Part 4

The nucleus
 4.1
The nucleus - Structure
Figure 09.F01: A cell from the human cervical carcinoma cell line HeLa has a
nucleus that is easily seen using light microscopy.
Major compartment

-Nuclear envelope: double membrane

* The nuclear pore complexes (NPCs)

- Nucleolus: rRNAs are synthesized

and ribosomal subunits are assembled

- Nucleoplasm: the non-nucleolar

regions of the nucleus

- Heterochromatin: highly compacted

- Euchromatin: less densely Compacted

Figure 09.F02: Many features of the nucleus of a lymphocyte are

easily seen by electron microscopy.
What is the advantage to a eukaryotic cell of having a nucleus?

Having a nucleus allows a cell to

have much more sophisticated
regulation of gene expression than
is possible in prokaryotic cells

The nucleus protects the DNA of

the cell

FIGUrE 9.3 In prokaryotes, transcription

and translation are coupled (left). In
eukaryotes, transcription and translation
occur in separate compartments (right)
 Nuclei vary in appearance according to cell type and organism

 Nuclei range in size from about one micron (1 μm) to more than 10 μm in
diameter

Most cells have a single nucleus, but some cells contain multiple nuclei, and a
few cell types lack nuclei

The percentage of the genome that is heterochromatin varies among cells and
increases as cells become more differentiated

Figure 09.F04: A Drosophila

embryo at the multinucleate stage
Immature erythroblasts differentiate
into mature erythrocytes, more and more
of the DNA becomes heterochromatin

Figure 09.F05: As erythroid cells

differentiate, the fraction of the genome
that is heterochromatin increases, and the
cells become smaller.
 Chromosomes occupy distinct territories

 Although the nucleus lacks

internal membranes, nuclei are
highly organized and contain many
subcompartments.

Each chromosome occupies a

distinct region or territory, which
prevents chromosomes from
becoming entangled with one
another.

The nucleus contains both

chromosome domains and
interchromosomal regions.

Figure 09.F06: Individual chromosomes occupy

distinct areas of the nucleus called chromosome
territories.
 The nucleus contains subcompartments that are not membrane-bounded

 rRNA is synthesized and ribosomal subunits are assembled in the nucleolus.

Genes that encode rRNAs are present on multiple chromosomes that cluster
together to form nucleolar subcompartments.
 mRNA splicing factors are stored in nuclear s and move to sites of transcription
where they function. peckles
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
Splicing factors are concentrated in nuclear speckles
The nucleus may contain a nucleoskeleton that could help to organize
nuclear functions

A sort of filamentous network,

called the nuclear matrix,
may exist in the nucleoplasm

Network is seen only if nuclei are

treated with detergents, DNase,
and high salt concentration

The enzymatic machines that replicate DNA and splice

RNA may be anchored to a nuclear matrix.
The nuclear envelope

-Double membranes.

-- The outer nuclear membrane is continuous

with the membranes of the ER, and the
lumen of the nuclear envelope is continuous
with the lumen of the ER.

-The nuclear envelope contains numerous

Figure 09.F12: The nuclear envelope is
NPCs, the only channels for transport of continuous with the endoplasmic
reticulum.
molecules and macromolecules between the
nucleus and the cytoplasm
Nucleus origin

The nucleus may have arisen by endosymbiosis, a process in which one prokaryotic cell
engulfs another cell, which then becomes a primitive nucleus
 Nuclear Lamina

 Located beneath the inner nuclear membrane and is physically connected to it

by lamina-associated integral membrane proteins.

 Plays a role in nuclear envelope assembly and may provide physical support for the
nuclear envelope

 Phosphorylation of lamins leads to the

disassembly of the structure during cell
division.

 Protein complexes that interact with the

nuclear lamina cross the nuclear envelope
and link the cytoskeleton to the nuclear
interior

Yeast and some other unicellular

eukaryotes lack a nuclear lamina
Figure 09.F16: The nuclear lamina is anchored to the
inner nuclear membrane by two types of interactions
 NPCs
Large molecules are actively transported between the nucleus and cytoplasm

Uncharged molecules smaller than 100 Da can pass through the membranes of the
nuclear envelope.

Molecules and macromolecules larger than 100 Da cross the nuclear envelope by
moving through NPCs
Particles up to 9 nm in diameter (corresponding to globular proteins up to 40 kDa)
can pass through NPCs by passive diffusion, as can metabolites, nucleotides, and
other small molecules

Larger macromolecules are actively transported through NPCs and must contain
specific information to be transported
 The nuclear pore is made of about 30-100
nucleoporin proteins.

Figure 09.F14: The nucleus may have arisen by

endosymbiosis, in which one prokaryotic cell
engulfs another, and then becomes a primitive
nucleus.

Many different classes of molecules and macromolecules are

transported through NPCs. Not shown are small, uncharged
molecules (<100 Da) that can diffuse through the membranes of
the nuclear envelope
Proteins are selectively transported into the nucleus through nuclear pores

Mature nuclear proteins contain sequence information required for their nuclear
localization.

Information for nuclear import lies in a small portion of the transported protein.

The signal within a protein that targets it to the nucleus is a stretch of amino acids
termed the NLS (nuclear localization sequence )

Cores do not contain information for

nuclear entry

nuclear pore is a selective channel that

allows only proteins with the proper
information in their amino acid sequence
to enter

Figure 09.F31: Injection of nucleoplasmin into the

cytosol or the nucleus of Xenopus oocytes shows the
importance of the C-terminal tail fragment.
Export of proteins from the nucleus is also receptor-mediated

Short stretches of amino acids rich in leucine act as the most common nuclear
export sequences (NESs)

A nuclear export receptor binds

proteins that contain NESs in the
nucleus and transports them to the
cytoplasm

The NESs were discovered in the

course of studies of the growth of
human HIV in infected cells

Figure 09.F36: Some proteins, such as HIV Rev,

shuttle between the nucleus and the cytoplasm.
Nuclear transport can be regulated

Both protein import and export are regulated.

Cells use nuclear transport to regulate many functions, including transit through
the cell cycle and response to external stimuli.

The localization of the transcription factor NF-κB illustrates how nuclear transport
is regulated
Multiple classes of RNA are exported from the nucleus

 mRNAs, tRNAs, and ribosomal subunits produced in the nucleus are exported
through NPCs to function during translation in the cytoplasm.

The same NPCs used for protein transport are also used for RNA export.

Export of RNA is receptor-mediated and energy-dependent.

Different soluble transport factors are required for transport of each class of
RNA.
Figure 09.F45: mRNA, tRNA, and ribosomal subunits are exported from the
nucleus and function in protein synthesis in the cytoplasm. Some tRNAs return
to the nucleus for further processing or storage before final export. U-snRNAs are
exported, processed, and assembled into RNA–protein complexes, and imported
into the nucleus where they participate in RNA processing.
Transport of most RNAs is unidirectional from the nucleus to the cytoplasm
 4.2
Chromatin - chromosomes
Bacteria- genetic material: in the form of a nucleoid

Eukaryotic: genetic material: the mass of chromatin within the nucleus

The centromere is the specialized DNA

sequence of a chromosome that links a pair
of sister chromatids
Different levels of DNA packing

The 30 nm solenoid structure fiber

forms loops whose base is attached
to scaffold proteins.
Decondensation of these loops
allows the transcription of genes
they encode.
 Chromatin-remodeling complexes decondense the
chromatin making it accessible to other proteins for replication, transcription
and their regulations

Figure 5-27b Essential Cell Biology (© Garland Science 2010)

Chromosomes have banding patterns

• Certain staining techniques cause the

chromosomes to have the appearance
of a series of striations called G-
bands.
• The bands are lower in G  C content
than the interbands.
• Genes are concentrated in the G  C-
rich interbands.
Figure 10.4: Every chromosome
has a distinct G-banding pattern.
The nucleosome is the subunit of all chromatin

• Micrococcal nuclease releases individual nucleosomes from chromatin as ~10-

nm particles.
• A nucleosome contains ~200 bp of DNA, two copies of each core histone (H2A,
H2B, H3, and H4), and one copy of H1.
• DNA is wrapped around the outside surface of the protein octamer.

Figure 10.27: The nucleosome consists of Figure 10.30: Sequences on the DNA
approximately equal masses of DNA and that tie on different turns around the
histones.. nucleosome may close together.
Nucleosomes have a common structure

 Nucleosomal DNA is divided into the core DNA and linker DNA depending
on its susceptibility to micrococcal nuclease.
 There are 1.65 turns of DNA wound around the histomer octamer.
 The core DNA is the length of 146 bp that is found on the core particles
produced by prolonged digestion with micrococcal nuclease.
 Linker DNA is the region of 8 to 114 bp that is susceptible to early cleavage
by the enzyme.
 Nucleosomes have a common structure

• Changes in the length of linker DNA

account for the variation in total length
of nucleosomal DNA.
• Linker histone is associated with linker
DNA and may lie at the point where
DNA enters or leaves the nucleosome.

Figure 10.35: Model for histone H1 interaction with the

nucleosome.
Do nucleosomes lie at specific positions?

• Nucleosomes may form at specific

positions as the result either of the
local structure of DNA or of proteins
that interact with specific sequences.
• A common cause of nucleosome
positioning is when proteins binding
to DNA establish a boundary.

Figure 10.52: Nucleosome positioning places restrictions sites at unique

positions relative to the linker sites cleaved by micrococcal nuclease.
Telomeres are the ends of chromosomes

 Protect ends
 Maintain length
Telomeres are replicated by a special mechanism

• The telomere is required for the stability of the chromosome end.

• A telomere consists of a simple repeat where a C+A-rich strand has the
sequence C>1(A/T)1-4.
• The protein TRF2 catalyzes a reaction in which the 3′ repeating unit of
the G+T-rich strand forms a loop by displacing its homologue in an
upstream region of the telomere.
Figure 10.16: Mutation in telomerase causes Figure 10.18: Telomeric DNA forms a
telomeres to shorten in each cell division. t-loop.
Telomerase activity identified
Telomerase allows telomere length equilibrium maintenance

TR

Replication

Telomerase
TERT
Why does telomerase matter?

It is required for cells that must divide many times

Cancer Tissue renewal

Histones are covalently modified

• Histones are modified by acetylation, methylation, phosphorylation,

and other modifications.
• Combinations of specific histones modifications define the function of
local regions of chromatin; this is known as the histone code.
• Histone acetylation occurs transiently at replication.

Figure 10.75: Modifying complexes have

several components.
 Histones are covalently modified

• Histone acetylation is associated with activation of

gene expression.
• Deacetylated chromatin may have a more
condensed structure.
• Transcription activators are associated with
histone acetyltransferase activities in large
complexes.
• Histone acetyltransferases vary in their target
specificity.
• Deacetylation is associated with repression of gene
activity.
 Histones play a role in the regulation of gene expression by their
posttranslational modifications

Potential posttranslational modifications on the N-terminal tail of Histone 3:

M – methylation
A – acetylation by histone-modifying enzymes
P – phosphorylation

Figure 5-28a Essential Cell Biology (© Garland Science 2010)

The 23 chromosome pairs of the human genome

FISH: fluorescent in situ hybridization Karyotype: chromosomes articially lined

up in order (e.g. for cytogenetic analysis)