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1.008

Hydride, Hydrogen and Proton. 1s. -. Proton. -. -. +. +. +. -. H. 1. 1.008. hydride. -. Hydrogen atom. Juang RH (2004) BCbasics. Proton Is Adsorbed or Desorbed. H +. N. H. N. Amino. H. H. H. High. Low. Low. High. H. O. O. C. Carboxylic. C. H +. O. O.

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1.008

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  1. Hydride, Hydrogen and Proton 1s - Proton - - + + + - H 1 1.008 hydride - Hydrogen atom Juang RH (2004) BCbasics

  2. Proton Is Adsorbed or Desorbed H+ N H N Amino H H H High Low Low High H O O C Carboxylic C H+ O O Proton：abundant and small, affects the charge of a molecule lone pair electrons pKa H+ pKa Ampholytecontains both positive and negative groups on its molecule Juang RH (2004) BCbasics

  3. pK2 ~ 9 R-C-H R-C-H R-C-H NH2H+ NH2 COO- COO- pK1 ~ 2 Acidic environment Neutral environment Alkaline environment NH2H+ COOH 5.5 0 +1 -1 Isoelectric point Juang RH (2004) BCbasics

  4. Amino Acids Have Buffering Effect 12 9 NH2H+ H-C-R 6 COO- pK1 + pK2 2 3 0 pH pK2 ★ pI Isoelectric point = ★ pK1 [OH] → Juang RH (2004) BCbasics

  5. Environment pH vs Protein Charge Buffer pH 10 9 8 7 6 5 4 3 Isoelectric point, pI + 0 - - Net Charge of a Protein Juang RH (2004) BCbasics

  6. pKa of Amino Acid Residues + + + + + + + H+ H+ H+ H+ H+ H+ H+ -COOH -COO- a a -COOH -COO- R R -Imidazole·H+ -Imidazole His His -SH -S- Cys Cys -OH -O- Tyr Tyr -NH3+ -NH2 a a -NH3+ -NH2 R R Residues on amino acids can release or accept protons pKa = 1.8~2.4 pKa = 3.9~4.3 pKa = 6.0 pKa = 8.3 pKa = 10 pKa = 8.8~11 pKa = 10~12.5 Smaller pKa releases proton easier Only His has the residue with a neutral pKa (imidazole) pKa of a carboxylic or amino groups is lower than pKa of the R residues Juang RH (2004) BCbasics

  7. pKa of Amino Acids pH pK1 + pK2 2 [OH-] Amino acids-COOH -NH2 -R Gly G 2.34 9.60 Ala A 2.34 9.69 Val V 2.32 9.62 Leu L 2.36 9.68 Ile I 2.36 9.68 Ser S 2.21 9.15 Thr T 2.63 10.4 Met M 2.28 9.21 Phe F 1.83 9.13 Trp W 2.38 9.39 Asn N 2.02 8.80 Gln Q 2.17 9.13 Pro P 1.99 10.6 Asp D 2.09 9.82 3.86 Glu E 2.19 9.67 4.25 His H 1.82 9.17 6.0 Cys C 1.71 10.8 8.33 Tyr Y 2.20 9.11 10.07 Lys K 2.18 8.95 10.53 Arg R 2.17 9.04 12.48 two pKa pK2 pI pK1 three pKa pK3 ? pK2 ? pI ? pK1 Juang RH (2004) BCbasics

  8. Aspartic acid H HOOC-CH2-C-COOH NH3+ H 2.1 + 3.9 HOOC-CH2-C-COO- 2 NH3+ H H -OOC-CH2-C-COO- -OOC-CH2-C-COO- -2 pK3 NH3+ NH2 -1 pK2 0 pK1 +1 first +1 Isoelectric point is the average of the two pKa flanking the zero net-charged form pK1 = 2.1 second 0 = 3.0 Isoelectric point pK2 = 3.9 -1 third pK3 = 9.8 -2 [OH] Juang RH (2004) BCbasics

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