Transcription Flashcards
Describe the Prokaryotic RNA polymerase holoenzyme and its roles.
A sigma subunit, two alpha, beta, and beta prime. Sigma is what locates and binds to the promoter.
Describe initiation, elongation, and termination in prokaryotic transcription
Binds to promoter via sigma factor. Elongation: ATP comes and sends it off once the 5’ to 3’ RNA to DNA linkage is made, no need for primer, addition of nucleotides to 3’ end. Sigma dissociates.
Termination: dissociation of the trimeric complex, RNA polymerase, transcript, DNA. Termination is done by DNA encoded RNA signals.
Describe the two types of termination.
Rho dependent: The Rho protein is encoded by DNA but binds to RNA. When it reaches the sequence, ATP fires the torpedo to the complex and it shoots up, boom termination.
Rho independent: uses hairpin structures, the ribosome stalls and then falls off.
What does rifampicin and amanitin do?
rifampicin inhibits Prokaryotic RNA polymerase and amanitin inhibits RNA polymerase II>
What are the three eukaryotic RNA polymerases.
Pol 1- rRNA
Pol 2- mRNA
Pol 3- 5S rRNA, tRNA.
What are the eukaryotic transcription elements?
TATA box (Binds TBP), a Downstream promoter element, the transcription start site = core promoter.
Proximal promoter = the CPG islands (upstream)
Enhancers are 250 bp from the start and function in either orientation. They are binding sites for activators.
The BRE binds TFIIB
Describe TFIID
Contains the TBP which binds to the TATA box. It also has TAFs, TBP associated factors. It nucleates the preinitiation complex. Then TFIIB binds to the BRE. Then a bunch of things come and it ends with TFIIH, which locally melts the double strand DNA so RNA polymerase can finally bind and elongation can start. TFIIH also couples transcription with DNA repair and mutation leads to XP, Cockayne,
RNA processing.
During elongation, a 5’ cap is added.
For termination, a cleavage signal is read and then onto the cleaved end, poly A tail is added in a nontemplated manner.
Energy requirements (transcription
NONE. As is for replication, all necessary energy is stored in the nucleotides.
PS, prokaryote DNA has no histones.
Splicing is ATP dependent!
The beta globin gene.
Exon 1 + intron 1 + exon 2 + intron 2+ exon 3.
Describe splicing.
Splicing is usually done co-transcriptionally. The 2’ OH on the branch site attacks the 5’ splice site (donator site). The 5’ Ss OH will attack the 3’ Splicesite (acceptor site). Two transesterfication reactions.
SPliceosome assembly
U1 binds the 5’ ss. U2 binds the 3’ ss. Recruits SNuRPs and other U proteins to assemble the spliceosome which bends the mRNA and faciliates that shit.
Describe steroid transcriptional regulation.
Steroids are all derived from cholesterol. Steroid hormone receptors have a DNA binding site and a ligand binding site along with an activation domain and a dimerization domain. They bind to enhancers which are palindromic. Then when the steroid binds it will recruit coactivators that may modify histones with tail modification or ATP dependent chromatin remodeling. The AD has no specificity and recruits activatiors.
Describe the glucacorticoid receptor and tamoxifen. Tamoxifen is an estrogen receptor antagonist. No conformational change in the receptor that will recruit the coactivators. Used to treat breast cancer.
Cortisol binds to the receptor before the Zinc finger DNA binding site is exposed. After that it can recruit basal transcription factors (TFIID), bring acetyl transferase, recruit ATP dependent chromatin remodeling enzymes to increase accesibility of RNA polymerase Ii
Estrogen receptors bind as dimers and recruit coactivators which recruit chromatin remodeling proteins.
How do repressors regulate gene expression?
Binding to operators- prokaryotes
