Transcription and mRNA Processing

Transcription: DNA to RNA

Overview of Genetic Information Flow

  • Transcription: The process of synthesizing RNA from a DNA template.
    • DNA strands are involved, with one serving as a template.
    • The resulting RNA has a sequence complementary to the template DNA strand.
    • DNA typically has bases A, T, C, G, while RNA has A, U, C, G (Uracil replaces Thymine).

Steps of Transcription

1. Initiation

  • Recognition: RNA polymerase recognizes and binds to a specific DNA sequence called the promoter.
    • The promoter is located "upstream" of the transcription unit, typically at the 5' end relative to the coding strand.
    • The transcription unit is the segment of DNA that is transcribed into RNA.
  • Unwinding: RNA polymerase unwinds the DNA double helix, separating the two strands.
  • Start Point: Transcription begins at a specific single nucleotide within the transcription unit, designated as the start point.
  • Directionality:
    • The template strand of DNA (3' to 5' orientation) is used to synthesize the new RNA molecule.
    • The nontemplate strand (5' to 3' orientation) is also known as the coding strand because its sequence is identical to the RNA transcript, except for T's in DNA being U's in RNA.

General Initiation in Eukaryotes (More Complex)

  • General Transcription Factors: These proteins bind to the promoter region (e.g., the TATA box), a common eukaryotic promoter element.
  • Transcriptional Activator Proteins: These proteins bind to distant DNA sequences called enhancer sequences.
  • Mediator Complex: A large protein complex is recruited, which can cause the DNA to bend, bringing the enhancer-bound activator proteins into proximity with the promoter.
  • RNA Polymerase Recruitment: The mediator complex then recruits RNA polymerase to the promoter.
  • Reason for Complexity: This elaborate initiation system allows for precise control over gene expression, integrating signals from multiple regulatory elements.

2. Elongation

  • RNA Synthesis: RNA polymerase moves along the template DNA strand in the 3' \to 5' direction, synthesizing a new RNA molecule in the 5' \to 3' direction.
  • Complementary Pairing: Only complementary RNA nucleoside triphosphates (ATP, UTP, CTP, GTP) fit into the active site of RNA polymerase.
    • Adenine (A) in DNA pairs with Uracil (U) in RNA.
    • Thymine (T) in DNA pairs with Adenine (A) in RNA.
    • Guanine (G) in DNA pairs with Cytosine (C) in RNA.
    • Cytosine (C) in DNA pairs with Guanine (G) in RNA.
  • Energy for Synthesis: The energy for RNA synthesis comes from the hydrolysis of two phosphate groups (PP_i) from the incoming nucleoside triphosphates, releasing energy to drive the phosphodiester bond formation.
  • DNA Rewinding: As RNA polymerase moves downstream, the unwound DNA behind the polymerase rewinds into a double helix.
  • RNA Transcript Growth: The RNA transcript progressively elongates, detaching from the DNA template as new nucleotides are added.

3. Termination

  • Terminator Sequence: RNA polymerase continues transcription until it reaches a specific DNA sequence called the terminator.
  • Release: Upon encountering the terminator, RNA polymerase detaches from the DNA template, and the newly synthesized RNA transcript is released.
  • Result: A completed RNA transcript is produced, which is then ready for further processing or translation.

Fate of the Primary Transcript

Differences between Prokaryotes and Eukaryotes

  • Prokaryotes: The primary RNA transcript (mRNA) is often directly translated into protein. Transcription and translation can occur simultaneously in the cytoplasm.
  • Eukaryotes: The primary RNA transcript, called pre-mRNA, undergoes significant processing in the nucleus before it can be translated into protein. This processed mRNA is then transported out of the nucleus to the ribosomes.

Eukaryotic Pre-mRNA Processing (mRNA Processing)

  • Purpose: Ensures transport from the nucleus, molecular stability, slows degradation, and facilitates attachment to ribosomes.
1. 5' Cap Addition
  • Structure: A modified guanine nucleotide, typically methylguanosine, is added to the 5' end of the pre-mRNA in a 5' \text{ to } 5' triphosphate linkage.
  • Function:
    • Aids in the export of mRNA from the nucleus to the cytoplasm.
    • Protects the mRNA from degradation by exonucleases.
    • Serves as a recognition signal for ribosomes to attach to the mRNA during translation.
2. Poly-A Tail Addition
  • Signal: The pre-mRNA contains a polyadenylation signal sequence, typically AAUAAA.
  • Process: After transcription past the polyadenylation signal, an enzyme adds 50-250 adenine nucleotides to the 3' end of the pre-mRNA.
  • Region: This series of adenines is called the Poly-A tail.
  • Function:
    • Aids in the export of mRNA from the nucleus.
    • Protects the mRNA from enzymatic degradation, increasing its stability and lifespan in the cytoplasm.
    • Helps ribosomes attach to the mRNA.
3. Splicing
  • Introns and Exons: Eukaryotic pre-mRNAs contain non-coding regions called introns (intervening sequences) and coding regions called exons (expressed sequences).
    • Example: An intron might span nucleotides 31-104 within a larger segment of 1-146 nucleotides.
  • Process: Introns are precisely cut out from the pre-mRNA, and the remaining exons are spliced (joined) together to form a continuous coding sequence.
  • Result: The mature mRNA contains the 5' cap, the united coding sequence (exons), untranslated regions (UTRs) at both 5' and 3' ends, and the Poly-A tail.
  • Untranslated Regions (UTRs): Present at both the 5' and 3' ends of the mRNA, these regions do not code for protein but help the mRNA interact with ribosomes for translation.