Chapter 9 DNA structure and organization

Broad course objective: a.) explain the molecular structure of

chromosomes as it relates to DNA packaging, chromosome function and
gene expression
Necessary for future material on: Chromosome Variation, Regulation of
Gene Expression

DNA PackagingWhy and How

If the DNA in a typical human cell were stretched out, what length would it be?
What is the diameter of the nucleus in which human DNA must be packaged?
What degree of DNA packaging corresponds with diffuse DNA associated
with G1? What kind of DNA packaging is associated with M-phase (condensed
DNA)?
What types of DNA sequences make up the genome? What functions do they
serve?
What are the differences between euchromatin and heterochromatin?
What types of proteins are involved in chromosome packaging?

How do nucleosomes and histone proteins function in DNA packaging?

What is chromosome scaffolding?

How much DNA do different organisms have?

Organism
T4 Bacteriophage
HIV
E. colibacteria
Yeast
Lily
Amoeba

haploid genome in bp

168,900
9,750
4,639,221
13,105,020
36,000,000,000
290,000,000,000

Frog

3,100,000,000

Human

3,400,000,000

DNA content does not directly coincide with complexity of the

organism. Any theories on why?

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Fungi
Vascular
plants
Insects
Mollusks
Simpsons Nature Photography

Fishes
Amphibians

(b) Plethodon richmondi

Salamanders

Reptiles
Birds
Mammals
106

107

108

109

1010

1011

1012

(a) Genome sizes (nucleotide base pairs per

haploid genome)
William Leonard

(c) Plethodon Iarselli

Brooker Fig 12.8

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Has a genome that is more than twice as

large as that of P. richmondi

12-21

Size measurements in the molecular world

1 mm (millimeter) = 1/1,000 meter
1 m (micron) = 1/1,000,000 of a meter (1 x 10-6)
1 nm (nanometer) = 1 x 10-9 meter

1 bp (base pair) = 1 nt (nucleotide pair)

1,000 bp = 1 kb (kilobase)
1 million bp = 1 Mb (megabase)
5 billion bp DNA ~ 1 meter
5 thousand bp DNA ~ 1.2 mm

Representative genome sizes

Phage virus: 168 kb 65 nm phage head (~1,000
x length)
E. coli bacteria: 1,100 mm DNA ~0.2 micron
space nucleoid region (5,500 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?
(Equivalent to fitting 690 miles of movie film into a 30-foot room)

An organisms task in managing its DNA:

1.) Efficient packaging and storage, to fit into very
small spaces (2.3 million times smaller)
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.

Chromosomal puffs in condensed Drosophila chromosome show states

of de-condensing in expressed regions

Prokaryotic genome characteristics

1. Circular chromosome (only
one), not linear
2. Efficientmore gene DNA,
less or no Junk DNA
3. One origin sequence per
chromosome

How does the bacterial chromosome remain

in its tight nucleoid without a nuclear
membrane?

Origin of
replication

Most, but not all, bacterial species

contain circular chromosomal DNA.
A typical chromosome is a few
million base pairs in length.
Most bacterial species contain a
single type of chromosome, but it
may be present in multiple copies.

Genes
Intergenic regions
Repetitive sequences

Brooker, fig 12.1

A few thousand different genes are

interspersed throughout the chromosome.

Intergenic regions play roles in DNA

folding, DNA replication, gene
regulation, and genetic recombination

Prokaryotic genome characteristics

Bacterial chromosome is normally supercoiled

(~ 40 kb)

Bacterial DNA released from

supercoiling

To fit within bacterial cell, the chromosome must be

compacted ~1000-fold
The looped structure compacts the
chromosome about 10-fold

Loop
domains
Formation of
loop domains

(a) Circular chromosomal DNA

Brooker, Fig 12.3

DNAbinding
proteins

(b) Looped chromosomal DNA with

associated proteins

DNA supercoiling is a second important way to compact the bacterial

chromosome
Supercoiling within loops creates a
more compact chromosome

Supercoiling

(b) Looped chromosomal DNA

(c) Looped and supercoiled DNA

Brooker, Fig 12.3 -- illustration of DNA supercoiling

12-8

Negative and
Positive
Supercoiling

Like Brooker, Fig 12.4

Area of
negative
supercoiling

Negative supercoiling
promotes DNA strand
separation

Brooker, Fig 12.5

Strand
separation

This enhances DNA

replication and
transcription

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.

(b) Overview of DNA gyrase function

Brooker, Fig 12.6

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Eukaryotic Chromosomes

Levels of DNA Packaging in Eukaryotes

Types of DNA sequences

making up the eukaryotic genome

DNA type
Function
Number/genome
Unique-sequence Protein coding and non-coding
1
Repetitive-sequence
Opportunistic?
few-107
Centromere

Cytoskeleton attachment

Telomere

Csome stability

1 region/csome
Ends of csome DNA

Percentage in the human genome

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100
80

59%

60
40
24%

20
0

15%

2%
Regions of
genes that
encode
proteins
(exons)

Brooker, Fig 12.9

Introns and
other parts
of genes

Unique
noncoding
DNA

Classes of DNA sequences

Repetitive
DNA

Centromere sequences

Repeating sequences
Non protein-coding
Sequences bind to centromere proteins, provide
anchor sites for spindle fibers

Reminder of function of kinetochores and

kinetochore microtubules

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

Chromosome
fragments lacking
centromeres are
lost in mitosis
(Figure 11.10)

Telomere sequences function to preserve the length of

the ends

Levels of DNA Packaging in Eukaryotes

Digestion of
nucleosom
es reveals
nucleosom
e structure

Nucleosomes shorten DNA ~seven-fold

nucleosome
diameter

H2A

H2A

Linker region
H3

DNA

H2B
H3
H2B

H4

11 nm

H4
Amino
terminal
tail

Histone
protein
(globular
domain)

Nucleosome
8 histone proteins (octamer) +
146 or 147 base
pairs of DNA

(a) Nucleosomes showing core histone proteins

Brooker, Fig 12.10a

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Non-histone proteins play role in

chromosomes organization and compaction
Histone
octamer
Nonhistone
proteins

Histone H1

Linker
DNA

Nucleosomes showing linker histones and nonhistone

proteins

Nucleosomes closely associate to form 30 nm fiber

(shortens total DNA by another 7 fold)
30 nm
30 nm
Core
histone
proteins
Irregular configuration
where nucleosomes
have little face-to-face
contact
Regular, spiral
configuration
containing six
nucleosomes per
turn

Solenoid model

Zigzag model

Brooker, Fig 12.13

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Levels of DNA Packaging

2 nm
DNA double helix

Histone H1

Wrapping of DNA around

a histone octamer

11 nm
Histone
octamer

Nucleosome

(a) Nucleosomes (beads on a string)

Formation of a three-dimensional zigzag structure
via histone H1 and other DNA-binding proteins

30 nm

(b) 30 nm fiber

Nucleosome
Anchoring of radial loops to the
nuclear matrix

Brooker, Fig 12.17a and b

Radial loop bound to a nuclear matrix

fiber
Gene

Scaffold-attachment
regions (SARs)

Gene

or

Gene

Matrix-attachment
regions (MARs)

Radial loop
25,000 to
200,000 bp

Protein
fiber
MAR

30-nm
fiber
MAR

(d) Radial loop bound to a nuclear matrix fiber

Brooker, Fig 12.14

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MARs are anchored to

the nuclear matrix,
thus creating radial
loops

Compaction level in
euchromatin
(interphase)
300 nm
(c) Radial loop domains

Protein scaffold
Further compaction of
radial loops

Levels of DNA
Packaging, cont.

700 nm

Compaction level in
heterochromatin
Formation of a scaffold from the nuclear matrix
and further compaction of all radial loops

1400 nm

(d) Metaphase chromosome

Brooker, Fig 12.17

Metaphase Chromosomes
DNA strand

Scaffold

2 m
Peter Engelhardt/Department of Virology, Haartman Institue

Metaphase
chromosome

Dr. Donald Fawcett/Visuals Unlimited

Metaphase chromosome treated with high salt to remove

histone proteins

Brooker, Fig 12.18

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