Chapter 5: Transcription Flashcards Preview

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Flashcards in Chapter 5: Transcription Deck (57):

RNA polymerase??

- DNA dependent RNA polymerase


Transcription is what?

ran synthesis


RNA polymerase has a template of ____ (non coding strand)

- ssDNA


the Gene is what?

coding strand/ non template


RNA polymerase uses _/_ strand of DNA to create the transcript..



Ex: Question : RNA?

5' AGACTCC 3' (coding DNA sequence)
3' TCTGAGG 5' (template)
5' AGACTCC 3' (primary transcript is the exact sequence of the coding sequence..)



- messenger RNA
-transcript of protein coding genes



- transfer RNA
- brings amino acid to ribosome during translation



- ribosomal RNA
- component of the ribosome which translates mRNA



-responsible for eukaryotic mRNA processing


Anything to the left is ___ of the gene. Anything to the right is ___ of the gene. NO MATTER HOW YOU ARE LOOKING AT THE GENE.

- upstream
- downstream


Three steps in transcription??

- Initiation
- Elongation
- termination


Steps of Transcription(prokaryotes) :
1. Initiation
L>Promoter?? also called the _ spot.
L> location?
L> RNA Poly?
L> what does the promoter sequence serve as?

- a sequence upstream of the start of the gene that encodes the RNA. The RNA polymerase interacts with the promoter
L> + 1 spot
L> the promoter sequence serves to orient the RNA poly to start transcribing at the beginning of the gene and ensures that the initiation of synthesis of every RNA occurs at the same time


Steps of Transcription(prokaryotes) :
1. Initiation
L>RNA coding sequence?

- the DNA sequence transcribed by RNA Polymerase into the RNA transcript


Steps of Transcription(prokaryotes) :
1. Initiation

- specifying where transcription stops.


Steps of Transcription(prokaryotes) :
1. Initiation
L>What type of RNA polymerase is found in bacteria?

- Holoenzyme which consists of core enzymes
( bound to 2 alpha, beta and beta prime polypeptide)


Steps of Transcription(prokaryotes) :
1. Initiation
L>The RNA polymerase (holoenzyme) is bound to what polypeptide?

- Sigma factor which ensures that RNA polymerase binds in a stable way only at PROMOTE REGIONS.
L> it is not required for elongation and termination stages of transcription


Steps of Transcription(prokaryotes) :
1. Initiation
L>RNA polymerase binds more tightly to the promoter at ___ region accompanied by the local untwisting go the DNA in that region.

- -10 region which is upstream from the +1 promoter region


Steps of Transcription(prokaryotes) :
1. Initiation
L>Sigma factor binds to what two regions of promoter?

- -35 and -10


Steps of Transcription(prokaryotes) :
1. Initiation
L>RNA synthesis does not need a ___.
L> Once transcribing has begun what is released?

- primer
- sigma factor


Steps of Transcription(prokaryotes) :
1. Elongation
L> after initiation has occurred the RNA polymerase beings ??

- moving along the DNA and the sigma factor is released.


Steps of Transcription(prokaryotes) :
2. Elongation
L> During this stage the RNA polymerase does what?
L> moves along?
L> behind the untwisted region what exists?
L> what occurs there
L> what exists the enzyme?

- it moves along untwisting DNA double helix ahead of itself exposing a new segment of single stranded template DNA.
L> behind the untwisted region the two DNA strands reform into a double strand.....within the untwisted region about 9 RNA nucleotides are base paired to the DNA in a temporary RNA-DNA hybrid, the rest of the newly synthesized RNA exits the enzyme as a SS.


Steps of Transcription(prokaryotes) :
3. Termination
L> general description?

- termination of bacterial gene transcription is singled by terminator sequences


Steps of Transcription(prokaryotes) :
3. Termination
L> Ro-independent Terminators?

-the terminators of transcription


Steps of Transcription(prokaryotes) :
3. Termination
L> Ro-Indpendent terminators consist of what?

- inverted repeat sequence about 16-20 base pairs upstream of the transcription point...followed by a string of 4-8 A-T pairs


Steps of Transcription(prokaryotes) :
3. Termination
L> Ro-Indpendent terminators - because of the inverted repeat arrangement the RNA folds into what? Causing the RNA poly to do what?

- hair pin loop
- slow and then pause in its catalysis of RNA synthesis....the string of U nucleotides downstream of the hairpin destabilizes the pairing between the new RNA chain and the DNA template.....RNA poly dissociates from the template and transcription is complete.


Transcription in Eukaryotes:
L>What are the three different RNA polymerases that transcribe the genes for four main types of RNA?

1. RNA Poly I
2. RNA Poly II
3. RNA Poly III


Transcription in Eukaryotes:
L> RNA Poly I?
- location
- makes?(3)

located in the nucleolus.....synthesizes 28S, 18S and 5.8S rRNA that make up ribosomes


Transcription in Eukaryotes:
L> RNA Poly II?
L> located?

- located in nucleoplasm
L> synthesizes mRNA and some snRNA


Transcription in Eukaryotes:
L> RNA Poly III?

- located in the nucleoplasm
- makes:
L> 53 rRNA (small RNA molecule found in each ribosome)
L> snRNA not made by Poly II


Transcription in Eukaryotes:
-One is the only thing transcribed into protein from the RNA polys?

L> Poly II


Transcription in Eukaryotes:
- Core Promoter elements??

- needed for transcription to start RNA synthesis at the correct site.


Transcription in Eukaryotes:
-What are the core promoter elements (2)

1. TATA box located at -30 nt
L> 5' TATAAAA 3' consensus sequence
2. Inr (initiator) : promoter region aka +1


Transcription in Eukaryotes:
- Promoter Proximal Elements location in comparison to TATA box?

- -50 to -200 nts from the start of transcription which are upstream from the TATA box.


Transcription in Eukaryotes:
-What are the two proximal elements?Locations?

1. CAAT box at -75 nt
2. GC box at -90nt


Transcription in Eukaryotes:
-Promoter proximal elements are important in determining what?

- how and when a gene is expressed


Transcription in Eukaryotes:
- Activators?

- transcription regulatory proteins that determine the efficiency of transcription initiation.


Transcription in Eukaryotes:
- Enhancers?

- thousands of nt away from the promoter region and are required to bind to an activator .....function normally upstream of the gene they control...


Transcription in Eukaryotes:
- Unlike in prokaryotes, in eukaryotes non of the RNA plus can bind directly to DNA...instead they have ___?

- general transcription factors which bind first to the DNA and recruit the RNA Poly to form a complex.... other GIF's than bind and transcription begins.


Transcription in Eukaryotes:
- What binds with the TATA box to form the initial committed complex?

L> which as TATA binding proteins (TBP) and TBP associated factors (TAF)


Transcription in Eukaryotes:
- After TFIID binds to the TATA box what other transcription factors (3) come in and ind to the initial committed complex?

- TFIIA and TFIIB bind
L> followed by TFIIF and RNA Poly II =
minimal transcription initiation complex.


Transcription in Eukaryotes:
- Once the minimal transcription complex is formed what are the last two transcription factors to bind? What does this make?

- TFIIH : helices like activity begins to unwind the promoter DNA and transcription is ready to start activating Poly II
L> they both bind making the Complete Transcription initiation complex/ pre initiation complex


Transcription in Eukaryotes:
L> What is the general structure of mature active mRNA in both prokaryotes and eukaryotes consist of? (3)

- 5' untranslated region (UTR) also called the leader sequence at the 5' end
- Protein coding sequence : specifies the aa sequence of a protein during translation
- 3' untranslated region (3'UTR) : trailer sequence
** translation starts at 5'UTR end (translating the PCS) and stops at the 3'UTR.


Transcription in Eukaryotes:
L> UTR regions are involved in regulating what?

- translation efficiency
- regionalization on free ribosomes or the rER
L> transcript inteself dictates where it will be translated..( either outside of cell or cell membrane
- mRNA stability


Transcription in Eukaryotes:
- The 3'UR has what??

polyadenylation signals.... 50-20 AAAAAA tail


Translation differences

1. RNA transcript functions directly as mRNA molecule.....base pairs are collinear with the bases of the translated mRNA..........since they lack a nucleus mRNA begins translation on ribosome before being transcribed completely...called coupled transcription and translation
2. RNA transcript (pre mRNA) must be processed to mature mRNA in the nucleus.....which the mRNA migrates to the cytoplasm where ribosomes are to begin translation.


Transcription in Eukaryotes:

intervening sequence
- non amino acid coding sequences
L> they need to come out!
beneficial for helping with mistakes


Transcription in Eukaryotes:
Exons ??

expressed sequence
- 5' and 3' UTR and amino acid coding regions of RNA sequence.
L> dictate which aa are in the polypeptide


Transcription in Eukaryotes:
- 5' Capping??

- once RNA Poly II has made about 20 to 30 nt of pre mRNA....a capping enzyme adds m7 G( 7-mehyl guanosine) to the 5' end creating a 5' to 5' linkage. The next two sugars are modified by m7 G...this remains in the mature protects it from degradation by exonucleases...its also important for the binding of ribosome...initial step of translation.


Transcription in Eukaryotes:
- 3'Poly A Tail??
L> transcription occurs ___?
L> the addition of? via cleaving of?
L> Does it have a DNA template?
L> Functions in what?

- transcription occurs past the tail.
- addition of 50-250 adenine nucleotides called a poly A tail to 3' end.... via cleaving 3' end and PAP synthesizes tail
L> does not have a DNA template.. it remains when pre mRNA is processed to mature... called pol A+ mRNA.
L> it functions in transporting mRNA into the cytoplasm... protecting it from early degradation and has a role in initiation of translation and in some regulations of the stability of mRNA.


Transcription in Eukaryotes:
- Splicing Mechanism!
L> Spliceosome???

- complex of pre mRNA bound to small nuclear ribonucleoprotein particles (snRPs)


Transcription in Eukaryotes:
-Splicing Mechanism
L> Five principle sRNA's?

U1 U2 U3 U4 U5 and U6 which form snRNPs with proteins.


Transcription in Eukaryotes:
- Splicing Mechanism!
- U1 binds where?
- U2 binds where?
- U4/U6 and U5 bind to what?

- at intron 5' site
- to the branch point sequence (upstream from intron 3' splice site)
- U1 and U2 regions....causing an intron to loop bringing its junctions together...= spliceosome! U4 leaves making the spliceosome active.


Transcription in Eukaryotes:
- Splicing Mechanism!
L> what is the branch point nucleotide?

- A in the intron


Transcription in Eukaryotes:
- Splicing Mechanism!
L> mature mRNA only consists of what?



Transcription in Eukaryotes:
- Splicing Mechanism!
L> 5' Cleavage of Intron?

- snRPs cleave intron from exon 1 at the 5' splice junction...the now free 5' end binds to the branch point nucleotide A. (RNA lariat structure)


Transcription in Eukaryotes:
- Splicing Mechanism!
L> 3' cleavage of intron ???

-the spliceosome excises the intron still in lariat shape via cleaving the 3' splice junction and then ligates axons 1 and 2 together.
L> snRNPs are now released and this is done for each intron.
= mature mRNA