Advanced Molecular, Transcription Regulation

4 domains of a transcription factor

DNA binding domain, transactivation domain, dimerization domain, regulatory domain

DNA binding domain is sensitive to what

methylation, secondary structure

DNA binding domain adhesion

fits into major groove of the alpha helix, 6-8 specific nucleotides in a consensus sequence

main focus of a transactivation domain

activates transcription by interactions with mediator, polymerase, etc

transactivation domains can sometimes have a negative effect

pull things out of position

2 hybrid assay

uses the ability of the DBD and AD to separate from each other to search for protein interactions

dimerization domain

TF can dimerize and form homo/hetero dimers that results in a wide variety of dna binding sites and expression

what is it called when the dimerization domain uses just a few TF for binding sites

combinational control

regulation domain

changes the shape of TF to change the function such as metabolites in prokaryotes

activator metabolites in prokaryotes

+effector, activator binds, -effector, takes activator off

repressor metabolites in prokaryotes

corepressor, repressor binds, -effector/inducer, takes repressor off

T/F eukaryotes have more than one promoter that is used dependent of splicing

true

rho dependent transcription termination in prokaryotes

rho attaches to rut site on RNA, polymerase pauses at termination site for rho to catch up. rho unwinds the DNA/RNA hybrid in transcription bubble. rho,rna polymerase, rna released

rho independent termination in prokaryotes

rna poly reaches T site which contains sequence for hairpin loop. loop followed by AAA which disrupts H bonding and causes everything to fall apart

more than one rho-independent terminator can be found located on the 5’ end. this is called an

attenuator

trp 2+3 form, this is a

preemptor loop, trp is put in slow, we need to keep making more

trp 3+4 form this is a

attenuator loop, trp is put in fast, we can stop early

can humans form attenuation loops

no

additional way to control loop formation in prokaryotes

riboswitches, example lysine as an anti-anti terminator loop