Organic Chemistry and Macromolecules Notes

Organic Chemistry

  • Compounds containing carbon are referred to as organic compounds.
  • All living organisms have similar proportions of major elements.
  • Important landmark experiment by Stanley Miller demonstrated the formation of organic molecules from inorganic compounds.

Importance of Carbon

  • Carbon's ability to form stable bonds with other elements enables the diversity of organic compounds necessary for life.
  • Carbon can form four covalent bonds, allowing for complex structures and varied functional groups.

Bonding to Carbon

  • Carbon compounds:
    • Hydrocarbons: Composed of carbon and hydrogen (e.g., Ethane, Propane).
    • Aromatic compounds: Contain cyclic structures with delocalized electrons (e.g., Benzene).
    • Illustrations of common hydrocarbons include butane and methylpropane.

Polycyclic Aromatic Hydrocarbons (PAHs)

  • Example: Benzo[a]pyrene, a PAH found in charred foods and tobacco smoke, acts as a pro-carcinogen.
  • Metabolized by liver enzymes to form a more reactive compound that can bind to DNA, increasing cancer risk.

Designing Experiments

  • Observational studies may show correlation (e.g., PAHs and cancer), but experiments are needed for causation testing.
  • Key elements of experimental design:
    • Independent Variable: Variable manipulated in the experiment.
    • Dependent Variable: Variable measured to determine effects.
    • Control Groups: Negative and positive for comparison.
    • Experimental Group: Receives the treatment being tested.
    • Use of statistics for data analysis.

Functional Groups

  • Hydroxyl ( + a), Carbonyl (C=O), Carboxyl (COOH), Amino (NH2), Sulfhydryl (SH), Phosphate (OPO3), Methyl (CH3).
  • Each functional group imparts specific chemical properties to the molecules.

Classes of Biological Molecules

  • Major classes include carbohydrates, proteins, nucleic acids, and lipids.
  • Macromolecules are formed by polymers from smaller building blocks called monomers.
  • Functions include energy storage, structural support, and biochemical signaling.

Carbohydrates

  • General formula: CH2O.
  • Can exist in linear or ring forms; classified as aldoses or ketoses.
  • Functions include serving as energy sources and structural components.
  • Examples of monosaccharides: glucose, galactose, fructose.

Polysaccharides

  • Formed by linking monosaccharides through glycosidic bonds.
  • Types include:
    • Storage: Starch (plants), Glycogen (animals).
    • Structural: Cellulose (plant cell walls), Chitin (fungi and arthropods).

Lipids

  • Groups include fats, phospholipids, and steroids.
  • Functions: energy storage, insulation, and forming cellular membranes.
  • Basic structure of fats: glycerol bonded to three fatty acids, forming triglycerides.
  • Differentiation in saturation: saturated vs. unsaturated fat.

Proteins

  • Functions include catalysis (enzymes), defense (immune response), storage, transport, signaling, movement, and providing structural support.
  • Monomers are amino acids; there are 20 different amino acids.
  • Structure determines function, with four levels of protein structure:
    • Primary: Sequence of amino acids.
    • Secondary: Local folding via hydrogen bonds (e.g., alpha helices, beta sheets).
    • Tertiary: 3D shape formed by interactions (hydrophobic, ionic).
    • Quaternary: Assembly of multiple polypeptides into functional units.

Protein Folding

  • The correct folding of proteins is essential for their function; misfolding can lead to diseases.
  • Chaperonins assist in proper protein folding, providing a protected environment during the process.
  • Factors affecting folding include pH, temperature, and ionic composition.

Nucleic Acids

  • Functions to store and transmit genetic information through DNA and RNA.
  • Nucleotide monomers consist of a nitrogenous base, sugar, and phosphate group.
  • Structural differences between DNA and RNA influence their functions, including base pairing.

Sequencing

  • Example: Human Genome Project; costs have dramatically decreased over the years due to advances in sequencing technology.
  • The diagram representing the reduction in genome sequencing costs highlights the rapid technological progress in the field.