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SECTION 1:AMINO ACIDS, PEPTIDES, AND PROTEINS

Properties of Amino Acids......................................................................................................................................................... 3

Data on the Naturally Occurring Amino Acids......................................................................................................................................................... 7

Structures and Symbols for Synthetic Amino Acids Incorporated into Synthetic Polypeptides............................................................................................................................................ 43

Properties of the a-Keto Acid Analogs of Amino Acids....................................................................................................................................................... 55

a,/3-Unsaturated Amino Acids....................................................................................................................................................... 57

Amino Acid Antagonists.............................................................................................................................................. 59

Coefficients of Solubility Equations of Certain Amino Acids in Water....................................................................................................................................................... 65

Heat Capacities, Absolute Entropies, and Entropies of Formation of Amino Acids and Related Compounds............................................................................................................................................. 67

Heat of Combustion, Enthalpy and Free Energy of Formation of Amino Acids and Related Compounds............................................................................................................................................. 69

Solubilities of Amino Acids in Water at Various Temperatures........................................................................................................................................... 71

pH of solutions of amino acids

Surface Tension of Amino Acids

Partial Specific Volumes of Amino acids

Heats of Solution of Amino Acids in Aqueous Solution at 25C........................................................................................................................................................ 75

Free Energies of Solution and Standard Free Energy of Formation of Amino Acids in Aqueous Solution at 25C........................................................................................................................................................ 77

Introduction to The Optical Properties of Proteins

Far Ultraviolet Absorption Spectra of Amino Acids....................................................................................................................................................... 79

UV Absorption Characteristics of N-Acetyl Methyl Esters of the Aromatic Amino Acids, Cystine

and of N-Acetylcysteine......................................................................................................................................... 81

Numerical Values of the Absorbances of the Aromatic Amino Acids in Acid, Neutral and Alkaline Solutions................................................................................................................................................. 83

Near-infrared spectroscopy of proteins

Raman Spectroscopy of Proteins

Luminescence of the Aromatic Amino Acids....................................................................................................................................................... 89

Luminescence of Derivatives of the Aromatic Amino Acids....................................................................................................................................................... 91

Luminescence of Proteins Lacking Tryptophan.............................................................................................................................................. 93

Luminescence of Proteins Containing Tryptophan.............................................................................................................................................. 95

Hydrophobicities of Amino Acids and Proteins................................................................................................................................................... 99

Chemical Specificity of Reagents for Protein Modification........................................................................................................................................... 115

Reagents for the Chemical Modification of Proteins................................................................................................................................................... 117

Rate Constants for Maleimide Modification of CysteineProtein pK Values.................................................................................................................................................... 137

Protease Inhibitors and Protease Inhibitor Cocktails................................................................................................................................................ 141

Assay of Solution Protein Concentration......................................................................................................................................... 155

Assay of Peptide Concentration

Spectrophotometric Determination of Protein Concentration in the Short-Wavelength Ultraviolet.............................................................................................................................................. 161

Extinction Cofficients for Some Proteins

Protein Fluorescence and Fluorescence Standards

Fluorescence of Tryptophan and Tryptophan Containing Peptides

Fluorescence of Tyrosine and Tyrosine Containing Peptides

Fluorescence of Phenylalanine and Phenylalanine Containing Peptides

Protein Splicing Reactions

Proeteins of Extracellular Matrix

Protein Glycosylation

Fusion Partners for Protein Purification (Protein Tags)

Collagens

Albumin

SECTION 2: ENZYMESE

Enzyme Kinetics

Matrix Metalloproteinase

ADAM and ADAMTS

Therapeutic Enzymes and Chemicallly Moeificd Therapeutic Enzymes (Moved from physical and chemical data)

Thermophilic Proteases

Pyschrotropic Proteases

 

SECTION 3LIPIDOMIC AND LIPIDOMES

A Comprehensive Classification System for Lipids..................................................................................................................................................... 165

Properties of Fatty Acids and Their Methyl Esters..................................................................................................................................................... 189

Densities, Specific Volumes, and Temperature Coefficients of Fatty Acids from C8to C12.......................................................................................................................................................... 191

Composition and Properties of Common Oils and Fats........................................................................................................................................................ 193

Androgens.............................................................................................................................................. 199

Bile Acids..................................................................................................................................................... 201

Corticoids.............................................................................................................................................. 203

Estrogens............................................................................................................................................... 205

Progestogens.......................................................................................................................................... 207

Sterols.................................................................................................................................................... 209

Prostaglandins and Related Fatty-Acid Derived Materials................................................................................................................................................ 221

Lipidomes and Lipodomics

Lipid Composition of Membranes

Lipid Composition of Brain

Raman Spectroscopy of Lipids

SECTION 4: VITAMINS AND COENZYMES

Properties of Vitamins................................................................................................................................................ 225

Biological Characteristics of Vitamins................................................................................................................................................ 237

Properties for Ascorbic Acid and Ascorbate-2-Sulfate................................................................................................................................................... 241

Vitamers................................................................................................................................................ 243

Vitamin Names Discarded.............................................................................................................................................. 251

Spectral Analysis of Viitamins

 

 

SECTION 5: METABOLOMICS

Metabolic Pathways.....................................................................................................................................................

State State Metabolite Concentrations............................................................................................................................................

Perturbation of metabolite Concentrations............................................................................................................................................

 

SECTION 6: NUCLEIC ACIDS

UV Spectral Characteristics and Acidic Dissociation Constants of 280 Alkyl Bases, Nucleosides,

and Nudeotides............................................................................................................................................ 255

Ultraviolet Absorbance of Oligonucleotides Containing 2'-0-Methylpentose Residues .............................................................................................................................................................. 263

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Spectrophotometric Constants of Ribonucleotides................................................................................................................................... 265

Purines, Pyrimidines, Nucleosides, and Nucleotides: Physical Constants and Spectral Properties............................................................................................................................................. 269

Chemical Modification of Nucleic Acids.................................................................................................................................................... 359

Transfection Technologies......................................................................................................................................... 373

DNA Sequence Methods

Some Commonly Used Nucleases

Determination of Oligonucleotide ConcentrationList of Data Bases for Nucleic Acid Research

RNA aptamers used for purification of RNA-protein complexes

Fluorophore-aptamer tags

Specificity of Restriction Endonucleases

DNA melting analysis

Extracellular Nucleic Acids

Classifications of Histones

SECTION 7: GLYCOSCIENCE

Introduction to Carbohydrates...................................................................................................................................... 383

Natural Alditols, Inositols, Inososes, and Amino Alditols and Inosamines........................................................................................................................................... 407

Natural Acids of Carbohydrate Derivation............................................................................................................................................ 417

Natural Aldoses................................................................................................................................................ 431

Natural Ketoses................................................................................................................................................ 457

Carbohydrate Phosphate Esters................................................................................................................................................... 473

The Naturally Occurring Amino Sugars.................................................................................................................................................. 491

Oligosaccharides (Including Disaccharides)...................................................................................................................................... 499

Mucopolysaccharides (Glycosaminoglycans).......................................................................................................................... 533

Chemical Modification of Carbojydrates

Methods for Determination of Polysacharide Concentration

Viscosity of Glycosaminoglycans

Advanced Glycation End Products

Glycomics

Heparin Sulfate Binding Proteins

Physical properties of Hyaluronan

SECTION 8: CHEMICAL BIOLOGY

Affinity Reagents for Protein Modification

Activity-Based Probes and Activity-Based Profiling ...................................................................................................................................................................

Bioorthogonal Modification ...................................................................................................................................................................

Click Chemistry

Protein Staplng

Unnatural Amino Acids for Incorporation into Proteins................................................................................................................................................... 53

Stapled Peptides

Mtabolic Labeling

Ligand-Directed Tosyl Chemistry

SECTION 9: PHYSICAL AND CHEMICAL DATA

Recommendations for Nomenclature and Tables in Biochemical Thermodynamics.................................................................................................................................. 537

Standard Transformed Gibbs Energies of Formation for Biochemical Reactants............................................................................................................................................. 551

Enthalpy, Entropy, and Free Energy Values for Biochemical Redox Reactions............................................................................................................................................. 555

Oxidation-Reduction Potentials, Absorbance Bands and Molar Absorbance of Compounds Used

in Biochemical Studies................................................................................................................................................. 557

Calorimetric AH Values Accompanying Conformational Changes of Macromolecules in Solution................................................................................................................................................ 565

Oxidation-Reduction Potential Indicators

Differential Scanning Calorimetry

Isothermal Calorimetry and Enzyme Kinetics

Buffer Effects in Isothermal Calorimetry

Reagents for Electron Paramagnetic Resonance

Reactive Oxygen Species

Reaciive Nitrogen Species

Free Energies of Hydrolysis and Decarboxylation.................................................................................................................................. 579

Deci-Normal Solutions of Oxidation and Reduction Reagents.............................................................................................................................................. 585

Guidelines for Potentiometric Measurements in Suspensions Part A. The Suspension Effect................................................................................................................................................... 587

Ionization Constants of Acids and Bases.................................................................................................................................................... 595

Guidelines for NMR Measurements for Determination of High and Low pK.Values............................................................................................................................................ 637

Measurement and Interpretation of Electrokinetic Phenomena.......................................................................................................................................... 645

Measurement of pH Definition, Standards, and Procedures........................................................................................................................................... 675

General Comments on Buffers (Revise)............................................................................................................................................... 693

List of Buffers (Add more recent references ............................................................................................................................................................. 695

Br0nsted Acidities (Revise )........................................................................................................................................................... 707

Measurement of pH....................................................................................................................................................... 709

Buffer Solutions............................................................................................................................................. 715

Amine Buffers Useful for Biological Research............................................................................................................................................... 719

Preparation of Buffers for Use in Enzyme Studies................................................................................................................................................ 721

Buffer for Acrylamide Gels (Single-Gel Systems).............................................................................................................................................. 725

Buffer for Acrylamide Gels with More Than One Layer................................................................................................................................................... 726

Starch Gels..................................................................................................................................................... 729

Indicators for Volumetric Work and pH Determinations.................................................................................................................................... 731

Acid and Base Indicators............................................................................................................................................ 735

Specific Gravity of Liquids (Add second table with alphabitized list of 50 commonly used liquids ............................................................................................................................................................ 739

Viscosity and Density Tables.................................................................................................................................................. 743

A Listing of Log P Values, Water Solubility, and Molecular Weight for Some Selected Chemicals............................................................................................................................................ 747

Chemicals Commonly Used in Biochemistry and Molecular Biology and Their Properties............................................................................................................................................ 751

Common Detergents Used in Biochemical Research.............................................................................................................................................. 811

Some Properties of Detergents and Surfactants Used in Biochemistry and Molecular Biology................................................................................................................................................ 813

Some Biological Stains and Dyes..................................................................................................................................................... 819

Mordant Dyes.................................................................................................................................................... 843

Metal Chelating Agents................................................................................................................................................. 847

Stability Constants of some complexing agents

Formation of complexes between metabolites and divalent cations

Binding of Metal Ions to Biological Polymers

Water.................................................................................................................................................. 855

Stability of Solutions for GLP and cGMP Use...................................................................................................................................................... 857

General Information on Spectroscopy....................................................................................................................................... 859

Near-Infrared Spectroscopy for tissues

Microplates........................................................................................................................................... 861

Plastics................................................................................................................................................. 863

Chemical and Physical Properties of Various Commercial Plastics................................................................................................................................................ 869

Generic Source-Based Nomenclature for Polymers............................................................................................................................................. 871

Definitions of Terms Relating to Reactions of Polymers and to Functional Polymeric Materials............................................................................................................................................. 877

Definitions of Terms Related to Polymer Blends, Composites, and Multiphase Polymeric Materials............................................................................................................................................. 887

Organic Name Reactions Useful in Biochemistry and Molecular Biology............................................................................................................................................... 899

Enzymes in Synthetic Organic Chemistry........................................................................................................................................... 927


Table of Contents ix

Weights of Cells and Cell Constituents........................................................................................................................................... 943

Particle Diameter................................................................................................................................................ 945

Ion-Exchange Matrices

Hydrophobic Affinity Matrices

Appendix A: Abbreviations and Acronyms........................................................................................................................................................ 947

Appendix B: Glossary of Terms Useful in Biochemistry................................................................................................................................................... 959

Index............................................................................................................................................................. 1075


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