Representative genome sizes
• Phage virus: 168 kb  65 nm phage head (~1,000 x length)
• E. coli bacteria: 1mm DNA  ~0.2 micron space nucleoid region
(1000 x)
• Human cell: 7.5 feet of DNA  ~3 micron nucleus (2.3 million times
longer than the nucleus)
DNA packaging: How does all that DNA fit into one
nucleus?
An organism’s task in managing its DNA:
1.) Efficient packaging and storage, to fit into very
small spaces
2.) Requires “de-packaging” of DNA to access correct
genes at the correct time (gene expression).
3.) Accurate DNA replication during the S-phase of the
cell-cycle.
Packaging of Prokaryotic DNA
• DNA is organized as a single chromosome
that contains ds circular supercoil
• Eg; E. coli 1mm chromosome need to be
packed in 1µm cell
• Bacterial chromosomes are organized into
compacted structure-nucleoids- interaction
with HU protein –
forming DNA-HU
complex
4
To fit within the bacterial cell, the chromosomal DNA must be compacted about a
1000-fold This involves the formation of loop domains. The number of loops varies
according to the size of the bacterial chromosome and the species.
E. coli has 50-100 with 40,000 to 80,000 bp of DNA in each loop.
The looped structure compacts
the chromosome about 10-fold

DNA super coiling is a second important way to compact the
bacterial chromosome
Supercoiling within loops creates
a more compact DNA
A SCHEMATIC ILLUSTRATION OF DNA SUPER COILING
Negative and Positive Supercoiling
Model for coiling activity of Topoisomerase II (Gyrase)
Upper jaws
DNA wraps around
the A subunits in a
right-handed direction.
DNA binds to
the lower jaws.
Lower jaws
A subunits
DNA
B subunits
Upper jaws
clamp onto DNA.
DNA held in lower jaws is cut. DNA
held in upper jaws is released and
passes downward through the
opening in the cut DNA (process
uses 2 ATP molecules).
(a) Molecular mechanism of DNA gyrase function
Circular
DNA
molecule
DNA gyrase
2 ATP
2 negative
supercoils
Cut DNA is ligated back
together, and the DNA is
released from DNA gyrase.
EUKARYOTIC CHROMOSOMES

Eukaryotic species contain one or more sets of chromosomes
◦ Each set is composed of several different linear chromosomes

If stretched end to end, a single set of human chromosomes will be over 1 meter
long!
 Yet the cell’s nucleus is only 2 to 4 mm in diameter
 Therefore, the DNA must be tightly compacted to fit

The compaction of linear DNA in eukaryotic chromosomes involves interactions
between DNA and various proteins
 Proteins bound to DNA are subject to change during the life of the cell
 These changes affect the degree of chromatin compaction
Levels of DNA Packaging in Eukaryotes
NUCLEOSOMES


The repeating structural unit within eukaryotic
chromatin is the nucleosome
It is composed of double-stranded DNA
wrapped around an octamer of histone
proteins

Consists of a nucleosome core, linker
DNA, one H1 histone.

Nucleosome core


An octamer is composed two copies each of four
different histones
146 bp (154bp - 260bp) of DNA wound around the
octamer in 1 ¾ turn.

Histone proteins are basic
 They contain many positively-charged amino acids
 Lysine and arginine
 These bind with the phosphates along the DNA backbone

There are five types of histones
 H2A, H2B, H3 and H4 are the core histones
 Two of each make up the octamer
Linker DNA: Size varies from 8bp to 114bp
H1 HISTONE: Each nucleosome contains one molecule of H1 histone
Not the part of nucleosome core
Binds where DNA enters and leaves nucleosome
Vary in length between 20 to 100 bp,
depending on species and cell type

Overall structure of connected nucleosomes resembles “beads on a
string”

This structure shortens the DNA length about seven-fold!!!!!!!!!!
Diameter of the
nucleosome
Nucleosomes Join to Form a 30 nm

Nucleosomes associate with each
other to form a more compact zigzag structure fiber of 30 nm.
Play a role in the
organization and
compaction of the
chromosome
Nucleosome Solenoid Model

Two models have been proposed
 Solenoid model
 Three-dimensional zigzag model
Regular, spiral
configuration
containing six
nucleosomes per turn
Irregular
configuration where
nucleosomes have
little face-to-face
contact
Solenoid is a coiled structure :
6 nucleosomes/turn
6 turns/ solenoid
Further Compaction of the chromosome
Non-Histone Chromosomal
(NHC) Proteins:
During interphase
most chromosomal
regions are
euchromatic
Compaction level
in euchromatin
Compaction level
in heterochromatin
The number of loops has not changed
However, the diameter of each loop is smaller
During interphase,
condensin is in the
cytoplasm
Condesin binds to
chromosomes and
compacts the
radial loops
Condesin travels
into the nucleus
THE CONDENSATION OF A METAPHASE
CHROMOSOME BY CONDENSIN
Summary of Chromosome Folding
Level of folding
Consists of
Base pair/turn
DNA double helix
Nucleotides
10
Nucleosomes
200 bp each
100
30 Nanometer fiber
6 Nucleosomes /turn
1,200
Loops
50 Solenoids/loop
60,000
Miniband
18 loops
1,080,000
Chromatid
1,000,000 minibands