6.3 RNA Structure and Types

RNA is the versatile cousin of DNA, playing crucial roles in genetic information transfer and regulation. Unlike DNA's double helix, RNA's single-stranded nature allows it to form complex structures like hairpin loops, essential for its diverse functions.

From messenger RNA carrying genetic instructions to transfer RNA delivering amino acids, RNA types are key players in protein synthesis. Regulatory RNAs like microRNAs and siRNAs fine-tune gene expression, showcasing RNA's importance beyond just information transfer.

RNA Structure

Single-Stranded Structure and Hairpin Loops

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• RNA molecules consist of a single strand of nucleotides, unlike the double-stranded structure of DNA
• Single-stranded nature allows RNA to form complex secondary structures through intramolecular base pairing
• Hairpin loops form when complementary bases within the same RNA strand pair up, creating a stem-loop structure
• Hairpin loops play crucial roles in RNA function and stability (tRNA cloverleaf structure, ribozyme catalytic sites)
• Base pairing in RNA follows Watson-Crick rules, with adenine (A) pairing with uracil (U) and guanine (G) pairing with cytosine (C)

Codons and Anticodons in Genetic Information Transfer

• Codons represent three-nucleotide sequences in mRNA that specify amino acids during protein synthesis
• 64 possible codons exist, including start and stop codons (AUG, UAA, UAG, UGA)
• Anticodons are complementary three-nucleotide sequences found on tRNA molecules
• Anticodons base pair with codons during translation, facilitating the transfer of genetic information
• Wobble base pairing allows some tRNAs to recognize multiple codons, increasing translation efficiency

RNA Modifications: 5' Cap and 3' Poly-A Tail

• 5' cap consists of a modified guanine nucleotide added to the 5' end of eukaryotic mRNA
• 5' cap enhances mRNA stability, facilitates nuclear export, and aids in ribosome recruitment
• 3' poly-A tail comprises a string of adenine nucleotides added to the 3' end of eukaryotic mRNA
• Poly-A tail typically ranges from 50 to 250 nucleotides in length
• Functions of the poly-A tail include mRNA stability, nuclear export, and translation efficiency
• Both 5' cap and 3' poly-A tail protect mRNA from exonuclease degradation

Types of RNA

Messenger RNA (mRNA) Structure and Function

• mRNA carries genetic information from DNA to ribosomes for protein synthesis
• Transcribed from DNA template strand in the nucleus
• Undergoes processing in eukaryotes, including splicing to remove introns
• Contains untranslated regions (UTRs) at both 5' and 3' ends, which regulate translation and stability
• Serves as a template for protein synthesis during translation
• Lifespan varies from minutes to hours in prokaryotes, and hours to days in eukaryotes

Transfer RNA (tRNA) and Its Role in Translation

• tRNA molecules transport amino acids to the ribosome during protein synthesis
• Distinctive cloverleaf secondary structure with three hairpin loops
• Anticodon loop contains the anticodon sequence that base pairs with mRNA codons
• Acceptor stem carries the amino acid attachment site
• Approximately 20 different types of tRNA molecules exist in cells, corresponding to the 20 standard amino acids
• tRNAs undergo post-transcriptional modifications to enhance their function and stability

Ribosomal RNA (rRNA) in Protein Synthesis Machinery

• rRNA forms the structural and catalytic core of ribosomes
• Comprises about 60% of the ribosome's mass
• Four types of rRNA in eukaryotes: 18S, 5.8S, 28S, and 5S
• Three types of rRNA in prokaryotes: 16S, 23S, and 5S
• rRNA catalyzes peptide bond formation during protein synthesis (peptidyl transferase activity)
• Highly conserved across species, making it useful for evolutionary studies and taxonomic classification

Regulatory RNAs

Small Nuclear RNA (snRNA) in Pre-mRNA Processing

• snRNAs participate in splicing of pre-mRNA molecules in eukaryotes
• Form complexes with proteins to create small nuclear ribonucleoproteins (snRNPs)
• Major spliceosomal snRNAs include U1, U2, U4, U5, and U6
• U1 snRNA recognizes the 5' splice site, while U2 snRNA binds to the branch point sequence
• Minor spliceosomal snRNAs (U11, U12, U4atac, U6atac) process a small subset of introns
• snRNAs undergo extensive post-transcriptional modifications to enhance their stability and function

MicroRNA (miRNA) and Gene Expression Regulation

• miRNAs are short, non-coding RNAs that regulate gene expression post-transcriptionally
• Typically 20-24 nucleotides in length
• Processed from longer precursor molecules by enzymes Drosha and Dicer
• Bind to complementary sequences in target mRNA 3' UTRs
• Regulate gene expression through mRNA degradation or translational repression
• Play crucial roles in development, differentiation, and disease processes (cancer, cardiovascular diseases)

Small Interfering RNA (siRNA) in Gene Silencing

• siRNAs are double-stranded RNA molecules involved in the RNA interference (RNAi) pathway
• Generally 20-25 base pairs in length
• Derived from longer double-stranded RNA precursors or introduced exogenously
• Incorporated into the RNA-induced silencing complex (RISC)
• Guide RISC to complementary mRNA targets for cleavage and degradation
• Utilized in research for gene knockdown studies and potential therapeutic applications (viral infections, genetic disorders)
• Differ from miRNAs in their origin and degree of complementarity to target mRNAs