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Cell Biology > Nucleus > Flashcards

Nucleus Flashcards

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1
Q

Functions of the nucleus

(3)

A
  1. Storage of DNA
  2. Transcription of RNA to DNA
  3. Mechanical element
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2
Q

The genetic material in eukaryotes is _____ whereas it is not in prokaryotes

A

compartmentalised

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3
Q

Benefits of compartmentalisation

(4)

A
  1. Protect DNA – critical information storage.
  2. Increase surface area for membrane-localised reactions.
  3. Increase efficiency of transcription and synthesis.
  4. More ways to regulate gene expression.
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4
Q

The nucleus has a ____ membrane

A

double

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5
Q

ER

A
  • Site of protein production by ribososomes
  • Site of protein folding
  • Site of glycosylation
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6
Q

Nuclear lamins

A
  • 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
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7
Q

Type ____ nuclear lamins are the most likely to associate with DNA

A

B

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8
Q

Nuclear lamina and the cytoskeleton

(5)

A
  • 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
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9
Q

Chromosomes

A
  • DNA-protein complexes specially packaged for cell division.
  • Humans have 23 pairs.
  • Exist in discrete territories within the nucleus,
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10
Q

Chromatin

A
  • 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.
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11
Q

Euchromatin

A
  • “true” chromatin
  • Less visible by microscopy
  • Not so densely packed
  • Majority of the genome (~90%)
  • Localised mostly in the central part of nucleus.
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12
Q

Heterochromatin

A
  • “different” chromatin
  • Looks dark under the microscope.
  • Tightly packed, condensed DNA
  • Localised around lamina and nucleoli.
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13
Q

The spatial arrangement of chromatin

A
    • LADs: Lamina-Associated Domains
  • “B” type chromatin = heterochromatin
  • “A” = euchromatin)
  • Low level of mRNA transcription in LADs
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14
Q

Functions of the nucleolus

A
  • Transcription of rRNAs
  • Assembly of ribosomal subunits
  • Sensing and responding to stress.
  • Cell cycle regulation
  • Cancer
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15
Q

Nucleolus is composed of …

A
  • Segments of 10 chromosomes encoding rRNA genes
  • Proteins for processing rRNAs
  • Ribsomal subunit proteins
  • Small nucleolar RNA (snoRNA) oligonucleotides that help process rRNAs.
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16
Q

Cajal bodies

A
  • 0.2 – 2 µm diameter
  • RNA processing
  • Genome organization (chromosome domain boundaries)
  • Dense foci of coilin protein
  • Resemble coiled balls of yarn under EM.
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17
Q

PML bodies

A
  • 0.1 – 1 µm diameter
  • Often associated with Cajal bodies
  • DNA repair
  • Cell proliferation
  • Programmed cell death
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18
Q

Speckles

A
  • 20 nm – 1 µm diameter
  • Gene transcription
  • mRNA processing (splicing to make various versions of genes)
  • Bit of a catch-all.
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19
Q

Central dogma

A

DNA to RNA
RNA goes to cytoplasm
Protein get back into the nucleus

20
Q

Export of RNA and ribosomes

A
  • mRNA – messenger (genes)
  • rRNA – ribosomal
  • tRNA – transfer (protein synthesis)
  • Assembled ribosomal subunits
21
Q

Import proteins from the cytoplasm

A
  • RNA polymerase
  • Ribosomal proteins
  • Transcription factors
  • All other structural proteins
22
Q

Nuclear pore complex

A
  • 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
23
Q

The two types of movement thhrough the NPC

A
  1. Passive transport
  2. Facilitated transport
24
Q

Passive transport

A
  • Does not require energy
  • Transports small molecules and proteins
  • Up to ~40 kDa
25
Q

Facilitated transport

A
  • 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
26
Q

mRNP

A
  • a mRNA-protein complex
  • includes processing, capping, splicing proteins and export factors.
  • Can go in or out through the NPC
27
Q

mRNA export as part of the processing complex

A
  • 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.
28
Q

Ran-GDP exists in the …

A

… cytosol

29
Q

Ran-GTP exists in the …

A

… nucleus

30
Q

The difference in Ran-GTP in nucleus vs cytoplasm maintains …

A

… gradient for import-export

31
Q

GTPases as molecular switches

A
  • 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.
32
Q

GTP hydrolysis to GDP is assisted by…

A

GAPs
GTPase Activating Proteins

33
Q

GTP loading after hydrolysis is assisted by…

A

GEFs
Guanine nucleotide Exchange Factors

34
Q

Ran-GAPs

(2)

A
  • In cytosol
  • Inactivate Ran
35
Q

Ran-GEFs

(2)

A
  • In the nucleus
  • Activate Ran
36
Q

To maintain the gradient, Ran-GTP is ….

A

…converted to Ran-GDP in the cytoplasm.

37
Q

Ran-GTP in the nucleus

(2)

A

1) facilitates export of proteins to the cytoplasm
2) facilitates release of cargo brought in from cytoplasm.

38
Q

Protein nuclear import

A
  • 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
39
Q

Importins

A
  • Bind cargo proteins in cytoplasm.
  • Interact with FG-Nups
  • Releases cargo in nucleus.
  • Karyopherins, aka nuclear transport receptors, aka importins
40
Q

Protein nuclear export

A
  • 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
41
Q

Exportins

A
  • Bind cargo proteins in the nucleus
  • Interact with FG-Nups
  • Release cargos in the cytoplasm
42
Q

Nuclear Localisation Signal (NLS)

A
  • 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
43
Q

Nuclear Export Signal (NES)

A
    • Sequence with four hydrophobic amino acids (most often leucine, L)
  • E.g. LxxxLxxLxL, where x is any other amino acid
  • Binds to exportins
44
Q

Nucleocytoplasmic shuttling

A
  • 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.
45
Q
A

Cell Biology (16 decks)

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