Ch.11 - The Nucleus Flashcards
What contains the genome?
the nucleus
What is the main distinguishing feature between eukaryotic and prokaryotic cells?
the nucleus
What plays a key role in eukaryotic gene expression?
the separation of the genome from the site of mRNA translation
what does the nuclear envelope divide?
divides nuclear contents from cytoplasm
What does the nuclear envelope do?
controls protein and RNA traffic using nuclear pore complexes
What is critical in regulating gene expression?
the nuclear envelope
what are the 3 parts of the nuclear envelope?
1) two nuclear membranes
2) underlying nuclear lamina
3) nuclear pore complexes
What is the outer membrane of the nuclear envelope continuous with?
the ER
The space between inner and outer membranes is called what?
perinuclear space
The perinuclear space is directly connected with the ________
lumen of the ER
What does the inner membrane of the nuclear envelope have?
integral proteins (including ones that bind the nuclear lamina)
Nuclear membranes are phospholipid bilayers permeable only to small ____ molecules.
nonpolar
What are the only channels for small polar molecules, ions, and macromolecules?
nuclear pore complexes
What is nuclear lamina?
fibrous mesh
What is the function of nuclear lamina?
gives structural support
what are lamins?
class of intermediate filament proteins
What associates to form higher order structures?
lamins
Two lamins interact to for what?
a dimer
What do lamins bind to?
inner membrane proteins
What are 2 examples of lamins?
1) emerin
2) lamin B receptor (LBR)
How are lamins connected to the cytoskeleton?
LINC protein complexes (linker of nucleoskeleton and cytoskeleton)
What can lamins also bind to (besides the cytoskeleton)?
chromatin
What is an example of mutations in lamin genes?
progeria
What are nuclear pore complexes (NPC)?
1) large
2) about 30 proteins (nucleoporins)
What things cam exit the NPCs?
RNA, ribosomes, etc.
Entering the NPCs requires what?
proteins needed for nuclear functions
What are the 2 mechanisms for molecular traffic through the nuclear pore complexes?
1) passive diffusion
2) selective transport
Which mechanism for molecular traffic through the nuclear pore complexes needs energy?
selective transport
How many subunits (organized around a large central channel) do NPCs have?
8
Protein filaments extend to form the ____ (in the nuclear envelope and traffic between the nucleus and the cytoplasm).
rings
Where does the basketlike structure form?
on the nuclear side
Proteins that must enter the nucleus have ____ _____ ______
nuclear localization signals
What is recognized by nuclear transport receptors?
proteins that have nuclear localization signals
Nuclear localization signals were identified what year?
1984
How were nuclear localization signals identified?
using viral replication protein SV40 T antigen
How was the amino acid sequence responsible for nuclear localization determined?
using T antigen mutants (same sequence attached to other proteins results in transport to the nucleus)
What is a T antigen nuclear localization signal?
a single stretch of amino acids
what do importins do?
carry proteins through NPC
What works in conjunction with Ran?
importins
What is Ran?
a GTP-binding protein
What does Ran do?
controls directionality
Importins bind to the ___ of a protein
NLS (nuclear localization signals)
What happens after the receptor and protein are bound (importins and NLS)?
complex is transported into the nucleus
What does the Ran GAP stimulate?
the Ran-GTPase to cleave the GTP to GDP in the cytoplasm, releasing the importin
what signals export proteins from the nucleus?
nuclear export signals (NES)
exportins do what?
direct protein transport to the cytoplasm
many importins and exportins are members of a family of nuclear transport receptors known as what?
karyopherins
what import karyopherin has proteins with a basic amino acid nuclear localization signal?
importin
what import karyopherin has snRNPs (U1, U2, U4, U5)?
snurportin
what import karyopherin has mRNA binding proteins and ribosomal proteins?
transportin
what import karyopherin has histone H1 and ribosomal proteins
Importin7
what export karyopherin has proteins with a leucine-rich nuclear export signal, snurportin, snRNAs, and ribosomal subunits?
Crm1
what export karyopherin has tRNAs?
exportin-t
what export karyopherin has miRNAs?
Exportin 5
Exportins form stable complexes with what in association with the Ran-GTP in the nucleus?
cargo proteins
In the cytoplasm, for nuclear export, what leads to dissociation of the cargo protein?
GTP hydrolysis and release of Ran-GDP
RNAs are transported to the cytoplasm as what?
ribonucleoprotein complexes (RNPs)
What do karyopherin exportins NOT transport?
mRNA
What do karyopherin exports transport?
tRNAs, rRNAs, miRNAs
mRNA transport does not use karyopherins or ______
Ran
What does mRNA use to move through the nuclear pore?
distinct transporter complex
Where is the helicase located, nucleus or cytoplasm side?
cytoplasm
Using the distinct transporter complex for mRNA transport ensures what?
unidirectional transport
Many noncoding RNAs (snRNAs and snoRNAs) function where?
within the nucleus
snRNAs are initially exported from the nucleus by what?
exportin (Crm1)
snRNAs associate with proteins in the cytoplasm to form what?
snRNPs
What are snRNPs recognized by?
an importin
Transcription factor NF-kB is complexed with what in the cytoplasm?
IkB
What happens if IkB is phosphorylated and degraded by ubiquitin-mediated proteolysis?
NF-kB can enter the nucleus and activate transcription of its target genes
Other transcription factors are regulated directly by what?
phosphorylation
During mitosis, what happens to chromatin?
becomes highly condensed to form the compact metaphase chormosomes
During interphase, what happens to chromatin?
most decondense and distributes throughout the nucleus
During interphase, transcriptional activity of a gene is correlated with what?
its position
Where does DNA replication and transcription take place?
in clustered regions within the nucleus
Chromosome territory was first suggested when?
1885
What was confirmed in 1984 by studies of polytene chromosomes in Drosophila salivary glands?
chromosome territory
What is chromosome territory?
each chromosome occupies a discrete region of the nucleus
Situ hybridization with fluorescent probes specific for repeated sequences on individual chromosomes has been used to visualize what?
the location of chromosomes within a nucleus
In living cells, what do chromosome conformation capture (3C) techniques reveal?
sites of interaction between chromosomal regions
How were the interactions between chromosomal regions identified?
by cross-linking interacting DNA sequences then were amplified and identified by high-throughput sequencing
Where is euchromatin located in the cell?
throughout the nucleus
Which is transcribed, euchromatin or heterochromatin?
euchromatin
Why is euchromatin transcribed and not heterochromatin?
euchromatin is decondensed while heterochromatin is highly condensed
What is heterochromatin often associated with?
the nuclear envelope or periphery of the nucleolus
Some human chromosomes are rich in what while containing relatively few genes?
transcribed genes
What does fluorescent in situ hybridization show?
gene-rich chromosomes located in the center of the nucleus
Where are gene-poor chromosomes located?
at the periphery
How are genomes divided?
into looped domains
What does the interaction of genomes look like?
regions within a domain interact frequently with one another + rarely with regions in other domains
Domains associated with the nuclear lamina are called what?
lamina-associated domains (LADs)
Genes within LADs are generally what?
transcriptionally repressed
What is an example of a gene within LADs?
heterochromatin
where are LADs found?
in the inner membrane of the nucleus
What is the term for the nucleolus being surrounded by heterochromatin?
nucleolus-associated domains (NADs)
DNA sequences found in NADs substantially overlap with what?
those in LADs
Where does DNA replication take place?
in large complexes (replication factories)
What can be seen by labeling cells with bromodeoxyuridine (an analog of thymidine), then staining with fluorescent antibodies?
replication factories
Where does transcription occur?
clustered sites (transcription factories) that contain newly synthesized RNA
Coregulated genes may be transcribed in ______ factory.
the same
What are nuclear bodies?
organelles within the nucleus that concentrate proteins and RNAs for specific processes
Nuclear bodies are not enclosed by what?
membranes
What are nuclear bodies maintained by?
dynamic structures are maintained by protein-protein and protein-RNA interactions
What are the 2 functions of the nucleolus?
1) rRNA transcription and processing
2) ribosome assembly
What is the function of cajal body?
snRNP assembly
What is the function of speckle?
storage of pre-mRNA splicing factors
What is the function of polycomb body?
gene silencing
What makes the rRNAs?
RNA polymerase I
Where does transcription of the 5S rRNA occur?
outside the nucleolus
What is the transcription of 5S rRNA catalyzed by?
RNA polymerase III
Where are 5.8S, 18S, and 28S rRNAs transcribed?
in the nucleolus
Following cell division, nucleoli associate with what?
nucleolar organizing regions
What do nucleolar organizing regions contain?
5.8S, 18S, and 28S rRNA genes
Transcription of 45S pre-rRNA leads to what?
the fusion of small prenucleolar bodies
In most cells, the nucleoli initially separate then do what?
fuse to form a single nucleolus
What are the 3 regions of nucleoli?
1) fibrillar center
2) dense fibrillar component
3) granular component
what does the fibrillar center do?
stores genes
In what region of the nucleoli does transcription take place
dense fibrillar component
What do the 3 regions of the nucleoli represent?
sites of progressive stages of rRNA transcription, processing, and ribosome assembly
In higher eukaryotes, the primary transcript of rRNA genes is what?
the 45S pre-rRNA
How is the pre-rRNA processed in higher eukaryotes?
via a series of cleavages
Processing of pre-rRNA also includes what?
addition of methyl groups to bases and ribose residues, and conversion of uridine to pseudouridine
Nucleoli have over 300 proteins and 200 _______________ that function in pre-rRNA processing.
small nucleolar RNAs (snoRNAs)
snoRNAs are complexed with proteins, forming ______.
snoRNPs
What are snoRNPs?
modify rRNA (guide RNAs to direct specific base modifications of pre-rRNA)
Two families of snoRNAs associate with different proteins , which does what?
catalyze ribose methylation or pseudouridine formation
snoRNAs have sequences complementary to what rRNAs, which include the sites of base modification?
18S or 28S
What does the formation of ribosomes require?
assembly of pre-rRNA with ribosomal proteins and 5S rRNA
Ribosomal proteins are produced where?
cytoplasm
Where are ribosomal proteins imported to after produced?
the nucleolus
What 2 things assemble to form pre-ribosomal particles?
additional ribosomal proteins and the 5S rRNA
Pre-ribosomal particles are exported to where?
cytoplasm
What do pre-ribosomal particles yield?
40S and 60S ribosomal units
How do polycomb proteins repress transcription?
a methyl group is added to lysine 27 on the histone H3
What shows the proteins are concentrated in domains called polycomb bodies?
immunofluorescence
What are snRNAs modified by?
ribose methylation and pseudouridylation
What is the enzyme for RNA methylation?
fibrillarin
What enzyme for RNA methylation is concentrated in cajal bodies?
fibrillarin
Cajal bodies have small cajal _________
body-specific RNAs (scaRNAs)
What do scaRNAs do?
serve as guides to direct methylation and pseudouridylation of snRNAs
What do cajal bodies appear to play a role in?
assembly of telomerase, which replicates the ends of chromosomal DNA
What is another thing that cajal bodies promote?
assembly of the RNA-protein telomerase complex and facilitate its delivery to telomeres
Following assembly and maturation in cajal bodies, _____ are transferred to speckles.
snRNPs
What are speckles recruited to do?
to actively transcribe genes where pre-mRNA processing occurs
