Biochemistry Fundamentals

Metabolic Pathways

• Definition: Series of chemical reactions that occur within a cell to convert energy and nutrients into ATP and other molecules
• Types:
  • Catabolic pathways: Break down molecules to release energy (e.g. glycolysis, citric acid cycle)
  • Anabolic pathways: Build molecules to store energy (e.g. gluconeogenesis, fatty acid synthesis)
• Key players:
  • Substrates: Molecules that undergo chemical changes
  • Products: Molecules resulting from chemical changes
  • Intermediates: Molecules formed during the pathway
  • Coenzymes: Molecules that facilitate chemical reactions
• Regulation:
  • Feedback inhibition: End products inhibit earlier enzymes in the pathway
  • Allosteric regulation: Binding of molecules to enzymes affects their activity
  • Post-translational modifications: Chemical changes to enzymes affect their activity

Enzyme Kinetics

• Definition: Study of the rates of enzyme-catalyzed reactions
• Key concepts:
  • Substrate binding: Enzyme binds to substrate, forming an enzyme-substrate complex
  • Catalysis: Enzyme facilitates chemical reaction, releasing product and regenerating enzyme
  • Michaelis-Menten equation: Describes the kinetics of enzyme-catalyzed reactions
  • Km (Michaelis constant): Concentration of substrate at which enzyme is half-saturated
  • Vmax (maximum velocity): Maximum rate of reaction at saturating substrate concentrations

Protein Structure

• Primary structure: Sequence of amino acids in a protein
• Secondary structure: Local arrangements of amino acids (e.g. alpha helices, beta sheets)
• Tertiary structure: 3D arrangement of amino acids in a protein
• Quaternary structure: Arrangement of multiple polypeptide chains in a protein
• Protein folding: Process by which a protein assumes its native structure
• Denaturation: Loss of native structure, often due to changes in temperature, pH, or solvent

Lipid Metabolism

• Fatty acid synthesis:
  • Acetyl-CoA is converted to malonyl-CoA, then to fatty acyl-CoA
  • Fatty acyl-CoA is elongated and desaturated to form unsaturated fatty acids
• Fatty acid oxidation:
  • Beta-oxidation: Fatty acids are broken down into acetyl-CoA, releasing energy
  • Alpha-oxidation: Fatty acids are broken down into acetyl-CoA, releasing energy
• Cholesterol metabolism:
  • Synthesis: Acetyl-CoA is converted to cholesterol through the mevalonate pathway
  • Regulation: Feedback inhibition by cholesterol and bile acids

Nucleic Acid Synthesis

• DNA replication:
  • Unwinding of double helix by helicase
  • Binding of primers to template strands
  • Synthesis of new strands by DNA polymerase
• RNA synthesis (transcription):
  • Binding of RNA polymerase to promoter region
  • Synthesis of RNA strand from template DNA
• DNA repair:
  • Base excision repair: Repair of damaged bases
  • Nucleotide excision repair: Repair of bulky lesions

Protein Metabolism

• Protein synthesis (translation):
  • Initiation: Binding of ribosome to mRNA
  • Elongation: Addition of amino acids to growing polypeptide chain
  • Termination: Release of completed polypeptide chain
• Protein degradation:
  • Proteasomal degradation: Breakdown of proteins by proteasomes
  • Lysosomal degradation: Breakdown of proteins by lysosomal enzymes
  • Ubiquitin-proteasome pathway: Targeted degradation of proteins marked with ubiquitin