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  <head>
    <title>087-01 Water, chemical bonding, acid–base chemistry, and biological macromolecules</title>
    <ownerName>Integrated Medical Foundations</ownerName>
  </head>
  <body>
    <outline text="Water, bonding, acid-base, and macromolecules">
      <outline text="Chemical foundations">
        <outline text="Organised non-equilibrium systems">
          <outline text="Crowding, compartments, catalysts, energy input"/>
        </outline>
        <outline text="Covalent bonds share electron pairs">
          <outline text="Geometry and electron distribution set shape"/>
        </outline>
        <outline text="Carbon: four bonds, chains, rings, stereoisomers"/>
        <outline text="N, O, P, S add acid-base, redox, transfer"/>
        <outline text="Functional groups confer recurring properties"/>
      </outline>
      <outline text="Noncovalent forces">
        <outline text="Electronegativity makes bonds polar">
          <outline text="Water: partial negative O, partial positive H"/>
        </outline>
        <outline text="Hydrogen bonds: weak singly, strong collectively">
          <outline text="Water, secondary structure, base pairing"/>
          <outline text="Reversible at physiological temperature"/>
        </outline>
        <outline text="Ionic interactions depend on water, salt, distance"/>
        <outline text="Van der Waals forces matter at close fit"/>
        <outline text="Hydrophobic effect from water and entropy">
          <outline text="Drives membrane formation and folding"/>
        </outline>
      </outline>
      <outline text="Water and solutions">
        <outline text="Hydration shells and high dielectric constant"/>
        <outline text="Cohesion, heat capacity, heat of vaporisation">
          <outline text="Temperature stability and evaporative cooling"/>
        </outline>
        <outline text="Takes part in hydrolysis, condensation, redox"/>
        <outline text="Moles, molarity, osmotically active particles">
          <outline text="Per litre versus per kilogram of solvent"/>
        </outline>
        <outline text="Activity governs non-ideal solutions"/>
        <outline text="Tonicity depends on nonpenetrating solutes">
          <outline text="Urea raises osmolarity, adds little tonicity"/>
        </outline>
      </outline>
      <outline text="Acids, bases, and buffers">
        <outline text="Strong acids dissociate, weak acids equilibrate"/>
        <outline text="pKa: pH of equal conjugate pair">
          <outline text="Henderson-Hasselbalch relation"/>
        </outline>
        <outline text="Buffers work best near pKa"/>
        <outline text="Bicarbonate links lungs and kidneys"/>
        <outline text="Phosphate and proteins, especially histidine"/>
        <outline text="Buffering does not remove acid">
          <outline text="Excretion or metabolism required"/>
        </outline>
        <outline text="Ionisation changes with pH">
          <outline text="Isoelectric point: zero net charge"/>
          <outline text="Uncharged forms cross membranes readily"/>
        </outline>
      </outline>
      <outline text="Redox and energetics">
        <outline text="Oxidation loses, reduction gains electrons"/>
        <outline text="Reduction potential: tendency to accept"/>
        <outline text="Energy captured by carriers and gradients"/>
        <outline text="Negative free energy says nothing about rate">
          <outline text="Enzymes leave equilibrium position unchanged"/>
        </outline>
        <outline text="Coupling to ATP hydrolysis"/>
      </outline>
      <outline text="Carbohydrates and lipids">
        <outline text="Monosaccharides cyclise and form anomers"/>
        <outline text="Glycosidic bond orientation and specificity">
          <outline text="Starch digested, cellulose not efficiently"/>
        </outline>
        <outline text="Glycogen: highly branched, many ends"/>
        <outline text="Glycosaminoglycans and glycan recognition">
          <outline text="Blood-group antigens"/>
        </outline>
        <outline text="Cis double bonds bend chains, raise fluidity"/>
        <outline text="Triacylglycerols store energy without water"/>
        <outline text="Amphipathic lipids self-assemble into bilayers"/>
        <outline text="Cholesterol: fluidity and precursor"/>
      </outline>
      <outline text="Proteins and nucleic acids">
        <outline text="L amino acids and side-chain classes"/>
        <outline text="Essential amino acids come from diet"/>
        <outline text="Peptide bond restricts rotation"/>
        <outline text="Sequence determines folding and fate"/>
        <outline text="Nucleotides: base, pentose, phosphate">
          <outline text="Purines fused rings, pyrimidines one ring"/>
        </outline>
        <outline text="DNA has thymine, RNA usually uracil"/>
        <outline text="Phosphodiester backbone and directionality"/>
        <outline text="Pairing gives complementarity, stacking stability"/>
        <outline text="Diverse RNA roles, nucleotide signals"/>
      </outline>
      <outline text="Assembly and synthesis">
        <outline text="Noncovalent assembly into complexes">
          <outline text="Ribosomes, membranes, chromatin"/>
        </outline>
        <outline text="Weak bonds reversible, covalent bonds durable"/>
        <outline text="Polymers built from activated monomers">
          <outline text="Enzymes control sequence and direction"/>
        </outline>
        <outline text="Name groups, forces, compartment, energy source"/>
      </outline>
    </outline>
  </body>
</opml>
