Biology Chapter: Transcription Mechanisms

Chapter Objectives

• Describe the features of transcription
• Discuss the requirements and steps in transcription
• Explain the different mechanisms in RNA processing

Transcription

• Transcription is a DNA-dependent synthesis of RNA
• Template: DNA
• Product:
  • Messenger RNA (mRNA)
  • Ribosomal RNA (rRNA)
  • Transfer RNA (tRNA)
  • miRNA, siRNA, and other regulatory RNAs

Features of Transcription

• It involves certain regions of DNA that code for RNA, but other regions do not.
• It consists of three general steps: initiation, elongation, termination.
• It is the major point of control of gene expression.
• The main enzyme for transcription is RNA polymerase.

RNA Polymerase

• DNA-directed
• Adds ribonucleotides to the 3' end of the RNA chain.
• Builds RNA in the 5' to 3' direction.
• Can initiate synthesis of strands on DNA templates.
• Makes an error for every 10⁴-10⁶ ribonucleotides incorporated.
• Has no proofreading ability.
• Prokaryotic vs. Eukaryotic

Bacterial RNA Polymerase Subunits

• 2α - aids in promoter recognition
• β - binds ribonucleotide substrate
• β' - binds DNA template
• σ - recognizes and binds tightly to promoter
• ω - facilitates assembly
• 2αββ' = core enzyme; (2αββ')σ = holoenzyme

Eukaryotic RNA Polymerases

• Three types of eukaryotic RNA polymerases (I, II, and III)
• I - located in the nucleolus, transcribes rRNA.
• II - located in the nucleoplasm, transcribes hnRNA (precursor of mRNA).
• III - located in the nucleoplasm, transcribes tRNA, 5s rRNA, and small stable RNAs.

Definition of Some Terms

• Gene - basic unit of a gene which extends from the promoter to the terminator.
• Promoter - a sequence that "promotes" or helps gene expression; the binding site for RNA polymerase.
• Terminator - the end of a gene sequence.
• Upstream - regions close to the promoter.
• Downstream - regions farther away from the promoter.
• (+1) - base pair in DNA which corresponds to the first RNA nucleotide added by RNA polymerase.
• (+) - nucleotide position number toward the direction of transcription.
• (−) - nucleotide position number toward the opposite/away from the direction of transcription.
• Consensus sequence - nucleotide sequence that, when aligned, have certain nucleotides that appear frequently at particular positions.

Prokaryotic Promoter

• Consensus sequence of -35 sequence and -10 sequence.
• Upstream from Pribnow box.

Eukaryotic Promoters

• One promoter for each type of RNA polymerase because there is a specific RNA polymerase for each type.
• Types:
  • For RNA polymerase II: promoter for RNA pol II.
  • For RNA polymerase I: promoter for RNA pol I
    • Includes upstream control element (UCE) and core promoter.
  • For RNA polymerase III: promoter for RNA pol III, located within the gene.
• General structure: includes TATA box, CAAT box, and GC box.
• Roles:
  • A-T rich region simplifies initial RNA polymerase binding.
  • The location relative to the startpoint affects RNA polymerase binding.
  • Auxillary protein binding facilitates RNA polymerase binding.

Promoter Mutation

• Two types of promoter mutation:
  • 1. mutation - causes deviation from the consensus sequence.
  • 2. mutation - causes a given sequence to become more/exactly similar to an established consensus sequence.

General Transcription Factors

• Necessary protein factors for the transcription of any eukaryotic gene.
• Sufficient to direct transcription from many core promoters.
• Position RNA polymerase at the appropriate position.

Assembly of Transcription Initiation Complex in Eukaryotes

• Steps of TFs binding to DNA and other TFs.

Gene-specific Transcription Factors

• Proteins involved in the interaction and activation of particular genes or groups of genes.
• Different sets in different cell types result in different patterns.
• Examples include steroid hormone receptors and myogenic proteins.

Transcription Initiation

• RNA polymerase binds to a promoter.
• RNA polymerase melts the DNA.
• RNA polymerase remains stationary.
• RNA polymerase incorporates the first ribonucleotide.
• RNA polymerase retains all three phosphate groups.

Transcription Elongation

• Nucleotides are added one by one to the growing RNA chain..
• 5' to 3' in the direction of RNA growth
• Rapid, about 50 nucleotides/sec in E. coli.

Transcription Termination

• RNA polymerase stops transcription at designated sequence signals.
  • Two types:
    • Rho-independent
    • Rho-dependent

Two Types of Termination

• Rho-independent: Simple termination; no need for rho factor. Ends in a stretch of GC-rich sequences from the mRNA that forms a hairpin structure that facilitates termination
• Rho-dependent: Termination that requires a protein called rho; a characteristic sequence is required; usually less GC rich and there isn't a sequence of UUUU's at the end of the RNA. Rho binds to the RNA at a recognition site, pursuing RNA pol until it catches up and unwinds the DNA-RNA helix, causing the transcript to release.

Additional Information Summarized

• Rifampicin binds to bacterial RNA polymerase and inhibits transcription initiation.

Explore the essential features and processes of transcription in this quiz. Learn about the requirements, steps involved, and the role of RNA polymerase in synthesizing RNA from DNA. Test your understanding of different types of RNA and the importance of transcription in gene expression.