Chapter 9 Flashcards
1
Q
Why is having a nucleus advantageous for eukaryotic cells? (2)
A
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
2
Q
Nuclei size mirrors
A
amount of DNA inside
3
Q
Number and size of nucleus of most cells
A
one nucleus and spherical/oblong
4
Q
What are the three exceptions of the size and number of nucleus?
A
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
5
Q
Stages of immature erythroblast differentiating into mature erythroblast
A
- erythroblast
- polychromatophilic erythroblast: stage 1
- polychromatophilic erythroblast: stage 2
- mature erythroblast
6
Q
Decrease in euchromatin is due to large number of genes that are what?
A
that are permanently silenced during the maturation process
7
Q
Structure of the chromosome during interphase
A
not stretched out throughout the nucleus and not intertwined
8
Q
Chromosome territories/domain is maintained due to
A
telomere anchors to the nuclear envelope
9
Q
Adjacent to chromatin free regions what domains are there?
A
interchromosomal domains
10
Q
Interchromosomal domains are often located near
A
NPCs
11
Q
Highly transcripted genes located at what region?
A
periphery of chromatin domains
12
Q
Interchromosomal domains contain what two things?
A
poly A and RNAs undergoing processing
13
Q
What is the most prominent subcompartment?
A
nucleolus
14
Q
Other than nucleus, what are other prominent subcompartments? (5)
A
speckles, Cajal bodies, Gemini bodies, interchromatin granules, and PML bodies
15
Q
Nucleolus contains materials for what 2 main things?
A
a. ribosomal subunit assembly
b. processing the rRNA molecules
16
Q
Materials for ribosomal subunit assembly requires what 3?
A
a. rRNA genes from multiple chromosomes
b. ribosomal proteins
c. enzymes for tcr rRNA genes
17
Q
How many rRNA genes from multiple chromosomes are there in humans?
A
10
18
Q
When does nucleolus disappear?
A
when rRNA transcription is prevented
19
Q
What are the 2 functions of the nucleolus?
A
a. transcription of tRNA genes
b. tRNA processing
20
Q
Function of speckles
A
store RNA splicing factors
21
Q
What happens at interchromatin granules?
A
diffused areas where pre-mRNA splicing occurs
22
Q
What happens at cajal bodies and gemini bodies?
A
snRNAs and snoRNAs are posttranscriptionally modified and assembled into snRNPS and snoRNPs
23
Q
Nuclear matrix is composed of
A
intermediate filaments, action, and other proteins
24
Q
DNA replication seems to be orderly through what phase?
A
S phase
25
Space between outer and inner nuclear membranes
nuclear envelope lumen
26
Why did cytoplasm of the large cell lose ALL of its genome?
cells genetic material became sequestered into specialized compartments
27
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
28
What is a nuclear lamina?
meshwork of intermediate filaments
29
Where does nuclear lamina lie?
inside the inner nuclear membrane
30
Lamin proteins are related to what proteins?
Keratin cytoskeletal proteins
31
Lamin proteins and keratin cytoskeletal proteins are both what?
intermediate filaments
32
Lamin contains IMPs called what?
lamina-associated proteins (LAPs)
33
Lamina is anchored to what three things?
IMPs, NPCs, and membrane lipids
34
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
35
Particles 9nm in diameter or smaller move through NPC via what transport?
passive diffusion
36
Particles larger than 9nm are moved through NPC via what transport?
actively and selective transport
37
NPCs have what fold symmetry?
8-fold rotational symmetry?
38
__________ or _______ is the collection of fibrils
nuclear basket; fish trap
39
A nuclear basket or fish trap is the collection of fibrils that extend to what 2 places?
nucleus and cytoplasm
40
Annulate lamellae
cytoplasmically located stacks of double membranes containing NPCs
41
What have short repeats with Phe-Gly pairs?
Nucleoporins
42
Repeats with Phe-Gly pairs are referred to as
FG repeats
43
Nucleoporins is a sites where what binds to what during transport?
cargo molecules bind to NPC
44
FG repeats-containing nucleoporins are found lining what three?
central channel of NPC, compartments of the cytoplasmic filaments, and nuclear basket
45
Locations of nucleoporins within NPCs can be studied via
immunoelectron microscopy
46
Proteins destined for the nucleus either have ______ or ______?
targeting signals or bind to to a protein that contains one
47
What action at NPC does not require energy?
docking of cargo proteins
48
What action at NPC does require energy?
transport of proteins across NPC
49
Most common NLS contains several what?
basic amino acid residues
50
NLS can be ______ aa residues or it can be ________ aa residues brought together by folding
continuous; separated
51
NLS receptors are what kind of proteins?
soluble cytoplasmic proteins
52
NLS receptor binds to what two?
cargo protein and nuclear pore
53
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
54
Nuclear import receptors are part of large family called
karyopherins
55
Importin alpha binds to
NLS
56
Importin beta interact with
nucleoporins
57
NES
nuclear export signal
58
NES is comprised of
leucine residues
59
What signals are needed for proteins to go back and forth between nucleus and cytoplasm
NLS and NES
60
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
61
Nuclear export receptor
exportin
62
Exportin is a member of what protein family?
karyopherin protein family
63
Ran function
hydrolyzes GTP to GDP at a very slow rate
64
Ran-GAP function
stimulates Ran to hydrolyze its GTP to GDP
65
Where is Ran-GAP found?
in the cytoplasm
66
Ran-GEF function
helps RAn-GDP get rid of its GDP and bind to GTP
67
Where is Ran-GEF found?
in the nucleus
68
Where is Ran-GDP and Ran-GTP higher?
Ran-GDP higher in the cytoplasm and Ran-GTP higher in the nucleus
69
Steps of import of proteins from the cytoplasm into the nucleus
1. Importins bind to NLS and cargo proteins
2. It goes into nucleus
3. It binds to Ran-GTP
4. conformational change in importing
5. cargo protein is released and NLS detached
70
Steps of the export of proteins from nucleus to cytoplasm
1. Exportin binds NES (cargo) and Ran-GTP forming a trimeric complex
2. trimeric complex goes to cytoplasm
3. it encounters Ran-GAP
4. Ran hydrolyzes GTP to GDP
5. Cargo released
6. Ran GDP is imported back into nucleus where Ran-GEF helps reload it with GTP
71
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
72
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
73
Binding of NF-kB and I-kB hides what?
NLSs of both NF-kB and I-kB
74
What does the binding of NLS on NF-KB with an importin result in?
enters the nucleus and regulates transcription of target genes
75
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
76
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
77
Most RNAs do not have export signals so they bind to?
bind to NES-containing proteins in order to exit
78
What is the most abundant proteins and RNAs in the cell?
ribosomal components
79
The nuclear import of ribosomal proteins involve what two proteins?
karyopherins and Ran-GTPase
80
Export of ribosomal subunits require what two proteins?
exportin and Ran-GTPase
81
Exportin-t binds to what two?
tRNA molecules and Ran-GTP
82
The binding of exportin-t with tRNA and Ran-GTP results in
passing NPC into the cytoplasm
83
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
84
Aminoaccylation of tRNA occurs in
cytoplasm and nucleus
85
Aminoacyl tRNA synthetase exports what tRNA more efficiently?
charged tRNA
86
hnRNPs
heterogeneous nuclear ribonucleoprotein particles
87
What are hnRNPs?
complexes of pre-mRNA associated with proteins
88
What two proteins are not considered hnRNP proteins?
cap-binding proteins and poly-A tail binding proteins
89
When are hnRNP proteins removed?
before or as or after the hnRNP moves out of nucleus
90
What is an example virus that export their entire genome of RNA out of the nucleus without intron removal?
HIV
91
What protein does HIV produce?
Rev
92
RRE
rev response element
93
Where is RRE?
on unspliced HIV-1 mRNA
94
Rev contains an NES so it can
export along with mRNA
95
What example mRNA are constitutive?
ribosomal protein mRNA and cytoskeletal fiber protein mRNA
96
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
97
Steps of transcription
1. capping - addition of 5' 7-methylGuanosine cap
2. RNA Splicing occurs
3. 3' end generated by endonuclease
4. polyadenylation (poly-A tail addition by poly A polymerase)
98
What is still at work as transcription is continuing?
RNA poly II
99
After poly-A tail is added, what is bound to pre-mRNA?
hnRNP proteins
100
hnRNP and mRNA are diffused through where to an NPC?
interchromosomal spaces
101
Which export is more complex?
mRNA export more complex than protein export
102
EJC
exon junctional complex
103
After splicing, what protein complex remains bound near the splice junction?
EJC
104
What is the one of the EJC protein used in the RNA export process?
Aly
105
What is Aly?
mRNA export factor
106
Function of Aly
interacts with a component of the spliceosome and with TAP
107
What is TAP?
receptor which binds to FG repeats in some nucleoporins
108
mRNP
messenger ribonucleoprotein particle
109
After Aly binds to spliceosome and TAP, mRNA is part of?
mRNP
110
What is mRNP?
a complex of mature mRNA and mRNA-binding protein
111
What is an exosome?
complex of ribonuclease
112
Where is exosome located?
near transcription sites
113
Function of exosome
degrades mRNAs that are processed incorrectly
114
Removal of mRNP proteins involve what enzyme?
Dbp5
115
What is Dbp5?
mRNA export protein
116
Dbp5 is a member what proteins?
DEAD-box proteins
117
Function of Dbp5
hydrolyze ATP to ADP and function in mRNA metabolism
118
What is U snRNA?
RNA of a snRNP
119
U snRNA made by
RNA pol II
120
What does U snRNA have and not have?
have 5' 7-meGuanosine cap added but no 3' poly A tail
121
U snRNA cap is a signal for
nuclear export
122
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
123
After methylation and U snRNP complex formation, U snRNP is imported into where via what?
nucleus via snurportin adaptor and importin B
124
microRNAs are transcribed by RNA poly II in?
nucleus
125
Where are miRNAs usually found?
in introns of protein-coding genes or in intergenic regions
126
miRNAs are important in
gene regulation for development, differentiation, and apoptosis
127
miRNAs bind to what in the cytoplasm?
mRNA
128
What does miRNA binding to mRNA cause?
blocking of translation and promotes mRNA degradation
129
Where is precursor miRNA processed in?
nucleus
130
What enzyme processes miRNA?
Drosha
131
What enzymes process miRNA in the cytoplasm to yield the functional miR?
Dicer
