Types of RNA and Processing Mechanisms

Types of RNA: Importance of understanding various RNA types, their structures, and functions.
Focus on mRNA: Special attention to messenger RNA (mRNA) and its processing mechanisms.

Transcription: RNA is synthesized from DNA via transcription.
RNA Polymerases: Different RNA polymerases exist in eukaryotes:
- RNA Polymerase I: Primarily synthesizes rRNA (ribosomal RNA).
- RNA Polymerase II: Synthesizes mRNA. Special distinctions will be noted in its structure and function.
- RNA Polymerase III: Produces tRNA (transfer RNA) and other small RNAs.

Pre-mRNA: Initial mRNA produced from DNA transcription, referred to as pre-mRNA.
- Structure: Chain of nucleotides from the 5' to 3' end.
- Functional Role: Acts as a template for protein synthesis.

Concurrent Processing: mRNA processing occurs simultaneously with transcription due to specific features of RNA Polymerase II.

C-terminal domain (CTD): Characterized by a long tail with repeating amino acid patterns.
- Serine Phosphorylation: Specific amino acids (serine 5 and serine 2) within the pattern are phosphorylated, providing binding sites for processing enzymes.

Serine 5 Phosphorylation:
- Binding site for the capping enzyme.
- Occurs early in elongation during transcription.
Serine 2 Phosphorylation:
- Serves as a binding site for splicing machinery.
- Occurs later in transcription.
Post-Transcriptional Modifications:
- After transcription, the phosphorylation of serine 5 is reversed, allowing for polyadenylation.

7-Methylguanylate Cap:
- Structure: A guanosine nucleotide with a methyl group on the seventh nitrogen.
- Linkage: Attached via a unique 5' to 5' linkage (phosphate bridge), differing from typical RNA connections.
- Protection from Degradation: Prevents RNA degradation by enzymes (RNases) that recognize 5' to 3' linkages. The unique cap structure disguises the mRNA, allowing it to avoid the degradation pathways.

Function: A string of adenine nucleotides added to the 3' end of mRNA.
Protection Mechanism: Competes with nucleases that degrade RNA from the 3' end, thus prolonging the lifespan of mRNA.
Tail Addition:
- Initial addition occurs in the nucleus, with further extensions possible in the cytoplasm.

Overview: mRNA processing includes the removal of non-coding regions (introns) and the joining of coding regions (exons).
Exons vs. Introns:
- Exons: Retained in mature mRNA.
- Introns: Removed through splicing mechanisms.

Key Sites: Splicing regulated by specific nucleotide sequences:
- GU at the 5' end of exons (donor site).
- AG at the 3' end of exons (acceptor site).
- A branch point adenine within the intron region.
Splicing Steps:
1. Attack on the 5' Splice Site: The free 2' hydroxyl of the branch point A attacks the 5' splice site, resulting in a break and initiating lariat formation.
2. Formation of Phosphodiester Bond: The 3' hydroxyl group of the first exon attacks the 5' phosphate of the following exon, sealing the bond and excising the intron as a lariat.

Spliceosome Role: A complex of small nuclear ribonucleoproteins (snRNPs) coordinated by RNA molecules serving as catalysts (rather than proteins).
Lariat Removal: The intron, shaped as a lariat, can be degraded or repurposed for generating small regulatory RNAs (sRNAs).

5' Cap Protection: Exclusive 7-methylguanylate cap prevents degradation by RNases.
3' Poly-A Tail: Protects against cleavage from nucleases and can be elongated post-export.
Splicing via Spliceosome: Removal of introns via a coordinated mechanism involving snRNPs, enhancing protein coding efficiency.
Simultaneous Processes: These modifications are closely linked to transcription, with enzymes interacting directly with RNA Polymerase II during the transcription process.