Repetitive DNA Junk or Treasure?
Repeats are often described as 'junk' and
dismissed as uninteresting. However, they
actually represent an extraordinary trove of
information about biological processes. The
repeats constitute a rich palaeontological
record, holding crucial clues about evolutionary
events and forces. As passive markers, they
provide assays for studying processes of mutation
and selection. It is possible to recognize
cohorts of repeats 'born' at the same time and to
follow their fates in different regions of the
genome or in different species. As active agents,
repeats have reshaped the genome by causing
ectopic rearrangements, creating entirely new
genes, modifying and reshuffling existing genes,
and modulating overall GC content. They also shed
light on chromosome structure and dynamics, and
provide tools for medical genetic and population
genetic studies. From Initial sequencing and
analysis of the human genome. Nature 409,
860 - 921 (2001)
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Highly Repetitive DNA

• Satellite DNA
• Highly repetitive DNA found in genome
• Centromere DNA
• highly conserved DNA maintains
  chromosome structure
• Yeast centromeres have three regions
  (I,II, III)
• -Region I and III - short highly
  conserved (8-26 bp)
• -Region II longer (80-85 bp) and A-T rich
• Telomere DNA
• GGGGTT in Tetrahymena and GGGATT in
  Humans
• Highly conserved

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Yeast Centromeric Structure
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VNTRs and Dinucleotide Repeats

• Tandem repeats that vary in number -
  variable number tandem repeats
• Repeats of 15-100 bp are minisatellites
• Repeats of 5 and 50 bp are microsatellites
• CA dinucleotide repeats are common in humans

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DNA as Evidence
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Inheritance of VNTR Alleles is Mendelian
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What Do You Think?
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Repetitive Transposed Sequences
Sequence that can move about the genome
Short Interspersed Elements (SINES) less than
500 bp but 1,500,000 copies in the human genome
best characterized is the Alu family
Long Interspersed Elements (LINES)
bigger than SINES best example is
the L1 family 6400 bp in length and present up
to 100,000 copies per genome LTR
retrotransposons retrovirus-like elements
DNA transposons
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Transposon-Derived Repeats
Most human repeat sequence is derived from
transposable elements
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Chromatin Organization
What do you get when you put all of these
components together?
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Chromosomes
G-banding
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Estimates of Chromosome Size