t-4

• Topic 4


  Amino Acids & Protein Structure
• Structure of biological molecules

  • Proteins
• Amino acids


  Monomers that define the structure and function of proteins
• Amino acids


  • Stereochemistry
  • Structure
  • Classification
  • Conformation
  • Directionality
• Primary structure


  Amino acid sequence linked by peptide bonds
• Peptide bond formation


  1. Amino group of one amino acid reacts with carboxyl group of another

  2. Releases water
• Peptide bond


  • Planar
  • Rigid
  • Trans configuration
• Disulfide bridges


  Covalent cross-links between cysteine residues
• Levels of protein structure

  • Primary
  • Secondary
  • Tertiary
  • Quaternary
• Secondary structure


  • Local conformation of backbone atoms held together by hydrogen bonds
  • Includes alpha helix, beta sheet, turns, and loops
• Phi and psi angles

  Backbone bond rotations that determine polypeptide folding
• Steric hindrance limits rotation of the polypeptide backbone
• Cys


  covalent cross-link
• insulin


  • A6-A11
  • A7-B7
  • A20-B19
• Protein structure


  • 1° (amino acid sequence)
  • 2° (local backbone conformation)
  • 3° (spatial arrangement of all atoms)
  • 4° (arrangement of subunits)
• 4 levels of protein structure, increasing in complexity
• 2° structure


  • Local conformation of backbone atoms
  • Does not involve side chains
  • Held together by backbone H-bonds
  • Repetitive H-bonding pattern
  • Repetitive backbone conformation
• 2° structure


  • α-helix
  • β-sheet
  • reverse turn
  • loop
• Why do proteins form regular 2° structure?

  • Backbone folding is limited by:
  • Bond rotation
  • Steric hindrance
  • Proline
• Peptide bond rotation is limited, only possible about single bonds, not peptide bonds
• Phi (φ) and Psi (ψ) are the backbone bonds around which rotation is possible
• Steric hindrance limits rotation of the polypeptide backbone, some conformations are unfavourable
• Proline limits rotation of the polypeptide backbone, as its phi (φ) is part of a ring
• In regular 2° structure (α, β), all backbone NH & CO are engaged in H-bonding
• α-helix


  • Polypeptide chain is coiled
  • H-bonds between residues at i, i+4
  • All peptide bonds point in the same direction
  • 1 polypeptide chain
• Side chains in α-helix

  • Amphipathic helix
  • Coiled coil
• β-sheet


  • Polypeptide chain is extended ("pleated" sheet)
  • Consists of multiple aligned β-strands
  • Side chains above & below plane of sheet
  • H-bonds between backbone NH & C=O of neighbouring strands
• β-sheets


  • Parallel
  • Antiparallel (or mixed)
• Irregular secondary structure includes reverse turns & loops that connect sheets & helices
• Protein structure levels


  • 1° (amino acid sequence)
  • 2° (local backbone conformation)
  • 3° (spatial arrangement of all atoms)
  • 4° (arrangement of subunits)
• 3° structure


  Spatial arrangement of all atoms in protein, including main chain, side chains, and prosthetic groups
• 3° structure


  • Globin fold
  • Immunoglobulin fold
• 3° structure stabilization


  • Non-covalent forces: H-bonds, electrostatic interactions, hydrophobic effect
• Hydrophobic effect


  Non-polar molecules/groups aggregate in water, decreasing total surface area and releasing ordered water molecules
• Hydrophobic effect is a major driving force for protein folding, due to changes in entropy of protein and solvent
• Hydrophobicity scale


  Measures relative amino acid hydrophobicity, hydrophobic residues are usually in interior of protein
• Thermodynamics of protein stability

  ΔG = ΔH - TΔS
• Disulfide bridges


  Covalent cross-links, eg. in Bovine Pancreatic Trypsin Inhibitor
• Prosthetic groups


  Non-amino-acid components permanently attached and integral to the 3D structure of a folded protein
• 4° structure


  • Arrangement of subunits in proteins with more than one subunit (multi-subunit protein)