Nucleus Flashcards
(20 cards)
How are lamins associated with the inner nuclear membrane?
The nuclear lamina is a meshwork of intermediate filaments beneath the inner nuclear membrane that provides structural support. Two lamins form a dimer in the alpha helix region of two polypeptide chains wound in each other to make a coiled coil. Then the lamin dimers associate with each other to form the filaments that make up the nuclear lamina. Lamins bind to specific inner nuclear membrane proteins (lamin B receptors) and directly connect to the cytoskeleton by protein complexes.
Which molecules can traffic freely through the nuclear pore complex? Which can’t?
The nuclear pore complex (NPC) is the only channel that allows molecules (proteins and RNA) to pass across the nuclear envelope. Small molecules are able to pass freely through the NPC by passive diffusion. Macromolecules (proteins and RNA) can selectively transport in either direction, depending on signals. This is an energy-dependent process.
Why is transportation of RNA and proteins needed?
RNA in nucleus must go to cytoplasm for protein synthesis. Proteins (transcription factors) must be transported from cytoplasm to nucleus for gene expression.
What are the roles of nuclear localization signals (NLSs) and nuclear export signals?
Proteins are targeted to the nucleus by nuclear localization signals (specific AA sequences); these signals are recognized by nuclear transport receptors like importin, which carry proteins in the nucleus. Proteins targeted for export from the nucleus by specific AA sequences are called nuclear export signals, and are rich in hydrophobic AA leucine. The export signals are recognized by export receptors like exportin.
How do levels of Ran/GTP determine directionality of nuclear import?
In cytoplasm, Ran/GTP turns into Ran/GDP, releasing importin, and Ran/GDP is transported to the nucleus by its own import receptor. A high concentration of Ran/GTP in the nucleus creates a gradient that drives importin proteins to bind cargo in the cytoplasm, then release it in the nucleus.
What are the roles of guanine exchange factors (GEF), GTPase-activating proteins, and nuclear transport factor 2 (NTF2) in nuclear transport?
Transport begins when the nuclear localization signal of a cargo protein is recognized by an importin. The cargo/importin complex binds to a nuclear pore protein in the cytoplasmic filaments and goes through the pore. In the nuclear side, Ran/GTP binds to importin, releasing the cargo protein. The importin/Ran/GTP complex then exports through the nuclear pore, and GTPase activating protein (Ran GAP) stimulates the hydrolysis of GTP to GDP, releasing importin. Ran/GDP then goes back into the nucleus with the NTF2 receptor. In the nucleus, Ran GEF (bound to chromatin) stimulates the exchange of GDP to GTP, maintaining the high concentration of Ran/GTP in the nucleus.
What proteins are directly interacting with carrier proteins, and what is their role in crossing the nuclear membrane pore?
Proteins like histones, DNA and RNA polymerases, gene regulatory proteins, and RNA processing proteins bind to carrier proteins to coordinate nuclear and cytoplasmic functions like regulating transcription factors.
What is the overall mechanism of snRNA transport between the nucleus and the cytoplasm?
In contrast to mRNAs which function in the cytoplasm, snRNAs (small nuclear RNAs) are involved in the pre-mRNA splicing functions within the nucleus. snRNAs are initially transported from nucleus to cytoplasm by exportin. In the cytoplasm, snRNAs associate with proteins to form snRNPs (small nuclear ribonucleoproteins), which are recognized by an importin (snurportin), which mediates transport back into the nucleus.
What is the mechanism of mRNA export?
mRNAs are transported out of the nucleus by a mechanism independent of Ran. After the completion of splicing and polyadenylation, mRNAs are bound by an exporter complex, which mediates their transport through the NPC. Directionality of this process is established by an RNA helicase associated with the cytoplasmic face of the NPC as it releases the mRNA into the cytoplasm.
How is the import and export of RNA and proteins another level of regulation (aside from transcription and translation)?
Regulation of transcription factor import and export is a novel means for gene expression control because transcription factors are only functional in the nucleus.
What is the regulation of nuclear import of transcription factors?
Transcription factors are only functional when present in the nucleus, so their regulation is key for controlling gene expression. For example, the transcription factor NF-kB, when binding to lkB, is an inactive complex, masking its nuclear localization signals in the cytoplasm. When extracellular signals phosphorylate lkB, lkB is targeted and degraded by ubiquitin proteolysis, allowing the import of NF-kB into the nucleus. Also, the yeast transcription factor Pho4 is maintained in the cytoplasm by phosphorylation, and dephosphorylation of Pho4 unmasks nuclear localization signals and allows Pho4 to be transported to the nucleus.
What are the differences between euchromatin and heterochromatin, and what role do they have in regulation of transcription?
Chromatin is generally a mixture of DNA and proteins that make up chromosomes. Euchromatin is the majority of chromatin, decondensed, and transcriptionally active, located toward the interior of the nucleus. Heterochromatin is a minority of chromatin, highly condensed, and not transcribed, and usually found around the nuclear envelope and nucleolus.
What are LADs, NADs, and TADs?
Chromatin in the nucleus is divided into looped domains, which restricts the interaction of chromosomes. Heterochromatin is localized to the nuclear lamina by binding to lamins and the lamin B receptor. Looped domains of transcriptionally inactive heterochromatin are associated with lamina-associated domains (LADs) or nucleolus-associated domains (NADs). Transcriptionally active domains (TADs) are localized to the interior of the nucleus. Domain boundaries are formed by CTCF (CCCTC-binding factor) and cohesin.
What are clustered regions?
Where replication and transcription take place; transcription factories are clustered sites of RNA polymerases and transcription factors where multiple domains of active chromatin are transcribed.
How are cytoplasmic and nuclear bodies organized?
Nuclear bodies are a variety of discrete organelles that compartmentalize specific processes within the nucleus and concentrate proteins and RNAs that function in specific nuclear processes. Unlike cytoplasmic bodies, they are not enclosed in membranes and are maintained by protein and RNA interactions, allowing for dynamic structures.
What is the nucleolus?
The middle of the nucleus, the site of rRNA transcription, rRNA processing, and ribosomal assembly. It consists of fibrillar center (FC), dense fibrillar component (DFC), and granular component (G).
What are the steps in ribosome assembly?
Ribosomal proteins are imported to the nucleolus from the cytoplasm and begin to assembly on pre-rRNA prior to its cleavage. As the pre-rRNA is processed, additional ribosomal proteins and the 5S rRNA assemble to form pre-ribosomal particles. The final steps follow the export of pre-ribosomal particles to the cytoplasm, yielding 40S and 60S ribosomal subunits.
Which ribosomal subunits make up the 40S and 60S?
The 40S subunit is made up from one rRNA molecule 18S. The 60S subunit is made up from three rRNA molecules, 28S, 5.8S, and 5S.
What are the roles of small nucleolar RNAs (snoRNAs) in rRNA processing?
They help the processing of pre-rRNA by functioning in pre-rRNA cleavage, ribose methylation, and pseudouridylation.
What is the role of polycomb bodies in transcriptional control?
Polycomb bodies function in gene silencing (transcriptional repression of genes) via methylation of histone H3 lysine 27 residues. They generate domains of repressed chromatin, so polycomb bodies are associated with heterochromatin, consistent with gene repression.
