Transcription Flashcards
Explain the concept of wobbling taking G:C as an example
Compared to a C:G base pair, the wobble T:G is shifted up so that the bases wobble. Only two hydrogen bonds.
Taumerisation
Taumerization is that the ring in the bases has two different forms, of which one can form an alternate (incorrect) base pair. This equilibrium between the two forms can lead to incorrect base pairing and translation of the genetic code.
DNAP, Induced fit
DNA-Polymerase has a clamp that closes at correct base-pairing, giving a tighter active seat and reaction speed.
The two roles of K-acetylation by HATs
Catalyses the reaction of acetylation of lysine.
Makes DNA recognisable by bromo-domains.
A complex that runs acetylation
SAGA
What domain of what protein recognizes acetylated lysine
Bromo-domains of co-activators, which has it because it’s a catalytic subunit that catalyzes hyperacetylation of histones near the promotor region. Co-activators are a type of translational co-regulator to increase the rate of transcription, which means that if the co-activator has this domain, it can then make it accessible for the transcription factors
Methylated lysine is recognizes by what domain?
Chromo-shadow-domains
H3K9 methylation results in gene silencing, how?
HP1 has chromo-shadow-domain and also binds H3K9 HTM (histone methyl transferase) to methylate another nucleosome
to create a binding site for the chromo domain
of the next HP1.
HP1 proteins associate with each other as well, through their chromo-shadow domains.
HP1 binding spreads the chromatin leading to its condensation into heterochromatin.
H2K27me3 is recognized by the polycomb complex.
RNAPII CTD
RNAPII CTD is the RNAPII’s C-terminal domain, involved in initiation of DNA transcription. Contains a repeat sequence of hepta-peptides with a consensus of YSPTSPS
CTD phosphorylation on Ser5
Is done by the Cyclin H-Cdk7 cyklin-kinase of TFIIH
Mediator (RNAPII initiation)
A huge multi-protein complex that interacts with the activation domains of the transcription factors together with the RNAP
What is the role of Mediator in the activation of transcription by RNAPII?
Conducts the activation signals from activators (transcription factors for example TFIID) bound to their response elements (specific DNA sequences) of the promotor (enhancers, TATA box for example) to the RNAP. It only plays a part during initiation
Why does mediator detach from RNAPII after initiation?
To make RNAPII available for further transcription initiation and does so when CTD is phosphorylated by TFIIH.
At which stage of mRNA synthesis does the CAP attachment to pre-mRNA occur
During transcription, when pre-mRNA is about 25 bases long
CAP
Catabolite Activator Protein
Cap formation is done by?
The capping enzyme attaches CAP during transcription, RNA at about 25 bases long
What are the roles of the Cap?
Protecting RNA from degradation
Recruits complexes involved with RNA processing, export and translation
Marks RNA as “self”
Spliceosome
Complex that splices introns from pre-mRNA
(pro) How are introns recognised in pre-mRNA?
By base pairing U1 and U2 which then recroute the rest of compex
Branching A in intron is defined how?
By jutting out when base-pairing U2:RNA
SF1/BBP and U2AF at splicing
U2AF promotes binding of U1 and U2
Intron recognition in high eucaryotes
Are super long and hard to define, so exons are
mRNA poly-adenylation
Poly-A-Polymerase (PAP) creates the poly-A tail after mRNA release from RNAP.
Signal of nuclear mRNA poly-adenylation
AAUAA
EJCs
Exon Junction Comlpexes
EJCs role in mRNA transport to cytoplasm
EJC forms where introns where, has Aly, acting as a bridge to RNA transporter Tap-15
Dbp5 helicase role in RNA transportation to cytoplasm
Hydrolysis of it stops RNA from “slipping” back, Browninan Ratchet model
TATA? No! Inr and DPE sequence recognition
Inr (Initiator) interacts with TAF1 and TAF2 and DPE (Downstream Promoter Element) interacts with TAF6 and TAF9
ISWI function
Organize the nucleosome by imposing regular and proper spacing between Nucleosomes (NSes) that lead to chromatin organization and condensation
SWI function
Roll NSes on DNA to open the binding sites for TFs
SWR1 function
Modulate histone composition in NSes. They replace the H2A histone with its promotor-boundry-specific H2A.Z variant, which is easily evicted from the chromatin by SWI machines
(euc) Repressors
Bind at or near the promotor and lock the access of RNAP to it
trigger loop
closes over active site of RNAP at correct (WC) base pairing
