Lecture Notes: DNA Transcription

Introduction

• DNA Transcription: Process of converting DNA into RNA.
  • Occurs in both eukaryotic and prokaryotic cells.
• Key Proteins/Enzymes: Required for transcription to occur.

Differences Between Prokaryotic and Eukaryotic Transcription

Prokaryotic Transcription

• Promoter Region: Nucleotide sequence in DNA for protein binding.
• RNA Polymerase Holoenzyme:
  • Core Enzyme: Consists of 2 alpha, 2 beta (beta prime), and omega subunits.
  • Sigma Subunit: Binds to promoter region.
• RNA Types: Single RNA polymerase makes all RNAs (mRNA, tRNA, rRNA).

Eukaryotic Transcription

• Promoter Regions: TATA box, CAT box, GC box.
• RNA Polymerases:
  • RNA Polymerase I: Makes rRNA.
  • RNA Polymerase II: Makes mRNA and snRNA.
  • RNA Polymerase III: Makes tRNA and some snRNA.
• General Transcription Factors: Required for polymerase binding to promoter.

Transcription Process

Initiation

• Prokaryotes:
  • Promoter regions (negative 35, Pribnow box).
  • RNA polymerase holoenzyme binds using sigma subunit.
• Eukaryotes:
  • TATA box, CAT box, GC box.
  • RNA polymerase II with transcription factor 2D (contains TATA binding protein).

Elongation

• DNA Strands:
  • Template/Antisense Strand: Read by RNA polymerase.
  • Coding Strand: Not read.
• Direction: RNA synthesized 5’ to 3’; DNA read 3’ to 5’.
• Functions: Opens DNA, stabilizes strands, unwinds DNA, synthesizes RNA.

Termination

• Prokaryotes:
  • Rho-Dependent: Rho protein helps detach RNA polymerase.
  • Rho-Independent: Formation of hairpin loop triggers enzyme cleavage.
• Eukaryotes:
  • Polyadenylation signal (AAUAAA) triggers RNA cleavage.

Post-Transcriptional Modification

• Only in Eukaryotes
  • 5’ Capping: Addition of 7-methylguanosine to protect RNA and aid translation.
  • 3’ Poly-A Tail: Addition of adenine nucleotides for stability and transport.
  • Splicing: Removal of introns, joining exons; involves SNRPs.

Special Topics

Gene Regulation

• Enhancers: Increase transcription rate.
• Silencers: Decrease transcription rate.

Alternative RNA Splicing

• Variants: Different proteins from one gene by varying exon combinations.
  • Examples: Antibody variations, dopamine receptors, tropomyosin in muscles.

RNA Editing

• Example with ApoB Proteins:
  • ApoB100: Unedited mRNA in hepatocytes.
  • ApoB48: Edited mRNA in enterocytes using cytidine deaminase.

Key Takeaways

• Prokaryotic vs Eukaryotic transcription differences.
• Roles of different RNA polymerases.
• Importance of post-transcriptional modifications.
• Understanding gene regulation and RNA splicing/editing.