Genome organisation, rRNA processing and nuclear transport Flashcards
(31 cards)
What are the characteristics of the nucleus
Has its own biochemical and molecular profile (repository for genetic code)
Traffic is highly regulated and involves the movement of nucleic acids and specific proteins
In micrograms, densely stained regions usually show regions with a lot of heterochromatin – chromatin that is used frequently will be found near pores
Chromatin is organised into eugenic and heterogenic domains
What is the structure of the nucleus
Partitioned from the cytoplasm by a double membrane known as the nuclear envelope
Outer membrane is continuous with the ER
Lamin proteins form a mesh over the nucleus to form a “scaffold” and hold the spherical shape
Nuclear pores are protein complexes in excess of 1250 KDa and regulate what enters and leaves the nucleus
What receptors are present on the nucleus and what do they trigger
Lamin-B receptors have several N-terminal SR domain and involve protein-protein interactions and exist in a large protein complex
The Lamin mesh dissolves and the nucleus dissappears during nuclear disassembly (mitosis)
Phosphorylation of LBR by LBR kinase is central for this process
LBR also interacts directly with the chromatin proteins like HP1 (heterochromatin protein)
Lamin mesh of filaments (lamin A,B and C proteins)
What facilitates gene transcription
Ring finger binding protein (RFBP) interacts with RUSH which facilitates gene transcription which forms RFBP-RUSH
How can gene expression be altered
Histone proteins complexes have subunits which can be methylated to alter gene expression – they can also be acetylated which loosens the core and increases gene expression
DNA and histone methylation patterns also contribute to chromatin and the nuclear architecture
DNA methylation – heterochromatin (epigenetics)
Euchromatin transcription hotspots (highly organised)
How does DNA exist in the nucleus
DNA exists as a nucleoprotein complex known as chromatin (the protein is a histone)
Histones have 5 different classes 1H1, 2H2a, 2H2b, 2H3 and 2H4 =9)
What parts do histones control in the cell cycle
DNA replication during the S phase
Chromatin condensation (chromosomes)
What can phosphorylate histones
Cyclin dependent kinases (CDK)
Where are the sites of post-translational modification
The N-terminal histone tails are the sites of post-translational modification (including phosphorylation)
What does histone acetylation refer to
Up to 4 acetyl groups can be added to H3 and H4 by histone acetylases or HAT enzymes which loosens the nucleosome
During interphase nucleus chromosomes become highly organised
Methyl transferase can methylate DNA, phosphatases and histone deacetylases (HDAC) remove acetyl groups and phosphate groups (condense the DNA)
What regions do chromosomes occupy in the nucleus and what happens there
Chromosome territories
Interactions with the nucleoskeletal proteins, inner membrane proteins (lamin) and chromatin provide organised euchromatin – these are regions where gene transcription will occur
CTCF = (CCCTC) binding factor (zinc finger protein)
How does DNA organisation differ in stem cells to terminally-differentiated cells
DNA structure can be modified biochemically which alters how tightly this wrap is
Loose wrap = euchromatin
Tight wrap = heterochromatin
What effects the how tightly wrapped DNA is
Phosphate groups give DNA negative charge due to their negative dipoles (due to the oxygen atoms they contain)
Methyl groups lack oxygen but are hydrophobic
Adding methyl groups creates “sticky” patches resulting in heterochromatin
Acetate is negatively charged which repels the already negative histones resulting in euchromatin
What gene codes from DNA methyltransferase and what cells express it
Embryonic stem cells express the gene DNMT3L which codes for a DNA methyltransferase chromatin remodelling enzyme
This results in euchromatin that allow for the expression of stem cell specific genes like hTERT
Genes that are required for tissue specific differnetiation are closed off
This is what allows stem cells to remain unspecialised and immortal
What is the nucleolus
An organised nuclear domain which is the site for ribosome synthesis
What are nucleolar organising regions
(NOR)
on p arms of chromosome 13,14,15,21 and 22 aggregate, along with rRNA and ribosomal proteins (densely stained regions within the nucleus)
What are ribosomes composed of
Ribosomes are proteins / rRNA complexes
There are 2 subunits 40s and 60s in higher eukaryotic cells
How is rRNA transcribed
Initiation factors (UBF, SL1 and TIFIA) bind to upstream of rDNA gene which promotes RNA polymerase I binding
A t-Utp sub-complex is necessary for the transcription of the pre-rRNA molecule
What does the nuclear pore complex have to prevent large molecules entering freely
Has a hydrophobic cloud that surrounds the pore which allows for the regulation of traffic
What is the weight threshold for molecules entering the nucleus
Anything larger than 40KDa cannot leave through a nuclear pore unless a carrier protein is bound to it to transport it
How is mRNA exported out of the nucleus
Requires many steps due to its size
Is a complex between nucleic acid and protein (RNP)
How is mRNA modified
RNA is extensively edited (5’ methyl cap and the 3’ poly-A tail)
Splice factor proteins associate with splice sites
What factors are used to export mRNA
Nuclear export factor (NXF1) and nuclear export transporter (NXT1) are made of hydrophobic residues and associate with RNA and ancillary proteins
What is the function of NXF1 and NXT1
This will carry RNP through the pore
These will diffuse back into the nucleus after they are released from the RNP
