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Handbook
of
Biochemistry
and
Molecular Biology
CRC Handbook
of
Biochemistry
and
Molecular Biology
3rd Edition
Physical and Chemical Data
Volume I
Editor
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Handbook
of
Biochemistry
and
Molecular Biology
3rd Edition
Gerald D. Fasman
Editor
MEMBERS
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
Irvine, California 92664
Philip Leder
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)
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:
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
PREFACE TO PHYSICAL AND CHEMICAL DATA, MISCELLANEOUS:
ION EXCHANGE, CHROMATOGRAPHY, BUFFERS,
MISCELLANEOUS, E.G., VITAMINS, VOLUME I
This section of the Handbook o f Biochemistry and Molecular Biology on Physical and
Chemical Data is divided into two volumes.
The first volume contains data on amino acids which consists of the coefficients of
solubility in water, heat capacities, entropies of formation, and heats of combustion.
Oxidation-reduction potentials of compounds of biochemical interest and of hemopro-
teins and metalloproteins are listed. Heats of proton ionization, pK and related thermo
dynamic quantities, free energies of hydrolysis and decarboxylation, and calorimetric
AH values accompanying conformational changes of macromolecules in solution are
listed. Information on the measurement of pH, buffer solutions, pH indicators, and the
ionization constants of acids and bases are detailed.
Tables of refractive index of water, various solvents, salt solutions, liquids, tempera
ture dependence, and Lorentz corrections are available.
Specific gravity of liquids, sucrose solutions, CsCl solutions, isokinetic glycerol and
sucrose gradients for density gradient centrifugation, and the temperature dependence for
selected compounds are included.
This collection of data, for which the editor alone is responsible, is highly selective in
nature. It is hoped that this volume will be of assistance to those working in the field of
biochemistry and molecular biology.
Gerald D. Fasman
Editor
March 1976
THE EDITOR
NOMENCLATURE
Biochemical Nomenclature ......................................................................................................................3
IUPAC Tentative Rules for the Nomenclature of Organic Chemistry Section E. Fundamental
S tereochem istry....................................................................................................................................20
The Citation of Bibliographic References in Biochemical Journals Recommendations (1971) . . 58
Nomenclature of Labeled C o m p o u n d s....................................................................................................62
Definitive Rules for the Nomenclature of Carotenoids ........................................................................63
INDEX . 541
Nomenclature
3
BIOCHEMICAL NOMENCLATURE
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) J. 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 PLACES3
Arch. Biochim.
Biochem. Biophys. Eur. J. J. Biol. Pure Appl. Biochimie Molek. Z. Phys.
Biophys. Biochem. J. Biochemistry Acta Biochem. Chem. Chem.b (Bull. Soc.)c Biol.d Chem. e
Clf 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
ABBREVIATIONS
Abbreviations are distinguished from symbols as follows (taken from Reference Al):
[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.]
2. Coenzymes, vitamins
3. Miscellaneous
4. Nucleic Acids
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 as examples of the use of symbols:
Dimethylsulfoxide Me, SO a
Tetranitromethane ( N O ,) ,C b
Guanidine hydrochloride Gdn • HC1 c
Guanidinium chloride GdmCl
Cetyltrimethylammonium bromide CtMe,NBr d
Ethyl methanesulfonate MeS03 Et
Methylnitronitrosoguanidine MeN2 0 3 Gdn
-nitrosourea -Nur e
-nitrosamine -Nam **
-fluorene -Fin
Aminofluorene NH2 Fin
Acetylaminofluorene AcNHFln g
Acetoxyacetylaminofluorene Ac(AcO)NFln
W-Acetylneuraminic acid AcNeu b
aReplaces DMSO.
bReplaces TNM.
c Replaces Gu, Gd, and G.
^Replaces CTAB (similarly for other ammonium
compounds).
eReplaces NU.
^Replaces NA.
^Replaces AAF.
hNot NANA.
8 Handbook o f Biochemistry and Molecular Biology
TRIVIAL NAMES
“The term vitamin A should be used as the generic description for all 0-ionone
derivatives, other than provitamin A carotenoids, exhibiting qualitatively the biological
activity of retinol. Thus, phrases such as ‘vitamin A activity,’ ‘vitamin A deficiency,’ and
‘vitamin A in the form o f . . .’ represent preferred usage. . . .”
“The term provitamin A carotenoid should be used as the generic descriptor for all
carotenoids exhibiting qualitatively the biological activity of jS-carotene. When referring
to the biological activity of the provitamin A carotenoids, the phrase ‘provitamin A
activity’ represents preferred usage.” *
in tern atio n al Union of Nutritional Science (I.U.N.S.), Nutr. Abstr. Rev., 40, 395 (1970).
Name(s)
“The term vitamin D should be used as the generic descriptor for all steroids exhibiting
qualitatively the biological activity of cholecalciferol.* Thus, phrases such as ‘vitamin D
activity’ and ‘vitamin D deficiency’ represent preferred usage.” **
“The term vitamin E should be used as the generic descriptor for all tocol and
tocotrienol derivatives exhibiting qualitatively the biological activity of a-tocopherol.
Thus, phrases such as ‘vitamin E activity,’ ‘vitamin E deficiency,’ and ‘vitamin E in the
form o f . . .’ represent preferred usage.” *
“The term vitamin K should be used as the generic descriptor for 2-methyl-l ,4-
naphthoquinone and all derivatives exhibiting qualitatively the biological activity of
phytylmenaquinone (phylloquinone). Thus, phrases such as ‘vitamin K activity’ and
‘vitamin K deficiency’ represent preferred usage.” *t
in tern atio n al Union of Nutritional Science (I.U.N.S.), Nutr. Abstr. Rev., 40, 395 (1970).
^American Institute of Nutrition (A.I.N.), J. Nutr., 99, 244 (1969).
10
Summary o f Chemical Relationships and Nomenclature of Some Biologically Active Quinones with Isoprenoid
Side-Chains, Including Vitamins E and K and Coenzyme Q (Recommended Names are in Boldface)
Aromatic nucleus Side-chain Trivial name(s) Abbreviations Cyclized form Trivial names Abbreviations
1,4-Naphthoquinone 3-(prenyl)n Menaquinone-n MK-n 2//-N aphtho| 1,2b | pyran-6-ol M enachromenol-(n-l) MK-n-el
2-methyl- Preny Imenaquinone-n * MQ-n' (2,5-substituted)
Menaquinone* n = 10: vitamin K2 (50)**
(Menadione) n = 7: vitamin K 2 (35)**
n- 6: vitamin Kj (30)**
♦Proposed by Committee on Nomenclature of IUNS [Nutr. Abstr. Rev.,] 40, 395, (1970), where differing from those recommended here.
♦♦Names previously used (see first paragraph in introductory section), are not recommended.
11
12 Handbook o f Biochemistry and Molecular Biology
Group in position
Group in position
4 5 2 6 Name
aFor use in combination with similar symbols (e.g., Lys, Me, P) or names, in accord with
general rules of symbolism (pp. 5 et. seq. )
bNot recommended. Use full name (see Footnote c).
cOr -5-P or 5'-P- for 5'phosphate (or -P alone).
king ... for ever] i.e. the kingdom is to abide with David and his
descendants. That the promise, however, was not to be interpreted
as independent of moral conditions, see below verse 9 ad fin.
⁵and of all my sons, (for the Lord hath given
me many sons,) he hath chosen Solomon my
son to sit upon the throne of the kingdom of
the Lord over Israel.
5. many sons] compare iii. 1‒9.
the throne of the kingdom of the Lord] Compare xxix. 23, the
throne of the Lord. The Chronicler regards the king as the deputy of
Jehovah.
9‒21.
David’s Charge to Solomon.
11. the pattern] Compare verse 12; Exodus xxv. 9. The Temple,
like the tabernacle, was to be constructed according to a pattern or
model communicated by inspiration (see verse 19). A verbal
description rather than a drawing is meant.
12. that he had by the spirit] i.e. that had come to him by
revelation and rested with him waiting for realisation. Margin, that he
had in his spirit (i.e. in his mind) is a less likely translation.
for the courts] The last verse dealt with the Temple itself; this one
with the courts and detached buildings.
19. All this, said David, have I been made to understand in writing
from the hand of the Lord, even all the works of this pattern]
Compare verse 11, note. As in the case of Moses and the tabernacle
(Exodus xxv. 9, 40), so David’s plans for the Temple are said to be of
Divine origin.
stones for inlaid work] Compare Isaiah liv. 11, I will lay thy stones
with fair colours (the same word is used in Hebrew).
the houses] i.e. the porch, the greater house, and the most holy
house; 2 Chronicles iii. 4, 5, 8.
6‒9.
The Offerings of the Chiefs of Israel.
⁶Then the princes of the fathers’ houses, and
the princes of the tribes of Israel, and the
captains of thousands and of hundreds, with
the rulers over the king’s work, offered
willingly;
6. over the king’s work] See xxvii. 25‒31.
ten thousand darics] A daric was a Persian gold coin worth about
22 shillings. Used thus in connection with the reign of David, the
word is of course a curious anachronism. The translation of
Authorized Version drams (i.e. drachmæ) may possibly be right. The
value of a gold drachma was about 9s. 5d.
10‒19.
The Blessing of David.
14. be able] Literally retain strength. David praises God for the
great success of the efforts of so transitory a creature as man.
20‒22.
The Great Rejoicing.
²⁰And David said to all the congregation, Now
bless the Lord your God. And all the
congregation blessed the Lord, the God of
their fathers, and bowed down their heads,
and worshipped the Lord, and the king.
20. worshipped] i.e. prostrated themselves.
22. the second time] Compare xxiii. 1. The first time which is
described in 1 Kings i. 39 (Solomon hastily anointed in order to
assert his claim to the throne against his brother Adonijah) is omitted
in Chronicles, unless perhaps the vague phrase of xxiii. 1 “Now
David ... made Solomon his son king over Israel” is intended to refer
to it.
Zadok] One of Solomon’s earliest acts seems to have been to put
an end to the double priesthood by deposing Abiathar; compare 1
Kings ii. 27, 35. The Chronicler appears to have this in mind, but he
avoids narrating anything so derogatory to the high-priesthood.
23‒25.
The Beginning of Solomon’s Reign.
24. the mighty men] Compare 1 Kings i. 10, 38, from which it is
clear that the faithfulness of Benaiah and the Cherethites and
Pelethites was the main factor in the elevation of Solomon to the
throne.