biochemistry

1. Amino Acids, Peptides,
and
Proteins

8. H2O ↔ H+ + OH¯
K = [H+][OH¯] / [H2O]
K = 1.8 x 10-16
1 liter H2O contains 55.56 moles H2O
K[H2O] = [H+][OH¯]
K[H2O] = KW
K[H2O] = 1.8 x 10-16 x 55.56 = 1 x 10-14
KW = [H+][OH¯] = 1 x 10-14

9. H2O ↔ H+ + OH¯
KW = [H+][OH¯] = 1 x 10-14
[H+] = [OH¯]
KW = [H+] [H+] = [H+]2 = 1 x 10-14
[H+] = 1 x 10-7
[H+] = [OH¯] = 1 x 10-7
If [H+] > 1 x 10-7 acidic reaction
If [H+] < 1 x 10-7 basic reaction

10. pX = log 1/ X = – logX
pH = – log [H+]
pH = – log [1 x 10-7] = – (– 7) = 7
If pH = 7 neutral reaction
If pH < 7 acidic reaction
If pH > 7 basic reaction

11. HCOOH Formic Acid
CH3-COOH Acetic Acid
CH3-CH2-COOH Propionic Acid
CH3-CH2-CH2-COOH Butyric Acid
CH3-CH2-CH2-CH2-COOH Valeric Acid
CH3-CH2-CH2-CH2-CH2-COOH Caproic Acid
ε δ γ β α
CH3-CH2-CH2-CH2-CH2-COOH
6 5 4 3 2 1
Monocarboxylic Acids

12. COOH COOH COOH
│ │ │
COOH CH2 CH2
Oxalic Acid │ │
COOH CH2
COOH Malonic Acid │
│ COOH
CH2 Succinic Acid
│
CH2
│
CH2
│
COOH
Glutaric Acid
Dicarboxylic Acids

13. CH3-COOH ↔ H+ + CH3-COO¯
Acid Base
Conjugated Base
(Acetate)
HA ↔ H+ + A¯
Acid Base
NH3 + H2O ↔ NH4
+ + OH¯
Base Acid Acid Base
R-NH2 + H+ ↔ R-NH3
+
Base Acid Acid (Conjugated)

14. HA ↔ H+ + A¯
Ka = [H+][A¯] / [HA]
CH3-COOH ↔ H+ + CH3-COO¯
Ka = [H+][CH3-COO¯] / [CH3-COOH]
Ka (CH3-COOH) = 1.8 x 10-5
pKa = – logKa
pKa(CH3-COOH) = – log 1.8 x 10-5 = – (– 4.74) = 4.74

17. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.2 General structure of the common amino acids.

18. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.8 Absolute configuration of an amino acid.

21. Hydroxyphenyl
OH
Phenyl

22. NH
Indole

27. H2N C NH
NH
Guanidine

28. Imidazole
N NH

29. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.6 Guanidinium and imidazolium groups of arginine and histidine.

34. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.14 Ionic forms of leucine.

35. For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
pH < 2.4
Charge + 1
NaOH (mole) ─

36. pH = pKa + log [A¯] / [HA]
[A¯] – Conjugate Base (-COO¯, or NH2)
[HA] – Conjugate Acid (-COOH, or NH3
+)
For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
After + 0.5 mole NaOH:
1.0 (α-COOH) + 0.5 OH¯ → 0.5 H2O + 0.5 (α-COO¯)
and remained 0.5 (α-COOH)
pH=pKa1 + log [α-COO¯] / [α-COOH] = 2.4 +log [0.5] / [0.5]=
= 2.4 +log1 = 2.4 +0 = 2.4
pH = pKa1 = 2.4

37. For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
pH < 2.4 2.4
Charge + 1 +0.5
NaOH (mole) ─ +0.5

38. pH = pKa + log [A¯] / [HA]
For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
After + 0.5 mole NaOH (total 1.0 mole NaOH):
0.5 (α-COOH) + 0.5 OH¯ → 0.5 H2O + 0.5 (α-COO¯)
and 0 (α-COOH)
Total 1.0 (α-COO¯)
0 (α-COOH)
pH = pKa1 + log [α-COO¯] / [α-COOH] = 2.4 +log [1.0] /[0] =
= 2.4 +? = ?
pH = pI = ?

39. For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
pI
pH < 2.4 2.4 ?
Charge + 1 +0.5 0
NaOH (mole) ─ +0.5 +1.0

40. pH = pKa + log [A¯] / [HA]
For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
After + 0.5 mole NaOH (total 1.5 moles NaOH):
1.0 (α-NH3
+) + 0.5 OH¯ → 0.5 H2O + 0.5 (α-NH2)
and remained 0.5 (α-NH3
+)
pH = pKa2 + log [α-NH2] / [α-NH3
+] = 9.6 +log [0.5] / [0.5] =
= 9.6 +log1 = 9.6 +0 = 9.6
pH = pKa2 = 9.6

41. For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
pI
pH < 2.4 2.4 ? 9.6
Charge + 1 +0.5 0 - 0.5
NaOH (mole) ─ +0.5 +1.0 +1.5

42. pH = pKa + log [A¯] / [HA]
For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
After + 0.5 mole NaOH (total 2.0 mole NaOH):
0.5 (α-NH3
+) + 0.5 OH¯ → 0.5 H2O + 0.5 (α-NH2)
and 0 (α-NH3
+)
Total 1.0 (α-NH2)
0 (α-NH3
+)
pH = pKa2 + log [α-NH2] / [α-NH3
+] = 9.6 +log [1.0] / [0] =
= 9.6 +? = ?
pH > 9.6

43. For Leucine pKa1(α-COOH) = 2.4
pKa2(α-NH3
+) = 9.6
pI
pH < 2.4 2.4 ? 9.6 >9.6
Charge + 1 +0.5 0 - 0.5 - 1
NaOH (mole) ─ +0.5 +1.0 +1.5 +2.0
pI = (pKa1 + pKa2) / 2 = (2.4 + 9.6) / 2 = 6.0

44. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.15 Titration curve of leucine.

46. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.9 Peptide bond formation.

48. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.10 Electronic isomer structures of a peptide bond.

49. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.12 (a) Trans peptide bond. (b) The rare cis peptide bond.

50. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

56. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.69 Edman reaction.

57. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.70 Specificity of some polypeptide cleaving reagents.

58. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.71 Ordering of peptide fragments by overlapping sequences produced by specific
proteolysis of a peptide.

59. Trypsin cleavage fragments:
T1 – Ser-Met-Tyr-Thr-Met-Glu-Pro-Arg
T2 – Phe-Leu-Gly-Val
T3 – Asp-Val-Ile-Lys
Chymotrypsin cleavage fragments:
C1 – Leu-Gly-Val
C2 – Asp-Val-Ile-Lys-Ser-Met-Tyr
C3 – Thr-Met-Glu-Pro-Arg-Phe
T3 – T1 – T2; C2 – C3 – C1
Asp-Val-Ile-Lys-Ser-Met-Tyr-Thr-Met-Glu-Pro-
-Arg-Phe-Leu-Gly-Val

61. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.25 Helix pitch (p) for a helix with n=4.
Reprinted with permission from Dickerson, R. E., and Geis, I. The Structure and Action of Proteins. Menlo Park, CA: Benjamin, 1969, 26.

64. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

65. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

66. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

69. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.31 Tertiary structure of trypsin.

71. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

72. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.41 Derived amino acids in collagen

73. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.42 Diagram of collagen demonstrating the necessity for glycine in every third residue to
allow different chains to be in close proximity in the structure.
Redrawn with permission from Dickerson, R.E., and Geis, I. The Structure and Actions of Proteins. Menlo Park, CA: Benjamin, 1969, 41, 42.

74. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.43 Covalent cross-link formed in collagen through allysine intermediates.

76. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.46 Correspondence of plasma lipoprotein density classes with electrophoretic mobility
in a plasma electrophoresis.
Reprinted with permission from Soutar, A.K., and Myant, N.B. In Offord, R.E. (Ed) Chemistry of Macromolecules, IIB. Baltimore, MD:
University Park, Press, 1979.

77. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.47 Generalized structure of plasma lipoproteins.
Part (a) redrawn from segrest, J.P., et all. Adv Protein Chem. 45:303, 1994; and part (b) redrawn from Schumaker, V.N., et all., Protein Chem.
45: 205, 1994.

78. Figure
Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

79. Figure
Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

80. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 3.49 Examples of glycosidic linkages to amino acids in proteins.

81. Pyrrole
N
H

83. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.20 Structure of heme.

84. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.21 Ligand bonds to ferrous atom in oxyhemoglobin.

87. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.26 Steric hindrance between proximal histidine and porphyrin in deoxyhemoglobin.
Redrawn from Perutz, M. Sci. Am. 239:92, 1978. Copyright (1978) by Scientific American, Inc. All rights reserved.

90. MbO2 ↔ Mb + O2
K = [Mb] [O2] / [MbO2]
[O2] = pO2 , K = [Mb] · pO2 / [MbO2]
Degree of Mb saturation - Y
Y = number of binding sites occupied / total number of
binding sites in solution
Y = [MbO2] / [Mb] + [MbO2]
Y is variable from 0 to 1
when Y = 0.5, pO2 is designated as P50 , and it is constant

91. MbO2 ↔ Mb + O2
K = [Mb] · pO2 / [MbO2]
In equilibrium state P50 = K
P50 = [Mb] · pO2 / [MbO2]
hence [MbO2] = [Mb] · pO2 / P50 (1)
Substitution into Eq. Y = [MbO2] / [Mb] + [MbO2]
of the value of [MbO2] obtained from Eq. (1)
Y = pO2 / P50 + pO2

92. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.24 Oxygen-binding curves for myoglobin and hemoglobin..

93. Figure
Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

94. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.23.
Reprinted with permission from Fersht, A. Enzyme Structure and Mechanism. San Francisco: Freeman, 1977, 12 and 13.

97. Hb(O2)4 ↔ Hb + 4O2
K = [Hb] · (pO2)4 / [Hb(O2)4]
Y = (pO2)4 / (P50)4 + (pO2)4
Hb(O2)n ↔ Hb + nO2
Y = (pO2)n / (P50)n + (pO2)n

98. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.24 Oxygen-binding curves for myoglobin and hemoglobin..

99. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.28 Stick and space-filling diagrams drawn by computer graphics showing movements of residues in
heme environment on transition from deoxyhemoglobin into oxyhemoglobin.
Redrawn with permission from Baldwin, J., and Chothia, C. J. Mol. Biol. 129:175, 1979. Copyright © 1979 by Academic Press, Inc. [London] Ltd.

106. Hb-BPG + 4O2 ↔ Hb(O2)4 + 2,3-BPG

108. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Affinity decreases by actions: high concentrations of 2,3-BPG, CO2, and [H+] – Saturation
curve shift to right

109. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.32

110. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.33

111. Figure
Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.

113. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.2 Diagrammatic structure of IgG.
From Cantor, C. R., and Schimmel, P. R. Biophysical Chemistry, Part I. San Francisco: Freeman, 1980. Reproduced with permission of Mr. Irving
Geis, New York.

114. Textbook of Biochemistry with Clinical Correlations, 7e edited by Thomas M. Devlin © 2011 John Wiley & Sons, Inc.
Figure 9.8

121. Ion exchange chromatography
http://higheredbcs.wiley.com/legacy/college/devlin/047028
1731/animated_figures/fdevprotiensps2.html

123. Gel filtration chromatography
http://higheredbcs.wiley.com/legacy/college/devlin/0470281731/ani
mated_figures/fdevprotiensps3.html