Introduction to Biochemistry III

Properties of water

  • Polar: electrons shared unequally causing a difference in change from one side of the molecule to the other
    • Enables water to act as a universal solvent
  • Molecules form a dipole, tetrahedral shape
  • Molecules are held together with H bonds

Hydrophobic effect

  • The observed tendency of non-polar substances to aggregate in aqueous solution and exclude water molecules - micelles, lipid bilayer, ‘oil slick’

Amphipathic molecules

  • Amphipathic molecules are moelcules with a polar (hydrophilic) ‘head’ and a non-polar (hydrophobic) tail
  • Form micelles, and the lipid bilayer of membranes
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Amino acids

Structure of amino acids

  • ⍺-carbon bonded to:
    • Amino group (-NH2)
    • Carboxyl group (-COOH)
    • A hydrogen (-H)
    • A side chain (-R)
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Classification of amino acids

  • Non-polar, hydrophobic
  • Polar, hydrophobic
  • Acidic
  • Basic

Peptide bonds

  • Join amino acids
  • Produced by a condensation reaction
  • Important for folding of proteins

Acids and bases

Base

  • Proton acceptors

Acid

  • Molecule that can donate a proton (H+)
  • Strength of acid depends on how readily it donates a proton to a base
    • Measured by the acid dissociation constant Ka
      • Ka = [H+][A-]/[HA]
      • pKa = -log10[Ka]

pH

  • The measurement of the number of protons in a solution
  • pH = -log10[H+]

Henderson-Hasselbalch equation

  • Connects the Ka of a weak acid with the pH of a solution containing this acid
  • pH = pKa + log[A]/[HA]

Buffers

  • A solution used to control the pH of a reaction mixture
  • When the concentration of acid is equal to the concentration of the conjugate base, pH = pKa
  • At their pKa value, buffers tend to resist a change in pH on addition of moderate amounts of acid or base

pH and proteins

  • Change in pH can change the ionisation of protein, therefore change its structure and function
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