Transcriptional circuits in prokaryotes and eukaryotes Flashcards
What is a transcriptome?
The transcriptome is the segment of the genome that is transcribed.
What percentage of a prokaryotic genome is transcribed?
Only about 50%.
What is an abundant transcript?
It is a type of gene which gives rise to many copies of RNA.
What is a rare transcript?
It is a type of gene which does not produce many RNA copies.
What is a no transcript?
It is a type of gene that produces no RNA copies.
What is an inducible gene?
The transcription is induced via a stimulus (turning it from a no/rare transcript to an abundant transcript).
How many directions does RNA polymerase move in?
RNA polymerase only moves in one direction.
What are enhancers? Where do they reside? What do they contain?
- An enhancer is a short DNA sequence that can be bound to a protein to increase the chances of transcription of a particular gene.
- They can reside 5’ or 3’ to a transcription unit and can also be found in the introns. They are not immediately adjacent to the site of transcription.
- They contain DNA sequences that are very strong binding sites for transcription factors.
Expand on the stability of recruitment of RNA Polymerase II to promoters.
- In both eukaryotes and prokaryotes, RNA polymerases can’t make stable contacts with DNA, they simply slide along.
- Once stably recruited, the RNA polymerases convert from a closed complex to an open complex.
The recognition of promoters is mediated by initiation factors. What are these factors in prokaryotes?
It is the sigma factor, which recognises the -35 and -10 motifs common to prokaryotic promoters and enables the RNA polymerase to make stable contact with DNA.
The recognition of promoters is mediated by initiation factors. What are these factors in eukaryotes?
It is the TFII basal transcriptional machinery (TFIIA, TFIIB, etc.). [RNA synthesis lecture]
What is the function of regulatory transcription factors?
- They function to dramatically alter the level of recruitment of RNA polymerase and/or its ability to initiate transcription.
- In eukaryotes they can influence local chromatin structure.
What are the transcriptional switches in prokaryotes (1) and eukaryotes (3).
Prokaryotes:-
- The lac operon
Eukaryotes:-
- Oestrogen - responsive transcription.
- Tissue - specific transcription (beta-globin).
- A complex regulatory circuit (cell cycle).
Describe the lac operon.
- It is found in prokaryotes. It is activated when lactose is available (and glucose is not). Its function is to use lactose as an energy supply.
- There are 3 genes associated with this: lacZ, lacY and lacA. (LacZ encodes the enzyme beta-galactosidase, which breaks lactose down to its monomers, galactose and glucose. LacY encodes the protein lactose permease, which is a transmembrane ‘pump’ that allows the cell to import lactose. LacA encodes an enzyme known as transacetylase that attaches a particular chemical group to target molecules). (the genes are extra info)
When lactose is present:-
- When lactose is present it binds to the repressor causing the repressor to change shape so it can no longer bind to rage operator site.
- The CAP protein binds to the promoter and this allows RNA polymerase II to bind to the promoter.
When lactose is absent:-
- The regulatory gene produces a lac repressor (a transcription factor) that binds to the operator site on the lac operon.
- This blocks transcription as RNA polymerase cannot bind to the promoter.
Structure of lac operon.
- There is a CAP site (catabolite activator protein site) before the promoter (site of RNA polymerase binding), and an OPERATOR site after it.
- The CAP site is a positive regulatory site (when CAP is bound it promotes transcription) bound by the catabolite activator protein.
- The operator site is a negative regulatory site (when lac repressor is bound it prevents transcription)
Can an intact DNA molecule present information to the cell, and why?
Yes, it can, because regulatory factors can recognise their target sequences by interacting with the DNA; the DNA double helix doesn’t need to be unwound.
Describe oestrogen-responsive transcription.
- An oestrogen molecule binds to a free oestrogen receptor complex, which binds to the oestrogen-responsive element on the mRNA.
- This stimulates the recruitment of general transcription factors and RNA polymerase.
What is tamoxifen? What can it be used to treat?
- Tamoxifen is an antagonist of oestrogen-responsive transcription.
- Its binding to the oestrogen-responsive element will prevent transcription of oestrogen.
- It can be used to treat breast cancer.
Describe tissue-specific transcription (specifically beta-globin).
It has a beta-globin specific transcription factor, GATA-1, which makes the cell lose its nucleus, etc.
