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Chemistry of amino acids

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General structure, classification, reactions and functions of amino acids.

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Chemistry of amino acids

  1. 1. Biochemistry for medicswww.namrata.co Biochemistry For Medics 7/5/2012 1
  2. 2. Provide the monomer units from which thelong polypeptide chains of proteins aresynthesized L-amino acids and their derivativesparticipate in cellular functions as diverse asnerve transmission and the biosynthesis ofporphyrins, purines, pyrimidines, and urea.Short polymers of amino acids calledpeptides perform prominent roles in theneuroendocrine system as hormones,hormone-releasing factors,neuromodulators, or neurotransmitters. Biochemistry For Medics 7/5/2012 2
  3. 3. Each amino acid (except proline) has acarboxyl group, an amino group and adistinctive side chain bonded to the alphacarbon atom. At physiological pH thecarboxyl group is dissociated forming thenegatively charged carboxylate ion(-COO-),and the amino group is protonated(-NH3+) Biochemistry For Medics 7/5/2012 3
  4. 4.  Amino acids can be classified in 4 ways: 1. Based on structure 2. Based on the side chain characters 3. Based on nutritional requirements 4. Based on metabolic fate Biochemistry For Medics 7/5/2012 4
  5. 5. I. Aliphatic Amino Acids:a) Mono-amino mono-carboxylic acids:  Simple amino acids: Glycine , Alanine Biochemistry For Medics 7/5/2012 5
  6. 6. I. Aliphatic Amino Acids:a) Mono-amino mono-carboxylic acids:Branched chain amino acids: Valine,Leucine and Isoleucine Biochemistry For Medics 7/5/2012 6
  7. 7. I. Aliphatic Amino Acids:a) Mono-amino mono-carboxylic acids:-OH group-containing amino acids: Serineand Threonine Biochemistry For Medics 7/5/2012 7
  8. 8. I. Aliphatic Amino Acids:a) Mono-amino mono-carboxylic acids:Sulfur-containing amino acids: Cysteine,Cystine(Formed by linking of two cysteineresidues) and Methionine. Biochemistry For Medics 7/5/2012 8
  9. 9. I. Aliphatic Amino Acids:a) Mono-amino mono-carboxylic acids:  Amide group-containing amino acids: Glutamine and Asparagine Biochemistry For Medics 7/5/2012 9
  10. 10. I. Aliphatic Amino Acids:a) Mono-amino di-carboxylic acids: Aspartic acid and Glutamic acid Biochemistry For Medics 7/5/2012 10
  11. 11. I. Aliphatic Amino Acids:a) Di- basic mono-carboxylic acids: Arginine and Lysine Biochemistry For Medics 7/5/2012 11
  12. 12. ii ) Aromatic amino acids- Phenyl alanine and tyrosine Biochemistry For Medics 7/5/2012 12
  13. 13. iii) Heterocyclic Amino Acids: Tryptophanand Histidine Biochemistry For Medics 7/5/2012 13
  14. 14. iv) Imino acid- Proline Biochemistry For Medics 7/5/2012 14
  15. 15. V. Derived Amino Acids:  Non-α-amino acids e.g.: β-alanine, γ-amino butyric acid (GABA), δ-amino Levulinic acid  Derived and Incorporated in tissue proteins: e.g.: Hydroxy-proline, hydroxy-lysine  Derived but not incorporated in tissue proteins: e.g.: Ornithine, Citrulline, Homocysteine, Argino succinic acid Biochemistry For Medics 7/5/2012 15
  16. 16. A. Amino acids with a non-polar side-chain:e.g.: Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, ProlineEach of these amino acids has a side chain thatdoes not bind or give off protons or participates inhydrogen or ionic bonds.Side chains of these amino acids can be thoughtof as “Oily” or lipid like, a property that promoteshydrophobic interactions. Biochemistry For Medics 7/5/2012 16
  17. 17. B) Amino acids with a polar but uncharged side-chain: e.g.: Glycine, Serine, Threonine, Tyrosine, Cysteine, Asparagine and Glutamine. These amino acids are uncharged at neutral pH,although the side chains of cysteine and Tyrosinecan lose a proton at an alkaline pH.Serine , Threonine and Tyrosine each contains a polarhydroxyl group that can participate in hydrogen bondformation. Side chains of Asparagine and Glutamine contain a carbonyl group and amide group, they can also participate in hydrogen bond formation. Biochemistry For Medics 7/5/2012 17
  18. 18. C) Amino acids with a charged side-chain: a) Amino acids with a positively charged side- chain: 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. Biochemistry For Medics 7/5/2012 18
  19. 19. 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. Biochemistry For Medics 7/5/2012 19
  20. 20. The carbon skeleton of amino acids can beused either for glucose production or for theproduction of ketone bodies, Based on thatI. Both glucogenic and ketogenic amino acids: Isoleucine, Tyrosine, Phenylalanine and TryptophanII. Purely Ketogenic amino acids: Leucine and LysineIII. Purely Glucogenic amino acids: The remaining 14 amino acids are glucogenic. Biochemistry For Medics 7/5/2012 20
  21. 21. Of the over 300 naturally occurring aminoacids, 20 constitute the monomer units ofproteins. These 20 amino acids are calledthe Primary or Standard amino acids.Seleno cysteine is the 21st Amino AcidThe other are Pyroglutamate and Pyrolysine. Biochemistry For Medics 7/5/2012 21
  22. 22. Each amino acid has three letter (code) andone letter (Symbol) abbreviations- Examples-1) Unique first letterCysteine- Cys- CHistidine- His- H2) Priority of commonly occurring aminoacidsAlanine- Ala- A (Preference over Aspartate) Glycine- Gly-G (Preference overGlutamate) Biochemistry For Medics 7/5/2012 22
  23. 23. 3) Similar sounding names- Some one lettersymbols sound like the amino acids theyrepresent- Example Tryptophan – W (Twyptophan) Phenyl alanine – F4) Letters close to initial letterAspartate- Asx- B( near A)Lysine Lys- K(near L) Biochemistry For Medics 7/5/2012 23
  24. 24.  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. Biochemistry For Medics 7/5/2012 24
  25. 25. Physical properties-ColorlessCrystallineMay be sweet(Glycine, Alanine, Valine),tasteless(Leucine) or bitter(Arginine,Isoleucine). Aspartame- An artificialsweetener contains Aspartic acid and Phenylalanine.Soluble in water, acids, alkalis but insolublein organic solventsHigh melting point(More than 200 c) 0 Biochemistry For Medics 7/5/2012 25
  26. 26. Amino acids can exist as ampholytes orzwitterions in solution, depending upon pH of themedium.The pH at which the amino acids exist aszwitterions, with no net charge on them is calledIsoelectric 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 is also minimum at Isoelectric pH Biochemistry For Medics 7/5/2012 26
  27. 27. Biochemistry For Medics 7/5/2012 27
  28. 28. If HCl is added drop wise to am amino acidsolution, at a particular p H, 50 % of themolecules are in the cationic form and 50%are in the zwitterion form. This pH ispK1(with regard to COOH)If the titration is done from the Isoelectricpoint with NaOH, molecules acquire theanionic form. When 50 % of the molecules arein the anionic form and 50% are in thezwitterion form. This pH is pK2(with regardto NH2) Biochemistry For Medics 7/5/2012 28
  29. 29. For mono aminomono carboxylicamino acids-pI = pK1+pK2 ------------- 2The bufferingaction is maximumin and aroundpK1or at pK2 but isminimum at pI Biochemistry For Medics 7/5/2012 29
  30. 30. The α carbon of each amino acid is attached to fourdifferent groups and is thus a chiral or opticallyactive carbon atom.Glycine is exceptional because there are twohydrogen substituents at the α carbon, thus it isoptically inactive.Amino acids with asymmetric centre at the α carboncan exist in two forms, D and L forms that are mirrorimages of each other and are called Enantiomers.All amino acids found in proteins are of L-configurationD- amino acids are found in some antibiotics and inbacterial cell walls. Biochemistry For Medics 7/5/2012 30
  31. 31. 1) Reactions due to amino group2) Reactions due to carboxyl group3) Reactions due to side chain4) Reaction due to both amino and carboxyl groups Biochemistry For Medics 7/5/2012 31
  32. 32.  Oxidativedeamination-α 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. 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. Biochemistry For Medics 7/5/2012 32
  33. 33. Formation of carbamino compoundCO2 binds to α amino acid on the globinchain of hemoglobin to form carbaminohemoglobinThe reaction takes place at alkaline pHand serves as a mechanism for the transferof Carbon dioxide from the tissues to thelungs by hemoglobin. Biochemistry For Medics 7/5/2012 33
  34. 34. 1) Decarboxylation- Amino acids undergo alpha decarboxylation to form corresponding amines. Examples- Glutamic acid GABA Histidine Histamine Tyrosine Tyramine2) Formation of amide linkage• Non α carboxyl group of an acidic amino acid reacts with ammonia by condensation reaction to form corresponding amides Aspartic acid Asparagine Glutamic acid Glutamine Biochemistry For Medics 7/5/2012 34
  35. 35. 1) Ester formation OH containing amino acids e.g. serine, threonine can form esters with phosphoric acid in the formation of phosphoproteins. OH group containing amino acid can also form: Glycosides – by forming O- glycosidic bond with carbohydrate residues. Biochemistry For Medics 7/5/2012 35
  36. 36. 2) Reactions due to SH group (Formation ofdisulphide bonds)Cysteine has a sulfhydryl group( SH) group andcan form a disulphide (S-S) bond with anothercysteine residue. The dimer is called CystineTwo cysteine residues can connect twopolypeptide chains by the formation of interchaindisulphide chains. Biochemistry For Medics 7/5/2012 36
  37. 37. 3)TransmethylationThe methyl group of Methionine can betransferred after activation to an acceptor forthe formation of important biologicalcompounds. Biochemistry For Medics 7/5/2012 37
  38. 38. Reactions due to side chains4)Reactions due to both amino & carboxylgroupsFormation of peptide bond Biochemistry For Medics 7/5/2012 38
  39. 39.  Incorporated in to tissue proteins Niacin, Serotonin and melatonin aresynthesized from TryptophanMelanin, thyroid hormone, catecholaminesare synthesized from TyrosineGABA (neurotransmitter) is synthesizedfrom Glutamic acidNitric oxide, a smooth muscle relaxant issynthesized from Arginine. Act as precursors for haem, creatine andglutathione, Porphyrins, purines andpyrimidines. Biochemistry For Medics 7/5/2012 39
  40. 40. S.No. Test Significance1) Ninhydrin reaction Given by all Alpha amino acids2) Xanthoproteic test Given by aromatic amino acids3) Millon’s test Confirmatory test for Tyrosine4) Biuret test Not given by free amino acids5) Sakaguchi test Given by Arginine6) Hopkins Cole reaction Confirmatory test for Tryptophan7) Lead acetate test Given by cysteine and cystine but not given by Methionine8) Nitroprusside reaction Given by SH group containing amino acids Biochemistry For Medics 7/5/2012 40