Amino Acids and Proteins PDF

Amino acids , Proteins Karma Wangchuk Agriculture  Amino acids Building blocks of proteins are essential components of peptides and proteins Amino acids are organic molecules that, when linked together with other amino acids, form a protein Amino acids are a...

Amino acids , Proteins Karma Wangchuk Agriculture  Amino acids Building blocks of proteins are essential components of peptides and proteins Amino acids are organic molecules that, when linked together with other amino acids, form a protein Amino acids are a group of organic compounds containing two functional groups -amino and carboxyl. 20 amino acids occurs repeatedly in proteins Structure of amino acid  Structure of amino acid Generally, amino acids have the following structural properties: A carbon (the alpha carbon) A hydrogen atom (H) A Carboxyl group (-COOH) An Amino group (-NH2) A "variable" group or "R" group  Amino acids and symbols Amino acids 3 lettter 1 letter Alanine Ala A Cysteine Cys C Aspartic acid Asp D Glutamic acid Glu E Phenylalanine Phe F Glycine Gly G Histidine His H  Amino acids and symbols Amino acids 3 letter 1 letter Isoleucine Ile I Lysine Lys K Leucine Leu L Methionine Met M Asparagine Asn N Proline Pro P Glutamine Gln Q  Amino acids and symbols Amino acids 3 letter 1 letter Arginine Arg R Serine Ser S Threonine Thr T Valine Val V Tryptophan Trp W Tyrosine Tyr Y  Classifications of amino acid Amino acids Structur Nutrition Metaboli polarity al al c rate Structural classifications of amino acid Based on structure – 1. Amino acids with aliphatic side chain 2. Hydroxyl group containing amino acids 3. Sulfur containing amino acid 4. Acidic amino acids and their amide 5. Basic amino acids 6. Aromatic amino acids 7. imino acids Amino acids with aliphatic side chain - These are monoamino monocarboxylic acid - Can be of simple and branched chain amino acids - Includes glycine, alanine, valine, leucine and isoleucine Hydroxyl group containing amino acids - Contains hydroxyl group Sulfur containing amino acid Basic amino acids - have basic side chains Aromatic amino acids -that includes an aromatic ring imino acids - it has an imino group (=NH), instead of an amino group (-NH2) - Proline  Based on the polarity A.A can be of 1. Non-polar amino acids - hydrophobic - no charge on R group Eg. alanine, leucine, isoleucine, valine, methionine, phenylalanine, tryptophan and proline  Based on the polarity 2. Polar amino acids with no charge on 'R' group - has charge on R group - possess groups such as hydroxyl, sulfhydryl and amides Eg. glycine, serine, threonine, cysteine, glutamine, asparagine and tyrosine. 3. Polar amino acids with positive 'R' group - Positively charged side chain - Eg. lysine, arginine and histidine  Based on the polarity 4. Polar amino acids with negative 'R'group - Are hydrophilic in nature - Negatively charged - The dicarboxylic monoamino acids - aspartic acid and glutamic acid are considered in this group.  Based on nutritional requirement It can be of 3 types – 1. Essential amino acids - The amino acids which cannot be synthesized hy the body and, therefore, need to be supplied through the diet are called essential amino acids -required for proper Browth and maintenance of the individual Eg. Arginine, Valine, Histidine, lsoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan  Based on nutritional requirement 2. Non essential amino acids - The body can synthesize about '10 amino acids to meet the biological needs, hence they need not be consumed in the diet Eg. glycine, alanine, serine, cystei ne, aspartate, asparagine, glutamate, glutamine, tyrosine and proline 3. semi-essential amino acid - A.A which can be synthesized by adults but not by child - arginine and histidine  Based on metabolic rate - The carbon skeleton of amino acids can serve as a precursor for the synthesis of glucose (glycogenic) or fat (ketogenic) or both. It can be of 3 types 1. Glycogenic amino acids - alanine, aspartate, glycine, methionin 2. Ketogenic amino acids -leucine and lysine 3. Glycogenic and ketogenic amino acids- isoleucine, phenylalanine, tryptophan, tyrosine  Physical properties of A.A Amino acids are colorless, crystalline solid. All amino acids have a high melting point greater than 200o Solubility: They are soluble in water, slightly soluble in alcohol and dissolve with difficulty in methanol, ethanol, and propanol. R-group of amino acids and pH of the solvent play important role in solubility. On heating to high temperatures, they decompose. All amino acids (except glycine) are optically active.  Physical properties of A.A Amino acid as ampholytes - Amino acids contain both acidic (-COOH) and basic (-NH2) groups. They can donate a proton or accept a proton, hence amino acids are regarded as ampholytes Zwitter ionic property A zwitterion is a molecule with functional groups, of which at least one has a positive and one has a negative electrical charge. The net charge of the entire molecule is zero. Amino acids are the best- known examples of zwitterions. They contain an amine group (basic) and a carboxylic group (acidic). The -NH2 group is the stronger base, and so it picks up H+ from the -COOH group to leave a zwitterion. The (neutral) zwitterion is the usual form amino acids exist in solution. Chemical properties of A.A 1) Reactions due to amino group 2) Reactions due to carboxyl group 3) Reactions due to both amino and carboxyl groups 4) Reaction due to side chain  Reactions due to amino group i) Oxidative deamination-Αn amino group is removed and corresponding α-keto acid is formed. α -keto acid produced is either converted to glucose or ketone bodies or is completely oxidized.  Reactions due to amino group (contd.) ii) Transamination-Transfer of an α amino group from an amino acid to an α keto acid to form a new amino acid and a corresponding keto acid. 5  2) Reactions due to carboxyl group i) Decarboxylation- Amino acids undergo alpha decarboxylation to form corresponding amines. Examples- Glutamic acid GABA Histidine Histamine Tyrosine Tyramine  2) Reactions due to carboxyl group (contd.) ii) Formation of amide linkage carboxyl group of an acidic amino acid reacts with ammonia by condensation reaction to form corresponding amides Aspartic acid Asparagine Glutamic acid Glutamine 8 3)Reactions due to both amino & carboxyl groups Formation of peptide bond- Carboxyl group of an amino acid binds with amino group of another amino acid forming a peptide bond with the loss of one molecule of water.  Reactions due to side chains 1) Ester formation  OH containing amino acids e.g. serine, threonine can form esters with phosphoric acid in the formation of phosphoproteins (figure- 1)  OH group containing amino acid can also form: Glycosides – by forming O- glycosidic bond with carbohydrate residues (figure-2)  Reactions due to side chains 2) Reactions due to SH group (Formation of sulphide bonds) Cysteine has a sulfhydryl group( SH) group and can form a disulphide (S-S) bond with another cysteine residue.  The dimer is called Cystine  Formation of disulphide bond Two cysteine residues can connect two polypeptide chains by the formation of interchain disulphide chains. Colour reactions of amino acids N  Chemical properties of A.A Reaction with ninhydrin : The amino acids react with ninhydrin to form a purple, blue or pink colour complex (Ruhemann's purple). Amino acid + Ninhydrin Keto acid + NH2+CO2+Hydrindantin Hydrindantin + NH3 + Ninhydrin Ruhemann's purple  Chemical properties of A.A Reaction with base – produce salt and water NH2-CH2-COOH + NaOH = NH2-CH2-COONa + H20 Reaction with alcohol- produce ester and water NH2-CH2-COOH + CH3OH = NH2-CH2- COOCH3 + H20 Reaction with acid – produce salt NH2-CH2-COOH + HCL = NH2-CH2-COOCl + H20 Peptides  Peptides - A peptide consists of two or more amino acids linked by a peptide bond formed between the carboxyl group of one amino acid and the amino group of another with the removal of one mole of water during a peptide bond. -  Types of peptides 1. Dipeptides: Compound formed when two amino acids linked by 1 peptide bond. Examples: Carnosine ( β-alanyl-L-histidine) Anserine (β-alanyl-N-methylhistidine) Aspartame (Asparagine-phenylalanine) 2. Tripeptides Compound formed when three amino acids linked by 2 peptide bond. Examples; Glutathione ( Glutamyl-cystinyl-glycine) Opthalmic acid (L-γ-Glutamyl-α-L-amino butyrl-glycine)  Types of peptides 3. Oligopeptides Compound formed when more than 2 and less than 20 amino acids are linked by peptide bonds. Examples; Tetrapeptide; Tulfsin ( thrionine-lysine-proline-Arginine) Endomorphin-1 ( Tyrosine-proline-tryptophan-phenylalanine) Amanitin ( Decapeptide) Netropsin 4. Polypeptides Compound formed when more than 20 amino acids are linked by peptide bond. Examples: Insulin Growth hormone  Proteins - protein is derived from a Greek word proteios meaning holding the first place - Proteins are made up of polypeptide chains, which are amino acids joined together with peptide bonds. - Proteins are polymer of amino acids  Structure of Proteins Alpha helix secondar Beta y plates Beta Primary Protein turns structure Tertiary Quartena ry  Structure of Proteins 1. primary structure- - The linear sequence of amino acids forming the backbone of proteins (polypeptides). - number of amino acids residues in proteins - sequence of amino acids - the primary structure is stabilized by peptide bonds Structure of Proteins Structure of Proteins  Secondary structure refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone The spatial arrangement of protein by twisting of the polypeptide chain. Stabilized by H-bond types 1. α helix and 2. β pleated sheet 1. α helix - Pauling and corey (1951) 2. β pleated sheet - Pauling and Corey -are composed of two or more segments of fully extended peptide chain - ln the β -sheets, the hydrogen bonds are formed between the neighboring segments of polypeptide chains.  Beta pleated sheets can be of two types – a. Parellel b. Anti parallel N terminal C- terminal N  Tertiary structure The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces Tertiary structure  Quartenary structure Many proteins are made up of a single polypeptide chain and have only three levels of structure. However, some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure. The individual polypeptide chains are known as monomers, protomers or subunits. A dimer consits ol two polypeptides while a tetramer has four  Quartenary structure Bonds in quaternary structure: The monomeric subunits are held together by nonconvalent bonds namely hydrogen bonds, hydrophobic interactions and ionic bonds Eg. Haemoglobin , DNA polymerase Quartenary structure  Classification of proteins proteins are classifed based -on their function, -chemical nature and solubility properties and - nutritional importance  Based on functions Structural proteins : Keratin of hair and nails, collagen of bone. 2. Enzymes or catalytic proteins : Hexokinase, pepsr n. 3. Transport proteins: Hemoglobin, serum albumin. 4. Hormonal proteins: Insulin, growth normone. 5. Contractile proteins : Actin, myosin. 6. Storage proteins: Ovalbumin, glutelin. 7. Genetic proteins : Nucleoproteins. 8. Defense proteins : Snake venoms, lmmunoglobulins. 9. Receptor proteins for hormones, viruses Classification of proteins  Nutritional importance 1. Complete protein - contains all ten essential amino acids eg, egg albumins, milk caesin 2. Partially complete proteins - These proteins are partially lacking one or more essential amino acid eg. Rice and wheat protein 3. Incomplete protein - completely lack one or more essential amino acids Eg. Gelatins  Chemical properties 1. Hydrolysis 2. reaction involving COOH 3. Reaction involving NH2 4. Reaction involving both COOH and NH2 5. Reaction involving R group 6. SH group  Functions 1. Repair and Maintenance 2. Energy 3. Hormones 4. Enzymes 5. Transportation and storage 6. Enzymes  Denaturation of proteins Denaturation can be defined as the disruption of the secondary, tertiary and quaternary structure of the native protein resulting in the alterations of the physical, chemical and biological characteristics of the physical, chemical and biological characteristics of the protein by a variety of agents.  Denaturation of proteins The phenomenon of disorganization of native protein structure is known as Denaturation of protein. In other words, the denaturation of proteins is defined as any noncovalent changes in the structure of the protein. Denaturation results in the loss of the secondary, tertiary and quaternary structure of proteins. This involves a change in physical, chemical and biological properties of protein molecules. The primary structure or the amino acid sequence remains the same after the denaturation process.  Denaturating agents Physical agents: Heat Exposure to UV light Vigorous shaking High pressure Ultrasound Radiation (radioactive compound) etc.  Denaturating agents Chemical agents: pH High concentrations of acids and alkali Certain solvents i.e ethanol, acetone etc Urea Heavy metal salts Mercaptoethanol Performic acid Sodium dodecyl sulfate  Biologically important peptides 1. Glutathione: Tripeptide. Exists as reduced or oxidized state 2G-SH↔ G-S-S-G Reduced Oxidized – Serves as coenzyme – Prevents oxidation of –SH groups essential for protein functions. E.g., enzymes – Correct disulfide bonds with the help of glutathione reductase – Reduced glutathione protects RBCs structure and Hb from oxidizing agents – Involved in the transport of AAs in the intestine and kidney – Involved in detoxification process – Glutathione peroxidase removes free radicals 2 GSH + H2O2→G-S-S-G + 2 H2O 2. Thyrotropin Releasing Hormone: Tripeptide from the hypothalamus casuses the release of TSH from pituitary 4. Vasopressin (ADH): Nonapeptide from posterior pituitary responsible for water absorption in kidneys 5. Angiotensin: Angiotensin I (10 AAs) converted to Angiotensin II (8 AAs). Angiotensin II exerts hypertensive effect. It also causes release of aldosterone from adrenal. 6. Methionine Enkephalin: Pentapeptide from the brain. Functions as an opiate and relieves pain. 7. Bradykinin and Kallidin: Nonapeptide and decapeptide, respectively. Act as vasodilators. 8. Peptide Antiobiotics: Bacitracin, actionomycin, gramicidin are available in nature. 9. Aspartame: Dipeptide of aspartic acid and phenylalanine. Artificial sweetener in soft drinks 10.Gastrointestinal hormones: Gastrin, Secretin, Cholecystokinin, etc are the gastrointestinal peptides which serve as hormones