Handbook of Biochemistry and Molecular Biology Fifth Edition PDF

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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 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2018 by Taylor & Fran...

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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 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2018 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed on acid-free paper International Standard Book Number-13: 978-1-138-03309-2 (Hardback) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged, please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. 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 http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com

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 1% Values for Proteins at Selected Wavelengths of the Ultraviolet and Visible Region .....................111 Molar Absorptivity and A1cm 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 C8 to C12 ...............................................................324 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

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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 pKa Values ...................................................................... 647 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...