GENOME STRUCTURE: From DNA To Chromosome

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GENOME STRUCTUREFrom DNA To Chromosome

• Lecture 2 of
• Introduction to Molecular Biology
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Packing Genetic Materials

• The length of the DNA as an extended molecule
  would vastly exceed the dimensions of the
  compartment that contains it therefore, the DNA
  (in some cases, the RNA) must be compressed
  exceedingly tightly to fit into the space
  available.

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Highly Organized DNA Molecule
The length to width ratio of a typical human
chromosome is over 10 million to one.
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Interphase DNA
When interphase nuclei are suspended in a low
ionic strength solution, they will swell and
rupture to release fibers of chromatin. In some
regions, the fibers consist

• of tightly packed material, but in regions that
  have become stretched, they can be seen to
  consist of discrete particles, called
  nucleosomes. A continuous duplex thread of DNA
  runs through the series of particles.

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Nucleosome

• The nucleosome contains 200 bp of DNA associated
  with a histone octamer that consists of two
  copies each of H2A , H2B, H3, and H4 (core
  histones).

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Composition of Nucleosome
The number of residues in H1 (or H5) is about
220. Other types of histones are smaller, each
containing 100-135 residues.
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Core and Linker DNA

• A nucleosome DNA can be further divided into 2
  regions
• 1. Core DNA 146 bp, resistant to digestion by
  nucleases.
• 2. linker DNA from as little as 8 bp to as much
  as 114 bp per nucleosome, sensitive to nucleases
  digestion.

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Beads on a String
When chromatin is examined in the electron
microscope, two types of fiber are seen the 10
nm fiber and 30 nm fiber. The 10 nm fiber
structure is obtained under conditions of low
ionic strength and does not require the presence
of histone H1.
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Solenoid
When chromatin is condensed, each nucleosome is
associated with an H1 (or H5) to form a solenoid
structure. H1 and H5 are called linker histones.
They are essential in stabilizing the solenoid
conformation.

• When chromatin is visualized in conditions of
  greater ionic strength, the 30 nm fiber is
  obtained.

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Loop of Chromosome Fiber

• The chromatin solenoid is also called 30 nm
  chromatin fiber. In the condensed form, the
  fiber is associated with scaffold proteins
  (notably topoisomerase II) to form loops. Each
  loop contains about 75 kb DNA. Scaffold proteins
  are attached to DNA at specific regions, called
  scaffold attachment regions (SARs), which are
  rich in nucleotides A and T.

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Chromosome

• Finally, the chromatin fiber and associated
  scaffold proteins coil into a helical structure
  (a chromosome). The AT-rich SARs are not evenly
  distributed along the longitudinal axis of the
  chromosome. G bands correspond to more closely
  spaced SARs. Hence, stains with dyes which
  preferentially bind AT-rich DNA, such as
  Quinacrine, will make G bands darker.

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Release of DNA from Histone
Histones contain a few lysine (K) residues at the
N terminus. Under normal cellular conditions, the
R group of lysine is positively charged, which
can bind to the negatively charged phosphates in
DNA. The positive R group of lysine may be
neutralized by acetylation (by histone
acetyltransferase, HAT), reducing the binding
force between histones and DNA. Such mechanism
has been demonstrated to play a major role in the
regulation of gene transcription.
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Modification of Histones

• 1. adding acetyl and methyl groups neutralizes
  the positive charges on Lys and Arg
• 2. adding phosphate groups adds negative charges
  to Ser and Thr residues
• 3. both actions would reduce the strength of the
  association between the highly-negative DNA and
  the highly-positive histones.

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Regenerates of Nucleosomes
Histones need to be removed before replication of
DNA can proceed.
Nucleosomes are quickly regenerated once the DNA
has been replicated
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Role of Nuclear Structure

• The replication factories were not diffusely
  spread throughout nuclei but concentrate in
  certain foci. Early in the S phase the foci is
  small and discrete later they become larger. The
  figure shows fluorescence micrographs of
  replication patterns found at different stages of
  S phase.

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Replication Pattern in S Phase