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Amino Acids, Peptides, Protein Primary Structure

Amino Acids, Peptides, Protein Primary Structure. Chapter 3. Amino Acids. Basic struct’l units of prot’s 3 common funct’l grps: -NH 2 , -COOH, -H Indiv aa’s each have diff R grp 4 grps att’d to a C Is this a chiral C? At neutral pH: dipole (zwitterion) Amino grp as NH 3 +

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Amino Acids, Peptides, Protein Primary Structure

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  1. Amino Acids, Peptides, Protein Primary Structure Chapter 3

  2. Amino Acids • Basic struct’l units of prot’s • 3 common funct’l grps: • -NH2, -COOH, -H • Indiv aa’s each have diff R grp • 4 grps att’d to a C • Is this a chiral C? • At neutral pH: dipole (zwitterion) • Amino grp as NH3+ • Carboxyl grp as COO-

  3. Chiral aC, so D,L stereo-isomers • L aa’s polymerize  prot’s

  4. Side chains vary: size, shape, charge, reactivity, H-bond capacity • Five aa groups, based on R grp similarities • Some notes: • Glycine – only optically inactive aa • Cysteine – highly reactive sulfhydryl grp • Histidine – R grp may be proton donor or acceptor at physio pH

  5. 1)Nonpolar w/ aliphatic R grps • Glycine (Gly, G) • Alanine (Ala, A) • Proline (Pro, P) • Valine (Val, V) • Leucine (Leu, L) • Isoleucine (Ile, I) • Methionine (Met, M)

  6. 2) Aromatic R grps • Phenylalanine (Phe, F) • Tyrosine (Tyr, Y) • Tryptophan (Trp, W) • Hydrophobic

  7. 3) Polar w/ uncharged R grps • Serine (Ser, S) • Threonine (Thr, T) • Cysteine (Cys, C) • Asparagine (Asn, N) • Glutamine (Gln, Q)

  8. 4) Polar w/ + charged R grps at physio pH • Lysine (Lys, K) • Histidine (His, H) • Arginine (Arg, R)

  9. 5) Polar w/ - charged R grps at physio pH • Aspartate (Asp, D) • Glutamate (Glu, E)

  10. Cysteine/Cystine • Cys reactive SH grp oxidizes  disulfide bond • Forms cystine • Hydrophobic • Impt to protein 3D structure

  11. Amino Acid Titration Curves • Aa’s – weak acids • Titration curves for each • REMEMBER: Meas D pH as titrate w/ OH-. Plot OH- added on x axis vs. pH on y axis • 2 abstractable H’s, both on grps att’d to a C (bottom p. 81) • Carboxyl grp • Amino grp

  12. 2 inflection pts • Shape of each sim to inflection seen w/ monoprotic acid (Chpt 2) • Each aa has at least 2 pKa’s • At titration midpoint([OH-]=1 eq), cmpd fully dipolar • No net electrical charge • “Isoelectric point” • Isoelectric pH = pI • Each aa has characteristic pI • At any pH<pI, aa has net + charge • At any pH>pI, aa has net - charge

  13. pKa1 <<<< pKa2 • First H+ released: much more easily given up than second H+ • 2 pKa’s = 2 regions of buffering capacity • Aa’s w/ ionizable R grps (lys, arg, his) have 3rd pKa

  14. Peptide Bonds • Link two aa’s •  Dipeptide • Condensation rxn • What mol is removed?? • Endothermic • Stable under physio cond’s • Broken w/ boiling in strong acid/base • a carboxyl of aa1 joined to a amino of aa2 • In cells, bond form’n assisted by ribosomes during translation

  15. Oligopeptide = several aa’s joined by peptide bonds • Polypeptide = many aa’s = small protein • Protein commonly MW > 10,000 • Amino terminus = aa residue w/ free amino grp • Carboxy terminus = aa residue w/ free carboxyl grp

  16. At neutral pH, all peptides have 1 free NH3+ and 1 free COO- • BUT R grps on indiv aa may be ionized •  Characteristic pI for each peptide • Peptide ionization = sum of all R grp charges of aa’s in peptide

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