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lecture4_print - Protein Structure and Function! Lecture 4:...

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Protein Structure and Function Lecture 4: pH, pKa and pI
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Defnition oF pH and pK a pH is a measure oF the concentration oF H + . ±or a weak acid, The pK a oF an acid is the pH at which it is halF-dissociated. + 10 pH log [H ] = HA ! " ! # ! ! H + + A ! , K a = [H + ][A ! ] [HA] aa pl o g KK =
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Henderson-Hasselbalch equation + 11 [ A ] [H ] [HA] a K = + [A ] log[H ] log [HA] a K = + [A ] pH p a K =+
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Amino acid pK a Amino acid Ionizable group s.c. b.b. NH 3 + b.b. COOH Arginine -NHC(NH 2 ) 2 + 12.5 9.0 1.8 Aspartic Acid -COOH 3.9 10.0 2.0 Cysteine -SH 8.3 10.8 1.8 Glutamic acid -COOH 4.3 9.7 2.2 Histidine ImH + 6.0 9.2 1.8 Lysine -NH3 + 10.5 9.2 2.2 Tyrosine -C 6 H 4 -OH 10.1 9.1 2.2 In a polypeptide, the pK a s may shift about +/- 1 pH unit. In a folded protein, speciFc interactions may shift them even more.
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pKa and environment 2.0 3.9 2.2 4.3 2.2 10.0 9.7 9.2 10.5 Inductive effect COO is electron-donating NH3+ is electron-withdrawing Charge effect + H 3 N OH O OH O + H 3 N O OH OH O + H 3 N OH O NH 3 + CH 3 COOH ClCH 2 COOH Cl 3 COOH 4.8 2.9 0.6
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pKa and resonance forms H 2 N NH 2 + NH + H 2 N NH 2 NH H 2 N NH 2 NH + Arg side chain, pKa = 12.5 OH O - O O O Tyr side chain, pKa = 10.1
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Amides not protonated Amide has delocalized electrons and partial double bond character Same for internal amide bonds in a polypeptide H 3 N N N N N O R1 O R2 O R3 O R4 O R5 O H H H H + + H 3 N OH O NH 2 O + H 3 N OH O NH 2 + - O
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Amino acid pK a Amino acid b.b. NH 3 + b.b. COOH Alanine 9.9 2.3 Asparagine 8.8 2.0 Glutamine 9.1 2.2 Glycine 9.8 2.4 Isoleucine 9.7 2.4 Leucine 9.6 2.4 Methionine 9.1 2.3 Phenylalanine 9.1 1.8 Proline 10.6 2.0 Serine 9.2 2.1 Threonine 10.4 2.6 Tryptophan 9.4 2.4 Valine 9.6 2.3 In a polypeptide, amine pKa ~ 8, COOH pKa ~ 3
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Cyclic peptides HN N N N N R1 O R2 O R3 O R4 O R5 O H H H H H 3 N N N N N O R1 O R2 O R3 O R4 O R5 O H H H H + No free backbone carboxylate or ammonium
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Isoelectric point pI = p K 1 + p K 2 2 pI = pH at which the net charge = 0.
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Isoelectric point pH at which the molecule has no net charge From Biochemical Calculations, Irwin Segel
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Ionization state Group
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This note was uploaded on 10/21/2011 for the course BIOC 450 and 45 taught by Professor Various during the Fall '11 term at McGill.

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lecture4_print - Protein Structure and Function! Lecture 4:...

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