Horton 3-wa

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Horton 3-wa

  1. 1. Principles of BiochemistryFourth EditionChapter 3Amino Acids and the PrimaryStructures of ProteinsCopyright © 2006 Pearson Prentice Hall, Inc.Horton • Moran • Scrimgeour • Perry • RawnDr. Wisam Alsamah
  2. 2. Biological Functions of Proteins1. As enzymes (catalysts)2. Storage and transport (hemoglobin)3. Provide support and shape (collagen)4. Mechanical work (muscles contraction)5. Decoding information (translation)6. As hormones7. Specialized functions (antibodies)
  3. 3. General Structure of Amino Acids
  4. 4. General Structure of Amino AcidsZwitterionsChiralOrAsymmetric
  5. 5. General Structure of Amino AcidsBall-and-stick model ofserine
  6. 6. General Structure of Amino AcidsStereoisomers (enantiomers)
  7. 7. General Structure of Amino AcidsThe RS system
  8. 8. General Structure of Amino AcidsThe RS systemClockwise R configurationCounterclockwise S configuration
  9. 9. Structures of the 20 common Amino AcidsA. Aliphatic R Groups
  10. 10. A. Aliphatic R GroupsStructures of the 20 common Amino Acids
  11. 11. A. Aliphatic R GroupsStructures of the 20 common Amino AcidsPyrrolidine ring
  12. 12. A. Aliphatic R GroupsStructures of the 20 common Amino Acids●Valine, Leucine, and isoleucine are known asbranched-chain amino acids●All three amino acids are highly hydrophobic●Pyrrolidine ring of proline restricts the geometryof polypeptides●Proline is much less hydrophobic than the threeamino acids
  13. 13. B. Aromatic R GroupsStructures of the 20 common Amino Acids(Benzyl) (Phenol) (Indol)(260 nm) (280 nm) (280 nm)
  14. 14. C. Sulfur-Containing R GroupsStructures of the 20 common Amino AcidsDisulfide bond
  15. 15. C. Sulfur-Containing R GroupsStructures of the 20 common Amino AcidsNonpolarMethyl thioetherSulfhydryl
  16. 16. D. Side Chains with Alcohol GroupsStructures of the 20 common Amino Acidsα- carbonβ- carbonStereoisomers
  17. 17. E. Basic R GroupsStructures of the 20 common Amino AcidsImidazole ringGuanidiniumion
  18. 18. F. Acidic R Groups and Their Amide DerivativesStructures of the 20 common Amino AcidsAmide
  19. 19. F. Acidic R Groups and Their Amide DerivativesStructures of the 20 common Amino Acids●Aspartate, and glutamate are dicarboxylic amino acidsand have negatively charged hydrophilic side chains at pH 7.●These amino acids are often found on the surface of proteins.●Monosodium glutamate (MSG) is used as a flavor enhancer.●The polar amide groups of these amino acids can form hydrogenbonds with atoms in the side chain of other polar amino acids.
  20. 20. G. The Hydrophobicity of Amino Acids ChainsStructures of the 20 common Amino AcidsHydropathy
  21. 21. Other Amino Acids and Amino Acid Derivatives(GABA)
  22. 22. Other Amino Acids and Amino Acid Derivatives(21stamino acid)(22ndamino acid)
  23. 23. Ionization of Amino Acids
  24. 24. Ionization of Amino Acids
  25. 25. Ionization of Amino Acids
  26. 26. Ionization of Amino Acids
  27. 27. Ionization of Amino Acids
  28. 28. Ionization of Amino Acids
  29. 29. Peptide Bonds link Amino Acids in Proteins
  30. 30. Peptide Bonds link Amino Acids in ProteinsAspartame(aspartylphenylalanine methyl ester)
  31. 31. Protein Purification Techniques●Column chromatography /eluate/●HPLC●Ion-exchange chromatography●Gel-filtration chromatography●Affinity chromatography
  32. 32. Column chromatography /eluate/
  33. 33. Analytical Techniques●Polyacrylamide gel electrophoresis (PAGE)●Mass spectrometry●Electrospray mass spectrometry●Matrix-assisted desorption ionization (MALDI)
  34. 34. Polyacrylamide gel electrophoresis (PAGE)
  35. 35. Matrix-assisted desorption ionization (MALDI)
  36. 36. Matrix-assisted desorption ionization (MALDI)MALDI-TOF
  37. 37. Matrix-assisted desorption ionization (MALDI)
  38. 38. Amino Acids Composition of Proteins▪Peptide bonds of the protein are cleaved by acid hydrolysis using6M HCl.▪Method of amino acid analysis :treatment of the protein hydrolysate with PITC at pH 9.0PTC-amino acid derivativesHPLC (column of fine silica beads+short hydrocarbon chains)Detection at 254 nm (peak absorbance of the PTC moiety)▪1 picomole of a protein that contains about 200 residues▪Glutamate + glutamine Glx or ZAspartate + asparagine Asx or B▪Side chain of Tryptophan is almost destroyed by acid hydrolysis
  39. 39. Amino Acids Composition of ProteinsAcid hydrolysis
  40. 40. Amino Acids Composition of Proteins(phenylisothiocyanate)(phenylthiocarbomyl)
  41. 41. Amino Acids Composition of Proteins
  42. 42. Determing the Sequence of Amino Acid ResiduesEdman degradation procedure
  43. 43. Determing the Sequence of Amino Acid ResiduesEntire procedure can be repeated seriallyusing a sequenator
  44. 44. Determing the Sequence of Amino Acid Residues2-mercaptoethanol
  45. 45. Protein Sequencing Strategies▪Most proteins contain too many residues cleave peptide bondsproteases (trypsin, staphylococcus aureus V8 protease)or certain chemical reagents (BrCN)▪BrCN reacts with Methionine C-terminal homoserine lactoneResidues + new N-terminal residues▪Trypsin carbonyl side of lysine and Arginine residues(positively charged side chains)▪Staphylococcus aureus V8 protease carbonyl side ofglutamate and Aspartate residues (negatively charged side chain)▪Chymotrypsin carbonyl side of uncharged residueswith aromatic or bulky hydrophobic side chains ( Phe, Tyr, Trp)
  46. 46. Protein Sequencing Strategies▪The amino acid sequence of a protein can be deduced fromthe sequence of nucleotides in the corresponding gene.▪A sequence of three nucleotides specifies one amino acid.
  47. 47. Comparisons of the Primary Structures of Proteinsreveal Evolutionary Relationships▪The protein cytochrome c (single polypeptide chain of about104 residues) example of evolution at the molecular level▪Protein sequences from distantly related species aresimilar enough proteins are homologous▪Cytochrome c sequences of humans and chimpanzees areIdentical.
  48. 48. Comparisons of the Primary Structures of Proteinsreveal Evolutionary Relationships

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