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AMINO ACIDS AND PROTEINS(Dr.GIREESH KM)
- 2. Chemistry of amino acids and proteins MAHE INSTITUTE OF DENTAL SCIENCES & HOSPITAL Gireesh Kumar K.M Assistant Professor Department of Biochemistry
- 3. Functions of proteins Proteins are the most abundant macromoleules in living cell Protein is the most important of cell constituents All enzymes are proteins Many hormones are proteins(insulin) Defense function ex:immunoglobulins(antibodies)
- 4. Protiens carry (transport) compounds across cell membrane Proteins act as buffers to maintain pH of the cell
- 5. Amino acids Amino acids are the simplest units of a protein molecule They form the building block of protein An amino acid has an amino group and a carboxyl group Carbon atom which – COOH group is attached is called α carbon In amino acids , both amino and COOH group are attached to α carbon .
- 6. Proteins are the chains of amino acids that are linked by peptide bonds Each protein has specific and unique sequence of amino acid. 20 amino acids are involved in formation of proteins They differ in the R group.
- 7. Peptide bond In proteins successive amino acids are joined by peptide bonds A dipeptide contain one peptide bond If the first amino acid is alanine and the second amino acid is glycine a dipeptide can be written as Ala-Gly Tripeptide Glu-Cys-Gly(Glutamate –cysteine – glycine)
- 8. Amino acid exhibit two types of isomerism due to the presence of assymetric carbon Stereoisomerism Optical isomerism Stereoisomerism All amino acids except glycine exist in D and L forms In D amino acids, -NH2 group is on the right side , in L it is on left Only L amino acids are utilized in our body
- 9. Optical isomerism All amino acids except glycine exhibit optical activity as they rotate the plane polarised light. Glycine ,Gly(optically inactive amino acid)
- 10. Importance of amino acids formation of proteins Some amino acids are converted to carbohydrate and are called glucogenic amino acids Enzyme activity Transport and storage form of ammonia Detoxification reactions Formation of biologically important compounds(explanation later)
- 11. Classification of amino acids Based on structure Based on nutritional status Based on metabolic fate Based on side chain
- 12. 1. Based on structure According to this type , amino acids are classified as Aliphatic aminoacids Mono amino mono carboxylic amino acids Simple amino acids Branched chain amino acids Hydroxy aminoacids Sulphur containing amino acids Amino acids with amide group Dicarboxylic acid and their amides Diamino acids Aromatic amino acids Heterocyclic amino acids Imino acids
- 14. Simple amino acids Glycine ,Gly(optically inactive amino acid) Alanine, Ala Branched chain Valine , val (branch chain) Leucine (branch chain, Leu Isoleucine (branch chain,Ile
- 15. Aliphatic amino acids Branched chain Valine , val (branch chain) Leucine (branch chain, Leu Isoleucine (branch chain,Ile
- 17. Hydroxy aminoacids Amino acids having –OH group in the side chain Serine , Ser Threonine, Thr Tyrosine , Tyr(aromatic also)
- 19. Sulphur containing amino acids Cysteine, Cys Methionine, Met
- 20. Amino acid with amide group Glutamine(amide of glutamic acid), Gln Aspargine (amide of aspartic acid), Asn
- 21. mono amino Dicarboxylic acid Amino acids having carboxylic acids in their side chain(COOH >NH2)- acidic amino acids Glutamic acid, Glu Aspartic acid, Asp
- 22. (Diamino acids) Di amino monocarboxylic acids -Lysine, Lys -Arginine,Arg -Histidine , His (aromatic also)
- 23. Aromatic amino acids Contain aromatic ring Phenylalanine,(Phe)- contain benzene ring Tyrosine , (Tyr)- contain phenol group Tryptophan (Trp)- indole group Histidine (His)-imidazole group
- 24. Heterocyclic amino acids Tryptophan (Trp)- indole group Histidine (His)-imidazole group
- 25. Imino acids or heterocyclic Amino acids have secondary amino(imino,-NH) group Eg proline
- 27. Special groups in amino acids Phenylalanine,(Phe)- contain benzene ring Tyrosine , (Tyr)- contain phenol group Tryptophan (Trp)- indole group Histidine (His)-imidazole group Proline-pyrrolidine group Arginine – guanidium group
- 28. Based on nutritional status
- 29. According to this type amino acid classified as Nutritionally essential or indispenible amino acids Nutritionally non essential or dispensible Semi essential amino acids
- 30. Essential amino acids Amino acids cannot be synthesized by the body and must be essentially supplied through the diet Tryptophan Valine Threonine Isoleucine Lysine Leucine Phenyl alanine Methionine T.V TILL 8 P.M
- 31. 31 MAHTT VIL PhLy M methionine A arginine T threonine T tryptophan V valine I isoleucine L leucine Ph phenylalanine Ly lysine H Histidine
- 32. SEMI ESSENTIAL HISTIDINE AND ARGININE are called semi essential amino acids because they are not synthesised only in small quantities So the synthesis is not suffecient during the period of growth So GROWING CHIDREN REQUIRE THEM IN FOOD
- 33. NON ESSENTIAL THE REMAINING 10 AMINO ACIDS ARE NON ESSENTIAL THEY CAN BE SYNTHESIZED BY THE BODY THEY ARE REQUIRED FOR NORMAL PROTEIN SYNTHESIS GLYCINE,ALANINE, PROLINE, SERINE, GLUTAMIC ACID, GLUTAMINE,TYROSINE,CYSTEINE, ASPARTIC ACID, ASPARGINE
- 34. BASED ON METABOLIC FATE
- 35. After the removal of amino group of amino acid . If the carbon skelton can be converted to glucose they are called PURELY GLUCOGENIC AMINO ACIDS- (Those which can be converted in to glucose) After the removal of amino group of amino acid . If the carbon skelton can be converted to ketone body then they are called PURELY KETOGENIC AMINOACIDS-Those which can be converted in to ketone bodies
- 36. After the removal of amino group of amino acid . If the carbon skelton splits in to two parts, one of which can be converted to glucose and other parts become ketone body such amino acids are BOTH GLUCOGENIC AND KETOGENIC-Those which can be converted in to both types
- 37. KETOGENIC BOTH KETOGENIC AND GLUCOGENIC (I like Aromatic amino acids) GLUCOGENIC LEUCINE(purely ketogenic) LYSINE ISOLEUCINE PHENYL LANINE TYROSINE TRYPTOPHAN GLYCINE ALANINE SERINE ASPARTIC ACID ASPARGINE GLUTAMIC ACID GLUTAMINE PROLINE HISTIDINE ARGININE METHIONINE THREONINE VALINE
- 38. BASED ON SIDE CHAIN
- 39. ACCORDING TO THIS AMINO ACIDS ARE CLASSIFIED IN TO 2 HYDROPHILIC OR POLAR AMIOACIDS HYDROPHOBIC OR NON POLAR AMINOACIDS
- 40. HYDROPHILIC OR POLAR The side chains of hydrophilic amino acids contain polar groups that may be either Charged Uncharged Positively charged side chains- Basic amino acids Negatively charged side chains- acidic amino acids These amino acids are relatively hydrophilic (water loving) because they possess polar functional groups (in side chains) i.e. oxygen and nitrogen, which can participate in hydrogen bonding with water so capable of interacting with water
- 41. UNCHARGED HYDROPHILIC The uncharged side chains of other amino acid have O, S , N atoms enabling them to form hydrogen bond with water Threonine and serine-------OH gp in the side chain Aspargine and glutamine------amide gp
- 42. HYDROPHOBIC –non polar The side chain of hydrophobic amino acids interact poorly with water Side chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings) are non-polar . Examples include valine, alanine, leucine, isoleucine, phenylalanine
- 44. Classification on the basis of Function Shape and size Physical and chemical properties Nutritional classification.
- 45. Proteins Shape &size Function Soluability & physical properties Nutritional classificato Fibrou s protei n Globul ar protein Keratin collagen Myoglobi n Hb Simple protein Conjugated protein Derived protein Albumin Glycoproteins Primary Seconda ry Globulin Lipoproteins Glutelin Nucleo proteins Protamin es Chromoprotein s Histones Phosphoprotei ns Prolamin es Metalloproteins Catalytic protein Transport protein Storage protein Contractile protein Structural protein Defense protein Regulatory Nutritionally rich protein or Incomplete protein Poor protein
- 46. Based on function 1 ..Catalytic proteins or enzymes Protein act as enzymes Glucokinase Dehydrogenases Transaminases Hydrolytic enzymes, pepsin, trypsin
- 47. 2..Transport proteins Involved in the process of transportation Hb transports oxygen Transferrin transports iron Albumin transports fatty acids and bilirubin
- 48. 3..Storage proteins Proteins serves as storage form Apoferritin stores iron in the form of ferritin Myoglobin stores oxygen in muscles Ovalbumin & glutelin
- 49. 4..Contractile proteins Some proteins have the ability to contract and function in the contractile system of skeletal muscle Actin Myosin
- 50. 5..Structural proteins Many protein serves as supporting frame work of cells to give biological structure , strength or protection Collagen in bone Elastin of ligaments Keratin of hair, nail
- 51. 6..Defense protein Many proteins involved in defense mechanism against foreign substances such as viruses, bacteria Immunoglobulin or antibodies Fibrinogen and thrombin
- 52. 7..Regulatory proteins(hormonal protein) Proteins regulate cellular or physiological activity Many hormones Insulin , regulate sugar metabolism Growth hormone of pituitory gland regulates growth of cells
- 53. 8.Protein as buffers Plasma proteins are involved in the buffringi in plasma Hb is an important buffer inside RBC
- 54. 9. PROTEIN AS TOXINS Clostridium botulinum toxin which cause bacterial food poisoning
- 55. 9.. Protein as antivitamin Avidin of raw egg white which binds biotin(vitamin) and interfere with its absorption
- 56. Based on shape and size Fibrous protein: they are elongated or needle shaped molecules Have axial ratio of length : width >10 Ex: keratins Elastin collagen
- 57. Globular proteins: they are spherical in shape Have axial ratio of length : width <10 Ex plasma globulins , fibrinogen,albumin, myoglobin, Hb etc
- 58. Based on physical and soluability(chemical) properties of protein Simple proteins Conjugated proteins Derived proteins
- 59. Simple Conjugated Derived Albumin Nucleoprotein Primary coagulated protein Proteans Metaproteans Globulin Glycoprotein Secondary Proteoses Peptones Peptides Glutelin Chromo protein Protamines Phospho protein Histones Lipo protein Prolamines metalloprotein Scleroproteins
- 60. Simple proteins Defined as those proteins that upon hydrolysis, yield only amino acids or their derivatives They are classified according to their solubility and heat coagulability. They are
- 61. Name Soluability Examples Albumin Soluble in water Coagulated by heat Egg albumin Serum albumin Lactalbumin Globulin Insoluble in water, soluble in dilute neutral salt solutions Heat coagulable Ovaglobulin of egg yolk Serum globulin Myosin of muscle Glutelin Soluble in dilute acids and alkalies Insoluble in neutral solvents Plant proteins Glutelin of wheat Oryzenin of rice Prolamines Soluble in 70-80-% alcohol Insoluable in water, neutral solvent or absolute alcohol Plant proteins Zein of corn Gliadin of wheat Protamines Soluble in water Not heat coagulable Nucleoproteins Sclero proteins Insoluable in water and salt solution Collagen and elastin Histones Soluable in water Nucleoproteins
- 62. Conjugated proteins Composed of simple protein combined with some non protein substances(prosthetic group) Examples Nucleoproteins Glycoproteins Chromoprotein Phosphoprotein Lipoprotein Metaloproteins
- 63. Conjugated protein Non protein part Examples Glycoproteins Carbohydrate Blood group antigens , serum proteins Lipoproteins Lipids Serum, lipoproteun(HDL, LDL Nucleo proteins Nucleic acids Histones Chromoproteins Colored group Hemoglobin , flavoprotein (riboflavin yellow ) Phosphoproteins Phosphorus Casein of milk , vitellin of egg yolk Metalloproteins Metal ions Hb(iron), Carbonic anhydrase(Zn), Xanthine Oxidase(Molybdenum)
- 64. Derived proteins This includes those substances derived from simple and conjugated proteins Derived proteins are divided in to two Primary derived proteins Secondary derived proteins
- 65. Primary derived proteins These protein derivatives are formed by agents( heat, acids, alkalies) which cause only slight changes in the protein molecule and its properties, without cleavage of peptide bond examples are
- 66. Proteans –earliest product of protein hydrolysis by the action of dilute acids or enzymes eg, fibrin from fibrinogen Metaproteins Are formed by further action of
- 67. Secondary derived proteins Substances are formed in the progressive hydrolytic cleavage of peptide bond of metaproteins in to smaller molecules ex. Proteoses Peptones
- 68. Note –Gelatin is another example for deived protein , derived from collagen(connective tissue protein)
- 70. 70 CLASSIFICATION BASED ON NUTRITIONAL VALUE
- 71. Class Definition Example Nutritionally rich proteins They contain all essential amino acids in required proportion casein of milk Incomplete proteins They are protein which lack one essential amino acid. Proteins from pulses (defecient in methionine) Protein from cereals ( def: in lysine Poor proteins They lack in many essential amino acids: zein of corn ( def: in tryptophan and lysine
- 73. The average nitrogen content of protein is 16% • Solubility-Proteins form colloidal solution instead of true solution in water • Mol.wt- Proteins vary in the mol.wt, which depend on the number of amino acid residues Shape- Wide variation in shape-scleroproteins are in the form of fibers Isoelectric pH-At isoelectric pH protein exists as ZWITTERIONS
- 74. Isoelectric pH of casein-4.6 Albumin 4.7 globulin -6.4
- 75. Hydration of proteins Proteins when contact with water, it absorbs and swell up Polar groups of protein(COOH, NH2, OH) binds with water to form hydrogen bonds to hold a considerable amount of water Thus a relatively immobile shell like layer of water(solvation layer) is held around each protein in aqueous medium
- 76. Precipitation of proteins The stability of protein in solution depends on Charge and hydration of protein molecule The factors which neutralize the charge or remove hydration , causes PRECIPITAT ION OF PROTEIN
- 77. Factors used for precipitation of protein are Precipitation by Salting out Precipitation at Isoelectric pH Precipitation by Organic solvents Precipitation by Anionic or alkaloid reagents Precipitation by salt of heavy metals
- 78. Salting out The process of protein precipitation by the addition of neutral salt such as ammonium sulfate is known as salting out. Explained on the basis of dehydration of proteins by salts
- 79. Mineral ions attract water molecules and consequently remove shell of hydration (solvation layer) around protein molecules Since water layer around protein molecule is removed , protein is precipitated, called salting out
- 80. Amount of salt required for protein precipitation depends on size(mol. Wt) of protein High mol. Wt protein require less salt to precipitate than low mol. Wt Albumin -69,000 Globulin -1,60,000
- 81. Serum globulins are precipitated by half saturation with ammonium sulfate solution while albumin is precipitated by full saturation with solid ammonium sulfate crystals. Precipitation at isoelectric pH All proteins are least soluble at their isoelectric pH Precipitation by organic solvents Org. solvents like alcohol-dehydrates and precipitates proteins
- 82. Precipitation by salts of heavy metals Heavy metas like pb2+, Fe2+,Zn2+, Cd2+ cause precipitation of proteins. These metals are positively charged, when added to a protein solution (-vely charged) in alkaline medium reults preipitation
- 83. Precipitation by anionic or alkaloidal reagents Proteins can be precipitated b trichoro acetic acid, sulphosaliylic acid,Phospho tungstic acid, tannic acid etc By the addition of these acids , protein existing as cations are precipitated by the anionic form of acids to produce protein-sulphosalicylate , protein- tungstate, etc
- 84. Colour reactions of protein Proteins give several colour reactions which are used to identify the nature of amino acids present in them . Colour reactions are ;
- 85. Reaction Specific group/amino acid Biuret reaction 2 peptide linkage Ninhydrin reaction Alpha amino acids Xanthoproteic reaction Benzene ring of aromatic amino acids(phe, Tyr, Trp) Millons reaction Phenolic group Hopkins coles reaction Aldehyde test Indole ring(Trp) Nitroprusside test Sulfhydril group(cys) Sulphur test Sulfhydril group(cys) Pauly’s test Imidazole ring(his)
- 86. Denaturation of protein The three dimensional conformation, the 1o,2o,3o and even some cases of 4ostructure is characteristics of native protein.(the natural biological conformation of a protein is called native state) The conformation can upset and disorganized ,only by the breakage of bonds which stabilize the structure The phenomenon of disorganization of native protein structure is known as denaturation
- 87. Agents of denaturation Physical agents Heat ,x-rays, uv rays can denature protein Chemical agents Acids, alkalies, and certain solutions of heavy metals (Hg,Pb,detergents) organic solvents like alcohol,ethers, urea etc denature protein • Mechanical agents Vigorous shaking and grinding leads to denaturation
- 89. Characteristics of denaturation Native structure of protein is lost Denaturation results in the loss of secondary structure, tertiary and quaternary structure Primary structure of protein remain intact Involves changes in the physical, chemical and biological properties of protein Loses biological activity Denatured protein becomes insoluble in solvent, in which is
- 90. Viscosity of Denatured protein increases Denatured protein is easily digested Denatured protein is irreversible(omlet can be prepared from egg protein albumin. But the reversal is impossible) Some times reversible.(renaturation) Hb undergo denaturation by salicylate. By removal of salicylate , Hb is renatured.
- 91. Coagulation The term coagulum refers to semi solid viscous precipitate of a protein Irreversible denaturation results in coagulation Albumin and globulin are coagulable protein Heat coagulation test is commonly used to detect the presence of albumin in urine
- 92. Structure of protein (levels of organization of proteins )
- 93. Primary structure Secondary structure Teritiary structure Quaternary structure
- 94. Primary structure of protein Primary structure refers to the order and sequence of amino acids in a polypeptide chain and the location of disulphide bonds , if any Each amino acid in a polypeptide chain is called a residue or moiety
- 95. Each polypeptide chain is having free amino group at one end called N terminal and free carboxyl group at other end called C terminal
- 97. This amino acid sequence of a protein is referred as PRIMARY STRUCTURE Understanding of primary structure of a protein is important because many genetic diseases result due to an abnormal amino acid sequence
- 98. Forces keeping the primary structure Peptide linkage Disulphide linkage
- 99. Secondary structure of proteins For stability of primary structure , hydrogen bonding between hydrogen of NH and oxygen of C=O groups of polypeptide chain occurs, which give rise to folding or twisting of primary structure
- 100. Regular folding or twisting of polypeptide chain by hydrogen bonding is called structure is called secondary structure of protein 2 types of secondary structures are - helix ß - pleated
- 101. H -bonding
- 103. - helix Most common & stable conformation - helix is a spiral structure Is a tightly coiled structure with amino acids side chains extent outward from central axis The polypeptide bonds forms the backbone
- 104. All the peptide bonds participate in H bonding except first and last Each turn of - helix contain 3.6 amino acid and travels a distance of 0.54nm, spacing of each amino acid is 0.15nm Each turn has 3 complete amino acid and two atoms from the next one
- 105. The helix is stabilized by H bond between the NH & C-O groups of the same chain. N-O distance 2.8 Ao
- 106. ß pleated sheet structure In the ß sheets H bonds are formed between NH & CO groups in different poly peptide chains. The poly peptide chains in the ß sheets may be arranged either in parallel (same direction) or antiparellel (opposite direction)
- 107. Parellel pleated sheet The polypeptide chain lie side by side and in same direction(with respect to to N and C terminal), so that their N terminal residues are at the same end (N terminal faces to N terminal) and stabilized by hydrogen bonding
- 108. Antiparellel sheet The polypeptide chain lie in opposite direction, ie N terminal end of one is next to the C terminal of other (N terminal faces to C terminal) and stabilized by hydrogen bonding
- 109. Tertiary structure The peptide chain , with its secondary structure, may folded and twisted about itself forming . Three dimensional arrangement of polypeptide chain or 3-dimensional structure is formed when alpha helices and beta sheets are held together Hydrogen bonds Hydrohphobic interactions Van der Waals force Disulphide bond Ionic bond Stabilize tertiary structure
- 111. Quaternary structure Some protein contain more than one polypeptide chain. They are known as oligomeric protein(multi subunit) Each subunit possesses primary,secondary,and tertiary chain have quaternary structure
- 112. When these subunits are held together by non covalent interactions or by covalent cross linked , it is referred as quaternary structure
- 113. Certain polypeptides will aggregate to form one functional protein Depending on the number of monomers the protein may be termed as dimer(2), tetramer(4)
- 114. Examples –glycolytic enzymes Aldolase,LDH,PDH Hemoglobin Creatine kinase Alkaline phosphatase IMMUNOGLOBULIN aspartate transcarbamoylase Collagen
- 115. The forces that keep the quaternary structure are hydrogen bonds, disulphide bonds,electrostatic bonds, hydrophobic bonds and van der Waals forces.
- 117. 117 Primary structure Sequence of amino acids Secondary structure Alpha helix; Beta pleated sheets Tertiary structure 3-dimensional structure is formed when alpha helices and beta sheets are held together Quaternary structure consists of more than one polypeptide chain Levels of Organisations of Proteins