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Cell Biology > Ch.11 - The Nucleus > Flashcards

Ch.11 - The Nucleus Flashcards

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1
Q

What contains the genome?

A

the nucleus

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2
Q

What is the main distinguishing feature between eukaryotic and prokaryotic cells?

A

the nucleus

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3
Q

What plays a key role in eukaryotic gene expression?

A

the separation of the genome from the site of mRNA translation

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4
Q

what does the nuclear envelope divide?

A

divides nuclear contents from cytoplasm

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5
Q

What does the nuclear envelope do?

A

controls protein and RNA traffic using nuclear pore complexes

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6
Q

What is critical in regulating gene expression?

A

the nuclear envelope

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7
Q

what are the 3 parts of the nuclear envelope?

A

1) two nuclear membranes
2) underlying nuclear lamina
3) nuclear pore complexes

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8
Q

What is the outer membrane of the nuclear envelope continuous with?

A

the ER

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9
Q

The space between inner and outer membranes is called what?

A

perinuclear space

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10
Q

The perinuclear space is directly connected with the ________

A

lumen of the ER

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11
Q

What does the inner membrane of the nuclear envelope have?

A

integral proteins (including ones that bind the nuclear lamina)

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12
Q

Nuclear membranes are phospholipid bilayers permeable only to small ____ molecules.

A

nonpolar

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13
Q

What are the only channels for small polar molecules, ions, and macromolecules?

A

nuclear pore complexes

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14
Q

What is nuclear lamina?

A

fibrous mesh

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15
Q

What is the function of nuclear lamina?

A

gives structural support

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16
Q

what are lamins?

A

class of intermediate filament proteins

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17
Q

What associates to form higher order structures?

A

lamins

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18
Q

Two lamins interact to for what?

A

a dimer

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19
Q

What do lamins bind to?

A

inner membrane proteins

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20
Q

What are 2 examples of lamins?

A

1) emerin
2) lamin B receptor (LBR)

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21
Q

How are lamins connected to the cytoskeleton?

A

LINC protein complexes (linker of nucleoskeleton and cytoskeleton)

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22
Q

What can lamins also bind to (besides the cytoskeleton)?

A

chromatin

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23
Q

What is an example of mutations in lamin genes?

A

progeria

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24
Q

What are nuclear pore complexes (NPC)?

A

1) large
2) about 30 proteins (nucleoporins)

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25
Q

What things cam exit the NPCs?

A

RNA, ribosomes, etc.

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26
Q

Entering the NPCs requires what?

A

proteins needed for nuclear functions

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27
Q

What are the 2 mechanisms for molecular traffic through the nuclear pore complexes?

A

1) passive diffusion
2) selective transport

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28
Q

Which mechanism for molecular traffic through the nuclear pore complexes needs energy?

A

selective transport

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29
Q

How many subunits (organized around a large central channel) do NPCs have?

A

8

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30
Q

Protein filaments extend to form the ____ (in the nuclear envelope and traffic between the nucleus and the cytoplasm).

A

rings

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31
Q

Where does the basketlike structure form?

A

on the nuclear side

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32
Q

Proteins that must enter the nucleus have ____ _____ ______

A

nuclear localization signals

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33
Q

What is recognized by nuclear transport receptors?

A

proteins that have nuclear localization signals

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34
Q

Nuclear localization signals were identified what year?

A

1984

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35
Q

How were nuclear localization signals identified?

A

using viral replication protein SV40 T antigen

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36
Q

How was the amino acid sequence responsible for nuclear localization determined?

A

using T antigen mutants (same sequence attached to other proteins results in transport to the nucleus)

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37
Q

What is a T antigen nuclear localization signal?

A

a single stretch of amino acids

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38
Q

what do importins do?

A

carry proteins through NPC

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39
Q

What works in conjunction with Ran?

A

importins

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40
Q

What is Ran?

A

a GTP-binding protein

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41
Q

What does Ran do?

A

controls directionality

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42
Q

Importins bind to the ___ of a protein

A

NLS (nuclear localization signals)

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43
Q

What happens after the receptor and protein are bound (importins and NLS)?

A

complex is transported into the nucleus

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44
Q

What does the Ran GAP stimulate?

A

the Ran-GTPase to cleave the GTP to GDP in the cytoplasm, releasing the importin

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45
Q

what signals export proteins from the nucleus?

A

nuclear export signals (NES)

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46
Q

exportins do what?

A

direct protein transport to the cytoplasm

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47
Q

many importins and exportins are members of a family of nuclear transport receptors known as what?

A

karyopherins

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48
Q

what import karyopherin has proteins with a basic amino acid nuclear localization signal?

A

importin

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49
Q

what import karyopherin has snRNPs (U1, U2, U4, U5)?

A

snurportin

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50
Q

what import karyopherin has mRNA binding proteins and ribosomal proteins?

A

transportin

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51
Q

what import karyopherin has histone H1 and ribosomal proteins

A

Importin7

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52
Q

what export karyopherin has proteins with a leucine-rich nuclear export signal, snurportin, snRNAs, and ribosomal subunits?

A

Crm1

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53
Q

what export karyopherin has tRNAs?

A

exportin-t

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54
Q

what export karyopherin has miRNAs?

A

Exportin 5

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55
Q

Exportins form stable complexes with what in association with the Ran-GTP in the nucleus?

A

cargo proteins

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56
Q

In the cytoplasm, for nuclear export, what leads to dissociation of the cargo protein?

A

GTP hydrolysis and release of Ran-GDP

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57
Q

RNAs are transported to the cytoplasm as what?

A

ribonucleoprotein complexes (RNPs)

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58
Q

What do karyopherin exportins NOT transport?

A

mRNA

59
Q

What do karyopherin exports transport?

A

tRNAs, rRNAs, miRNAs

60
Q

mRNA transport does not use karyopherins or ______

A

Ran

61
Q

What does mRNA use to move through the nuclear pore?

A

distinct transporter complex

62
Q

Where is the helicase located, nucleus or cytoplasm side?

A

cytoplasm

63
Q

Using the distinct transporter complex for mRNA transport ensures what?

A

unidirectional transport

64
Q

Many noncoding RNAs (snRNAs and snoRNAs) function where?

A

within the nucleus

65
Q

snRNAs are initially exported from the nucleus by what?

A

exportin (Crm1)

66
Q

snRNAs associate with proteins in the cytoplasm to form what?

A

snRNPs

67
Q

What are snRNPs recognized by?

A

an importin

68
Q

Transcription factor NF-kB is complexed with what in the cytoplasm?

A

IkB

69
Q

What happens if IkB is phosphorylated and degraded by ubiquitin-mediated proteolysis?

A

NF-kB can enter the nucleus and activate transcription of its target genes

70
Q

Other transcription factors are regulated directly by what?

A

phosphorylation

71
Q

During mitosis, what happens to chromatin?

A

becomes highly condensed to form the compact metaphase chormosomes

72
Q

During interphase, what happens to chromatin?

A

most decondense and distributes throughout the nucleus

73
Q

During interphase, transcriptional activity of a gene is correlated with what?

A

its position

74
Q

Where does DNA replication and transcription take place?

A

in clustered regions within the nucleus

75
Q

Chromosome territory was first suggested when?

A

1885

76
Q

What was confirmed in 1984 by studies of polytene chromosomes in Drosophila salivary glands?

A

chromosome territory

77
Q

What is chromosome territory?

A

each chromosome occupies a discrete region of the nucleus

78
Q

Situ hybridization with fluorescent probes specific for repeated sequences on individual chromosomes has been used to visualize what?

A

the location of chromosomes within a nucleus

79
Q

In living cells, what do chromosome conformation capture (3C) techniques reveal?

A

sites of interaction between chromosomal regions

80
Q

How were the interactions between chromosomal regions identified?

A

by cross-linking interacting DNA sequences then were amplified and identified by high-throughput sequencing

81
Q

Where is euchromatin located in the cell?

A

throughout the nucleus

82
Q

Which is transcribed, euchromatin or heterochromatin?

A

euchromatin

83
Q

Why is euchromatin transcribed and not heterochromatin?

A

euchromatin is decondensed while heterochromatin is highly condensed

84
Q

What is heterochromatin often associated with?

A

the nuclear envelope or periphery of the nucleolus

85
Q

Some human chromosomes are rich in what while containing relatively few genes?

A

transcribed genes

86
Q

What does fluorescent in situ hybridization show?

A

gene-rich chromosomes located in the center of the nucleus

87
Q

Where are gene-poor chromosomes located?

A

at the periphery

88
Q

How are genomes divided?

A

into looped domains

89
Q

What does the interaction of genomes look like?

A

regions within a domain interact frequently with one another + rarely with regions in other domains

90
Q

Domains associated with the nuclear lamina are called what?

A

lamina-associated domains (LADs)

91
Q

Genes within LADs are generally what?

A

transcriptionally repressed

92
Q

What is an example of a gene within LADs?

A

heterochromatin

93
Q

where are LADs found?

A

in the inner membrane of the nucleus

94
Q

What is the term for the nucleolus being surrounded by heterochromatin?

A

nucleolus-associated domains (NADs)

95
Q

DNA sequences found in NADs substantially overlap with what?

A

those in LADs

96
Q

Where does DNA replication take place?

A

in large complexes (replication factories)

97
Q

What can be seen by labeling cells with bromodeoxyuridine (an analog of thymidine), then staining with fluorescent antibodies?

A

replication factories

98
Q

Where does transcription occur?

A

clustered sites (transcription factories) that contain newly synthesized RNA

99
Q

Coregulated genes may be transcribed in ______ factory.

A

the same

100
Q

What are nuclear bodies?

A

organelles within the nucleus that concentrate proteins and RNAs for specific processes

101
Q

Nuclear bodies are not enclosed by what?

A

membranes

102
Q

What are nuclear bodies maintained by?

A

dynamic structures are maintained by protein-protein and protein-RNA interactions

103
Q

What are the 2 functions of the nucleolus?

A

1) rRNA transcription and processing
2) ribosome assembly

104
Q

What is the function of cajal body?

A

snRNP assembly

105
Q

What is the function of speckle?

A

storage of pre-mRNA splicing factors

106
Q

What is the function of polycomb body?

A

gene silencing

107
Q

What makes the rRNAs?

A

RNA polymerase I

108
Q

Where does transcription of the 5S rRNA occur?

A

outside the nucleolus

109
Q

What is the transcription of 5S rRNA catalyzed by?

A

RNA polymerase III

110
Q

Where are 5.8S, 18S, and 28S rRNAs transcribed?

A

in the nucleolus

111
Q

Following cell division, nucleoli associate with what?

A

nucleolar organizing regions

112
Q

What do nucleolar organizing regions contain?

A

5.8S, 18S, and 28S rRNA genes

113
Q

Transcription of 45S pre-rRNA leads to what?

A

the fusion of small prenucleolar bodies

114
Q

In most cells, the nucleoli initially separate then do what?

A

fuse to form a single nucleolus

115
Q

What are the 3 regions of nucleoli?

A

1) fibrillar center
2) dense fibrillar component
3) granular component

116
Q

what does the fibrillar center do?

A

stores genes

117
Q

In what region of the nucleoli does transcription take place

A

dense fibrillar component

118
Q

What do the 3 regions of the nucleoli represent?

A

sites of progressive stages of rRNA transcription, processing, and ribosome assembly

119
Q

In higher eukaryotes, the primary transcript of rRNA genes is what?

A

the 45S pre-rRNA

120
Q

How is the pre-rRNA processed in higher eukaryotes?

A

via a series of cleavages

121
Q

Processing of pre-rRNA also includes what?

A

addition of methyl groups to bases and ribose residues, and conversion of uridine to pseudouridine

122
Q

Nucleoli have over 300 proteins and 200 _______________ that function in pre-rRNA processing.

A

small nucleolar RNAs (snoRNAs)

123
Q

snoRNAs are complexed with proteins, forming ______.

A

snoRNPs

124
Q

What are snoRNPs?

A

modify rRNA (guide RNAs to direct specific base modifications of pre-rRNA)

125
Q

Two families of snoRNAs associate with different proteins , which does what?

A

catalyze ribose methylation or pseudouridine formation

126
Q

snoRNAs have sequences complementary to what rRNAs, which include the sites of base modification?

A

18S or 28S

127
Q

What does the formation of ribosomes require?

A

assembly of pre-rRNA with ribosomal proteins and 5S rRNA

128
Q

Ribosomal proteins are produced where?

A

cytoplasm

129
Q

Where are ribosomal proteins imported to after produced?

A

the nucleolus

130
Q

What 2 things assemble to form pre-ribosomal particles?

A

additional ribosomal proteins and the 5S rRNA

131
Q

Pre-ribosomal particles are exported to where?

A

cytoplasm

132
Q

What do pre-ribosomal particles yield?

A

40S and 60S ribosomal units

133
Q

How do polycomb proteins repress transcription?

A

a methyl group is added to lysine 27 on the histone H3

134
Q

What shows the proteins are concentrated in domains called polycomb bodies?

A

immunofluorescence

135
Q

What are snRNAs modified by?

A

ribose methylation and pseudouridylation

136
Q

What is the enzyme for RNA methylation?

A

fibrillarin

137
Q

What enzyme for RNA methylation is concentrated in cajal bodies?

A

fibrillarin

138
Q

Cajal bodies have small cajal _________

A

body-specific RNAs (scaRNAs)

139
Q

What do scaRNAs do?

A

serve as guides to direct methylation and pseudouridylation of snRNAs

140
Q

What do cajal bodies appear to play a role in?

A

assembly of telomerase, which replicates the ends of chromosomal DNA

141
Q

What is another thing that cajal bodies promote?

A

assembly of the RNA-protein telomerase complex and facilitate its delivery to telomeres

142
Q

Following assembly and maturation in cajal bodies, _____ are transferred to speckles.

A

snRNPs

143
Q

What are speckles recruited to do?

A

to actively transcribe genes where pre-mRNA processing occurs

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