Protein sturucture


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Protein sturucture

  1. 1. Protein Structure and Function Compiled & Edited by Dr. Syed Ismail VN Marathwada Agril. University Parbhani
  2. 2. DEFINITIONS OF PROTEIN • Proteins are one of the essential building blocks of the human body. • They provide amino acids, which are a nutritional requirement of the body to produce its own proteins and a variety of nitrogen-based molecules. • It is common for programs to recommend a minimum of 50 grams of protein per day to maintain healthy levels. • Proteins vary in structure as well as function. They are constructed from a set of 20 amino acids and have distinct three-dimensional shapes.
  3. 3. General Characteristics of Proteins • They are the most complex and most diverse in chemical composition, conferring upon the different tissues. • Protein molecule contains elements of C, H, O,N, S, and P together with traces of Fe, Cu, I, Mn, and Zn. • It has a molecular weight of 5,000 to 3,000,000 • They are the most important of the biologic substances being the fundamental constituent of cell cytoplasm. • They supply not only heat and energy but also material for building and repair. • Unlike carbohydrates and lipids, only small amounts of protein is temporarily stored in the body, and which can be quickly used up upon demand.
  5. 5. FUNCTIONS OF PROTEIN • Antibodies - are specialized proteins involved in defending the body from antigens (foreign invaders). One way antibodies destroy antigens is by immobilizing them so that they can be destroyed by white blood cells. • Enzymes - are proteins that facilitate biochemical reactions. They are often referred to as catalysts because they speed up chemical reactions. Examples include the enzymes lactase and pepsin. Lactase breaks down the sugar lactose found in milk. Pepsin is a digestive enzyme that works in the stomach to break down proteins in food. • Hormonal Proteins - are messenger proteins which help to coordinate certain bodily activities. Examples include insulin, Insulin regulates glucose metabolism by controlling the bloodsugar concentration.
  6. 6. FUNCTIONS OF PROTEIN • Contractile Proteins - are responsible for movement. Examples include actin and myosin. These proteins are involved in muscle contraction and movement. • Structural Proteins - are fibrous and stringy and provide support. Examples include keratin, collagen, and elastin. Keratins strengthen protective coverings such as hair, quills, feathers, horns, and beaks. Collagens and elastin provide support for connective tissues such as tendons and ligaments. • Storage Proteins - store amino acids. Examples include ovalbumin and casein. Ovalbumin is found in egg whites and casein is a milk-based protein. • Transport Proteins - are carrier proteins which move molecules from one place to another around the body. Examples include hemoglobin and cytochromes. Hemoglobin transports oxygen through the blood. Cytochromes operate in the electron transport chain as electron carrier proteins.
  7. 7. Classification of Proteins Based on Composition: • Simple proteins – composed of entirely amino acids only. Ex. Albumin, Globulin • Complex or Conjugated proteins – made up of amino acids and other organic compounds. The nonamino acid group is termed as the prosthetic group. Ex. Nucleoproteins, lipoproteins, glycoproteins, metalloproteins
  8. 8. Classification of Proteins Based on Axial Ratio: Axial ratio is the ratio of the length to the breath. • Globular proteins – with axial ratio less than 10 but not below 3 or 4. They are compactly folded and coiled. Ex. Insulin, plasma albumin, globulin, enzymes • Fibrous proteins – with axial ratio greater than 10. They are spiral and helical and are cross linked by disulfide and hydrogen bonds. Ex. Keratin, myosin, elastin, collagen
  9. 9. Globular Proteins • Globular proteins have their axial ratio less than 10 but not below 3 or 4. They are compactly folded and coiled. • Examples are insulin, plasma albumin, globulin, enzymes
  10. 10. Fibrous Proteins • Fibrous proteins are spiral and helical and are cross linked by disulfide and hydrogen bonds • Examples are keratin, myosin, elastin, collagen
  11. 11. Based on Biological Functions • Structural proteins: collagen, elastin, keratin, fibroin of silk and webs • Transport proteins: hemoglobin, myoglobin, lipoproteins • Protective proteins: immunoglobulins, fibrinogen, thrombin, snake venoms, bacterial toxins • Contractile proteins: actin, myosin, tubulin • Catalytic proteins: enzymes • Regulatory proteins: hormones • Storage proteins: ferritin, hemosiderin, gluten, casein, ovalbumin • Reception of Stimuli: rhodopsin, membrane receptor proteins, acethylcholine, insulin • Germicidal proteins: Polymyxin B1, Gramicidin S
  12. 12. Shape = Amino Acid Sequence • Proteins are made of 20 amino acids linked by peptide bonds • Polypeptide backbone is the repeating sequence of the N-C-C-N-C-C… in the peptide bond • The side chain or R group is not part of the backbone or the peptide bond
  13. 13. Proteins Composed of a chain of amino acids. 20 possible groups R | H2N--C--COOH | H
  14. 14.   NH 3  C  COO -  NH 3  C  COO   NH 3  C  CO  NH  C  COO -  H2 0
  15. 15. Different Amino Acid Classes H2N H O C C C H H2N OH Generic H H Non-polar H O C O C C C Acid OH H O Amine H2N Aspartic acid H2N H OH ?R C C HS C Polar Acid C Cysteine C O Alanine OH H H OH O H H2N H H Basic C C H+N C C C H NH C Histidine OH H
  16. 16. Non-Polar Amino Acids Glycine O H2N C C OH Valine O H H H2N H H C C OH H C C C H H CH3 OH H H2N CH3 H H3C C C C H C H H C H O Isoleucine H3C H OH H C C OH H H C C C C H3C H PhenylalanineO H2N H2N H H C H3C H C H C OH C H2N Leucine O C H2N Alanine O MethionineO OH H H3C TryptophanO H2N H H S C C C H NH H2C H2C OH H Proline O H2N+ C C CH2 H Protein Structure OH
  17. 17. Polar Amino Acids Serine O H2N H C C C H2N OH H H H CH3 HO Cysteine O H HS C C C H C C C H2N H H O OH H H C C OH H C H H Asparagine O OH H2N OH C H H2N Tyrosine O Threonine O C C C C H NH2 Glutamine O HO H2N OH H H H O H H NH2 C C C C C H OH
  18. 18. Acidic Amino Acids O Aspartic O acid C H2N C H H C C OH H H OH O Glutamic O acid C H2N C H H C H C C H OH OH
  19. 19. Basic Amino Acids Histidine O H2N H C C H+N C C C H2N H H H NH C Lysine O OH H H H C +H N 3 C C C C OH Arginine O H H2N H C H H H H H H +H N 2 N C C C C C OH H H C H H H NH2 Protein Structure
  20. 20. Levels of Protein Organization • Primary Structure - The sequence of amino acids in the polypeptide chain • Secondary Structure - The formation of  helices and b pleated sheets due to hydrogen bonding between the peptide backbone • Tertiary Structure - Folding of helices and sheets influenced by R group bonding • Quaternary Structure - The association of more than one polypeptide into a protein complex influenced by R group bonding
  21. 21. Levels of Protein Organization Primary Structure Met-Gly-Ala-Pro-His-Ile-Asp-Glu-Met-Ser-Thr-.. The sequence of amino acids in the primary structure determines the folding of the molecule. Protein Structure
  22. 22. Protein Secondary Structure • The peptide backbone has areas of positive charge and negative charge • These areas can interact with one another to form hydrogen bonds • The result of these hydrogen bonds are two types of structures:   helices  b pleated sheets
  23. 23. H N C O C C O C Protein Secondary Structure:  Helix H N H N C H N H N C O C O C O C O C C C O H C N H H H N H H - O N C C C + H O N H H C H HO C C H H OH
  24. 24. H N Protein Secondary Structure: H C  Helix C N O H C C O N H - + C H O H O C N O C C O H N H N C O H C O C C C O H N H H N C C C N H H C H HO C H C H OH
  25. 25. Protein Secondary Structure:  Helix R groups stick out from the  helix influencing higher levels of protein organization R R R R R R R R R R R R R R
  26. 26. M L L S R Q S I R F T L F K A R C Y P P S L The order of the amino acids determines the hydrogen bonding Neutral Non-polar Polar Basic Acidic MLSLRQSIRFFKPATRTLCSSRYLL T S R Yeast Cytochrome C Oxidase Subunit IV Leader • This would localise specific classes of amino acids in specific parts of the helix
  27. 27. Protein Secondary Structure: b Pleated Sheet C O C H C N N H O C N H C C O C C O H N C O C H C N N H O C N H C C O C C O H N C O C H C N N H O C N H C C O C C O H N C O C H C N N H O C N H C C O C O H N C
  28. 28. Protein Secondary Structure: b Pleated Sheet C O C N H O C C H C N N H O C N H C C O C O H N H C N C C O O C N H O C C C H C N N H O C N H C C O C O H N H C N C C O O C N H O C C C H C N N H O C N H C C O C O H N H C N C C O O C N H O C C C H C N N H O C N H C C O C O H N H C N C O C
  29. 29. Levels of Protein Organization Tertiary Structure • Tertiary structure results from the folding of  helices and b pleated sheets • Factors influencing tertiary structure include: • Hydrophobic interactions • Hydrogen bonding • Disulphide bridges • Ionic bonds
  30. 30. Hydrophobic interactions Valine O H2N H H3C C C C H CH3 OH Glycine O H2N H H2C H2C C C OH H Proline O H2N+ C C CH2 H OH
  31. 31. Hydrogen Bonding Glutamine O Asparagine O H2N H O C C C C H NH2 H2N OH H H H O N-------H (+) slightly C C H H C C C H NH2 (-) O -------C slightly OH
  32. 32. Disulphide bridges Cysteine O H2N H HS C C C H Cysteine O OH H2N H H Cysteine O H2N H HS C C C H S C C C OH H H Cysteine O OH H2N H H S C C C H H OH
  33. 33. Ionic Bonds H O Glutamic O acid C H2N C H H C Arginine O H C C OH H2N H H O- H H +H N 2 N C NH2 C H C C H C H H C H OH
  34. 34. e.g.G-3-P Dehydrogenase Tertiary Structure
  35. 35. Levels of Protein Organization Quaternary Structure • Quaternary structure results from the interaction of independent polypeptide chains • Factors influencing quaternary structure include: • Hydrophobic interactions • Hydrogen bonding • The shape and charge distribution on amino acids of associating polypeptides
  36. 36. G-3-P Dehydrogenase from Bacillus stearothermophilus
  37. 37. Protein structure
  38. 38. Globular • e.g. haemoglobin • 3º structure normally folds up in a ball • hydrophilic R groups point outwards • Hydrophobic R groups point inwards • soluble • metabolic functions and Fibrous • e.g. collagen • 2º structure does not fold up, form fibres • not surrounded by hydrophilic R groups • insoluble • structural functions
  39. 39. Haemoglobin • Haemoglobin is a globular protein with a prosthetic ‘iron’ group • In adults, hemoglobin is made up of 4 polypeptides (2  polypeptide chains and 2 b polypeptide chains) • Each polypeptide surrounds a prosthetic ‘haem’ group • Hydrophobic interactions between side groups pointing inwards maintain the structure • Hydrophilic side chains point outwards making it soluble  b Fe  b
  40. 40. Polypeptide Backbone
  41. 41. Amino Acids (magic 20) You need to know these Hydrophilic Hydrophobic
  42. 42. Protein Folding • The peptide bond allows for rotation around it and therefore the protein can fold and orient the R groups in favorable positions • Weak non-covalent interactions will hold the protein in its functional shape – these are weak and will take many to hold the shape
  43. 43. Non-covalent Bonds in Proteins
  44. 44. Globular Proteins • The side chains will help determine the conformation in an aqueous solution
  45. 45. Hydrogen Bonds in Proteins • H-bonds form between 1) atoms involved in the peptide bond; 2) peptide bond atoms and R groups; 3) R groups
  46. 46. Protein Folding • Proteins shape is determined by the sequence of the amino acids • The final shape is called the conformation and has the lowest free energy possible • Denaturation is the process of unfolding the protein – Can be done with heat, pH or chemical compounds – The chemical compound can be removed and have the protein renature or refold
  47. 47. Refolding • Molecular chaperones are small proteins that help guide the folding and can help keep the new protein from associating with the wrong partner
  48. 48. Protein Folding • 2 regular folding patterns have been identified – formed between the bonds of the peptide backbone • -helix – protein turns like a spiral – fibrous proteins (hair, nails, horns) • b-sheet – protein folds back on itself as in a ribbon – globular protein
  49. 49. b Sheets • Core of many proteins is the b sheet • Form rigid structures with the Hbond • Can be of 2 types – Anti-parallel – run in an opposite direction of its neighbor (A) – Parallel – run in the same direction with longer looping sections between them (B)
  50. 50.  Helix • Formed by a H-bond between every 4th peptide bond – C=O to N-H • The  helix can either coil to the right or the left • Can also coil around each other – coiled-coil shape – a framework for structural proteins such as nails and skin
  51. 51. Protein Structure
  52. 52. Domains • A domain is a basic structural unit of a protein structure – distinct from those that make up the conformations • Part of protein that can fold into a stable structure independently • Different domains can impart different functions to proteins • Proteins can have one to many domains depending on protein size
  53. 53. Domains
  54. 54. Useful Proteins • There are thousands and thousands of different combinations of amino acids that can make up proteins and that would increase if each one had multiple shapes • Proteins usually have only one useful conformation because otherwise it would not be efficient use of the energy available to the system • Natural selection has eliminated proteins that do not perform a specific function in the cell
  55. 55. Protein Families • Have similarities in amino acid sequence and 3-D structure • Have similar functions such as breakdown proteins but do it differently
  56. 56. Proteins – Multiple Peptides • Non-covalent bonds can form interactions between individual polypeptide chains – Binding site – where proteins interact with one another – Subunit – each polypeptide chain of large protein – Dimer – protein made of 2 subunits • Can be same subunit or different subunits
  57. 57. Single Subunit Proteins
  58. 58. Different Subunit Proteins •Hemoglobin – 2  globin subunits – 2 b globin subunits
  59. 59. Protein Assemblies • Proteins can form very large assemblies • Can form long chains if the protein has 2 binding sites – link together as a helix or a ring • Actin fibers in muscles and cytoskeleton – is made from thousands of actin molecules as a helical fiber
  60. 60. Types of Proteins • Globular Proteins – most of what we have dealt with so far – Compact shape like a ball with irregular surfaces – Enzymes are globular • Fibrous Proteins – usually span a long distance in the cell – 3-D structure is usually long and rod shaped
  61. 61. Important Fibrous Proteins • Intermediate filaments of the cytoskeleton – Structural scaffold inside the cell • Keratin in hair, horns and nails • Extracellular matrix – Bind cells together to make tissues – Secreted from cells and assemble in long fibers • Collagen – fiber with a glycine every third amino acid in the protein • Elastin – unstructured fibers that gives tissue an elastic characteristic
  62. 62. Collagen and Elastin
  63. 63. Stabilizing Cross-Links • Cross linkages can be between 2 parts of a protein or between 2 subunits • Disulfide bonds (S-S) form between adjacent -SH groups on the amino acid cysteine
  64. 64. Proteins at Work • The conformation of a protein gives it a unique function • To work proteins must interact with other molecules, usually 1 or a few molecules from the thousands to 1 protein • Ligand – the molecule that a protein can bind • Binding site – part of the protein that interacts with the ligand – Consists of a cavity formed by a specific arrangement of amino acids
  65. 65. Ligand Binding
  66. 66. Formation of Binding Site • The binding site forms when amino acids from within the protein come together in the folding • The remaining sequences may play a role in regulating the protein’s activity
  67. 67. Antibody Family • A family of proteins that can be created to bind to almost any molecule • Antibodies (immunoglobulins) are made in response to a foreign molecule ie. bacteria, virus, pollen… called the antigen • Bind together tightly and therefore inactivates the antigen or marks it for destruction
  68. 68. Antibodies • Y-shaped molecules with 2 binding sites at the upper ends of the Y • The loops of polypeptides on the end of the binding site are what imparts the recognition of the antigen • Changes in the sequence of the loops make the antibody recognize different antigens specificity
  69. 69. Antibodies