The Cell Nucleus

The presence of a nucleus confined in a nuclear membrane is a key feature of Eukaryotic cells.

The nucleus is the specialized area of the cell where processes related to gene expression occur &
hence controls all cell activities.
 Store cell DNA  RNA processing & export
 DNA replication  Ribosome biogenesis
 DNA repair

GENERAL FEATURES

 Stores very long DNA molecules as structures called chromosomes

 Contains all the machinery that allows DNA to replicate

 Contain all the RNA transcription & post-transcriptional processing machinery

 Its structure, tightly regulates the traffic with the cytoplasm

DNA PACKAGING -humans have 23 pairs of chromosomes contain 6 x 109 bp of DNA-protects DNA

 Chromosomes + associated proteins = CHROMATIN

 FIRST LEVEL
o Histones: proteins responsible for the 1st level of packaging
 DNA + HISTONES = NUCLEOSOMES
 NUCLEOSOMES structure increases DNA packaging 7 fold

 SECOND LEVEL
o NUCLEOSOMES pack themselves in 30nm fibres constituting the 2nd level of packaging
 Increases packaging 6 fold

 THIRD LEVEL
o 30nm fibres pack themselves into 80-100nm fibres constituting the 3rd level of packaging
 Increases packaging 3 fold

 FOURTH LEVEL
o Represented by the mitotic chromosome
 Represents 10,000 fold increase
CHROMOSOME

 A single molecule of DNA

 Linear in eukaryotes
 Contains genes

 Structural elements: all chromosomes have

o Telomeres: At either ends of the chromosome
 Protect the chromosome ends
 Ensure the entire chromosome is replicated during cell division

o Centromere: Divide the chromosome into 2 parts (not equally)

 Ensure the chromosome attaches to the mitotic spindle via Kinetochore during
cell division
o Origins of replication: places where replication of the chromosome starts
The banding pattern
and other features observed in the chromosomes are used to identify & correlate to genetic
anomalies.
G-banding: spanning pattern on chromosomes. Take Cell sample,
Centromere=point of attachment culture them so they are growing and use hypotonic solution to
swell them up big so when they are dropped onto a slide they
burst. All chromosomes spread=metaphase spread. You get a
banding pattern.

Cytogenetics: scientifically looking at banding pattern to see how

many chromosomes an organism has, and the chromosome
number and organisation in cancer cells would be different to
healthy cells because the genes are disrupted (abnormal events).
Also used when you have recurrent miscarriages to see if you
have an extra part of a chromosome.

Metacentric: Centromere roughly in the

middle
Karyotyping: Lining up all the chromosomes in
order to count them and Submetacentric: Centromere towards one compare banding
pattern to ensure the side slightly. P&Q arms genome is normal.

Acrocentric (5 chromosomes): P arm has

nothing on it except ribosomal RNA genes.
Q is variable depending on chromosomes.
 Small deletions/ insertions won’t be seen, but large chromosomal rearrangements will be seen.
Spectral Karyotyping: use chromosome paints to colour the chromosomes different colours, so you
can see how they are organised inside the nucleus. Conclusion of experiment using paints: the
chromosomes form non-overlapping domains within the interphase nucleus, and their locations are
distinct. Initially done in chickens. Also used to back up the theory that heterochromatin is on the
outside and euchromatin is on the inside.

HETEROCHROMATIN VS EUCHROMATIN

Heterochromatin Euchromatin
Chromosomal material that is darkly stained & generally Chromosomal material that consists of uncoiled threads
inactive during interphase, I genetically active, & stains lightly with
basic dye
 Gene poor
 Found near the periphery of the nucleus  Location for active genes
 Found near centromeres & telomeres (centromeres &  Less condense
telomeres are heterochromatin)  Majority of the genome is made up of Euchromatin
 Highly condensed- compact-neighbouring gene is also  Found in the interior of the nucleus
usually resistant to gene expression due to
heterochromatic effect
 Often associated with the nuclear envelope-periphery
 In a typical cell 10%of the genome is Heterochromatin
 Can exists as :
o Constitutive (always condensed)
o Facultative (inactive during specific stages or cell
types)

HETEROCHROMATIN
EUCHROMATIN

The location of ribosomal RNA genes: 200 rRNA gene copies per haploid genome- the genes are located in
tandem (repeating) copies on the acrocentric chromosomes (13,14,15,21,22). Chromosomes can have up to 30
copies of rRNA genes, why? Compared to single genes, whose mRNA strand can be translated many times to
give amplification of final product (depending on stability of mRNA), the rRNA is not translated into protein as
the transcribed RNA is the final product. Cells need lots of ribosomes. Thus, lots of genes.
Why does the cell need DNA?

- Transcription to make mRNA

- DNA replication during S phase so we can make new cells
- DNA repair
- To make ribosomes so we can make proteins

NUCLEAR COMPARTMENTS

Functional compartmentalisation of the nucleus

Subnuclear compartments exist despite the absence of internal membranes. Every single protein can
be marked with an antibody and its precise location in 3D can be looked at.

 Chromosome territories: store DNA and control access to DNA.

 Replication factories: nascent DNA production
 Transcriptions factories: nascent RNA production
 Spliceosome: irregular domain containing splicing factors
 Nucleoli: Ribosome biogenesis
 PML nuclear bodies: possible nuclear depot

DNA REPLICATION FACTORIES

 DNA replication takes place in replication factories – thought to be factories where lots of
DNA was replicated together, but this is not actually the case.
 Factories contain all the enzymes & other factors required to produce 2 new DNA strands

RNA TRANSCRIPTION FACTORIES

 Factories contain RNA polymerase II, template DNA strand & newly synthesized nascent
mRNA

NUCLEOLUS

The largest substructure in the nucleus- can be circular or any other shape

Functions

 Transcription of rRNA to produce large 45S tRNA precursor. Small nucleolar organising RNAs
come together and through cleavage and modification can make
 Cleavage/modification of rRNA into 18S, 5.8S & 28S rRNA subunits. Leave nucleus
separately.
 Assembly of ribosomal subunits in the cytoplasm
o 18S- small ribosomal subunit
o 5.8S, 28S (and 5S) – large ribosomal subunit

3 Distinct Zones by electron microscopy

FC: ribosomal RNA genes

DFC: rRNA transcripts
GC: processing & assembly
NUCLEAR ENVELOPE FUNCTION

 Nuclear envelope:
o Compartmentalized the nucleus: molecules can move from the nucleus to cytoplasm
and vice versa
o Constitutes inner membrane (IM) & outer membrane (OM)
o Made of two lipid bilayers

 OM: continuous with the endoplasmic reticulum (ER)

 IM: proteins such as lamins are anchored to the IM

LAMINS-Only found in nuclei of multicellular eukaryotes

Function
- Intermediate filament proteins
- Form meshwork at inside of inner nuclear membrane (INM), some extend into nucleoplasm
- Nuclear strength & architecture
- DNA replication & mRNA transcription
- Involved in apoptosis

Lamin alteration can lead to multiple abnormalities as they are not only structural but also functional

THE NUCLEAR PORE COMPLEXES: 3000-4000

 Movement through the nuclear pore is strictly controlled-allow communication

 Only small water soluble molecules can diffuse freely through the pore
 Very stable structure, are formed, remain in situ

Larger molecules must be actively transported through the nuclear pore

 NUCLEAR EXPORT: e.g. ribosomal subunits & mRNA proteins. Proteins require a nuclear
export signal (NES)
 NUCLEAR IMPORT: e.g. histones, DNA/RNA polymerase & other nuclear proteins. Proteins
require a nuclear localisation sequence (NLS)