Chapter 4 - Protein Structure and Function

  1. Introduction
    1. Proteins
  2. Shape & Structure of Proteins
    1. Primary structure
      1. aas
      2. peptide bonds
      3. ends
      4. naming
        1. peptide, polypeptides, protein
      5. size
        1. daltons - kDa
    2. Secondary structure
      1. a helix
      2. b sheet
        1. parallel
        2. antiparallel
      3. b turn
      4. irregular structure
      5. random coil
    3. Tertiary structure
      1. non-covalent bonds
      2. hydrophobic interactions
      3. disulfide bonds
      4. broad categories
    4. Quaternary structure
      1. homomeric
      2. heteromeric
  3. Additional Structures
    1. Structural motifs
      1. coiled-coil
      2. leucine rich repeats
      3. helix-turn-helix
        1. EF hand
        2. basic helix-loop-helix
        3. zinc finger
    2. Domains
      1. classes
    3. Fundamental classes
    4. Proteome
  4. Protein Folding
    1. Planar peptide bonds
    2. Directing protein folding
      1. native state
      2. denaturation
    3. Chaperones
      1. families
        1. molecular chaperones
        2. chaperonins
    4. Alternative folding
    5. How Proteins Work
    6. Binding
      1. ligand
      2. binding site
      3. specificity
      4. affinity - Kd
    7. Enzymes
      1. background
      2. substrates
      3. active Site
      4. example
        1. serine proteases
      5. cofactors
        1. metals / ions
        2. small organic cpds
          1. vitamins
        3. altered and replaced
      6. Common pathway association
        1. protein machines
  5. How Proteins Are Controlled
    1. Introduction
    2. Non-covalent Mods.
      1. allostery
        1. allosteric binding site
          1. feedback inhibition
      2. Ca++ switching
        1. switch proteins
      3. GTPase switching
    3. Covalent Mods.
      1. phosphorylation
        1. kinase
        2. phosphatase
      2. proteolytic cleavage
        1. proteinase
        2. zymogens