Lecture 1

• covalent bonds

  electron is shared, serve as basic link in organic compounds, relatively permanent, strongest bonds in biomolecules are non polar covalent bonds

  common elements: C, N, H, O, P, S
• Ionic bonds

  electron is donated, charge-charge interactions, organic, carboxyl and amino groups carry/ form ionic bonds
• H Bonds

  partially charged atoms attract each other, polar covalent compounds, interact, partially negative and partially positive atoms interact, oxygen and nitrogen are the most common en atoms in H bonds
• Weak non polar interactions

  van der waals: result from transient dipoles that form within non-polar groups

  hydrophobic interactions: non polar groups cluster together in aq solutions
• Non polar covalent bonds

  atoms have identical or very similar electronegativity, the electrons are shared equally and no atom has a charge
• polar covalent bonds

  the atoms differ in electronegativity. electrons spend more time around the more en atom, giving it a partial negative charge, other atoms have a partial positive charge
• H bonds important

  essential for protein structure, binding of enzymes to their substrates

  hold the DNA double helix together

  Individual H bonds are weak, but collectively they can exert great strength
• H bonds and properties of water

  Responsible for the unique properties of water

  1. cohesiveness/adhesiveness
  2. high heat capacity
  3. high heat of vaporization
  4. expansion upon freezing
  5. versatility as a solvent
• van der waals interactions

  caused by induced electrical interactions between closely approaching atoms

  strength depends on the size of the atoms and their distance

  bigger electron clouds form stronger interactions

  atoms need to be about 0.2nm apart
• Bronsted acid/ base theory

  Bronsted acid = carboxyl groups and phenolic hydroxyl groups

  conjugate base are different types of amino acid groups

  A) proton donor

  B) proton acceptor

  
• Strong acid

  dissociates completely when dissolved in water

  ex: HCl and H2SO4
• Weak acid

  only partially dissociates when dissolved in water

  ex: acetic acid and other carboxylic acids