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Molecular Biology

Basic Molecular Theory

Basic Molecular Theory explains the flow of information from the stable storage form (DNA, organized in chromosomes) through replication (copying the storage), transcription (accessing specific information into RNA), processing (splicing in eukaryotes), translation (building proteins from the RNA instructions), ultimately resulting in functional proteins whose structure determines their role in the cell. Disruptions at any stage can lead to disease, making these processes central to understanding and diagnosing conditions in the clinical molecular laboratory

Here’s an overview connecting these key processes:

Chromosome Structure (The Library & Its Organization)

  • Core Idea: DNA, the massive instruction manual, needs to be incredibly organized and compacted to fit within the cell (nucleus in eukaryotes, nucleoid in prokaryotes)
  • Eukaryotes: Use histones to wrap DNA into nucleosomes, forming chromatin, which further folds into linear chromosomes. Key features include centromeres (for segregation) and telomeres (protective ends). Packing density (euchromatin vs. heterochromatin) regulates gene access
  • Prokaryotes: Typically have a single, circular chromosome compacted by supercoiling and nucleoid-associated proteins in the cytoplasm
  • Clinical Relevance: Detecting abnormalities in chromosome number or structure (via karyotyping, FISH, CMA) is crucial for diagnosing genetic disorders and cancers

Extrachromosomal Structure (Plugins & Mobile Apps)

  • Core Idea: Not all genetic information resides on the main chromosomes. These are independent DNA (or RNA) elements
  • Plasmids (Bacteria): Small, circular DNA carrying accessory genes (like antibiotic resistance!), replicating independently. Key tools in lab cloning
  • Bacteriophages (Viruses): Infect bacteria, can integrate (lysogeny) or replicate and lyse cells. Transfer genes via transduction
  • Mitochondrial DNA (Eukaryotes): Small, circular DNA in mitochondria, essential for energy production, maternally inherited
  • Clinical Relevance: Plasmid-mediated antibiotic resistance, phage-encoded toxins, mitochondrial diseases, mtDNA in forensics

Replication (Photocopying the Entire Library)

  • Core Idea: The process of making an exact copy of the entire DNA genome before cell division
  • Mechanism: Semiconservative, where each parental strand serves as a template. Key enzymes include helicase (unwinds), primase (lays RNA primers), DNA polymerase (synthesizes 5’->3’, proofreads), and ligase (seals gaps). Proceeds via leading and lagging strands at replication forks
  • Clinical Relevance: Basis of PCR, target for antiviral/anticancer drugs, defects cause genome instability

Transcription (Making a Working Copy of One Chapter)

  • Core Idea: Synthesizing an RNA copy from a specific DNA segment (a gene). The first step in gene expression
  • Mechanism: RNA polymerase binds to a promoter, unwinds DNA, and synthesizes RNA complementary to the template strand (using U instead of T). No primer needed. Ends at a terminator sequence
  • Clinical Relevance: Basis for gene expression analysis (RT-PCR, RNA-Seq), detecting RNA viruses, target for some antibiotics

Exons, Introns, and Splicing (Editing the Working Copy - Eukaryotes)

  • Core Idea: Eukaryotic genes contain coding regions (exons) interrupted by non-coding regions (introns). The initial transcript (pre-mRNA) must be processed
  • Mechanism: Splicing, carried out by the spliceosome, removes introns and joins exons together. Alternative splicing allows one gene to produce multiple protein variants
  • Clinical Relevance: Many genetic diseases are caused by mutations affecting splice sites; splicing is a target for therapies (e.g., ASOs)

Translation (Reading the Edited Copy to Build the Product)

  • Core Idea: Decoding the sequence of codons on the mature mRNA to synthesize a specific sequence of amino acids, forming a polypeptide
  • Mechanism: Occurs on ribosomes. tRNA molecules act as adapters, matching mRNA codons with specific amino acids. Governed by the genetic code. Proceeds through initiation (start codon AUG), elongation (peptide bond formation, translocation), and termination (stop codons)
  • Clinical Relevance: Target for many antibiotics (bacterial ribosomes), nonsense/frameshift mutations cause disease, protein detection via immunoassays

Protein Structure (The Final Functional Product)

  • Core Idea: The resulting polypeptide chain folds into a specific three-dimensional shape, essential for its function. Structure dictates function!
  • Levels: Primary (amino acid sequence), Secondary (α-helices, β-sheets via backbone H-bonds), Tertiary (overall 3D shape of one chain via R-group interactions), Quaternary (multiple subunits associating)
  • Folding & Denaturation: Folding is complex (chaperones help); denaturation (loss of structure) causes loss of function
  • Clinical Relevance: Misfolded proteins cause disease (sickle cell, CF, prions), enzyme activity assays, immunoassays rely on protein structure