Molecular Biology: RNA Functions and Structure

RNA Structure and Transcription

• RNA is a polymer of ribonucleotides linked by 3'-5' phosphodiester linkages.
• RNA is typically single-stranded but can form secondary structures like hairpin loops.
• RNA nucleotides contain ribose sugar, a phosphate group, and a nitrogenous base (adenine, guanine, cytosine, or uracil).
• RNA comprises only 5% of the total RNA in a cell.
• RNA is heterogeneous in size and base sequence.
• All RNA molecules function as messengers carrying genetic information from a gene to the protein synthesizing machinery.
• rRNA forms 80% of cellular RNA and is the most abundant type. Synthesized in the nucleus, particularly in the nucleolus, and combines with proteins to form ribosomes, which are essential for protein synthesis.
• rRNA is involved in the formation of the peptide bond between amino acids during protein synthesis.
• Ribosomes provide the necessary infrastructure for mRNA, tRNA, and amino acids to interact during translation.
• tRNA molecules transfer amino acids to ribosomes during protein synthesis and act as adapters between mRNA and amino acids.

Types of RNA

• mRNA (messenger RNA): Encodes proteins; carries genetic information from DNA to ribosomes for protein synthesis.
• tRNA (transfer RNA): Transfers amino acids to ribosomes during protein synthesis. Adapts mRNA codons to amino acids.
• rRNA (ribosomal RNA): Forms the ribosomes, the protein synthesis machinery

DNA vs RNA

• DNA consists of deoxyribose sugar with a double helix structure.
• RNA is single-stranded with ribose sugar.
• Uracil is the RNA base, not thymine.

Transcription

• The synthesis of RNA molecules using DNA as a template.
• Transcription involves three main phases: initiation, elongation, and termination.
• Initiation involves recognizing the promoter region of the DNA.
• Elongation involves the synthesis of mRNA from the DNA template.
• Termination involves the stopping of RNA synthesis
• The DNA-dependent RNA polymerase is the enzyme responsible for synthesizing RNA during transcription.
• The prokaryotic RNA polymerase is a multiple-subunit protein, whereas the eukaryotic system comprises three different RNA polymerases with multiple subunits, involved in the transcription of different types of RNA
• Promoters, -35 regions, and -10 regions are critical in initiating prokaryotic transcription.
• Differences between prokaryotes and eukaryotes' transcription involve different enzymes, mechanisms, location within the cell, and presence of other factors involved in the initiation of transcription.
• Transcription is unidirectional. The information flows from DNA to RNA.

Post-transcriptional Modification of RNA

• Primary transcript (pre-mRNA) is extensively modified post-transcriptionally.
• Capping, polyadenylation (poly-A tail), and splicing are common modifications in eukaryotes.
• Capping involves adding a modified guanine nucleotide to the 5' end.
• Polyadenylation involves adding a poly(A) tail to the 3' end.
• Splicing removes non-coding introns from the pre-mRNA; only exons are retained in mature mRNAs.

Alternative mRNA Processing

• Alternative splicing allows the generation of different mature mRNA molecules from one pre-mRNA transcript.
• Alternative splicing achieves this by varying the use of 5' and 3' splice sites or by retaining or removing certain exons.

RNA Editing

• RNA editing is an unusual form of RNA processing
• It changes the sequence of the primary transcript after transcription.

Pre-mRNA Methylation

• Methylation of certain bases in pre-mRNA is a final modification step.
• This methylation event regulates gene expression.
• The methylation event takes place on mature mRNA (after transcription).

Reverse Transcription

• Reverse transcription is the process of converting RNA into DNA
• It uses the enzyme reverse transcriptase.

Retrovirus Replication

• Retroviruses replicate using reverse transcription.
• The virus's RNA is converted to DNA, integrating into the host's DNA, forming a provirus.
• The provirus is transcribed and used to produce new viral RNA and proteins.
• The resulting virus particles bud from the host cell.

Ribosomal RNA Subunits and Composition

• Prokaryotic ribosomes are composed of 70S ribosomes with 50S and 30S subunits.
• Eukaryotic ribosomes are composed of 80S ribosomes with 60S and 40S subunits.

Differences Between Replication and Transcription

• Replication involves replicating the entire genome; transcription involves a segment of the DNA template.
• The enzyme used in replication is DNA polymerase; the enzyme in transcription is RNA polymerase.
• The product of replication is double-stranded DNA; the product of transcription is single-stranded RNA.
• Base pairings are somewhat similar, but uracil (U) replaces thymine(T) in RNA.

Important Terms

• Coding strand: The DNA strand whose sequence specifies the amino acid sequence of the encoded protein; also called the sense strand.
• Template strand: The DNA strand from which RNA is transcribed; also called the antisense strand.
• Promoter: The DNA sequence that the RNA polymerase recognizes and binds to initiate transcription.
• UTR: untranslated region; sequence on the mRNA that is not translated to protein.
• Introns: non-coding regions of the gene that are removed during RNA processing to produce mature mRNA; found in most eukaryotic genes.
• Exons: coding regions of the gene present in mature mRNA; they are expressed into proteins.
• Spliceosome: A complex molecular machine that performs splicing of pre-mRNA.
• hnRNA: heterogeneous nuclear RNA; primary transcript produced from DNA transcription; found in the nucleus.
• Cis-acting elements: specific DNA sequences on the DNA template that regulate the transcription of a specific gene or group of genes.
• Trans-factors proteins are involved in transcription regulation, binding to cis-elements in the DNA.

This quiz covers key concepts in molecular biology, focusing on the different types of RNA and their roles in protein synthesis and transcription. Questions range from the function of ribosomal RNA to the structure of transfer RNA and details about prokaryotic RNA polymerase. Test your understanding of these essential biological molecules.