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Proteins structure and classification

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  1. 1. PROTEINS Dr. Daxaben N. Mehta Principal Smt. Sadguna C.U.Shah Home Science and C. U. Shah Arts & Commerce Mahila College, Wadhwancity, Dist: Surendranagar Home Science Proteins
  2. 2. Proteins • We need protein to build our muscles. • Even our hair and nails need protein. • We get protein from meat, poultry, eggs, cheese, and beans. Home Science Proteins
  3. 3. Proteins (Greek = “of first importance”) Functions: Structure - skin, bones, hair, fingernails Catalysis - biological catalysts are enzymes Movement - muscle: actin and myosin Transport - hemoglobin, transport thru membranes Home Science Proteins
  4. 4. Proteins Functions: Hormones - insulin, oxytocin, etc. Protection - antigen-antibody reactions, fibrinogen in clotting Storage - casein in milk, ovalbumin in eggs, ferritin in liver-stores iron Regulation - control in expression of genes Home Science Proteins
  5. 5. Proteins • Protein types: 9000 different proteins in a cell Individual human being >100,000 different Fibrous Protein Insoluble in H2O • Used mainly for structural purposes Globular Protein Partly soluble in H2O • Usually not used for structural purposes Home Science Proteins
  6. 6. Proteins Natural Polymers • Proteins are constructed in the body from many repeating units call amino acids • Just like other polymers the amino acids (monomers) are joined together to make long chains (polymers) – but we call them proteins instead • All of the polymer information applies to proteins – cross linking, rings, polarity etc Home Science . Proteins
  7. 7. Amino Acids • The Building Blocks of proteins Contains an amino group and an acid group Nature synthesizes about 20 common AA All but one (proline) fit this formula: AA Proline: H COOH N H proline Home Science R C COOH NH 2 Proteins
  8. 8. Amino Acids • Amino Acids (AA) The twenty common are Called alpha amino acids One and three letter codes given to 20 common AA All but glycine (where R=H) H exist as a pair of enantiomers R C COOH • nature usually produces the L amino acid NH 2 Home Science Proteins
  9. 9. Amino Acids • Amino Acids (AA) Sometimes classified as AA with: • nonpolar R groups • polar but neutral R groups • acidic R groups • basic R groups Home Science Proteins
  10. 10. H CH3 Glycine CH2 CH2 Alanine Phenylalanine Home Science OH Tyrosine Proteins
  11. 11. Acidic & Amide AA Aspartic acid Glutamic Acid Asparagine CH2 COO– COO– COO– Aspartate CH2 CH2 CH2 CH2 CH2 COO– C=O C=O NH2 NH2 Glutamate Home Science Glutamine Proteins
  12. 12. . Amino Group Arginine CH2 CH2 Lysine Histidine CH2 CH2 CH2 CH2 CH2 CH2 HN NH+ NH +H NH3+ Epsilon amino Home Science 2N=C NH2 Imidazole Guanidinium Proteins
  13. 13. Sulphur Group Serine CH2OH Threonine H-C-OH Cysteine CH2SH CH3 Methionine CH2 CH2 S CH3 Home Science Proteins
  14. 14. hydrophobic amino acids Valine Leucine Isoleucine C C – C C C C C C C C C Home Science Proteins Ethyl group
  15. 15. Proline Tryptophan H2C CH2 CH2 C H2C N H N H Indole Home Science Proteins H COO–
  16. 16. Zwitterions • Zwitterion = compound where both a positive charge and a negative charge exist on the same molecule • AA are ionic compounds • They are internal salts • In solution their form changes depending on the pH Home Science Proteins AA’s
  17. 17. Zwitterions pH = 1-5 pH = 10-14 more acidic more basic excess H+ excess OH- H R C H H COOH NH 3 + Home Science R C COO- R NH 3 + C COO- NH 2 Proteins AA’s
  18. 18. Zwitterions pH = 1-5 pH = 10-14 more basic more acidic excess H+ H R C COOH NH 3 + Home Science at pI (isoelectric point) charge = 0 H R C excess OHH R COO- NH 3 C COO- NH 2 + Proteins AA’s
  19. 19. pI • The pI is the “isoelectric point” • The pI is the pH where NO charge is on the AA: (Not necessarily at a neutral pH) at pI charge = 0 H R C COO- NH 3 + Home Science Proteins
  20. 20. Cysteine • The AA Cysteine exists as a dimer: H 2 HS CH 2 C [O] COOH [H] NH 2 cysteine H HCOO C H CH 2 S S NH 2 CH 2 C COOH NH 2 cystine a disulfide linkage Home Science Proteins AA’s
  21. 21. Peptides • AA are also called peptides • They can be combined to form... H H 2N O CH 3 O CH C OH + H 2 N CH C OH glycine alanine -H 2 O AA’s Home Science Proteins
  22. 22. Peptides • A dipeptide. H H 2N O CH C OH CH 3 O + H 2N glycine CH -H 2 O C OH alanine H H 2N O CH C CH 3 O NH CH a peptide bond Home Science Proteins C OH
  23. 23. Peptides • Known as a “dipeptide” H H 2N amine end O CH C CH 3 O NH CH a peptide bond C OH acid end glycylalanine (Gly-Ala), a dipeptide Home Science Proteins
  24. 24. Peptides • Addition of peptides (head to tail) Formation of: • dipeptides • tripeptides • tetrapeptides • pentapeptides • polypeptides • Proteins Home Science Proteins AA’s
  25. 25. Proteins • Proteins usually contain about 30+ AA • AA known as residues One letter abbreviations G, A, V, L Three letter abbreviations • Gly, Ala, Val, Leu • N terminal AA (amine end) on LEFT • C terminal AA (carboxyl end) on RIGHT glycylalanine Gly-Ala G-A Home Science Proteins AA’s
  26. 26. Polypeptides • Polypeptides R R side chains R R R R N CH C N CH C N CH C N CH C N CH C N CH C H O H O H O H O H O H O amino acid residues peptide bonds peptide bonds AA’s Home Science Proteins
  27. 27. Solubility • Polypeptides or Proteins If there is a charge on a polypeptide, it is more soluble in aqueous solution If there is No charge (neutral at pI), it is Least soluble in solution H R C H COOH charged R NH 3 + Home Science C COO- NH 2 Proteins
  28. 28. Protein Structure • Primary Structure 1o Linear sequence of AA • Secondary Structure 2o Repeating patterns ( helix, pleated sheet) • Tertiary Structure 3o Overall conformation of protein • Quaternary Structure 4o Multichained protein structure Home Science Proteins
  29. 29. Protein Structure • Primary Structure Linear sequence of AA R R R 1o R R R N CH C N CH C N CH C N CH C N CH C N CH C H O H O H O H O H O H O AA 1 AA 2 AA 3 AA 4 AA 5 With any 6 AA residues, the number of possible combinations is 6 x 6 x 6 x 6 x 6 x 6 = 46656 Home Science Proteins AA 6 AA’s
  30. 30. Protein Structure • Primary Structure R R R R R R N CH C N CH C N CH C N CH C N CH C N CH C H H H H H H O AA 1 O AA 2 AA 3 O O AA 4 O AA 5 O AA 6 With any 6 of the 20 common AA residues, the number of possible combinations is 20 x 20 x 20 x 20 x 20 x 20 = 64,000,000 (and this is not nearly large enough to be a protein!) AA’s Home Science Proteins
  31. 31. Protein Structure • Primary Structure A typical protein could have 60 AA residues. This would have 2060 possible primary sequences. 2060 = 1078 This results in more possibilities for this small protein than there are atoms in the universe! Home Science Proteins
  32. 32. Protein Structure • Primary Structure Sometimes small changes in the 1o structure do not alter the biological function, sometimes they do. AA’s Home Science Proteins
  33. 33. Changes and Effect of AA change • Cattle and hog insulin is used for humans but is different • Sickle cell anemia – only one change in an amino acid – changes the hemoglobin Home Science Proteins
  34. 34. Protein Structure • Secondary Structure Repeating patterns within a region Common patterns helix pleated sheet Originally proposed by • Linus Pauling • Robert Corey Home Science AA’s Proteins
  35. 35. Protein Structure • Secondary Structure Helix Single protein chain Shape maintained by intramolecular H bonding between -C=O and H-NHelical shape helix is clockwise Home Science AA’s Proteins
  36. 36. Protein Structure • Secondary Structure pleated sheet Several protein chains Shape maintained by intramolecular H bonding and other attractive forces between chains Chains run anti-parallel and make U turns at ends Home Science AA’s Proteins
  37. 37. Protein Structure • Secondary Structure • Random Coils Few proteins have exclusively helix or pleated sheet Many have nonrepeating sections called: Random Coils Home Science AA’s Proteins
  38. 38. Collagen Protein Structure • Secondary Structure • Triple Helix of Collagen Structural protein of connective tissues • bone, cartilage, tendon • aorta, skin About 30% of human body’s protein Triple helix units = tropocollagen Home Science Proteins AA’s
  39. 39. Tertiary Structure The Three dimensional arrangement of every atom in the molecule Includes not just the peptide backbone but the side chains as well These interactions are responsible for the overall folding of the protein This folding defies its function and it’s reactivity AA’s Home Science Proteins
  40. 40. Tertiary Structure The Tertiary structure is formed by the following interactions: Covalent Bonds Hydrogen Bonding Salt Bridges Hydrophobic Interactions AA’s Metal Ion Coordination Home Science Proteins
  41. 41. Tertiary Structure Covalent Bonding • The most common covalent bond in forming the tertiary structure is the disufide bond • It is formed from the disulfide Interaction of cysteine H 2 HS CH 2 C H [O] HCOO COOH [H] NH 2 cysteine Home Science H C CH 2 S S NH 2 CH 2 C COOH NH 2 cystine Proteins
  42. 42. Tertiary Structure Hydrogen Bonding • Anytime you have a hydrogen connected to a F O of N – you can get hydrogen bonding • These interactions can occur on the side chain, backbone or both Home Science Proteins
  43. 43. Tertiary Structure Salt Bridge • Salt bridges are due to charged portions of the protein. • Opposite charges will attract and Form ionic bonds • Some examples are the NH3+ and COO- areas of the protein Home Science Proteins
  44. 44. Tertiary Structure hydrophobic interactions • Because the nonopolar groups will turn away from the water and the polar groups toward it, hydrophobic interactions take place. • These interactions are strong enough to help define the overall structure of a protein Home Science Proteins
  45. 45. Tertiary Structure Metal Ion Coordination • Two side chains with the same charge would normally repel each other • However, if a metal is placed between them, they will coordinate to the metal and be connected together. • These metal coordinations are Important in tertiary structure formation Home Science Proteins
  46. 46. Tertiary Structure Home Science Proteins
  47. 47. Quaternary Structure Highest level of organization Determines how subunit fit together Example Hemoglobin (4 sub chains) • 2 chains 141 AA • 2 chains 146 AA - Example - Collagen Home Science Proteins
  48. 48. Home Science Proteins
  49. 49. Home Science Proteins
  50. 50. Denaturation • Any physical or chemical agent that destroys the conformation of a protein is said to “denature” it Examples: • Heat (boil an egg) to gelatin • Addition of 6M Urea (breaks H bonds) • Detergents (surface-active agents) • Reducing agents (break -S-S- bonds) Home Science Proteins
  51. 51. Denaturation • Denaturation Examples: • Acids/Bases/Salts (affect salt bridges) • Heavy metal ions (Hg2+, Pb2+) Some denaturation is reversible • Urea (6M) then add to H2O Some is irreversible • Hard boiling an egg Home Science Proteins
  52. 52. Denaturation • Denaturation Home Science Proteins