Bonev - Protein complexes Flashcards
What is the motif found at promoter regions upstream of the coding gene?
TATA box
There are three pathways following the initial binding of the trnacription factor to the promoter region, what are they?
- Binding of a secondary TF protein to the initial TF
- Binding of a secondary TF protein to DNA adjacent to the promoter region
- Secondary TF binds to a region further away from the promoter region, possibly at -75. This can cause the DNA to bend.
RNA Pol2 requires TFII, where does TFII bind at?
-10 position promoter site
How is the TFII able to recognise the TATA box?
It contains TBP (TATA box Binding Proteins)
What do these TBPs do?
Bend and unwind the protein to allow further proteins to act on the DNA
How does this bending of DNA help TFII(D)?
The bending allows the TFIID to come into closer proximity with the specific TF found at the enhancer and this causes a protein-protein interaction to initiate transcription
TFIID, where does it recognise DNA?
In the minor groove
Why is this important?
It leaves the major groove available for other proteins to act on the DNA
Which fits into the minor groove of DNA, beta sheets or alpha helix?
Beta sheets
TFIID contains Phenylalanine, what is the role of this aromatic amino acid?
Phe intercalates between specific bases of DNA and forms ring-ring hydrophobic interactions. This stabilises the interaction between the DNA promoter region and TFIID. Bending at about 110º
What does the binding of TFIID to the minor groove help RNA Pol2 to do?
RNA Pol2 can then bind to DNA at the major groove
Which two transcription factors are involved in the switching of lyosegnic state to lytic state in the E.coli when it has been infected by a bacteriophage?
The lambda repressor and Cro
How does lambda repressor transcription factor work?
It binds to the operator sites of the lambda DNA which prevents the expression of genes necessary for the lytic cycle. It blocks the promoter and prevents the RNA Polymerase from working. Therefore, it remains in the lysogenic cycle.
How does cro work?
Cro protein binds to the same operator sites as the lambda repressor and outcompetes it and disrupts its binding. This means RNA Polymerase can initiate transcription and the lytic cycle can start properly.
How does lambda repressor bind to DNA?
Using the helix-turn-helix motif
How is the stability of the HTH motif maintained?
Hydrophobic interactions between the surfaces of the two helices between each other
Where is the binding to the DNA by the HTH motif?
At the major groove. Alpha helices is 12º in size, major groove is 12º in width, making it a good fit.
How is the HTH motif able to recognise and be specific to the major groove?
Hydrogen bonding between the sidechains of residues in the helix, and the exposed portions of base pairs found at the major groove DNA