BMSC200 MODULE 2

• Water is the most abundant molecule in living organisms
• Passive role of water


  The structure (hence function) of biomolecules form in response to interaction with water. For example, protein folding is driven to bury hydrophobic residues.
• Active role of water

  Water is a participant in many biochemical reactions. For example, peptide bond formation releases a water molecule.
• While the presence of water on another planet does not ensure life, it is difficult to imagine life (at least as we know it) in the absence of water
• The presence of water on other planets is a critical determinant of their habitability by humans
• Scientists have started to contemplate alternate liquids, such as ammonia or formamide, that might also be suitable for life
• Oxygen and hydrogen differ in their electronegativities

  Oxygen is more electronegative than hydrogen, giving water a permanent dipole
• The dipole of a water molecule influences its ability to


  • Form electrostatic interactions with charged molecules
  • Form hydrogen bonds (including with other water molecules)
• Hydrogen bonds


  Electrostatic interactions between an electronegative atom with a hydrogen covalently linked (donor) to another electronegative atom with a free electron pair (acceptor)
• Hydrogen bonds


  • Relatively weak, ~5% the strength of a covalent bond
  • About double the length of a covalent bond
  • Strength depends on geometry (e.g. anti-parallel beta sheets are more stable than parallel)

  
• Each water molecule can donate and accept two hydrogen bonds
• Within water, each water molecule has the potential to participate in four hydrogen bonds with four other water molecules

  
• In liquid water, each molecule participates in an average of 3.4 hydrogen bonds in dynamic "flickering clusters"

  
• Heat of Vaporization


  The amount of heat required to vaporize a liquid at its boiling temperature
• Specific Heat Capacity


  The amount of heat required to raise the temperature of a substance one degree
• Water has a higher melting point, boiling point, and heat of vaporization than most common solvents

  
• Isothermic


  Living organisms that need to regulate and maintain their temperatures
• The high composition of water within our bodies, coupled with the high specific heat capacity of water, helps us to regulate our temperature
• In ice, each water molecule participates in four hydrogen bonds with other water molecules

  
• The ordered arrangement of ice has a lower density than liquid water, as a consequence, ice floats on water
• Polywater


  A new form of water with a higher boiling point, lower freezing point, and much higher viscosity than ordinary water
• Polywater was proposed to result from a novel arrangement of interaction between water molecules

  
• There was considerable concern that the unusual networking of water molecules within polywater was self-propagating and could be used as a weapon

  
• An American scientist demonstrated that his own sweat had properties remarkable similar to polywater, suggesting the unique properties reflected the influence of impurities
• Electrostatic interactions


  Water molecules can interact, and dissolve, charged solutes through formation of layers of hydration
• Hydrogen bonds


  Biomolecules have functional groups that can form hydrogen bonds with water molecules

  
• Solubility of molecules in water

  • Depends on the ability to interact with water molecules
  • Molecules that carry charge (+/-) and/or participate in hydrogen bonds have the greatest solubility
  • Hydrophilic (water-loving) molecules are polar
  • Hydrophobic (water-fearing) molecules are non-polar
  • Amphipathic molecules contain both hydrophobic and hydrophilic portions

  
• Many biologically important gases, such as CO2 and O2, are non-polar and therefore have limited solubility in water (and blood)

  
• Hydrophobic interactions


  The forces that hold the non-polar regions of an amphipathic molecule together when mixed with water
• Hydrophobic drive is a primary driving force in formation and stabilization of biomolecular structures
• Non-covalent interactions


  • Transient, dynamic interactions
  • Flexibility of structure and function
• Non-covalent interactions within biomolecules

  • Hydrogen bonds
  • Ionic (electrostatic) interactions
  • Hydrophobic interactions
  • Van der Waals interactions
• Hydrogen bonds


  Critical for the specificity of biomolecular interactions but not for the formation of biomolecular structures

  
• Ionic (electrostatic) interactions


  Magnitude of contribution is reduced by the shielding of these groups by water molecules
• Van der Waals forces

  Interaction between permanent and induced dipoles; short range, low magnitude interactions
• Hydrophobic effect


  Drive to have polar groups interacting with water and non-polar regions shielded away from water
• Ionic interactions


  • Can be attractive (oppositely charged groups) or repulsive (similarly charged groups)
  • Magnitude of contribution to biomolecular structures is reduced by shielding of these groups by water molecules
• Water shielding of charged groups

  Greatly diminishes the strength of ionic interactions
• Strength of electrostatic interactions

  Depends on the distance separating the atoms and the nature of the intervening medium
• Van der Waals forces

  • Interaction between permanent and induced dipoles; short range, low magnitude interactions
  • Attraction is maximal when two atoms are separated by the sum of the van der Waals radii
  • Abundant in the core of folded proteins