Detailed Notes on Transcription: Prokaryotic and Eukaryotic Systems

Overview of Transcription in Prokaryotes vs Eukaryotes

• Transcription Basics: The process of converting DNA sequences into RNA.
• Conservation of structure and function: Both prokaryotic and eukaryotic systems share fundamental functional similarities despite differences in components.

Key Differences in RNA Polymerases

• Bacterial System: Only one RNA polymerase.
• Eukaryotic System: Three types of RNA polymerases:
  • RNA Polymerase I (Pol I): Synthesizes ribosomal RNA (rRNA).
  • RNA Polymerase II (Pol II): Synthesizes messenger RNA (mRNA) and some small nuclear RNAs.
  • RNA Polymerase III (Pol III): Synthesizes transfer RNA (tRNA) and other small RNAs.

RNA Polymerase II

• Core Promoter Elements: Key sequences for Pol II in initiation include:
  • TATA Box: Important for binding of TATA Binding Protein (TBP).
  • INR: Initiator element that aids in transcription initiation.
  • DPE: Downstream promoter element for polymerase recognition.
• Initiation Steps: Recruitment involves:
  • TF2D binding to core promoter.
  • Subsequent recruitment of TF2B, TF2E, and other factors.
  • Phosphorylation of Pol II to activate transcriptional mode, transitioning from scanning to elongation.
• Phosphorylation: Crucial for moving to the active phase of transcription.

RNA Polymerase I and III

• Pol I:
  • Also recognized by core elements but includes upstream control elements (UCE).
  • UBF (Upstream Binding Factor) binds UCE, enhancing Pol I recruitment.
• Pol III: Very distinct from Pol I and II
  • Lacks a core promoter in traditional sense.
  • Utilizes box A and box B for tRNA synthesis.

Comparing RNA Polymerases

• Similarities: All three rely on specific DNA sequences for recruitment and activation.
• Differences:
  • Pol I has additional UCE for recruitment.
  • Pol II involves significant phosphorylation.
  • Pol III operates without a core promoter structure.

Regulation of Transcription in Eukaryotes

Promoter Region Composition

• Core Promoter vs Upstream Elements:
  • Eukaryotic gene expression can be regulated by various DNA sequences and transcription factor interactions.
  • TATAbinding protein presence can vary, impacting the transcription initiation efficiency.
• Chromatin Accessibility: Open chromatin structure facilitates transcription machinery access and also aids DNA repair processes.

Transcription Factor Role

• Specific Factors: They facilitate or inhibit the recruitment of RNA polymerases, impacting transcription levels.
  • Example: NF-kappa B enhances transcription for certain genes.

Termination of Transcription

• Mechanisms:
  • Similar to prokaryotes, with row-dependent and independent mechanisms.
  • Termination can lead to the exposure of RNA to exonucleases, affecting stability and processing (e.g., polyadenylation following termination).

Gene Regulation in Prokaryotes (Operon Models)

Operon Functionality

• Control of Multiple Genes: Allows coordinated expression via operator sites (e.g., Lac operon, Trp operon).
• Repressors and Inducers: Mechanistically controls operon activity primarily through repressor protein binding.

Riboswitches in Gene Regulation

• Structure-Function Relationship: Riboswitches can influence transcription independently of the coding region by forming alternative RNA structures.
  • Ligand binding stabilizes structures preventing RNA polymerase from completing transcription.