Polypeptides

• Polypeptides

  • Two amino acids join to form dipeptide (peptide bond, condensation)
  • Many amino acids joined form polypeptide
  • Polypeptide chains (100s of amino acids long) form proteins
  • Have “Amino” end (-NH_2) and “Carboxyl” end (-COOH)
  • No branches
  • Amino acids sequence determined by genetic code
  • Number, types, and arrangements in chain is infinite
  • Pontetial for huge variety
  • Fold up to form specific functional 3D shapes; essential for function, broken down to four levels:
  • Primary
  • Secondary
  • Tertiary
  • Quarternary
• Polypeptide Formation

  Label

  A) Variable

  B) Carboxylic (acid) groups

  C) Amine Groups

  D) Peptide bond

  E) H_2O

  
• Primary Structure

  • Specific sequence of Amino acids in chain determined by DNA
  • Present in every proteins
  • Only has peptide bonds
  • Finding primary sequence is called protein sequencing
  • First done by Fredrick Singer
  • Sequenced insulin
  • Won Nobel prize, 1958
• Secondary Structure

  • Primary structure folded into regular 3D shapes
  • Maintained by h bonds
  • Individually weak
  • Collectively give stability
  • Enabled by peptide bond groups carrying small positive and negative charges

  Two types of folding

  • α-helix:
  • H-bonds form between C=O of one amino acids and N-H of another
  • Twists it into a helix
  • May take up whole chain, or just small part
  • β-pleated sheets:
  • H-bonds form between C=O of one chain and N-H of adjacent one (run anti-parallel)
  • Gives high tensile strength
  • Supple but no stretch
• Quaternary Structure

  • When protein has multiple polypeptide chains (e.g. many functional proteins)
  • Same bonding types as tertiary
  • Polypeptide chain may have a non-protein molecule attached
  • Prosthetic group
  • E.g. “haem” in haemoglobin
  • Makes it a conjugated protein
• Tertiary Structure

  • Further folding of polypeptide into more complex 3D shapes
  • Bonds are between the R groups (H-bonds, disulphide bonds, ionic bonds and hydrophobic/philic interactions)
  • Not in all proteins (e.g. fibrous)
  • Vital to function; forms receptor/active sites shape (e.g. hormone or enzyme)
  • Heating Effect:
  • Increases kinetic energy
  • Atoms vibrate, causing some weaker bonds break (e.g. hydrogen, ionic and hydrophobic/philic)
  • Irreversibly changes 3D shape; denatured
  • Same result from pH changes, organic solvents, high salt concentration, and heavy metal ions presence
• Tertiary Strcture; bonding

  Hydrogen Bonds

  • Between electropositive (δ^+) H atoms and electronegative (δ^-) O in other
  • Weakest

  Disulphide Bonds

  • Strong covalent bonds
  • Between amino acids, like cysteine, that contain -SH groups

  Ionic Bonds

  • Between oppositely charged ions
  • Still fairly weak

  Hydrophobic/philic Interactions

  • Hydrophobic
  • R-groups with just H and Carbon
  • In cell’s aqueous environment, they orientate away
  • Interact together by a weak bond
  • Hydrophilic
  • Polar groups in molecule, containing oxygen or nitrogen
  • Orientate out to interact with water in cell