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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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Definition of pH and pK a pH is a measure of the concentration of H + . For 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] a a p log K K =
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Henderson-Hasselbalch equation + 1 1 [A ] [H ] [HA] a K = + [A ] log[H ] log log [HA] a K = + [A ] pH p log [HA] 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, specific 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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