UNIT 3: RNA Structure and Transcription
Exam Focus: The major difference between prokaryotic and eukaryotic transcription (single vs. multiple RNA polymerases, presence of transcription factors/enhancers in eukaryotes) is crucial. Know the specific roles of the **Sigma factor** and the TATA box/Promoter in initiating prokaryotic transcription.
Table of Contents
1. RNA: Structure and Function
RNA (Ribonucleic Acid) is generally single-stranded, uses **ribose** sugar (instead of deoxyribose), and contains **Uracil (U)** instead of Thymine (T).
mRNA (messenger RNA)
Carries the genetic information transcribed from DNA to the ribosome for protein synthesis.
rRNA (ribosomal RNA)
A major component of the ribosomes, the cellular machinery that catalyzes protein synthesis (translation).
tRNA (transfer RNA)
Acts as an adaptor molecule, linking specific amino acids to their corresponding mRNA codons during translation. It has a characteristic clover-leaf secondary structure. [Image of tRNA structure]
2. Transcription in prokaryotes
Transcription is the synthesis of RNA from a DNA template.
Prokaryotic RNA polymerase
Prokaryotes (like E. coli) have **only one type of RNA polymerase** responsible for transcribing all three types of RNA (mRNA, tRNA, rRNA).
- **Holoenzyme:** Core enzyme (α2 β β' ω) plus the **Sigma (σ) factor**.
- **Core Enzyme:** Catalyzes the polymerization reaction.
Role of sigma factor
The **Sigma (σ) factor** is essential for **initiation**. It recognizes and binds specifically to the promoter region on the DNA, ensuring that the polymerase starts transcription at the correct site.
Promoter
A specific DNA sequence upstream of the gene where RNA polymerase binds to initiate transcription. In prokaryotes, key sequences include the -35 region and the -10 region (**Pribnow box**).
Initiation, elongation and termination of RNA chains
- **Initiation:** Holoenzyme binds to the promoter. σ factor directs the unwinding of the DNA (creating the transcription bubble) and synthesis of the first few ribonucleotides. σ factor dissociates after initiation.
- **Elongation:** The core enzyme moves along the DNA, synthesizing the RNA strand.
- **Termination:** Transcription stops either by **Rho-dependent** (requires the Rho protein) or **Rho-independent** mechanisms (involves a hairpin loop structure in the RNA followed by a poly-U tract).
3. Transcription in eukaryotes
Eukaryotic transcription is more complex, involving multiple RNA polymerases and accessory factors.
Eukaryotic RNA polymerase
Eukaryotes have three main RNA polymerases, each responsible for transcribing different genes:
- **RNA Pol I:** Transcribes most rRNA genes.
- **RNA Pol II:** Transcribes all protein-coding genes (pre-mRNA) and some small non-coding RNAs.
- **RNA Pol III:** Transcribes tRNA genes and the small rRNA gene.
Transcription factors (TFs)
Proteins required for RNA polymerase (especially Pol II) to recognize and initiate transcription at the promoter. **General TFs** (e.g., TFII D) form the pre-initiation complex at the promoter; **Specific TFs** bind to regulatory sequences (enhancers/silencers) to control gene expression levels.
Promoters
Contain specific conserved sequences where TFs and RNA Pol bind. For Pol II, the common core promoter element is the **TATA box**.
Enhancers
DNA sequences, often located far away from the gene, that bind specific TFs. When bound, enhancers greatly **increase the rate of transcription** by looping the DNA to interact with the promoter/Pol II complex.
Mechanism of transcription
Involves the assembly of the pre-initiation complex at the promoter, recruitment of RNA Pol, unwinding of DNA, and synthesis of the pre-mRNA molecule.