Amino acid sdk (biochem)

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Amino acid sdk (biochem)

  1. 1. AMINO ACIDSDKFebruary 2, 2013
  2. 2. Amino Acids, Peptides, ProteinsOBJECTIVES• What are Amino acids• Structure and naming of amino acids• Standard and Non-standard amino acids• What is peptide bond and peptides• Ionization behavior of amino acids and peptides• Structure and properties of peptides
  3. 3. AMINO ACIDSØAmino acids are organic acids containing an amine group, they arethe building units of proteins.ØThere are about 300 amino acids occur in nature. Only 20 of themoccur in proteins.
  4. 4. Structure of amino acids:ØEach amino acid has 4 different groups attached to α- carbon ( which is C-atom next toCOOH).ØThese 4 groups are :ØAmino Group,ØCOOH GroupØHydrogen AtomØSide Chain (R)COOH|H2N—C — H|R side chain
  5. 5. Structure of amino acids:
  6. 6. • The most common amino acids are alpha-amino(a-amino acids) acids and the most common aminoacids are the L- alpha-amino acids.• Biochemical designation: start from a-carbon andgo down the R-groupStructure of amino acids:
  7. 7. D & LAmino Acids
  8. 8. At physiological PH (7.4), COOH group is dissociated forming anegatively charged carboxylate ion (COO-) and H2N aminogroup is protonated forming positively charged ion (NH3+)forming Zwitter ionAmino Acids Physiological PH
  9. 9. • Both the –NH2 and the –COOH groups in an amino acidundergo ionization in water.• At physiological pH (7.4), a zwitterion forms– Both + and – charges– Overall neutral– Amphoteric• Amino group is protonated• Carboxyl group is deprotonated• Soluble in polar solvents due to ionic character• Structure of R also influence solubilityZwitterions
  10. 10. Classification of Amino acidsAmino acids are classified on following bases1. On the basis of protein formation2. On the basis of Side chain3. Nutritional classification4. On the basis of polarity
  11. 11. • The building blocks of proteins• These 20 A.A. are the only A.A. coded for by DNA .• Each amino acid (except proline) has a carboxyl group, an amino group, and adistinctive side chain “R-group” bonded to the a -carbon atom.• Proline has imino (NH)groupStandard & Nonstandard amino Amino Acids:Nonstandard amino acids are not coded for protein synthesisby DNA. eg. Ornithine, Citrulline
  12. 12. Non-standard amino acids↕collagenMyosinCa2+ bindingproteinsCa2+ElastinRedoxProteins
  13. 13. Classification on the basis of side chain• Acidic side chain• Basic side chain• Neutral– Aliphatic side chain– Aromatic side chain• Hetero cyclic– Hydrocarbon side chain– Hydroxylic side chain– Sulphur – containing side chain– Imino side chain
  14. 14. Sulfur containing•Cysteine•MethionineNeutral Acidic•Aspartic•Glutamic•Asparagine•GlutamineBasic•Arginine•LysineAliphatic Aromatic•Phynylalanine•TyrosineHeterocyclic•Tryptophan•Proline•HistidineWith a hydrocarbonside chain•Glycine•Alanine•Valine•Leucine•IsoleucineHydroxylcontaining•Serine•Threonine1. Chemical classification of amino acids
  15. 15. Sulfur containing•Cysteine•MethionineNeutral Acidic•Aspartic•Glutamic•Asparagine•GlutamineBasic•Arginine•LysineAliphatic Aromatic•Phynylalanine•TyrosineHeterocyclic•Tryptophan•Proline•HistidineWith a hydrocarbonside chain•Glycine•Alanine•Valine•Leucine•IsoleucineHydroxylcontaining•Serine•Threonine1. Chemical classification of amino acids
  16. 16. Aliphatic Side Chain• Glycine , Alanine , Valine Leucine IsoleucineCCOOHHH2N H CCOOHHH2N CH3Glycine Alanine
  17. 17. Aromatic Side Chain• Phenylalanine Tryptophan & tyrosineCCOOHHH2N CH2NHTryptophan
  18. 18. Sulphur – Containing Side Chain• Cysteine MethionineCCOOHHH2N CH2 CH2 S CH3CCOOHHH2N CH2 SHMethionineCysteine
  19. 19. CystineCCOOHHH2N CH2 S S CH2 CHNH2COOH
  20. 20. Acidic Side ChainCCOOHHH2N CH2 COO-CCOOHHH2N CH2 CH2 COO-Aspartic acidGlutamic acid
  21. 21. Basic Side ChainCCOOHHH2N CH2 CH2 CH2 CH2 NH3+CCOOHHH2N CH2 CH2 CH2 NH CNH2+NH2CCOOHHH2N CH2HN NLysineArginineHistidine
  22. 22. Amide Side ChainCCO O HHH2N CH2 CON H2CCOOHHH2N CH2 CH2 CONH2AsparagineGlutamine
  23. 23. Hydroxylic Side ChainCCOOHHH2N CH2 OHCCOOHHH2N CH CH3OHSerineThreonine
  24. 24. Imino Side ChainCCOOHHNCH2CH2CH2HProline
  25. 25. 2. Nutritional Classification• Essential amino acid/ Indispensable amino acid• Nonessential amino acid/ Dispensaable aminoacid.
  26. 26. Classification of amino acids based on theirnutritional value1-Essential amino acids ;They are those amino acids that cannot be synthesized inthe body thus they are essential in the diet.Essential amino acids include the following amino acids ;MATT VIL PHLY2- Non-essential amino acids; They are those amino acids that can be synthesized inthe body thus they are non-essential in the diet.
  27. 27. 3-Classification according to the polarity ofthe side chain R.a)Non-polar amino acids.Each of these amino acids has a non-polar side chain that does not bind or giveoff protons or participate in hydrogen or ionic bonds.b)Polar amino acids1-Polar uncharged amino acidsThese amino acids have zero net charge at neutral pH2-Polar charged amino acidsØ Polar acidic or positively charged amino acids.The amino acids acid are proton donorsØ Polar basic or negatively charged amino acidsThe side chains of the basic amino acids accept protons
  28. 28. Peptide Bond• Acid amide linkage.• α-carboxyl group of one amino acid join withthe α-amino group of another amino acid.• It is covalent linkageCHCR1H2NOOH + CHCR2H2NOOH CHCR1H2NON CHCHR2OOH + H2OPeptide bond
  29. 29. Characteristic of Peptide bonds• Peptide bonds are not broken by conditions that denatureproteins, such as heating or high concentrations of urea.• Prolonged exposure to a strong acid or base at elevatedtemperatures is required to hydrolyze these bonds non-enzymatically.• The peptide bond has a partial double-bond character, that is, itis shorter than a single bond,• It is rigid and planar.• The peptide bond is generally a trans bond
  30. 30. Peptide bond formationMake sure you clearlyindicate whether wateris a product or reactant!Zwitterion formFormation: dehydration reactionHighlight the peptide bond
  31. 31. • More amino acids can be added using the samecondensation reaction– oligopeptide/polypeptide/proteinPeptides and ProteinsFig 3-14R1 R2 R3 R4 R5
  32. 32. CHCO OHH2NC H3++ H2OCHC OO HH2NHCHCO O HH2NCH2O H+Glycine ( Gly )Alanine ( Ala ) Serine (Ser )2CHCH2NCH3ONHCHHCONHCHCH2OHCOO HAlanylglycylserine (Ala-Gly-Ser)Peptide Bond
  33. 33. Clinical Importance1. Synthesis of body proteins.2. Synthesis of essential nitrogen compounds e.g ( Histamine,DNA,RNA).3. Synthesis of glucose, fat, energy.4. Synthesis of hormones(Thyroid Hormones)5. Synthesis of neurotransmitters(dopamine, epinephrine,norepinephrine, serotonin, and histamine)
  34. 34. Thank you

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