The concise encyclopedia of biochemistry

147 10

Sleeman D and Brown J Seds (1982) 'Intelligent Tutoring Systems'. Academic, London 11 Colin A J T (1980) 'Strathclyde Basic', Audiogenic Ltd, Reading RG1 2SN 12 Beynon R J and Place G A (1982) Biochern Educ 10, 104-107 13 Kibby M R (1981) Biochemistry Computer Group Newsletter No 4, 14-16 14 Keat R (1982)JChem Educ 59, 128-129 15 Dessy R E (1982)JChem Educ 59, 320-327 16 Bryce C F A and Stewart A M (1981) 'Computers in Education' Lewis R and Tagg D eds, 351-358, North-Holland, Amsterdam 17 Kibby M R (1983)Unpublished work 18 Beveridge W T (1982) 'Educational Computer Package Evaluation and Design', Scottish Microelectronics Development Program, Glasgow G12 9JN 19 Spencer T (1983) Biochem Educ 11, 27-29 20 Scottish Microelectronics Development Programme (1983) Private communication 21 Robertson I (1983) Private communication 22 (1982) See Scottish Education Review special issue 2, 79-81 23 Published by the Department of Biochemistry, University of Liverpool 24 Smith A e t al (1983)Practical Computing 6 (4), 107-129

T h e Concise E n c y c l o p e d i a o f B i o c h e m i s t r y * This is not an independent review, but a brief account of the events leading to the production of the above book, and the trials and tribulations of one of the author-translators. The abe Biochemie, published in 1976 by Brockhaus in Leipzig, is not well known to English-speaking biochemists. In the tradition of German Handbiicher, it is of small format and fairly chubby; the print is small, and an extremely large amount of information is documented in 560 double column pages. Biochemical compounds, concepts, hypotheses, abbreviations, mechanisms, etc are listed alphabetically, accompanied by definitions or explanations that vary appropriately in length from a few lines to several paragraphs. A second German edition appeared in 1982, and its circulation will likewise be largely restricted to German-speaking countries. When I was asked by Waiter de Gruyter (who had acquired the translation rights from the Leipzig publisher) to undertake the translation, my immediate reaction was one of enthusiasm. There was no book of this kind for English-speaking biochemists. My delayed reaction was more cautious. Even at the time of publication, the first German edition was rather out of date; some entries needed revision, and there were several glaring omissions. A straight translation was therefore out of the question. It was finally decided, in 1979, to translate, revise and update the German work. This task I was to share with Mary Brewer, an American chemist living at that time in West Berlin. At our first policy meeting, we standardized our list of abbreviations, agreed to adopt American spelling, and divided the work into approximately equal portions: A to Ligase for Mary Brewer, and Lignin to Zymosterol for myself. Preparation of new entries and revision of existing material were undertaken by both of us, depending on personal preference and areas of expertise, and irrespective of alphabetical location. * The Concise Encylopedia of Biochemistry by M Brewer and T A Scott is published by Walter de Gruyter, Berlin and New York, 1983, at DM59 or $29.90. ISBN 3 - 1 1 - 0 0 7 8 6 0 - 0 .

B i o c h e m i c a l E d u c a t i o n 11(4) 1983

Colleagues were solicited widely for advice and criticism. The second German edition, the proofs of which were available during the translation period, included some new and revised entries, but the changes were unfortunately minimal, and made only a small contribution to our updating exercise. By way of acknowledgement, the German edition contains a list of sources of diagrams and there is also a list of suggested general reading, but these are no use for the reader who wants more information about a specific subject. We have therefore introduced literature references, especially for new and revised entries. Where possible, we have also given each enzyme its EC (Enzyme Commission) number, according to the Recommendations (1978) of the Nomenclature Committee of the International Union of Biochemistry. In German biochemistry there can still be detected the echo of a tradition from a time when the translation of 'die Biochemic' was not exactly 'biochemistry', but rather 'the chemistry of substances of biological interest'. This influence is very apparent in the German publication, and we debated whether to omit, eg many of the plant pigments and alkaloids and their accompanying chemical data. In the event, all this material has been retained, and some new natural products have even been added. It is not intended here to present a complete check list of all new and revised entries, but some examples may be of interest. Much of the biochemistry of the Aromatic Amino Acids has been revised and expanded. Especially Tryptophan Metabolism and its associated enzymes have been treated more extensively. Many aspects of Nitrogen Metabolism have been rewritten, in particular Ammonia Assimilation and the enzymology, physiology and genetics of Nitrogen Fixation. As in any reference work, some key words are cross referenced to other entries that embrace them. In the English edition we have accorded independent status to some of these subjects, eg Ionophores, which was cross referenced into Biomembranes, now stands alone as an independent and much expanded entry. Amongst the new additions is Attenuation, with a diagrammatic representation, which we hope will be an aid to understanding this complicated phenomenon. After returning to the USA to work in a department of Immunology, Mary Brewer, taking advantage of the good nature of her new colleagues, undertook a total revision of the section on Immunoglobulins; fortunately the original artwork was suitable for the revised version. Without doubt, the drawing of new illustrations was the most time consuming part of this venture. Nevertheless, the production of science artwork was a satisfying experience, in contrast to the 'translation' of existing diagrams, which was most tedious. Original printing blocks were available for the illustrations, but the translation of labels and annotations sometimes necessitated such extensive changes, that is was more economic to completely redraw many flow diagrams and reaction pathways. As might be predicted, all areas concerned with nucleic acids, protein synthesis and molecular genetics needed revision in the light of current research. But this is a game you cannot win. Conventional publishing techniques can never keep pace with the rate of progress in molecular biology. Omission of the immunological studies on ribosomal proteins, and the concept of ribosome structure

148 Co~nzyme F

100

Colchicum alkaloids

reaction in the el¢ctropbilic form, a n d the other in the n u d c o p h i l i c fon'a. The ieaermediatel in t l ~ I~oxidation of fatty ac-

~ ~ ~

iris ( ~ Fatty acid delnldJItion) are d¢fiVlfiVles of CoA, as are some intermediates in the synthesis of~ome alkaloids, ~-O~-C-~0~ ~'

;---~

~ ~ ¢ 1

• ,e

~o

H~

l

~

P~$~ote

h~ ~=0

~ i "~ ~ q - ~

O

)=/ c~

alkaloids (see) in which the nitrolen is p=e'r~nt as • substituted a m i n o iroup on I tficyclic skeleton The latter consists of an aromatic ring. • ~~ 1 lone rin$ and anolhet ?-memhered rin|. C.I. are synlhesized only by I few senera of the lily fami-

I

21

~,ll~f ~t o~

4

{~, f'o~

..,o

",.~,~ ,,e¢, ~,,~

:

o

a

t~co >

!-.2{~1~

pr~rlltatives of the Iroup are Colchicine (~e) amd demecolcine; the folm~tr often o~cul~ as the

,v, a~,~

$1ucc~ide (~olcbico~ide). ]n the lisht, the Iropo-

~h

HsCO~ H~CO

o

a 0 ~hco

t~ndrocymplne

~CO •

0emecok ,,e

~

•

o

h H

HlCO

~ .[3, O,-

co.espena,ng

COCH~

0

H~C~

autumnale L . the ra~adow ~lffron. The main re.

~

Collagen

101 a

# olphdk~l: ~ Pbospholipids. C t l 4 1 ~ l : Ire mo~ important of the Colchicure alkaloids (I¢¢). M r 399.4. mp.p 142 to 150 *C. Io]~ - 121 ° ( t - 0 . 9 in chloroform). C . is ex irl¢led from C o t c h ~ a~tumnat¢ L and is u ~ d mainly in plant $©netlol to inhibit mitosis and induc~ polyploidy In small do~'s, C, relieves pain and suppt~u~e~ inflammation, but it is highly toxic. 20 mShein$ l leil~l d o ~ It has been u ~ d iglins~ n¢opll~ic | r o a r .

|

C o l d - ~ n s i t i v e enzymes

O: see Ub/quinone. R: ~ V i ~ m i n • (vitamin H). I~l Ethenolamine.

ceF~,one

o~om'.

lone lin$ of the CJ. may rearranse to a C, and a

FiB 2. A c t l ~ f m d

C s tins (lamJc~l~hi¢i~s~

Kyt.CoA (r~en)

2a Synthesis of acetylphosphate (activated carboxyl group)

The C.I. are bi~ynthetized via a l-phenylethylisoquinoline alkaloid from which androcymbin is

2b

foxed

Citrate

synthesis

(acfivalcd

a-methylene

by h y d ~ x y l • t i o n , mcthoxylafion, attack

I~roup) .-n~

~ o c

H

l o CH] 0

~

i

h Oem~¢ol¢~ne

Co1¢hl(,ne Co~c" (OSlde

o

~, ~a CHI CH~ COCH3 CH 1 COCH~ Glucose

OCH3 Fi B I ~

~

F: ~ e Tetrahydrotoll¢ a c i d ~ ¢4 ~ Bsa: see 5'-D¢oxyaden~ylcolmlamine

~

~/¢lm

Ik~/~s

of phenol o x i d l ~ s and oxidative ¢ouplinl~, Androcymbin is then converted to demecolcine a n d fumher to colchicine ( F i g )

Cokl-I~'~dll~ ~ : • IrOUp of oligom©la (consisting o4" ~everal polypeplide chains) en zymes, of which about 25 are presently known, which Ioic tbelr itability •nd thai tnzym•fic •cliVity as the lemperaluR is decRalcd. The cau~ of this elTe¢l, which is often revertible, is the dis~ociafion of (he enzymes into their inacfive subunits due to the weahenin I of hydrophobic and/ or electrostatic and ionic intcrlc~iom. Examples of this clall • ~ lh~ mitochondnll idenoslnetriph~phatase and pyluvat¢ ¢ a t h o a y l ~ e , and gly~raldehyde-phouphate dehydrosenasc, yeast pynavat¢ hidll¢, fruclos¢ bispho~pEaulSe and earbamyIpho~phnl¢ synth~as¢ from muscle Colchis: t~e Toxic proteins, C~41111~m:i n e a t ~ c e i l u l a s p ~ c i n which is ~ sponsible for Ihe strength and flexibility ol" conhectare tissue• h accounts for 25 to 30% of the

Wne unusual sl~eturll F~'Ol~:rties of collagen are due to i l l amino acid ~rquenee. The a-chains con• •st of about I 0 ~ a m i ~ acid~ each, and thus

III;I 11 !I 1 111

.... i

protein in an animal. C in i l l mature t o n • is in-

soluble under physiOlolliCall conditions, |llhou|h it can be readily denatured by heal, mild acid or alkaline irealmenl. SI~ClUre (1 is arranlted in fibrils visible u n d e r a light m i e n • c o p e , which are scan under an decIron microscnpe to be composed of microfibt*h

These have a characleristic striation with a eepeat

oI~0

o%

\OH r~ o ~ ,,e

Phenyrptoz~ona]deh~d¢

FiB 2 B / ~ n ' ~ pa~e I01}

~/" ~

'"

OH

OH olkolo,d (continued on

ditlance of about 670 ./g. due Io the end-In-end alisnmem of the ba•i¢ molecldar unit. tropocol.

la$¢n IF• l . I). The tropocollalen molecule is • rilhlEanded Iriphe bell• composed of two idenlical pOlyl~l~ide chaida (all and one d i l h t l y different (~2) chain E~ICh CllChaln is i t . l l I left / handed helix with a pitcb of 9.~ A, while the supcrhellx has | pitch of IO4 A. The helical a n d sul~tlbelical stnl~ulx~ are Itabillaed by h y d r o | a n

bonds hel wt~n the H N Sroupof$1ycine in one chain •nd the 0 - C Stoup ofa proiineo~olher amino acid in an edjlcent chain. ~1~ Ir0pocollalgen molecules are also crosslinhed (see below).

hetrL A: a re$ion of short overlap. B: a long overlap region. C: an ov¢rlap teE•on eorrclpondin 8 to one hole zone i n d one re|ion of shorl overlap. and livin$ r i g to I11¢ dis[once of 668 A on the blinded slruelure of the microfibril. D: a ho~e tone. Each sin$1¢ a ~ w (lenl~h 4.4 x C) represents • lropo~ollllen molecule.

Reproduction of a double-page spread of the Encyclopedia (printed with the permission of the publishers). Actual size of page: 215 X 13.5 cm. derived from electron microscope studies of antibody-ribosome complexes was an obvious defect, which has now been corrected. It should be emphasized, however, that the great majority of the entries in this first English edition represent unmodified translations of the German text; the book retains the layout and indeed the flavour of the original abc Biochemie, which are so admirable. When we started translating, Mary, being on the spot in Berlin, was responsible for day-to-day dealings with the publisher, and for collating the final typescript. At the end of 1979, Mary returned permanently to the USA and I inherited the duty of liaising from Leeds with the publishers in Berlin; a duty made difficult by the geographical separation, but pleasant by Dr Rudolf Weber, director of the science publishing section of Waiter de Gruyter. Thus, the post travelled backwards and forwards between Leeds, Oregon and Berlin. Our exchange of typescripts and exercise of mutual criticism would have proceeded more quickly had we been in the same city. On the other hand, a thought must be considered in depth and expressed clearly, if it is to be written down and submitted to the international postal system with expectation of a response in no less than ten days; very dull for those accustomed to the rapid cut and thrust of ideas in the research laboratory, but highly commendable when writing a book! Biochemical Education 11(4) 1983

Stored alphabetically in loose leaf document Fdes, the completed typescript was bulky and heavy. Early in 1981, Dr Weber flew to Leeds to take personal delivery, but the size and weight were greater than he had bargained for, not surprising for a work that claims to embrace the whole of Biochemistry! We had to ship the precious cargo to Berlin by air freight from Leeds-Bradford airport. Caroline, the wife of my colleague, David Herries, who had kindly criticised much of the enzyme kinetics suggested the title "Concise Encyclopedia". Galley proofs started to arrive later in 1981, followed in 1982 by illustrations and finally page proofs. Here, the method of typesetting used by Walter de Gruyter proved advantageous, because it was still possible, in the very advanced stages of proof reading, to make extensive alterations and introduce new material. I received my final page proofs on October 18, 1982, just before leaving for a visit to Khartoum, to teach and to act as external examiner in Biochemistry at the Faculty of Medicine. I had to collect the proofs as air-freight from KLM in Cargo Editor's Note: The "Dictionary of Biochemistry" by Stensh (Pub John Wiley & Sons, 1976) was reviewed in Biochemical Education 4, 38 (1976). Your Editor noted the entry Macdougallin (a sterol from cactus) in the Concise Encyclopedia and looks forward to Macdonaldin being extracted from hamburgers in time to be included in the Second Edition.

149 Village on my way through London's Heathrow airport. Cargo Village is literally miles away from the passenger terminals on the other side of the airport, and I nearly missed my connection for the Sudan. To my knowledge, that was the only crisis (or near crisis) associated with the production of the book. Relaxing on the terrace of the Grand Hotel, overlooking the Blue Nile, just a short walk from the palace where Gordon of Khartoum was murdered by the followers of the Mahdi, I tried to ignore my exotic surroundings and bring some degree of objectivity to bear on the correction of the proofs. Subsequently, as a source of information for final-year lecture and MSc seminars, and for answering queries from students, the Concise Encyclopedia (in the form of a complete set of page proofs) proved remarkably effective. Since it places equal emphasis on all areas of Biochemistry, we hope this book will be just as useful to clinical, microbiological and plant biochemists, in both teaching and research. Already we have started collecting, classifying and revising for the second edition. Criticisms of the first edition and suggestions for new entries will be gratefully received. All new material will be thoroughly researched, edited to the style of the Concise Encyclopedia, and, with any luck read in proof on the banks of the great grey-green, greasy Limpopo river.

Note added in proof: By analogy with humans and elephants, it is to be expected that the gestation period of an article in

Biochemical Education will be somewhat shorter than that of an encyclopedia, albeit a concise one. Barely six months have elapsed between submission and typesetting of the present manuscript. During this period the Concise Encyclopedia has been published and there has even been time for a preliminary assessment of its success. Several biochemists have already written to express enthusiasm for the project (eg "I have dipped into it very frequently since my volume arrived here, and I have been very delighted by the type of information that you have put into the book"), and valuable suggestions for future entries have started to arrive. Sales in the USA have been brisk, and a second printing has been ordered by the publishers; this has given us the opportunity to correct some minor printing errors. Thgmas A Scott

This is w h a t F r a n k Vella t h o u g h t o f the Concise Encyclopedia: This is a useful and handy reference work on biochemistry. For me, it will replace the scurrying through the index pages of several textbooks (often to no avail) when I need to find out something about an unfamiliar biochemical compound or process. There are over four thousand entries. They vary in length from one line to an eleven-page essay (with fourteen figures and a table) on vitamins, and are extensively crossreferenced. Some entries contain references to the literature. Microbiological, animal, and plant areas are well represented. The writing is clear, concise and complemented by structural formulae, metabolic pathways, figures and tables. If updated periodically, this book could quickly become an important source book of value to teachers, graduate students, and many others in all areas of biological science.

B i o c h e m i c a l E d u c a t i o n 11(4) 1983

Practical A b b r e v i a t i o n s in A p p l i e d B i o c h e m i s t r y J M MACARULLA and A MARINO

Department of Biochemistry University of Pais Vasco Bilbao, Spain Introduction Abbreviated forms of representing the name and/or structure of biomolecules are often found in biochemical literature. Tentative or definite rules are periodically established by IUPAC-IUB1,2,3 in order to consolidate efforts of rationalizing the biochemical nomenclature. One of the main objectives of these rules is to avoid any ambiguity or imprecision. With these ideas in mind, we would like to propose a series of minimal abbreviations that, in the same way as longer and more widely accepted ones, could designate monomers as well as more complex substances, unambiguously. Many of the abbreviations proposed here consist of a single letter. However, their meaning is made clear by the context. Indeed, this is what happens with some of the initials currently in use. For instance, the letter G can symbolize, according to the context, guanine, guanosine, glycine, Gibbs free energy, a class of immunoglobulins, glycerate, etc. In the same way, it could mean glucose. 4 Aim of this paper Our suggested abbreviations do not intend to modify the rules established by IUPAC-IUB, but rather to help biochemistry teachers to express the formulae and structures of biomolecules in a clear and concise way. Our abbreviations could be used in textbooks and research papers as long as IUPAC-IUB does not define more universal ones. According to the context, a capital A following the abbreviated name of an aldose indicates the corresponding aldonic acid, while a U means the uronic acid. In this case we prefer U over A because the acid, under physiological conditions, ie at neutral pH, will be in the salt form (A: aldonate, U: uronate), and the letter U is more specific. Generally speaking, if the structure of the molecule under consideration is very complex, shorter abbreviations may be used for each of its components, since the danger of ambiguity is obviated by the context.

Rules (1) Abbreviated names are based on the English name of the substance, and should be used in the same form even in other languages. (2) The most common substances are designated by a single letter and the less frequent ones by more than one letter. (3) The same abbreviation may have different meanings if ambiguities are avoided by the context. If not, the use of abbreviations is precluded. (4) Speaking of carbohydrates, a lower case 'u' means a ketose, eg R = ribose, Ru = ribulose. (5) Similarly, an T indicates a polyol: R1 = ribitol, Inl = inositol. (6) Ac stands for acetyl and Ac for acyl. N indicates the location of these radicals: NAc = N-acetyl, NAc = N-acyl.