Elongation phase: Transcription bubble
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Transcript of Elongation phase: Transcription bubble
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Elongation phase: Transcription bubble
50 nt/sec
• unwound region 17 bp•RNA-DNA hybrid duplex 8 bp
•Mistakes 1 per 104- 1 per 104 nucleotides
Separation of RNA-DNA duplex
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RNA Synthesis in Bacteria
Start of Gene
Several RNA Pol transcribing the same gene
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In bacteria, the new RNA can be immediately translated
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Termination of RNA Polymerization
Two mechanisms possible
1) Rho () protein independent termination
stable hairpin formation
2) Rho () protein-mediated termination
G
GC
U
U
5'-U•C•C•C•A•C A•U•U•U-3'
G•C A•U C•G C•G G•C C•G C•G G•C
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-independent termination
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-dependent termination
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Antibiotic inhibitors of RNA polymerization
Rifampicin inhibits initiation by blocking a channel within RNA polymerase:
Actinomycin intercalates in ds DNA, inhibiting strand separation:
phenoxazone
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RNA synthesis in Eukaryotes
See Stryer 5th edition p. 792-798Or 4th edition p.
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Eukaryotic vs prokaryotic transcription
Prokaryotes:
• no membrane-bound nucleus
• transcription and translation are coupled
Eukaryotes:
• DNA is located in membrane-bound nucleus
• Transcription and translation are separated in space and time
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Amanita phalloides (the death cap)
-amanitin
RNA Pol II Inhibitor
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Actinomycin D
•Antitumor antibiotic from Streptomyces genus• Aromatic ring intercalates between GC base pairs, while the peptides bind to the minor groove• Binds to GpC sequences in double-stranded DNA, stabilizing the duplexand inhibiting transcription• Inhibitor of eukaryotic RNA Pol I
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Eukaryotic RNA Polymerase II
RNA Pol II is responsible for transcription to pre-mRNA
- 8-12 subunits
- Two large subunits are responsible for RNA synthesis
- Regulated by phosphorylation of carboxyl-terminal domain (CTD) of the largest subunit- Unphosphorylated form is involved in initiation and phosphorylated form in elengation
- some subunits are shared for RNA Pol I-III
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Type II Eukaryotic Promoters
Consensus sequence:
Examples:
Promoter sequenceStart site
Coding sequence
CAAT Box
(TATAAAA)
5'
-90 -25 +1
3'GC Box
-70
(GGGGCG)(GGNCAATCT)TATA box
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Initiation of transcription in eukaryotes
• RNA Pol II can not initiate transcription by itself
• Transcription factors (TFII) are required
• The key initiation step is the recognition of TATA box by TBP
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TATA box-binding protein (TBP)
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Hydrogen bond donors and acceptors on each edge of a base pair
NH
N
N O
NH2
N NN
H2N
O
HN
N
O
O
NN
N
N NH2
G•C A•T
NO
H
OH
N H
O
NN
O
Major groove
Minor groove
To deo
xyrib
ose
To deoxyribose
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Formation of RNA Polymerase II pre-initiation complex
IIA stabilizes IID binding to promoter
IID contains TBP that binds TATA box
IIB binds initiation sequence
IIE stimulates transcription
IIH has kinase and helicase activity
Pol II binds IIB
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Transcriptional control in eukaryotes
Coding region
Basal promoter
Upstream elements(CAAT, GC)
Regulated expression
Proximal elements(TATA box)
Enhancers
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Enhancer sequences examples in eukaryotes
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Post-transcriptional modifications of mRNA in eukaryotes
1. 5’ end CAP2. polyA tail3. splicing
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Eukaryotic mRNA is 5’-Capped
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PolyA Synthesis and termination of transcription
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RNA splicing in eukaryotes
Primary transcript,hnRNA
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RNA Synthesis: Take Home Message
1) DNA sequences are translated into RNA messages by RNA polymerases.
2) The initiation of RNA synthesis is controlled by specific DNA promoter sequences.
3) The synthesis of RNA is governed by initiation, elongation, and termination steps.
4) Eukaryotic mRNA is extensively processed