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
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
3
Q
chromatin
A
complex of protein and DNA
4
Q
euchromatin
A
-stains more lightly and is less condensed DNA that is being actively expressed
5
Q
heterochromatin
A
-stains more darkly and is more condensed DNA that is not in the process of being expressed
6
Q
nucleolus 1
A
non membrane bound subcompartment of the nucleus where ribosome biogenesis occurs
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
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
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
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
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
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
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
14
Q
detailed mechanism of transport-import
A
- cargo binds to importin
- importin-cargo complex diffuses through pore
- Ran-GTP binds to complex, causing a release of cargo
- 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
15
Q
detailed mechanism of transport-export
A
- cargo and Ran GTP bind to exportin
- diffuse through NPC
- Ran-GTP hydrolysis by GAP releases cargo and exportin.
- Exporting and Ran-GDP cycled back across
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
