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Amino Acids, Peptides, Protein Primary Structure Chapter 3 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- • Chiral aC, so have D,L stereoisomers – L form aa’s polymer -ize prot’s • 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 • 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) • 2) Aromatic R grps – Phenylalanine (Phe, F) – Tyrosine (Tyr, Y) – Tryptophan (Trp, W) – Hydrophobic • 3) Polar w/ uncharged R grps – – – – – Serine (Ser, S) Threonine (Thr, T) Cysteine (Cys, C) Asparagine (Asn, N) Glutamine (Gln, Q) • 4) Polar w/ + charged R grps at physio pH – Lysine (Lys, K) – Histidine (His, H) – Arginine (Arg, R) • 5) Polar w/ - charged R grps at physio pH – Aspartate (Asp, D) – Glutamate (Glu, E) Cysteine/Cystine • Reactive SH grp of cys oxidizes disulfide bond • Forms cystine – Hydrophobic mol – Impt to protein 3D structure 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 • 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 • 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 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 • 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 • 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