BIO206H5 Study Guide - Final Guide: Guanosine, Purine, Deoxyribonuclease

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1 Apr 2016

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Table of summary Transcription, Translation
DNA Storage
- Stored in nucleoid & plasmids
- Stored in nucleus & plastids
o Plastids: mitochondria/chloroplast
Prok & Euk Genes
- Contains a promoter, exons, & UTRs
- Smaller genome
- Less complex organization
- Contains a promoter, exons, introns, & UTRs
- Larger genome
- More complex organization condensed chromatin w/ histone
Product of Biosynthesis
- mRNA
o No need for further processing
- Is either monocistronic or polycistronic
o Carries info for one/many genes
- hnRNA or pre-mRNA
o “hetereogeneous nuclear mRNA”
o This is processed to become mature mRNA
- Is monocistronic
The Key Enzyme of RNA Synthesis
- RNA Polymerase
o Core + Sigma (σ)
o Sigma is the variable unit, in that they’re what
recognizes the different promoter regions.
o Core contains 5 subunits:
2α recognizes upstream element at (-40
to -70)
β performs polymerase activity deals
with initiation & elongation
β’ binds to DNA
ω stabilizes polymerase & acts as a
molecular chaperone (maintain tertiary
structure) for the RNA poly
o Sigma:
σ recognizes (-10 to -35) region, binds
there, & recruits the core complex
Forming a holoenzyme!
- RNA Polymerase -- I, II, & III
Synthesizes larger rRNAs (28S, 18S, 5.8S)
Located in nucleolus
Synthesizes mRNAs, snRNAs, snoRNAs,
telomerase RNA
Located in chromatin & nuclear matrix
Synthesizes smaller RNAs (tRNA, 5S
rRNA, U6 snRNA)
Located in chromatin & nuclear matrix
- Initiator Complex
o Composed of:
Mediator protein which interacts with
distal enhancer/repressor sequences
Chromatin Remodelling Complex
assists the movement of the complex,
opens & removes chromatin-making
molecules would around DNA ; also
Histone Modifying Enzyme changes
acetylation of DNA
o 4-5 signals have to be met, which causes the bending
of DNA onto itself, before transcription can start
- RNA Polymerase II
o Contains a CTD with 52 repeats of YSPTSPS
amino acids for phosphorylation
o Uses general transcription factors (GTFs) instead of
Sigma to assist in binding to DNA -- TFIIA, TFIIB,
TFIIA & TFIID, binds to TATA box, to
form DA complex
TFIIB binds to that, making the DAB
TFIIF & RNA Poly II binds to -34 to +17,
to form the DABPolF complex
TFIIE & TFIIH bind to finish it all up, to
have the DABPolFEH complex
- Consensus sequences -- sequences of nucleotides most
- GTFs bind to these promoter sites before RNA poly II does
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commonly found at that particular site
- Promoter Regions
o -35bp = TTGACA
o -10bp = TATAAT/TATATT < Pribnow box
o (These are recognized on the coding/sense strand!)
- After RNA poly attaches to the DNA strand, the closed
complex of DNA changes into an open complex
o Where there’s a transcription bubble!
- DNA becomes intimate with β’ & β
o 1) Sigma orients the RNA poly onto promoter
o 2) Sigma & β distorts the DNA strands, causing the
two strands of DNA to separate, & kept apart by a
o 3) Then there’s sequential addition of
ribonucleotides to the DNA approximately 2-15
o 4) Sigma factor is released & initiation completed!
o Class II Promoters = promoters that’re recognized by
RNA poly II
- Promoter Regions
o 4 Core Proximal Promoter Elements:
-35bp = SSRCGCC < “BRE box” – B
recognition element
-25bp = TATAWAAR < “TATA box”
+1bp = YYANWYY < Inr Initiation
+35bp = RGWYV < DPE -- Downstream
Promoter Element
o 2 Distal Promoter Elements:
-80bp = GCYCAATCT < “CAAT box”
~-200bp = GGGCGG < “GC box”
- THE STEPS (details):
o 1) TFIID (with TBPtatabindingprotein & TAFs
TBP associated factors as subunits) binds to the
TATA box, causing a kink to happen in the DNA
TA weaker bonds to break; thus good
place to start
TBP, a symmetrical, saddle-shaped protein
with long beta sheet & long alpha helix;
this allows it to insert itself into the minor
groove of DNA & bend it
o 2) TFIIB is recruited (sometimes with TFIIA) to the
BRE region.
o 3) RNA Poly II & TFIIF is recruited.
This RNA Poly has a CTD & several other
CTD C-terminal Domain; has binding
sites for RNA-processing enzymes, located
near where RNA emerges, involved in
processing, & activation of the PIC
o 4) Then, TFIIE & TFIIH come in to complete the
pre-initiation complex (PIC)
- It just keeps goin’ & goin’ & goin’.
- Unwinding (melting) & rewinding (reannealing), as
ribonucleotides are added 20-50 per second
o Helicase assists with unwinding. (:
- 1) TFIIH, using helicase activity & energy from ATP, unwinds
DNA at Inr site, beginning initiation
o It also has kinase activity & phosphorylates the CTD
of the RNA Poly II, causing it to change shape &
release most of the GTFs + bind strongly with DNA
to proceed with elongation
o The phophorylation is really important too because it
will later contribute to the co-transcriptional
- 2) TFIIH begins to unwind the DNA (helicase activity)
- 3) Elongation factors (ELL & SII) unbinds the RNA poly to
begin the elongation process
o Kinases add phosphate groups to the hydroxyl of a
serine group of the CTD, making phosphoserine; this
allows the release of RNA poly from the promoter
- 4) PTEFb assists in the formation of transcription bubbles
AND phosphorylates the CTD
- Then, it keeps goin’ & goin’ & goin’.
Co -Transcriptional Modifications
- N/A
- All modifications occur in the nucleus
- This happens as the mRNA is being synthesized
- RNA Capping:
o 1) Once hnRNA is ~25rn long, a phosphatase
removes a pyro from GTP & gamma phosphate from
first base of hnRNA (an ATP)
o 2) Guanyltransferase creates the 5’-5’ triphosphate
linkage “phosphylester linkage”
o 3) N7 of guanosine is methylated
o 4) Held together by the CBC (Cap-binding Complex)
- RNA Splicing:
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