Biomolecules amino acids and proteins

properties, classification and nature of amino acids and proteins

1. BIOMOLECULES DEVIPRIYA P V M PHARM Amino acids and proteins.

2. AMINO ACIDS AND PROTEINS Proteins are the most abundant organic molecules of the living system. They are high molecular weight nitrogen rich substances. The term protein is generally used for a polypeptide containing more than 50 amino acids. The amino acids are held together in a protein by covalent peptide bonds. Peptide bonds are formed when the amino group of the amino acid combines with the carboxyl group of another amino acid

3. Proteins are the polymers of L- α -amino acids Only 20 amino acids (standard amino acids ) are found in the structure of proteins. Amino acids are a group of organic compounds containing two functional groups- amino and carboxyl The amino group (-NH 2 ) is basic while the carboxyl group(-COOH) is acidic in nature. If both the –COOH and –NH 2 group are attached to the same carbon atom , the amino acids are termed as α - amino acids . The α - carbon atom binds to a side chain represented as R which is different for each of the 20 amino acids found in proteins Amino acids mostly exists in ionized form in biological system Except amino acids except glycine have optical isomers (In glycine R=H)

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5. Functions of proteins Proteins perform variety of specialised and essential functions in living cells which are broadly grouped as static and dynamic Structural functions/ static functions These proteins are responsible for the structure and strength of body. These include collagen and elastin found in bone matrix, vascular system and other organs and α -keratin present in epidermal tissues. Dynamic function: These include proteins acting as enzymes, hormones, blood clotting factors, immunoglobulins, membrane receptors, storage proteins, besides their function in genetic control, muscle contraction, respiration etc. Proteins performing dynamic functions are regarded as the working horses of cell

6. Elemental composition of Proteins: Proteins are predominantly constituted by five major elements: Carbon:50-55% Hydrogen:6-7.3% Oxygen:19-24% Nitrogen:13-19% Sulphur:0-4% Contain other elements like P, Fe, Cu, I, Mg, Mn , Zn etc.

7. Classification of amino acids There are different ways of classification of amino acids based on the structure and chemical nature, nutritional requirement, metabolic fate etc. Amino acid classification based on structure: Amino acids with aliphatic side chains: These are mono amino mono carboxylic acids Hydroxyl group (-OH)containing amino acids. Sulphur containing amino acids Acidic amino acids and their amides Basic amino acids Aromatic amino acids Imino (=NH group) acids

8. Name Symbol Special group present 3 letters 1 letter Amino class with aliphatic side chain Glycine Gly G Alanine Ala A Valine Val V Branched chain Lucine Leu L Branched chain Isolucine Ile I Branched chain Amino acids containing hydroxyl (-OH) groups Serine Ser S Hydroxyl Threonine Thr T Hydroxyl Sulfur containing amino acids Cysteine Cys C Sulfhydryl Methionine Met M Thioether

9. Acidic amino acids and their amides Aspartic acid Asp D β -Carboxyl Asparagine Asn M Amide Glutamic acid Glu E γ -Carboxyl Glutamine Gln Q Amide Basic amino acids Lysine Lys K ε- Amino Arginine Arg R Guanidine Histidine His H Imidazole Aromatic amino acids Phenylalanine Phe F Benzene or Phenyl Tyrosine Tyr Y Phenol Tryptophan Trp W Indole Imino acids Proline Pro P Pyrrolidine

10. Amino acid classification based on polarity: (a)Non polar amino acids: Hydrophobic amino acids and have no charge on ‘R’ group It includes Alanine, Leucine , Isoleucine , Valine , Methionine , Phenyl alanine, Trytophan and Proline . (b)Polar amino acids with no charge on ‘R’ group: These possesss groups like hydroxyl, sulfhydryl and amide and participate in the hydrogen bonding of protein synthesis. Glycine, serine, threonine , cysteine , glutamine, asparagine and tryrosine are included in this group (c)Polar amino acids with positive ‘R’ group: Lysine, arginine and histidine are included in this group (d)Polar amino acids with negative ‘R’ group: The dicarboxylic monoamino acids – aspartic acid and glutamic acid are included in this group

11. Nutritional classification of amino acids: (a)Essential or indispensable amino acids: The amino acids which cannot be synthesised by the body and need to be supplied through diet. These are required for proper growth and maintenance of the individual. It includes arginine , valine , histidine , Isoleucine , Leucine , Lysine, Methionine , Phenyl alanine, threonine and tryptophan Arginine and Histidine can be synthesised by adults and not by growing children, so these are considered as semi-essential amino acids (b)Non- essential or dispensable amino acids: The amino acids which are synthesised by the body to meet the biological needs Includes Glycine, alanine, serine, cysteine , aspartate , glutamate, glutamine, tyrosine and proline

12. Amino acid classification based on their metabolic fate: The carbon skeleton of amino acid can serves as a precursor for the synthesis of glucose(Glycogenic) or fat (Ketogenic) or both. Glycogenic amino acids : These amino acids serve as a precursors for the formation of glucose or glycogen Eg : alanine, aspartate , glycine, methionine etc Ketogenic amino acids: Fats can be synthesised from these amino acids. Leucine and Lysine are exclusively ketogenic Glycogenic and Ketogenic amino acids: Isoleucine , phenylalanine, trptophan and tryrosine are precursors for the synthesis of glucose as well as fat

13. Properties of amino acids Physical properties: Solubility: usually soluble in water and insoluble in organic solvents Melting point: often above 200°C Taste: sweet( Gly , Ala, Val), tasteless( Leu ) or bitter( Arg , Ile) Optical properties: all the amino acids except glycine possess optical isomers due to the presence of asymmetric carbon atom. Amino acids as ampholytes : amino acids contain both acidic and basic groups, they can donate & accept protons. Each amino acid has a characteristic pH at which it carries both +ve and -ve charges and exists as zwitter ions

14. Chemical properties: Amino acids form salts(- COONa ) with bases and esters (-COOR´) with alcohols. Amino acids undergo decarboxylation to produce corresponding amines. The carboxyl group of dicarboxylic amino acids react with ammonia to form amide. Eg : Aspartic acid + NH 3 Asparagine The α - amino acids react with ninhydrin to form purple, blue or pink color complex. Transamination : Transfer of amino group from an amino acid to a keto acid to form a new amino acid. Amino acids undergo Oxidative deamination to liberate free ammonia

15. Properties of proteins Solubility: form colloidal solutions in water Molecular weight: 4000- 440,000 Shape: globular, oval, fibrous or elongated At Isoelectric pH, the protein exists as zwitterions or dipolar ions. They are electrically neutral with minimum solubility, maximum precipitability and least buffering capacity Undergo several color reactions like biuret reaction, Ninhydrin reaction, millions reaction, xanthoproteic reaction etc The phenomenon of disorganisation of the protein structure by physical and chemical agents is called Denaturation :

16. Classification of proteins Functional classification of proteins: Structural proteins: keratin of hair and nails, collagen of bones Enzymes or catalytic proteins: Hexokinase, pepsin Transport proteins: Hemoglobin, serum albumin Hormonal proteins: Insulin, growth hormones Contractile proteins: Actin , Myosin Storage proteins: Ovalbumin , Glutelin Genetic proteins: Nucleoproteins Defense proteins: Snake venoms, Immunoglobulins Receptor proteins for hormones, viruses.

17. Protein classification based on chemical nature and solubility: (a)Simple proteins : These are composed of only amino acid residues (b)Conjugated proteins : Besides the amino acids, these proteins contain a non-protein moiety known as prosthetic group or conjugating groups (c)Derived proteins: These are denatured or degraded products of simple and conjugated proteins. The above 3 classes are further subdivided into different groups

18. Simple proteins: Globular proteins: These are spherical or oval in shape, soluble in water or other solvents and digestible. (a)Albumins: soluble in water and dilute salt solutions and conjugated by heat. Eg : serum albumin, ovalbumin (egg), lactalbumin (milk). (b)Globulins: soluble in neutral and dilute salt solutions. Eg : serum globulins, vitelline (egg yolk) (c) Glutelins : soluble in dilute acids and alkalies and mostly found in plants. Eg : glutelin (wheat), oryzenin (rice) (d) Prolamines : soluble in 70% alcohol. eg : gliadin (wheat), zein (maize)

19. (e) Histones : Strongly basic proteins, soluble in water and dilute acids but insoluble in dilute ammonium hydroxide eg : thymus histones , histones of codfish serum (f)Globins: These are generally considered along with histones . However, globins are not basic proteins and are not precipitated by ammonium hydroxide (g) Protamines : They are strongly basic and resembles histones but smaller in size and soluble in NH4OH. Protamines are also found in association with nucleic acids. Eg : sperm proteins

20. (2)Fibrous proteins: These are fiber like in shape, insoluble in water and resistant to digestion. Albuminoids or scleroproteins constitute the most abundant group of fibrous proteins. Collagens: These are connective tissue proteins lacking tryptophan. Collagens on boiling with water or dilute acids, yields gelatin which is soluble and digestible Elastins : These proteins are found in elastic tissues such as tendons and arteries. Keratins: These are present in exoskeletal structures , eg : hair, nails, horns

21. Conjugated proteins: (a)Nucleoproteins: Nucleic acid (DNA or RNA) is the prosthetic group Eg : nucleohistones , nucleoprotamines (b)Glycoproteins: The prosthetic group is carbohydrate, which is less than 4% of protein. The term mucoprotein is used if the carbohydrate content is more than 4%. Eg : mucin (saliva), ovomucoid (egg white) (c)Lipoproteins: Proteins found in combination with lipids as the prosthetic group Eg : serum lipoproteins, membrane lipoproteins. (d) Phosphoproteins : Phosphoric acid is the prosthetic group. Eg : casein(milk), vitelline (egg yolk) (e) Chromoproteins : The prosthetic group is coloured in nature Eg : hemoglobins , cytochromes (f) Metalloproteins : These proteins contain metal ions such as Fe, Co, Zn, Cu, Mg etc. Eg : ceruloplasmin (Cu), carbonic anhydrase (Zn)

22. Derived proteins: (1)Primary derived proteins: These are the denatured or coagulated or first hydrolysed products of proteins (a)Coagulated proteins: These are the denatured proteins produced by agents like heat, acids, alkalies etc. Eg : cooked proteins, coagulated albumin(egg white) (b) Proteans : These are the earliest products of enzyme hydrolysis by enzymes, dilute acids, alkalies etc which are insoluble in water. Eg : fibrin formed form fibrinogen (c) Metaproteins : These are the second stage products of protein hydrolysis obtained by treatment with slightly stronger acids and alkalies . Eg : acid and alkali metaproteins (2)Secondary derived proteins: These are the degraded (due to breakdown of peptide bonds) products of proteins/ Progressive hydrolytic products of protein hydrolysis. These include proteoses , peptones, peptides and polypeptides

23. Nutritional classification of proteins: (a)Complete proteins: These proteins have all the 10 essential amino acids in the required proportion by the human body to promote good growth. Eg : egg albumin, milk casein (b)Partially Incomplete proteins: These proteins are partially lacking one or more essential amino acids and hence can promote moderate growth. Eg : wheat and rice proteins (c)Incomplete proteins: These proteins completely lack one or more essential amino acids and hence they do not promote growth at all Eg : gelatin , zein

24. Structure of proteins The structure of proteins can be divided into 4 levels of organization. Primary structure : The linear sequence of amino acids forming the backbone of proteins Secondary structure : The spatial arrangement of proteins by twisting of the polypeptide chain. 3 types : α- helix, β- pleated sheet and collagen helix Tertiary structure: The 3 dimensional structure of a functional protein Quaternary structure: Some of the proteins are composed of 2 or more polypeptide chains called subunits. The spatial arrangement of these subunits is known as quaternary structure