Handbook of Biochemistry and Molecular Biology

1019 Pages·2018·39.42 MB·English

by  Roger L. Lundblad

Handbook of
BIOCHEMISTRY and
MOLECULAR BIOLOGY
Fifth Edition

Handbook of
BIOCHEMISTRY and
MOLECULAR BIOLOGY
Fifth Edition
Edited by
Roger L. Lundblad
Fiona M. Macdonald
CRC Press
Taylor & Francis Group
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Library of Congress Cataloging‑in‑Publication Data
Names: Lundblad, Roger L., editor. | Macdonald, M. (Fiona), 1960- editor.
Title: Handbook of biochemistry and molecular biology / editors, Roger L. Lundblad,
Fiona M. Macdonald.
Description: Fifth edition. | Boca Raton : Taylor & Francis, 2018. | Includes
bibliographical references and index.
Identifiers: LCCN 2017055451 | ISBN 9781138033092 (hardback : alk. paper)
Subjects: | MESH: Biochemical Phenomena | Tables
Classification: LCC QH345 | NLM QU 16 | DDC 572--dc23
LC record available at https://lccn.loc.gov/2017055451
Visit the Taylor & Francis Web site at
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This work is dedicated to the many scientists of the “The Greatest Generation” who
contributed to the base of our knowledge of biochemistry and molecular biology.
Roger L. Lundblad, Ph.D.
Dedicated to James Ivan Yanchak, my husband
Fiona M. Macdonald, Ph.D., F.R.S.C.

TABLE OF CONTENTS
Preface ..................................................................................................................................................................................................................................xi
Acknowledgments ..........................................................................................................................................................................................................xiii
Editors .................................................................................................................................................................................................................................xv
SECTION I: AMINO ACIDS, PEPTIDES, AND PROTEINS
Properties of Amino Acids ...................................................................................................................................................................................2
Data on the Naturally Occurring Amino Acids ..............................................................................................................................................6
Coefficients of Solubility Equations of Certain Amino Acids in Water ...................................................................................................31
Heat Capacities, Absolute Entropies, and Entropies of Formation of Amino Acids and Related Compounds ...............................32
Heat of Combustion, Enthalpy, and Free Energy of Formation of Amino Acids and Related Compounds .....................................34
Solubilities of Amino Acids in Water at Various Temperatures ................................................................................................................36
Heats of Solution of Amino Acids in Aqueous Solution at 25° C ..............................................................................................................37
Free Energies of Solution and Standard Free Energy of Formation of Amino Acids in Aqueous Solution at 25° C ......................39
Far Ultraviolet Absorption Spectra of Amino Acids ....................................................................................................................................40
UV Absorption Characteristics of N-Acetyl Methyl Esters of the Aromatic Amino Acids, Cystine, and of N-Acetylcysteine .......42
Numerical Values of the Absorbances of the Aromatic Amino Acids in Acid, Neutral, and Alkaline Solutions ..........................43
Hydrophobicities of Amino Acids and Proteins ............................................................................................................................................48
Partial Volumes of Amino Acids .......................................................................................................................................................................63
Deamidation of Asparagine ................................................................................................................................................................................66
Michael Reactions of Proteins ............................................................................................................................................................................70
Molecular Weights of Proteins and Some Other Materials Including Sedimentation, Diffusion, and Frictional
Coefficients and Partial Specific Volumes .......................................................................................................................................................74
Molar Absorptivity and A11c%m Values for Proteins at Selected Wavelengths of the Ultraviolet and Visible Region .....................111
Temperature Coefficients of Apparent Partial Specific Volumes of Proteins Expressed in ml/g/deg (dV/dT) .............................225
Protein pK Values ................................................................................................................................................................................................226
Intrinsic Viscosity of Proteins .........................................................................................................................................................................230
Infrared Spectra of Proteins .............................................................................................................................................................................232
Volume Changes for Some Macromolecule Association Reactions ........................................................................................................233
Assay of Solution Protein Concentration .....................................................................................................................................................234
Spectrophotometric Determination of Protein Concentration in the Short-Wavelength Ultraviolet ............................................239
SECTION II: ENZYMES
Turnover of Enzymes in Tissues .....................................................................................................................................................................242
Molecular Turnover of Cytochromes in Animals ......................................................................................................................................246
Matrix Metalloproteinases ...............................................................................................................................................................................247
Proteases in the Interstitial Space ...................................................................................................................................................................259
Enzymes in Synthetic Organic Chemistry ....................................................................................................................................................267
Therapeutic Enzymes .........................................................................................................................................................................................278
Protease Inhibitors and Protease Inhibitor Cocktails ................................................................................................................................282
SECTION III: LIPIDOMICS AND LIPIDOMES
Evolution of the Classification and Nomenclature of Lipids .....................................................................................................................296
A Brief Glossary for Lipidomics .......................................................................................................................................................................297
A Comprehensive Classification System for Lipids .....................................................................................................................................298
Properties of Fatty Acids and Their Methyl Esters......................................................................................................................................322
Densities, Specific Volumes, and Temperature Coefficients of Fatty Acids from C to C ...............................................................324
8 12
Composition and Properties of Common Oils and Fats ............................................................................................................................325
Spectral Properties of Fatty Acids ..................................................................................................................................................................329
IR Active Bands of Phosphatidylethanolamines (PE) .................................................................................................................................336
Concentration of Some Fatty Acids in Human Blood, Blood Plasma or Blood Serum ......................................................................340
Some Unusual Fatty Acid Structures ............................................................................................................................................................346
SECTION IV: VITAMINS AND COENZYMES
Properties of Vitamins .......................................................................................................................................................................................352
Biological Characteristics of Vitamins ..........................................................................................................................................................362
Vitamers ................................................................................................................................................................................................................365
Vitamin Names Discarded................................................................................................................................................................................373
vii
viii Table of Contents
SECTION V: NUCLEIC ACIDS
Some Definitions for Nucleic Acids ...............................................................................................................................................................376
UV Spectral Characteristics and Acidic Dissociation Constants of 280 Alkyl Bases, Nucleosides, and Nucleotides ...............380
Ultraviolet Absorbance of Oligonucleotides Containing 2′-O-Methylpentose Residues ...................................................................387
Spectrophotometric Constants of Ribonucleotides ...................................................................................................................................388
Purines, Pyrimidines, Nucleosides, and Nucleotides: Physical Constants and Spectral Properties ...............................................391
Chemical Modification of Nucleic Acids .......................................................................................................................................................479
Polymerase Chain Reaction ..............................................................................................................................................................................492
Gene Editing ........................................................................................................................................................................................................495
SECTION VI: GLYCOSCIENCE
Nomenclature of Carbohydrates ....................................................................................................................................................................500
Chemical Modification of Carbohydrates .....................................................................................................................................................507
Some Properties of Glycosaminoglycans ......................................................................................................................................................516
Sugar Mimetics ....................................................................................................................................................................................................522
Intrinsic Viscosity of Polysaccharides ............................................................................................................................................................525
SECTION VII: CHEMICAL BIOLOGY AND DRUG DESIGN
Unnatural Amino Acids for Incorporation into Proteins ..........................................................................................................................530
Structures and Symbols for Synthetic Amino Acids Incorporated into Synthetic Polypeptides .....................................................532
Properties of the α-Keto Acid Analogs of Amino Acids ...........................................................................................................................540
α,β-Unsaturated Amino Acids .......................................................................................................................................................................542
Amino Acid Antagonists ..................................................................................................................................................................................543
Particle Diameter ...............................................................................................................................................................................................549
Weights of Cells and Cell Constituents .........................................................................................................................................................550
Click Chemistry ..................................................................................................................................................................................................551
A Listing of Log P Values, Water Solubility, and Molecular Weight for Some Selected Chemicals ................................................555
SECTION VIII: PHYSICAL AND CHEMICAL DATA
IUBMB-IUPAC Joint Commission on Biochemical Nomenclature (JCBN) Recommendations for Nomenclature and
Tables in Biochemical Thermodynamics ......................................................................................................................................................560
Standard Transformed Gibbs Energies of Formation for Biochemical Reactants ...............................................................................572
Enthalpy, Entropy, and Free Energy Values for Biochemical Redox Reactions .....................................................................................575
Oxidation-Reduction Potentials, Absorbance Bands, and Molar Absorbance of Compounds Used in Biochemical Studies .....576
Calorimetric ΔH Values Accompanying Conformational Changes of Macromolecules in Solution ..............................................583
Free Energies of Hydrolysis and Decarboxylation .......................................................................................................................................594
Deci-Normal Solutions of Oxidation and Reduction Reagents ................................................................................................................598
Guidelines for Potentiometric Measurements in Suspensions Part A — The Suspension Effect ......................................................599
Ionization Constants of Acids and Bases .....................................................................................................................................................606
Guidelines for NMR Measurements for Determination of High and Low pK Values ......................................................................647
a
Measurement and Interpretation of Electrokinetic Phenomena ............................................................................................................654
Measurement of pH Definition, Standards, and Procedures ....................................................................................................................682
General Comments on Buffers .........................................................................................................................................................................699
List of Buffers .......................................................................................................................................................................................................701
Brønsted Acidities...............................................................................................................................................................................................713
Buffer Solutions ...................................................................................................................................................................................................714
Amine Buffers Useful for Biological Research .............................................................................................................................................718
Preparation of Buffers for Use in Enzyme Studies ......................................................................................................................................719
Indicators for Volumetric Work and pH Determinations .........................................................................................................................723
Acid and Base Indicators ...................................................................................................................................................................................725
Specific Gravity of Liquids ................................................................................................................................................................................729
Properties of Some Solvents .............................................................................................................................................................................733
Chemicals Commonly Used in Biochemistry and Molecular Biology and their Properties .............................................................737
Common Detergents Used in Biochemical Research .................................................................................................................................797
Some Properties of Detergents and Surfactants Used in Biochemistry and Molecular Biology ......................................................799
Some Biological Stains and Dyes ....................................................................................................................................................................806
Mordant Dyes ......................................................................................................................................................................................................829
Metal Chelating Agents .....................................................................................................................................................................................832
Metallomics: Guidelines for Terminology and Critical Evaluation of Analytical Chemistry Approaches
(IUPAC Technical Report) ...............................................................................................................................................................................840
Water .....................................................................................................................................................................................................................847
General Information on Spectroscopy ..........................................................................................................................................................849
Plastics ...................................................................................................................................................................................................................851
Table of Contents ix
Chemical and Physical Properties of Various Commercial Plastics........................................................................................................857
Chemical Resistance of Plastics .......................................................................................................................................................................858
Generic Source-Based Nomenclature for Polymers ...................................................................................................................................860
Definitions of Terms Relating to Reactions of Polymers and to Functional Polymeric Materials ..................................................866
Definitions of Terms Related to Polymer Blends, Composites, and Multiphase Polymeric Materials ............................................874
Terminology for Biorelated Polymers and Applications (IUPAC Recommendations 2012) .............................................................885
Intrinsic Viscosity of Poly(ethylene glycol) ...................................................................................................................................................901
International Union of Pure and Applied Chemistry ................................................................................................................................903
Organic Name Reactions Useful in Biochemistry and Molecular Biology ............................................................................................917
Brief Guide to the Nomenclature of Inorganic Chemistry ......................................................................................................................944
Properties of Fluorescent Probes Commonly Used for Membrane Studies ..........................................................................................951
Chromatography .................................................................................................................................................................................................953
Blotting Technologies ........................................................................................................................................................................................971
Oxidation of Thiols .............................................................................................................................................................................................973
Partial Volumes for Some Selected Compounds .........................................................................................................................................976
Appendix: Abbreviations and Acronyms ..................................................................................................................................................................979
Index ..................................................................................................................................................................................................................................993