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BIOC221 - Transcription in eukaryotes
Terms in this set (70)
RNA polymerase B (subunits of RNA Pol II).
C-terminal domain of the RPB1 subunit of RNA polymerase II that is phosphorylated during transcription.
An enzyme that cataluses the transfer of a phosphoryl group from ATP to another molecule (phosphorylates proteins).
An enyme that hydrolyses phosphryl esters groups (dephophorylates proteins).
Rpb1 and 2
Catalytic RNAP subunit. Similar to beta subunits of prokaryotic RNAP.
Rpb3 and 11
Involved in complex formation. Similar to alpha subunits of prokaryotic RNAP.
Involved in complex formation. Similar to the omega subunit of prokaryotic RNAP.
Not essential in vitro. These subunits are involved in stability, neculeosome remodelling and mRNA processing in vivo.
Makes most rRNA. Located in the nucleolus. Is essential.
Makes mRNA, snoRNA and some snRNA. Located in the Nucleoplasm. Is essential.
Makes tRNA, 5s rRNA, some snRNA and other small ncRNAs. Located in the nucleoplasm. Is essential.
RNAP IV and V
Makes regulatory ncRNA. Located in the nucleoplasm.
Nuclear encoded polymerase
Makes rRNA, tRNA and mRNA. Located in mitochondria and plastids. Of viral origin.
Plastid encoded polymerase
Makes rRNA, tRNA and mRNA. Located in plastids. Of bacterial origin.
Basic parts of RNAP II
Cleft, clamp, wall, pore, catalytic site, bridge, DNA-RNA hybrid helix, rudder and exit.
(RNAP II) DNA enters and is unwound. This part of RNAP II has helicase activity.
(RNAP II) Closed when RNAP II is active.
(RNAP II) Bends template strand into active site.
(RNAP II) NTPs enter.
(RNAP II) Template base is exposed to NTPs. When correct NTP binds, a new phosphodiester bond is formed.
(RNAP II) Pushes paired nucleotide from active site.
DNA-RNA hybrid helix
(RNAP II) 8 to 9 base pairs after the RNAP II active site. Is important for stability during transcription and aids in proof reading.
(RNAP II) Separates DNA and RNA.
(RNAP II) RNA transcript leaves.
(RNAP II) 1) Mismatch is detected, due to tension in the DNA-RNA hybrid helix. RNAP II backtracks over the DNA and 3' end of RNA enters the pore.
2) Nuclease in the pore will remove the mistake.
3) Transcription resumes since the 3' end is in the active site once corrected.
(of Rpb1) A heptapeptide repeat (Tyr-Ser-Pro-Thr-Ser-Pro-Ser) involved in interacting with other proteins. It can be reversibly phosphorylated (at Ser2 or Ser5) to alter interactions with other proteins during transcription.
Transcription start site.
The DNA sequence at which the general transcription factors bind and recruit RNAP II.
The entire regulatory region around the transcription start site. Includes the core promoter.
Conserved basic proteins to which DNA is bound.
The complex of a histone octamer and ~200 bp of DNA.
(HAT) Enzyme that catalyses the acetylation of histones.
(HDAC) Enzyme that removes acetyl groups from histones.
(HMTase) Enzyme that transfers a methyl group from a donor to a histone.
Enzyme that removes a methyl group.
Also called a chromatin remodeler. An ATP-dependent complex which either moves, ejects or restructures nucleosomes.
A protein which binds histones and prevent them from interacting with DNA.
(CRE) A DNA motif to which activators and repressors bind (cis = "on the same molecule").
A short recurring pattern in DNA that is presumed to have biological function. Often indicate sequence-specific binding sites for proteins.
Proteins that activate/promote transcription. A type of transcription factor.
A protein complex recruited by activators that aids in chromatin remodeling at the core promoter and PIC formation.
N-terminal tails of histone
These extend beyond the nucleosome ad are accessible for chemical modification, altering the nucleosome.
Bind to acetylated lysine residues of histone.
Bind to methylated lysine and arginine residues of histone.
(PIC) A complex formed by RNAP II, activators, co-activators, re-modelers and general transcription factors.
General transcription factor
(GTF) Eukaryotic proteins required for the recruitment of RNAP II to the core promoter and formation of the pre-initation complex.
(GTF) Recognises the core promoter and recruits other GTFs.
TATA binding protein, a part of TFIID.
TBP-associated factor, a part of TFIID.
A region of DNA in some core promoters, recognised by the TBP.
(Inr) The region around the transcriptional start site (TSS) and part of some core promoters recognised by TAFs.
Downstream promoter element. A region of DNA in some core promoters recognised by TAFs.
(GTF) Stabalises binding and helps recruit RNAP II.
(GTF) Stabalises binding.
(GTF) Helps recruit RNAP II to the PIC. It binds to RNAP II and escorts it to the complex.
(GTF) Interaction with DNA and aids recruitment of TFIIH.
(GTF) ATP-dependent helicase activity and kinase activity for the phosphorylation of the CTD.
An enzyme that unwinds a double stranded nucleic acid.
(CE) Adds an inverted guanine to the 5' end of the an mRNA transcript. Has triphosphatase and guanylyltransferase activity.
(RNMT) Adds a methyl group onto nitrogen 7 of the guanine base on the 5' end of an mRNA transcript.
Positive transcription elongation factor b, is a kinase that phosphorlates Ser2 of the CTD and promotes elongation.
Proteins associated with the CTD of RNAP II that recognise and bind to splice sites in the mRNA transcript. They mark the sites where introns will be removed.
Transcription elongation factors
Proteins tat enable rapid transcription by RNAP II.
Cleavage and polyadenylation specificity factor.
Cleavage stimulation factor.
Poly-A polymerase, it adds multiple A bases to the 3' end of an mRNA transcript.
An enzyme that degrades nucleic acids from the ends.
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