Transcriptional Circuits in Prokaryotes and Eukaryotes Flashcards
What is the name of the segment that is apart of the genome and is transcribed
Transcriptome- only a fraction of the transcriptome is transcribed at any one time.
What are the different levels that genes can be transcribed at?
- Abundant transcript: housekeeping genes e.g. glycolic enzymes
- Rare transcript: not expressed as much
- No transcript: tissue specific e.g. globin
What is a stimuli?
Stimuli can activate activated transcription to create mRNA scripts such as hormones; these are inducible genes.
What does transcription require for it to occur?
They require recognition sequences that can be found on the outside of the transcribed region.
What are promoters?
It is the sequence that is found before the 5’ end and it has the job to recruit RNA polymerase to a DNA template.
What are enhancers?
Sequences of the DNA that are not immediately adjacent to where transcription starts, have the role to enhance the recruitment of RNA polymerase to a promoter.
They can reside 5’ or 3’ to a transcription unit and can even be located within an intron.
They contain DNA sequences that are very strong binding sites for transcription factors.
By definition:
Enhancers are DNA sequences that activate transcription in a position (you can delete the enhancer
from a gene and we can copy it and the enhancer will still work) in a dependant manner and also in orientation (we can cut the DNA and reverse it in the same position and the enhancer will still work) in a dependant manner.
What is the difference between a promoter and an enhancer?
Promoters contain a TATA box and if you cut the DNA and place it in an intron the RNA polymerase will bind and start transcription downstream, meaning it will not activate the expression of the gene; even if you were to reverse the RNA polymerase in the same position, the RNA polymerase will still move to the other end.
What is an issue with RNA polymerases?
They are not able to make stable contacts with DNA- they slide along the DNA without being able to recognise the promoters so it is difficult for them to be able to transcribe without the aid of initiation factors.
What are initiation factors?
Initiation factors are able to help mediate RNA polymerase recognise promoter regions.
In prokaryotes the initiation factor is called the sigma factor which binds to the promoter to recruit RNA Polymerase II.
In eukaryotes, the TFII basal transcriptional machinery are the initiation factors which recruit RNA Polymerase II.
What forms when RNA polymerase is able to be stably recruited to the DNA?
The RNA polymerase is able to convert from a closed complex to an open complex.
What is a consensus sequence and how does it work in prokaryotes?
It is an ideal promoter sequence which can be found in prokaryotes at -35 (TTGACA) and at -10 (TATAAT)- the closer the sequence is to the consensus sequence the stronger the promoter will be so the better it will be to bind to the RNA polymerase, and thus more mRNA can be created.
These sequences are not bound directly by RNA polymerase so the sigma factor recognises the -35 and -10 motifs common to prokaryotic promoters and enables RNA polymerase to make stable contacts with DNA.
Where is the eukaryotic promoter located?
The sequence is not directly by RNA polymerase II and has a consensus sequence. The TATA box is recognised by TBP (TATA binding factor). This consists of 10 binding proteins which includes the TATA binding protein which identifies the region.
What are the transcription factors that are required by Eukaryotic RNA polymerase II?
TFIID is a transcription factor which consists of TBP- this binds directly to the TATA box.
TFIIB bind and helps stablise the TFIID-TBP complex and helps RNA polymerase II recognise the +1 nucleotide in order to start transcription.
RNA polymerase II can now recruit TFIIE and TFIIH which helps initiate transcription.
What are the regulatory transcription factors?
-The ability of sigma factor and TFII to recruit RNA polymerases to promoters are GENERIC – i.e. they happen at every promoter
o This does not account for the ability to VARY the
level of transcription from a promoter.
-Regulatory changes are mediated by a different class of transcription factors = Regulatory Transcription Factors
-In both prokaryotes and eukaryotes they function to dramatically alter the level of recruitment of RNA polymerase and/or its ability to initiate transcription
-Additionally, in eukaryotes they can influence local chromatin structure (see CMB2.07 Chromatin structure and the histone code.
What are transcriptional switches?
They are examples of transcription factors. One well known example of a transcriptional switch is the Lac operon in prokaryotes (E.Coli) - a prokaryotic paradigm for the regulation of transcription. This was the first system where we understood how transcription was regulated.
