Which sequence marks the end of transcription in prokaryotes?
The terminator sequence signals the end of transcription in prokaryotes.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance Transcription - Mechanism and RNA Polymerase
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Which region of a gene acts as the termination site for transcription?
The terminator sequence signals RNA polymerase to stop transcription and release the RNA transcript.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance Transcription - Mechanism and RNA Polymerase
Torpedo model of termination involves
Torpedo model explains Pol II termination via cooperation between cleavage and exonucleolytic degradation. After endonucleolytic cut at polyadenylation site, downstream nascent RNA attached to elongating polymerase bears exposed five prime monophosphate lacking cap. Nuclear exonuclease Xrn2 in mammals, Rat1 in yeast, associates with Serine two phosphorylated CTD via Rtt103 and Pcf11, binds uncapped end, degrades RNA processively in five prime to three prime direction. Kinetic chase overtakes polymerase, destabilizes RNA-DNA hybrid and induces allosteric release of polymerase from template, completing termination and allowing recycling.
Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: Torpedo model 5'-3' exonuclease Xrn2; Nature Struct Mol Biol, Mechanism of Pol II termination
Termination of RNA pol II transcription occurs
Termination of RNA polymerase II transcription is coupled to three prime end processing and occurs after recognition of polyadenylation signal AAUAAA. CPSF-CstF machinery cleaves nascent RNA downstream of signal while polymerase continues transcribing one to two kilobases beyond cleavage site. Uncapped five prime monophosphate of downstream fragment becomes substrate for nuclear 5' to 3' exonuclease Xrn2 Rat1 torpedo that degrades RNA faster than elongation, eventually catching polymerase and triggering dissociation. Allosteric model also proposes conformational change after polyadenylation signal causing loss of elongation factors.
Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: Pol II termination after polyadenylation signal; Alberts et al., Torpedo model of termination
Rho protein is best described as
Rho protein functions as homohexameric motor translocating along nascent RNA toward polymerase, coupling ATP hydrolysis to RNA displacement. Structural analysis reveals each subunit contains N-terminal oligonucleotide-binding domain forming primary C-rich rut binding site and C-terminal RecA-like ATPase domain providing RNA-dependent ATPase and 5' to 3' helicase activities. Mechanism resembles ring helicase threading RNA through central pore. Rather than simple endonuclease or ligase, Rho acts mechanical translocase unwinding RNA-DNA hybrid within elongation complex. Inhibitor bicyclomycin targets ATPase pocket, validating RNA-dependent ATPase helicase classification essential for factor-dependent termination pathway.
Ref: Lodish Molecular Cell Biology Chapter 8: Rho RNA-dependent ATPase helicase structure function; Alberts Chapter 6: Rho hexameric translocase model
Run-off transcription assay is used to:
Run-off transcription assay quantitatively measures promoter-dependent transcription initiation in defined in vitro system. Linearized DNA template containing promoter and downstream truncated coding sequence is incubated with purified RNA polymerase, general transcription factors and radiolabeled NTPs. Polymerase initiates at transcription start site and synthesizes RNA until reaching DNA end where it falls off, generating transcript of predictable length. Product size on denaturing gel confirms initiation fidelity, while band intensity reflects efficiency. Assay is ideal for testing activators, repressors and promoter mutations and is distinct from degradation or cloning assays.
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.