Biochemistry

• Water


  The most abundant substance in living systems, making up 70% or more of the weight of most organisms
• Cell structure and function

  • Adapted to water (aqueous) environment
• Hydrogen bonds


  Provide the cohesive forces that make water a liquid at room temperature and a crystalline solid (ice) at cold temperatures
• Polar biomolecules


  Dissolve readily in water because they can replace water-water interactions with more energetically favorable water-solute interactions
• Nonpolar biomolecules


  Poorly soluble in water because they interfere with water-water interactions but are unable to form water-solute interactions; in aqueous solutions, nonpolar molecules tend to cluster together
• Hydrogen bonds, ionic, hydrophobic, and van der Waals interactions are individually weak, but collectively they have a very significant influence on the 3D structures of proteins, nucleic acids, polysaccharides, and membrane lipids
• Water has a higher melting point, boiling point, and heat of vaporization than most other common solvents
• Hydrogen Bonding

  Gives water its unusual properties
• 1. O-H bond angle

  • 104.5°
• Oxygen


  More electronegative, attracts electrons more strongly than hydrogen nucleus (a proton)
• Hydrogen atom

  Bears a partial positive charge (δ+)
• Oxygen atom


  Bears a partial negative charge equal in magnitude to the sum of the two partial positives (2δ-)
• Hydrogen bond


  A weak electrostatic attraction between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom
• Hydrogen bonds in liquid water have a bond dissociation energy (the energy required to break a bond) of about 23 kJ/mol, compared with 470 kJ/mol for the covalent O-H bond
• Hydrogen bonds


  Strongest when the bonded molecules are in a straight line – that is, when the acceptor atom is in line with the covalent bond between the donor atom and H
• Water


  A polar solvent, readily dissolves most biomolecules, which are generally charged or polar compounds
• Nonpolar solvents


  Such as chloroform and benzene are poor solvents for polar biomolecules but easily dissolve those that are hydrophobic – nonpolar molecules such as lipids and waxes
• Water

  Dissolves salts such as NaCl by hydrating and stabilizing the Na+ and Cl- ions, weakening the electrostatic interactions between them and thus counteracting their tendency to associate in a crystalline lattice
• Water

  Readily dissolves charged biomolecules, including compounds with functional groups such as ionized carboxylic acids, protonated amines, and phosphate esters or anhydrides
• Nonpolar gases


  CO2, O2, and N2 are poorly soluble in water
• The movement of molecules from the disordered gas phase into aqueous solution constrains their motion and the motion of water molecules and therefore represents a decrease in entropy
• Some organisms


  • Have water-soluble "carrier proteins" (hemoglobin and myoglobin) that facilitate the transport of O2
• CO2


  Forms carbonic acid (H2CO3) in aqueous solution and is transported as the bicarbonate ion (HCO3-)
• NH3, NO, and H2S

  Polar gases – readily dissolve in water, ionize in aqueous solutions
• Nonpolar compounds


  Such as benzene and hexane are hydrophobic – they are unable to undergo energetically favorable interactions with water molecules
• Clathrates


  Crystalline compounds of nonpolar solutes and water; the ordering of water molecules reduces entropy
• Amphipathic compounds


  Contain regions that are polar and regions that are nonpolar. Many biomolecules are amphipathic; proteins, pigments, certain vitamins, and the sterols and phospholipids of membranes all have both polar and nonpolar surface regions
• Hydrophobic effect


  When an amphipathic compound is mixed with water, the polar, hydrophilic region interacts favorably with the water and tends to dissolve, but the nonpolar, hydrophobic region tends to avoid contact with the water. The nonpolar regions of the molecules cluster together to present the smallest hydrophobic area to the aqueous solvent, and the polar regions are arranged to maximize their interaction with the solvent
• Micelle


  An aggregate of amphipathic molecules in water, with the nonpolar portions in the interior and the polar portions at the exterior surface, exposed to water
• Hydrophobic interactions


  Forces that hold the nonpolar regions of the molecules together
• van der Waals interaction (London forces)


  Weak intermolecular forces between molecules as a result of each inducing polarization in the other
• van der Waals radius

  A measure of how close that atom will allow another to approach
• Four Types of Noncovalent ("Weak") Interactions among Biomolecules in Aqueous Solvent


  • Hydrogen bonds (between neutral groups and between peptide bonds)
  • Ionic interactions (attraction, repulsion)
  • Hydrophobic interactions
  • van der Waals interactions
• Solutes


  Alter certain physical colligative properties of the solvent, water: vapor pressure, boiling point, melting point (freezing point), and osmotic pressure
• The concentration of water is lower in solutions than in pure water
• The effect of solute concentration on the colligative properties of water is independent of the chemical properties of the solute; it depends only on the number of solute particles (molecules or ions) in a given amount of water
• Osmotic pressure


  Produced when two different aqueous solutions are separated by a semipermeable membrane, and when water molecules diffuse from the region of higher water concentration to the region of lower water concentration
• Osmosis


  Water movement across a semipermeable membrane
• Osmotic pressure


  The force necessary to resist water movement, approximated by the van't Hoff equation: Π = icRT
• van't Hoff factor (i)

  A measure of the extent to which the solute dissociates into two or more ionic species