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36 Cards in this Set

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  • Back
describe the function of -35 and -10 elements in bacterial promotors
at these consesus sequences the sigma subunit binds and enables the RNA polymerase to recognize the promoter site.
Which subunit of bacterial RNA polymerase increases the affinity and specificity for binding of the polymerase to the promotor?
sigma subunit
function of sigma subunit
recognize and bind RNA polymerase to core promoter
steps of bacterial transcription initiation
1.RNA poly finds genes promotor. The initial complex of RNA poly and promotor is closed binary complex.
2.RNA poly unwinds short segment of DNA around transcriptional start site making an open complex which allows RNA poly to have a single DNA strand
3. RNA poly initiates mRNA synthesis . the complex of RNA poly, DNA, and RNA is known as the ternary complex
4. RNA begins transcription and sigma falls off and elongation begins
How do different sigma factors induce different gene expression?
different sigma factors recognize and promote binding of RNA poly to diff -35 and -10 elements that are in diff core promoters that control expression of another gene
how does lactose affect lac operon expression?
with lactose, a lac repressor binds to the operator in the lac promotor so that RNA polymerase cant bind to the promotor so there is no lac operon expression.

When lactose is present, the lac repressor binds to allolactase and dissociates from the operator so the promotor is free and the RNA polymerase can bind and the lac operon can be expressed if glucose is lo and lactose it hi
How does glucose affect lac operon expression?
when glucose is lo the cAMP conc is hi. CRP is complex with cAMP will bind to CRP site upstream of lac promotrer. The CRP bound helps RNA polymerase to bind to the promotor enhancing lac operon expression.

with hi glucose, cAMP is lo so CRP does not bind to site. Without CRP, RNA polymerase wond bind to lac promoter effiently and lac operon wont be expressed
How trp repressor regulates trp operon expression
when tryptophan conc. is hi, trp repressor binds to tryptophan and this binds to the operator at the trp promotor so RNA poly can bind to trp promotor and tryptophan is not expressed.

when tryptophan is not v.hi, but still hi, the trp repressor will not bind to the operator bc no trp is bound to it, so RNA poly binds to promoter and transcribes trpL the first gene in typ operon
what happens if bacteria is grown in both glucose and lactose?
the lac repressor binds to allolactase and is inhibited BUT cellular cAMP is lo therefore CRP is lo so lac operon genes are shut off
only way trp repressor is capable of binding to trp operator
in presecne of hi tryptophan bc tryptophan is the corepressro
only time trp is repressed
when very high. the trp binds to the repressor which binds to the operator which binds to the promoter so RNA poly cant binds. IT IS REPRESSED
what are the roles of 1-4 in trpL mRNA and the rate of translation of trpL mRNA in attenuation of trp operon trancription?
when trp conc is hi, trpL DNA is transcribed by RNA poly, making trpL mRNA that contains sequences 1-4. Ribosome quickly translates sequence one, blocking sequence 2 before 3 is transcribed. 3 forms attenuator site with 4. this terminates transcription of trp enzymes and gens. the trp operon expression is ATTENUATED.

when trp is low, the ribosomes pause at the trp codons in sequence one so sequence 2 and 3 can form a bond. this stops 3 from pairing with 4 so ATTENUATIOIN wont occur and transcription of trp enzymes and genes will continue and trp operon will be expressed
basic steps of transcription initiation by eukaryotic RNA polymerase II
1. RNA poly II and IF assemble at core promotor to form closed complexed (before initiation occurs)
2. RNA poly II and IF form open complex but need ATP
3.RNA poly initiates mRNA synthesis by catalyzing first phosphodiester bond using DNA as template
4. IF are released and elongation occurs
2 ways Bacterial and eukaryotic transcription initiation differ
1. eukaryotic RNA poly II cant bind independent to core promotor, it needs assistance from TF (similiar to sigma)

2.Eukaryotic RNA poly II needs ATP to make a open complex where bacteria does not need ATP is just uses isomerization
What is the role of TFIID (TBP and TAF)in eukaryotic transcription initiation?
TFIID is the 1st TF that binds to the core promoter. Through its TBP subunit, TFIID binds the TATA box in the core promoter formind the nucleus for initiation complex assembly. The other subunits in TFIID are TBP associated factors or TAFs. TAFs bind to the initiaor element in the core promoter. Other TAFs contain bromodomains that bind acetyl lysine residues in a histone tail.
binds to site upstream of TAFs. stabilizes the TFIIB and TBP to promotor
binds to TBP at core promotor and recruits RNA poly to the promotor
binds to RNA poly II. stabizes binding of RNA polyII to TFIID and TFIIB at core.

Required for entry of TFIIE and TFIIH into preinitiation complex
TFIIE works with TFIIH to promote ATP dep. formation of open complex
last transcription factor being assembeld into the initiation complex. TFIIH contains ATP dep. DNA helicase that hydrolyzes the ATP and unwinds the DNA near the start of transcription forming an open complex. TFIIH has kinase to phosphorylate the CTD of RNA of poly II releasing the polymerase from the initation complex at promoter to start elongation
What are the locations ofTATA box, UAS and enhancer in eukaryotic gene and the function of these DNA elements in regulating gene expression?
TATA is used to locate core promoter and is the binding site of TFIID (TBP).

UAS is at fixed distance from core promoter. Binding site for transactivatiors that activate the transcription initiation. binding here causes initation complex. The orientation between spacing betwee 2UAS are fixed

Enhancer is at variable distance from core promoter either US or DS or wi it. it is the binding site for transactivators that activate ther transcription of initiation (enhancer increases promoter activity)
How can DNA binding transactivator bound to an enhancer thousand base pairs away from core promoter affect the activity of RNA polymeraseII bound to core promoter?
DNA between the enhancer and core promoter is looped so that the transactivator and polymerase are close. Co activators can mediate the interaction between the transactivator and the polymerase
What are the functions of helix turn helix, zinc finger, and leucine zipper?
helix turn helix is the most common DNA binding domain in prokarotic transcriptional regulatory proteins.(seen on proteins that bind to DNA as dimers Ex: trp repressor

ZincFinger is a DNA binding motif commonly found in eukaryotic transcriptional regulatory proteins.

leucine zipper is a protein binding motif found in eukaryotic transcriptional regulatory proteins
problem for eukaryotic gene expression
nucleus is small and tons of DNA so DNA must be packaged so assemble DNA into chromosomes. Chromosomes consist of linear DNA moleuces associated w/protein that fold and pack it called chromatin
basic structural element of chromatin
What seperate nucleosome
linker DNA
describe components of nucleosome core, histone core, and nucleosome.
nucleosome core has 146 bp of DNA and a histone core.

The histone core has 8 histone proteins(2 copies of H2A,H2B,H3,and H4)

Nucleosome contains 166 bp of DS DNA wrapped around a histone core, and another histone protein, H1.
distinguish transcriptionally active and inactive regions of chromatin by two characteristics
transcriptionally active regions of chromosmes are found in a more loosely packed structure and transcriptionally inactive regions of chromosomes are found in more tightly packed structure
What kind of enzymes can be recruited to chromatin by transactivators that bind enhancer or UAS?
Histone acetylase and chromatin remodeling enzyme
How does Histone aceylase and chromatin remodeling enzyme enhance gene expression?
hisone acetylase acetylates histone proteins, reducing the nuceosome packing. Chromatin remodeling enzyme shifts the position of nucleosomes along the DNA. both rxns expose the chromosomal DNA for binding of regulatory protins and transciption crap
What is the effct of histone acetylation on nucleome packing?
histone acetylation unpacks the nucleosome
What are the proteins that can bind aceylated histones?
the TF like TAFII250 (which have 2 bromodomains) and the chromatin remodeling enzymes that have 2 bromodowmains
How Myc-Max dimer activates gene expression
Myc-Mac dimer binds to the E box element in DNA, recruits co activators that contain the histone aceylase activy. suggests that the myc protein may activate transcription through regulation of histone acetylation
How Mad-Max dimer represses gene expression
mad-max dimer binds to E box in DNA and recruits repressors like histone deaceylase which cause transcriptional silencing
How does estrogen receptor regulate transcription
Binding of estrogen to estrogen receptor changes the conformation of the receptor so that the receptor can recruit a co activator.

basically estrogen binds to a receptor, the receptor has a ligand binding domain and a DNA binding domain which modifies expression of genes by binding to control elements in DNA called estrogen response elements. The DNA binding domain binds the ERE through Zinc finger motiff.
How does anti cancer drug tamoxifen work?
treats breast cancer. binding of tamoxifen to estrogen receptor changes the conformation of the receptor so that the receptor cant recruit the co activator so tamoxifen inhibits the activation of gene expression by extrogen receptor and the growth of the estrogen dep breast tumors:)