Ch 2

• Orbitals and shells


  Fill with electrons in order from lowest to highest energy
• Valence shell


  Outermost shell containing electrons
• Valence electrons


  Electrons in the valence shell
• Oxygen has 6 valence electrons
• Oxygen needs 2 more electrons to fill its valence shell
• Atoms with incomplete valence shells


  Are reactive and interact with other atoms to complete their valence shells
• Chemical Bond


  Attraction between atoms that holds them together due to sharing or exchanging electrons
• Types of chemical bonds in biological systems

  • Strong bonds: Covalent and ionic
  • Weak bonds: Hydrogen bonds

  
• Covalent Bond


  Sharing of electrons by two atoms to complete their valence shells
• Single bond


  1 electron pair shared
• Double bond


  2 electron pairs shared
• Electronegativity (χ)


  The attraction of an atom for the electrons in a covalent bond
• Hydrogen has an electronegativity of 2.1
• Carbon has an electronegativity of 2.5
• Nitrogen has an electronegativity of 3.0
• Oxygen has an electronegativity of 3.5
• Non-polar covalent bond


  Electrons are shared equally between atoms of the same electronegativity
• Non-polar covalent bonds


  • H-H
  • C-C
  • C-H

  
• Polar covalent bond


  Electrons are not shared equally between atoms of different electronegativity
• Methanol has 5 covalent bonds, 2 of which are polar
• Ionic Bond


  Atom with high electronegativity takes the lone valence electron from atom with low electronegativity, producing ions
• Strong attraction forms between anion and cation in an ionic bond
• Hydrogen Bond


  Attraction between the δ+ H atom of one polar covalent bond and the δ- atom of a second polar covalent bond

  
• Rules of hydrogen bonding

  • Each atom in the H-bond is covalently bonded to something else
  • An H-bond always involves a hydrogen atom
  • The second atom in an H-bond is always electronegative (usually O or N)
  • Electrons are not shared in an H-bond, it is an attraction between partial charges
  • Each H atom can form only one H-bond

  
• Hydrogen bonds are weak in biological settings, but very important
• Water can hydrogen bond with polar molecules

  
• Hydrophilic molecules


  Have polar covalent bonds, form hydrogen bonds with water, and dissolve in water
• Hydrophobic molecules


  Have non-polar covalent bonds, have little affinity for water, and interact with other non-polar molecules and exclude water
• Hydrocarbons


  Carbon-hydrogen only chains
• Variations in carbon chains

  • Benzene
  • Cyclohexane
  • Hexane
  • 2-methylpentane
  • 3-methylpentane
  • 3-methylpentene
  • Hexene

  
• Geometric isomers


  Atoms are in the same order, but with a different spatial arrangement
• Functional groups


  Can replace an H on a carbon skeleton and give the molecule unique properties
• Functional groups


  • Aldehyde
  • Ketone
• Methyl group


  Decreases water solubility when added to a carbon skeleton, found in nucleic acids and hormones