THE CELL NUCLEUS

A typical cell nucleus is bound by a nuclear envelope made up of two membranes. This serves
to protect the DNA from the mechanical forces generated by the cytoplasmic filaments in
eukaryotes. A typical cell nucleus has two networks of intermediate filaments that provide
mechanical support for the nuclear envelop. The intermediate filaments inside the nucleus form
the nuclear lamina
Chromosomal DNA
Parts of a typical nucleus A chromosome is formed from a single,
enormously long DNA molecule that
contains a series of many genes. A gene
is a nucleotide sequence in a DNA
molecule that acts as a functional unit for
the production of an RNA molecule

Specialized Nucleotide Sequences in the DNA

1. DNA replication origin

Each chromosome has many origins of replication.
2. A centromere serves to hold the two copies of the duplicated chromosome together and to
attach them, via a protein complex called a kinetochore, to the mitotic spindle fiber
(accurate segregation of chromosomes to daughter cells)
3. A telomere allows the DNA molecule to be replicated
These three (3) DNA elements are needed to produce a stable linear eucaryotic chromosome

Most chromosomal DNA does not code

for proteins or RNAs (“introns”). The
mammalian genome is enough to
code for 3 million proteins but in reality
not more than 60,000 essential
proteins constitute a mammal (or any
organism) . In higher eucaryotes,
gene length is commonly 100,000 bp,
occassionally 2M bp. Proteins of
average size is 300-400 aa and is
encoded by 1000 bp only

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 The amount of DNA in the haploid
genome of an organism has no
systematic relationship to the
complexity of the organism

Each gene produces an RNA molecule

A mRNA codes for a protein while rRNA and tRNA are structural RNAs

Chromatin - complex of proteins with the DNA

Nucleosome - the fundamental packing unit of the chromatin structure (discovered in 1974)
Two H2A-H2B dimers flank an H3-H4 tetramer

Nucleosomal Proteins
• Histone proteins
Nucleosomal histones - small proteins responsible for
coiling the DNA into nucleosomes (H2A, H2B, H3, H4)
H1 histones are larger
• Nonhistone chromosomal proteins

A nucleosome has a histone octamer composed of two each of

the histone molecules. It is the protein core around which the
double stranded DNA helix (146 bp) is wound twice
(Total mass = 100,000 daltons)

Linker DNA – 0 to 80 bp between nucleosomes

Histones are the principal structural proteins

of eucaryotic chromosomes

They are relatively small with high proportion of

positively charged amino acids (lysine and arginine); the
positive charge helps the histones bind tightly to DNA
(negatively charged)

The bending of
DNA in a
nucleosome

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 Histone H1 binds
through its globular
portion to a unique
site on a
nucleosome, and its
arms extend to
contact other sites
30 nm chromatin fiber
on the histone cores
(higher-order structures)
of adjacent
Histone H1 molecules are thought to
nucleosomes, so
be responsible for pulling
that the
nucleosomes together to form the 30
nucleosomes are
nm fiber
pulled together into
a regular repeating
array.

NUCLEASE-HYPERSENSITIVE SITES
• short regions where the chromosomal DNA is unusually vulnerable to digestion by
DNAse I
• interruption of the regular nucleosomal structure
If the organization of the chromatin is just the 30nm fiber, then the length of a typical human
chromosome would be 0.1 cm and would span the nucleus more than 100 times (not possible!)
Implication: there must still be a higher level of folding

Model of Chromatin Packing

The many orders of chromatin
postulated to give rise to the highly
condensed mitotic chromosome

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Evidences for the existence of higher order chromatin structure
Specialized structures are visible under the light microscope
1. Lampbrush Chromosomes- vertebrate oocytes
2. Polytene Chromosomes – insect giant secretory cells

Polytene chromosomes
Homologous chromosomes lie side by side forming a single giant polytene chromosome
Source: insect (fly) salivary gland cells

After several cycles of replication, no separation

occurs. Identical strands of chromatin are lined up side by
side. Regions that are actively transcribed at a period can be
identified (labeling with radioactive RNA precursor 3H-Uridine
and locating the transcripts by autoradiography)
Active parts are decondensed, forming chromosome
puffs. During the different life stages of the insects, new puffs
would appear and old would recede indicating the activation
and deactivation of transcription units.
This activity is controlled by the hormone ecdysone

Lampbrush Chromosomes
Have unusually stiff and extended chromatin
loops that are covered with newly transcribed
RNA packed into dense RNA-protein complexes.
Majority of the chromatin are in the condensed
areas which are not transcribed.
condensed – inactive
extended portions or loops – actively
being transcribed

Interphase Chromatin
Heterochromatin – compact and transcriptionally inactive; approx 10% of genome is
packed into heterochromatin
Euchromatin – less condensed (10% active, 90% inactive)

Interphase Chromosomes
- too extended
- thin
- not easily discernible
Mitotic chromosomes
coiled up and condensed
- shorter (a 5 cm DNA could become 5 micrometers)

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- chromatin resembles heterochromatin
- transcriptionally inactive; RNA polymerase has no access to the DNA (due to condensation)

Chromosome Replication
• Takes place during the S phase, a specific part of interphase
• Usually last for about 8 hours in typical higher eukaryotic cells
• By the end of S, each chromosome has been replicated to produce two complete copies,
which remain joined together at their centromeres until the M phase

Karyotype - display of chromosomes at mitosis

Identification of individual chromosomes possible through stains (usually flourescent)
G bands – rich in A-T
R bands – rich in G-C
Bands are discernible along the chromosome

A typical metaphase chromosome

Each sister chromatid contains one of two identical daughter DNA molecules generated earlier
in the cell cycle by DNA replication