Chapter 9 Flashcards
Why is having a nucleus advantageous for eukaryotic cells? (2)
a. protects more loosely-compacted DNA in interphase from breakage by shear forces generated by the cytoskeleton
b. allows much more sophiscated regulation of gene expression than is possible in prokaryotic cells
Nuclei size mirrors
amount of DNA inside
Number and size of nucleus of most cells
one nucleus and spherical/oblong
What are the three exceptions of the size and number of nucleus?
a. mature, differentiated cells with no nucleus
b. multi-nucleated cells due to many karyokinetic events without cytokinesis
c. mutli-lobed nucleus in cells like mammalian neutrophils, eosinophils, and basophils
Stages of immature erythroblast differentiating into mature erythroblast
- erythroblast
- polychromatophilic erythroblast: stage 1
- polychromatophilic erythroblast: stage 2
- mature erythroblast
Decrease in euchromatin is due to large number of genes that are what?
that are permanently silenced during the maturation process
Structure of the chromosome during interphase
not stretched out throughout the nucleus and not intertwined
Chromosome territories/domain is maintained due to
telomere anchors to the nuclear envelope
Adjacent to chromatin free regions what domains are there?
interchromosomal domains
Interchromosomal domains are often located near
NPCs
Highly transcripted genes located at what region?
periphery of chromatin domains
Interchromosomal domains contain what two things?
poly A and RNAs undergoing processing
What is the most prominent subcompartment?
nucleolus
Other than nucleus, what are other prominent subcompartments? (5)
speckles, Cajal bodies, Gemini bodies, interchromatin granules, and PML bodies
Nucleolus contains materials for what 2 main things?
a. ribosomal subunit assembly
b. processing the rRNA molecules
Materials for ribosomal subunit assembly requires what 3?
a. rRNA genes from multiple chromosomes
b. ribosomal proteins
c. enzymes for tcr rRNA genes
How many rRNA genes from multiple chromosomes are there in humans?
10
When does nucleolus disappear?
when rRNA transcription is prevented
What are the 2 functions of the nucleolus?
a. transcription of tRNA genes
b. tRNA processing
Function of speckles
store RNA splicing factors
What happens at interchromatin granules?
diffused areas where pre-mRNA splicing occurs
What happens at cajal bodies and gemini bodies?
snRNAs and snoRNAs are posttranscriptionally modified and assembled into snRNPS and snoRNPs
Nuclear matrix is composed of
intermediate filaments, action, and other proteins
DNA replication seems to be orderly through what phase?
S phase
Space between outer and inner nuclear membranes
nuclear envelope lumen
Why did cytoplasm of the large cell lose ALL of its genome?
cells genetic material became sequestered into specialized compartments
How did the circular chromosome of the small cell become linear and acquire telomeres?
One circular chromosome fragmented into linear pieces and telomeres acquired to stabilize the new chromosome ends
What is a nuclear lamina?
meshwork of intermediate filaments
Where does nuclear lamina lie?
inside the inner nuclear membrane
Lamin proteins are related to what proteins?
Keratin cytoskeletal proteins
Lamin proteins and keratin cytoskeletal proteins are both what?
intermediate filaments
Lamin contains IMPs called what?
lamina-associated proteins (LAPs)
Lamina is anchored to what three things?
IMPs, NPCs, and membrane lipids
What are 7 molecules that leave the nucleus through NPCs?
a. protein shuttling
b. ATP
c. protein
d. RNA
e. virus capside
f. ions
g. glucose
Particles 9nm in diameter or smaller move through NPC via what transport?
passive diffusion
Particles larger than 9nm are moved through NPC via what transport?
actively and selective transport
NPCs have what fold symmetry?
8-fold rotational symmetry?
__________ or _______ is the collection of fibrils
nuclear basket; fish trap
A nuclear basket or fish trap is the collection of fibrils that extend to what 2 places?
nucleus and cytoplasm
Annulate lamellae
cytoplasmically located stacks of double membranes containing NPCs
What have short repeats with Phe-Gly pairs?
Nucleoporins
Repeats with Phe-Gly pairs are referred to as
FG repeats
Nucleoporins is a sites where what binds to what during transport?
cargo molecules bind to NPC
FG repeats-containing nucleoporins are found lining what three?
central channel of NPC, compartments of the cytoplasmic filaments, and nuclear basket
Locations of nucleoporins within NPCs can be studied via
immunoelectron microscopy
Proteins destined for the nucleus either have ______ or ______?
targeting signals or bind to to a protein that contains one
What action at NPC does not require energy?
docking of cargo proteins
What action at NPC does require energy?
transport of proteins across NPC
Most common NLS contains several what?
basic amino acid residues
NLS can be ______ aa residues or it can be ________ aa residues brought together by folding
continuous; separated
NLS receptors are what kind of proteins?
soluble cytoplasmic proteins
NLS receptor binds to what two?
cargo protein and nuclear pore
After NLS binds to its receptor, what happens?
accompanies cargo through NPC, releases cargo in the nucleus, and returns cytoplasm for another round of transport
Nuclear import receptors are part of large family called
karyopherins
Importin alpha binds to
NLS
Importin beta interact with
nucleoporins
NES
nuclear export signal
NES is comprised of
leucine residues
What signals are needed for proteins to go back and forth between nucleus and cytoplasm
NLS and NES
What proteins have NES? Why?
some proteins that does not belong in the nucleus. Having NES helps them get out of nucleus as it reforms during telophase
Nuclear export receptor
exportin
Exportin is a member of what protein family?
karyopherin protein family
Ran function
hydrolyzes GTP to GDP at a very slow rate
Ran-GAP function
stimulates Ran to hydrolyze its GTP to GDP
Where is Ran-GAP found?
in the cytoplasm
Ran-GEF function
helps RAn-GDP get rid of its GDP and bind to GTP
Where is Ran-GEF found?
in the nucleus
Where is Ran-GDP and Ran-GTP higher?
Ran-GDP higher in the cytoplasm and Ran-GTP higher in the nucleus
Steps of import of proteins from the cytoplasm into the nucleus
- Importins bind to NLS and cargo proteins
- It goes into nucleus
- It binds to Ran-GTP
- conformational change in importing
- cargo protein is released and NLS detached
Steps of the export of proteins from nucleus to cytoplasm
- Exportin binds NES (cargo) and Ran-GTP forming a trimeric complex
- trimeric complex goes to cytoplasm
- it encounters Ran-GAP
- Ran hydrolyzes GTP to GDP
- Cargo released
- Ran GDP is imported back into nucleus where Ran-GEF helps reload it with GTP
To method of transport of karyopherins with FG repeat binding sites
a. FG repeat interacts weakly in a meshwork of nucleoporins (facilitated transport)
b. transporters with FG binding sites selectively partition through the NPC
When would selective interactions of transporters with FG-rich regions of the central pore be favored?
Rapid kinetics through the NPC and transport of at least 10 substrate molecules with their receptors at the same time
Binding of NF-kB and I-kB hides what?
NLSs of both NF-kB and I-kB
What does the binding of NLS on NF-KB with an importin result in?
enters the nucleus and regulates transcription of target genes
How is the transcription activated by NF-kB terminated?
newly-made I-kB enters the nucleus, binds to NF-kB, and together they exit the nucleus using NES of I-kB
How is mRNA exported to the cytosol?
U-snRNA in the nucleus binds to the proteins in cytosol at cytosol, becoming a spliceosome and together they move into the nucleus helping in RNA splicing
Most RNAs do not have export signals so they bind to?
bind to NES-containing proteins in order to exit
What is the most abundant proteins and RNAs in the cell?
ribosomal components
The nuclear import of ribosomal proteins involve what two proteins?
karyopherins and Ran-GTPase
Export of ribosomal subunits require what two proteins?
exportin and Ran-GTPase
Exportin-t binds to what two?
tRNA molecules and Ran-GTP
The binding of exportin-t with tRNA and Ran-GTP results in
passing NPC into the cytoplasm
When that trimeric complex reach cytoplasm, what happens?
Ran-GAP stimulates hydrolysis of GTP to GDP, complex dissociates, and tRNA is ready to be aminoacylated
Aminoaccylation of tRNA occurs in
cytoplasm and nucleus
Aminoacyl tRNA synthetase exports what tRNA more efficiently?
charged tRNA
hnRNPs
heterogeneous nuclear ribonucleoprotein particles
What are hnRNPs?
complexes of pre-mRNA associated with proteins
What two proteins are not considered hnRNP proteins?
cap-binding proteins and poly-A tail binding proteins
When are hnRNP proteins removed?
before or as or after the hnRNP moves out of nucleus
What is an example virus that export their entire genome of RNA out of the nucleus without intron removal?
HIV
What protein does HIV produce?
Rev
RRE
rev response element
Where is RRE?
on unspliced HIV-1 mRNA
Rev contains an NES so it can
export along with mRNA
What example mRNA are constitutive?
ribosomal protein mRNA and cytoskeletal fiber protein mRNA
What example mRNA is regulated?
in a heat shock response, most poly A + RNAs are not exported instead heat shock genes are up-regulated, these mRNAs are preferentially exported
Steps of transcription
- capping - addition of 5’ 7-methylGuanosine cap
- RNA Splicing occurs
- 3’ end generated by endonuclease
- polyadenylation (poly-A tail addition by poly A polymerase)
What is still at work as transcription is continuing?
RNA poly II
After poly-A tail is added, what is bound to pre-mRNA?
hnRNP proteins
hnRNP and mRNA are diffused through where to an NPC?
interchromosomal spaces
Which export is more complex?
mRNA export more complex than protein export
EJC
exon junctional complex
After splicing, what protein complex remains bound near the splice junction?
EJC
What is the one of the EJC protein used in the RNA export process?
Aly
What is Aly?
mRNA export factor
Function of Aly
interacts with a component of the spliceosome and with TAP
What is TAP?
receptor which binds to FG repeats in some nucleoporins
mRNP
messenger ribonucleoprotein particle
After Aly binds to spliceosome and TAP, mRNA is part of?
mRNP
What is mRNP?
a complex of mature mRNA and mRNA-binding protein
What is an exosome?
complex of ribonuclease
Where is exosome located?
near transcription sites
Function of exosome
degrades mRNAs that are processed incorrectly
Removal of mRNP proteins involve what enzyme?
Dbp5
What is Dbp5?
mRNA export protein
Dbp5 is a member what proteins?
DEAD-box proteins
Function of Dbp5
hydrolyze ATP to ADP and function in mRNA metabolism
What is U snRNA?
RNA of a snRNP
U snRNA made by
RNA pol II
What does U snRNA have and not have?
have 5’ 7-meGuanosine cap added but no 3’ poly A tail
U snRNA cap is a signal for
nuclear export
Out in the cytoplasm, what happens to the U snRNA cap?
7-methyl-Gcap is methylated to trimethyl-Gcap and associated with proteins to be assembled into a U snRNP complex
After methylation and U snRNP complex formation, U snRNP is imported into where via what?
nucleus via snurportin adaptor and importin B
microRNAs are transcribed by RNA poly II in?
nucleus
Where are miRNAs usually found?
in introns of protein-coding genes or in intergenic regions
miRNAs are important in
gene regulation for development, differentiation, and apoptosis
miRNAs bind to what in the cytoplasm?
mRNA
What does miRNA binding to mRNA cause?
blocking of translation and promotes mRNA degradation
Where is precursor miRNA processed in?
nucleus
What enzyme processes miRNA?
Drosha
What enzymes process miRNA in the cytoplasm to yield the functional miR?
Dicer
