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EoM Exam 2 - Richardson > Nucleus > Flashcards

Nucleus Flashcards

1
Q

What are the 3 functions of the Nucleus?

A
  1. ) DNA Replication
  2. ) Trancription
  3. ) RNA Processing
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2
Q

How is the Nucleus separated from the Cytoplasm?

Why is this important?

A
  1. ) The Nucleus is separated from the Cytoplasm by a double membrane.
  2. ) This is important for keeping Nuclear processes separated from Cytoplasmic processes (protein synthesis and metabolism).
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3
Q

Why does the Nucleus require a transport mechanism?

A

The Nucleus uses a transport mechanism because proteins are often required to regulate replication and transcription. Some proteins that function in the Nucleus are made in the Cytoplasm and vice versa.

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4
Q

What is the structure of the Nucleus?

A

The Nucleus contains genetic material (DNA and associated proteins like Histones) packaged as Chromatin with other functional domains (RNA metabolism) in discrete locations then all surrounded by a double membrane that is continuous with the ER and mediates transport between the Cytoplasm and Nucleoplasm.

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5
Q

What is the internal structure of the Nucleus?

A

During cell cycle, Mitosis is the active phase then the rest is Interphase.
Interphase Nuclei have Heterochromatin (varies among cell types) in dark staining patches along membrane and within the Nucleoplasm that is not actively transcribed, Euchromatin that is light gray within the Nucleoplasm and is actively transcribed, and 46 chromosomes in a small space, each occupying their own discrete domains.
(See pictures in Notes)

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6
Q

What are the functional regions of the Nucleus?

How can the locations of these regions be determined?

A

Functional regions of the Nucleus are those that are involved in RNA processing. These include:
1.) Red nuclear speckles (mRNA splicing),
Green cajal bodies (Ribonucleoprotein RNP assembly), Nucleolus (rRNA genes, ribosome assembly)
2.) Antibodies can be used to determine location of these regions.

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7
Q

What are the two main functions of the Nucleolus?

A

The Nucleolus actively transcribes/processes RNA and assembles ribosomes.

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8
Q

What are the 3 distinct regions of the Nucleolus?

What are the functions of each?

A

The 3 distinct regions of the Nucleolus are:
1.) Fibirllar center (darker, location of rRNA genes)
2.) Dense fibrillar componenet (transcription of rRNA)
3.) Granular component (speckled light grey area, site of ribosome assembly).
(See pictures in Notes)

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9
Q

What is the structure of the Nuclear Envelope?

A

Nuclear Envelope is a double bilayer with space in between:
Outer nuclear membrane is continuous with endoplasmic reticulum (ER).
Perinuclear space is lumen and continuous with the ER.
Inner nuclear membrane binds nuclear lamina then chromatin bind to the nuclear lamina.
(See picture in Notes)

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10
Q

What is the Nuclear Lamina?

A

1.)Nuclear Lamina is the meshwork underlying the inner nuclear membrane that provides shape and stability to the Nuclear Envelope.

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11
Q

How does the Nuclear Lamina give structure to the Nuclear Envelope?
What are its other functions?

A
  1. ) The Nuclear Lamina gives structure by determining the size and shape of Nucleus, providing strength to prevent deformation, and determining the position of nuclear pore complexes by binding nuclear pore proteins.
  2. ) The Nuclear Lamina mediates transcription and RNA processing by binding inactive regions of hetero-chromatin while Lamins are associated with internal regions active in replication, transcription, RNA processing, and DNA repair.
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12
Q

What are the 2 components of the Nuclear Lamina?

A
  1. ) Lamins are the major component of the Nuclear Lamina. They are proteins of the intermediate filament family that form dimers associated end to end like long strings then side to side associations of polymers give very strong ropelike structure that goes on to give meshwork structure.
  2. ) Associated proteins include integral membrane proteins that attach then Nuclear Lamina to the membrane (Lamin B) and determine heterochromatin or euchromatin (Emerin).
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13
Q

What are the 2 types of Lamins?

A
  1. ) Type A Lamins - Lamin A and C are peripheral proteins that are broken up into small vesicles by the nuclear membrane during mitosis then dispersed to the Cytoplasm.
  2. ) Type B Lamins - Lamin B is an integral protein that is attached to the membrane by a prenyl group and by binding to other integral membrane proteins. It remains attached to membrane vesicles that disperse during mitosis then come back after to reform membrane.
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14
Q

What are Nuclear Lamina mutations?

With what diseases are they associated?

A

Nuclear Lamina mutations interfere with lamina assembly and are associated with Congenital lipodystrophy, Dilated cardiomyopathy, Emery-Dreifuss muscular dystrophy, and Hutchinson-Gilford progeria.

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15
Q

What are the 2 forms of Emery-Dreifuss muscular dystrophy?

A

1.) The autosomal dominant form (most common) is associated with mutations in Lamins A and C.
2.) The X-linked form is associated with mutations in Emerin (laminin responsible for determining hetero or euchromatin).
(They are different proteins but have the same presentation of symptoms.)

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16
Q

What is the cause and presentation of Hutchinson-Gilford progeria?

A

Hutchinson-Gilford progeria is caused by a mutation in Lamin A. It presents as features and diseases associated with aging. (Boy in photo died of old age when he was 15 years old.),

17
Q

What mutation in Lamin A causes Hutchinson-Gilford progeria?

A

In normal post-translational processing of Lamin A, a farnesyl group is added to the C terminal of Lamin A for it to interact with the membrane then the farnesyl is removed.
In HGP, a mutation in the cleavage site keeps farnesyl from being removed. Lamin A never comes together appropriately, resulting in downstream effects on gene transcription due to improper heterochromatin and euchromatin binding.

18
Q

Why does the farnesyl group need to be cleaved from Lamin A?

A

The farnesyl group probably helps Lamin A first associate with membrane then once the prenyl group forms, the farnesyl group is no longer needed.

19
Q

What are Nuclear Pores?
What is their function?
How do they allow for the transport of various molecules?

A
  1. ) The Nuclear Pores are a large multi-subunit complex of more than 50 proteins (125 x 10^6 Daltons) with pore size ranging from 9 to 25nm.
  2. ) Nuclear Pores regulate transport of RNA, proteins, and other small molecules into and out (bidirectional) of the Nucleus.
  3. )The pore size adjusts to size of transported molecule so that small molecules freely diffuse and large molecules require a specific transport mechanism.
20
Q

What makes up the Nuclear Pore?

What is their structure?

A
  1. ) The Nuclear Pore is made of Nucleoporins that form a ring structure that is anchored to the Membrane and Nuclear Lamina.
  2. ) Fibrils on the cytoplasmic side (outside) bind cargo and direct transport through the pore, while fibrils on the nuclear side (inside) form a basket-like structure.
21
Q

What are the main players of Nuclear Transport?

What do the mechanisms require?

A

1.) Nuclear Transport involves Cargo (packages) with either a Nuclear Localization Signal (return address) or a Nuclear Export Signal (mailing address), and Importin and Exportin Receptors (delivery trucks).
2.) The mechanism is different for import and export but both require GTP hydrolysis.
(Remember: mRNA uses ATP hydrolysis.)

22
Q

What signals are used for Import and Export?

How were Import signals confirmed?

A

1.) Import uses a Nuclear Localization Signal (NLS) made of a stretch of basic amino acids (Lys-Lys-Lys-Arg-Lys) that can be linear or bipartite (comes together when protein folds.)
Export uses a Nuclear Export Signal (NES) that is rich in Leucine.
2.) The NLS sequence was put into a protein that did not normally localize in the Nucleus, but the protein did so after the addition.

23
Q

What comprises the Receptors?

What are the 2 methods of Import?

A
  1. )The Receptors (delivery trucks) are a Karyopherin family of proteins. Import uses Importin Receptors and may also use an Adapter. Export uses Exportins.
  2. )Importin may recognize NLS on the Cargo then bind and import it or Adapter may recognize NLS on Cargo, bind it, then Importin will recognize NLS signal on Adapter, and bind/import the Adapter with the Cargo.
24
Q

What is the Ras superfamily of small GTPases?

A

Small monomeric GTPases act as molecular switches.
They come from a very large family of related proteins (in which Ras is the prototype) that are involved in regulation of a variety of processes and are also similar to the larger trimeric G proteins.

25
Q

What is the number of proteins, function, and location of the Ras family?

A

Ras (3) function is growth signals and are located on the cytoplasmic face of the plasma membrane.

26
Q

What is the number of proteins, function, and location of the Ran family?

A

Ran (1) function is nuclear transport and are located shuttling between the Nucleus and Cytoplasm.

27
Q

What is the number of proteins, function, and location of the Arf/Sar family?

A

Arf/Sar (8) function is vesicular traffic and are located shuttling between the cytoplasm and cytoplasmic face of various organelles and the plasma membrane.

28
Q

What is the number of proteins, function, and location of the Rab family?

A

Rab (50) function is vesicular traffic and are located shuttling between the cytoplasm and cytoplasmic face of various organelles and the plasma membrane.

29
Q

What is the number of proteins, function, and location of the Rho family?

A

Rho (14) function is cytoskelton organization and are located shuttling between the cytoplasm and cytoplasmic face of the plasma membrane.

30
Q

What other proteins help the Ras superfamily of small GTPases cycle between the GTP and GDP form?

A

Ras superfamily of small GTPases cycle between GTP bound (active) and GDP bound (inactive). GTPase Activating Proteins (GAPs) stimulate the intrinsic GTPase activity. Guanine Nucleotide Exchange Factors (GEFs) promote the exchange of GDP for GTP. GDP Dissociation Inhibitors (GDIs) maintain the inactive form.

31
Q

What is Ran?
What is Ran-GAP?
What is Ran-GEF?
What drives transport?

A
  1. ) Ran is the GTPase.
  2. ) Ran-GAP facilitates the hydrolysis of GTP to GDP and is localized in the Cytoplasm.
  3. ) Ran-GEF exchanges GDP for GTP and is localized in the Nucleus.
  4. ) Localization of Ran-GAP (Cytoplasm) and GEF (Nucleus) is what drives transport because binding of GTP or GDP to Ran determines whether Ran will then bind Importin or Exportin.
32
Q

What is the Ran cycle?

What determines the ability of Ran to bind Importins and Exportins?

A
  1. ) Ran cycles between the Cytoplasm and Nucleoplasm. In Cytoplasm, Ran-GTP binds Ran-GAP and Ran hydrolyzes GTP to GDP. Ran-GDP comes back through the pore into the Nucleoplasm where it binds GEF, and GEF replaces GDP with GTP.
  2. ) The ability of Ran to bind Importins and Exportins depends on if it is bound to GTP or GDP.
33
Q

What is Import Cargo?

What are some examples?

A
  1. ) Import Cargo includes proteins that are synthesized in the Cytoplasm but function in the Nucleus.
  2. ) These include: Histones, Replication/Transcription machinery, Ribosomal proteins, Transcription Factors.
34
Q

What is the mechanism of action for Import?

A
  1. ) Ran-GTP-Importin goes from Nucleoplasm to Cytoplasm where GAP hydrolyzes GTP to GDP causing the dissociation of Importin.
  2. ) Importin binds Cargo and associates with Fibrils to go through NPC into Nucleus. Ran-GDP follows along.
  3. ) In the Nucleoplasm, Ran-GDP associates with GEF to exchange GDP for GTP.
  4. ) Ran-GTP dissociates the Cargo from the Importin so it can bind the Importin and repeat the process.
35
Q

What is Export Cargo?
What are some examples of Ran-dependent Cargo?
What is Ran-independent Cargo?

A
  1. ) Export Cargo includes proteins and RNAs that are either Ran-dependent or Ran-independent.
  2. ) Ran-dependent Export Cargo includes: Proteins that shuttle between Nucleus and Cytoplasm (TFs), Ribosomal subunits, RNAs transported as Ribonucleoprotein complexes, and tRNA.
  3. ) Ran-independent Export Cargo includes: mRNA
36
Q

What is the mechanism of action for Ran-dependent Export?

How does it differ from Import?

A

1.) In the Nucleoplasm, Ran-GDP associates with GEF to become Ran-GTP and bind Exportin.
2.) Ran-GTP-Exportin bind Cargo and entire Complex associates with the Nuclear Pore Complex (NPC) to be transported to the Cytoplasm.
3.) In Cytoplasm, GAP will hydrolyze GTP to GDP and cause dissociation of the entire complex.
4.) Ran-GDP and Exportin move back through the NPC (independent of one another) to repeat the process.
(Difference: Ran is bound to the Exportin-Cargo Complex as it goes through the NPC.)

37
Q

What is the mechanism of action for Ran-independent Export of mRNA.

A
  1. ) As mRNA is transcribed mRNP particles will associate with different proteins:RNA Helicase Dbp5 and Nuclear Export Complex Tap+Nxt1
  2. ) Once transcription is finished, Dbp5 moves the mRNA-Exporter Complex through NPC to Cytoplasm.
  3. ) Helicase Dbp5 becomes active in Cytoplasm and hydrolyzes ATP to ADP.
  4. ) Export Complex is removed from mRNA and immediately replaced by ribosomes.
  5. ) Dbp5, Tap, Nxt1 go back through NPC to Nucleus (independent of one another) and bind new mRNP.
38
Q

Why is Nuclear Transport regulated?

A

Some proteins (like TFs) are only transported into the Nucleus after a stimulus indicates their need. In these cases the TF’s NLS will be masked until it is unmasked by either phosphorylation or dephosphorylation.

39
Q

What are 2 examples of Nuclear Transport Regulation?

A
  1. ) TF NFkappaB has its NLS blocked when inactive by Inhibitor IkappaB. When NfkappaB is signaled to move into Nucleus, IkappaB is removed by phosphorylation and proteolysis, unmasking the NLS so NFkappaB can bind Importin.
  2. ) TF Pho4 has its NLS masked by phosphorylation when inactive. When Pho4 is signaled to move into Nucleus, Phosphotase removes the Phosphate (dephosphorylates) to unmask the NLS so Pho4 can bind Importin.

EoM Exam 2 - Richardson (1 decks)

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