Biological Molecules

• Calculating pH from concentration:

  • pH = -log(H⁺)
  • pOH = -log(OH⁻)
• pH = power of hydrogen
• pOH = power of hydroxide
• pH + pOH = 14
• Acids release H⁺ ions when they dissociate (fall apart into separate ions) and alkalis release OH⁻ ions.

  e.g. H₂SO₄ (sulfuric acid) releases 2 H⁺ ions when it dissociates.
• To find the pH of an alkali, find the pOH using the formula and subtract the answer from 14.
• pH is equal to the negative logarithm (the power to which 10 must be raised) of the hydrogen ion concentration of a solution.
• pH example questions:

  • Determine the pH of a 0.010M HNO₃ solution.

  pH = -log(0.010) = -log(1.0 x 10⁻²) = -(-2.0) = pH 2

  • What is the pH of a 2.5 x 10⁻⁶M solution of HCl?

  pH = -log(2.5 x 10⁻⁶) = pH 5.6 (2 d.p.)

  • Calculate the pH of a 0.0010M NaOH solution.

  pH = -log(0.0010) = 3 = 14 - 3 = pH 11

  • What is the pH of a 0.020M Sr(OH)₂ solution?

  pH = -log(0.020) = 1.7 (2 d.p.) = 14 - 1.7 = pH 12.3
• Organic chemistry is the study of organic compounds.
• Organic compounds are any compound containing carbon (C) and found in living organisms.
• Four major categories of organic compounds:

  • carbohydrates
  • lipids
  • proteins
  • nucleic acids
• The functional group carbonyl has the symbol CO and consists of a carbon atom joined to an oxygen atom by a double bond. The compounds formed by carbonyl include ketones and aldehydes (e.g. acetone, propanol).
• The functional group hydroxyl has the symbol -OH and consists of a hydrogen atom bonded to an oxygen atom which is bonded to the molecule's carbon skeleton. Hydroxyl groups form the alcohol compound (e.g. ethanol).
• The functional group carboxyl has the symbol -COOH and consists of an oxygen atom double-bonded to a carbon atom bonded to a hydroxyl group. The compounds formed by carboxyl include carboxylic acids and organic acids (e.g. acetic acid in vinegar).
• The functional group amino has the symbol -NH₂ and consists of a nitrogen atom bonded to two hydrogen atoms and the carbon skeleton. The compounds formed by amino are amines (e.g. glycine, an amino acid because it also contains a carboxyl group).
• The functional group sulfhydryl has the symbol SH and consists of a sulfur atom bonded to a hydrogen atom. The compounds formed by sulfhydryl are thiols (e.g. cysteine, an amino acid).
• The functional group methyl has the symbol CH₃ and consists of a carbon atom bonded to three hydrogen atoms. The compounds formed by methyl are called methylated compounds (e.g. 5-methyl cytidine).
• The functional group phosphate has the symbol -OPO₃²⁻ and consists of a phosphate atom bonded to four oxygen atoms, one of which is bonded to the carbon skeleton and two carrying negative charges. The compounds formed by the phosphate group are organic phosphates (e.g. glycerol phosphate, the backbone of phospholipids).
• Condensation reactions are used to join monomers by chemical bonds through the elimination of a water molecule.
• Covalent bonds are strong bonds created through the sharing of electrons.
• Hydrolysis is a reaction which separates a large molecule into smaller ones and consumes a water molecule as a reactant.
• A monomer is a small repeating unit from which larger molecules (polymers) are made
• An isomer is a molecule with the same molecular formula but a different structural arrangement.
• Dipole-dipole forces are attractive forces between the positive end of the polar molecule and the negative end of another polar molecule.
• Hydrogen bonding occurs when hydrogen atoms covalently bonded to highly electronegative elements like oxygen, nitrogen, fluorine, and sulfur form weak dipoles with other nearby electronegative atoms.
• Ionic bonds involve electrostatic attraction between oppositely charged ions.
• Catabolism is the breakdown of complex molecules into simpler ones to release energy.
• Metabolism is the sum of all reactions that take place inside the cell.
• Anabolism is the build-up of larger, more complex molecules from smaller, simpler ones, which requires energy.
• Scientists studied two species of North American seahorses. They thought that these two species were closely related.

  Describe how comparisons of biological molecules in these two species could be used to find out if they are closely related.

  • compare DNA;
  • sequence of bases;
  • compare same protein;
  • sequence of amino acids;
  • immunological evidence:
  • inject seahorse protein into animal;
  • obtain antibodies;