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CSD > Nucleus > Flashcards

Nucleus Flashcards

1
Q

why do we need a nucleus?

A

genome organization, genome integrity, control of gene regulation, coordination of genome activities, make faithful copies of itself and genome

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2
Q

Major structures of nucleus?

A

nuclear envelope (outer and inner), heterochromatin/euchromatin, nuclear pore, nucleolus, contiguous with rough ER

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3
Q

T/F. Inner nuclear membrane is continuous with the ER

A

False, Outer membrane

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4
Q

What components of the nucleus interact with chromatin?

A

inner nuclear membrane and lamina

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5
Q

T/F. Nuclear envelope has two lipid bilayers, it is contigueous with the ER, it is connected with the cytoskeleton

A

All true

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6
Q

T/F. INM and ONM are contiguous and have the same resident proteins

A

False, they are contiguous but have very different protein compositions

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7
Q

Proteins larger than what size need to be actively transported?

A

40kDa

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8
Q

Features of FG repeat Nups

A

Line length of nuclear pore complex, believed to form intermolecular interactions, creating a semi-permeable mesh that restricts translocation.
Binding sites for transport receptors.

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9
Q

Sole determinant of directionality of nuclear transport

A

Ran-GTP gradient, Ran-GDP should be higher in cytoplasm and Ran-GTP in the nucleus

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10
Q

NLS

A

nuclear localization signal, Lys-Arg rich, binding site for importins. Not always sufficient for import

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11
Q

How do importin and imported cargo protein dissociate?

A

Through binding of Ran-GTP to importin in the nucleus. Ran-GDP then produced through dephosphorylation activity of Ran GAP, allowing for release of Ran-GDP and restarting of the cycle

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12
Q

How do you reinstate Ran-GTP from Ran-GDP?

A

Through action of Ran GEF in nucleus

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13
Q

Ran-GTP gradient cycle

A

Be able to draw with import/export

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14
Q

Example of disease caused by mutations in an NPC

A

ALADIN mutants, cause Triple A syndrome, autosomal recessive disorder which leads to all kinds of physical and nuero issues

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15
Q

T/F. Ratio of Ran-GTP : Ran-GDP in a normal cell is higher in the cytoplasm

A

False, it is higher in the nucleus

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16
Q

T/F. Ratio of Ran-GTP : Ran-GDP in a normal cell is dependent on RAN-GAP and RAN-GEF

A

True

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17
Q

Strategy to detect lamina or INM interactions with chromatin

A

DamID, where you exogenously label GATC in DNA stretches close to where the fused Dam/protein of interest is bound

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18
Q

Examples of different components throughout the nucleoplasm that contribute to gene regulation

A

Cajal bodies, nucleoli, nuclear speckles

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19
Q

Two types of lamins

A

Lamin A type - found in differentiated cells, Lamin B type found in virtually all cells

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20
Q

Lamin structure

A

Intermediate filaments that form coiled coils and have disordered region at C-terminus

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21
Q

Lamin A processing

A

Farnesylation, carboxymethyltransferase, etc, and dysregulation in this leads to disease - ex progeria

22
Q

T/F. Nuclear lamins are inner nuclear membrane proteins, intermediate filament proteins, and very stable

A

False, the first statement is false – they are associated with the inner nuclear membrane but are not a part of it.

23
Q

Proximity tagging methods

A

DamID for DNA, APEX-ID or BIO-ID to biotinylate/otherwise label adjacent proteins or DNA. Can do Mass spec

24
Q

Nuclear envelope breakdown controlled by

A

Cyclin B1 - CDK1 complex, phosphorylation events

25
Q

what is the largest structure in the nucleus

A

chromosomes

26
Q

largest sub-nuclear structure

A

nucleolus

27
Q

nucleolus assembly

A

at loci containing rRNA gene arrays - on short arms of 5 different somatic chromosomes

28
Q

nucleoli purpose

A

factories to assemble rRNAs into ribosomes. Precursor RNA is processed, co-assembled with ribosomal proteins. Then small and large subunits are exported to cytoplasm. Assembly of other RNA-protein complexes also happen here

29
Q

additional subnuclear bodies (6) and their putative purposes

A

speckles (recycle mRNA splicing machinery?), cajal bodies (snRNP assembly?), gems (snRNP assembly), PcG bodies (polycomb group proteins), cleavage bodies (pre-mRNA cleavage), and PML bodies (transcriptional regulation)

30
Q

components of the nuclear envelope (5)

A

inner membrane, outer membrane, lumen, NPCs, peripheral lamina structure

31
Q

T/F. Nuclear lamina has different characteristics depending on cell type

A

True, for example liver cell nucleus has unusually thick lamina

32
Q

T/F. Lamin filaments are typically unstable

A

False, they are very stable

33
Q

Name three nuclear activities that lamins support, either directly or indirectly

A
  1. Scaffolds for proteins involved in activating or inactivating chromatin
  2. Mechanical, adaptive protection of the genome
  3. Regulate signaling in specific tissues

Other answers:: import/export via NPCs, support replication and DNA repair, mechanically anchor cytoskeleton, rebuild nucleus post division

34
Q

What are the components and functions of LINC complexes?

A

SUNs + Nesprins, mechanically link nucleoskeleton and cytoskeleton

35
Q

Examples of laminopathies

A

Emery-dreifuss muscular dystrophy, progeria, lipodystrophy

36
Q

what are some essential factors that NPCs mediate import of from cytoplasm?

A

signaling, regulatory, ribosomal and nucleolar proteins. histones, transcription factors

37
Q

what are some essential factors that NPCs mediate EXPORT of from cytoplasm?

A

ribosome subunits, mRNA complexes, tRNA, snRNA

38
Q

What two amino acids create the hydrophobic barrier within nuclear pores (nups)?

A

Phe-Gly, AKA FG repeats

39
Q

How does the nuclear envelope structure help ensure chromosome segregation fidelity?

A

Through nuclear disassembly and reformation, mediated by phosphorylation and subsequent desphosphorylation of lamins

40
Q

What protein is largely responsible for unifying chromosomes within a single nucleus?

A

BANF1 and its nuclear lamina partners

41
Q

what are the 4 distinct types of nuclear filaments?

A

A, C, B1, and B2

42
Q

What are some other nucleoskeletal proteins?

A

Titin, actin, myosins, spectrins

43
Q

Three types of NLS signals

A

Classic PKKKRKV (60%), bipartite, and proline-tyrosine rich

44
Q

What type of signal does nuclear export require?

A

A nuclear export signal (NES) on cargo protein.

45
Q

What are the primary differences between NLS and NES?

A

NES are hydrophobic, leucine rich, and have no strict consensus, contrary to NLS

46
Q

T/F. Protein unfolding required for nucleocytoplasmic transport

A

False, not required

47
Q

Requirement for NLS/NES use in import/export

A

Signal must be accessible on cargo surface - layer of regulation in mods or partners that hide (or expose) the signal

48
Q

Ran-GTP gradient responsible for (2)

A

importins taking cargo in, and exportins taking cargo out

49
Q

What does Ran need in order to bind and hydrolyze GTP

A

Binds GTP easily, but needs GAP in order to hydrolyze

50
Q

What does Ran need in order to kick out GDP?

A

GEF (GDP exchange factor)

51
Q

T/F. Ran-GEF is chromatin associated

A

True

CSD (13 decks)

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