RNA, the versatile cousin of DNA, plays crucial roles in gene expression and cellular function. Unlike DNA's stable double helix, RNA forms complex secondary structures as a single strand, allowing it to perform diverse tasks in the cell.

From mRNA carrying genetic instructions to tRNA and rRNA facilitating protein synthesis, RNA molecules come in various types. Regulatory RNAs like miRNA and lncRNA fine-tune gene expression, while ribozymes showcase RNA's catalytic abilities, blurring the line between genetic material and functional molecules.

RNA vs DNA Structure

Structural Differences and Chemical Composition

• RNA exists as single-stranded molecule forms complex secondary structures through intramolecular base pairing
• DNA maintains double-stranded helical structure limits formation of complex secondary structures
• RNA backbone contains ribose sugar includes additional hydroxyl group increases chemical reactivity and decreases stability
• DNA backbone contains deoxyribose sugar lacks additional hydroxyl group enhances stability and resistance to hydrolysis
• RNA incorporates uracil as one of four nucleotide bases pairs with adenine
• DNA utilizes thymine instead of uracil pairs with adenine in complementary strand
• RNA molecules range from few nucleotides to thousands of bases in length
• DNA molecules extend to millions of base pairs in length carry large amounts of genetic information

RNA Secondary Structures and Stability

• RNA forms various secondary structures (hairpins, loops, pseudoknots) crucial for specific functions
• DNA rarely forms complex secondary structures maintains stable double helix configuration
• RNA sugar-phosphate backbone more susceptible to hydrolysis contributes to shorter lifespan
• DNA sugar-phosphate backbone resistant to hydrolysis ensures long-term stability of genetic information
• RNA's transient nature allows for rapid response in cellular processes (gene expression, regulation)
• DNA's stability enables long-term storage and transmission of genetic information across generations

Types of RNA and their Roles

Protein Synthesis-Related RNAs

• Messenger RNA (mRNA) carries genetic information from DNA to ribosomes
  • Serves as template for translation
  • Determines amino acid sequence of proteins
  • Undergoes processing (capping, polyadenylation) in eukaryotes
• Transfer RNA (tRNA) functions as adaptor molecule in translation
  • Brings specific amino acids to ribosome based on mRNA codon sequence
  • Contains distinct anticodon complementary to mRNA codon
  • Possesses amino acid attachment site at 3' end
• Ribosomal RNA (rRNA) forms structural and catalytic component of ribosomes
  • Plays crucial role in peptide bond formation during protein synthesis
  • Helps maintain ribosome structure
  • Comprises majority of cellular RNA (80-90%)

Regulatory and Processing RNAs

• Small nuclear RNA (snRNA) involved in splicing pre-mRNA molecules
  • Forms part of spliceosome complex
  • Assists in removal of introns and joining of exons
  • Examples include U1, U2, U4, U5, and U6 snRNAs
• Small nucleolar RNA (snoRNA) guides chemical modifications of other RNAs
  • Modifies rRNAs, tRNAs, and snRNAs
  • Essential for proper RNA function and stability
  • Two main classes: box C/D snoRNAs (methylation) and box H/ACA snoRNAs (pseudouridylation)
• MicroRNA (miRNA) and small interfering RNA (siRNA) regulate gene expression
  • Participate in post-transcriptional gene silencing
  • Bind to complementary mRNA sequences
  • Inhibit translation or induce mRNA degradation
  • miRNAs typically 21-25 nucleotides long
  • siRNAs usually 20-25 nucleotides in length
• Long non-coding RNA (lncRNA) participates in various cellular processes
  • Involved in gene regulation, chromatin remodeling, and protein interactions
  • Typically longer than 200 nucleotides
  • Do not encode proteins
  • Examples include Xist (X-chromosome inactivation) and HOTAIR (gene silencing)

RNA Splicing and its Significance

Mechanism and Components of RNA Splicing

• RNA splicing removes introns (non-coding sequences) from pre-mRNA
• Process joins exons (coding sequences) to produce mature mRNA
• Occurs in nucleus of eukaryotic cells
• Spliceosome catalyzes splicing reaction
  • Complex of small nuclear ribonucleoproteins (snRNPs) and other proteins
  • Recognizes specific sequences at intron-exon boundaries (splice sites)
  • Major spliceosome components include U1, U2, U4, U5, and U6 snRNPs
• Splicing reaction involves two transesterification steps
  • First step: 5' splice site cleavage and lariat formation
  • Second step: 3' splice site cleavage and exon ligation

Significance and Implications of RNA Splicing

• Alternative splicing produces multiple mRNA isoforms from single gene
  • Selectively includes or excludes certain exons
  • Greatly increases protein diversity from limited number of genes
  • Allows for tissue-specific and developmental stage-specific gene expression
• RNA splicing crucial for gene expression regulation
  • Determines which protein isoforms are produced and in what quantities
  • Errors in splicing can lead to various genetic disorders (cystic fibrosis, spinal muscular atrophy)
• Self-splicing introns catalyze their own removal without spliceosome
  • Found in some lower eukaryotes and organelles
  • Examples include Group I introns (self-splicing rRNA in Tetrahymena) and Group II introns (found in mitochondrial and chloroplast genes)

Structure and Function of Ribozymes

Characteristics and Types of Ribozymes

• Ribozymes are RNA molecules with catalytic activity
• Perform specific biochemical reactions similar to protein enzymes
• Catalytic activity based on specific three-dimensional structure
  • Determined by primary sequence and intramolecular base pairing
  • Creates active sites for catalysis
• Ribozymes catalyze various reactions
  • RNA splicing (Group I and Group II introns)
  • RNA cleavage (hammerhead ribozyme, hairpin ribozyme)
  • Peptide bond formation (ribosomal RNA in ribosomes)
• Examples of naturally occurring ribozymes
  • RNase P (processes tRNA precursors)
  • Group I introns (self-splicing introns in rRNA)
  • Hammerhead ribozyme (found in plant viroids and satellite RNAs)

Implications and Applications of Ribozymes

• Discovery of ribozymes supports "RNA World" hypothesis
  • Suggests RNA molecules may have been first self-replicating molecules in early life forms
  • Blurs traditional distinction between genetic material and functional molecules
• Ribozymes demonstrate versatility of RNA in cellular processes
  • Combines informational and catalytic roles
  • Challenges central dogma of molecular biology
• Potential applications in biotechnology and medicine
  • Tools for RNA manipulation and gene regulation
  • Development of RNA-based therapeutics
  • Gene therapy applications (targeting specific mRNAs for cleavage)
• Engineered ribozymes for research and therapeutic purposes
  • Trans-cleaving ribozymes designed to target specific RNA sequences
  • Allosteric ribozymes activated by small molecule ligands
  • Riboswitches combining sensing and catalytic functions