W3: 3.2 Nucleus & Gated Transport Flashcards
What is a nucleolus and what are some of its features?
The ribosome factory (site production of ribosomal RNA molecules and ribosome subunits)
Features:
- located inside the nucleus.
- not a membrane bound compartment
- Nucleus Organizing Regions (NOR) of the chromosomes gather in the nucleolus
- takes of 20-25% of nuclear volume.
What structure provides mechanical support to the nuclear membrane? and what is its composition?
Nuclear laminas:
made of cytoskeletal filaments called intermediate filaments, which are very strong.
The function of this layer is to give mechanical support to the nuclear membrane
located inside the inner nuclear membrane by transmembrane protein anchors called LAP (lamin-associated proteins)
involved in tying/localizing chromosomes to specific sites on the membrane nucleus
What are the three types of proteins found in nuclear pores? What are their functions?
Peripheral, transmembrane, and anchored proteins.
Peripheral proteins - multiple copies of about thirty different kinds of peripheral proteins arranged in a ring and called nucleoporins
Integral/transmembrane proteins that span the membrane and anchor ring into the membrane
Anchored proteins - Lamins - anchor the pore complex to the nuclear lamina
NPC (nuclear pore complex) proteins regulate what enters/exits the nucleus and regulate gene expression
What are the functional parts of the nuclear pore?
Central channel (9nm pore)
Nuclear basket on inside of the pore made of protein filaments
Fibrilis: on inside it’s called nuclear fibrilis and on the outer membrane or systolic side it’s called cytosolic fibrilis
What are the major parts of a nuclear pore?
Ring subunits: form the upper and lower boundaries of the pore
Columnar subunits: line the channel of the pore
Annular subunits: stick into the channel w/in the pore & help prevent or facilitate movement of things through the pore
Luminal subunits: stick into the lumen of the perinuclear space. Important in anchoring the nuclear pore comples to the nuclear membrane
How small does a molecule need to be in order to move freely in and out of the nucleus?
molecules smaller than 5000 daltons can pass through nuclear pores by simple diffusion
How do molecules that are bigger than 5000 daltons move through a nuclear pore?
Through gated transport
Since the pore is 9nm some form of energy will be needed to move complexes that are larger - this movement is tightly regulated
What are the characteristics of an NLS (nuclear localization signal?)
code that causes proteins to enter the nucleus.
Common feature is the presence of several positively charged lysine (Lys) or Arginine (Arg) amino acids.
An inactivated nuclear receptor shows uniform localization in both the nucleus and cytoplasm. However, when it is activated, it is exclusively in the nucleus. Does activation likely involved a nuclear localization sequence or a nuclear retention sequence?
Nuclear localization since it causes proteins to move into the nucleus, where nuclear retention sequence can move proteins to move in and out. (CHECK ANSWER)
What are FG repeats and what is their role in nuclear import and export?
inner nuclear pore proteins that have phenylalaline and glycine repeats that work as stepping stones for nuclear import receptors. FG repeats help regulate movement of molecules.
Which of these would be found primarily in the cell cytoplasm: Ran-GEFS, RAN-GAPs, RAN-GTP, RAN-GDP
RAN GAP is found in the cytoplasm and converts GTP to GDP + Pi when GTP leaves the nucleus to enter the cytoplasm. RAN GDP can also be found in the cytoplasm (CHECK THIS PART)
Would a nuclear receptor making its way into the nucleus be bound to RAN GTP or RAN GDP?
It would be bound to RAN-GDP b/c ran-GDP moves into the nucleus while Ran-GTP moves out of the nucleus.
What is Dbp5 and what is its function?
Dbp5 is an RNA helicase protein (motor protein) that provides force for transport and releases the receptor and other mRNA associated proteins so that they can recycle back to the nucleus. It uses energy of ATP
Explain how Rev functions in the life cycle of HIV
Rev helps HIV virus get around the normal mechanism preventing the export of unprocessed mRNAs from cells
During the early phase of viral infection, mRNA encoding Rev is produced and processed normally by cells leading to the export of the mRNA for Rev and production of the Rev protein
Rev then reenters the nucleus and couples unprocessed viral mRNA molecules to a host cell nuclear export receptor that is exported using the Ran-GTP dependent process
What are the structural features of a nucleus?
subnuclear compartments
nuclear matrix
nucleolus
nuclear envelope
nuclear pore complex
nuclear localization
gated transport
Where are ribosomes and ribosomal RNA molecules assembled?
by the nucleolus inside the nucleus
Why do cells need to produce large amounts of ribosomes in molecules? How do cells accomplish this?
In order to make all the protein they need to live.
To accomplish this some chromosomes have multiple copies of genes coding for ribosomal RNA. The regions of chromosomes containing these genes are localized w/in the nucleolus
What is the nucleus organizing region?
Region in nucleolus that contains chromosome genes coding for ribosomal RNA
What are the similarities and differences of ribosomal subunits
Similarities: subunits are made in the nucleolus and joined in the cytoplasm
Difference: one subunit is small and the other large
What is the function of nuclear lamina?
made of cytoskeletal filaments called intermediate filament, which are very strong and the function of this layer is to give mechanical support to the nuclear membrane. Lamina also ties chromosomes to specific sites on the membrane
How does the nuclear pore complex (NPC) function?
NPC functions as a gate for molecules greater than 5000 daltons
What are the subunits of a nuclear pore? How many are there?
4 subunits:
Ring subunits
Column Subunits
Annular Subunit
Lamina Subunit
How do large molecules pass the nuclear pore?
An active process known as gated transport, which will require some form of energy
How do complexes move through nuclear pores in one direction while being prevented from moving through it in the other direction
When the cell is not in transition state protein is either inside the nucleus or outside the cytoplasm. However it is coded in their amino acid if a protein will move in it will bind to NLS if it moves out it will bind to NES
What is a common feature of NLS
Presence of several positively charged lysine (Lys) or arginine (Arg) amino acids
What is a common feature of NES?
contains large number of non-polar leucine (Leu) or isoleucine (Lle) amino acid
Where is ran-GAP found?
in the cytoplasm of the cell. Will hydrolyze GTP to GDP+ Pi
How does export of a protein work in the nucleus?
Nuclear export receptor floats around in nuclear pore
Once inside the nucleus it will bind to Ran-GTP and once this binding occurs it can pick up a protein cargo.
The GTP+Export Receptor+Protein will hop around FG repeats until they move out of the nucleus into the cytoplasm.
Once outside ran-GAP will hydrolyze GTP to GDP and the complex will separate
Empty nuclear export receptor can move through the nuclear complex
How does nuclear import work?
Nuclear import receptor will bind to cargo protein in the cytoplasm
Receptor and cargo float around on FG repeats to get into the nucleus.
Once inside the nucleus Ran-GTP will bind to the receptor and the protein will separate and be stuck in the nucleus. The GTP-Receptor complex will use FG to get out of the nucleus.
Once in the cytoplasm Ran-GAP will hydrolyse the GTP and the import receptor will free itself for another protein to dock
What mediates transport of RNA out of the nucleus?
Dpb5 (motor protein)
Why does REV reenter the nucleus?
Couples unprocessed viral mRNA molecules to a host cell nuclear export receptor.
What do nuclear receptor signals and nuclear shuttling sequences do?
(IDK)
In addition to NLS and NES what is needed for nuclear import and export?
Nuclear import and export receptors - soluble proteins that bind to the nuclear localization and export signals on different proteins.
Inner nuclear pore proteins with two amino acid repeats of phenylalanine and glycine amino aka FG repeats (they act as docking sites).
How can the activity of nuclear receptors be regulated?
FG act as stepping stones pathways through the nuclear pore complex and this gives cell a way of turning on and off the movement of cargo molecules through nuclear pores
During mitosis, does the nucleolus form or dissociates?
During mitosis it dissociates and after mitosis it will reform
Where is nuclear lamina located?
Inside the inner nuclear membrane and bound to this membrane by protein called LAP aka Lamin associated proteins
Why is it important for nuclear import receptors to be attached to either a cargo protein or a GTP?
b/c it has to be attached to either for it to bind to FG repeats on nuclear pore proteins. When nothing is bound to it, it doesn’t interact with the nuclear pore complex.
Can a nuclear export receptor interact to with the nuclear pore complex without being attached to a cargo protein or gtp?
Yes, unline nuclear import receptor. NER can move through the pore empty
How does a protein with both NSL and NES signals in their amino acid decide which signal is functional at a given time?
dependent on regulatory events like the phosphorylation sate of the protein or the calcium levels in the environment
ex: T cell protein called nuclear factor is activated by t cells or NF-AT.
When phosphorylated it reveals NES
Calcineurin dephosphorylates NF-AT when Ca2+ is high in cytoplasm and this hides NES and exposes NIS signal
What is a complete ribosome and how are they made?
a complete ribosome has 2 subunits, one large and one small. and the 2 subunits are joined in the cytoplasm but they are independently produces in the nucleolus.
How many NOR (nucleus organizing regions) have to merge in a human cell to form a nucleolus after mitosis?
10 NORs
What are cajal bodies?
sites where non-coding RNAs are assembled with other proteins. as well as assembly and storage of RNA based structures which handle messenger RNA splicing. These structures are called small nuclear rubonuclear proteins or snRNps.
Cajal bodies thn are said to be sites Where snRNP and snoRNP are assembled and recycled
What is interchromatin granule clusters (speckles)?
proposed to be a storage site for fully mature snRNPs
What are the sub nuclear components in the nucleus (not visible with normal light microscopy)?
- Cajal bodies
- interchromatin bodies
-these structures have no membranes and are relatively stable.
What are snRNPs?
-Small Nuclear RiboNuclear Proteins. They handle messenger RNA splicing
Where is the perinuclear space? what is it continuous with?
the space between the outer and inner membrane of the nucleus.
-perinuclear space is continuous with the ER membrane
What makes up the nuclear envelope?
1) membrane of nucleus (double membrane)
2) perinuclear space
3) nuclear pore complex
4) nuclear lamina
Where is nuclear lamina located?
located inside the inner nuclear membrane.
How are lamins attached to the inner nuclear membrane?
by transmembrane-protein anchors called lamina associated proteins (LAP)
What do proteins of the nuclear pore complex do?
regulate what enters/exits the nucleus (the gated transport) and thus regulate gene expression.
The bulk of the nucleus pore complex is made up of what type of proteins?
multiple copies of about thirty different types of peripheral membrane proteins arranged in a ring.
How to transmembrane proteins help the nucleus pore complex?
they anchor the ring structure (made up of peripheral proteins) into the membrane of the nucleus.
-lamin fibers are also present to anchor the pore complex to the nuclear lamina.
what units form the upper and lower boundaries of the nuclear pore complex?
the ring subunits.
Which subunit lines the channel of the nuclear complex pore?
columnar subunits
Which subunits stick into the channel within the pore and interact w/things moving through to facilitate or prevent movement?
annular subunits
Which subunits stick into the lumen of the perinuclear space and anchor the nuclear pore complex to the nuclear membrane?
luminal subunits
Why does the nuclear port complex, transport process (gated transport) require several types of molecular signals?
b/c of bidirectional transport in nucleus.
-protein is either inside the nucleus or outside the nucleus in the cytoplasm;
therefore, complexes can move through the pore in one direction, while being prevented
from moving through it in the other direction
What determines whether a protein leaves or enters the nucleus?
signals encoded in their amino acid sequence determines whether a protein enters or leaves (import or export codes)
What code causes a protein to enter the nucleus? What code causes a protein to leave the nucleus?
In: The nuclear localization signal or NLS
Out: Nuclear export sequences
Nuclear shuttling sequences and nuclear retention signals move in what direction?
in and out of the cell.
Apart from proteins, what else can pass through the nucleus? And what direction?
RNA molecules but they can only move OUT of the nucleus not in. Movement out depends heterodimeric mNRNA export receptor and Dbp5.
How does mRNA move out of the nuclear pore complex?
1) Heterodimeric mRNA expore receptor binds mRNA-protein complex (mRNPs) and then the nuclear pore complex
2) RNA helicase Dbp5 provides the force to transport and release the receptor and other mRNA associated proteins so they can recycle back to the nucleus.
- mRNA receptor binds only to fuly processed mRNA with proper processing accessory proteins
