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12 Cards in this Set

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What are the roles of the 3 Eukaryotic RNA polymerases

1.RNA polymerase I=transcribes genes that encode for rRNA




2.RNA polymerase II=transcribes genes that encode all proteins and micro-RNAs




3.RNA polymerase III=treanscribes genes that encode tRNAs as well as some other small RNAs

define gene expression

gene expression= the production of an active gene product( ex protein, mRNA)

Compare and contrast gene expression in prokaryotes to eurkayotes





describe the possible steps at which gene expression can be regulated in eukaryotes

1.intitaion of transcription


2.transcript processing(including alternative splicing)


3.export of mRNA from the nucleus


4.translatability of the message


5.localization of protein products in specific organelles in the cell


6.post-translational modification to the protein,(e.g. cleavage, phosphorylation....)

describe the 3 types of cis-acting elements:


promoters


promoter-proximal elements


enhancers

promoters- close to the gene, always including the initiation site for transcription (aka +1), sometimes contains TATA box, sometimes contain DPE( downstream promoter element),


binding RNA poly to TATA or DRE allows fro basal level transcription




Promoter-proximal elements- sequences 200bp upstream of promoter that bind transcription factors.(GC box CCAAT boxes),




Enhancers- are regulatory sites that can be quite distant from the promoter,binding of enhancer increase or decrease level of transcription





Describe the method to detect promoters and enhancers

can identify promoters and enhancers by making reporter constructs with a resumed regulatory region hooked up to a reporter gene(ex.LacZ GFP)


-used in vitro mutagenesis across the regulatory region and then reintroduce the reporter constructs into the genome by transformation, look for increase or decrease level of transcription

define transcription factor, including basal factor or TAFs

transcription factors- trans-acting proteins control transcrition intitaio.




basal factors assist in binding of RNA polymerase II to the promoter and the initiation of a low level of transcription called basal transcription




TAF= TBP- associated factor ( TBP=TATA binding protien)

describe how DNA binding sites can be found analyzed by chromatin immunoprecipitation (ChIP) techniques

ChIP=The use of antibodies to isolate specific regions of chromatin and to identify the regions of DNA to which regulatory proteins are bound.


1.treat proteins so they can cross-link with DNA


2.break chromatin into pieces


3. add antibody to target protein and purify


4.reverse crosslink to separate DNA and protein


5.amplify and sequences DNA segment of interest

compare and contrast activators and co-activators




make into multple questions



Activators


-increase transcription activity by binding to an enhancer element and directly or indirectly interacting with basal factors at the promoter



describe the role of a Mediator

Mediator = one of the most important protein coactivators, a large multiprotein complex composed of 25-30 proteins


-the mediator does not bind to DNA but serves as an essental bridge between promoter and enhancer for many of the pol II promoters in eukaryotic organisms



describe the common domains of transcription factors

d

compare repressors and co-repressors

Repressors


Co-repessors