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Understanding Amino acids: Structures, Significance, and Interactions

Explore the world of amino acids, proteins, and enzymes in this informative guide. Learn about the different types of amino acids, their non-protein significance, and classification based on R groups. Understand the concept of zwitterions, isoelectric point, and chirality. Dive into peptides, polypeptides, and primary structure importance in protein function. Discover the vital role of primary and secondary structures in shaping proteins, including a-helix and b-pleated sheet formations.

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Understanding Amino acids: Structures, Significance, and Interactions

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  1. Chapter 18 Amino Acids,Proteinsand Enzymes

  2. Amino Acids • 20 amino acids; all are α-amino acids:

  3. Essential AA’s Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine Arginine Histidine Non-Essential AA’s Alanine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Proline Serine Tyrosine 20 Amino Acids

  4. Serotonin • Non-protein significance of AA’s • Tryptophan precursor for serotonin, melatonin and niacin Melatonin Tryptophan Niacin • Glycine is a precursor for porphyrins such as heme Glycine Porphyrin Heme B

  5. ‘Non-Protein’ Amino Acids • β-Alanine • Carnosine • β-alanyl-L-histidine • Anserine • β-alanyl-N1-methyl-L-histidine • Glutathione • γ-L-glutamyl-L-cysteinylglycine

  6. Classification of AA R groups(Pg. 549) • Nonpolar Side Chains • Proline: a secondary amine • Methionine: contains S • Tryptophan & Phenylalanine: aromatic rings • Polar, Neutral Side Chains • Cysteine: S-H group • Tyrosine: aromatic ring • Acidic Side Chains • Basic Side Chains

  7. Zwitterions Although -amino acids are commonly written in the un-ionized form, they are more properly written in the zwitterion (internal salt) form. COOH donates H to NH2 • Unionized form doesn’t exist in aqueous soln. or solid state • All have high melting pts • All are soluble in water

  8. Isoelectric Point • Isoelectric point, pI: the pH at which the majority of molecules of a compound in solution have no net charge

  9. Handedness or Chirality “Left Handed” Stereocenter All but one of the AA’s are of the L configuration, which means that their configuration around the central Carbon is similar to that of L-glyceraldehyde.

  10. Enantiomers • Enantiomers (optical isomers): the 2 mirror image forms of a chiral molecule • Same formula but different arrangement • ALL enantiomers are stereoisomers • Same formula, same chemical groups (COOH, NH3, etc.) but different spatial arrangement (like cis-trans) • Enantiomeric pairs differ in effect on polarized light.

  11. Blue represents which atom? Red? White? Grey? Which AA is this? (Note: this is not the zwitterionic form)

  12. Peptides and Polypeptides • Peptide bond - Review • Naming Conventions • Amino end (N-terminal)Carboxyl end (C-Terminal) • ‘yl’ added to name except to C-Terminal AA • Ser-gly-ala not the same as Ala-gly-ser • Primary Structure = AA sequence

  13. Primary Structure • Primary structure: the sequence of amino acids in a polypeptide chain • The number peptides derived from the 20 protein-derived amino acids is enormous • there are 20 x 20 = 400 dipeptides possible • there are 20 x 20 x 20 = 8000 tripeptides possible • the number of peptides possible for a chain of n amino acids is 20n • for a small protein of 60 amino acids, the number of proteins possible is 2060 = 1078, which is possibly greater than the number of atoms in the universe!

  14. Primary Structure • Just how important is the exact amino acid sequence? • human insulin consists of two polypeptide chains having a total of 51 amino acids; the two chains are connected by disulfide bonds • in the table are differences between four types of insulin

  15. 1o Structure Crucial to Function • Hemoglobin and Sickle Cell Anemia • Normal Hb: -Thr-Pro-Glu-Glu-Lys-Ala Position: 4 5 6 7 8 9 • Sickle Cell: -Thr-Pro-Val-Glu-Lys-Ala

  16. Primary Structure • vasopressin and oxytocin are both nonapeptides but have quite different biological functions • vasopressin is an antidiuretic hormone • oxytocin affects contractions of the uterus in childbirth and the muscles of the breast that aid in the secretion of milk

  17. Primary Structure • The ‘linear’ AA sequence • Protein ‘Backbone’ consists of the alpha C, amino N and Carboxyl C. The 6 atoms, from alpha-C to alpha-C are arranged within an imaginary plane. • Important in 2o structure

  18. Shape-Determining Interactions in Proteins • H-bonding along backbone • R-group interactions • H-bonding • Hydrophobic interactions • Salt bridges • Covalent bonds • S-S

  19. Secondary Structure • Secondary structure: conformations of amino acids in localized regions of a polypeptide chain • the most common types of secondary structure are a-helix and b-pleated sheet • a-helix: a type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral • b-pleated sheet: a type of secondary structure in which two polypeptide chains or sections of the same polypeptide chain align parallel to each other; the chains may be parallel or antiparallel Interaction: H-bonding along backbone

  20. a-Helix Grey = C Blue = N Red = O Yellow = R-group White = H Hydrogen bonds are between the C=O of peptide bond and the H-N of another peptide linkage 4 AA’s further along the chain.

  21. b-Pleated Sheet Grey = C Blue = N Red = O Yellow = R-group White = H

  22. Beta-pleated sheet can be parallel or anti-parallel

  23. Fibrous Proteins (water-insoluble) Water Insoluble Secondary Structure determines nature Ex. Alpha-keratins Hair, fingernails, wool Composition of alpha-helixes; multiple strands twist together Ex. Fibroin Silk Composed of b-sheets Fibrous Proteins

  24. Collagen Triple Helix

  25. Tertiary Structure • Overall Conformation of a Peptide chain • How it folds, interactions between various AA’s along the chain. • Determined by interactions of R-groups • Hydrophobic • Salt-bridges • H-bonds • disulfide

  26. Example of a Globular Protein

  27. Myoglobin • Conjugated Globular Protein • Contains a heme group

  28. Quaternary Structure • Quaternary structure: the arrangement of polypeptide chains into a noncovalently bonded aggregation • the individual chains are held in together by hydrogen bonds, salt bridges, and hydrophobic interactions • Hemoglobin • adult hemoglobin: two alpha chains of 141 amino acids each, and two beta chains of 146 amino acids each • each chain surrounds an iron-containing heme unit • fetal hemoglobin: two alpha chains and two gamma chains; fetal hemoglobin has a greater affinity for oxygen than does adult hemoglobin

  29. Hemoglobin

  30. Chemical Properties of Proteins • Hydrolysis – breaking of peptide bonds • By enzymes • By acid • Denaturation – disruption of non-covalent bonds • Heat • Mechanical agitation • Detergents • pH change • Disrupt salt-bridges • Solvents • Disrupt hydrophobic interactions

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