Chemistry of amino acids&proteins

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  • 1.Chemistry of amino acids

2. Amino Acids Amino Acids are the building units of proteins. Proteins are polymers of amino acids linked together by what is called Peptide bond. There are about 300 amino acids occur in nature. Only 20 of them occur in proteins. Each amino acid has 4 different groups attached to - carbon ( which is C-atom next to COOH). These 4 groups are : amino group, COOH gp, Hydrogen atom and side, Chain (R)R 3. At physiological PH (7.4), -COOH gp is dissociated forming a negatively charged carboxylate ion (COO-) and amino gp is protonated forming positively charged ion (NH3+) forming Zwitter ion 4. Amino acid structures differ at the side chain (Rgroups). Abbreviations: three or one letter codes Amino acids (except glycine) have chiral centers: Rotate the plane of polarized light and are optically active. There are 20 commonly occurring amino acids that make up proteins, and the order of amino acids in proteins determines its structure and biological function. When amino acids are covalently linked to one another, this chain can twist and fold to form a unique three-dimensional structure that has a specific function. 5. Amino Acid Structure Amino acids contain two functional groups, a protonated amine and carboxylic acid in the form of a carboxylate group. Amino acid carbons are named in sequence using the Greek alphabet ( , , , , ) starting at the carbon between the carboxyl and amino groups. COO H3NCH CH2 CH2 CH2 CH2 NH 3 6. The carbon is also bonded to a hydrogen atom and a larger side chain. The side chain is unique for each amino acid. An amino acid, with a chiral center, has two forms called enantiomers, which are nonsuperimposable mirror images. 7. When drawing the Fischer projection, the carboxylate group is at the top of the structure and the side chain (R group) is at the bottom. The protonated amine group can be on the left-hand side (L form) or right-hand side (D form) of the structure. 8. The L-amino acids are the building blocks for proteins. Some D-amino acids occur in nature, but not in proteins. BUT L or D designation for an amino acid does NOT reflect its ability to rotate plane polarized light in a particular direction! COO H3NC CH3L-AlanineHCOO HH3NCHCH3(S)-Alanine3 H3CSC 1 NH 32 COO 9. The R group gives each amino acid its unique identity and characteristics. Twenty amino acids are found in most proteins. There are nine different families of organic compounds represented in the structures of different amino acids. They are as follows: 1. 2. 3. 4. 5. 6. 7. 8. 9.Alkanes Aromatics Thioethers Alcohols Phenols Thiols Amides Carboxylic acids Amines 10. Classification of amino acids Amino acids can be classified in 4 ways: 1. 2. 3. 4.Based on structure Based on the side chain characters Based on nutritional requirements Based on metabolic fate 11. 1)Classification based on structure According to number of COOH and NH2 groups i.e. according to net charge on amino acid. i) Aliphatic Amino Acids A- Monobasic, monocarboxylic amino acids i.e. neutral or uncharged:R 12. 1- GlycineR= H2- AlanineR= CH3 13. 3- Branched chain amino acids: R is branched such as in: a - Valineb- LeucineR= isopropyl gpR= isobutyl gp 14. c- Isoleucine R= isobutyl gpR is isobutyl in both leucine and isoleucine but branching is different: in leucine branching occurs on carbon in isoleucine branching occurs on - carbon 15. 4- Neutral Sulfur containing amino acids: e.g. Cysteine and Methionine. 16. 5- Neutral, hydroxy amino acids: e.g. Serine and Threonine 17. 6- Amide group-containing amino acids: e.g. Glutamine and Asparagine 18. i) Aliphatic Amino Acids B- Mono-amino di-carboxylic acids (Acidic): Aspartic acid and Glutamic acid 19. i) Aliphatic Amino Acids: C- Di- basic mono-carboxylic acids(Basic): Arginine and Lysine 20. ii ) Aromatic amino acids Phenyl alanine and tyrosine 21. iii) Heterocyclic Amino Acids: Tryptophan and Histidine 22. iv) Imino acidProline: In proline, amino group enters in the ring formation being -imino gp so proline is an -imino acid rather than -amino acid 23. v) Derived Amino Acids: Non--amino acids e.g.: -alanine, -amino butyric acid (GABA), -amino Levulinic acid Derived and Incorporated in tissue proteins: e.g.: Hydroxy-proline, hydroxy-lysineDerived but not incorporated in tissue proteins: e.g.: Ornithine, Citrulline, Homocysteine, Argino succinic acid 24. 2) Classification based on side chain characters Amino Acids with a Non-polar side-chain: e.g.: Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Proline A.Eachof these amino acids has a side chain that does not bind or give off protons or participates in hydrogen or ionic bonds. Sidechains of these amino acids can be thought of as Oily or lipid like, a property that promotes hydrophobic interactions. 25. B) Amino acids with a polar but uncharged side-chain: e.g. Serine, Threonine, Tyrosine, Cysteine, Asparagine and Glutamine. These amino acids are uncharged at neutral pH, although the side chains of cysteine and Tyrosine can lose a proton at an alkaline pH. Serine , Threonine and Tyrosine each contains a polar hydroxyl group that can participate in hydrogen bond formation. Side chains of Asparagine and Glutamine contain a carbonyl group and amide group, they can also participate in hydrogen bond formation. 26. C) Amino acids with a charged side-chain a) Amino acids with a positively charged sidechain: The basic amino acids- Lysine, Arginine and Histidine b) Amino acids with a negatively charged side-chain: The acidic amino acids- Glutamic acid and Aspartic acid They are hydrophilic in nature. 27. 3)- Classification based on nutritional requirements I.Essential amino acids:These amino acids cannot be synthesized in the body and have to be present essentially in the diet. Examples-Valine, Isoleucine, Leucine, Lysine, Methionine, Threonine, Tryptophan and Phenylalanine.II. Semi-essential amino acids: These amino acids can be synthesized in the body but the rate of synthesis is lesser than the requirement(e.g. during growth, repair or pregnancy) Examples-Arginine and Histidine.III. Non-essential amino acids: These amino acids are synthesized in the body, thus their absence in the diet does not adversely affect the growth. Examples- Glycine, Alanine, and the other remaining amino acids. 28. Essential AA Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan ValineNonessential AA Alanine Arginine ** Asparagine Aspartic Acid Cysteine ** Glutamic acid Glutamine ** Glycine ** Proline ** Serine Tyrosine ** 29. 4)-Classification based on metabolic fate The carbon skeleton of amino acids can be used either for glucose production or for the production of ketone bodies, Based on that I. Both glucogenic and ketogenic amino acids: Isoleucine, Tyrosine, Phenylalanine and Tryptophan II. Purely Ketogenic amino acids: Leucine and Lysine III. Purely Glucogenic amino acids: The remaining 14 amino acids are glucogenic. Alanine,valine ,serine, threonine, glycine, methionine, asparagine, glutamine, cysteine, cystine, aspartic acid, glutamic acid, histidine and arginine. 30. Non standard amino acids Of the over 300 naturally occurring amino acids, 20 constitute the monomer units of proteins. These 20 amino acids are called the Primary or Standard amino acids. Seleno cysteine is the 21st Amino Acid The other are Pyroglutamate and Pyrolysine. 31. Naming of Amino acids Each amino acid has three letter (code) and one letter (Symbol) abbreviationsExamples-1) Unique first letter Cysteine- Cys- C Histidine- His- H 2) Priority of commonly occurring amino acids Alanine- Ala- A (Preference over Aspartate) Glycine- Gly-G (Preference over Glutamate) 32. Naming of Amino acids 3) Similar sounding names- Some one letter symbols sound like the amino acids they represent- Example Tryptophan W (Twyptophan) Phenyl alanine F 4) Letters close to initial letter Aspartate- Asx- B( near A) Lysine Lys- K(near L) 33. Amino acid abbreviations 34. Special groups in amino acids Arginine- Guanidinium group Phenyl Alanine- Benzene group Tyrosine- Phenol group Tryptophan- Indole group Histidine- Imidazole group Proline- Pyrrolidine Proline has a secondary amino group, hence it is an imino acid. 35. Properties of amino acids Physical propertiesColorless Crystalline May be sweet(Glycine, Alanine, Valine), tasteless(Leucine) or bitter(Arginine, Isoleucine). Aspartame- An artificial sweetener contains Aspartic acid and Phenyl alanine. Soluble in water, acids, alkalis but insoluble in organic solvents High melting point(More than 2000c) 36. Isoelectric point Amino acids can exist as ampholytes or zwitterions in solution, depending upon pH of the medium. The pH at which the amino acids exist as zwitterions, with no net charge on them is called Isoelectric pH or Isoelectric point. In acidic medium, the amino acids exist as cations In alkaline medium , they exist as anions. Due to no net charge, there is no electrophoretic mobility at Isoelectric pH. Solubility and buffering capacity are also minimum at Isoelectric pH 37. Isoelectric point 38. Isoelectric pH pH at which amino acids exist as the zwitterion (neutral) and carries no net charge. Thus molecule is electrically neutral. The pl value can be calculated by taking the average pKa values corresponding to the ionizable groups. For example leucine has two ionizable groups , and its pl value can be calculated as follows. 39. Leucine exists as cation at pH below 6 and anion at pH above 6. at the ispelectric pH leucine is found as Zwitterions . Titration curve of Amino acid: in the graphical representation of Leucine titrarion at low pH , Leucine exists in fully protonated forms as cation. As the titration proceeds with NaOH, Leucine loses its protons and at isoelectric pH its become Zwitterions. Further titration results in formation of anionic form of Leucine. 40. The isoelectric point (pI) of an amino acid is the pH at which it has no n