Molecular Biology

1. Biomolecular Interactions
   1. Enzyme-Substrate Interactions
      1. Enzyme structure
         1. Active site composition
         2. Three-dimensional conformation
         3. Allosteric sites and regulation
      2. Catalytic mechanisms
         1. Enzyme-substrate complex formation
         2. Transition state stabilization
         3. Strategies of catalysis
            1. Acid-base catalysis
            2. Covalent catalysis
            3. Metal ion catalysis
         4. Enzyme kinetics
            1. Michaelis-Menten kinetics
            2. Lineweaver-Burk plot
         5. Inhibition types
            1. Competitive inhibition
            2. Non-competitive inhibition
            3. Uncompetitive inhibition
   2. Receptor-Ligand Interactions
      1. Types of receptors
         1. G protein-coupled receptors (GPCRs)
         2. Receptor tyrosine kinases
         3. Ion channel-linked receptors
         4. Intracellular receptors
      2. Signal transduction
         1. Signal amplification and pathways
         2. Second messengers (e.g., cAMP, calcium ions)
         3. Cross-talk between signaling pathways
      3. Hormone and neurotransmitter interactions
         1. Specificity and affinity in binding
         2. Agonists and antagonists
         3. Receptor desensitization and downregulation
   3. Nucleic Acid-Protein Interactions
      1. DNA-binding proteins
         1. Structural motifs (helix-turn-helix, zinc finger, leucine zipper)
         2. Role in gene regulation
            1. Transcription factors
            2. Enhancers and silencers
            3. Operon models in prokaryotes
      2. RNA-binding proteins
         1. RNA recognition motifs (RRMs)
         2. Role in RNA processing and stability
         3. RNA interference and regulatory RNAs
      3. Chromatin remodeling proteins
         1. Histone modification and its effects
         2. Nucleosome positioning
         3. Chromatin accessibility and epigenetic regulation
   4. Protein-Protein Interactions
      1. Interaction motifs and domains
         1. SH2, SH3 domains
         2. Coiled-coil motifs
         3. PDZ, WW domains
      2. Methods for studying interactions
         1. Yeast two-hybrid system
         2. Co-immunoprecipitation
         3. Surface plasmon resonance (SPR)
      3. Importance in cellular functions
         1. Signal transduction pathways
         2. Complex formation (e.g., ribosome, spliceosome)
         3. Protein transport mechanisms
   5. Lipid-Protein Interactions
      1. Membrane protein association
         1. Integral vs. peripheral membrane proteins
         2. Lipid rafts and membrane microdomains
      2. Lipid signaling
         1. Role of phospholipids in signal transduction
         2. Eicosanoid signaling (prostaglandins, leukotrienes)
      3. Lipid modifications
         1. Prenylation, myristoylation, palmitoylation
         2. Glycosylphosphatidylinositol (GPI) anchors
   6. Carbohydrate-Protein Interactions
      1. Glycoproteins and proteoglycans
         1. Glycosylation types (N-linked, O-linked)
         2. Functional implications in cell recognition
      2. Lectin interactions
         1. Specificity and biological roles
         2. Pathogen recognition and immune response
   7. Small Molecule-Protein Interactions
      1. Interaction dynamics
         1. Binding affinities and thermodynamics
         2. Induced fit vs. conformational selection models
      2. Drug design and discovery
         1. Structure-based drug design
         2. High-throughput screening techniques
         3. Challenges in specificity and off-target effects