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MCP Unit 2 > Nuclear Structure and Function > Flashcards

Nuclear Structure and Function Flashcards

1
Q

Functions of the nucleus

A
  • protect chromosomes from damage
  • repair chromosomes when damaged
  • replicate chromosomes
  • facilitate the expression of genetic programs through the transcription of gene sets
  • synthesize ribosomes
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2
Q

nuclear structure

A
  • surrounded by cage of IF and enclosed by double membrane nuclear envelope
  • envelope punctuated by nuclear pores that are the conduits for traffic of everything in and out
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3
Q

chromatin

A

complex of protein and DNA

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4
Q

euchromatin

A

-stains more lightly and is less condensed DNA that is being actively expressed

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5
Q

heterochromatin

A

-stains more darkly and is more condensed DNA that is not in the process of being expressed

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6
Q

nucleolus 1

A

non membrane bound subcompartment of the nucleus where ribosome biogenesis occurs

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7
Q

nuclear envelope

A
  • double membrane
  • outer membrane continuous with membrane of ER and has active ribosomes attached to it
  • proteins translated on outer membrane are inserted into the lumen b/n membranes
  • inner membrane attached to and supported by nuclear lamina
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8
Q

nuclear lamina

A
  • meshwork of IF
  • lamin A, B, C
  • attached to inner membrane of nuclear envelope and helps stabilize nuclear envelope and organize chromosomes
  • phosphorylation of lamins at mitosis induces disassembly of the nuclear lamina which causes nuclear breakdown
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9
Q

nuclear dynamics during mitosis

A 
before:
-transcription ceases
-nucleolus dissolves
-chromosomes condense
-modification of lamins
after:
-lamin A dephosphorylated
-nuclear envelope vesicles fuse onto decondensing chromosomes
-chromosomes fuse
-transcription of rDNA repeats leads to re-formation of nucleolus
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10
Q

nuclear pores (NPCs)

A
  • proteinaceous channels through the nuclear envelope
  • conduits through which all molecules move into and out of the nucleus
  • form a 9mm diameter, 15nm length, semi-selective channel
  • solutes and proteins (<44kDa can diffuse alone) is facilitated
  • ~125 mega daltons, ~100 proteins arranged in 8-fold symmetry
  • most cells have 3-4,000 functionally equivalent NPCs
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11
Q

general mechanism of transport in and out of nucleus

A
  • process is facilitated by carrier proteins that recognize transport substrates via signals on substrates.
  • nuclear localization=import
  • export signals
  • carrier binds substrate binds and acts as escort through the pore
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12
Q

Ran in transport

A
  • energy comes from GTP hydrolysis by Ran
  • Ran-GDP on cytoplasmic side (GAP changes GTP to GDP when it gets to cytosolic side)
  • Ran-GTP on nuclear side (GEF changes GDP to GTP when it gets to nuclear side)
  • creates PE gradient
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13
Q

nuclear localization signal

A
  • required to recognize and direct proteins for import into the nucleus. recognized by importin complex
  • 4-8 positively charged amino acids (lysine and/or arginine)
  • can occur anywhere in primary sequence
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14
Q

detailed mechanism of transport-import

A
  1. cargo binds to importin
  2. importin-cargo complex diffuses through pore
  3. Ran-GTP binds to complex, causing a release of cargo
  4. Ran-GTP and importin diffuse back across pore, and GAP helps hydrolysis to Ran-GDP and release of importin
    * Ran GDP cycled back into nucleus and GEF changes it to GTP for next cargo-importin complex
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15
Q

detailed mechanism of transport-export

A
  1. cargo and Ran GTP bind to exportin
  2. diffuse through NPC
  3. Ran-GTP hydrolysis by GAP releases cargo and exportin.
  4. Exporting and Ran-GDP cycled back across
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16
Q

GAP and GEF

A

GAP in cytoplasm
GEF in nucleus

Ran-GDP moves from cytoplasm to nucleus, is GEFed to Ran-GTP, moves back, and is hydrolyzed with help of GAP

17
Q

Ran GTPase

A
  • provides energy for transport in the form of PE stored as a chemical gradient
  • it helps form export complexes and accompanies these complexes out of the nucleus
  • catalyze release of the transport complex after transport and thus ensures irreversibility
18
Q

nucleolus 2

A
  • non membrane bound sub-compartment of the nucleus
  • assembled on the rDNA repeats of 5 different autosomes with two homologues each for a total of 10 chromosomes
  • primary function is ribosome biogenesis
19
Q

three regions of the nucleolus

A
  • fibrillar center-contains DNA that isn’t being actively transcribed
  • dense fibrillar component-contains rRNA molecules being actively synthesized
  • granular component-maturing ribosomal precursor particles
20
Q

transcription of rDNA genes

A
  • 3 of 4 rRNA species are transcribed as a large 45S pre-cursor
  • ~200 rDNA genes per haploid genome are located in tandem array on 5 chromosomes (2 homologues= 10)
  • ~100 transcription units/gene are simultaneously transcribed by RNA Pol I.
21
Q

45S rRNA precursor processing

A
  • 13,000 nucleotide precursor is processed in the pre-ribosome by endo and exonucleases to 28S, 18S, and 5.8S rRNAs
  • 18S is incorporated into the small subunit
  • 28S, 5.8S, and 5S (from RNA Pol III somewhere else) are incorporated into the large subunit
22
Q

Ribosome biogenesis

A
  • about 80 ribosomal proteins assemble on the 45S precursor (and the 5S)
  • 45S rRNA is processed in the particle with nucleases to create the other sized S rRNAS and immature small and large sub-units
  • process is completed following export from the nucleus
23
Q

human chromosomes

A
  • extremely long (1.7-8.5cm), linear polymers of double stranded DNA
  • 22 different autosomes and 2 different sex chromosomes
  • diploid cells have 44 autosomes and 2 sex chromosomes
  • haploid genome contains ~3x10^9 base pairs (1000x size of E. coli)
  • chromosomes coated in structural and regulatory proteins- chromatin
  • human genome has been sequenced
24
Q

elements required for stability and propagation of chromosomes

A
  • replication origins-initiation of DNA replication (~100,000)
  • centromeres-segregation of duplicated chromosomes at mitosis and meiosis
  • telomeres-stability and replication of the chromosome ends
25
Q

information content on chromosomes

A
  • surprisingly little of the sequence codes for anything. that which does code is broken down into functional unit called gene
  • other substance includes: Alu sequences, transposons, and pseudogenes
26
Q

split genes

A
  • genes code for RNAs- rRNA, tRNA, mRNA
  • other classes include snRNA and snoRNA
  • recently discovered micro-RNA
  • in mRNA, most of the precursor is removed by splicing that joins exons and removes introns
  • exon/intron system plays critical role in evolution of genes
27
Q

chromosome packaging

A
  • mediated by histones (pos charge)- highly conserved
  • abundant, positively charged DNA binding proteins
  • 5 kinds- H1, H2A (H2AZ) H2B, H3, H4
  • mitosis has high level of packaging called chromosome condensation
28
Q

nucleosome

A
  • histone octamer
  • formed from 2 copies each of h@a, H2B, H3. H4
  • 146 bp’s of DNA is wrapped around the barrel-shaped octomer
  • including linker DNA, 200 bps of DNA is packaged per nucleosome, leading to a 1/3 linear reduction of length
29
Q

30 nm chromatin fiber

A
  • one H1 per nucleosome coils and binds the linker DNA and stabilizes nucleosomes in 30 nm fiber
  • disrupted by regulatory proteins to allow for transcription of genes
30
Q

chromosome looping

A
  • additional levels of packaging not well understood
  • involves organization of chromosomes into loops
  • at mitosis the chromosomes condense, achieving highest level of packaging
31
Q

epigenetics and histone tails

A
  • histone N terminal tails protrude from nucleosome
  • lysine residues in the tails can be modified by methylation and acetylation
  • patterns of acetylation are regulated and are metastable in that they can persist through many cell divisions
  • acetylation locally alters chromatin structure and protein composition affecting accessibility to, or the recruiting of regulatory proteins
32
Q

chromosome organization

A

-fractal globules

33
Q

nuclear architecture

A
  • nuclear matrix is an underlying fibrous network that facilitates further organization
  • chromosomes are attached to the nuclear matrix via Matrix associated Regions (MARs)
  • euchromatin is organized into a small number of foci
  • there are open channels to the nuclearpores
34
Q

nucleus and diease

A
  • lupus-AI disease produce antibodies to nuclear antigens
  • acute promyelocytic leukemia-reciprocal translocation that fuses the retinoic acid receptor to the protein PML creating altered activites
  • spinal muscular atrophy-childhood neuromuscular disease. inherited mutation in SMN1-RNA processing factor

MCP Unit 2 (10 decks)

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