Download Transcription Outline RNA Structure

Transcription
PHENOTYPE
GENOTYPE
Chapter 13
Outline
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Key Questions
Structure of RNA
Types of RNA
Ingredients for Transcription
Bacterial Transcription
– Initiation, Elongation, Termination
• Eukaryotic Transcription
– Initiation, Elongation, Termination
Transcription: Key Questions
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RNA Structure
What ingredients are required?
Where does transcription start?
How does transcription proceed?
Where and why does it stop?
2’ Carbon Atom
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Wow! This must be IMPORTANT!!!
Prokaryotes
and
Eukaryotes
Eukaryotes
only
Transcription:
SELECTIVE synthesis of RNA
Ingredients
• rNTPs
• DNA Template
• Enzymes
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DNA Template
• Transcription is highly selective
• RNA is synthesized from one DNA strand (the
TEMPLATE STRAND)
• RNA is synthesized complementary and
antiparallel to template strand
Template Strand(s)
The Transcription Unit
• Stretch of DNA that codes for an RNA
molecule and the sequences necessary for
transcription
How does the transcription
apparatus know which
strand to read, where to
start, and where to stop?
The Transcription Unit
• Stretch of DNA that codes for an RNA molecule and
the sequences necessary for transcription
• 3 critical regions:
– PROMOTER
– RNA CODING REGION
– TERMINATOR
-Y
+1
The PROMOTER is a DNA
sequence that is recognized
and bound by the
transcription apparatus. It
indicates the template strand,
and the direction of
transcription.
+X
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Transcription Apparatus
• RNA Polymerase
• Bacterial Transcription Apparatus
– Sigma factor (involved in promoter recognition)
– Holoenzyme (core RNA Pol + Sigma)
– Rho (involved in termination)
• Eukaryotic Transcription Apparatus
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RNA Pol I: Large rRNA
RNA Pol II: Pre-mRNA, some snRNA, snoRNA
RNA Pol III: tRNA, small rRNA, snRNA
Many accessory proteins (transcription factors)
Ribonucleoside triphosphates (rNTPs)
rNTPs) are substrates used in RNA synthesis
Many bacteria have
multiple types of sigma
factors, which help in the
recognition of multiple
classes of promoters.
The bacterial RNA polymerase
Bacterial Transcription:
Initiation
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Promoter Recognition
Formation of Transcription Bubble
Bond creation between rNTPs
Escape of transcripton apparatus from
promoter
Promoters and Consensus
Sequences
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A Consensus Sequence is
a short stretch of DNA that
is conserved among
promoters of different
genes.
There are two consensus
sequences upstream of the
start site, at approximately
-10 and -35.
Gene
Sequence
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AATAAA
2
TTTAAT
3
TATTTT
4
TAAAAT
Consensus
TATAAT
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Pribnow Box
Bacterial Initiation
Bacterial Transcription:
Elongation
• RNA polymerase unwinds DNA ahead of
it, and rewinds the DNA at the end of
transcription.
• Transcription occurs in the Transcription
bubble
Bacterial Transcription:
Termination
Rho-independent Termination
1) Two inverted repeats in the DNA
sequence are transcribed
• Transcription ends after a terminator is
transcribed
• Two types of terminators in bacteria:
– Rho-dependent terminators
– Rho-independent terminators
2) A string of ~6 Adenines
follows the second inverted
repeat
3) The inverted repeats form
a hairpin structure pausing
the polymerase
4) The A-U bonds break and
the RNA molecule
separates from the
template
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The Hindenberg Lecture
Rho-dependent
Termination
1) Rho binds a stretch of DNA
that encodes RNA
upstream of the terminator.
2) DNA causes a pause in
transcription and Rho
catches up.
3) Rho unwinds DNA-RNA
hybrid using helicase
activity
Eukaryotic Transcription
Eukaryotic Transcription is Horribly
Complicated!
¾Three different polymerases
¾Multiple promoter types
¾Many proteins required for promoter
recognition
Eukaryotic Initiation
Promoters
– Always found adjacent to gene a fixed number of
nucleotides away from start site
Enhancers
– Can be thousands of nucleotides away, and exact
location can be variable
– Increase the rate of transcription
Promoter recognition accomplished by accessory
proteins that recruit the appropriate Polymerase
RNA Polymerase II
(PROTEINS)
PROTEINS)
• Core promoter
– Immediately upstream of the gene
– Includes one or more consensus sequences
(most common is the TATA box:
box TATAAA)
– Located -25 to -35
Basal Transcription Apparatus
• Consists of general transcription factors,
RNA polymerase, Mediator
• Binds to DNA near start site
• Is necessary for transcription at minimal
levels
• Additional proteins (transcriptional
transcriptional
activators)
activators bind to other promoters and
enhancers affecting the RATE of
transcription.
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Figure 13.17
Figure 13.17
Figure 13.17
ZZZZZZZ…
TATA Binding Protein
Transcription factors
RNA Polymerase I (Large
Large rRNAs)
rRNAs
• Same idea: transcription factors bind to
consensus sequence and recruit RNA
Polymerase I.
• RNA Pol I promoters have 2 key elements
– Core element,
element surrounds start site and is
sufficient to initiate transcription
– Upstream control element increases
efficiency
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Figure 13.20
RNA Polymerase I Promoters
RNA Polymerase III (tRNA
tRNA,, small
rRNA,
rRNA, snRNA)
snRNA
• Recognizes several types of promoters
– Several contain consensus sequences and
are also used by RNA pol II (including the
TATA box)
• Promoters for rRNA and tRNA
– Contain internal promoters downstream of
transcription site
Figure 13.21
Eukaryotic Termination
• Three RNA Polymerases use different
mechanisms for termination
• RNA pol I: requires a termination factor
• RNA Pol II: termination can end at
multiple sites (Chapter 14)
• RNA Pol III: requires transcription of a
string of Uracils (hairpin not required)
Summary
• Transcription: making RNA from a DNA
template to transfer information from the
genome
• Ingredients: rNTPs, DNA template,
Transcriptional Apparatus
• Stages: Initiation, Elongation,
Termination
• Bacteria vs. Eukaryotes: Compare and
Contrast (Problem Set)
Archea,
Archea, Eubacteria,
Eubacteria, and
Eukaryotes
• Transcription has strong similarities
between Archea and Eukaryotes
– Archea have TBP
– Archea have TFIIB
• Both of these are not in Eubacteria
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What are the major
similarities and differences
between bacterial and
eukaryotic
transcription,
and why should
I care?
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