The Nucleus

The nucleus is the headquarters of the

cell. It is the most obvious organelle in
any eukaryotic cell and appears as a
large dark spot in EUKARYOTIC cells. It
controls all cell activity.

 The Nucleus is a membraneenclosed organelle which house

most of the genetic information
and regulatory machinery
responsible for providing the cell
with its unique characteristics.

Nucleus is the most important organelle in cell.

In mammalian cells, excepting RBC,
all cells else are the nucleus contained cells.
In prokaryotic cells, there is no membrane
to package the nucleic acid substance, so,
we call this nucleic substance enriched
area as Nucleoid.

The major structures of nucleus include:

nuclear envelope.
nucleolus.
nuclear matrix.
chromatin.
nuclear lamina.

The major functions of nucleus:

inheritance: maintain the genetic
continuity of generation by the
replication of DNA chromatin and the
proliferation of cell.
development: regulate the cell
differentiation by the regulation of
spatiotemporal sequence of gene
expression.
6

 THE NUCLEUS:
FUNCTIONS

It stores the cell's hereditary material, or DNA.

Site of DNA replication
Site of DNA transcription to mRNA
Ribosomal formation
Nucleolus: RNA & protein required for ribosomal
synthesis
It coordinates the cell's activities, which include
growth, intermediary metabolism, protein synthesis,
and reproduction (cell division) by regulating gene
expression.

nuclear
envelope
nucleolus
nuclear
pores

chromatin

nucleus

nuclear
pores

I. Nuclear envelope (Nuclear membrane)

Nuclear envelope is the lipid bilayer that packages
the nucleus.
Nuclear envelope separates the DNA from cell plasma
and forms a stable inner environment to:
protect the DNA from damage,
separate the replication of DNA from the
translation of RNA spatiotemporally,
the chromatin is anchored on to the nuclear
envelope, that is beneficial to be despiraled,
replicated, condensed, and distributed into new
nuclei equally,
the pores on the envelope are the channels for
the substance exchange.
11

Nuclear envelope is bilayer membrane:

Nuclear envelope is composed of
inner nuclear membrane,
outer nuclear membrane, and
perinuclear space.
There are nuclear pores on the membrane
that are linked with plasma.
12

 The NE consists of two cellular membrane, an

inner and an outer membrane, arranged
parallel to one another and separated by 10 to
50 nanometers (nm).
The outer nuclear membrane is continuous
with the membrane of the rough endoplasmic
reticulum (RER), and is similarly studded with
ribsomes.
The space between the membranes is called
the perinuclear space and is continuous with
the RER lumen.

 The inner surface of the NE is bound to

a thin filamentous network (lamins
polypeptides) called the nuclear
lamina. It provides mechanical support
to the NE and seeves as sites for
attachment for chromatin fibers.
Mutations in the lamin genes are
responsible for several distinct human
diseases (e.g. a rare form of muscular
dystrophy).

THE NUCLEAR PORE

The nuclear pores are the channels for the
substance transportation:
Nuclear proteins are synthesized in plasma, then
will be imported into nucleus by the pores.
The RNAs and the ribosome subunits synthesized
in nucleus will be exported into plasma by the
pores also.
In addition, it is indicated by a injection
experiment that small molecules can enter the
nucleus by diffusion from the pores.
16

Nuclear pores are composed of 50 different

nucleoporins at least, and we call these pore
structure as nuclear pore complex (NPC).
Usually, a mammalian nucleus contains 3,000
nuclear pores.
The more activities a cell takes, the more
nuclear pores the cell contains.
For example, a frog ovum can contain 37.7X106
nuclear pores, but a matured cell contains
150~300 nuclear pores only.
17

The structures of nuclear pore include

cytoplasmic ring located on the cell
plasma part of the pore complex
contains 8 filaments extending into
plasma.
nuclear ring located on the nuclear
plasma part of the pore complex
extending 8 filaments also.
transporter located in center of the
pore as a plug particle.
Spoke located on the edge of the pore
as the spines.
18

20

The nuclear pore structures on the cell plasma side after an extraction

21

The nuclear pore structures on the nuclear plasma side after an extraction
22

23

24

Nuclear plasma protein (nucleoplasmin) is

transported by the following steps:
The protein combines to the / dimer of
the receptor (imporin).
The complex of the protein transported
and the receptor used combines to the
filaments located on the NPC cytoplasmic
ring.
The filaments curve to the nuclear center,
the transporter structure will be changed
to form a hydrophilic channel, and the
protein passes through the channel.
25

 The complex of the protein transported

and the receptor used combines to RanGTP, the complex is disassembled and
releases out the protein transported.
The imporin combined with Ran-GTP will
be exported out of the nucleus, the GTP
combined with Ran will be hydrolyzed in
cell plasma, and the Ran-GDP will go back
to nucleus to be transformed to Ran-GTP
again.
The imporin will be transported back to
cell plasma with the help from exportin.
26

We know a little about how the macromolecules are

transported to cell plasma from nucleus.
In most of cases, the RNA in nucleus is
combined with protein to form an RNP complex,
then, transported into cell plasma.
There is nuclear exportation signal (NES) on the
protein of RNP complex that can combine to the
intracellular receptor, exportin, to form the
complex of RNP-exportin-Ran-GTP.
In the cell plasma, this complex will be
disassembled and release out the Ran-GTP,
Ran-GDP, exportin, and RNP protein.

RNA,

27

The nucleoplasmin is transported into nucleus

28

Chromosome
Chromatin was named by
W. Flemming in 1879.
Chromosome was named by
Waldeyer in 1888.
Chromatin and chromosome are
same substance with different shape
presentation in different cell cycle
phases.
29

The chemical components of chromatin:

DNA,
histone protein,
nonhistone protein, and
some RNA
at ratio about 1:1:(1-1.5):0.05.
DNA:
DNA is the carrier of genetic information.
DNA sequences can be sorted as 3 types:
nonrepeated fraction,
moderately repeated fraction (101-105), and
highly repeated fraction (>105).
DNA forms:
B-DNA,
Z-DNA, and
A-DNA.

30

DNA forms (Red color shows the couple backbones)

31

Chromosome DNA contains three basic sequences:

autonomously replicating DNA sequence (ARS).
ARS is the starting site of DNA replication.
In yeast genome, there are 200-400 ARSs
included, and most of them contain a AT
enriched 11bp sequence called as ARS
consensus sequence (ACS).
centromere DNA sequence (CEN) composed of
a lot of repeated sequences.
telomere DNA sequence (TEL).
TEL is similar in different bio organisms,
and composed of 5 10bp repeated
sequences. Human
TEL repeated sequence is TTAGGG.

32

In 1983, A. W. Murray et al constructed

yeast artificial chromosome (YAC)
contains ARS, CEN, TEL and
exogenous DNA with the length of 55kb.
YAC is very useful to transgenic
technology and construction of cDNA
library because the length of insert to
YAC can be much longer than that to
plasmid.

33

Three basic sequences of chromosome

34

HISTONE
Histone is positively charged and contains
arginine and lycine.
Histone is alkaline protein.
Histones can be sorted as two types:
1. Highly conserved core histone including H2A,
H2B, H3, and H4.
2. Non conserved linker histone including H1 only.

The core histone is highly conserved, especially the

H4 is.
For example, 2 of 102 amino acids of the H4 of
cattle and pea are different, but cattle has been evoluted
300 million years earlier than pea.
35

The reasons for that may be as the follows:

1. Most of the amino acids of core histone
interact with DNA or other histones, so,
any change of them will cause the fatal
mutation.
2. In all bio organisms, the DNA
phosphodiester skeleton that interacts
with histone is same.
H1 is easy to be mutated,
and it is species specific and tissue
specific.
36

NONHISTONE PROTEIN:
Nonhistone protein is
the protein that binds to the specific DNA sequence
of
chromosome, so, we call it as sequence specific
DNA binding protein.
The features of nonhistone protein are as the follows:
Nonhistone protein is negatively charged and
acidic protein that contains a large number of
aspartic acids and glutamic acids.
Nonhistone protein can be synthesized during
the whole cell cycle, but histone protein is
synthesized during the S phase only.
Nonhistone protein can recognize the specific
DNA sequence.
37

The functions of nonhistone are as the

follows:
Help DNA molecules to be pleated
and form different structure
domains that are beneficial to
DNA replication and gene
transcription.
Help to start DNA replication
reaction.
Regulate transcription and gene
expression.

38

FROM DNA TO CHROMOSOME:

There are 23 pairs of chromosomes in a human
nucleus.
If you open and extend the DNA molecule in
each chromosome, it will be 5 cm long.
If you link all DNA molecules in a nucleus
together, it will be 1.7 2.0 m long.
But, the diameter of nucleus is shorter
than
10m.
The primary structure formed by the powerful
compaction is called as nucleosome.

39

Nucleosome:
R. Kornberg figured out the model of nucleosome.
Nucleosome is a beaded structure composed of core
particles and linker DNA.
We can describe the structure as the follows:
Each nucleosome includes about 200bp DNA, one
histone core, and an H1.
The octameric histone core is composed of 8
molecules from H2A, H2B, H3, and H4 by two
molecules from each.
DNA molecule winds the core particle with a left
hand helix and 80bp for each circle. 1.75 circles for
each structure.
Adjacent core particles are linked by a 60bp linker
DNA.
40

Structures of nucleosome

41

Chromatin DNA filament:

The DNA is compacted to be shortened by 7
folds and forms the DNA filament in 11nm
diameter when it was transformed to the beaded
nucleosome chain.
Chromatin DNA exists in another style by that the
beaded nucleosome chain is condensed by 6
folds.
Under electron microscope, we can see the
chromatin DNA filament in 30nm diameter that is
formed by the overlapped helix structure of the
beaded nucleosome chain.
42

The DNA filaments in 30nm and 11nm diameter

(A) Is composed of (B)
43

For the advanced package of the chromosome, we keep detail unknown

so far. Probably, it is the serial overlapped or pleated like the follows:
From DNA to Chromosome:
DNA
11nm filament (beaded nucleosome chain)
30nm filament
pleat as loop chain
bind to the sites on nuclear skeleton where is AT
enriched
assembly of chromosome

44

Assembly of chromosome

45

Heterochromatin and euchromatin:

In the inter phase (G1 and G2) of cell cycle, the chromatin in the nucleus
can be sorted as heterochromatin and euchromatin.
Euchromatin is the DNA regions where the transcription is very active.
Euchromatin looks like loose loop and bright staining under electron
microscope. Euchromatin is easy to be cleaved by nuclease at some
hypersensitive sites.
Heterochromatin is condensed in G phase without any transcription, so, it
was named as inactive chromatin. Heterochromatin is the genetic lazy regions,
and replicated lately, condensed early, that is called as heteropyknosis.

46

Heterochromatin

Heterochromatin
(dark staining)
and euchromatin
(bright staining)

Euchromatin

47

Constitutive
heterochromatin is
heteropyknosed
chromatin in
each type of
cell and
located in
centromere
region.
The Fig shows
you the
Constitutive
heterochromatin
displayed by
fluorescence
hybridization in
situ.
48

Facultative heterochromatin
is heterochromatin appeared
in some special cell type or
developing stage. The X
chromosome of female
mammalians is the facultative
heterochromatin. Usually,
female mammalian cell
contains double X
chromosomes, and one of
them is heterochromatin
called barr body. When a
human embryo is developed
after 16 days, one X
chromosome will be
transformed as barr body with
dark staining. So, we can
identify the sex of a human
embryo by checking the barr
body of the embryo cells in the
amniotic fluid.
The barr body like a drumstick in a white cell

49

The structure of chromosome:

In the M phase of cell cycle, chromatin will be transformed as chromosomes
by the powerful condensation. Chromosomes are stick shape with different length.
The metaphase chromosome is the best stage to observe and number them
because the morphology of chromosome is stable at this time.
The number of chromosome is same in the same type of cells from different
individuals of one species. The chromosomes of sex cells are haploid, we mark it
as n. The chromosomes of other cells are diploid, we mark it as 2n. The
chromosomes of some cells of some species are polyploid, such as, 4n, 6n, and
8n.
The different cells from same individual can be different chromosome types.
For example, body cells of rat are 2n, but its liver cells can be 4n, 8n, and 16n. The
chromosome number of human endometrial cell is variable from 2n =17 - 2n =103,
that is not euploidy.
The chromosome number can be different in different species cells. For
examples, human 2n = 46, chimpanzee 2n = 48, fruit fly 2n = 8, wheat 2n = 42,
rice 2n = 24, onion 2n=16.
50

The terms used to the structure of chromosome:

1 Chromatid: Metaphase chromosome is composed of two chromatids with a
junction at the centromere site. Each chromatid is formed by the overlapped and
pleated DNA double strands. When the cell is dividing the chromatids can be
separated into two new cells.
2 Chromonema: In the S or G phase cells, each chromonema indicates a
chromatid.
3 Chromomere: Chromomere is the linear beaded particles chain DNA. The
chromomere of heterochromatin is bigger than that of euchromatin.
4 Primary constriction: It is a bright stained hang ditch on the metaphase
chromosome where the centromere is located, so, it can be called as centromere
region. Each chromosome has one localized centromere. The chromosome from
some species has centromere function every where. We call this chromosome as
holocentromere chromosome. For examples, ascarid (round worm) and other
nemas, butterfly. The chromosomes can be sorted by the location of centromere
as following: metacentric chromosome. submetacentric chromosome.
subtelocentric chromosome. telocentric chromosome.
5 Secondary constriction: Excepting primary constriction, the second ditch is
called as secondary constriction. The location of secondary constriction is
unmovable by that we can identify chromosome.
51

The terms of chromosome structure

52

6 Nucleolar organizing regions (NORs): They are the areas where the genes
for ribosome RNA are located. They can synthesize the 28S, 18S, and 5.8S rRNA
for ribosome. NORs can exist in secondary constriction.
7 Satellite: It is a ball part located at the terminal of chromosome, and linked to
the main part of chromosome by secondary constriction. The satellite located at
terminal of chromosome is called as terminal satellite, and located between two
secondary constrictions is called as intermediate satellite.
8 Telomere: It is the specialized part located at the terminal of chromosome.
The function of telomere is maintenance of the stability of chromosome. Telomere
is composed of the highly repeated fractions, and it is so conserved that it is
similar between the totally different life beings. The component of human
telomere is TTAGGG. Telomere is associated with aging. After each replication of
telomere DNA, the telomere will be shortened by 50 100bp. The replication of
telomere is droved by telomerase that has reverse transcriptase activity. This
enzyme lacks in normal cells, so, telomere will become short with the cell
proliferation. So, cell will be aging during this action.

53

III. Nucleolus
Nucleolus may be visible in G phase nucleus. They are spherical and 1 2 for
each cell usually. The number and size of nucleolus are depended on the cell type
and function. The more proteins synthesis and the faster proliferation the cell
takes, the more and bigger nucleoli the cell has. Nucleolus disappears before the
cell division, and appears in the end of division. The major functions of nucleolus
are rRNA transcription and ribosome assembly.
Structure of nucleolus:
No any membrane packages nucleolus area. There are three special areas
can be identified under electron microscope: fibrillar centers (FC) that are
surrounded by dense fibers, and low electric density. FC contains RNA polymerase
and rDNA that is naked molecule. dense fibrillar component (DFC) that is a loop
or half loop to surround FC. Transcription is carried out in the border region of FC
and DFC. granular component (GC) composed of 15-20nm particles that are
the RNPs in different manufactured steps. RNP means the RNA combined with
protein.
Nucleolus chromatins can be sorted as two types: heterochromatin and
euchromatin. The nucleolus heterochromatin is always located around the
nucleolus, so we call them as nucleolus peripheral chromatin. The nucleolus
euchromatin is located in nucleolus, and nucleolus organizing region in that the
rDNA is located.
54

Structure of nucleolus
55

IV. Ribosome
Ribosome is the manufacturing shop to synthesize proteins. There are about
20,000 ribosomes in an actively growing bacterium. Ribosome proteins are 10% of
total proteins of cell, and its RNA is 80% of cell total RNA.
Structure of ribosome:
The ratios of protein and RNA to ribosome components are 40% and 60%.
The ribosome subunits are composed of the combination of the protein and RNA.
The catalytic activities needed by the translation are presented by ribosome
protein, rRNA and other helper factors.
The ribosomes can be sorted as two types. 70S ribosome exists in bacteria,
mitochondrion, and chloroplast. 80S ribosome exists in the plasma of eukaryotic
cells.
Ribosome is composed of a large subunit and a small subunit. The both
subunits will be combined together when the ribosome synthesizes protein with
mRNA as template. After the translation, the ribosome will be separated as two
parts again. When a protein is translated on an mRNA, many ribosomes can bind
to the mRNA to synthesize the protein. We call these ribosomes for one protein
synthesis as polyribosome. The longer mRNA is used, the more ribosomes are
combined. The polyribosome enhances the efficiency of protein synthesis.
Prokaryotic 5S rRNA and eukaryotic 5.8S rRNA are very conserved for their
structures, so, they can be used to research the bio-evolution.
56

Assembly of ribosome:
The DNA fragment encoding rRNA is called as rRNA gene. There are about
200 copies of this gene in a human cell. rDNA contains no histone core, so, it is a
naked DNA.
To transcript rRNA, the RNA polymerase moves ahead along the DNA
molecule. The synthesized rRNA molecules extend out their molecules from the
complex of polymerase and DNA, and form a featherlike structure under
microscope.

57

rRNA transcription

The filaments are the

new synthesized 45S
rRNA that combines to
protein to form RNP
complex. The
methylated 45S rRNA
can be cleaved as the
two parts by RNase:
18S rRNA and 32S
rRNA the latter is
cleaved as 28S rRNA
and 5.8S rRNA. The
synthesized 5S rRNA
will be transported into
nucleolus to join the
assembly of the large
subunits of ribosome.

There is a 60bp non-transcription DNA

fragment between adjacent rRNA genes
58

Assembly of ribosome
59

Model of a
ribosome

mRNA

Synthesized protein

60

http://www.wadsworth.org

V. Nuclear matrix
Nuclear matrix is called as nucleoskeleton that is a meshwork in eukaryotic
cells, that is what I told you before. Because nuclear matrix is associated with
DNA replication, RNA transcription and modification, chromosome assembly, and
virus replication, nuclear matrix is now paid more attentions to.
Components of nuclear matrix:
Non-histone filaments at ratio of 96%. The nucleoskeleton contains three
scaffold proteins: SC , SC, and SC .
A little RNA and DNA: The RNA is important to maintain the skeleton
structure. The DNA is called as matrix /scaffold associated region (MAR or SAR)
where the AT is enriched to form the heterochromatin binding sites.
A little phospholipids (1.6%) and sugars (0.9%).
Nuclear skeleton nuclear lamina inter filaments pore complex is a
meshwork system with very good stability.

61

The function of nuclear skeleton:

1. Present the scaffolds for DNA replication. DNA can be anchored on to the
scaffold with a replication loop. The enzymes needed by DNA replication are
located on the skeleton, such as DNA polymerase , DNA primerase, DNA
topoisomerase II.
2. Is the place where gene can be transcripted and modified. There are RNA
polymerase binding sites on the skeleton. New synthesized RNA is combined
to the skeleton for further modification.
3. Is associated with the assembly of chromosome. The nuclear skeleton may
be same thing to chromosome skeleton. 30nm chromatin fibers are
combined to nuclear skeleton to form loops that will be packaged further in M
phase to be assembled as chromosome.

62

Chromatin bound on nuclear skeleton or chromosome skeleton

63