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223 Cards in this Set
- Front
- Back
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Where does transcription initiation start
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the TATA box
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what hapens at the TATA box
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TFIID binds the TATA box
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How does TFIID bind the TATA box
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by using the TATA boxes binding protein TBP
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Once TFIID has bound the TBP and the TATA box what happens
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TFIIA and TFIIB are recruited and bind
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Once TFIIA and TFIIB are bound, what happens
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the TBP distrorts the TATA box
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What happens when the TBP distorts the TATA box
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it provides a platform to recruit other TFs
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Once the TATA box is distorted what TF are recruited
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TFIIE TFIIH
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What is special a TFIIH
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it provides the helicase activity, and requires ATP
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Once all these have bound and the RNA Pol II is about to start, what happens
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it sheds many of the Transcription factors
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How does this happen
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by the phosphorlation of it C-terminal tail and by a kinase found in TFIIH
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First step in Transcribing Chromatin
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Activators help recruit TFa
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Which TFs do the activators recruit
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Polymerase
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How does is this recruit of the Pol by the activators monitiored
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The Mediator Complex
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How does the Mediator complex associate with the Pol II
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by the use of its Cterminal tail
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This preformed RNA Poll II-Mediator complex is called
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RNA Pol II Holoenzyme
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Once the RNA Poll II has shed its initation factors, they are replaced by
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elongation factors
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What part of the complex brings in these elongation factors
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the c terminal tail doamin (brings it all in at the same time)
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What is the first thing that happens to the c terminal tail
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it has a capping enzyme on the end of its tail
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Once the tail has been capped, what hapens
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RNA splicing machinery assembles
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after RNA splicing machinery has assembles what happens
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the factors responsible for cleavage and polyadenylation assemble
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The FACT complex is
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elongating RNA Pol that must deal with histones in its way
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What does the FACT complex have that helps it work through these histones
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Spt 16/SSRPI dimer
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What does the Spt16/SSRPI dimer do
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They work together to disociate an H2A-H2B dimer from the nucleosome
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Once this H2A-H2B dimer has been removed, what happens
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RNA Pol II can transcribe through the nucloesome
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Then what happens
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The nucleosome is reassembled
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How
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With Spt16/SSRPI and with help from SPT6
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Capping involves adding a lot of ? to ? end of the Cterminal tail domain
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Methyl groups
5' end |
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Polyadenylation involves adding a lot of ? to the ? end of the newly sytnthesized RNS
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Adenines
3' end |
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Once the end of a gene is reached RNA Pol II will
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signal the transfer of polyadenylation enzymes to the RNA
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The first step in the process of signaling the polyadenlyation enzymes to the RNA is
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two enzymes, cleavage and polydenylation specifity factor (CPSF) and cleavage stimulation factor (CstF) move from the CTD to the Poly-A sequence
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Once these CPSF and CstF are recuited to the RNA what happens
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the RNA is cleaved from the RNA Pol II
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After the RNA is cleaved, what happens
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Poly-A polymerase (PAP) add several more adenines to the 3' end of the RNA
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Once a lot of adenines have been added, what happens
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Poly-A binding proteins bind to the poly-A stretch
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LECTURE 16
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LECTURE 16
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The more introns you have,
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the more complex the organism
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Why is this the case
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bc the more introns you have, the more control you have during splicing so it is a more complex organism
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intron exon boundary
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site that will be spliced
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5' splice site
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boundary at the 5' end of the intron
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what is cut first
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the 5' intron/exon boundary
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3' binding site
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site at the 3' end of the intron exon
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what binds the 3' end
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the freed 5' end
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branch point site
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point where the spliced 5' intron make the lariet
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Where is the branch point site found
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entirely in the Intron
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First step in splicing
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the 2'-OH group from the A site attacks the Phosphate group of the G site
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What is a result of this
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the freed 5' end of the intron is joined to the branch site
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After that, what happens
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The 3'-OH group of the freed exon attacks the Phosphate group of the 3' splice site
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What is the result
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one intron lariet
and one spliced together exon |
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When you see the A site you know you are where
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In the Middle
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When you see the G site you know you are where
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Start
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What is it called when two exons from different RNAs get spliced together
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Trans-splicing
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What is the result of trans-splicing
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There is a Y-shaped structure insted of a lariet
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What does the Splicesome do
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It mediates the formation of the lariet and exons
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What is the first step in this
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Branch Point Binding Protein (BBP) protein binds the A site
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What binds the 5' splice site
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U1
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Once U1 is bound, what happens the BBP
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It is replaced by U2
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What does U2 do
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Distorts the A site
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What helps BBP bind to the A site
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U2FA
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Once U2 replaces BBP what happens
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U4 U5 and U6 join the complex
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How are the U4 U5 U6 are associated together
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U4 and U6 are more tightly held together then U5
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What is the main function of U4 U5 and U6
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they bring U1 and U2 together (5' splice site and branch site)
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Once U1 and U2 are brought together by U4 U5 U6, what happens
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U1 leaves
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When U1 leaves, what happens
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U6 replaces it one hte 5; site
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Once U6 is one the 5' site, what happens
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U4 leaves
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what does U4 leaving allow
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It allows U6 and U2 to interact
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When you U6 and U2 interact, what happens
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It generates the active site and the 5' intron exon boundary is spliced
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Then U5
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helps bring together the exons
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Pre-mRNA splicesome is the
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Most common
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Group II self-splicing are different because they
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do not use a splicesome
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Instead they
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simple fold on themselves
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Group I self splicing do not use
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a splicesome
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Instead group I
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bind guanine
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Group I self splicing is
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RARE
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One way that the accuracy of splice-site selection can be enhanced
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Loading splicing machinery during transcription
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What would do this, and how does it help improve
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CTD
The transcriptional loading of splicing proteins reduces the likely hood of an exon being skipped |
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Another way that accuracy of splice-site can be enhanced
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Proteins that only splice sites close to exons are recognized
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These proteins are called
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SR proteins
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Where do these SR proteins bind
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Exonic Splicing Enhancers (ESEs)
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And what do these SR proteins do
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recruit U2FA to the 3' splice site and U1 to the 5' splice site
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U1 U2 U3 U4 U5 U6 are all examples of
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snRNPs
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U1
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binds the 3' splice site
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U2
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Binds the branch site
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U6
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brings U1 and U2 together
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U4
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leaves so that U6 and U2 can from the active site
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U5
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Helps the exons to bind
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LECTURE 17
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LECTURE 17
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Synonyms are
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codons that code for the same amino acid
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What does degeneracy mean
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More than 1 codon can code for the same amino acid
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Mutations in the first nucleotide will often give
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similar if not the same amino acid
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Pyrimidines in the second position mostly code for
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hydrophobic amino acids
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Purines in the second position mostly code for
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polar amino acids
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Transition mutations in the 3rd poition
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rarely change the amino acid
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Does do they mean by Wobble
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Purified tRNA can bind more than one codon
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In some tRNAs an additional anticodon base was found
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inosine
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What can Inosine pair with
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A U C
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How does the wobble concept work
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The 5' end of the anti codon is not as restricted as the other two allowing it to form hydrogen bonds with several bases at the 3' end of the codon
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Which end of the anti codon is mist exposed:
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5' end
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Where is the 3' end
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towards the top and it is in the middle of a series of base stacking interactions so it is more restricted
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3 Rules that Govern the Genetic Code
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-Codons are read by Ribosomes in the 5'-3' direction
-Codons are non overlapping and mRNA contains no gaps -mRNA is translated in a fixed reading frame (from first AUG) |
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Three kinds of Point mutation
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Missense
Nonsense Frameshirt |
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Missense mutations
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changes a single base, which changes a single amino acid
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Do missense mutation effect the length of the polypeptide
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No
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Nonsense mutations
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change a single base, which changes an amino acid to a stop codon
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Do nonsense mutations effect length
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Yes
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Frameshift mutations
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insert or delete one or more bases, which changes the reading frame
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Do frameshift mutations effect the length
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maybe, you may encode for a stop codon sooner
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Two ways mutations can be reversed
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Reverse (back) mutations
Supressor mutations |
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Reverse (back mutations)
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just go to where the altered nucleotide is and change it back
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Supressor mutations
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mutations in another region of DNA can supress the harmful effect of the original mutation
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LECTURE 18
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LECTURE 18
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What does the ribosome do again
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corrdinates recognition of the mRNA by the tRNA and forms bonds between individual amino acids on the gorwin peptide chain
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Open reading frames (ORFs) are
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the regions of mRNA that are composed of non overlapping condons
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The most real ORF has
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the longest strand that has both a stop and start codon
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The ribosome is composed of two parts
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Small subunit
LArge subunit |
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The small subunit is the
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decoding center (where tRNAs read the mRNA codons)
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The large subunit is the
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peptidyl transferase center (where peptide bonds are formed)
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Prokaryotic ribosome is
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70s (30-Small,40-Large)
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The Eukaryotic ribosome is
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80s (40-Small,60-Large)
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In Prokaryotes how do they recruit the ribosome
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by the ribosome binding sites on their ORFs
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In Eukaryotes how do they recruite the ribosome
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by the use of their 5' cap on the 5' end
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Translation is slower in Pro or Euk?
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Eukaryotes
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why
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because translation and transcription take place in different ares of the cell
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where does translation take place
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cytoplasm
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where does transcription take place
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nucelus
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Why is it faster in prokaryotes
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transcription and translation machinery are located in the same compartment
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The compostion of the ribosome is split nearly in half with
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Proteins and rRNA
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The proteins are ? so there are ? or them
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smaller
more |
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The rRNAs are? so there are ? of them
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larger
less |
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First step in the Ribosome association and dissaciation process
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mRNA and initiator tRNA bind to the small Ribosome subunit
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after the mRNA/tRNA/Small subunit is formed
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it recuits a large subunit
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once the large subunit has formed
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initioation begins
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As the Ribosome moves from codon to codon
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More initiator tRNA are added to elongate the growing polypeptide chain
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How many ribosomes can translate a single mRNA
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MANY
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an mRNA bearing multiple ribosomes is caled
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Polyribosome or polysome
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Since many ribosome can translate one mRNA, this means that mRNA
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do not have to be abundant
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New amino acids are added to the
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C(carbon)-terminus of the growing poly peptide chain
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The substrates for each new amino acid addition are charged by two species of tRNA
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Aminoacyl-tRNA
Peptidyl-tRNA |
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The peptidyl-tRNA is located
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at the C-Terminus of the polypeptide
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What does the aminoacytl tRNA do
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it attack the peptide-tRNA
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how does the aminoactl tRNA attack the peptidyl tRNA
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in Amine group (N) attacks the attacks the carbonyl (C) group of the peptidyl tRNA
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what is the result
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a new peptide bond is formed
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This means proteins must grow from the ? to the ? terminus
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N to the C
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Ribosomes have 3 binding sites
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A site: Aminoacyl-tRNA site
P site: Peptidyl-tRNA site E site: Exit site |
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During the elongation process, which site is the first site occupied?
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P site
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What is the second site occupied
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A site
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LECTURE 19
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LECTURE 19
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First step n general prokaroytic translation
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all machinery is recruitted (mRNA, tRNA initiato complex, Small ribosome)
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Secdon step
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tRNA must be loaded to the P site
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Third
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large ribosome binds and it is positioned over a start codon
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WHat does IF3 do
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It binds the E site and prevents the large ribosome from binding
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What does IF1 do
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blocks the A site and prevents new tRNA from binding
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What does IF2 do
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IF2 is a GTPase that interacts with IF1 and the initiator tRNA to help bind the fMet-tRNA. and it helps block the A site
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First step
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Initiator tRNA is recruitted
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where does this initiator tRNA bind
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the P site
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After the initiator tRNA is bound and it finds a start codon what happens
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Once it binds a start codon IF3 is released
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what happens when IF3 is released
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a large ribosome can now bind the subunit
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What happens when the large subunit joins
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it stimulates IF2 to hydrolize its GTP
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What is the result of IF2 hydrolizing its GTP
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If2 and IF1 are released
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What happens when IF1 and IF2 are released
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Then A site is now open and can bind new tRNA
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In Eukaroytes there are ? more steps
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A LOT
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eIF1/3/5 all block the ? site and prevent the ?
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E site
the large ribosome from binding |
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eIF2-GTP/Met-tRNA complex is loaded to the
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P site
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What does EF-Tu do
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it escorts the aminoacyl-tRNA to the ribosome
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How does it do this
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EF-Tu utilizes GTP
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first step in this process
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The EF-Tu-GTP binds the 3' end of the aminoacyl tRNA
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What does this EF-Tu-GTP/Aminoacyl tRNA do next
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it takes the aminyl tRNA to the A site
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Once the complex is at the A site what happens
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The EF-tu-GTP comes in contact with the factor binding center
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What does this contact do
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Causes the EF-Tu to hyrolsize its GTP and dissociate from the amincyl tRNA
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Translocation in the ? subunit comes before translocation in the ? subunit
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Large comes before
Small |
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During the hyrbid state, once the peptide transfer is done, the ? site is open
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A
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What binds the A site
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EF-G
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EF-G bind the A site only when
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It has GTP with it
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This EF-G-ATP complex binds then A site, then what
|
The EF-G-GTP comes in contact with the factor binding center
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This contact with the factor binding center causes the EF-G-ATP to do what
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hydrolsize its GTP into GDP
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What happens when the GTP is hydrolosizes
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it changes the shape of the EF-G
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The shape change in the EF-G causes what
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the EF-G to reach down and scoop and translocate the A site tRNA
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LECTURE 20
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LECTURE 20
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Gene expression is controled by
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extracellular signals
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If there are no signals
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RNA Pol will bind weakly
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If there are repressive signals
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repressor protein binds the operator site and there is no transcription
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If there are activating signals
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Activator proteins bind the activating site
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In allostery the activator
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produces an allosteric change )shape) and it activates transcription
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in the Lac Operon, if lactose is absent
|
The lac Operon will be OFF
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If glucose is present
|
The Lac Operon will be OFF
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the lac Z gene
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cleaves lactose to produce glucose
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The lac Y gene
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encodes lactose permease and incorpporates itself into the cell
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The lac A gene
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encodes thiogalactoside and rids the cell of toxins
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Where is the Lac Repressor found and what encodes it
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Operator site
lacI |
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When are Lac z, Y, and A present
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in high levels of lactose
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The CAP site
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mediates the effect of glucose
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The CAP will bind only where and only when
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The CAP site
there is no glucose |
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Lac Repressor binds where and only when
|
Operator site
No lactose |
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If there is Glucose and Lactose,
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The CAP and Repressor do not bind
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When the CAP and Repressor do no bind, this is called
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Basal Transcription
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What part of the RNA Pol binds to the CAP site
|
The CTD
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What happens when they bind
|
RNA Pol is activated
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LECTURE 21
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LECTURE 21
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3 Main roles of the tro operon
|
regulate levels of tryptophan
Sense the levels Synthesize enzymes when levels are too low |
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The repressor bind the trp operon where
|
the operator site
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When does it bind and repress trp?
|
When trp levels are high
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When there is high trp
|
Repressor is on
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When there is low trp
|
repressor is off
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So lactose is a ? of transcription while trypophan is a ?
|
Promotor
Repressor |
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regions 3 and 4 on the trp operon are important because
|
They can form a hairpin structure
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what does the formation of this hairpin structure do
|
stops transcription
|
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what is this hairpin structue called
|
attenuator site
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When there are moderate to high levels of trp
|
sites 3 and 4 form a hairpin structure
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What does the formation of this hairpin structure do
|
Does not alow the ribosome to move along and therefore does not transcribe genes
|
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During low levels of trp
|
sites 2 and 3 form the hairpin
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What happens when sites 2 and 3 form the hairpin
|
The DNA Pol come apart and then attachs the to other side of the hairpin and continues transcribing
|
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Two different phage life cycles
|
lysogenic
lytic |
|
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Which gene is pro-lytic
|
cro
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which gene is pro-lysogenic
|
cI
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|
|
Which promotors are pro-lytic
|
Pr and Pl
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|
|
Which promotors are pro-lysogenic
|
Prm
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|
Pl and Pr make transcription
|
turn on
|
|
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why
|
because the lytic stage is active and the lysogenic stage is repressed
|
|
|
Pl and Pr produce a lot of
|
cro
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Prm produces a lot of
|
cI
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cI is called the
|
phage repressor , BUT it can also be an activator
|
|
|
as a repress it bind at the ? and therefore ?
|
Opperator
Blocks RNA Pol |
|
|
As an activator cI works like
|
CAP and recruits RNA Pol
|
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cro works only as a
|
repressor
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and cro binds DNA as A
|
dimer
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