Molecular Diagnostics

Molecular diagnostics is a discipline that applies the principles and techniques of molecular biology to medicine and healthcare. It involves the analysis of biological markers in an individual's genome and proteome—such as specific DNA sequences, RNA levels, and proteins—to diagnose disease, predict susceptibility, monitor treatment efficacy, and guide therapeutic decisions. By examining the molecular basis of health and illness, this field enables the highly sensitive and specific detection of infectious agents, inherited genetic disorders, and cancer, paving the way for personalized medicine and improved patient outcomes.

1. Fundamentals of Molecular Biology for Diagnostics
   1. The Central Dogma of Molecular Biology
      1. Overview of Information Flow
         1. DNA to RNA to Protein Pathway
         2. Exceptions to the Central Dogma
         3. Reverse Transcription in Retroviruses
      2. DNA Replication
         1. Molecular Machinery of Replication
            1. DNA Polymerases
            2. Helicases
            3. Primase
            4. Ligase
            5. Single-Strand Binding Proteins
         2. Replication Process
            1. Origin of Replication
            2. Replication Fork Formation
            3. Leading Strand Synthesis
            4. Lagging Strand Synthesis
            5. Okazaki Fragments
         3. Fidelity and Repair
            1. Proofreading Activity
            2. Mismatch Repair
            3. Base Excision Repair
            4. Nucleotide Excision Repair
      3. Transcription
         1. RNA Polymerases
            1. RNA Polymerase I
            2. RNA Polymerase II
            3. RNA Polymerase III
            4. Bacterial RNA Polymerase
         2. Transcription Initiation
            1. Promoter Recognition
            2. Transcription Factor Binding
            3. RNA Polymerase Recruitment
            4. Transcription Bubble Formation
         3. Transcription Elongation
            1. RNA Chain Extension
            2. Transcriptional Pausing
            3. Elongation Factors
         4. Transcription Termination
            1. Intrinsic Termination
            2. Rho-Dependent Termination
            3. Polyadenylation Signal Recognition
         5. Post-Transcriptional Processing
            1. 5' Capping
            2. 3' Polyadenylation
            3. Splicing Mechanisms
            4. Alternative Splicing
      4. Translation
         1. Ribosome Structure and Function
            1. Large and Small Subunits
            2. rRNA Components
            3. Ribosomal Proteins
            4. A, P, and E Sites
         2. Transfer RNA Function
            1. tRNA Structure
            2. Aminoacylation
            3. Codon-Anticodon Recognition
            4. Wobble Base Pairing
         3. Translation Process
            1. Initiation Complex Formation
            2. Elongation Cycle
            3. Termination and Release
            4. Ribosome Recycling
         4. Post-Translational Modifications
            1. Protein Folding
            2. Chemical Modifications
            3. Protein Targeting
   2. Structure and Function of Nucleic Acids
      1. Deoxyribonucleic Acid Structure
         1. Chemical Composition
            1. Nucleotide Components
            2. Purine Bases
            3. Pyrimidine Bases
            4. Deoxyribose Sugar
            5. Phosphate Groups
         2. Double Helix Architecture
            1. Watson-Crick Base Pairing
            2. Antiparallel Strands
            3. Major Groove
            4. Minor Groove
            5. Helical Parameters
         3. DNA Conformations
            1. B-Form DNA
            2. A-Form DNA
            3. Z-Form DNA
         4. Chromosome Organization
            1. Chromatin Structure
            2. Nucleosome Formation
            3. Histone Proteins
            4. Chromatin Condensation
            5. Euchromatin vs Heterochromatin
      2. Ribonucleic Acid Structure
         1. Chemical Differences from DNA
            1. Ribose Sugar
            2. Uracil Base
            3. Single-Strand Nature
         2. Secondary Structures
            1. Hairpin Loops
            2. Bulges
            3. Internal Loops
            4. Pseudoknots
         3. Functional RNA Types
            1. Messenger RNA
            2. Transfer RNA
            3. Ribosomal RNA
            4. Small Nuclear RNA
            5. MicroRNA
            6. Small Interfering RNA
            7. Long Non-Coding RNA
      3. Gene Structure and Organization
         1. Prokaryotic Gene Organization
            1. Operons
            2. Promoter Elements
            3. Regulatory Sequences
         2. Eukaryotic Gene Structure
            1. Exons and Introns
            2. Promoter Regions
            3. Enhancers and Silencers
            4. Untranslated Regions
   3. Gene Expression and Regulation
      1. Transcriptional Control
         1. Promoter Elements
            1. Core Promoter
            2. Proximal Promoter
            3. Distal Promoter
         2. Enhancers and Silencers
            1. Enhancer Function
            2. Silencer Mechanisms
            3. Chromatin Looping
         3. Transcription Factors
            1. DNA-Binding Domains
            2. Activation Domains
            3. Repressor Proteins
            4. Coactivators and Corepressors
      2. Epigenetic Regulation
         1. DNA Methylation
            1. CpG Islands
            2. Methyltransferases
            3. Demethylases
            4. Gene Silencing Mechanisms
         2. Histone Modifications
            1. Acetylation
            2. Methylation
            3. Phosphorylation
            4. Ubiquitination
            5. Chromatin Remodeling Complexes
         3. Non-Coding RNA Regulation
            1. MicroRNA Mechanisms
            2. Long Non-Coding RNA Functions
      3. Post-Transcriptional Regulation
         1. Alternative Splicing
         2. RNA Editing
         3. RNA Stability
         4. MicroRNA Targeting
   4. Genetic Variation and Mutation
      1. Types of Mutations
         1. Point Mutations
            1. Silent Mutations
            2. Missense Mutations
            3. Nonsense Mutations
         2. Insertion and Deletion Mutations
            1. Frameshift Mutations
            2. In-Frame Indels
         3. Large-Scale Mutations
            1. Chromosomal Rearrangements
            2. Copy Number Variations
      2. Mutation Mechanisms
         1. Spontaneous Mutations
         2. Induced Mutations
         3. DNA Repair Defects
      3. Polymorphisms
         1. Single Nucleotide Polymorphisms
         2. Tandem Repeats
         3. Structural Variants
      4. Population Genetics Concepts
         1. Allele Frequencies
         2. Hardy-Weinberg Equilibrium
         3. Linkage Disequilibrium