Genomics

Genomics is the comprehensive study of an organism's complete set of DNA, known as the genome, including all of its genes. Unlike classical genetics, which typically focuses on single genes and their roles in inheritance, genomics takes a broader, large-scale approach to understand the structure, function, evolution, and mapping of the entire genetic blueprint. This field utilizes high-throughput DNA sequencing and bioinformatics to analyze how genes interact with each other and the environment to influence an organism's traits, development, and susceptibility to disease.

1. Foundations of Genomics
   1. Defining Genomics
      1. Definition and Scope of Genomics
      2. Distinction from Classical Genetics
         1. Focus on Single Genes vs. Whole Genomes
         2. Methodological Differences
         3. Scale and Complexity Considerations
      3. The "Omics" Revolution
         1. Genomics
         2. Transcriptomics
         3. Proteomics
         4. Metabolomics
         5. Epigenomics
         6. Interactomics
      4. Historical Milestones in Genomics
         1. Discovery of DNA Structure
         2. Development of DNA Sequencing
         3. Early Genome Mapping Efforts
         4. Human Genome Project
         5. Post-Genomic Era Developments
   2. Molecular Foundations
      1. Central Dogma of Molecular Biology
         1. DNA Replication
            1. Semiconservative Replication
            2. DNA Polymerases
            3. Replication Fork Dynamics
         2. Transcription
            1. RNA Polymerases
            2. Promoter Recognition
            3. Transcriptional Regulation
         3. Translation
            1. Ribosome Structure and Function
            2. Genetic Code
            3. Protein Synthesis Mechanisms
      2. Structure of Nucleic Acids
         1. DNA Structure
            1. Nucleotide Composition
            2. Double Helix Structure
            3. Major and Minor Grooves
            4. DNA Packaging
         2. RNA Structure and Types
            1. Single-Stranded Structure
            2. Secondary Structure Elements
            3. Messenger RNA (mRNA)
            4. Transfer RNA (tRNA)
            5. Ribosomal RNA (rRNA)
            6. Regulatory RNAs
   3. Genome Organization
      1. Chromosomes and Chromatin
         1. Chromosome Structure
            1. Linear vs. Circular Chromosomes
            2. Centromeres and Telomeres
            3. Chromosome Banding Patterns
         2. Chromatin Organization
            1. Euchromatin vs. Heterochromatin
            2. Chromatin Remodeling
            3. Nuclear Organization
         3. Histones and Nucleosomes
            1. Histone Proteins
            2. Nucleosome Structure
            3. Higher-Order Chromatin Structure
      2. Prokaryotic vs. Eukaryotic Genomes
         1. Genome Size and Complexity
            1. C-Value Paradox
            2. Gene Density Differences
            3. Intergenic Regions
         2. Organization of Genetic Material
            1. Operons in Prokaryotes
            2. Gene Structure Differences
            3. Regulatory Mechanisms
         3. Plasmids in Prokaryotes
            1. Plasmid Types
            2. Horizontal Gene Transfer
            3. Antibiotic Resistance
      3. Organellar Genomes
         1. Mitochondrial Genomes
            1. Structure and Gene Content
            2. Maternal Inheritance
            3. Evolutionary Origin
         2. Chloroplast Genomes
            1. Gene Organization
            2. Photosynthesis Genes
            3. Endosymbiotic Theory
   4. Elements of a Genome
      1. Protein-Coding Genes
         1. Gene Structure
            1. Promoters
            2. Exons and Introns
            3. Untranslated Regions (UTRs)
            4. Regulatory Sequences
         2. Gene Expression Regulation
            1. Transcriptional Control
            2. Post-Transcriptional Regulation
            3. Alternative Splicing
            4. Epigenetic Regulation
      2. Non-Coding DNA
         1. Regulatory Elements
            1. Promoters
            2. Enhancers
            3. Silencers
            4. Insulators
            5. Locus Control Regions
         2. Non-Coding RNA Genes
            1. Transfer RNA (tRNA) Genes
            2. Ribosomal RNA (rRNA) Genes
            3. MicroRNA (miRNA) Genes
            4. Long Non-Coding RNA (lncRNA) Genes
            5. Small Nuclear RNA (snRNA) Genes
            6. Small Nucleolar RNA (snoRNA) Genes
         3. Repetitive DNA Sequences
            1. Tandem Repeats
               1. Satellite DNA
               2. Minisatellites
               3. Microsatellites
            2. Interspersed Repeats
               1. Transposable Elements
               2. Processed Pseudogenes
         4. Transposable Elements
            1. DNA Transposons
            2. Retrotransposons
               1. Long Terminal Repeat (LTR) Retrotransposons
               2. Non-LTR Retrotransposons
            3. Impact on Genome Evolution
            4. Regulation and Silencing