Biology, Chemistry



Water in Biochemistry

Water is essential in biochemistry

  • Nearly all biochemical reactions occur in water
    • Reactants, products, nutrients, waste depend on water
  • Water itself participates in chemical reactions:
    • \mathrm{H^+}
    • \mathrm{OH^-}
  • Biomolecules adjust their shape (and therefore function) in response to physical and chemcial properties of water

Hydrogen bond = attractive force between hydrogen bonded to an electronegative atom (e.g., O, N, F) and an unshared electron pair on another electronegative atom

  • In general, a hydrogen bond can be represented as D-H—-A
    • DH = weaky acidic donor group (e.g., OH, NH, sometimes SH)
    • A = weakly basic acceptor group (e.g., O, N, or sometimes S)
  • The energy of an individual hydrogen bond is only approximately 20 \mathrm{kJ} / \mathrm{mol} BUT the number of hydrogen bonds in a given system can accumulate so that the overall effect of hydrogen bonds is very significant
  • Note: hydrogen bonds are constantly forming and breaking in solution
    • Water “networks” break up and reform every 2 \cdot 10^{-11} \mathrm{sec}
    • Thus, liquid water can be seen as a rapidly chaning 3D network of hydrogen bonds
  • Importantly, weak molecular interactions dictate the structure of biomolecules
    • This includes hydrogen bonds as well as ionic/electrostatic interactions and van der Waals interactions

Water affects solubility

  • Hydrophilic = polar and ionic compounds
    • Water is a good solvent for these types of molecules
  • Hydrophobic = compounds that are virtually insoluble in water
  • Most biomolecules will have both hydrophillic and hydrophobic groups (the technical term for these molecules is amphiphilic or amphipathic)
    • Example: lipid bilayer of a cell membrane
  • Hydrophobic effect = the tendency of water to minimize contacts with hydrophobic molecules

Water can participate in chemical reactions

  • Water only has a slight tendency to minimize, but can form \mathrm{H^+} and \mathrm{OH^-} ions
  • \mathrm{H^+} associates with \mathrm{H_2 O} to form \mathrm{H_3 O^+}
    • Thus, \mathrm{H^+} is never free in solution
    • Proton jumping = when the \mathrm{H^+} of \mathrm{H_3 O^+} jumps to other molecules
      • Explains why acid-base reactions occur most quicky in aqueous solutions


  • high surface tension ⇒ concentrated into tiny droplets
  • low surface tenson ⇒ spreads out


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