Chapter 2

• Biology:

  • The study of life, based on the principles of chemistry and physics
  • each living organism is a collection of atoms and molecules bond together and interacting with each other
• Chemical elements essential for life in more organisms:

  • C, H, O, N -> make up 95.5% of atoms in living organisms
  • carbon is the building block of all living matter
  • nitrogen is found in proteins
  • Hydrogen and oxygen occur primarily in water
• Mineral elements (macroelements) make up less that 1%

  • Ca and P are important constituents of the skeleton
  • Na and K are key regulators of water movement and electrical current that occur across the surface of many cells
• trace elements (microelements) make up less that 0.01%

  • essential for normal growth and function
• Energy levels of electrons:

  • electrons exist only at fixed levels of potential energy called electron shells
• How electron shells are filled:

  • from the inside out
  • Electrons filling out the low energy shells closer to the nucleus before they move into the higher energy shells further out
• Valence electrons:

  • the outermost electrons
• valence shells:

  • the outermost shells
• Electron clouds or orbitals:

  • a space where the presence of an electron has the highest probability is referred to as an orbital or electron cloud
• Ions:

  • Atoms that have gained or lost an electron are no longer neutral, they have a charge (now called ions)
• electrolytes:

  • ions in the human body are called electrolytes, include:
  • Na+ (sodium) - tears, sweat, blood
  • K+ (potassium) - nerve cells, blood
  • Ca+ (calcium) - blood, nerve cells, muscle cells, bone
  • Cl- (Chloride) - blood, stomach acid
• Chemical bonds:

  • the formation and function of molecules depend on chemical bonding between atoms
  • atoms with incomplete valence shells can share or transfer valence electrons with/from certain other atoms
  • these interactions usually result in atoms staying close together, held by attractions called chemical bonds
• ionic bonds:

  • formed when electrons are donated from one atom to another
• covalent bonds:

  • formed when two atoms share a pair of electrons
  • the making and breaking of covalent bonds are violent events, and in living cells they are carefully controlled by highly specific catalysts, called enzymes
• nonpolar covalent bonds:

  • electrons are shared equally
• polar covalent bonds:

  • electrons are shared unequally
  • polar covalent bonds containing molecules with complementing charges create attraction to each other (Van der Waals force)
• polar and nonpolar bonds:

  • molecules that contain polar or slightly polar bonds can still be nonpolar as a whole because of mutual compensation of symmetric opposite charges
  • polar and nonpolar subtractions do not dissolve in each other
• hydrophilic molecules: (water loving)

  • readily dissolve in water
  • ions and molecules that contain polar covalent bonds
• hydrophobic molecules: (water fearing)

  • do not readily dissolve in water
  • nonpolar molecules like hydrocarbon (oil floating on water)
• amphipathic molecules: (combine both properties)

  • have both polar and ionized regions at one or more sites and nonpolar regions at other sites
  • may form micelles in water.
  • polar (hydrophilic) regions at the surface of the micelle and nonpolar (hydrophobic) ends are oriented towards the interior of the micelle
• hydrophobic substances:

  • one that does not have affinity for water
• hydrophilic substances:

  • one that has affinity for water
• hydrogen bonds:

  • result from the attraction between the partial positive charge on the hydrogen atom and the partial negative change on another atom
• Hydrogen bonds in DNA:

  • hydrogen bonds between DNA bases are responsible for complementary base pairing of opposite DNA strands
• Van der waals interactions:

  • proteins
  • water
  • polymers
  • graphic sheets
• Van der waals force:

  • keep the tertiary structure of polypeptide molecules
• shape of molecules:

  • a shape of a molecules is crucial for its biological function
  • similarities in shapes of molecules have tremendous importance for drug design
• importance of water for living things:

  • life is thought to have originated in water
  • water is the biological medium on earth
  • the abundance of water is the main reason earth is habitable
  • all living organisms require water more than any other substance
  • most cells are surrounded by water
  • the cells themselves are 70 - 95 % water
• 4 of waters properties that facilitate an environment for life:

  • cohesive and adhesive behavior
  • ability to moderate temperatures
  • expansion upon freezing
  • versatility as a solvent
• importance of water for living systems:

  • cohesion of water molecules allows plants to grow very tall
  • water has high surface tension
  • prevents large changes in temperature on earth because of its high specific heat
  • because of hydrogen bonds - ice density is lower than liquid water
  • dissolves minerals and organic substances making them available for biochemical reactions
• polar molecules for acids and bases in water:

  • acid: a molecules possessing a highly polar covalent bond between a hydrogen and a second atom dissolves in water - releasing a positively charged hydrogen nucleus
  • base: a molecule that can easily accept a proton and/or contain a completely or partially displaceable -OH group is a base
• the pH of a solution can affect:

  • the shapes and functions of molecules
  • the rates of many chemical reaction
  • the ability of two molecules to bind to each other
  • the ability of ions or molecules to dissolve in water
• concentration of pH is important in biological systems:

  • most of biological reactions are possible only at a certain pH
• colligative properties of water:

  • depend strictly on the concentration of dissolved solute particles and not on the specific type of particle
  • addition of solutes to water lowers its freezing point below 0C and raises its boiling point above 100C
  • some animals produce antifreeze molecules that dissolve in their body fluids - lowering the freezing point of the fluids - preventing their blood and cells from freezing
• properties of water:

  • high heat capacity - the water holds tight onto its heat and its temp falls more slowly than that of other liquids
  • high heat of vaporization - large number of hydrogen bonds must be broken before water boils
  • high heat of fusion - large amount of heat must be released to change from liquid to the solid state
• solutions:

  • concentration - amount of a solute dissolves in a unit volume of solution
  • molecular mass - equal the sum of the atomic mass of all atoms in the molecules
  • Molarity - 1 mole of a substance is the amount of the substance in grams equal to its atomic or molecular mass
• chemical reactions:

  • occur when one or more substances are changed into other substances - reactants -> product
• chemical reaction properties:

  • all require a source of energy
  • reactions in living organisms require a catalyst (enzymes)
  • proceed in a particular direction - eventually reach equilibrium
  • occur in liquid environment - water