Amino Acids, Peptides, Protein Primary Structure

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

2. Amino Acids • Basic structural units of proteins • All have 3 common functional grps: • -NH2, -COOH, -H • Individual aa’s each have diff R grp • These 4 grps att’d to a C • Is this a chiral C? • At neutral pH, exist as dipole (zwitterion) • Amino grp as NH3+ • Carboxyl grp as COO-

5. Chiral aC, so have D,L stereo-isomers • L form aa’s polymer-ize  prot’s

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

7. 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)

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

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

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

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

14. Cysteine/Cystine • Reactive SH grp of cys oxidizes  disulfide bond • Forms cystine • Hydrophobic mol • Impt to protein 3D structure

15. Amino Acid Titration Curves • Aa’s – weak acids • Construct titration curves for each • REMEMBER: Add OH-, measuring change in pH as titrate w/ OH-. Plot OH- added on x axis vs. pH on y axis • Have 2 abstractable H’s, both on grps att’d to a C (bottom p. 81) • One on carboxyl grp • One on amino grp

16. 2 inflection pts • Shape of each inflection sim to inflection seen w/ monoprotic acid (Chpt 2) • Each aa has 2 pKa’s • At midpoint of titration ([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

18. pKa1 <<<< pKa2 • First H+ released from aa is 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

21. Peptide Bonds • Links two aa’s •  Dipeptide • Condensation rxn; H2O removed • Endothermic rxn • Stable under physio cond’s; broken w/ boiling in strong acid/base • a carboxyl of aa1 joined to a amino of aa2 • In living systems, peptide bond form’n assisted by ribosomes in translation process

23. Oligopeptide = several aa’s joined by peptide bonds • Polypeptide = many aa’s = small protein • Protein commonly MW > 10,000 • Aa residue of peptide w/ free amino grp called amino terminus • Aa residue of peptide w/ free carboxyl grp = carboxy terminus

25. At neutral pH, peptides have 1 free NH3+ and 1 free COO- • BUT R grps on each aa may be ionized • Each peptide has characteristic pI • Peptide ionization = sum of all R grp charges of aa’s which make up the peptide