Term
| Post- transcriptional RNA modications are in -- and are : |
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Definition
EUK only
5' Capping
3' Polyadenylation
Splicing |
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Term
RNA vs DNA synthesis
polymerization-
repair-
initiation sites-
locations- |
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Definition
RNA polymerization slower than DNA polymerization
• Little or no repair of RNA
• Many more initiation sites in a cell for RNA synthesis
• Both mainly in nucleus of eukaryotes |
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Term
| in prok- where the division time is very short (20mins) |
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Definition
| transcription and replication occur at same time |
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Term
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Definition
Codes for proteins (exon regions of the RNA)
•Usually a single mRNA product
•Often multiple mRNAs transcribed by an operon |
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Term
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Definition
| •Structural core of ribosomes , building block of factories for rna |
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Term
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Definition
Carries activated amino acids to ribosomes for
protein synthesis |
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Term
| Small nuclear RNA (snRNA) |
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Definition
| Involved in processing DNA and RNA in nuclei (splicing) |
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Term
| Non-transcribed DNA regulatory elements |
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Definition
•Promoters
•Enhancers
•Repressors |
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Term
Transcription
-DNA as a template, whats the problem? |
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Definition
| Its dbl stranded and only one of the strands is the template. |
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Term
| outline of transcription: |
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Definition
-open it up.
- dbl -> 2 ss dna (bubble)
-BIND the rna polymerase, synthesis is running 5’ 3’
- signal to fall off |
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Term
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Definition
coding strand
it is the compliment so the sequence of this strand is identical to the transcript RNA |
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Term
RNA transcription in prokaryotes and eukaryotes requires:
-- template
-- to initiate
-- incorporated
--relieve
--something NOT req= |
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Definition
•dsDNA as a template
•Only one DNA strand is transcribed
•RNA polymerase to initiate and continue transcription
•The 4 ribonucleotides to be incorporated into the new
RNA strand (ATP, GTP, UTP, CTP)
•Topoisomerase to relieve supercoils (as in DNA
replication)
•A primer is not required (can add on to a pre existing) |
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Term
| RNA polymerase (RNAP) binds at the |
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Definition
| the promoter region runs along the DS DNA and unwinds it to ss dna and uses one as the template. |
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Term
Prok transcription:
RNA polymerase |
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Definition
| Holoenzyme has 6 subunits: α2ββ'ωσ |
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Term
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Definition
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Term
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Definition
•Synthesizes (5'→3') RNA complementary to template strand of DNA
•Separates ssRNA from the DNA template, releases product
•α2ββ'ω binds to and runs along the DNA template
•But very slowly |
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Term
| What is the most important protein in RNAP? bc: |
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Definition
Sigma subunit
gives specicicity to the polymerase
•σ helps bind the polymerase tightly to a specific promote |
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Term
| Transcription requires a promoter= |
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Definition
•= DNA sequence to which RNA polymerase may bind,
leading to initiation of transcription
•Upstream (i.e., 5' side) of the gene(s) to be transcribed
•= 3' side of the template strand |
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Term
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Definition
| •Avoids wasteful transcription by establishing specificity |
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Term
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Definition
•Bacteria have one core RNA polymerase but many
promoter-specific sigma proteins |
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Term
| 2 promoter regions in bacteria- |
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Definition
10 nt upstream (-10- pribnow)
35 nt upstreamt -35 box |
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Term
| --- alows easy acess to promoter site |
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Definition
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Term
| Holoenzyme (core + σ) forms and conducts a |
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Definition
"random
walk" along DNA.
•σ recognizes the promoter and binds
•specificity between sigma and the promoter |
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Term
•After adding ~13 bases, replacement of σ with the protein
NusA allows |
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Definition
transcription to continue at a faster rate
•Processive elongation is rapid |
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Term
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Definition
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Term
| # different sigma factors activated -- |
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Definition
7 different sigma factors activated under different
environmental conditions |
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Term
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Definition
"Housekeeping"
• Transcribes most genes in growing cells |
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Term
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Definition
σ54 Nitrogen-limitation
• σ38 Starvation/stationary-phase genes
• σ32 Heat shock genes (on when exposed
to heat)
• σ28 Flagellar genes
• σ24 Extracytoplasmic/extreme-
heat-stress genes
• σ19 Ferric citrate transport gene |
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Term
Termination of transcription in E. coli
•Two mechanisms |
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Definition
•Rho-independent = intrinsic
•No protein factor required
•Rho-dependent
•ρ protein factor required |
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Term
| each termination mechanism is responsible for: |
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Definition
~50 % of
termination events |
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Term
Careful timing of intrinsic and ρ-mediated termination
can produce a |
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Definition
variety of RNA molecules from a
single gene |
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Term
| Model for rho-independent (=intrinsic) termination of transcription in E. coli |
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Definition
We run along about 8 nt then the next 8 turn out to be a compliment to the last 8= intramolecular hydrogen bond which forms a stem loop/hair pin
Makes a stable dbl intra strand.
When this happens the RNA is attached to template less tightly (fewer h bonds) and right after the stem loop seq there about 4 A-U A-T pairing causing it to be weak. They are the only ones remaining- causing RNA to fall off. |
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Term
| Prokaryotic vs. eukaryotic transcription |
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Definition
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Term
| In Prok, once made an RNA it is -- EUK |
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Definition
done. In euk there are modifications to the RNA. = Processing to make it biological functional
Prok have no nucleus. In Euk transcription starts in nucleus, and ends in cytoplasm |
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Term
Promoters in Euk are different (not -10. -35)
• Promoters contain a |
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Definition
• TATA box (-25): TATAAT/A
• GC box (-40): GGGCGG
• CAAT box (-110) GGCCAATCT
• many enhancer and suppressor binding domains in
the DNA upstream or downstream from transcription
start site |
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Term
| Why no proofreading in RNA? |
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Definition
RNA does not carry permanent genetic information
• Change would affect only 1 generation
• RNA is rapidly degraded
• RNA has 2'-OH group to attack 5'→3' phospho-
diester bond, DNA does not
Might make the wrong protein but it will be such a small amount there won’t be a great effect. |
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