Gene Expression: I. Transcription – Cell Biology Study Notes

Gene Expression: I. Transcription

Introduction to Gene Expression

Gene expression is the process by which the information encoded in DNA is used to direct the synthesis of RNA and, subsequently, proteins. This process is fundamental to cellular function and regulation.

• Transcription is the synthesis of RNA from a DNA template.

• Translation is the synthesis of protein using the information in RNA.

• Some RNAs function directly as final products, not as templates for protein synthesis.

The Central Dogma of Molecular Biology

The central dogma describes the directional flow of genetic information in cells: DNA → RNA → Protein.

• DNA replication: DNA is copied to produce identical DNAmolecules.

• Transcription: DNA is used as a template to synthesize RNA.

• Translation: RNA is used as a template to synthesize proteins.

Exceptions: Some viruses (e.g., retroviruses) use RNA as a template for DNA synthesis via reverse transcription. RNA viruses may also replicate their RNA genomes directly.

Equation:

$\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$

Key Terms in Transcription

• Promoter: DNA sequence where RNA polymerase binds to initiate transcription.

• RNA Polymerase: Enzyme that synthesizes RNA from a DNA template.

• Protein Factors: Proteins that assist in the initiation, elongation, or termination of transcription.

• Termination Signals: DNA sequences that signal the end of transcription.

• Sigma Factor: Protein required for promoter recognition in prokaryotes.

• Transcription Factor: Proteins required for transcription initiation in eukaryotes.

• Pribnow Box: Conserved sequence in prokaryotic promoters (TATAAT at -10 position).

• Rho-factor: Protein involved in terminating transcription in some prokaryotic genes.

• Exon: Coding sequence in a gene that remains in mature RNA.

• Intron: Non-coding sequence removed during RNA processing.

• RNA Splicing: Removal of introns and joining of exons in eukaryotic pre-mRNA.

• 5' Cap/Poly(A) Tail: Modifications added to eukaryotic mRNA for stability and export.

Stages of Transcription

Overview of Transcription Stages

Transcription occurs in four main stages: binding, initiation, elongation, and termination.

1. Binding: RNA polymerase binds to the promoter region of DNA, causing local unwinding.

2. Initiation: RNA polymerase begins synthesizing RNA using one DNA strand as a template.

3. Elongation: RNA polymerase moves along the DNA, unwinding the helix and elongating the RNA chain in the 5' to 3' direction.

4. Termination: RNA polymerase encounters a termination signal, dissociates from DNA, and releases the newly synthesized RNA.

Comparison: Prokaryotic vs. Eukaryotic Transcription

While the basic mechanism of transcription is conserved, there are key differences between prokaryotes and eukaryotes.

• Location: Prokaryotes lack a nucleus; transcription and translation are coupled. Eukaryotes compartmentalize these processes.

• Promoters: Prokaryotic promoters contain conserved sequences like the Pribnow box; eukaryotic promoters are more varied and complex.

• RNA Polymerases: Prokaryotes have one RNA polymerase; eukaryotes have three (I, II, III), each transcribing different classes of RNA.

• Initiation Factors: Prokaryotes use sigma factors; eukaryotes use multiple transcription factors.

Types of RNA and Their Functions

Messenger RNA (mRNA)

mRNA carries genetic information from DNA to the ribosome, where it is translated into protein.

• Produced by transcription of protein-coding genes.

• Undergoes processing in eukaryotes (capping, polyadenylation, splicing).

Ribosomal RNA (rRNA)

rRNA is a structural and functional component of ribosomes, essential for protein synthesis.

• Transcribed from rRNA genes.

• Forms the core of ribosomal subunits.

Transfer RNA (tRNA)

tRNA molecules serve as adaptors, bringing amino acids to the ribosome during translation.

• Each tRNA recognizes specific codons in mRNA via its anticodon.

• tRNAs are processed and chemically modified after transcription.

Additional info:

• Central Dogma Exceptions: Retroviruses (e.g., HIV) use reverse transcriptase to synthesize DNA from RNA. Some viruses replicate RNA directly.

• RNA Processing: Eukaryotic pre-mRNAs undergo splicing, capping, and polyadenylation before becoming mature mRNAs.

• Key Equations: $\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$