Advanced Molecular Exam 3 Transcription regulation

a transcription factor has 4 domains

DNA binding, dimerization, regulatory, trans activation

binding domains are sensitive to

B dna and Z dna, in bdna it usually fits into the major groove

dna binding domains typically bind to ___ nucleotides and can be

6-8, consensus, methylation sensitive

trans activational domains can sometimes be 

negative, pull things out of position, can act as both a repressor and an activator 

2 hybridization assay

uses the ability of the activating domain and the binding domain to search for protein interactions and see where transcription is active

dimerization domain

hetero and homo dimers form which results in a wide variety of dna binding sites and different combonations that can be recognized by just a few TF this is called combonational control

regulatory domain

changing shape of the TF which will change the function.

positive vs negative effector activators 

+ effector activator binds and dna binds, - effector takes activator off and dna no longer binds 

positive vs negative repressor effector

+ repressor binds, no dna. - repressor is taken off, dna binds

where do negative effectors bind

at the allosteric site

rho dependent termination in prokaryotes 

Rho attaches to recognition site RUT, rna poly pauses at termination site, rho catches up. rho unwinds the dna-rna from the transcription bubble. rna poly,rho, and rna are released. 

rho independent prokaryotic termination

rna poly reaches t site, which contains sequences to form hairpin loops. T site RNA has AAA which disrupts hydrogen bonding and causes everything to fall apart.

what is the first rho terminator called? can there be multiple 

the attenuator, yes

attenuators are regulated by?

translation, decides whether the attenuator is used or if the final termination site is used

in translation, the RNA to make TRP can form two possible secondary structures

2&3 form preemptor loop when TRP is put in slow, 3&4 form attenuator loop if TRP is put in fast 

many essential amino acids needed are made in

prokaryotes because they require attenuation

loops can also be controlled by metabolites which are called

riboswitches

eukaryotic termination

termination coupled with adding the poly A tail or a nuclease cutting the RNA

non canonical eukaryotic 5’ caps

less common and include structures like NAD cap which can help with RNA folding and stability

key enzyme that adds the 5’ MG cap

guanalyl transferase

what does a phosphohydrolase do 

removes the gamma phosphate before the 7-methyl guanosine to the transferred chain

release of the capping enzyme allows for

splicing enzymes to be added next