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BIOL 2321 - Cell Biology > The Nucleus > Flashcards

The Nucleus Flashcards

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1
Q

What are the 7 main structures of the nucleus?

A

nuclear envelope

lamina

nuclear pores

matrix

nucleoplasm

perinuclear space

chromatin

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2
Q

T or F: all DNA is located in the nucleus

A

FALSE, some DNA is in the mitochondria and chloroplasts

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3
Q

About what percent of a cell’s volume does the nucleus occupy?

A

~10%

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4
Q

Describe the nuclear envelope

A

2 membrane bilayers separated by a 10-50 nm space (perinuclear space) that surrounds the nucleus

Each membrane has its own complement of proteins

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5
Q

Describe the perinuclear space

A

the 10-50 nm space between the two membrane bilayers of the nuclear envelope

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6
Q

How many membranes does the nuclear envelop consist of ?

A

2 membrane bilayers

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7
Q

What structure is the perinuclear space continuous with?

A

the ER lumen

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8
Q

The outer nuclear membrane is continuous with which structure?

A

the ER membrane

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9
Q

T or F: the rough ER membrane is the only membrane that can be have ribosomes attached

A

FALSE, the outer nuclear membrane can also be studded with ribosomes

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10
Q

Where are the two membrane bilayers (nuclear envelope) fused?

A

at nuclear pores

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11
Q

Describe nuclear pores

A

protein complexes that are the entry and exit of the nucleus

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12
Q

How many nuclear pores does the average mammalian cell contain?

A

thousands

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13
Q

Describe the nuclear lamina

A

A thin, filamentous meshwork on the inner surface of the nuclear envelope in animal cells

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14
Q

What is the function of the nuclear lamina?

A

Structural support for the nucleus, especially the envelope

to keep it round

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15
Q

What are the filaments of the nuclear lamina made of?

A

Lamina proteins

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16
Q

How is the lamina network assembled and disassembled?

A

by lamin phosphorylation

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17
Q

Why would the lamina network need to assemble and disassemble?

A

lamina would need to disassemble for cell division to separate cells and then would need to be reassembled in each new cell

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18
Q

During interphase, what 4 things would we see in the nucleus?

A
  1. nuclear matrix
  2. nucleoplasm
  3. chromosomes
  4. nucleolus
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19
Q

What is the nucleoplasm?

A

the fluid inside the nuclear envelope

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20
Q

What would the structure of chromosomes be during interphase?

A

highly extended fibres with both DNA and chromatin protein

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21
Q

Describe the nucleolus

A

an irregularly shaped electron dense region in the nucleus that functions in ribosomal RNA and ribosome synthesis

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22
Q

What is the function of the nucleolus?

A

ribosomal RNA and ribosome synthesis

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23
Q

Describe the nuclear matrix

A

a dynamic meshwork of insoluble filamentous scaffolding proteins within the nucleus

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24
Q

What is the nuclear matrix analogous to?

A

cytoskeleton in the cytosol

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25
Q

What is the function of the nuclear matrix?

A

to compartmentalize regions of the nucleus by binding to chromatin

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26
Q

What does assembly and disassembly of the nuclear matrix depend on?

A

phosphorylation

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27
Q

What 7 things does the nucleoplasm contain?

A

ions
nucleotides
phosphates (and other components of DNA and RNA)

RNA molecules (ex. RNA transcripts, rRNA, RNPs)

enzymes and proteins

CHROMATIN

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28
Q

1 micrometer of mitotic chromosome length typically contains how many cm of DNA? How much condensation is this?

A

1 cm of DNA

this is a 10,000 fold condensation

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29
Q

How many meters of DNA does the average cell contain?

A

2 meters!

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30
Q

T or F: chromosomes are more condensed in interphase than during mitosis

A

FALSE FALSE FALSE

way more condensed during mitosis

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31
Q

Describe eukaryotic chromatin

A

Composed of DNA, histone proteins, and non-histone chromosomal proteins in almost equal parts

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32
Q

What does prokaryotic DNA lack that eukaryotic chromatin has?

A

lacks histone proteins

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33
Q

Describe histones

A

proteins in eukaryotic chromatin that condense DNA so it will fit into the nucleus

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34
Q

How many major classes of histones are there? What are they?

A

5

H1
H2A
H2B
H3
H4
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35
Q

Describe the structure of histones

A

relatively small proteins with a lot of basic (POSITIVELY CHARGED) residue amino acids

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36
Q

Are histones positively or negatively charged?

A

positively charged

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37
Q

How does the charge of histones help them coil DNA?

A

DNA is negatively charged due to its sugar-phosphate backbone and histones are positively charged due to their basic residues so attractive forces help histones coil DNA

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38
Q

What is the basic packing unit of chromatin?

A

a nucleosome

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39
Q

Describe a nucleosome

A

DNA that is coiled around a histone protein core

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40
Q

How is a nucleosome formed?

A

DNA loops around a histone core twice (~150 base pairs of DNA coil around the histone)

~50 nucleotides act as a spacer between histones

Histone 1 will bind to the linker DNA

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41
Q

How many nucleotides and histones will 1 nucleosome involve?

A

200 nucleotides/base pairs

8 histones

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42
Q

What is the first level of coiling DNA? Describe it

A

nucleosomes form ‘beads on a string’

Histones are the beads and the DNA is the string

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43
Q

What is a key feature of histones?

A

they have long nitrogen-terminal tails that project outwards to interact with one another and aid in condensing even more

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44
Q

What is the second level of condensing?

A

solenoid

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45
Q

Describe the solenoid shape

A

Nucleosomes are coiled further into the solenoid shape which represents a wound garden hose

aka DNA already coiled around histones is coiled again into the solenoid

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46
Q

How thick is the fibre in the solenoid shape?

A

30 nm

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47
Q

What is the third level of condensing?

A

Loops

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48
Q

How is the third level of condensing achieved?

A

Chromatin fibres wrapped in the solenoid are coiled with NON-histone proteins (scaffold proteins) into loops and anchored onto the scaffold protein

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49
Q

What kind of protein is the solenoid structure coiled with and anchored to?

A

NON-histone scaffolding proteins

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50
Q

What is the fourth structure coiled chromatin makes?

A

the condensed mitotic chromosome

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51
Q

What are the 2 types of chromatin in the interphase nucleus?

A

euchromatin

heterochromatin

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52
Q

Describe euchromatin

A

loose chromatin ready for gene transcription

appears lighter on a micrograph

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53
Q

Describe heterochromatin

A

densely packed chromatin that cannot be transcribed

appears darker on a micrograph

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54
Q

What are the two kinds of heterochromatin?

A

constitutive

facultative

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55
Q

Describe constitutive heterochromatin. Give examples

A

heterochromatin that is always condensed in all cells

it is permanently silent

ex. the centromere and telomeres

56
Q

Describe facultative heterochromatin

A

heterochromatin that is specifically inactivated in certain life stages or in certain cells

57
Q

Describe epigenetic inheritance

A

the inheritance of phenotypic changes that do not result from changes in the nucleotide sequence of DNA

58
Q

How does an epigenetic change influence phenotypic changes?

A

it alters how DNA code is read

59
Q

what regulates epigenetic changes?

A

environmental factors, behaviour, nutrition, etc.

60
Q

Give a specific example of epigenetic inheritance

A

people born from mothers who were pregnant during the Dutch Winter Famine of 1944-1945 were more likely to develop heart diseases, schizophrenia, and type 2 diabetes because of the changes in methylation of certain genes

61
Q

Explain the effects on the people who were born from pregnant mothers during the Dutch Winter Famine of 1944-1945

A

pregnant mothers during a famine would be receiving less nutrition and therefore so would the baby

these people were more likely to develop heart diseases, schizophrenia, and type 2 diabetes due to epigenetic changes

62
Q

Describe the histone code

A

An epigenetic change that causes the disordered N-termini of histones to be phosphorylated, methylated, acetylated, glycosylated, etc.

these modifications are passed on to daughter cells because of replication and division

63
Q

What does the histone code hypothesis suggest?

A

the activity of a particular chromatin region depends on the specific modifications to the histone tails (N-termini) in that region

64
Q

Explain how histone modifications affect the degree of compaction

A

epigenetic changes to the histone code can cause heterochromatin which is harder to unpack to inactivate DNA that is not likely to be transcribed

65
Q

What is an example of facultative heterochromatin

A

calico cats

females have to inactivate one X chromosome randomly (facultative heterochromatin) =
some patches of the skin will inactivate brown colour –> orange patch
some will inactive orange –> brown etc.

66
Q

T or F: a huge amount of traffic moves into and out of the nucleus through pores

A

true

67
Q

How are replication and transcription related to nuclear pores

A

they require a lot of proteins that are synthesized in the cytoplasm to be transported into the nucleus via the pores

68
Q

How do mRNA, tRNA, and ribosomal subunits relate to nuclear pores?

A

they are manufactured in the nucleus and need to be transported out into to cytosol via the pores

69
Q

T or F: some cell components are synthesized in the nucleus, assembled into a functional unit in the cytoplasm, and shipped back into the nucleus to function

A

true

70
Q

How many macromolecules per second can each nuclear pore transport?

A

up to 1000 macromolecules a second

71
Q

T or F: each pore transports macromolecules in only one direction at a time

A

FALSE. pores move molecules in both directions at the same time

72
Q

What kind of technique would be good to visualize nuclear pores?

A

gold particles with an electron microscope

the particles can be seen moving into the nucleus through the pores

73
Q

What do nuclear pores contain that project into the nucleus and the cytoplasm?

A

a nuclear pore complex

74
Q

How many proteins make up a nuclear pore complex? are they all the same?

A

~30 different proteins

75
Q

What are the proteins called that make up a nuclear pore complex?

A

~30 nucleoporins make up the NPC

76
Q

What kind of symmetry does the overall nuclear pore complex have?

A

octagonal symmetry

77
Q

What kind of symmetry does each nucleoporin have?

A

octagonal symmetry

78
Q

How does the size of a nuclear pore complex compare to a ribosome?

A

~30x the size of a ribosome

79
Q

Describe the structure of a nuclear pore complex

A

a complex of about 30 different proteins (nucleoporins) with octagonal symmetry (each nucleoporin is also has octagonal symmetry) and it has a large, expandable central channel (the pore)

80
Q

What kind of molecules can move through the central channel/pore of a nuclear pore complex passively?

A

small polar molecules

81
Q

T or F: the central channel/pore of a nuclear pore complex can move fully folded proteins - why/why not?

A

true because it is large and expandable

82
Q

What kind of structure do some nucleoporins contain?

A

FG (phenylalanine/glycine) repeats of disordered structure along the lining of the channel

83
Q

What purpose do the FG domains of disordered structure serve?

A

they line the channel/pore to form a hydrophobic sieve to block the passive diffusion of large molecules through the pore/channel

84
Q

Does the FG domain create a hydrophilic or hydrophobic region in the nuclear pore? why does it do this?

A

hydrophobic

to block the passive diffusion of large molecules

regulates large protein movement

85
Q

What is FG?

A

repeats of 2 amino acids:

phenylalanine (F)
glycine (G)

86
Q

What must proteins destined for the nucleus possess in order to be moved into the nucleus?

A

a nuclear localization signal (NLS)

87
Q

What is a nuclear localization signal (NLS)?

A

A small, specific amino acid sequence (~6-7) (within a larger protein) that targets a protein to move into the nucleus

88
Q

describe an NLS

A

a small series (6-7) of positively charged amino acids within a larger protein that will target a protein to move to the nucleus

acts as a signal to move a protein into the nucleus

89
Q

Describe an importin

A

A family of proteins that binds to a nuclear localization signal on another protein

90
Q

What will an NLS on a protein bind to in the cytoplasm?

A

Importins

91
Q

What can each importin bind to?

A

A subset of ‘cargo’ proteins destined to the nucleus

92
Q

What is a cargo?

A

A protein that has an NLS and will bind to an importin to move to the nucleus

93
Q

Where are importins located?

A

in the cytoplasm

94
Q

What do importins carrying cargo interact with in the cytoplasm?

A

the fibrils extending into the cytosol from the nuclear pore complex

95
Q

How do importins move from the cytosol into the nucleus?

A

When they are carrying cargo, the importins will form temporary bonds with one FG domain (of the nuclear pore complex channel) and then another and another and move into the nucleus

96
Q

What happens once the importin and its cargo are inside the nucleus?

A

the importin dissociates from the cargo

97
Q

Describe the structure of an importin

A

Alpha helix and beta sheet subunits of importin form a dimer (CHECK THIS)

98
Q

What kind of structure does an importin have?

A

A dimer (2 subunits) 1 alpha helix + 1 beta sheet (is it a beta sheet??)

99
Q

Once the dimer is formed, what can the importin then do?

A

Bind to the cargo protein

100
Q

What happens after an importin binds to a cargo protein?

A

Importin ‘docks’

Binds to the cytoplasmic filaments of the nuclear pore complex

101
Q

What kind of micrograph can be used to see importin with cargo binding to the cytoplasmic filaments?

A

gold particles and an EM

102
Q

What happens after importin binds to the cytoplasmic filaments of the nuclear pore complex?

A

The filament that importin has bonded to undergoes a conformational change and folds inwards into the pore

103
Q

What is the purpose of importin binding to the cytoplasmic filaments of the NPC?

A

when it binds to the filaments, a conformational change occurs and the filaments fold into the pore, bringing the importin + cargo into contact with the FG domains

104
Q

T or F: after the importin dissociates from the cargo protein in the nucleus, the importin dimer stays in the nucleus

A

False

the importin dissociates from the cargo protein and must return to the cytosol to bring more cargo in

105
Q

Describe Ran GTPase

A

a monomeric protein that exists in 2 conformations that depends on whether GDP is bound or GTP is bound

106
Q

What subunit of importin will Ran bind to?

A

the beta importin

107
Q

What are the 2 conformations of RanGTPase? What do these depend on?

A 
On = bound to GTP
Off = bound to GDP
107
Q

What does Ran binding to the beta importin do?

A

Separates all the components of the importin

cargo
beta importin
alpha importin
all separate

108
Q

How many conformations does Ran GTPase have?

A

2

109
Q

T or F: alpha and beta importin move back to the cytosol together - why/why not?

A

False

When Ran binds to the beta importin, the components all separate so beta and alpha importin move back to the cytosol separately

111
Q

Why does Ran GTPase act like a molecular switch?

A

they have an active ‘on’ conformation and an inactive ‘off’ conformation

112
Q

What is GTP?

A

Guanine triphosphate

113
Q

What is GDP?

A

the hydrolyzed version of GTP

Guanine diphosphate

114
Q

What kind of structure does an Ran GTPase have (monomer, dimer, trimer…)?

A

Monomer

115
Q

T or F: the 2 conformations of Ran GTPase are found in the same location in the cell

A

False

116
Q

Where is the GTP-bound Ran GTPase more commonly located in the cell?

A

in the nucleus

117
Q

Where is the GDP-bound Ran GTPase more commonly located in the cell?

A

in the cytosol

118
Q

How does Ran GTPase switch from ON to OFF (ie., between conformations)?

A

GAP activates the ability of the Ran GTPase to hydrolyze GTP to form GDP and turn itself off

119
Q

Describe GAP and its function

A

GTPase Activating Protein that activates the ability of Ran GTPase to hydrolyze GTP to form GDP and turn off

120
Q

What does GAP stand for?

A

GTPase Activating Protein

121
Q

How does Ran GTPase switch from OFF to ON (ie., between conformations)?

A

GEF exchanges GDP for another new GTP

122
Q

Describe GEF and its function and what it stands for

A

Guanine nucleotide Exchange Factor

A protein that exchanges GDP for a new GTP

123
Q

Explain why Ran GTP is more common in the nucleus

A

When Ran GDP enters the nucleus it is quickly converted to Ran GTP by GEF and remains that way until it leaves the nucleus

124
Q

Explain why Ran GDP is more common in the cytosol

A

As soon as Ran GTP enters the cytosol, GAP converts it to Ran GDP

125
Q

In the nucleus, is Ran GTPase on or off? why?

A

ON

It will be converted from Ran GDP to Ran GTP by GEF

126
Q

In the cytoplasm, is Ran GTPase on or off? why?

A

OFF

it will be converted from Ran GTP to Ran GDP by GAP

127
Q

What does beta importin need to bind to in the nucleus after separating in order to return back to the cytosol?

A

the Ran GTP in the nucleus

128
Q

Describe how beta importin moves back to the cytosol from the nucleus

A

Beta importin binds to Ran GTP in the nucleus and moves with it through the nuclear pore

Ran GTP will be hydrolyzed in the cytosol to Ran GDP and will release the beta importin

129
Q

What is the importance of the conformational change from Ran GTP to Ran GDP when it enters the cytosol?

A

Ran GTP will be carrying beta importin with it through the nuclear pore

In order to release it, Ran GTP must be hydrolyzed to Ran GDP

130
Q

What is an NES?

A

Nuclear Export Signal

131
Q

What is an exportin?

A

A protein that binds to a protein with an NES signal in the nucleus

132
Q

Where are exportins mostly located?

A

in the nucleus

133
Q

What function does exportin have as part of the Ran cycle?

A

Exportin binds to Ran GTP and can bind with alpha importin and move the alpha importin through the nuclear pore and into the cytosol

134
Q

How does alpha importin return to the cytosol?

A

An exportin protein binds to the Ran GTP in the nucleus and the alpha importin and they all move into the cytosol and will be released when Ran GTP is hydrolyzed

135
Q

How is the alpha importin released from the exportin when they enter the cytosol?

A

the exportin is also bound to Ran GTP so when they enter the cytosol, Ran GTP will be hydrolyzed to Ran GDP and the conformational change will cause the alpha importin to be released

136
Q

Briefly describe the steps of transporting proteins into and out of the nucleus

A
  1. An importin (made of alpha and beta) protein binds to a protein with an NLS
  2. importin + cargo bind to the cytosolic filaments of the NPC causing the filaments to bend in
  3. importin now able to transiently bind to the FG domains of the nuclear pore and can move into the nucleus with the cargo
  4. Ran binds to the beta importin causing the alpha, beta and cargo to separate
  5. beta importin binds to Ran GTP and when they enter the cytosol, Ran GTP is hydrolyzed by GAP into Ran GDP and releases beta importin
  6. exportin proteins binds to an NES on a random protein, then it binds to Ran (Ran has alpha importin as a substrate)
  7. when they enter the cytosol, Ran GTP is converted to Ran GDP by GAP and releases the alpha importin

BIOL 2321 - Cell Biology (26 decks)

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