Ch. 23: RNA Synthesis-DNA Transcription Flashcards
What 3 identical but functionally different RNA molecules are transcribed from anti-sense (-) DNA (template strand)?
Which is the most abundant in the cell?
messenger RNA (mRNA) transfer RNA (tRNA) ribosomal RNA (rRNA) ➡️ most abundant
Describe the sequence of rRNA compare to that of mRNA.
What are the subunits & nucleotides found in prokaryote ribosomes? In eukaryote ribosomes?
Has sequence complementarity to regions of mRNA
Prokaryote: 5S (120), 16S (1541), 23S (2904)
Eukaryote: 5S (120), 5.8 (150), 18S (2100), 28S (5050)
What is the function of tRNA?
Binds an a.a. at one end, mRNA at other end
Acts as adaptor to carry a.a. of a protein to correct place as coded for by mRNA
Describe the 5’ terminus and 3’ terminus of tRNA.
What part of tRNA interacts with mRNA codon?
5’ terminus: base-paired
3’ terminus: 4 base single-stranded region, XCCA-3’-OH
(CCA = acceptor stem ➡️ adenine is a.a. attachment site)
Anticodon loop
What are the modified bases for tRNA?
dihydrouridine (DHU) ribosylthymine (rT) pseudouridine inosine (I) wyosine (Y)
What is the function of mRNA in DNA transcription?
photocopy of a gene (has sequence that is complimentary to 1 DNA strand and identical to other strand) ➡️ carries the info stored in DNA in nucleus to cytoplasm (for translation)
What is the start codon in mRNA to initiate translation?
What are the stop codons in mRNA to terminate translation?
Start codon: AUG
Stop codons: UAG, UGA, UAA
What makes prokaryotic mRNA different from eukaryote mRNA?
Polycistronic (polygenic): carry info for synthesis of several polypeptides from 1 mRNA
How is the timing of transcription and translation different in prokaryotes compared to eukaryotes?
Prokaryotes: transcription and translation are coupled (happens at the same time, since mRNA does not have to be stable)
Eukaryotes: transcription and translation happen separately
What makes mRNA in eukaryotes different from mRNA in prokaryotes?
1) Has info for only 1 polypeptide
2) it is heterogeneous nuclear RNA (hnRNA) = has introns & exons
3) goes through post-transcriptional modifications
4) transported to cytoplasm for translation
What are the post-transcriptional modifications eukaryote mRNA goes through?
What is the main purpose of these modifications?
5’ Capping
Poly A tailing
Splicing (alternative splicing, RNA editing)
Give mRNA stability, protection, ⬆️ lifespan
What is the function of small nuclear RNA (snRNA)?
Mediate the processing of primary transcripts (large precursor molecules formed from DNA transcription of genes for mRNA, tRNA, and rRNA) in nucleus ➡️ produces functional molecules for export to cytosol
In what direction does an RNA chain grow?
What enzyme initiates RNA synthesis? Is a primer needed?
‘5 to 3’ direction
RNA polymerase
No primer needed
What are 4 features specific to transcription (differ from DNA replication)?
1) Transcription has more initiation sites
2) More RNA polymerase molecules per cell than DNA polymerase
3) Rate of RNA polymerase (50-100 bases/s) slower than DNA polymerase (1000 bases/s)
4) RNA polymerization has ⬇️ fidelity than DNA
Prokaryote transcription:
Describe the structure of E. coli RNA polymerase and the function of its subunits.
Has 5 subunits ➡️ alpha2 beta beta’ sigma = holoenzyme
Beta’: binds to DNA
Beta: binds to rNTPs, interacts with sigma
Sigma: recognizes promoter sequences on DNA
What are the 3 promoter regions in prokaryotic transcription?
Initiation site (+1) Pribnow box (-10) -35 region
What are the 3 main steps of transcription & translation?
1) Initiation
2) Elongation
3) Termination
What occurs to transition from initiation ➡️ elongation in prokaryote transcription?
After initiation: RNA polymerase holoenzyme loses sigma subunit ➡️ becomes core enzyme ➡️ conducts elongation
Inhibitors of prokaryotic transcription initiation:
Rifamycin B: how does it ➖ transcription initiation?
Binds to beta subunit of RNA polymerase ➡️ blocks binding of incoming rNTPs at initiation site
Inhibitors of prokaryotic transcription initiation:
Rifampin (rifampicin): how does it ➖ transcription initiation?
Prevents translocation of RNA polymerase along DNA template
Inhibitors of prokaryotic & eukaryotic transcription initiation:
Actinomycin D: how does it ➖ transcription initiation?
What diseases can it be used to treat?
Binds to DNA
Useful to treat childhood neoplasms (Wilms’ tumor) & choriocarcinoma
What 3 characteristics are required for termination of transcription to occur at a specific base sequence?
Factor independent transcription termination:
1) inverted repeat base sequence with a central non-repeating segment
2) ⬆️ G + C content
3) ⬆️ A + T content resulting in 6-8 U’s in RNA
What factor is required in factor dependent transcription termination?
rho factor
What are the specific features of transcription in eukaryotes?
1) transcription & translation separated in space & time ➡️ better regulation of gene expression ➡️ variety of eukaryotic forms & functions
2) RNA stabilized via post-transcriptional modification
3) 3 types of RNA polymerases (I, II, III)
4) Promoters have a TATA box near start site
What types of RNA are each of the 3 classes of eukaryotic RNA polymerases used for?
I: rRNA (nucleolus)
II: mRNA, snRNA
III: tRNA, 5S rRNA
What are the sensitivities to amanitin (of specific 🍄) of each of the 3 classes of RNA polymerases?
I: insensitive to amanitin
II: strongly ➖ by amanitin
III: ➖ by ⬆️ [amanitin]
What makes promoters of eukaryotic transcription more complex than that of prokaryotes?
TATA box & CAAT box
Many non-polymerase factors needed for RNA polymerase binding to DNA
What are the structural features eukaryotic RNA polymerases I, II, and III have in common?
1) Big, multimeric proteijs (500-700 kD)
2) Have 2 large subunits (sequences similar to beta and beta’ in E. coli RNA polymerase)
3) have subunit homologs of alpha and omega in E. coli polymerase
What makes up the RNA polymerase II transcription initiation complex? What does each part do?
1) Activators: binds to genes at enhancer sites ➡️ help to decide which genres to switch on, ⬆️ transcription rate
2) Coactivators: “adapter” molecule integrate & relay signals from Activators ➡️ basal transcription factors
3) Basal transcription factors: position RNA polymerase at start of protein coding region
Also, repressors: binds to genes at silencer sites ➡️ interfere with activator function ➡️ slows transcription
Transcription factors for RNA polymerase II:
Step 1: Formation of DAB complex ➡️ what is the function of each TF?
TFIID: Binds to TATA box (TBP), bends DNA
TFIIA: stabilizes promoter binding by TBP
TFIIB: stabilizes TBP-TATA complex, recruits RNA polymerase II (essential)
Transcription factors for RNA polymerase II:
Step 2: Binding of RNA polymerase II to DNA ➡️ which TF is the polymerase complexed with?
TFIIF: Binds RNA polymerase II, positions template during initiation
Transcription factors for RNA polymerase II:
Step 3: Which TFs bind after RNA polymerase II binds to DNA? Functions of each TF?
TFIIE: Assists recruitment & activity of TFIIH, promoter melting (denaturation or promoter region)
TFIIH: ATPase, CTD kinase, helicase, promoter melting & escape
Transcription factors for RNA polymerase II:
Step 4: Elongation ➡️ what TF stimulates elongation for RNA polymerase II?
TFIIS (TFIIF may also help)
