Transcription Flashcards
What is a gene
- A region of DNA containing a sequence of bases that is transcribed into a functional product
- Several regions are responsible for the proper function of a gene
- Regulatory Region: Sequence of bases that control the initiation of transcription
- Coding Region: Sequence of bases that are read into a functional molecule
- Termination Region: Sequence of nucleotides that stops transcription
Compare and contrast RNA and DNA
- RNA contains the sugar ribose; DNA contains deoxyribose
- RNA contains uracil; DNA contains thymine instead
- RNA is single stranded; DNA is double stranded
- RNA is short (one gene long); DNA is long (many genes)
- RNA and DNA can store information
- RNA can catalyse chemical reactions (like proteins)
- RNA / protein hybrid structures are involved in protein synthesis (ribosome), splicing of messenger RNA) and telomere maintenance
What are the types of RNA and their functions
- rRNA: Structural and functional components of the ribosome
- mRNA: Carries genetic code for proteins, transcription
- tRNA: Helps incorporate AA into the polypeptide chain
- snRNA: Processing of pre-mRNA
- snoRNA: Processing and assembly of rRNA
- miRNA: Inhibits translation of mRNA
What is the central dogma of molecular biology
- Reflects the flow of genetic information from DNA to protein
- Not concerned with DNA replication
- Changes in proteins do not affect DNA in a systematic manner (can cause mutations)
- DNA → transcription → mRNA → translation → protein
- An exception to the central dogma is reverse transcription and prions
What are exceptions to the central dogma
Reverse Transcription
- Retroviruses contain reverse transcription which allows a viral DNA copy to be made
- viral DNA becomes permanent feature of genome
- flow of information from RNA to DNA
Prion Protein (PrPc)
- Protein folding abnormally creates PrPsc
- Causes mad cow disease
- Form of inheritance that doesn’t involve nucleic acids
What are σ factors
- Converts core of RNA polymerase to RNA polymerase holoenzyme
- Required for promoter recognition and transcription initiation in prokaryotes
- Analogous function as general transcription factors in eukaryotes
- σ70 (essential for cell growth)
- σ54 (nitrogen regulation)
- σ32 (response to heat shock)
What are bacterial promoters
- Equivalent to the eukaryotic TATA box
- Located upstream of transcription start site (TSS)
- Have –35 and –10 elements, some have UP element and some lack –35 element, but have extended –10 region
Describe the steps in prokaryotic / bacterial transcription
Initiation
- Sigma makes initial contact with promoter (AT rich region)
- Helix opens and template threaded through channel
- Incoming NTPs base pair complementary with template strand
- Sigma releases
Elongation
- One strand of DNA serves as template
- Multiple rounds of transcription may occur
Termination
- Transcription termination signal reached
- Formation of hairpin loop - RHO independent (RNA secondary structure)
- Disrupts interaction between RNA polymerase and transcript
- RHO dependent termination involves addition of RHO, removal of polymerase and no hairpin loop
Describe the steps in eukaryotic transcription
Initiation
- TFIID binds TATA box (initial committed complex)
- TFIIB binds RNApol II and TFIIF (minimal transcription initiation complex)
- TFIIE and TFIIH bind (complete transcription initiation complex)
Elongation
- Stimulation of transcription by activator binding to enhancer
Termination
- RNApol II transcribes beyond 3’ end of coding region and cleaved by endonucleases (premRNA)
What is RNA polymerase I
- Transcribes rRNA precursor genes (12S, 18S, 5.8S)
- Core Element: Located -45 to +20
- Upstream Control: Element (UCE), located -180 to -107, GC and AT rich segments
- TBP: TATA box binding protein, important protein involved in RNA polymerase complex
- SL1: Core binding factor that binds to core promoter
What is RNA polymerase II
- Transcribes mRNAs / some snRNAs
- Regulatory promoter
Core promoter - TFIIB (transcription factor II B) recognition element
- TATA box
- Initiator element (contains pyrimidines)
- Downstream core promoter element (drives transcription
What is RNA polymerase III
- Bipartite sequences
- Transcribes 5S rRNA (box A and C downstream)
- Transcribes tRNAs (box A and B downstream)
- Transcribes snRNAs (Oct, PSE, TATA upstream)
What are transcription factors (eukaryotes)
- Regulate rate of initiation of transcription
- Enhancer and silencer elements (sit upstream, recognised by regulatory proteins)
- TFs function analogous to sigma
- Interact with DNA independently of RNA polymerase
- Methylation of histones (silencer, condensed chromatin)
- Decondensed chromatin (activators) enhance TFs
What is transcription and a transcription unit
- Process of making an RNA copy of a single gene
- Uses RNA polymerase
- Proceeds 5- to 3’, starts at a region of DNA called a “promoter”
- All promoters would be similar to a consensus sequence, but not identical
- TU: Includes a promotor, an RNA-coding region and a terminator
What are important RNApol II promoters
- TATA: Positioning of promoter, binds TBP factor
- CAAT: Increases efficiency of promoter
- GC box: Common in promoters, binds to SP1
- Octamer: Common in promoters, binds to Oct-1 factor
