Notes

Basic Biochemistry Topics

1. Introduction to Biochemistry

  • Definition and scope
  • Historical background
  • Relationship with other sciences

2. Chemical Foundations of Biochemistry

  • Atomic structure and chemical bonds
  • Properties of water: Polarity, hydrogen bonding, solvent properties
  • Acid-base chemistry: pH, pKa, and buffers
  • Thermodynamics in biochemical reactions: Free energy, enthalpy, entropy

3. Biomolecules: Structure and Function

  • Carbohydrates
    • Monosaccharides: Glucose, fructose
    • Disaccharides: Sucrose, lactose
    • Polysaccharides: Starch, glycogen, cellulose
  • Lipids
    • Fatty acids: Saturated, unsaturated
    • Triglycerides and their roles
    • Phospholipids in membrane structure
    • Steroids: Cholesterol, hormones
  • Proteins
    • Amino acids: Structure, properties
    • Peptide bonds and protein primary structure
    • Secondary structure: Alpha-helix, beta-sheet
    • Tertiary and quaternary structures
    • Protein folding and stability
  • Nucleic Acids
    • DNA and RNA: Structure and function
    • Nucleotide structure: Bases, sugars, phosphates
    • Base pairing and double helix

4. Enzymes

  • Enzyme structure and classification
  • Mechanism of enzyme action: Active site, substrate binding
  • Enzyme kinetics: Michaelis-Menten equation, Km, Vmax
  • Enzyme inhibition: Competitive, non-competitive, uncompetitive
  • Regulation of enzyme activity: Allosteric control, feedback inhibition, covalent modification

Intermediate Biochemistry Topics

1. Carbohydrate Metabolism and Bioenergetics

  • Principles of metabolic pathways: Catabolism and anabolism
  • ATP: Structure, synthesis, and role as energy currency
  • Glycolysis: Steps, regulation, and energetics
  • Gluconeogenesis: Pathway and regulation
  • Pentose Phosphate Pathway: Functions and importance
  • Citric Acid Cycle (Krebs Cycle): Steps, regulation, and energy yield
  • Oxidative Phosphorylation: Electron transport chain, chemiosmosis, ATP synthesis
  • Energy-rich compounds: ATP, NADH, FADH2, GTP

2. Lipid Metabolism

  • Fatty acid oxidation (Beta-oxidation): Steps, regulation, energy yield
  • Ketogenesis and ketone bodies
  • Fatty acid synthesis: Steps, regulation
  • Metabolism of triglycerides and phospholipids
  • Cholesterol metabolism: Biosynthesis, regulation, transport

3. Amino Acid and Protein Metabolism

  • Amino acid catabolism: Transamination, deamination, urea cycle
  • Biosynthesis of non-essential amino acids
  • Specialized products of amino acids: Neurotransmitters, hormones, creatine
  • Protein turnover: Ubiquitin-proteasome system, autophagy

4. Nucleotide Metabolism

  • Purine metabolism: Synthesis, salvage pathways, degradation
  • Pyrimidine metabolism: Synthesis, salvage pathways, degradation
  • Disorders of nucleotide metabolism: Gout, Lesch-Nyhan syndrome

Advanced Biochemistry Topics

1. Genetics and Molecular Biology

  • DNA replication: Mechanism, enzymes involved, fidelity
  • DNA repair mechanisms: Mismatch repair, excision repair, recombination repair
  • Recombination: Homologous and non-homologous
  • Transcription: Initiation, elongation, termination, RNA polymerases
  • RNA processing: Capping, splicing, polyadenylation
  • Translation: Ribosome structure, initiation, elongation, termination, post-translational modifications
  • Regulation of gene expression: Operons, enhancers, silencers, transcription factors, epigenetic modifications

2. Signal Transduction

  • Types of receptors: G-protein coupled receptors (GPCRs), receptor tyrosine kinases (RTKs), ion channels
  • Signal transduction pathways: cAMP, phosphoinositide pathway, MAPK pathways
  • Secondary messengers: cAMP, IP3, DAG, Ca2+
  • Hormones: Types, mechanisms of action

3. Membrane Biochemistry

  • Structure and function of biological membranes: Lipid bilayer, fluid mosaic model
  • Membrane dynamics: Lateral diffusion, flip-flop movement
  • Membrane transport: Passive (simple diffusion, facilitated diffusion), active transport (primary and secondary)
  • Membrane proteins: Integral, peripheral, lipid-anchored
  • Signal transduction across membranes

4. Biochemical Techniques

  • Chromatography: Principles, types (HPLC, affinity, ion exchange, gel filtration)
  • Electrophoresis: Principles, SDS-PAGE, agarose gel electrophoresis
  • Spectroscopy: UV-Vis, fluorescence, NMR, mass spectrometry
  • Molecular cloning: Cloning vectors, restriction enzymes, ligation, transformation
  • PCR and DNA sequencing

5. Advanced Topics in Enzymology

  • Enzyme inhibition: Types, kinetics, applications in drug design
  • Enzyme regulation: Allosteric enzymes, covalent modification, zymogens
  • Kinetic isotope effects: Mechanistic insights
  • Enzyme evolution: Natural selection, directed evolution
  • Enzyme engineering: Rational design, site-directed mutagenesis

6. Structural Biology

  • X-ray crystallography: Principles, data collection, structure determination
  • NMR spectroscopy: Principles, structure determination, dynamics
  • Cryo-electron microscopy: Principles, single-particle analysis, resolution

7. Bioinformatics and Computational Biochemistry

  • Sequence alignment: Algorithms, tools (BLAST, Clustal)
  • Protein structure prediction: Homology modeling, ab initio methods
  • Molecular modeling: Docking, molecular dynamics simulations

8. Specialized Topics

  • Metabolomics: Techniques, data analysis, applications
  • Systems biology: Integration of omics data, network analysis
  • Proteomics: Techniques, mass spectrometry, applications
  • Chemical biology: Small molecule probes, target identification
  • Drug design: Structure-based, ligand-based approaches

9. Synthetic Biology

  • Genetic circuits: Design, construction, applications
  • Synthetic organisms: Genome synthesis, minimal genomes
  • CRISPR-Cas systems: Mechanism, applications in genome editing

10. Environmental Biochemistry

  • Biochemical cycles: Carbon, nitrogen, phosphorus cycles
  • Bioremediation: Principles, strategies, applications
  • Environmental biotechnology: Waste treatment, bioenergy

11. Biochemical Engineering

  • Enzyme reactors: Types, design, applications
  • Microbial bioreactors: Fermentation, scale-up, optimization
  • Industrial biochemistry: Production of biochemicals, pharmaceuticals

12. Personalized Medicine and Pharmacogenomics

  • Biochemical basis of personalized medicine: Biomarkers, targeted therapies
  • Pharmacogenomics: Genetic variability in drug response, applications

Additional Topics

1. Nutrition and Biochemistry

  • Macronutrients: Carbohydrates, proteins, lipids
  • Micronutrients: Vitamins, minerals
  • Nutritional biochemistry: Digestion, absorption, metabolism
  • Nutritional deficiencies: Scurvy, rickets, pellagra, beriberi
  • Obesity and metabolic syndrome: Biochemical basis, consequences

2. Diseases Related to Biochemistry

  • Metabolic disorders: Diabetes, phenylketonuria, glycogen storage diseases
  • Genetic disorders: Cystic fibrosis, sickle cell anemia, thalassemia
  • Neurodegenerative diseases: Alzheimer’s, Parkinson’s, Huntington’s
  • Cancer biochemistry: Oncogenes, tumor suppressors, metabolic reprogramming
  • Cardiovascular diseases: Atherosclerosis, hypertension, hyperlipidemia
  • Infectious diseases: Biochemical aspects of viral and bacterial infections
  • Inflammatory diseases: Biochemistry of inflammation, autoimmune diseases

This detailed list should provide a thorough and organized roadmap for studying biochemistry from foundational concepts to advanced and specialized topics.

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