Part 2 Flashcards
(18 cards)
Look at the differences between euchromatin and heterochromatin . What role do they have in regulation of transcription
Euchromatin: decondensed chromatin in interphase cells that are transcriptionally active
Heterochromatin: Highly condensed chromatin and generally not described. Contain highly repeated sequences
Genes that are transcribed in more decondensed state allows for transcription, heterochromatin inhibits transcription.
Look at the steps in ribosome assembly
1) Ribosome RNA genes are transcribed at the interface between fibrillar center and dense fibrillar component of the nucleus
2) Produces pre-rRNA, which undergoes initial processing steps within dense fibrillar component
3) Ribosomal proteins imported to the nucleus from the cytoplasm and being to assemble on pre-rRNA during their processing
4) Pre rRNA further processed additional ribosomal proteins
5) final steps of maturation follow the export of pre ribosomal particles to the cytoplasm yielding 40s and 60s ribosomal subunits.
How are lamins associated with the inner nuclear membrane?
Determine the stiffness of nuclear envelope. Association of lamins with inner nuclear envelope facilitated by post translational addition of lipids. Lamins binds to specific proteins, emerin or lamin B receptor directly connected with cytoskeleton. Lamins and inner nuclear membrane interact with chromatin.
Understand the basic function of replication factories and transcription hubs.
How are cytoplasmic and nuclear bodies organized?
Nuclear bodies found in nucleus cytoplasmic organelles found in cytoplasm. Nuclear bodies surrounded by double membrane and contain specialized proteins and RNA molecules for nuclear processing. Cytoplasmic organelles involved in a wider range of cellular processes and are typically larger in size.
Look at the roles of nuclear localization signals and nuclear export signals
Proteins responsible for all aspects of genome structure (DNA, RNA , TF) targeted to nucleus by nuclear localized signals (amino acids) recognized and bound by nuclear transport receptors direct protein transport through pore complex.
Understand how levels of Ran/GTP determines directionality of nuclear import
When Ran/GTP binds to an importin, it results in the cargo protein being released in the nucleus. When GTP is hydrolyzed, the importin goes OUT of the cell.
When Ran/GTP binds to an exportin, the it causes the exportin to leave the cell and the cargo protein is released outside of the cell. When GTP is hydrolyzed, this causes the exportin to go back INTO the cell.
Understand the overall mechanism of snRNA transport between the nucleus and cytoplasm
1)Small nuclear RNAs (snRNA) are initially exported from the nucleus to cytoplasm by an exportin (Crm1)
2) in cytoplasm the snRNA associate with proteins to form snRNPs
3) SnRNPs recognized by a protein called snorprotein also binds to importin results in transport back to nucleus.
Understand the role of polycomb bodies in transcriptional control
Polycomb bodies: polycomb proteins concentrated in a relativly small region, rather than disrupted throughout the nucleus.
Function: slices (transcriptional repression of genes) via methylation of histone H3 and lysine 27 residues
Generate domains of repressed chromatin so polycomb bodies are associated with heterochromatin consistent with gene expression
What are the roles of small nuclear RNAs in rRNA processing?
Small nuclear RNA (snoRNA) function in pre-rRNA cleavage, ribose methylation and pseudo uridylation
Understand how regulation of import and export of RNA and proteins is another level of regulation; transcription and translation
The cell controls gene expression not only by turning genes on/off (transcription) or by translating mRNA, but also by deciding whether RNAs and proteins are allowed in or out of the nucleus.
mRNA can be transcribed but it won’t be translated unless it leaves to nucleus. There are certain mechanisms that control when the mRNA leaves the nucleus.
Look at the overall findings of the ENODE Project
Advanced understanding of defnieing the functional elements of the human genome by transcribing 75% of the human genome, found out that non coding RNA make up a lot of the genome
Resulted in 20000 protein coding genes 18000 noncoding RNA 75% of genome transcribed and 8% of genome binding TF
Look at regulation of nuclear import of transcription factors
TF are only functional when present in the nucleues so their regulation is key for controlling gene expression
EX: TF NF-KB when binding to IKB is an inactive complex making its NLS in th ecytoplasm
Extracellular signals phosphorylated IKB, IKB is targeed and degraded by ubiquitin proteolysis allowing the import of NFKB into nucleus
Understand which proteins are directly interacting with carrier proteins and what their role is in crossing the nuclear membrane pore
Proteins that interact with carrier proteins: importins, Ran-GTP, Ran-Gap, exportins, NTFR, Ran-GEF
Importins bind to the carrier protein, which is identified by the NLS, in cytoplasm.
Ran/GTP and Ran-GDP both play a role in the directionality of the import/export processes.
Ran-GAP hydrolyzes Ran-GTP –> Ran-GDP, helping maintain the concentration gradient of the two molecules.
Exportins bind to carrier protein in nucleus.
NTF2 acts as a NLS, allowing exportins to come back into the nucleus.
Ran-GEF phosphorylates Ran-GDP –> Ran-GTP, helping maintain the concentration gradient of the two molecules.
Understand the roles of Guanine Echange Factors (GEF), GTPase-Activating Proteins, Nuclear Transport Factor 2 (NTF2) in nuclear transport
1) GTPase activating proteins associate with cytoplasmic filaments to stimulate hydrolysis of GTP to GDP
2) Release importin
3) RAN/GDP is transported back to the nucleus in association with its own receptor NTF2
4) In nucleus RNA - GEF stimulated the exchange of GDP bound to RNA for GTP leads to conversion of RAN/GDP to RAN/GTP
Look at the mechanism of mRNA export
1)Following processing, mRNA are bound by group of proteins called exporter complex mediates transport through nuclear pore complex
2) A helicase associated with the cytoplasmic face of the nuclear pore complexe rearranges the folding og the mRNA
3)Releases the mRNA from the exporter complex into cytoplasm
Look at trafficking of molecules through the nuclear pore complex
small molecules are able to pass freely through nuclear pore complex by passive diffusion
Contrast RNA pass through nuclear pore complex by selective transport (Carrier based on specific characteristics)
What are LADs, NADs and TADs?
LAD - genomic regions make molecular contract with the nuclear lamina, influencing gene expression and chromatin organization
TAD - Self-interacting genomic regions where DNA sequences interact more frequently with each other than with sequences outside of TAD
NAD - related to LADs defined by association with nuclear lamina affecting chromatin distribution and gene expression
