Nucleus Flashcards

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1
Q

What is the history of the nucleus?

A

A prokaryote organism was invaded by another, non-nucleated cell, setting up an endosymbiotic relationship, with the invading cell’s outer membrane forming the nuclear envelope (Pederson, 2011)

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2
Q

What is the nucleus?

A

Double membrane-enclosed organelle found in eukaryotic cells
Contains most of the cell’s genetic material and is the control centre of the cell

Can be multinucleated - 2 nuclei, 1 macronucleus and 1 micronucleus
Macronucleus governs all the general cellular activities such as water balance
Micronucleus is responsible for sexual reproduction

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3
Q

What is significant about leukocytes?

A

Most nuclei are spherical but in leukocytes we can find multilobed nuclei - polymorphonuclear (K Shrivastav, 2020)

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4
Q

What does the nucleus do?

A

Nucleus maintains the integrity of DNA and controls the activities of the cell by regulating gene expression and mediating the replication of DNA during the cell cycle
Separates nuclear and cytosolic enzymes – concentrated where needed to protect DNA from harsh cytosolic environment
Separates site for transcription from translation in the cytoplasm

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5
Q

What are some components of the nucleus?

A
Nuclear Envelope
Nucleolus
Nuclear Matrix
Nuclear Lamina
Chromatin 
Nuclear pore complex
Sub nuclear bodies
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6
Q

How can we visualise the nucleus?

A

Fluorescence Micrograph with markers for NPC, nucleolus and chromatin
Resolution limit of 200 nm (wavelength of visible light)
Used Confocal Microscopy

Electron micrograph - spatial resolution of 3-5 nm

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7
Q

Describe the nuclear envelope?

A

Nuclear envelope is a double lipid bilayer membrane that encloses the entire organelle
Outer membrane is continuous with the RER (similar structure with bound ribosomes)
The inner nuclear membrane contains many inner nuclear membrane proteins, mostly associated with the nuclear lamina
There is a perinuclear space between the two membranes 20-40 nm (K Shrivastav, 2020)

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8
Q

What does the nuclear envelope do?

A

Role - a physical barrier, separating the contents of the nucleus (nucleoplasm) from the chemical reactions in the cytoplasm
This allows reactions synthesising genetic material and RNA before replication

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9
Q

What is significant about the nuclear envelope?

A

The nuclear envelope disappears during prophase of mitosis into fragments (depolymerisation and phosphorylation)
It is reassembled as two new envelopes (repolymerisation and dephosphorylation) (BSCB)

Nuclear envelope is not a spherical coat - the surface invaginates to form deep or shallow tubules in the nucleoplasm
This could be to bring nuclear pores closer to deeper parts of the nucleoplasm (BSCB)

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10
Q

Describe the nucleolus?

A

Non-membrane bound dynamic element within the nucleus
It disappears in late prophase and reappears in telophase (during cell division)
The number of nuclei differ per nucleus changes

Structure consists of:
Fibrillar centers - contains rRNA (in the form of partly condensed chromatin)
Fibrillar component - they surround the fibrillar centers, which contain RNA molecules in the process of transcription
Granular regions - outer most regions having mature ribosomal precursor particles
(K Shrivastav, 2020)

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11
Q

Describe the nuclear matrix

A

A nuclear scaffold as it has a network of protein filaments providing a structural framework for the organisation of chromatin
It facilitates transcription and replication
It has a similar structure to the nuclear lamina except the nuclear matrix extends within the nucleoplasm

We can isolated the nuclear matrix from the nuclei (nucleolus) using: non-ionic detergents, nucleases and high salt buffers
(K Shrivastav, 2020)

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12
Q

Describe the nuclear lamina?

A
A dense (30 -100nm thick) fibrillar network inside the nucleus 
Composed of intermediate filaments and full of membrane associated proteins (lamin proteins)
Contains lamin A,C and B and is associated with emerin proteins
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13
Q

What does the nuclear lamina do?

A

Nuclear lamina regulates important cellular events such as DNA replication and cell division (not just mechanical support)

Participates in chromatin organization and it anchors the nuclear pore complexes embedded in the nuclear envelope - provides great stability

Similar to the cytoskeleton
This controls what happens to gene expression as it is involved in how compact the DNA is and therefore what can be expressed

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14
Q

What are laminopathy disorders?

A

Group of rare genetic disorders caused by mutations in genes encoding proteins of the nuclear lamina
Leads to defects in filament assembly and/or attachment to the nuclear envelope
Jeopardizes the nuclear envelope’s stability in physically stressed tissues such as muscle fibres, bone, skin and connective tissue
Two types: Emery-Dreifuss muscular dystrophy and Hutchison-Gilford progeria syndrome (HGPS)
First reports of laminopathies in the late 1990s

We can see abnormal looking nuclei
Large variety of clinical symptoms including skeletal and/or cardiac muscular dystrophy, lipodystrophy, neuropathies and progeria (premature aging)
No cure and treatment is largely symptomatic and supportive

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15
Q

Describe the laminopathy disorder: Emery-Dreifuss muscular dystrophy?

A

A condition that mainly affects skeletal muscles and cardiac muscle
Earliest features are joint deformities called contractures, restricting the movement of joints
Most affected individuals also experience slowly progressive muscle weakness and wasting
Almost all have heart problems, due to abnormalities of the electrical signals that control the heartbeat (cardiac conduction defects)

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16
Q

Describe the laminopathy disorder: Hutchison-Gilford progeria syndrome (HGPS)?

A

HGPS is a disease in which the physical aspects of aging are accelerated
Point mutation in the LMNA gene (single gene defect)
Results in the translation of a lamin A lacking 50 amino acids
The mutant protein (LAD50) incorporates abnormally into the nuclear lamina, leads to mechanical defects, thickening of the lamina, loss of peripheral heterochromatin, and increased DNA damage

17
Q

How is genetic material organised?

A

Humans have 23 pairs of chromosomes = total of 46
22 are autosomes
23rd = sex chromosome
XX - Female & XY - Male

DNA organizes itself into discrete individual patches called chromosome territories
They reside in a specific region - localisation within the nucleus

Key land mark for pathologists - intranuclear gene locations in relation to not only reciprocal translocations but in more recent work on gene repositioning in solid tumours (Pederson, 2011)

18
Q

How is DNA stored within the nucleus?

A

Chromatin
Two types: euchromatin and heterochromatin

Euchromatin - consists of DNA that is active/expressed, an open form of DNA that allows transcription factors to bind
DNA wraps around histone proteins forming nucleosomes; the “beads on a string” structure
Light Staining

Heterochromatin - Mostly inactive DNA where multiple histones wrap into a 30 nm fibre consisting of nucleosome arrays in their most compact form
This is often found near the nuclear membrane (doesn’t make sense as the chromatin that can be transcribed should be near the edge) - but linked to the nuclear lamina
Dark staining

19
Q

What are the types of heterochromatin?

A

Constitutive heterochromatin - never expressed (located around the centromere )

Facultative heterochromatin - which is differentially expressed (development/stress)
E.g. During the early stage of development when you want two arms to be grown/expressed, however, you want that to stop after they have been developed

20
Q

What is an interesting fact about certain heterochromatin?

A

In the rod photoreceptor cell nuclei of nocturnal animals, the heterochromatin is condensed into a large central domain in the nucleus with the euchromatin displaced to more peripheral locations, with plausible speculations as to the efficiency of light transmission and retinal harvesting
(Pederson, 2011)

21
Q

What are insulator elements?

A

They organize the chromatin fibre in the nucleus by establishing separate compartments of higher-order chromatin structure

Domains of open chromatin are flanked by insulators that interact together to form a loop
They are anchored in part to the nuclear periphery by interactions of the insulators with the nuclear lamina

22
Q

What are some regions within a chromosome?

A

Centromere - not located in the centre but is the constricted region of a chromosome, regions either side are the chromosome arms
Role - attachment site for microtubules and site of association of sister chromatids

Telomere - they cap the ends of the eukaryotic chromosomes, consisting of a long array of short tandem repeats
Tole - to protect DNA and prevent the shortening of genetic material each time replication occurs
Discovered through the macronuclear amplification of the ribosomal RNA genes (Pederson, 2011)

Origin of replication - the site where replication initiates, one chromosome can contain multiple origins of replication

23
Q

What is the nuclear pore complex?

A

NPC are elaborate multiprotein assemblies that span the nuclear membrane (thousands situated within the nuclear membrane - 3000-4000 pores) (BSCB)
Proteins and mRNA transverse the nuclear membrane through NPC

The nucleus is permeable to small proteins <40 kDa 
Larger macromolecules (mRNA and proteins) are transported across via an active mechanism that requires soluble nuclear transport factors
24
Q

Describe the structure of the Nuclear pore complex?

A

It has octagonally shaped symmetric cylindrical structure around the channel and is embedded within the two nuclear membrane (looks like an open ended cylinder with wider perimeters at its each end - like a sand timer)
Very complex - 125 mega Daltons (MDa)
Contains 30-50 nucleoporins

There are 8 composite rings of protein at the cytoplasmic surface and similar ring of eight at the inner surface of the nuclear membrane (they are connected to each other by spoke proteins)
8 cytoplasmic filaments (NUPs) stick into the cytoplasm and eight intranuclear filaments (NUPs) produce a basket like structure into the nucleus

Approximately 145 nm in diameter and 80 nm long
The central channel is about 69nm - expands and contracts when required

25
Q

Describe how proteins get into the nucleus?

A
  1. A protein with a nuclear localization signal sequence (NLS) is recognized by an importin complexed with Ran-GDP
    (NLS tells the nucleus that this protein should be coming into the cell)
  2. Importin then binds cytoplasmic filaments
  3. The complex is translocated through the pore by sequential binding to pore proteins
  4. Nuclear guanine nucleotide exchange factor (GEF) exchanges the GDP on Ran for GTP, allowing protein to be released
  5. Importin-Ran/GTP complex is re-exported - cytoplasmic GTP-ase activating protein (GAP) hydrolyses Ran-GTP to Ran-GDP (restart again)
26
Q

Describe importin?

A

Importin (a type pf karyopherin) has two subunits a and b, with a binding to the NLS as well as FG motifs on Nups and b binds to the NPC for transport into the nucleus

Importin α has 2 NLS binding sites:
Monopartite NLS (one site)
Bipartite NLS (both sites)
Contains mainly Lysine and Arginine in the binding sites

27
Q

Describe how proteins get out of the nucleus?

A

Proteins are targeted for export by specific amino acid sequences, called nuclear export signals (NESs) - contains a lot of leucine
Nuclear export signal are recognised by exportins, in the presence of Ran-GTP, within the nucleus that direct protein transport through the NPC to the cytoplasm.
Following transport to the cytoplasm, GTP hydrolysis leads to dissociation of the target protein, which is released into the cytoplasm

28
Q

What are some disorders linked to the nuclear pore complex?

A

Rare as most cause drastic effects on early stages of embryo development

Nup214 – facilitates export of NES bearing cargo
mutation can lead to accumulation of proteins in nucleus

Triple A syndrome:
Symptoms - muscle control of heart and of oesophagus / sphincter, adrenal insufficiency (affect hormone release) and mental retardation
This specifically affects the nuclear import of certain proteins : aparataxin; DNA ligase I, ferritin heavy chain All involved in protecting and repairing DNA under oxidative stress - cells more prone to oxidative damage

29
Q

How do viruses get into the nucleus?

A

Viruses that replicate in nucleus deliver their genetic material to the nucleus for replication

Small viruses, eg HBV (<36 nm capsid diameter) are able to cross NPC without the need for capsid disassembly
HBV capsids have NLSs

Large viruses HSV (125 nm capsid diameter) or adenovirus particles (90 nm diameter) dock to pore via importin B or Nup214, then releases its DNA through the NPC into the nucleoplasm

30
Q

Give an overview of how bulk mRNA exits the nucleus?

A

This is the majority of export out the nucleus
It is marked for nuclear export - during the process of splicing many proteins are associated/bound onto the mRNA forming mRNPs
The recruitment of multiple protein complexes make stable and export competent

The human trex protein (hTREX) component and NXF1–NXT1 heterodimers are essential to mark the mRNA
Made up of around 20 proteins
It recruits specific exportin to the mRNA to allow exit through the pore

31
Q

What is the process of how bulk mRNA exits the nucleus?

A
  1. The large complex approaches the nuclear pore complex (NPC) and attaches by a thin filament
  2. It then reaches the pore centre elongating into a 100–150Å broad rod
  3. The material passes the pore centre in a rod like form, assuming a typical dumbbell-shaped configuration
  4. Then the material rounds into a spherical particle (almost reforms it’s shape) and is deposited on the cytoplasmic side

Once in the cytoplasm hTREX dissociates and Dbp5 detaches NXF1 so the mRNA can then be used within translation
The mRNA changes conformation in order to sequeeze through the NPC

32
Q

What is involved in hTREX mutations?

A

This can cause high grade tumours as there is a degree of DNA damage / genomic instability

It enhances formation of R-loops
R-loops halt transcription and increase DNA damage

33
Q

What are the different NPC subcomplexes that the nucleoporins are split into?

A
Cytoplasmic Filaments -10
Y-complex - 10
Transmembrane nucleoporins -3
Nup93-complex - 5
Nup62-complex - 4
Nuclear basket - 3 

Numbers are the number of nucleoporin proteins

(A.Ashkenazy-Titelman, Y.Shav-Tal1, R.Kehlenbach, 2020)

34
Q

Does any RNA enter the nucleus?

A

snRNPs as components of the spliceosome
telomerase RNP
transport of tRNAs (under certain conditions)

(A.Ashkenazy-Titelman, Y.Shav-Tal1, R.Kehlenbach, 2020)