RNA

Control of Gene Expression

The Chemical Structure of RNA

• RNA vs. DNA
      - Both RNA and DNA are linear polymers made up of nucleotide subunits linked by phosphodiester bonds.
      - RNA differs from DNA in two main aspects:
          1. Sugar: RNA contains ribose while DNA contains deoxyribose.
          2. Nucleotide Bases: RNA has uracil (U) instead of thymine (T), which is found in DNA.

Base-Pairing Properties

• Uracil (U) can base-pair with adenine (A) similar to thymine (T) in DNA.

RNA's Structural and Functional Roles

• RNA's ability to fold into complex three-dimensional shapes enables it to:
      - Serve not only as an information carrier between DNA and proteins but also perform structural, regulatory, or catalytic functions.
      - DNA: Information storage, typically double-stranded.
      - RNA: Mostly single-stranded, allowing diverse structural configurations.

Types of RNA in Cells

• Cells produce various types of RNA:
      - Messenger RNAs (mRNAs): Direct synthesis of proteins.
      - Non-coding RNAs (ncRNAs): Perform regulatory, structural, and catalytic roles.
          - Ribosomal RNAs (rRNAs): Core structural and catalytic components of ribosomes.
          - Transfer RNAs (tRNAs): Act as adaptors in protein synthesis, choosing specific amino acids.
          - MicroRNAs (miRNAs): Regulators of gene expression in eukaryotes.

RNA as an Intermediary

• RNA acts as an intermediary in protein synthesis, allowing for multiple identical RNA copies from a single gene. This amplification enables rapid protein synthesis.
      - Each RNA molecule can direct the synthesis of numerous protein copies, permitting variable expression rates for different proteins based on cellular needs.

Transcription Process

• Transcription: The initial step of gene expression where DNA information is copied into RNA.
      - Similarities to DNA replication:
          - Involves opening the DNA double helix to expose bases.
          - One strand of DNA serves as a template for RNA synthesis.
      - Distinctions:
          - RNA does not remain hydrogen-bonded to the template strand; it displaces and releases as it synthesizes.
          - RNA molecules synthesized are generally shorter than the DNA templates.
          - RNA polymerase catalyzes the formation of phosphodiester bonds to link ribonucleotides, mimicking DNA polymerase in its action.

Key Aspects of RNA Polymerase

• Events during transcription:
      - RNA polymerase elongates the RNA strand in the 5′ to 3′ direction using ribonucleotides (ATP, CTP, UTP, GTP) as substrates.
      - No primer required for RNA polymerase; proofreading is not as rigorous as with DNA polymerases.
          - Error rate: RNA polymerase makes errors approximately once for every 10,000 bases copied.
          - DNA polymerase makes errors approximately once for every 10,000,000 bases copied.

Signals for Transcription Initiation and Termination

• Promoter Recognition: RNA polymerase recognizes promoters to start transcription, which contain specific nucleotide sequences upstream of the transcription start site.

• Transcription Initiation in Bacteria:
      - The sigma factor of bacterial RNA polymerase enables specific binding to promoter regions.
      - Once transcription starts, the sigma factor is released.

• Transcription Terminators: RNA polymerase stops transcription upon reaching terminator sequences, which are also transcribed.

Eukaryotic vs. Prokaryotic Transcription

• Eukaryotes utilize three types of RNA polymerase (I, II, III), while prokaryotes rely on a single polymerase.

• Eukaryotic transcription initiation involves complex assembly of general transcription factors and RNA polymerase at the promoter, unlike bacteria.

• Eukaryotic genes are often dispersed with longer sequences intervening between coding regions, requiring more elaborate regulatory mechanisms.

RNA Processing in Eukaryotes

• Eukaryotic mRNAs undergo several processing steps:
      - Capping: A 7-methylguanylate cap is added to the 5′ end shortly after transcription begins.
      - Polyadenylation: A series of adenine nucleotides is added to the 3′ end, stabilizing the mRNA and signaling for export.
      - Splicing: Introns (noncoding regions) are removed, and exons (coding regions) are joined together to form a mature mRNA.

• Alternative splicing allows different protein isoforms to be generated from a single gene, increasing protein diversity.

Role of Spliceosomes in RNA Splicing

• Spliceosomes: Large complexes of snRNPs (small nuclear ribonucleoproteins) and other proteins that facilitate the splicing of pre-mRNA.

• Special sequences at the ends of introns guide the splicing machinery for precise excision of introns into lariat structures.

Regulation of Gene Expression

• Gene expression can be regulated at multiple levels, including transcription, RNA processing, and translation.

• Regulatory RNAs (such as miRNAs and siRNAs) serve in post-transcriptional regulation, often by degrading mRNA or inhibiting translation.
      - miRNAs: Bind to target mRNAs, leading to their destruction or translational repression.
      - siRNAs: Utilize the RISC complex to seek and destroy foreign RNA, maintaining genomic stability during viral infections.

CRISPR as a Genetic Tool

• CRISPR allows for targeted modifications of genes and elucidation of gene functions through RNA-guided processes, simulating ancient bacterial defense mechanisms against phages.

Conclusion

• The regulation of gene expression is pivotal for cellular function and complexity, demanding intricate mechanisms to manage transcription, RNA processing, translation, and degradation. The central dogma serves as a baseline understanding of these processes, detailing how genetic information transforms from DNA to functional proteins.