The nucleus is a membrane-bound organelle that houses the cell's DNA. It contains several sub-compartments including the nucleolus, which is the site of ribosome biogenesis. The nuclear envelope, composed of two lipid bilayers separated by perinuclear space, encloses the nucleus and regulates transport between the nucleus and cytoplasm through nuclear pore complexes. Within the nucleus, DNA is organized into either loosely packed euchromatin or tightly packed heterochromatin. The nucleolus forms around clusters of rRNA genes and is the site of rRNA transcription and ribosome subunit assembly.

1. The nucleus

2. ◾Components of the nucleus
◾Nuclear Envelope
◾Nuclear pore
◾Nucleoplasm
◾Nucleolus

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. ◾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.

9. ◾ 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.
◾ 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.

10. NUCLEAR ENVELOPE
◾ Nuclear Membrane is a barrier 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

11. 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).

12. 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.

13. 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.
◾ 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.

14. • Nuclear pores, small channels that span the nuclear envelope, let substances enter and exit
the nucleus.
• Lined by a set of proteins, called the nuclear pore complex, that control what molecules can
go in or out. No. of pores = 3000-4000
• Highly selective, allowing only newly formed ribosome units to pass through, and restricts
the active ribosome units from entering.
• The nucleopore has multiple copies of roughly 30 proteins that are different from each
other. The specific proteins that interact among themselves to make the nuclear pore
complex are known as nucleoporins.
NUCLEAR PORE

15. NUCLEAR PORE CHANNEL (NPC)
 The Phospholipid bilayer is only permeable for non-polar micro-molecules. 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.
 The cylindrical multiprotein complexes that surround each nuclear pore and direct
the nucleocytoplasmic exchange are termed NPCs.
 Both concentric membranes of the nuclear envelop fuse with the multiprotein
complex that is manifested by 30 disparate proteins termed NUPs or Nucleoporins.

16. The nuclear pore complex
possesses octagonal symmetry. The
structure of the nuclear pore complex
comprises the following key elements:
• Nucleoporins scaffold
• Central channel or transporter
• Cytoplasmic filaments
• Nuclear basket
Nucleoporins scaffold
• It comprises of the Cytoplasmic,
Lumenal and Nucleo-plasmic rings, in
between which a central spoke ring is
allocated.
• NPC appears as an octagonal ring.

17. Central channel or transporter
• Some nucleoporins repeat account for the
formation of the central channel.
• The nucleoporins of the central channel
function as a selective barrier, which only
allows the import and export of large
biomolecules across the bilayer nuclear
envelop that carries specific amino acid
sequences.
• It is 36-38 nm wide.
• The central channel is encased by eightfold
symmetrical spokes.

18. Cytoplasmic filaments:
• They appear as short and thick stringy structures associated with the cytoplasmic ring.
• It has a diameter of 3.3 nm and extended towards the cytoplasm.
• It functions like a sensor that specifically binds with signal proteins tagging molecules
that have to be imported into the nucleus.
• These are eight in number and covers less space towards the cytoplasmic end.
Nuclear basket
• It seems like a large bin-like structure associated with the nuclear ring.
• It enables tethering of nucleoporins inwards the nucleus lumen. This basket plays a
significant role in exporting biomolecules.

19. 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.

20. NUCLEAR LAMINA
 It is a fibrous mesh work supports the inner nuclear
membrane called as 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.

21. 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

22. 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.

23. 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.

24. 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).

25. ◾ 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.

26. 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
chromosomes from
entangled with one
prevents
becoming
another.
 The nucleus contains both
chromosome domains and inter-
chromosomal regions.
Individual chromosomes occupy distinct areas
of the nucleus called chromosome territories.

27. 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.

28. 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.

29. 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

30. 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.

31. 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.

32. 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.

34. 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
RIBOSOMEASSEMBLY

35. Molecular trafficking into and out of nucleus

36. 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.

37. 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.

38. 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 protein, and amino
acids that are involved in these
localization signals are found close to
each other but not immediately adjacent
to each other.

39. OF SnRNAs BETWEEN NUCLEUS AND
TRANSPORT
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.
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.

40. 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.

41. 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.