Gene Editing

Gene editing, a revolutionary technology within genetics and genomics, encompasses a set of techniques that allow scientists to make precise and targeted changes to an organism's DNA. Functioning like molecular scissors, these tools, most notably the CRISPR-Cas9 system, can add, remove, or alter genetic material at specific locations within the genome. This powerful capability has profound implications, offering the potential to correct genetic defects responsible for diseases, enhance agricultural crops, and provide a deeper understanding of gene function and its role in biological processes.

1. Foundational Concepts in Genetics
   1. The Central Dogma of Molecular Biology
      1. Overview of Information Flow in Cells
      2. DNA Replication
         1. Enzymes Involved in Replication
            1. DNA Polymerases
            2. DNA Helicases
            3. DNA Primase
            4. DNA Ligase
         2. Replication Fork and Origin of Replication
            1. Origin Recognition Complex
            2. Replication Bubble Formation
            3. Bidirectional Replication
         3. Leading and Lagging Strand Synthesis
            1. Continuous vs. Discontinuous Synthesis
            2. Okazaki Fragments
         4. Proofreading and Error Correction
            1. 3' to 5' Exonuclease Activity
            2. Mismatch Repair Systems
      3. Transcription
         1. RNA Polymerase Function
            1. RNA Polymerase II Structure
            2. Promoter Binding
            3. Elongation Complex
         2. Promoter Recognition
            1. TATA Box
            2. Initiator Elements
            3. CAAT Box
         3. mRNA 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 Binding Sites
         2. tRNA and Codon-Anticodon Pairing
            1. tRNA Structure
            2. Aminoacyl-tRNA Synthetases
            3. Wobble Base Pairing
         3. Translation Process
            1. Initiation
            2. Elongation
            3. Termination
            4. Post-translational Modifications
   2. Structure of DNA and Chromosomes
      1. Nucleotides and Base Pairing
         1. Purines
            1. Adenine
            2. Guanine
         2. Pyrimidines
            1. Cytosine
            2. Thymine
         3. Hydrogen Bonding Rules
            1. Watson-Crick Base Pairs
            2. Base Pair Stability
      2. Double Helix Structure
         1. Antiparallel Strands
         2. Major and Minor Grooves
            1. Protein-DNA Interactions
            2. Groove Dimensions
         3. DNA Supercoiling
            1. Positive and Negative Supercoiling
            2. Topoisomerases
      3. Genes and Genomes
         1. Gene Structure
            1. Exons
            2. Introns
            3. Untranslated Regions
            4. Regulatory Sequences
         2. Genome Organization
            1. Prokaryotic Genome Structure
            2. Eukaryotic Genome Structure
            3. Operons vs. Individual Genes
         3. Non-coding DNA
            1. Intergenic Regions
            2. Repetitive Elements
            3. Pseudogenes
      4. Chromatin and Chromosome Organization
         1. Nucleosomes and Histones
            1. Core Histones
            2. Histone Octamer
            3. DNA Wrapping
         2. Chromatin States
            1. Euchromatin
            2. Heterochromatin
            3. Chromatin Accessibility
         3. Higher-Order Chromosome Structure
            1. Chromosome Territories
            2. Nuclear Organization
            3. Chromosome Condensation
   3. Gene Expression and Regulation
      1. Transcriptional Control Elements
         1. Promoters
            1. Core Promoter Elements
            2. Proximal Promoter Elements
         2. Enhancers
            1. Distal Regulatory Elements
            2. Enhancer-Promoter Interactions
            3. Chromatin Looping
         3. Silencers
            1. Negative Regulatory Elements
      2. Transcription Factors
         1. Types and Functions
            1. General Transcription Factors
            2. Specific Transcription Factors
         2. DNA Binding Domains
            1. Helix-Turn-Helix
            2. Zinc Fingers
            3. Leucine Zippers
         3. Transcriptional Machinery
            1. Co-activators
            2. Co-repressors
            3. Mediator Complex
      3. Epigenetic Modifications
         1. DNA Methylation
            1. CpG Islands
            2. DNA Methyltransferases
            3. Methylation Patterns
         2. Histone Modifications
            1. Histone Acetylation
            2. Histone Methylation
            3. Histone Phosphorylation
            4. Histone Code Hypothesis
         3. Chromatin Remodeling
            1. ATP-dependent Remodeling Complexes
            2. Nucleosome Positioning
         4. Non-coding RNAs in Regulation
            1. microRNAs
            2. Long Non-coding RNAs
            3. Small Interfering RNAs
   4. Genetic Variation and Mutation
      1. Types of Mutations
         1. Point Mutations
            1. Silent Mutations
            2. Missense Mutations
            3. Nonsense Mutations
            4. Transition vs. Transversion
         2. Insertions and Deletions
            1. Small Indels
            2. Large Indels
            3. Frameshift Mutations
            4. In-frame Mutations
         3. Chromosomal Rearrangements
            1. Duplications
            2. Deletions
            3. Inversions
            4. Translocations
            5. Copy Number Variations
      2. Mutation Mechanisms
         1. Spontaneous Mutations
            1. DNA Replication Errors
            2. Spontaneous Chemical Changes
         2. Induced Mutations
            1. Chemical Mutagens
            2. Radiation-induced Damage
      3. Natural DNA Repair Mechanisms
         1. Mismatch Repair
            1. Recognition of Mismatches
            2. Repair Pathway
         2. Base Excision Repair
            1. DNA Glycosylases
            2. AP Site Processing
         3. Nucleotide Excision Repair
            1. Global Genome Repair
            2. Transcription-coupled Repair
         4. Double-Strand Break Repair
            1. Homologous Recombination
            2. Non-homologous End Joining
            3. Single-Strand Annealing