|Transcription ||RNA synthesis|
|How is gene expression controlled? ||A reticulate network of regulatory mechanisms interact to control when and where gens are expressed|
|When do regulatory mechanisms occur? ||All levels!
|3 types of RNA ||mRNA
tRNA, snRNA, 5S rRNA|
|mRNA function ||encodes polypeptide sequence|
|What is the relative abundance of mRNA ||lowest|
|What RNA polymerase is used in mRNA? ||Pol II|
|rRNA function ||components of ribosomes|
|What is the relative abundance of rRNA? ||Highest; 90%|
|What RNA polymerase is used in rRNA? ||Pol I|
|Function of tRNA ||aa carriers|
|Relative abundance of tRNA, snRNA and 5S rRNA ||Moderate|
|RNA polymerase used in tRNA, snRNA, 5S rRNA ||Pol III|
|Function of snRNA ||splicing|
|Function of 5S rRNA ||ribosomes|
|What is downstream? ||3'|
|What is upstream? ||5'|
|What is the numbering system for RNA transcription? ||The base where transcription starts is numbered +1.
Upstream bases are negative.
Downstream bases are postitive|
|What is the promoter? ||A region of DNA used to activate or repress transcription of a gene.|
|What is an enhancer? ||A region of DNA that regulates transcription like a promotoer, but can be moved relative to the gene it controls.|
|Can a promoter be moved relative to the gene? ||NO|
|Where are regulatory regions on mRNA? ||upstream from the gene|
|Where is the promoter usually at? ||Immediately upstream|
|Where are enhancers usually located? ||upstream usually great distances from their genes|
|What is a distinguishing characteristic of an enhancer? ||its 5' - 3' orientatino can be flipped in a transgenic expression assay while a promoter cannot|
|What is a minimal promoter? ||The smallest region of a full promoter that will drive detectable transcription.
|Can minimal promoters regulate? ||NO|
|What is a TATA box? ||Most minimal promoters for Pol II possess teh consensus sequence TATAa/tA.|
|What are TATAless promoters? ||Promoters that lack any sequences similar to the TATA box.
Expressed at LOW levels|
|What are AT rich sequences? ||Held more weakly because adenosines adn thymidines only have 2 specific bonds.|
|What is the initiation complex? ||a cluster of proteins that assemble around the TATA box to initiate transcription|
|TBP ||TATA Binding Protein
Protein that actually binds to the TATA box|
|TAF ||TATA associated factors
Other proteins that bind TBP|
|Where is the start of transcription? ||This is usually a purine (A>G)
26-34 bp downstream from the TATA box|
|What is the mechanism of action to the start of transcription? ||TBP first binds several TAFs in the nucleoplasm
These complexes then find a TATA box
Other TAFs are then recruited to form an initiation complex.
These complexes then attract an RNA polymerase which looks for a purine.|
|What do promoters for Pol I and Pol III lack? ||TATA boxes
TBP is still part of their initiation complexes|
|What is required to elevate and regulate transcription? ||upstream promoter and enhancer sequences|
|What are recognition sequences? ||Promoters and enhancers bound by proteins known as particular transcription factors.|
|What is a recognition dequence for TBP? ||TATA box|
|CCAAT box ||second most common recognition sequence.
Raises baseline transcription.|
|What is CCAAT box bound to? ||transcription factor called CP1|
|SP1 recognition sequences ||Third most common recognition sequence
Consists of GC rich regions 20-50 bp long and bound by SP1 transcription factor.
Common in TATAless promoters|
|Transcription factors ||proteins that bind recognition sequences to control transcription|
|DNA binding domain ||a region of a transcription factor that recognizes and binds a specific sequence of DNA.
|Activation domain ||region of transcription factor that induces RNA synthesis by attracting an RNA polymerase.
|Acid Blob Model ||Negative charge with little structure and few specific interactions.
Attracts RNA polymerase.|
|Four Observations of Acid Blob Model ||1) Activation domains are generally the most variable regions found in any gene.
2) While DNA binding domains have specific structures, activation domains often do not.
3) DNA binding domains must recognize specific sequences. Activation domains, all at|
|Why can enhancers and promoters not? ||Enhancers are far enough away.
Promoter is so close to transcription it can't move around and work the same way.|
|How do enhancers and promoters interact? ||Enhancers and promoters start interacting and wrap up to form a complex all clustered together. Negative charge is pushed to the outside.|
|Initiation complex ||Promoter, enhancer, TBP/TAF clump together into an initiation complex. RNA polymerase is attracted to these negative charges.|
|How does transcription progress from here ||The RNA polymerase breaks the DNA bond and uncoils there by allowing RNA to be transcribed.|
|What happens to the DNA as RNA is transcribed ||RNA will move away and the DNA will rebind|
|What is the primary transcript? ||RNAs that have not been processed|
|What is the first part of processing? ||capping|
|What is capping? ||a guanosine is added to teh first nucleotide of teh primary transcript by an unusual 5' - 5' bond|
|Why does capping occur? ||Increases mRNA stability by preventing its degradation.|
|What is 3 areas are methylated? ||the cap, 2' hydroxyls of the first and third nucleotides|
|What is splicing? ||removal of a section of teh primary transcript.|
|What is teh region that is spliced out? ||Intron|
|What are the regions retained in splicing? ||Exons|
|What splices out the introns? ||spliceosomes|
|What are spliceosomes? ||Complexes of snRNPs (pronounced snirps)
small nuclear ribonucleoprotein particles|
|What composes snRNPs? ||proteins and snRNAs|
|What is polyadenylation? ||The final event of mRNA processing which adds 20-300 adenosines to the 3' end of the transcript.|
|What is poly A Polymerase ||Makes the poly-A tail to the end of RNA and promotes stability|
|Where is excess RNA cleaved? ||at a CA, 10-30 bp downstream of teh poly A signal|
|What are the four transcription factors? ||Helix-Turn-Helix
|What are Helix-Turn-Helix Family? ||Two α helices are positioned at right angles to each other, connected by a short linker region.|
|How are transcription factor families classified. ||Based on DNA binding domains|
|What are zinc fingers? ||Cysteine and histidine residues are chelated to a central zinc ion, creating several loops in the polypeptide.
These loops act like “fingers” wedging themselves into the major groove to bind DNA
|Three subfamilies of zinc fingers ||C2H2 zinc finger class
|What is C2H2 ||Pair of cysteins 2-4 amino acids apart, a linker region ~11 amino acids long|
|What is C4 ||Like C2H2 except that there are 2 pairs of cysteins with no histidines|
|What is C6 ||Three pairs of cysteines|
|What is Helix-Loop-Helix ||Like HTH factors but have two α helices separated by linker region.
Linker regions of HLH are longer and no sequence similarity between HLH and HTH
|What are leucine zippers ||All function as dimeric proteins.
Interaction domain specifically binds another protein.
Extensions of α helices which grip the recognition sequence on each side of the DNA