Chemistry in living systems

• Intramolecular forces


  Forces that hold atoms together within a molecule
• When two atoms with significantly different electronegativities share electrons in a covalent bond

  The electrons are more attracted to the atom with the higher electronegativity, causing that atom to assume a slightly negative charge and the other atom a partial positive charge
• Atoms with high electronegativity

  • Oxygen, Nitrogen, Chlorine
• Molecules with regions of partial negative and partial positive charge

  • Polar molecules
• Non-polar molecules


  • Cooking oil, Motor oil
• The natural clumping together of non-polar molecules in water is referred to as the hydrophobic effect
• Hydrophobic


  Non-polar molecules that are water-fearing and tend to clump together
• Atoms with lower electronegativity

  • Hydrogen, Carbon, Phosphorus
• Bonds within molecules

  • Covalent bonds formed when the electron shells of two non-metal atoms overlap so that valence electrons of each atom are shared between both atoms
• Polar covalent bond


  Unequal sharing of electrons in a covalent bond creating partial negative and partial positive charges
• When non-polar molecules interact with polar molecules

  Non-polar molecules have a natural tendency to clump together rather than mix with the polar molecules
• Hydrophilic


  Polar molecules that are water-loving and tend to form hydrogen bonds with water
• Non-polar bonds


  Covalent bonds formed between atoms with similar electronegativities, resulting in fairly equal sharing of electrons
• Hydrogen ions


  • Critical to many biological processes, including cellular respiration
• Ions


  Atoms or groups of atoms that have gained or lost electrons, giving them a positive or negative charge
• Hydrophobic effect


  The natural clumping together of non-polar molecules in water
• Substances that form ions in biological processes are almost never considered in the form of ionic compounds in cells
• Breaking the bonds in hydrocarbons releases a great deal of energy
• Properties of hydrocarbons

  • Non-polar
  • Do not dissolve in water
  • Have relatively low boiling points
  • Are flammable
• Important functional groups on biological molecules

  • Carbonyl
  • Carboxyl
  • Amino
  • Sulfhydryl
  • Phosphate
• Hydrocarbons are organic molecules made up of only carbon and hydrogen atoms
• Hydrophobic


  Referring to non-polar molecules that do not have attractive interactions with water molecules
• Sodium ions

  • Part of transport mechanisms that enable specific molecules to enter cells
• Ions are an important part of living systems
• Functional group


  An atom or group of atoms attached to a molecule that gives the molecule particular chemical and physical properties
• Hydrophobic effect


  Plays a central role in how cell membranes form and helps to determine the three-dimensional shape of biological molecules such as proteins
• Covalent bonds between carbon and carbon and between carbon and hydrogen in hydrocarbons are "energy-rich"
• The presence of hydroxyl or carbonyl groups on a molecule makes the molecule polar
• Functional groups provide the molecules to which they are bonded with those same chemical properties
• Functional groups contain atoms such as oxygen (O), nitrogen (N), phosphorus (P), or sulfur (S)
• Many functional groups, and therefore the molecules that contain them, can also participate in hydrogen bonding
• Fuels

  • acetylene
  • propane
  • butane
  • octane
• The three-dimensional shape of a molecule influences its behaviour and function
• A single line indicates a single covalent bond, double lines indicate a double bond, and triple lines indicate a triple bond
• Structural formulas show how the different atoms of a molecule are bonded together
• Common functional groups of biologically important molecules

  • Hydroxyl
  • Carbonyl
  • Carboxyl
  • Amino
  • Phosphate
• Functional group


  A cluster of atoms that always behaves in a certain way
• Molecular formula shows the number of each type of atom in an element or compound
• Certain chemical properties are always associated with certain functional groups
• A carboxyl functional group on a molecule will make it acidic, meaning it will easily release or donate a hydrogen atom to another molecule