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  1. 1. Proteins are of primary importance to the life of the cell • by dry weight proteins are the major components of an actively growing cell
  2. 2. Proteins are constructed of monomers, called:
  3. 3. How do we get the amino acids needed to build proteins? EATING Protein-Rich Foods
  4. 4. Proteins ingested are digested by proteases enzymes called……………………
  5. 5. Essential amino acids:  must be taken in with the diet  the body cannot make them (e.g. methionine) Non-essential amino acids:  can be synthesised by the body (e.g. cysteine)
  6. 6. Structure of an amino acid molecule
  7. 7. R = Side group/chain [varies] What is an ‘amino acid’? An organic molecule possessing both carboxyl and amino groups
  8. 8. Sometimes books give this [amino acid in solution]:
  9. 9. The α carbon atom is:  the first carbon that attaches to a functional group asymmetrical
  10. 10. Amino acids exist in two isomeric forms: • D-amino acids (dextro, “right”) • L-amino acids (laevo, “left”)—this form is found in organisms
  11. 11. How many different amino acids: exist:  over 170 are known are commonly found in proteins:  20
  12. 12. Amino acids can be grouped based on side chains
  13. 13. Table 3.2 (Part 1) The various side groups of amino acids NONPOLAR Leucine Amino acids are nonpolar.
  14. 14. Table 3.2 (Part 1) The various side groups of amino acids POLAR UNCHARGED Glycine: simplest amino acid
  15. 15. Table 3.2 (Part 1) The various side groups of amino acids POLAR CHARGED Glutamic acid Amino acids are polar.
  16. 16. Table 3.2 (Part 1) The R-groups also have functional groups: Glutamic acid: e.g. carboxyl Arginine [polar, positively charged] e.g. amino group
  17. 17. Table 3.2 (Part 1) The various side groups of amino acids AROMATIC [NONPOLAR] Phenylalanine
  18. 18. Let’s mention three amino acids of special interest:  Proline  Methionine  Cysteine
  19. 19. Table 3.2 (Part 4) Proline: causes kinks in chains
  20. 20. Table 3.2 (Part 3) Methionine: - is often the first amino acid in a polypeptide - contains sulfur
  21. 21. Table 3.2 (Part 4) Cysteine:  contains sulfur  can form disulfide bridges Sulfhydrl group
  22. 22. A Disulfide Bridge
  23. 23. When hair is permed – disulfide bridges in keratin are broken and reformed Disulfide bridges in straight hair Disulfide bridges broken & reformed
  24. 24. Same happens when hair is straightened
  25. 25. Why do amino acids differ in their chemical and physical properties (size, water solubility, electrical charge)? Because of their different R groups
  26. 26. Table 3.2 (Part 1) The side groups of amino acids determine folding of polypeptide
  27. 27. Side chains of amino acids:  show a wide variety of chemical properties  are important to determine the:  3D structure of the protein  function
  28. 28. hydrophilic amino acids hydrophobic amino acids Where do you expect these types of amino acids to be placed in the ion channel spanning the plasma membrane?
  29. 29. WHY? hydrophilic amino acids hydrophobic amino acids Ions (black) can only pass through the pore of the ion channel because this is the only part with hydrophilic amino acids lining the pore (green = area of ion channel with hydrophilic water-loving amino acids). The rest of the ion channel mostly consists of hydrophobic amino acids (purple).
  30. 30. ORDER of the side chains of amino acids in a protein : determines how it folds into a three dimensional configuration
  31. 31. From amino acids to proteins two amino acids three amino acids more than 50 amino acids 6 000-1000 000 dipeptide tripeptide polypeptide protein
  32. 32. All proteins can be hydrolysed into amino acids • Some: need time & a particular medium • All proteins are broken when: heated in 6M HCl at 115C for several hours
  33. 33. Let’s discover how two amino acids link together
  34. 34. Amino acids are joined together by a condensation reaction H H2N C Carboxyl group O Amino group H + C OH N C CH3 H2O H2N C C C OH H H O H H O H H O N C C H CH3 OH Peptide bond A peptide bond is a covalent C-N bond formed by condensation between the -NH2 of one amino acid and -COOH of another
  35. 35. Many amino acids joined together = Polypeptide chain N-terminus C-terminus H H H O H H O H H O H H O H N C N C C C C C H C CH3 N N C CH2 CH2 OH C OH H O H H O H H O H H O N C C N C C N C N C C CH2 CH H3C CH3 C CH2 CH2 SH O OH OH
  36. 36. Note R groups alternate in the Polypeptide chain Show the position of a peptide bond
  37. 37. C-N atoms of the peptide bonds: lie in the same plane to form the backbone Side chains of the individual amino acids: are arranged transversal to each other across the backbone – this confers stability to the molecule
  38. 38. A protein molecule:  contains 100’s and 1000’s of amino acids joined together by peptide links into one or more chains 3 chains in collagen (in mouse tail)
  39. 39. Polypeptide chains can be folded in various ways
  40. 40. Proteins are unbranched, not like carbohydrates Branched molecule Unbranched molecule Protein
  41. 41. Many different types of proteins exist. How can this be? MILLIONS of Antibodies exist A LARGE NUMBER OF ENYZMES
  42. 42. Because any of 20 different amino acids might appear at any position • E.g. a protein containing 100 amino acids could form any of 20100 different amino acid sequences • this is 10130, i.e. 1 followed by 130 zeros
  43. 43. Number and Sequence of amino acids determine the protein 6 amino acids 5 amino acids 6 amino acids but in a different sequence 7 amino acids
  44. 44. Test for Protein: Biuret Test Protein present
  45. 45. Test for Protein: Biuret Test Cheese is rich in protein. pestle mortar Add an equal amount of NaOH to the solution followed by 1-2 drops of CuSO4 solution
  46. 46. When a protein reacts with copper(II) sulfate (blue), the positive test is the formation of a violet colored complex. Purple / Lilac: Positive test
  47. 47. Proteins have many functions: hormones enzymes structural proteins What dictates the function of each protein? The exact sequence of amino acids.
  48. 48. Where is the information stored in a cell that determines the sequence of amino acids?
  49. 49. Scrambled sequences of amino acids are useless: in some cases, just one wrong amino acid can cause a protein to function incorrectly What is the cause of ‘scrambled sequences of amino acids’?
  50. 50. Is the amino acid sequence really important? Let’s illustrate by an example: PKU (phenylketonuria) a genetic disorder no enzyme is present to process phenylalanine phenylalanine builds up – causes mental retardation
  51. 51. A person with PKU must avoid foods that are high in protein, such as milk, cheese, nuts or meats
  52. 52. • Enzyme has about 452 amino acids • One amino acid is present instead of another
  53. 53. PKU: no cure Testing at birth
  54. 54. Glycine is one of the 20 amino acids that occur in proteins. Proteins, in turn are useful organic components of cells. Proteins play various roles within a cell. On the otherhand, glycine, is the simplest amino acid, having hydrogen as the radical and could have formed much more easily than the other amino acids. Complex machinery is required to convert amino acids to functional proteins.
  55. 55. Structure of a Protein • each protein has a characteristic three dimensional shape called its conformation • four levels of organisation exist:1) Primary structure 2) Secondary structure 3) Tertiary structure 4) Quaternary structure
  56. 56. Structure of a Protein
  57. 57. Primary structure of a protein:  the number and sequence of amino acids held together by peptide bonds in a polypeptide chain  the primary structure of each type of protein is unique
  58. 58. Primary structure of insulin: 51 amino acids
  59. 59. Secondary structure: • the way in which the polypeptide is arranged in space • secondary structure of many different proteins may be the same • bonds present: 1. Peptide 2. Hydrogen
  60. 60. Hydrogen bonds between amino acids lead to the secondary structure of a protein Two common secondary structures are the -helix and pleated sheet
  61. 61.  helix is in a right-handed coil
  62. 62.  helix  is in a right-handed coil, maintained by H-bonds between:  CO of one amino acid and  NH group of the fifth amino acid  radical groups jut out in all directions
  63. 63.  helix: the most common form of secondary structure
  64. 64. Keratin:  is entirely helical and thus fibrous  hardness & stretchability of keratin varies with degree of disulfide bridges
  65. 65. -pleated sheet  occurs when two adjacent peptide chains bind to one another
  66. 66. 2) -pleated sheet  chains run parallel but in opposite directions
  67. 67. Side chains stick perpendicular to the plane of the chains assuming a zig-zag pattern -pleated sheet
  68. 68. Silk is an example of a pleated sheet Silk Protein Structure
  69. 69. Elastin in elastic connective tissue consists of many cross-linked polypeptides
  70. 70. It is common for a polypeptide to be partly:  an -helix a - beta pleated sheet: -helix - beta pleated sheet
  71. 71. Tertiary structure: • is when the polypeptide chain bends and folds extensively to form a precise compact • is a complex, three-dimensional that determines the final configuration of the polypeptide
  72. 72. Tertiary structure is determined by interactions of R-groups: • • • • Disulfide bonds Aggregation of hydrophobic side chains Ionic bonds Hydrogen bonds
  73. 73. Further folding of the polypeptide chain contributes to the tertiary structure of a protein Which amino acid forms disulfide bridges? Cysteine
  74. 74. Hydrophobic Interactions are a major force in the folding of globular proteins
  75. 75. Myoglobin:  153 amino acids in a single polypeptide chain  no disulfide bridges  molecule is unusual as it consists almost entirely of helices Haem
  76. 76. Quaternary structure: • the precise arrangement of the aggregation of polypeptide chains held together by hydrophobic interactions, H-bonds and ionic bonds • occurs in many highly complex proteins • a huge variety of quaternary structures
  77. 77. Quaternary structure of various proteins Antibodies comprise four chains arranged in a Y-shape.
  78. 78. Quaternary structure of various proteins Actin - hundreds of globular chains arranged in a long double helix
  79. 79. Quaternary structure of various proteins ATP synthase - 22 chains forming a rotating motor.
  80. 80. The joining of more than one polypeptide chain leads to the quaternary structure of proteins
  81. 81. Collagen is:  a triple helix  a fibrous protein  cannot be stretched due to Hbonds connecting the chains
  82. 82. Collagen is found in:  cartilage  tendons (attach muscles to bones) cartilage tendon
  83. 83. Collagen is found in: cornea  the underlayers of skin  cornea of the eye
  84. 84. Haemoglobin: - 574 amino acids - 4 polypeptide chains -chain -chain -chain -chain
  85. 85. (a) Haemoglobin (b) Iron-containing haem group (one molecule of oxygen binds to one haem)
  86. 86. - haem is an iron-containing porphyrin, acting as prosthetic group of several pigments - prosthetic group is a non-protein group which when firmly attached to a protein results in a functional complex (a conjugated protein) - porphyrin is a macromolecule composed of four subunits
  87. 87. How is it possible for foetal haemoglobin to obtain oxygen from the maternal haemoglobin?
  88. 88. Foetal haemoglobin is structurally different from that of an adult : as it has gamma chains instead of beta What does this difference in structure result in?
  89. 89. Structural difference results in foetal haemoglobin being able to obtain oxygen from the placenta as it has a higher affinity for oxygen than the mother’s haemoglobin
  90. 90. Structure of foetal haemoglobin varies from that of maternal haemoglobin.
  91. 91. The final three-dimensional shape of a protein can be classified as: Fibrous  Tough  Insoluble in water Globular  Soluble Keratin Silk Collagen Enzymes Antibodies
  92. 92. A few proteins have both structures e.g. the muscle protein : myosin long fibrous tail a globular head
  93. 93. Proteins have tertiary and quaternary structure. The tertiary and quaternary structures of proteins create a variety of molecules, each able to carry out a particular function.
  94. 94. Since proteins can twist and fold in many ways, forming a variety of active site shapes.
  95. 95. Two Types of Protein SIMPLE : only amino acids e.g. albumins, histones CONJUGATED : globular proteins + non-protein material (prosthetic group)
  96. 96. Name Prosthetic group Haemoglobin Haem Glycoprotein Carbohydrate Lipoprotein Lipid Location Red blood cells Blood plasma Cell membranes
  97. 97. Denaturation & Renaturation
  98. 98. The loss of the specific three-dimensional conformation (secondary structure) of a protein A protein spontaneously refolds into its original structure under suitable conditions
  99. 99. Why is denaturation of proteins considered as harmful to an organism? The molecule unfolds and cannot perform its normal biological functions.
  100. 100. Denaturation agents can be: i) Heat ii) Strong acids & alkalis and high concentrations of salts iii) Heavy metals (e.g. mercury) iv) Organic solvents and detergents
  101. 101. i) Heat - weak hydrogen bonds and non polar hydrophobic interactions are disrupted - Why?
  102. 102. Heat increases the kinetic energy Causes the molecules to vibrate so rapidly and violently that bonds break
  103. 103. protein coagulates
  104. 104. ii) Strong acids & alkalis + high concentrations of salts ionic bonds are disrupted the protein is coagulated
  105. 105. Coagulation of milk by adding salts
  106. 106. Breakage of peptide bonds may occur if the protein remains in the reagent for a long time
  107. 107. iii) Heavy metals cause the protein to precipitate out of the solution Cations (+) form strong bonds with carboxylate anions (COOH-) and often disrupt ionic bonds
  108. 108. iv) Organic solvents & detergents disrupt hydrophobic interactions form bonds with non-polar groups this in turn disrupts intramolecular H-bonding
  109. 109. Why does the solution become purple when beetroot discs are placed in detergent? 1. Proteins in cell membrane & tonoplast are denatured. 2. Phospholipid bilayer is damaged.
  110. 110. Why is the skin wiped with alcohol before an injection is given? Alcohol is used as a disinfectant. It denatures the protein of any bacteria present on the skin.
  111. 111. What change has a protein undergone if it has been denatured When a protein is denatured it loses its three dimensional shape in space. Its tertiary structure is destroyed and cannot fold properly. Hydrogen bonds, ionic bonds and hydrophobic interactions that are useful to determine the final shape of the molecule are destroyed.
  112. 112. List TWO agents that may cause denaturation of a protein. (2) Extreme changes in pH Heat Heavy metals Organic solvents Detergents
  113. 113. Buffering capacity of proteins
  114. 114. A buffer can donate or accept H+ to stabilise the pH.
  115. 115. Why are buffers needed? To keep solution at a constant pH.
  116. 116. The need of buffers in organisms Reactions in cells change pH in blood. Proteins change shape if pH changes.
  117. 117. Name THREE buffers in organisms: Hydrogen carbonate
  118. 118. Buffering capacity of amino acids Zwitterion: a compound with both acidic and basic groups Isoelectric point is that pH at which a zwitterion carries no net electrostatic charge
  119. 119. Buffering actions by phosphate and hydrogen carbonate
  120. 120. Functions of Proteins Type Example Occurrence / function Structural Collagen Component of bone, tendons, cartilage cartilage
  121. 121. Functions of Proteins Type Example Occurrence / function Structural Keratin Skin, feathers, hair, nails, horns
  122. 122. Functions of Proteins Type Example Occurrence / function Structural Elastin Elastic connective tissue (ligaments)
  123. 123. Functions of Proteins Type Example Structural Fibrin Occurrence / function Forms blood clots Viral coat proteins ‘Wraps up ‘ nucleic acid of virus
  124. 124. Functions of Proteins Type Enzymes Example Hydrolytic enzymes Proteases Hormones Insulin Occurrence / function Cleave polysaccharides Break down proteins Regulate blood sugar level
  125. 125. Functions of Proteins Type Example Occurrence / function Transport Haemoglobin Carries O2 and CO2 in blood Myoglobin Stores O2 in muscle
  126. 126. Functions of Proteins Type Example Occurrence / function Transport Serum albumin Transport in blood e.g. lipids Cytochrome Electron transport Lipoprotein Electron carriers
  127. 127. Functions of Proteins Type Example Transport Membrane transporters e.g. glucose transporters Occurrence / function Transport sugars into cells
  128. 128. Functions of Proteins Type Example Protective Antibodies Occurrence / function Mark foreign proteins for elimination
  129. 129. Functions of Proteins Type Example Protective Fibrinogen Thrombin Occurrence / function Precursor of fibrin in blood clotting Involved in clotting mechanism
  130. 130. Functions of Proteins Type Motion Example Myosin Actin Occurrence / function Contraction of muscle fibres Contraction of muscle fibres
  131. 131. Functions of Proteins Type Example Occurrence / function Storage Caesin Stores ions in milk
  132. 132. Functions of Proteins Type Example Storage Ferretin Occurrence / function Stores iron, especially in spleen
  133. 133. Type Example Toxins Bacterial neurotoxins Occurrence / function Prolonged muscle contraction Patient Suffering From Tetanus. Painting by Sir Charles Bell, 1809.
  134. 134. Functions of Proteins Type Example Antifreeze Glycoproteins Occurrence / function In arctic flea
  135. 135. Functions of Proteins Type Example Occurrence / function Receptors Rhodopsin Light receptor in retina
  136. 136. THE END