A very brief introduction to nucleus structure and function.

1. The nucleus
Presented By: Group 1
Afsha Zia,
Alizay,
Ayesha Khalid,
Noor-ul-naeem,
Tehreem Ishtiaq,
Tehreem Tariq

2. CONTENTS
 Introduction
 Nuclear Envelope
 Transport Through Nucleus
 Internal Organization of Nucleus
 Assembly of RNAs

3. THE NUCLEUS
 When you look at a eukaryotic cell in a light microscope nucleus is the
largest visible compartment.
 The presence of a nucleus distinguishes eukaryotic cells from
prokaryotic cells.
 The nucleus houses all of the eukaryotic cell’s genome and acts as a
center for controlling cellular activities.
 Processes such as DNA replication, transcription, and RNA processing
all takes place within the nucleus.

5. DISCOVERY
 Antony van Leeuwenhoek (1632–
1723) was probably the first to
observe nucleus in the blood cells of
birds and amphibians.
 But Felice Fontana (1730–1805) was
the actual discoverer of nucleus by
observing epidermal cells of eel.
 The Scottish botanist, Robert Brown
(1773–1858) observed the nucleus in
plant cells and was the first to call
these structures ‘nuclei’.

6. STRUCTURE
 A double membrane called nuclear envelope encloses the nucleus.
 The lumen separates the two membranes and is continuous with the Endoplasmic
Reticulum.
 Macromolecules pass between the nucleus and cytoplasm through the Nuclear Pore
complexes (NPCs) that are channels spanning the envelope.
 The nucleus has non-enveloped sub-compartments with specialized function.
 Nucleolus is the most clearly visible structure.
 Regions other than the nucleolus are referred to as the nucleoplasm.
 Other sub-compartments include speckles, cajal bodies and PML bodies etc.
 Inside the nucleus the DNA can be found in the compacted and highly stained form,
heterochromatin or in the less densely compacted form the euchromatin.

7. Structure

8. ADVANTAGES TO EUKARYOTES IN HAVING A NUCLEUS
 By separating the genome from the
cytoplasm, the nuclear envelope allows
gene expression to be regulated by
mechanisms that are unique to
eukaryotes.
 In prokaryotes mRNAs are translated
before their transcription is completed,
eukaryotic mRNAs are produced from
precursor RNAs through complete
processes before being transported
from the nucleus to the cytoplasm.
 When DNA is replicating during
interphase the nucleus protects the
relaxed DNA from breakage by force of
cytoskeleton.

9. NUCLEI VARY IN NUMBER AND APPEARANCE
 Nuclei can vary in size
according to the amount of
DNA they contain. The single
celled organism
Saccharomyces cerevisiae
has a nucleus of 1µ in
diameter.
 Many multicellular organisms
have a nucleus of size 5-10µ
in diameter.
 The percentage of volume
occupied by nuclei in
different cells varies.
 Volume occupied by nucleus
in yeasts cells is 1%-2%,
10% in somatic cells and
40%-60% in cells that do not
have many cytoplasmic
functions.

10.  In most cells the nucleus is
oblong or oval shaped to
minimize surface area of
enclosure. We can identify
different cells from the shape of
their nucleus.
 Example: During leukemia an
excess of white blood cells are
produced which have different
shapes of nuclei at different
stages of development. The type
of leukemia can be diagnosed by
studying the morphology of
nuclei of the cells produced in
excess.
 Most cells are mononucleate, some
are multi nucleate and some are
anucleate.
 Example: Multinucleate cells include
those of Drosophila melanogaster in
embryonic stages.
 Myocytes formed by fusion of
myoblasts are also multinucleate.
 Cells like the mammalian red blood
cells and cells of lens of vertebrate
eye lack nucleus.
Figure:
A Drosophila embryo at the
multinucleate stage

11. Nuclear envelope

12. NUCLEAR MEMBRANE
 Nuclear Membrane is a fence between
nucleus and cytoplasm to stave off free
transmission of molecules.
 It provides nucleus an identity of separate
biochemical compounds.
 The nuclear membrane consists of:
1. Outer nuclear membrane
2. Inner nuclear membrane
3. Perinuclear space
4. Nuclear pores
5. Nuclear lamina

13. OUTER NUCLEAR MEMBRANE
 The outer nuclear membrane is
continuous with endoplasmic reticulum,
therefore the lumen of nuclear membrane
is directly connected with lumen of ER.
 The outer nuclear membrane is
functionally homologous to ER
membrane.
 The cytoplasmic surface of outer nuclear
membrane has ribosomes that are
different in composition of protein and
these ribosomes are enriched in
membrane proteins (for cytoskeleton
binding).

14. PERINUCLEAR SPACE
 Space is present between ONM
and INM and is called Perinuclear
space or lumen of envelope.
 The thickness of each nuclear
membrane is 7-8nm thick while
perinuclear space is 20-40nm
thick.

15. INNER NUCLEAR MEMBRANE
 Proteins that are specific to nucleus are present in
INM such as those that bind the nuclear lamina.
 Including Lamin B receptor (LBR), lamina-
associated polypeptide (LAP) 1, LAP2, emerin,
MAN1 and nurim.
 Most of these proteins interact with lamins and
chromatin.
 Mutations in emerin and nuclear lamins have been
associated with muscular dystrophies and
lipodystrophy.
 Integral proteins of the inner nuclear membrane are
synthesized on the rough ER and reach the inner
nuclear membrane by lateral diffusion in the
connected ER and nuclear envelope membranes.

16. NUCLEAR PORE CHANNEL (NPC)
 The Phospholipid bilayer is only
permeable for non-polar
micromolecules.
 The only channel through which
transmission of polar
micromolecules and
macromolecules occurs is through
Nuclear Pore Complex.
 NPCS are the points where lNM
and ONM are continuous.
Figure:
The inner and outer membranes of the
nuclear envelope are fused at the NPC.

17. NUCLEAR LAMINA
 In multicellular eukaryotes, a fibrous mesh work supports
the inner nuclear membrane called Nuclear Lamina
 The nuclear lamina is present inside the nuclear
envelope.
 Lamins are 60-80 kilo Dalton fibrous proteins that
makeup the nuclear lamina
 Some associated proteins are also present.
 Lamins belong to a class of intermediate filament
proteins.
 Nuclear Lamina disease:
1. Emery-Dreifuss muscular dystrophy
2. Hutchinson-Gilford progeria syndrome

18. MODEL OF LAMIN ASSEMBLY
• Association of lamins with each other occurs to form higher order structure called nuclear
lamina.
• Attachment of lamins to the nuclear envelope is mediated by prenylation and binding to
specific inner nuclear membrane proteins such as emerin and Lamin B receptor.

19. DURING MITOSIS THE NUCLEAR ENVELOPE DISASSEMBLES
Onset
 The nuclear membrane disassembles and
the nuclear lamina depolymerizes due to
phosphorylation of nuclear lamins by Cyclin-
dependant protein kinase.
 The nuclear envelope membrane proteins
also dissemble by phosphorylation leading
to disassembling of NPCs.
 NPC proteins become bound to nuclear
import receptors, which play an important
part in the reassembly of NPCs at the end of
mitosis.
 Motor proteins on microtubules also help in
tearing down the nuclear membrane.
Offset
 The nuclear envelope forms around
chromatin. Chromatin is surrounded by a
shroud of Ran-GTP.
 The assembly of NPCs is started by
nuclear import receptors from NPC
proteins displaced by the Ran-GTP cloud.
 Alongside the nuclear envelope
membrane proteins with
dephosphorylated lamins start attaching
to chromatin again.
 Membranes from ER fuse over the
chromatin until a complete Nuclear
envelope is formed.

21. Nuclear Pore:
transport through nucleus

22. WHAT ARE NUCLEAR PORES?
 Small polar molecules, ions and macro-molecules can only move in
between the nucleus and cytoplasm through channels.
 The large circles with diameter of 120nm and molecular mass of ̴125
million Dalton and 30X the size of ribosomes are pores that are
collectively called as Nuclear Pore complex.
 They are composed of several proteins of 30 different types.
 Those specialized proteins are named as Nucleoporins.

23. VARIATION IN NUMBER OF NPCS IN
MEMBRANES
 Requirement of nuclear transmission
of a cell decides the number of NPCs.
 150-250 NPCs are present in the much
smaller yeast cell's nuclear envelope.
 Some cells contain millions of NPCs
(e.g. Xenopus) because they are very
active transcriptionally and
translationally.
FIGURE The surface of the nuclear envelope
of a Xenopus laevis oocyte is covered with
NPCs.

24. MODEL OF THE NUCLEAR
PORE COMPLEX
 The complex consists of an
assembly of eight spokes attached
to rings on the cytoplasmic and
nuclear sides of the nuclear
envelope.
 The spoke-ring assembly surrounds
a central channel containing the
central transporter.
 Cytoplasmic filaments extend from
the cytoplasmic ring, and filaments
forming the nuclear basket extend
from the nuclear ring.

25. FUNCTIONS OF NUCLEAR PORE
 Nuclear pores play an important role in physiology of eukaryotic cells
by controlling the traffic of molecules between nucleus and cytoplasm.
 RNAs that are synthesized in nucleus are carried out through the
nuclear pores in order to synthesize proteins in the cytoplasm.
 Conversely, proteins required for nuclear functions (e.g., transcription
factors) must be transported to the nucleus from their sites of synthesis
in the cytoplasm.
 Many proteins shuttle continuously in between nucleus and cytoplasm
which is also a very specialized function of nuclear pore.

26. MOLECULAR TRAFFIC THROUGH NUCLEAR PORE
COMPLEXES
 Small molecules are able to pass
rapidly through open channels in
the nuclear pore complex by passive
diffusion.
 In contrast, macromolecules are
transported by a selective, energy-
dependent mechanism that acts
predominantly to import proteins to
the nucleus and export RNAs to the
cytoplasm.

27. NUCLEAR LOCALIZATION SIGNALS
Figure:
The nuclear localization signal of
nucleoplasm is bipartite, consisting
of a Lys-Arg sequence, followed by a
Lys-Lys-Lys-Lys sequence located
ten amino acids farther downstream.
 These proteins are targeted to the
nucleus by specific amino acid
sequences called nuclear localization
signals.
 These localization signals are detected
by nuclear transport receptors
(Importins) as they carry proteins into
the nucleus.
 They direct protein transport through
nuclear pore complex.
 Nuclear localization signals have yet
been observed in many proteins, and
amino acids that are involved in these
localization signals are found close to
each other but not immediately
adjacent to each other.

28. TRANSPORT OF RNAs
 Since proteins are synthesized in the cytoplasm, the export of mRNAs, rRNAs, tRNAs,
and microRNAs (miRNAs) is a critical step in gene expression in eukaryotic cells.
 As proteins are selectively transported from cytoplasm to nucleus in the same way
RNAs are transported from nucleus to cytoplasm to synthesize these proteins.
 Like protein import, the export of all RNAs through the nuclear pore complex is an
active, energy-dependent process requiring the transport receptors to interact with the
nuclear pore complex.
 Karyopherin, importins and exportins transport most tRNAs, rRNAs, miRNAs and small
nuclear RNAs.
 In contrast to mRNAs, tRNAs, and rRNAs, which function in the cytoplasm, many small
RNAs (snRNAs and snoRNAs) function within the nucleus as components of the RNA
processing machinery.

29. TRANSPORT OF SnRNAs BETWEEN NUCLEUS AND
CYTOPLASM
 snRNAs firstly get transported into the
cytoplasm from nucleus.
 Then they associate with proteins to form
functional snRNPs.
 And then go back to the nucleus.
 Crm1 and other transport receptor proteins that
bind to the 5' 7-methylguanosine caps of
snRNAs are involved in the export of the
snRNAs to the cytoplasm. Figure: Small nuclear RNAs are initially exported
from the nucleus to the cytoplasm, where they
associate with proteins to form snRNPs.
The assembled snRNPs are then transported back
into the nucleus.

30. ACTIVE TRANSPORT OF MACROMOLECULES
 Uncharged molecules including
water, can diffuse freely through
phospholipid bilayers.
 Other macromolecules that are
transported across the nuclear
envelope move through NPCs.
 The process of moving through
the NPC is called translocation.

31. Internal organization of nucleus

32. INTERNAL ORGANIZATION OF NUCLEUS
 A loosely organized matrix of
nuclear lamins extends from
nuclear lamina into the interior of
nucleus in animal cell, which
serves as sites of chromatin
attachment and bind other proteins
into the nuclear bodies.
 Chromatin is organized into large
loops of DNA and regions of these
loops are bound to the lamin
matrix by lamin binding proteins.
 Many other nuclear proteins form
Lamin-dependent complex

33. CHROMOSOMES AND HIGHER ORDER CHROMATIN
STRUCTURES
 During interphase the heterochromatin remains highly condensed and
inactive and euchromatin is de-condensed and distributed throughout
the nucleus, a heterochromatin is of two types:
 Constitutive heterochromatin remains permanently in heterochromatin
stage, having DNA sequences that are not transcribed.
 Facultative heterochromatin consist of euchromatin that takes on the
staining and compactness characteristics of heterochromatin during
some phase of development, having DNA sequences that are
transcribed in cell which we are studying but are transcribed in other
cells.

34.  Although interphase chromatin
appears to be uniformly
distributed, the chromosomes are
actually arranged in an organized
fashion and divided into discrete
functional domains that play an
important role in regulating gene
expression.
Heterochromatin in interphase nuclei
The euchromatin is distributed throughout the nucleus. The
heterochromatin is indicated by arrowheads and the
nucleolus by an arrow.

35. SUB-COMPARTMENTS WITHIN THE NUCLEUS
 The internal organization of nucleus is
the result of localization of nuclear
processes to specific regions of
nucleus.
 Many enzymes and proteins of nucleus
are organized to discrete sub-nuclear
bodies. The nature and function of
these nuclear bodies are not clear.
 Replication of multiple DNA molecules
takes place on the cluster site of nuclei
in mammalian cell.
Sub-compartments within the nucleolus,
as

36.  Actively transcribed genes appears to be distributed
throughout the nucleus.
 Components of mRNA splicing machinery are concerted
in nuclear speckles. Immunoflourescent staining
showed that rather than being distributed uniformly
throughout the nucleus the components of RNA splicing
apparatus are concerted in these 20-50 discrete
structures:
 Speckles: storage sites of splicing components where
pre mRNA processing occurs. In addition to speckles
nuclei also contain PML and cajal bodies.
 PML bodies: transcription factors & chromatin-modifying
enzymes localize here.
 Cajal bodies/coiled body: involved in snRNP biogenesis,
histone mRNA processing & telomere maintenance.
 Gemini Bodies: are not found in all cells, and some of
their components are also found in Cajal bodies,
suggesting they may not perform distinct functions.
Cajal bodies and Gemini bodies
can be detected by using specific
antibodies and indirect immuno-
fluorescence.

37. CHROMOSOMES OCCUPY DISTINCT TERRITORIES
 Although the nucleus lacks
internal membranes, nuclei are
highly organized and contain
many sub-compartments.
 Each chromosome occupies a
distinct region or territory, which
prevents chromosomes from
becoming entangled with one
another.
 The nucleus contains both
chromosome domains and inter-
chromosomal regions.
Individual chromosomes occupy distinct areas
of the nucleus called chromosome territories.

38. NUCLEAR SUB COMPARTMENTS ARE NOT
MEMBRANE-BOUNDED
 Nuclear sub compartments are not membrane-bounded.
 rRNA is synthesized and ribosomal subunits are assembled in the
nucleolus.
 Genes that encode runs are present on multiple chromosomes that
cluster together to form nucleoli sub-compartments, mRNA splicing
factors are stored in nuclear speckles and move to sites of transcription
where they function.
 Other nuclear bodies have been identified using antibodies; some of
these bodies are believed to concentrate specific nuclear proteins, but
the functions of most nuclear bodies are unknown.

39. nucleolus

40. THE NUCLEOLUS
 The most prominent nuclear body is the nucleolus.
 It is the site of rRNA transcription and processing as well as aspects
of ribosome assembly.
 The nucleolus is a ribosome production factory, designed to fulfill
the need for regulated and efficient production of rRNAs and
assembly of the ribosomal subunits.
 Actively growing mammalian cells, for example, contain 5 million to
10 million ribosomes that must be synthesized each time the cell
divides.
 Recent evidence suggests that nucleoli also have a more general
role in RNA modification and that several types of RNA move in and
out of the nucleolus at specific stages during their processing.
Nucleoli in amphibian
oocytes The amplified rRNA
genes of Xenopus oocytes
are clustered in multiple
nucleoli (darkly stained
spots).

41. RIBOSOMAL RNA GENES AND THE ORGANIZATION OF THE
NUCLEOLUS
 The nucleolus is associated with the chromosomal regions that contain
the genes for the 5.8S, 18S, and 28S rRNAs.
 Ribosomes of higher eukaryotes contain four types of RNA designated
the 5S, 5.8S, 18S, and 28S rRNAs.
 The 5.8S, 18S, and 28S rRNAs are transcribed as a single unit within the
nucleolus by RNA polymerase I, yielding a 45S ribosomal precursor
RNA.
 Transcription of the 5S rRNA, which is also found in the 60S ribosomal
subunit, takes place outside the nucleolus in higher eukaryotes and is
catalyzed by RNA polymerase III.

42. rRNA Genes
 The human genome, for example, contains about 200 copies
of the gene that encodes the 5.8S, 18S, and 28S rRNAs and
approximately 2000 copies of the gene that encodes 5S RNA.
 The genes for 5.8S, 18S, and 28S rRNAs are clustered in
tandem arrays on five different human chromosomes
(chromosomes 13, 14, 15, 21, and 22)
 The 5S rRNA genes are present in a single tandem array on
chromosome 1.

43. RIBOSOMAL RNA GENES
Each rRNA gene is a single transcription unit containing the 185, 5.85, and 285
rRNAs as well as transcribed spacer sequences. The rRNA genes are organized
in tandem arrays, separated by non-transcribed spacer DNA

44. IMPORTANCE OF RIBOSOME PRODUCTION
 The importance of ribosome production is particularly evident in
oocytes in which the rRNA genes are amplified to support the synthesis
of the large numbers of ribosomes required for early embryonic
development.
 In Xenopus oocytes, the rRNA genes are amplified approximately two-
thousand-fold, resulting in about one million copies per cell.
 These amplified rRNA genes are distributed to thousands of nucleoli,
which support the accumulation of nearly 1012 ribosomes per oocyte.
 Recently, it has been shown that ribosome biogenesis is intimately
linked to multiple cellular signaling pathways and that defects in
ribosome production can lead to a wide variety of human diseases.

45. TRANSCRIPTION AND PROCESSING OF rRNA
 Each nucleolar organizing region contains a cluster of tandemly
repeated rRNA genes separated from each other by non-transcribed
spacer DNA.
 These genes are very actively transcribed by RNA polymerase I,
allowing their transcription to be readily visualized by electron
microscopy.
 In such electron micrographs, each of the tandemly arrayed rRNA
genes is surrounded by densely packed growing RNA chains forming a
structure that looks like a Christmas tree.
 The high density of growing RNA chains reflects that of RNA polymerase
molecules, which are present at a maximal density of approximately one
polymerase per hundred base pairs of template DNA.

46. RIBOSOME ASSEMBLY
 Early in ribosome assembly, the processing of the two nascent
ribosomal subunits occur separately
 Processing of the smaller subunit, which contains only the 18S rRNA, is
simpler and involves only four endonuclease cleavages.
 In higher eukaryotes, this is completed within the nucleus but in yeast
the final cleavage to the mature 18S rRNA actually occurs after export of
the 40S subunit to the cytosol.
 Processing of the larger subunit, which contains the 28S, 5.8and 5S
rRNAs, involves extensive nuclease cleavages and is completed within
the nucleolus. Consequently, most of the pre-ribosomal particles in the
nucleolus represent precursors to the large (60S) subunit.
 The final stages of ribosomal subunit maturation follow the export of
pre-ribosomal particles to the cytoplasm, forming the active 40S and
60S subunits of eukaryotic ribosomes.

48. Ribosomal proteins
are imported to the
nucleolus from the
cytoplasm and begin
to assemble on pre-
rRNA prior to its
cleavage.
As the pre-rRNA is
processed, additional
ribosomal proteins and
the 55
rRNA (which is
synthesized elsewhere
in the nucleus)
assemble to form
preribosomal
particles. The final
steps of maturation
follow the export of
preribosomal
particles to the
cytoplasm, yielding the
RIBOSOME ASSEMBLY

49. THANK
YOU

50. REFERENCES
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 Google Images