Transcription Flashcards
RNAs transcribed in both prokaryotes and eukaryotes
- mRNA (messenger)
- rRNA (ribosomal)
- tRNA (transfer)
RNA produced only in eukaryotes
- pre-mRNA (pre-messenger)
- snRNA (small nuclear)
- snoRNA (small nucleolar)
- miRNA (micro)
- siRNA (small interfering)
- piRNA (piwi-interacting)
RNA produced only in prokaryotes
CRISPR RNA (crRNA)
Function of rRNA
Ribosomal rna : structural and functional components of ribosome
Function of mRNA
Messenger RNA: Carrie’s genetic code for proteins
Function of tRNA
Transfer RNA: helps incorporate amino acids into polypeptide chain
Function of snRNA
Small nuclear RNA: processing of pre-mRNA
Function of snoRNA
Small nucleolar RNA : processing and assembly of tRNA
Function of miRNA
MicroRNA: inhibits translation of mRNA
Function of siRNA
Small interfering RNA: triggers degradation of other RNA molecules
Function of piRNA
Piwi-interacting RNA : suppresses the transcription of transposable elements in reproductive cells
function of crRNA
CRISPR RNA: assists destruction of foreign DNA
What direction does transcription proceed
5’ —> 3’
Components of bacterial RNA polymerase
- 2x α subunits, β, β’,ω & σ
Core enzymes (without σ) is catalytically active, but binds non-specifically
σ directs RNA polymerase to the promoter
What are the 3 stages of bacterial transcription
Initiation
Chain elongation
Termination
What happens in initiation of bacterial transcription
- promoter recognition
- formation of transcription bubble
- creation of first bonds between rNTPs
- escape of transcription apparatus from promoter
What happens during chain elongation of bacterial transcription
RNA polymerization reaction
What happens during termination of bacterial transcription
- ρ dependent termination
- ρ independent termination
What is TTGACA
Consensus sequence on bacterial promoter with charge -35
What is TATAAT
The pribnow box consensus sequence on bacterial promoter with charge -10
What charge does the transcription start site on bacteria have
+1
6 steps of initiation of transcription in bacteria
- Sigma factor associates with core enzyme to form Holoenzyme
- Bind to -35 and -10 consensus sequences in promoter
- Holoenzyme bind the promoter tightly and unwinds the double stranded DNA
- RNTP complementary to base at start site serves as first nucleotide in RNA molecule
- Two phosphate groups are cleaved from subsequent nRTP, creating rna nucleotide that is added to 3’ ends of growing mRNA
- Sigma factor released as the RNA polymerase moves beyond promoter
Discuss DNA bending in the operon- promoter complex
- rna polymerase forms a closed complex in which dna is not unwound
- stable open complex forms where the -10 region is unwound
- an mg2+ dependent isomerization further unwinds the DNA from -12 to +2
How does transcription bubble occur
Nucleophilic attack by the 3’-OH of the first nucleotide on the α-phosphate of the seconds nucleotide forms a phosphodiester bind in a manner analogous to dna replication (5’ to 3’)
As process continues, the dna is continuously unwound in a transcription bubble
What does topoisomerase do during elongation
Remove negative supercoils
What does gyrase do during elongation
Introduce negative supercoils
Is rna polymerase activity continuous or discontinuous ?
Explain
Discontinuous
When the RNA polymerase reaches a site difficult to transcribe it may pause or shift backwards
Transcription can then resume either by the polymerase sliding forward or by cleavage of the non-base-paired part of the transcript
6 steps of rho -independent transcription termination in bacteria
- Rho-independent terminator contains an inverted repeat followed by a string of approximately 6 adenine nucleotides
- The inverted repeated are transcribed into rna
- String of Us cause the rna polymerase to pause
- The inverted repeats fold into a hairpin
- Destabilize DNA-RNA pairing
- Rna transcript separates from the template, terminating transcription
3 steps of Rho-dependent termination in bacteria
- Rho binds to rut site and moves toward the 3’ end
- When rna polymerase encounters a terminator sequence it pauses and rho catches up
- Using helicase activity, rho unwinds the dna-rna hybrid and brings an ends to transcription
3 steps of factor-dependent termination
- Binding of ρ to dna-rna-polymerase complex
- ρ moves toward 3’ end, displacing dna template strand
- Weakens interaction between template and transcript, causing them the dissociate
What happens during the initiation of eukaryotic mRNA transcription
- assembly of basal transcriptional apparatus on core promoter
- binding of TFs to enhancers
- formation of transcription bubble
- first binds between rNTPs
- escape of rna polymerase II from promoter
What are the 4 regions on the eukaryotic core promoter
- TFIIB recognition element (-35)
- TATA box (-25)
- Initiator element (+1)
- Downstream core-promoter element (+30)
5 steps of eukaryotic transcription initiation
- TFIID binds to TATA box in core promoter
- Transcription factors and RNA polymerase II bind to core promoter
- Transcriptional activator proteins bind to sequences in enhancers
- Dna loops out, allowing the proteins bound to the enhancer to interact with the basal transcription apparatus
- Transcriptional activator proteins bind to sequences in the regulatory promoter and interact with the basal transcription apparatus through the mediator
- Steps of eukaryotic transcription termination
- Rna polymerase II transcribed well past coding sequence
- Cleavage near 3’ end of rna
- Rna polymerase continues to transcribe
- Rat1 endonuclease attached to 5’ ends of trailing rna
- Moves toward rna polymerase degrading the rna as it goes
- When rat1 reaches the polymerase, transcription is terminated
What does mRNA processing involve
- capping
- cleavage of transcript
- polyadenylation
- splicing
- rna export from nucleus
What function does the addition of 5’ cap have
Facilitates binding of ribosome to 5’ end of mRNA, increases rna stability and enhances RNA splicing
What functions do 3’ cleavage and addition of polyAtail have
Increases stability of mRNA, facilitates binding of ribosome to mRNA
What function does RNA splicing have
Removes non coding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced through alternative splicing
What is alternative splicing
Producing different mRNAs from the same nRNA by linking together different combinations of potential exons
