Nucleus Flashcards
Functions of the nucleus
(3)
- Storage of DNA
- Transcription of RNA to DNA
- Mechanical element
The genetic material in eukaryotes is _____ whereas it is not in prokaryotes
compartmentalised
Benefits of compartmentalisation
(4)
- Protect DNA – critical information storage.
- Increase surface area for membrane-localised reactions.
- Increase efficiency of transcription and synthesis.
- More ways to regulate gene expression.
The nucleus has a ____ membrane
double
ER
- Site of protein production by ribososomes
- Site of protein folding
- Site of glycosylation
Nuclear lamins
- Related to intermediate filaments.
- Form meshwork on inner nuclear membrane (give shape and elasticity)
- Associate with DNA (functional)
- Two types: A/C and B
- “Laminopathies” cause muscular dystrophy and progeria
Type ____ nuclear lamins are the most likely to associate with DNA
B
Nuclear lamina and the cytoskeleton
(5)
- Protein complex that links nuclear lamina with cytoskeleton
- Inner membrane: SUN/KASH proteins
- Outer membrane: nesprins
- Nesprins connect to the cytoskeleton
- Mechanical linkage between cytoplasm and nucleus
Chromosomes
- DNA-protein complexes specially packaged for cell division.
- Humans have 23 pairs.
- Exist in discrete territories within the nucleus,
Chromatin
- complex of DNA, RNA, and proteins.
- Organised around a protein-rich nuclear matrix
- the spatial arrangement allows for co-regulation of genes on different chromosomes if they are next to each other.
Euchromatin
- “true” chromatin
- Less visible by microscopy
- Not so densely packed
- Majority of the genome (~90%)
- Localised mostly in the central part of nucleus.
Heterochromatin
- “different” chromatin
- Looks dark under the microscope.
- Tightly packed, condensed DNA
- Localised around lamina and nucleoli.
The spatial arrangement of chromatin
- LADs: Lamina-Associated Domains
- “B” type chromatin = heterochromatin
- “A” = euchromatin)
- Low level of mRNA transcription in LADs
Functions of the nucleolus
- Transcription of rRNAs
- Assembly of ribosomal subunits
- Sensing and responding to stress.
- Cell cycle regulation
- Cancer
Nucleolus is composed of …
- Segments of 10 chromosomes encoding rRNA genes
- Proteins for processing rRNAs
- Ribsomal subunit proteins
- Small nucleolar RNA (snoRNA) oligonucleotides that help process rRNAs.
Cajal bodies
- 0.2 – 2 µm diameter
- RNA processing
- Genome organization (chromosome domain boundaries)
- Dense foci of coilin protein
- Resemble coiled balls of yarn under EM.
PML bodies
- 0.1 – 1 µm diameter
- Often associated with Cajal bodies
- DNA repair
- Cell proliferation
- Programmed cell death
Speckles
- 20 nm – 1 µm diameter
- Gene transcription
- mRNA processing (splicing to make various versions of genes)
- Bit of a catch-all.
Central dogma
DNA to RNA
RNA goes to cytoplasm
Protein get back into the nucleus
Export of RNA and ribosomes
- mRNA – messenger (genes)
- rRNA – ribosomal
- tRNA – transfer (protein synthesis)
- Assembled ribosomal subunits
Import proteins from the cytoplasm
- RNA polymerase
- Ribosomal proteins
- Transcription factors
- All other structural proteins
Nuclear pore complex
- Ring structure with 8-fold symmetry.
- Pass through both layers of nuclear membrane.
- 30 different nuclear pore proteins called Nups
- Central channel filled with FG - Nups that form selective barrier to transport.
- Common ancestry with COP I, COP II, and clathrin
- Basket shapes on nuclear side
The two types of movement thhrough the NPC
- Passive transport
- Facilitated transport
Passive transport
- Does not require energy
- Transports small molecules and proteins
- Up to ~40 kDa
Facilitated transport
- RNAs, larger proteins, macromolecular complexes
- Facilitated transport requires energy:
- ATP hydrolysis for mRNA
- GTP hydrolysis for proteins, tRNA, and ribosomes
- Requires nuclear transport receptors: karyopherins
mRNP
- a mRNA-protein complex
- includes processing, capping, splicing proteins and export factors.
- Can go in or out through the NPC
mRNA export as part of the processing complex
- ATP hydrolysis causes the release of Dbp5 in the cytoplasm and mRNP dissociation
- Energy from ATP hydrolysis is needed to maintain a gradient of transport
- There is net movement of molecules across the barrier rather than an equilibrium.
Ran-GDP exists in the …
… cytosol
Ran-GTP exists in the …
… nucleus
The difference in Ran-GTP in nucleus vs cytoplasm maintains …
… gradient for import-export
GTPases as molecular switches
- Small GTPases bind GTP and hydrolyse a phosphate group to GDP
- This causes a conformational change in the GTPase, which changes the binding to effector proteins.
GTP hydrolysis to GDP is assisted by…
GAPs
GTPase Activating Proteins
GTP loading after hydrolysis is assisted by…
GEFs
Guanine nucleotide Exchange Factors
Ran-GAPs
(2)
- In cytosol
- Inactivate Ran
Ran-GEFs
(2)
- In the nucleus
- Activate Ran
To maintain the gradient, Ran-GTP is ….
…converted to Ran-GDP in the cytoplasm.
Ran-GTP in the nucleus
(2)
1) facilitates export of proteins to the cytoplasm
2) facilitates release of cargo brought in from cytoplasm.
Protein nuclear import
- Facilitated by importins
- Cargo release enabled by Ran-GTP binding to importin-β
- This causes conformational change that results in complex coming apart
- Importin + Ran-GTP goes back to out to the cytosol
- In the cytosol, Ran-GTP converted to Ran-GDP by Ran GAP
Importins
- Bind cargo proteins in cytoplasm.
- Interact with FG-Nups
- Releases cargo in nucleus.
- Karyopherins, aka nuclear transport receptors, aka importins
Protein nuclear export
- Facilitated by exportins
- Cargo loading enabled by Ran-GTP binding to exportin.
- Conformational change that results in complex assembly
- Ran-GTP hydrolysed to Ran-GDP in cytoplasm by Ran GAP
Exportins
- Bind cargo proteins in the nucleus
- Interact with FG-Nups
- Release cargos in the cytoplasm
Nuclear Localisation Signal (NLS)
- Protein motif typically 8 amino acids long
- Can occur anywhere in the protein.
- Many basic residues such as lysine (K), arginine (R), and proline (P)
- Binds to importins
- Sequence with four hydrophobic amino acids (most often leucine, L)
- E.g. LxxxLxxLxL, where x is any other amino acid
- Binds to exportins
Nucleocytoplasmic shuttling
- NLS of the transcription factor NF-κB is masked when bound to its inhibitor IκB in the cytoplasm …
- Until a signal such as a cytokine (TNFa) triggers degradation of IκB, exposing the NLS
- Then NF-kB can be imported to the nucleus, where it turns on inflammatory genes
- NF-kB relocalises to the cytoplasm via exportins binding to its NES.
