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 Handbook
of
Biochemistry
and
Molecular Biology
 Handb ook
of
Bioche mistry
and
Molecu lar Biology
3rd Edition
Proteins -Volume I
EDITOR
Gerald D. Fasn1an, Ph. D.
Rosenfield Professor of Biochemistry
Graduate Department of Biochemistry
Brandeis University
Waltham, Massachusetts

Boca Raton London New York

CRC Press is an imprint of the

Taylor & Francis Group, an informa business
 First published 1976 by CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742

Reissued 2018 by CRC Press

© 1976 by CRC Press, Inc.

©1970, 1968 by The Chemical Rubber Co.
CRC Press is an imprint of Taylor & Francis Group, an Informa business

No claim to original U.S. Government works

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
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 Handbook
of
Biochemistry
and
Molecular Biology
3rd Edition

Proteins

Volume I

Editor
Gerald D. Fasman, Ph. D.
Rosenfield Professor of Biochemistry
Graduate Department of Biochemistry
Brandeis University
Waltham, Massachusetts

The following is a list of the four major sections of the Handbook,

each consisting of one or more volumes

Ptoteins - Amino Acids, Peptides, Polypeptides, and Proteins

Nucleic, Acids — Purines, Pyrimidines, Nucleotides, Oligonucleotides,

tRNA, DNA, RNA

Lipids, Carbohydrates, Steroids

Physical and Chemical Data, Miscellaneous - Ion Exchange, Chromatog­

raphy, Buffers, Miscellaneous, e.g., Vitamins
 ADVISORY BOARD

Gerald D. Fasman
Editor

Herbert A. Sober (deceased)

Consulting Editor

MEMBERS

Bruce Ames Victor Ginsburg

Professor, Department of Biochemistry Chief, Biochemistry Section, National
University of California Institute of Arthritis, Metabolism and
Berkeley, California 94720 Digestive Diseases
Department of Health, Education, and
Sherman Beychok Welfare
Professor, Department of Biological National Institutes of Health
Sciences Bethesda, Maryland 20014
Columbia University
New York, New York 10027
Walter Gratzer
Waldo E. Cohn MRC Neurobiology Unit
Senior Biochemist, Biology Division Department of Biophysics
Oak Ridge National Laboratory Kings College
Oak Ridge, Tennessee 37830 University of London
London
England
Harold Edelhoch
National Institute Arthritis, Metabolism
and Digestive Diseases Lawrence Grossman
Department of Health, Education, and Professor, Department of Biochemical and
Welfare Biophysical Sciences
National Institutes of Health School of Hygiene and Public Health
Bethesda, Maryland 20014 The Johns Hopkins University
Baltimore, Maryland 21205
John Edsall
Professor Emeritus, Biological Laboratories Frank Gurd
Harvard University Professor, Department of Chemistry
Cambridge, Massachusetts 02138 Indiana University
Bloomington, Indiana 47401
Gary Felsenfeld
Chief, Physical Chemistry Laboratory
Laboratory of Molecular Biology William Harrington
National Institute of Arthritis, Professor, Department of Biology
Metabolism, and Digestive Diseases The Johns Hopkins University
National Institutes Of Health Baltimore, Maryland 21218
Bethesda, Maryland 20014
William P. Jencks
Edmond H. Fischer Professor, Graduate Department of
Professor, Department of Biochemistry Biochemistry
University of Washington Brandeis University
Seattle, Washington 98195 Waltham, Massachusetts 02154
 ADVISORY BOARD (continued)

0 . L. Kline Julius Marmur

Executive Officer Professor, Department of Biochemistry
American Institute of Nutrition and Genetics
9650 Rockville Pike Albert Einstein College of Medicine
Bethesda, Maryland 20014 New York, New York 10461

1. M. Klotz
Alton Meister
Professor, Department of Chemistry
Professor, Department of Biochemistry
Northwestern University
Cornell University Medical College
Evanston, Illinois 60201
New York, New York 10021

Robert Langridge
Professor, Department of Biochemistry Kivie Moldave
Princeton University Professor, Department of Biochemistry
Princeton, New Jersey 08540 California College of Medicine
University of California
Philip Leder Irvine, California 92664
Chief, Laboratory of Molecular Genetics
National Institute of Child Health D. C. Phillips
and Human Development Professor, Laboratory of Molecular
National Institutes of Health Biophysics
Bethesda, Maryland 20014 Department of Zoology
Oxford University
I. Robert Lehman Oxford
Professor, Department Biochemistry England
School of Medicine
Stanford University William D. Phillips
Stanford, California 94305 The Lord Rank Research Centre
Ranks Hove, McDougall Ltd.
Lawrence Levine Lincoln Road, High Wycombe
Professor, Graduate Department of Bucks
Biochemistry England
Brandeis University
Waltham, Massachusetts 02154
G. N. Ramachandran
John Lowenstein Professor, Molecular Biophysics Unit
Professor, Graduate Department of Indian Institute of Science
Biochemistry Bangalore
Brandeis University India
Waltham, Massachusetts 02154
Michael Sela
Emanuel Margoliash Professor, Department of Chemical
Professor, Department of Biological Immunology
Sciences The Weizmann Institute of Science
Northwestern University Rehovot
Evanston, Illinois 60201 Israel
 ADVISORY BOARD (continued)
Waclaw Szybalski
Professor, McArdle Laboratory for
Cancer Research
The University of Wisconsin
Madison, Wisconsin, 53706
Serge N. Timasheff
Professor, Graduate Department of
Biochemistry
Brandeis University
Waltham, Massachusetts 02154
Ignacio Tinoco, Jr.
Professor, Department of Chemistry
University of California
Berkeley, California 94720
Bert L. Valiee
Professor, Biophysics Research
Laboratory
Peter Bent Brigham Hosoital
Harvard Medical School
Boston, Massachusetts 02115
 PREFACE

The rapid pace at which new data is currently accumulated in science presents one of
the significant problems of today — the problem of rapid retrieval of information. The
fields of biochemistry and molecular biology are two areas in which the information
explosion is manifest. Such data is of interest in the disciplines of medicine, modern
biology, genetics, immunology, biophysics, etc., to name but a few related areas. It was
this need which first prompted CRC Press, with Dr. Herbert A. Sober as Editor, to
publish the first two editions of a modern Handbook o f Biochemistry, which made
available unique, in depth compilations of critically evaluated data to graduate students,
post-doctoral fellows, and research workers in selected areas of biochemistry.
This third edition of the Handbook demonstrates the wealth of new information
which has become available since 1970. The title has been changed to include molecular
biology; as the fields of biochemistry and molecular biology exist today, it becomes more
difficult to differentiate between them. As a result of this philosophy, this edition has
been greatly expanded. Also, previous data has been revised and obsolete material has
been eliminated. As before, however, all areas of interest have not been covered in this
edition. Elementary data, readily available elsewhere, has not been included. We have
attempted to stress the areas of today’s principal research frontiers and consequently
certain areas of important biochemical interest are relatively neglected, but hopefully not
totally ignored.
This third edition is over double the size of the second edition. Tables used from the
second edition without change are so marked, but their number is small. Most of the
tables from the second edition have been extensively revised, and over half of the data is
new material. In addition, a far more extensive index has been compiled to facilitate the
use of the Handbook. To make more facile use of the Handbook because of the increased
size, it has been divided into four sections. Each section will have one or more volumes.
The four sections are titled:

Proteins —Amino Acids, Peptides, Polypeptides, and Proteins

Nucleic Acids — Purines, Pyrimidines, Nucleotides, Oligonucleotides, tRNA, DNA,
RNA
Lipids, Carbohydrates, Steroids
Physical and Chemical Data, Miscellaneous - Ion Exchange, Chromatography,
Buffers, Miscellaneous, e.g., Vitamins

By means of this division of the data, we can continuously update the Handbook by
publishing new data as they become available.
The Editor wishes to thank the numerous contributors, Dr. Herbert A. Sober, who
assisted the Editor generously, and the Advisory Board for their counsel and cooperation.
Without their efforts this edition would not have been possible. Special acknowledgments
are due to the editorial staff of CRC Press, Inc., particularly Ms. Susan Cubar Benovich,
Ms. Sandy Pearlman, and Mrs. Gayle Tavens, for their perspicacity and invaluable assistance
in the editing of the manuscript. The editor alone, however, is responsible for the
scope and the organization of the tables.
We invite comments and criticisms regarding format and selection of subject matter, as
well as specific suggestions for new data (and their sources) which might be included in
subsequent editions. We hope that errors and omissions in the data that appear in the
Handbook will be brought to the attention of the Editor and the publisher.

Gerald D. Fasman
Editor
August 1975
 PR E F A C E TO AM INO ACID S, PEPT ID E S, PO LY PEPTID ES, AND
P R O T E IN S , VOLU M E I

The section of the Handbook o f Biochemistry and Molecular Biology on Amino acids,
Peptides, Polypeptides and Proteins is divided into three volumes. The first volume
contains information relating to the naturally occurring amino acids, a, /3-unsaturated
amino acids, amino acid antagonists, and a-keto analogues of amino acids.
Data on ultraviolet absorption, fluorescence, optical rotatory dispersion and circular
dichroism of amino acids and their derivatives are contained herein.
Relevant data on peptide synthesize is included: Amino acid derivatives, preparation
of sequential polypeptides, solid state synthesize, and poly-a-amino acids.
The second and third volumes will contain material mainly on proteins.
Although the data, for which the editor alone is responsible, are far from complete,
it is hoped these volumes will be of assistance to those working in the field of biochemistry
and molecular biology.

Ge rald D. F asm an
Editor
January 1976
 THE EDITOR

Gerald D. Fasman, Ph.D., is the Rosenfield Professor o f Biochemistry, Graduate

Department of Chemistry, Brandeis University, Waltham, Massachusetts.
Dr. Fasman graduated from the University of Alberta in 1948 with a B.S. Honors
Degree in Chemistry, and he received his Ph.D. in Organic Chemistry in 1952 from the
California Institute of Technology, Pasadena, California. Dr. Fasman did postdoctoral
studies at Cambridge University, England, Eidg. Technische Hochschule, Zurich,
Switzerland, and the Weizmann Institute of Science, Rehovoth, Israel. Prior to moving to
Brandeis University, he spent several years at the Children’s Cancer Research Foundation
at the Harvard Medical School. He has been an Established Investigator of the American
Heart Association, a National Science Foundation Senior Postdoctoral Fellow in Japan,
and recently was a John Simon Guggenheim Fellow.
Dr. Fasman is a member of the American Chemical Society, a Fellow of the American
Association for the Advancement of Science, Sigma Xi, The Biophysical Society,
American Society of Biological Chemists, The Chemical Society (London), the New York
Academy of Science, and a Fellow of the American Institute of Chemists. He has
published 180 research papers.
The Editor and CRC Press, Inc. would like to dedicate this
third edition to the memory of Eva K. and Herbert A.
Sober. Their pioneering work on the development of the
Handbook is acknowledged with sincere appreciation.
 TA B LE O F C O N TEN TS

NOMENCLATURE
Biochemical Nomenclature........................................................................................................................... 3
Nomenclature of Labeled Compounds........................................................................................................16
The Citation of Bibliographic References in Biochemical Journals........................................................ 17
1UPAC Tentative Rules for the Nomenclature of Organic Chemistry Section E.
Fundamental Stereochemistry...............................................................................................................21
Abbreviations and Symbols for the Description of the Conformation of Polypeptide Chains
Tentative Rules (1969)............................................................................................................................59
A One-letter Notation for Amino Acid Sequences Tentative R u le s ....................................: ............ 75
Symbols for Amino Acid Derivatives and Peptides Recommendations (1971).................................... 79
Abbreviated Nomenclature of Synthetic Polypeptides (Polymerized Amino Acids)
Revised Recommendations (1 9 7 1 )....................................................................................................... 91
Structures and Symbols for Synthetic Amino Acids Incorporated into Synthetic Polypeptides. . . .96

AMINO ACIDS
Data on the Naturally Occurring Amino A c id s.................................................................................... I l l
a,j3-Unsaturated Amino A c id s.................................................................................................................. 175
Amino Acid Antagonists.............................................................................................................................177
Properties of the a-Keto Acids Analogues of Amino Acids.................................................................... 181
Far Ultraviolet Absorption Spectra of Amino Acids...............................................................................183
UV Absorption Characteristics of W-Acetyl Methyl Esters of the Aromatic Amino Acids, Cystine,
and TV-Acetylcysteine.............................................................................................................................186
Numerical Values of the Absorbances of the Aromatic Amino Acids in Acid, Neutral and
Alkaline Solutions..................................................................................................................................187
Ultraviolet Spectra of Derivatives of Cysteine, Cystine, Histidine, Phenylalanine, Tyrosine, and
T ryptophan............................................................................................................................................ 192
Luminescence of the Aromatic Amino A c id s ........................................................................................ 200
Luminescence of Derivatives of the Aromatic Amino Acids................................................................. 201
Luminescence of Proteins Lacking Tryptophan...................................................................................... 204
Luminescence of Proteins Containing Tryptophan.................................................................................205
Covalent Protein Conjugates.................................................................................................................... 208
Hydrophobicities of Amino Acids and Proteins......................................................................................209
Specific Rotatory Dispersion Constants for 0.1 M Amino Acid Solutions.........................................244
Circular Dichroism (CD) Spectra of Metal Complexes of Amino Acids and Peptides....................... 245
Errors of Amino Acid M etabolism .......................................................................................................... 317
Errors of Organic Acid Metabolism.......................................................................................................... 326
Free Amino Acids in Amniotic Fluid in Early Pregnancy (13 to 18 Weeks) and at T e rm ............... 327
Free Amino Acids in Blood Plasma of Newborn Infants and Adults................................................... 328

PEPTIDES AND POLYPEPTIDES

A List of Sequential Polypeptides, Their Method of Preparation and Product Analysis..................331
Peptides Prepared by Solid Phase Peptide Synthesis.............................................................................. 374
Poly (a-Amino Acids), Their Solubility and Susceptibility to Enzymatic Activities......................... 393

INDEX 401
Nomenclature
 3

BIOCHEMICAL NOMENCLATURE

This synopsis of the recommendations of the IUPAC-IUB Commission on Biochemical

Nomenclature (CBN) was prepared by Waldo E. Cohn, Director, NAS-NRC Office of
Biochemical Nomenclature (OBN, located at Biology Division, Oak Ridge National
Laboratory, Oak Ridge, TN 37830), from whom reprints of the CBN publications listed
below and on which the synopsis is based are available.
The synopsis is divided into three sections: Abbreviations, symbols, and trivial names.
Each section contains material drawn from the documents (A 1 to C l, inclusive) listed
below, which deal with the subjects named.
Additions consonant with the CBN Recommendations have been made by OBN
throughout the synopsis.

RULES AND RECOMMENDATIONS AFFECTING BIOCHEMICAL NOMENCLATURE

AND PLACES OF PUBLICATION (AS OF FEBRUARY 1975)

I. IUPAC-IUB Commission on Biochemical Nomenclature

A l. Abbreviations and Symbols [General; Section 5 replaced by A6 ]
A2. Abbreviated Designation o f Amino-acid Derivatives and Peptides (1965) [Revised 1971; Expands Section 2
of A ll
A3. Synthetic M odifications o f Natural Peptides (1966) [ Revised 1972]
A4. Synthetic Polypeptides (Polymerized Amino Acids) (1967) [Revised 1971 ]
A5. A One-letter Notation for Amino-acid Sequences (1968)
A6. Nucleic Acids, Polynucleotides, and their Constituents (1970)

B1. (Nomenclature o f Vitamins, Coenzymes, and Related Compounds)

a. Miscellaneous [A, B’s, C, D’s, tocols, niacins; see B2 and B3]
b. Quinones with Isoprenoid Side-chains: E, K, Q [Revised 1973]
c. Folic Acid and Related Compounds
d. Corrinoids: B-12’s [Revised 1973]
B2. Vitamins B-6 and Related Compounds [Revised 1973]
B3. Tocopherols (1973)

C l. Nomenclature o f Lipids (1967) [Amended 1970; see also II, 2]

C2. Nomenclature o f a-Amino Acids (1974) [See also II, 5]

D l. Conformation o f Polypeptide Chains (1970) [See also III, 2]

E l. Enzyme Nomenclature (1972) a [Elsevier (in paperback); Replaces 1965 edition.]

E2. Multiple Forms o f Enzymes (1971) [Chapter 3 o f E l ]
E3. Nomenclature o f Iron-sulfur Proteins (1973) [Chapter 6.5 o f E l ]
E4. Nomenclature o f Peptide Hormones (1974)

II. Documents Jointly Authored by CBN and CNOC [See III]

1. Nomenclature o f Cyclitols (1968) [Revised 1973]
2. Nomenclature o f Steroids (1968) [Amended 1971; Revised 1972]
3. Nomenclature o f Carbohydrates-I (1969)
4. Nomenclature o f Carotenoids (1972) [Revised 1975]
5. Nomenclature o f a-Amino Acids (1974) [Listed under I, C2 in the following table]

III. IUPAC Commission on the Nomenclature o f Organic Chemistry (CNOC)

1. Section A (Hydrocarbons), Section B (Heterocyclics): J. Am . Chem. Soc., 82, 5545; a Section C (Groups
containing N, Hal, S, Se/Te): Pure Appl. Chem., 11, Nos. l - 2 a [A, B, and C Revised 1969:a Butterworth’s,
London (1971)]
2. Section E (Stereochemistry):15 J. Org. Chem., 35, 2489 (1970); Biochim. Biophys. Acta, 2 0 8 ,1 (1970); Eur.
J. Biochem., 1 8 ,1 5 1 (1970) [See also I, D l]

aNo reprints available from OBN; order from publisher.

^ Reprints available from OBN (in addition to all in IA to ID and II).
4 Handbook o f Biochemistry and Molecular Biology

RULES AND RECOMMENDATIONS AFFECTING BIOCHEMICAL NOMENCLATURE

AND PLACES OF PUBLICATION (AS OF FEBRUARY 1975)(continued)

IV. Physiochemical Quantities and Units (IUPAC)a J. Am. Chem. Soc., 82, 5517 (1960) [Revised 1970: Pure Appl.
Chem., 21, 1 (1970)]

V. Nomenclature of Inorganic Chemistry (IUPAC)/. Am. Chem. Soc., 82, 5523a [Revised 1971: Pure Appl. Chem.,
28, No. 1 (1971)] a
VI. Drugs and Related Compounds or Preparations
1. U.S. Adopted Names (USAN) No. 10 (1972) and Supplement [U.S. Pharmacopeial Convention, Inc., 12601
Twinbrook Parkway, Rockville, Md.]
2. International Nonproprietary Names (INN) [WHO, Geneva]
 CBN RECOMMENDATIONS APPEAR IN THE FOLLOWING PLACES*

Arch. Biochim.
Biochem. Biophys. Eur. J. J. Biol. Pure Appl. Biochimie Afolek. Z. Phys.
Biophys. Biochem. J. Biochemistry Acta Biochem. Chem. ChemA (Bull. Soc.)c BiolA Chem.e

A lf 136,1 101,1 5,1445 1,259 241,527 50,3 1,872 348,245

A2(Revised) 150,1(R) 126,773(R) 11,1726(R) 263,205(R) 27,201(R) 247,977(R) 40,(R) 49,121 * 2,282 * 348,256 *
A 3 (Revised) 121,6 * 104,17* 6,362 * 133,1* 1,379* 242,555 * 31,649(R) 49,325 * 2,466 * 348,262 *
A4(Revised)g 151,597(R) 127,753(R) 11,942(R) 278,211(R) 26,301(R) 247,323(R) 33,439(R) 51,205 * 5,492(R) 349,1013 *
A5 125(3),i 113,1 7,2703 168,6 5,151 243,3557 31,641 50,1577 3,473 350,793
A6h 145,425 120,449 9,4022 247,1 15,203 245,5171 40, 6,167 351,1055

B l* 118,505 102,15 1 07,l(a—c) 2,1 241,2987 49,331 348,266

B lb( Revised) 165.1(R) 147,15(R) 387,397(R) 53,15(R) 38,439
Bld( Revised) 161(2),iii(R) 147,1(R) 13,1555(R) 45,7(R)
B2( Revised) 162,1(R) 137,417(R) 13,1056(R) 354,155(R) 40,325(R) 245,4229 * 33,447(R) 351,1165*
B3(Revised) 165,6(R) 147,11(R) 46,217(R)

c if 123,409 105,897 6,3287 152,1 2,127 242,4845 50,1363 2,784 350,279

Amendments 116(5) 202,404 12,1 245,1511
C2 14,449 53,1

Dl* 145,405 121,577 9,3471 229,1 17,193 245,6489 7,289

E2 147,1 126,769 10,4825 258,1 24,1 246,6127 54,123 353,852

E3 160,355 135,5 12,3582 310,295 35,1 248,5907
E4 151,1 14,2559 250,3215

II,I(Revised) 128,269 * 112,17* 165,1* 5,1* 243,5809 * 37,285(R) 51,3 * 350,523*

II, 2f 136,13 113,5 8,2227 164,453 10,1 l 31 285(R) 51,819 351,663
Amendments 147,4 127,613 10,4994 248,387 25,2 j
11,3 125,673 10,3983 244,223 21,455 247,613
H,4 127,741 10,4827 286,217 25,397 247,2633
Amendments 151,507 14,1803

3Reprints availab le from OBN. *Also• in other journals.

b No reprints available from OBN; order from publi sher. gAlsc>in Biopolymers, 1 1 , 321.
cIn French. hJ. Mtol. Biol., 55, 299.
^ In Russian. V. M,ol B iol, 52, 1.
e In German.
5

* First, unrevised version.

(R) = revised version.
6 Handbook o f Biochemistry and Molecular Biology

ABBREVIATIONS

Abbreviations are distinguished from symbols as follows (taken from Reference A l):

a. Symbols, for monomeric units in macromolecules, are used to make up

abbreviated structural formulas (e.g., Gly-Val-Thr for the tripeptide glycylvalylthreonine)
and can be made fairly systematic.
b. Abbreviations for semi-systematic or trivial names (e.g., ATP for adenosine
triphosphate; FAD for flavinadenine dinucleotide) are generally formed of three or four
capital letters, chosen for brevity rather than for system. It is the indiscriminate coining
and use of such abbreviations that has aroused objections to the use of abbreviations in
general.

[Abbreviations are thus distinguished from symbols in that they (a) are for
semi-systematic or trivial names, (b) are brief rather than systematic, (c) are usually
formed from three or four capital letters, and (d) are not used - as are symbols —as units
of larger structures. ATP, FAD, etc., are abbreviations. Gly, Ser, Ado, Glc, etc., are
symbols (as are Na, K, Ca, O, S, etc.); they are sometimes useful as abbreviations in
figures, tables, etc., where space is limited, but are usually not permitted in text. The use
of abbreviations is permitted when necessary but is never required.]

1. Nucleotides (N = A, C, G, 1,0 , T, U, X, ^ - see Symbols)

NMP Nucleoside 5 '-phosphate

NDP Nucleoside 5'-di(or pyro)phosphate
NTP Nucleoside 5 '-triphosphate

Prefix d indicates deoxy.

2. Coenzymes, vitamins

CoA(or Co ASH) Coenzyme A

CoASA c Acetyl Coenzyme A
DPN a D ip ho sp ho pyridine nucleotide
FAD Flavin-adenine dinucleotide
FMN Riboflavin 5 '-phosphate
GSH Glutathione
GSSG Oxidized glutathione
NAD b Nicotinamide-adenine dinucleotide (cozymase, Coenzyme I, diphosphopyridine
nucleotide)
NADP b Nicotinamide-adenine dinucleotide phosphate (Coenzyme II, triphosphopyridine
nucleotide)
NMN Nicotinamide mononucleotide
TPN C Triphosphopyridine nucleotide

3. Miscellaneous

ACTH Adrenocorticotropin, adrenocorticotropic hormone, or corticotropin

CM-cellulose 0-(Carboxym ethyl)cellulose
DEAE-cellulose 0-(D iethy laminoe thy l)ceUulose
DDT 1,1,1 -Trichloro-2,2-b is(p-chlorophenyl)ethane
EDTA Ethy lened iaminetetraacetate
Hb,HbCO,HbOa Hemoglobin, carbon m onoxide hemoglobin, oxyhemoglobin
P, Inorganic orthophosphate

a Replaced by NAD (also DPN* by NAD*, DPNH by NADH).

bGeneric term; oxidized and reduced forms are NAD*, NADH (NADP*, NADPH).
c Replaced by NADP (also TPN* by NADP*, TPNH b y NADPH).
 7
PPj Inorganic pyrophosphate
TEAE-cellulose 0-(Triethylam inoethyl)cellulose
Tris Tris(hydroxymethyl)aminomethan (2-amino-2-hydroxymethylpropane-l,3-diol)

4. Nucleic Acids

DNA, RNA Deoxyribonucleic acid, ribonucleic acid (or -nucleate)

hnRNA Heterogeneous RNA
mtDNA Mitochondrial DNA
cRNA Complementary RNA
mRNA Messenger RNA
nRNA Nuclear RNA
rRNA Ribosomal RNA
tRNA Transfer RNA (generic term; sRNA should not be used for this or any other
purpose)
tRNAAla Alanine tRNA; tRNA^*a, tR N A ^ a : isoacceptor alanine tRNA’s
AA-tRNA Aminoacyl-tRNA; aminoacylated tRNA; “ charged” tRNA (generic term)
Ala-tRNA or
Ala-tRNA*1® Alanyl-tRNA
tRNAMet Methionine tRNA (not enzymically formylatable)
tRNAm e t or
tR N A ^ e * Methionine tRN A, enzymically formylatable to . . .
fMet-tRNA Formylmethionyl-tRNA (small f, to distinguish from fluorine F)

SYMBOLS

Symbols are distinguished from abbreviations in that they are designed to represent
specific parts of larger molecules, just as the symbols for the elements are used in
depicting molecules, and are thus rather systematic in construction and use. Symbols are
not designed to be used as abbreviations and should not be used as such in text, but they
may often serve this purpose when space is limited (as in a figure or table). Symbols are
always written with a single capital letter, all subsequent letters being lower-case (e.g., Ca,
Cl, Me, Ac, Gly, Rib, Ado), regardless of their position in a sequence, a sentence, or as a
superscript or subscript.
Some abbreviations expressed in symbols (see also Section II F below), as examples of
the use of symbols:

Dimethylsulfoxide Me, SO *
Tetranitromethane (NOa)4C b
Guanidine hydrochloride Gdn • H Q c
Guanidinium chloride GdmCl
Cetyltrimethylammonium bromide CtMea NBr d
Ethyl methanesulfonate M eS03 Et
Methylnitronitrosoguanidine MeN20 3Gdn
-nitrosourea -Nur e
-nitrosamine -Nam f
-fluorene -Fin
Aminofluorene NH2 Fln
Acetylaminofluorene AcNH Fln *
Acetoxyacetylaminofluorene Ac(AcO)NFln
jy-Acetylneuraminic acid AcNeu b

“ Replaces DMSO.
^ Replaces TNM.
c Replaces Gu, Gd, and G.
d Replaces CTAB (similarly for other ammonium
compounds).
e Replaces NU.
f Rep laces NA.
^ Replaces AAF.
^ Not NANA.
8 Handbook o f Biochemistry and Molecular Biology

I. Phosphorylated Compounds (Reference A l)

-P 0 3H2 (or its ions) -P(or P-) (“p” in Nucleic Acids; see IV)
-P 02 H-(or its ion) -P-(hyphen in Nucleic Acids; see IV)
-P 02 H-P03 H2 (or ions) -P-P or -PP or PP- (cf. PPj in Abbreviations)

Examples:3

Glucose 6-phosphate Glucose-6-P (or Glc-6-p; see II below).

Phosphenolpyruvate (pyruvenol phosphate) P-ewo/Pyruvate or ewo/Pyruvate-P or e Prv-Pb
Fructose 1,6-bisphosphate (not di) Fructose-1,6-P2 (or Fru-1,6-P2; see II below).
Creatine phosphate Creatine-P
Phosphocreatine P-Creatine

aNote that symbols are hyphenated even where names are not.
b Recommended by OBN.

II. Peptides and Proteins (References A l—A5)

A. Symbols (Reference A 2 - A 5 )

1. Common amino acids

Symbol Symbol

Name Three-letter 2 One-letter^ Name Three-letter3 One-letted

Alanine Ala A Lysinee Lys K

Arginine Arg R Methionine Met M
Asparagine Asn c ’d -e N Phenylalanine Phe F
Aspartic acid Asp d>e D Proline Pro P
Cysteine Cys e C Serinee Ser S
Glutamic acid Glu f E Threonine e Thr T
Glutamine Gin e >f’8 Q Tryptophan e Trp W
Glycine Gly G Tyrosine e Tyr Y
Histidine His e H Valine Val V
Isoleucine lie I Unknown or AAh X
Leucine Leu L ‘other'

a One capital, two small letters, at all times.

^ For special uses and with special conventions; see III, I following.
cOr Asp (NH2 ); see Footnotes e and g.
U n certainty as between Asp and Asn may be designated by Asx (or B).
S ub stitution on a functional group may be indicated, as shown in Footnotes c and g, by parenthesis following the symbol,
e.g., Cys (Cme), Ser (P); see C 2 below.
U ncertainty, as between Glu and Gin, may be designated by Glx (or Z); pyroglutamate is pGlu or <Glu, not PCA.
gOr Glu (NH2); see Footnotes c and e.
h See Abbreviations, Part 4 (AA-tRNA).
 9

2. Less common amino acids

Name Symbol

/3-Alanine /3Ala
Alloisoleucine alle
2-Aminoadipic acid Aad
3-Aminoadipic acid /3Aad
2-Aminobutyric acid Abu
6-Aminocaproic acid 3 eAhx a
2-Aminopimelic acid Apm
2,4-Diaminobutyric acid A2bu b
2,2'-Diaminopimelic A2pm b
2,3-Diaminopropionic acid A2p r b
Af-Ethylglycine, etc. EtGly, etc.
Hydroxylysine Hyl
fl//o-Hydroxylysine flHyl
3-Hydroxyproline 3H yp c
4-Hydroxyproline 4Hyp c
A-Methylglycine (sarcosine) MeGly or Sar
A-Methylisoleucine Melle
N-Methylvaline, etc. MeVal, etc.
Norleucine Nle
Norvaline Nva
Ornithine Orn

a6-Aminohexanoic acid is preferred; see Reference C2.

bThe use of D (for di), T (for tri or tetra), etc., is
undesirable. Hence, in this context, A2 for diamino is
recommended (cf. II F below).
cOr Pro(PH) for hydroxyproline.

B. Sequence, Direction, and Bonding (Reference A2)

-+ peptide bond, originating in peptide -00-

— peptide bond, originating in peptide -CO- of residue at left.
, separates symbols in unknown sequence (the entire unknown sequence is enclosed in parentheses).
I bond originating in first letter of symbol of a residue having a substituted functional group
(-SH, 3- or 4-COOH, -OH, 6-NH2 , etc., or the remaining H o f a peptide bond; see C2 below).

C. Substitution (Reference A2)

Groups substituted for hydrogen or for hydroxyl may be indicated either by their
structural formulae, or by symbols, or by combinations of both, e.g.,

Benzoylglycine (hippuric acid) PhCo-Gly or C6 H s CO-Gly or Bz-Gly

Glycine methyl ester Gly-OCH3 or Gly-OMe
Trifluoroacetylglycine CF3CO-Gly

1. In a-NH2 or a-COOH groups: horizontal dash (hyphen) to left or right, respectively.

A-Acetylglycine Ac-Gly /V-Tosylphenylulanyl

Glycine ethyl ester Gly-OEt chloromethyl ketone (TPCK) Tos-Phe CH2Cl
yV2-Acetyllysine Ac-Lys
Serine methyl ester Ser-OMe Et
O 1-Ethyl A-acetylglutamate Ac-Glu-OHt A'-Fthyl-A'-inethylglycine ht-(Me-)Glv or
Isoglutamine G1u-NH2
10 Handbook o f Biochemistry and Molecular Biology

2. On functional group: Vertical bond (see B above) or parentheses (see II A1 above,

Footnote e).

J Me Me
sp or Asp or AsptOMe) 0-MethyItyrosine Tyr or Tyr or Tyr (Me)
OMe lile

Ac Et
*
Ar-Acetyllysine
I
Lys or ^ys or Lys( Ac) S-Ethylcyteine
I
Cys or Cys or Cys(Et)
Ac Et

P Me
I r[
O-Phosphoserine Ser or Ser or Ser( ) A^-Metbylhistidine* (see 3.3) His or His or Hist rMe)
j, (/c'/rmethylhistidine) Tj{(je

similarly for substitution (prosmethylhistidine)

yV-Glycylsarcosine G ly------ j— Gly or Gly-(Me-)Gly or Gly-Sar

Me

Ac

/V-GlycykV-acetylglycine G ly------ ■
I Gly or Gly-tAc-)Gly or
Ac\ ^ ^ G ly

G ly— , G ly /

/V,/V-Diglycylglycine n ■
G ly------ Gly or Gly2 > Gly or c,y\ ^>G ly
G ly /^

♦ The prolonged and well-entrenched ambiguity in the nomenclature o f the N -1 being the
biochemist’s N - 3 and vice versa) led to a new trivial system for designating these substances:
The imidazole N nearer the alanine residue is designated pros (symbol rr) and the one farther
tele (symbol r), to give the following names and symbols: prosmethylhistidine or
w-methylhistidine, His(irMe); fe/emethylhistidine or r-methylhistidine, His(rMe).

D. Polypeptides: Follow Rules for Substitution (C above) (Reference A z)

Glycylglycine Gly-Gly
-Gly
Ma-(«lutumylglycinc
;V-7-Glutamylglycine
Glu-Gly
Glu or
j
Glu or LTL,
Glu «---- Gly

I------- Gly

Glutathione Glu or Glu

LiIII i------ Cys-Gly or Glut-Cys-Gly)

- Cys-Gly
7
i__r
Not Glu or Glu CysGly

Cys-Gly

N* -o-Glutamyllysine Glu or Glu _r Lys or Glu-elys

n
Lys

/V6 -7 -GLiUaniyllysine Glu or Glu Lys or

I I
Glu Lys or Glu(eLys)

Lys
 11

Glycyllysylglyeine dihydrochloride +H2— Gly*Lys-Gly—OH • 2HCI

Its A^-formylderivative Gly-Lys-Gly -or Gly-Lys(CHO)-Gly

CHO

E. Cyclic Polypeptides (Reference A2)

1. Homodetic: Gramicidin S

cyc/o-Val-Orn-Leu-DPhe-Pro-Val-Orn-Leu-DPhe-Pro
Val-OrivLeu-D Phe-Pro-Val-Orn-Leu-D Phe-Pro

c
Val Orn —►Leu — DPhe —*• Pro— i

Pro DPIve«— Leu — Orn«— Va!«-J

2. Heterodetic:

Oxytocin Cys-Tyr-lle-Asn-Gln-Cys-Pro-Leu-Gly-NLL

Cyclic ester of threonylglycylglycylglycine

Thr-Gly-Gly-Gly H H Thr-Gly-Gly-Gly-
II

F. Substituents (Reference A2)

1. NH2 protecting groups of the urethan type (partial list)

Benzyloxycarbonyl- Z- or p-M ethoxyphenylazobenzyloxycarbonyl- Mz-

Cbz-a
p-Nitrobenzyloxycarbonyl- Z (N 0 2)- p-Phenylazobenzyloxycarbonyl- Pz-
p-Bromobenzyloxycarbonyl- Z(Br)- r-Butoxycarbonyl- Boc-b or
ButOCO-
p-Methoxybenzyloxycarbonyl- Z(OMe)- Cyclopentyloxycarbonyl- Poc- or
cPeOCO-

2. Other N- protecting groups (partial list)

Acetyl- Ac- Maleoyl- Mal-e or

(—OC—CH=CH—CO—) Mal<
Benzoyl-(Ce H5 CO-) PhCO- or Maleyl- Mal-
Bz- (HOOC—CH=CH—CO—)
BenzyL (C6H5CH2-) PhCH2 - or Methylthiocarbamoyl- MeNHCS-8 or
Bzl Mtc-f
Benzylthiomethyl- PhSCH2- or o-Nitrophenylthio- Nps-
Btm-
Carbamoyl- NH2CO- Phenylthiocarbamoyl- PhNHCS-a or
(preferred to Cbm) Ptc-f
Phthaloyl- -P h t- or
Pht<
l-Carboxy-2-nitrophenyl-5-thio- Nbs- Phthalyl- Pht-
3-Carboxypropionyl- Suc- Succinyl- -S u c- or
(H OO C-CH, -C H 2 - C O - ) (-O C -C H 2 -C H 2 - C O - ) Suc<
T etrahydropyrany i- H4 pyran-c>g
12 Handbook o f Biochemistry and Molecular Biology

Dansyl-(5-dimethylamino- Dns-Cor Tosyl- Tos- or

naphthalene-inonaphthalene- dansyl3 (p-tolylsulfonyl) tosyl
1 -sulfonyl)
Dinitrophenyl- N 2 ph-a,c or Trifluoroacetyl- CF 3 CO- or
Dnp F 3 Ac-a,h
Formyl- HCO-d or Trityl- Ph3 C-a,i or
CHO- (triphenylmethyl) Trt-
p-1 o do phenylsulfony 1 Ips or
(pipsyl) pipsyl

3. Substituents at carboxyl group

Benzyloxy- (benzyl ester) —OCH2 Ph or p-Nitrophenoxy- —ONph

—OBzl (p-nitrophenyl ester)
Cyanomethoxy- -OCH2CN or p-Nitrophenylthio- -SNph
(cyanomethyl ester) -OMeCN
Diphenylmethoxy- -OCHPh 2 or Phenylthio- -SPh
(benzhydryl ester) —OBzh (phenylthiolester)
Ethoxy- (ethyl ester) —OEt 1-Piperidino-oxy- -OPip
Methoxy- (methyl ester) -OMe 8-Quinolyloxy- -OQu
Succinimido-oxy- —ONSuc
Tertiary butoxy- -OBu*
(f-butyl ester)

Preferred.
bNot BOC or /BOC.
cThe use o f D for di and T for tri (or tetra) is discouraged. Recognized symbols with numerical subscripts are
recommended.
dfMet is approved for formylmethionine.
eMalNEt is recommended for 7V-ethylmaleimide (not NEM).
f Mtc and Ptc have been used to denote methyl- and phenylthiohydantoins (e.g., Ptc-Leu). Since this incorrectly
implies the substitution of an amino acid by a “phenyl (or methyl) thiohydantoyl” group, the correct
representation,,CS-Leu:NPh or,PhNCS-Leu-t or, in text, Leu>PhNCS, is recommended.
gNot THP or Thp (see Footnote c).
hNot TFA (see Footnote c).
*Or trityl.

4. Other substituents (and reagents)

2-Aminoethyl-a -(CH2 ) 2 NH2 or Chloroethylamine C1(CH2 ) 2 NH2 or

Aet-a>b AetCl
Carbamoylmethyl- -CH2 CONH2 or Chloroacetamide ClCH2 CONH2 or
Ncm- NcmCl
Carboxymethyl- -CH2 C 0 2H or Chloroacetic acid C1CH 2C 0 2 H or
Cxm- CxmCl
p-Carboxyphenylmercuri- -HgBzOH p-Chloromercuribenzoate ClHgBzO-c
l-Carboxy-2-mitrophenyl-5-thio- Nbs- 5,5 '-Dithiobis(2-nitrobenzoic acid) Nbs2 d
nitrophenyl-5-thio- ( 2 -nitrobenzoic acid)
Diazoacetyl- N 2 CHCO- or
N 2 <A c-
-Diisopropylphosphor iPr2/ >-e Diisopropylfluorophosphate iPr2/>-F f
Dinitrophenyl- N2ph g Fluorodinitrobenzene N 2 ph-F b
Hydroxyethyl- -(CH2)2OH or Ethylene oxide (CH2 )2 0 or
HOEt- E t> 0
N-Ethylmaleimide MalNEt1
Tetrahydrofuran H4 furan J
Tosyllysyl chloromethyl Tos-LysCH2Cl k
ketone
 13

Tosylarginine methyl Tos-ArgOMe 1

ester
Trifluoroacetyl- F 3Ac- m Trifluoroacetic acid F 3A cOH
Trimethylsilyl- Me3Si-n Tetramethylsilane Me4 S i n

aFor -ethylamine, -Etn; for -ethanolamine (see Lipids), -OEtn.

bN ot AET.
c Replaces PCMB, pCMB, and CMB.
d Replaces DTNB.
e Replaces, DIP and Dip.
f Replaces DPF, DFP, DIPF, etc.
gReplaces DNP and Dnp.
h Re places FDNB.
^Replaces NEM.
^Replaces THF. Similarly, H„ folate.
k Repiaces TLCK (similarly for TPCK, e ta ).
R eplaces TAME (similarly for other N-substituted amino-acid esters. See C l above).
m Replaces TFA.
n Not TMS- or TMS. Similarly, Me2 SO, not DMSO; N A c3, not NTA.

G. Polymerized Amino Acids (Synthetic Polypeptides) (Reference A4)

1. Linear polymers (only normal peptide links are involved).

a. Homopolymer: polylysine; poly(Lys) or (Lys)n (n may be replaced by a

number).
b. Copolymer, alternating sequence: poly(alanine-lysine); poly(AJa-Lys) or
(Ala-Lys)n.
c. Copolymer, random sequence, composition unspecified: poly(alanine, lysine);
poly(Ala,Lys) or (Ala,Lys)n.
d. Copolymer, random sequence, molar percentages (2 = 100%) known:
poly(DLGlu56Lys38DTyr6) or (DLGlu56Lys38DTyr6)n (only lysine is L).
e. Block polymer of poly(Glu) linked via a-COOH to a-NH2 of poly(Lys):
poly(Glus 6)-poly(Lys4 4 ) or (GluS6)„<Lys44)n.
f. Block polymer, a repeating series of the known sequence Glu-Lys-Lys-Tyr:
poly(Glu-Lys2-Tyr) or (Glu-Lys2-Tyr)n.
g. Block polymer of two repeating series: poly (Glu-Lys)2S-poly(Ala-Tyr2-
Glu) 12*5 or (Glu-Lys)n5-(Ala-Tyr2-Glu)n2*5 (molar percentages = 100).

2. Branched graft polymers (functional groups are involved).

a. Main chain is a repeating sequence (see If above), sidechain is of random

sequence, connection is from e-NH2 of a lysine to an unknown group in the
sidechain

poly(Asp30Glu50) or (Asp30Glu5 ° )n

i i
poly(Glu-LySj -Tyr)5 (Glu-LySj -Tyr)^

or

I
poly(Glu-LySj-Tyr)5
I I
poly(Asp30Glu50) or (Glu-Lys,-Tyr)^
I
(Asp30Glu50)n
14 Handbook o f Biochem istry and Molecular Biology

b. Main chain of unknown sequence, linked via e-NH2 of a lysine to the a-COOH
of an L-tyrosine in the sidechain, which is a block polymer (no analytical data):

or

poly(DLAla,Lys) (poly (Ala )-poly(T yr)—1 or poly (DLAla,Lys)--poly(Ala)-poly(Tyr)

Note: The points of attachment of Lys and Tyr cannot be specified in the last example.
This system, depending on double hyphens to express functional group involvement, is not
recommended.

c. Two linear copolymers of unknown sequence, triply linked between e-NH2

groups of lysines and 7-COOH residues of glutamates:

(See comment under b with respect to last example).

d. Linear, random-sequence chain attached via terminal a-COOH group (of either
Tyr or Glu) to NH2 terminal of poly(DLalanine) in turn connected, via terminal
COOH, to e-NH2 groups(s) of poly(L-lysine) (no analytical data):

H. Synthetic Modifications o f Natural Peptides (Reference A3)

Modification and Name Abbreviation

I. Replacement:
a. o f 8th residue in vasopressin by citrulline:
[8-Citrulline] vasopressin [Cit* ] vasopressin
b. at 5 and 7 positions in hypertensin II:
[5-Isoleucine, 7-alanine] hypertensin II [lie5, Ala7}hypertensin II
2. Extension of X by valyl residue, at N and C terminals:
valyl-X Val-X
X(yl)-valine X(yl)-V al
3. Insertion of tyrosine residue between 4th and 5th residue
4a-endo-tyrosine-hypertensin II endo-Tyr4 a-hypertensin II
4. Removal o f proline from position 7 in oxytocin:
des-7 -proline-oxytocin des-Pro7-oxytocin
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