Lecture 1

• Covalent Bonds


  • Electrons are shared
  • Stable and strong – 50 to 200 kcal/mole
  • Atoms very close (~0.1 to 0.2 nm apart)
  • Usually represented by -, : (usually a line)

  
• Non polar covalent bonds


  Electrons are shared equally
• Polar covalent bonds


  Electrons are not shared equally
• Electronegativity of an atom dictates equal or unequal sharing of electron pairs
• N and O are electronegative in polar covalent bonds
• Non-Covalent Bonds


  • Binding interactions that do not involve shared electrons
  • Weak bonds: 1 – 7 kcal/mole
  • Distance between atoms: ~0.3nm
  • Reversible
  • Hydrogen Bonds
  • Van der Waals Attraction
  • Hydrophobic Effect
  • Ionic Bonds

  
• Hydrogen Bonds


  • When a H atom is covalently bond to an electronegative atom (N and O), the H atom becomes slightly polarized and slightly positive in charge
  • The H atom that is slightly positive can form a weak non-covalent interaction with electron rich (electronegative) atom of another molecule

  
• Specific Molecules


  • Water
  • Ethanol
  • Dimethyl ether
• Ethanol is more soluble in water than Dimethyl ether because it donates and accepts H-bonds; polar molecule (water loving)
• Molecules that can not form Hydrogen Bonds

  • Non Polar
  • Hydrophobic (water hating)
  • No H-bond donor
  • No H-bond acceptor
  • No electronegative atom
• Van der waals attraction

  • Weak non-covalent interaction between non polar hydrophobic molecules
  • 1 kcal/mole
• Hydrophobic Effect


  Molecules that can not form H-bonds with water will form a separate phase (e.g. oil and water)
• Ionic bonds


  • Non-covalent - no electrons shared
  • One atom donates electron to another
  • Fills outer shell of both atoms – produces positive and negative ion
  • 3-7 kcal/mole
• Water can Ionize
• pH


  • pH = -Log [H+]
  • pH inside cell is ~7.4
• Acids and bases can ionize inside the cell


  • Acetic acid donates more H+ to water – increases [H+] to [10-3 M] ; pH = 3
  • Ammonia steals H+ from water – to liberate OH-decreases [H+] to [10-10 M] ; pH = 10
• Biology is the interplay between covalent and non-covalent chemistry
• Covalent arrangement of atoms in a biological molecule determine the non-covalent interactions and behavior that define the functions of that molecule
• Functional Groups


  • Hydroxyl group (—OH)
  • Carboxyl group (—COOH)
  • Amino group (—NH2)
  • Sulfhydryl group (—SH)
  • Phosphate group (—OPO3^2−)
  • Methyl group (—CH3)
• Functional Groups that are always negatively charged at physiological pH include phosphate and sulfhydryl
• Amphipathic molecules


  Hydrophobic and hydrophilic
• Amphipathic molecules in water form micelles to solve the containment problem
• Phospholipids


  • The solution to the containment problem
  • Form a sheet of amphipathic molecules - a phospholipid bilayer
  • Closed structure occurs so that there are no water hating (hydrophobic) edges
  • Inner aqueous environment separated from outer aqueous environment
  • Bilayer is poorly permeable to ions and to big molecules
  • Stable formation – but not to stable!