Table Of ContentWe shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time
from Little Gidding, in Four Quartets by T. S. Eliot
This we know. All things are connected like the blood which
unites one family. All things are connected.
Whatever befalls the earth befalls the sons of the earth. Man
did not weave the web of life; he is merely a strand in it.
Whatever he does to the web, he does to himself.
From Chief Seattle's letter to
the Great White Chief in Washington
in 1854 in reply to an offer for
a large area of Indian land.
BiochelDistry and
Oral Biology
Second edition
s.
A. Cole, B.Sc.,Ph.D.,
SeniorLecturerin Biochemistry (retired), University ofBristol
J. E. Eastoe, D.Sc., Ph.D., F.D.S.R.C.S., D.I.C.A.R.C.S.,
ProfessorofOralBiology, University ofNewcastle upon Tyne
withcontributionsby
JohnMcGivan, M.A.,Ph.D.
M. L. Hayes, B.D.S.,M.Sc.,Ph.D.,
A. C. Smillie, M.D.S., Ph.D.
WRIGHT
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is an imprint of Butterworth Scientific.
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This book is sold subject to the Standard Conditions of Sale of Net Books and
may not be re-sold in the UK below the net price given by the Publishers
in their current price list.
First edition published by John Wright, Bristol, 1977
Reprinted, 1978,1979,1980,1983
Second edition, 1988
Butterworth International Edition, 1988
ISBNO 7236 17511
© Butterworth & Co. (Publishers) Ltd, 1988
British Library Cataloguing in Publication Data
Cole, A. S.
Biochemistry and oral biology—2nd ed.
1. Biochemistry—For dentistry
I. Title II. Eastoe, J. E. (John Eric)
574.19'2'0246176
ISNB 0-7236-0834-2
Library of Congress Cataloging in Publication Data
Cole, Anne S.
Biochemistry and oral biology/A. S. Cole and J. E. Eastoe;
with contributions by M. L. Hayes and A . C. Smillie—2nd ed. |
p. cm.
Bibliography: p.
Includes index.
ISBN 0-7236-0834-2
1. Biochemistry. 2. Mouth. 3. Dental chemistry.
I. Eastoe, John E. II. Hayes, M. L. III Smillie, A. C.
IV. Title.
QP514.2.C64 1988
612'.015'0246176—dc 19
Typeset by EJS Chemical Composition, Midsomer Norton, Bath
Printed and bound in Great Britain by Anchor Brendon Ltd, Tiptree, Essex
Foreword
Professor G. N. Jenkins
Department of Oral Physiology, Dental School, Newcastle upon Tyne
Textbooks in pre-clinical subjects for dental students have always presented a problem. Very
few books in physiology and biochemistry have been written specifically for dental students.
This has meant that they have had to use texts designed for medical or science students
containing more detail on many topics while omitting altogether or discussing superficially
subjects of outstanding dental importance. Although a number of books are now available
covering these dentally orientated topics the present book by Anne Cole and John Eastoe, and
other contributors, is, I believe, the first work covering both the general and the dental aspects
of a pre-clinical subject and will be warmly welcomed on that account .I am particularly pleased
to note that prominence has been given to nutrition, a subject clearly of outstanding importance
to all humanity yet frequently neglected in medical and dental courses. This subject, bristling
with challenging intellectual and practical problems, has inexplicably become the Cinderella of
biochemistry. The unique combination of a modern exposition of biochemistry at a level
eminently suitable for dental students, linked with nutrition and with the fascinating but highly
controversial questions of dental biochemistry will, I am sure, be a very valuable addition to the
dental literature. I congratulate the authors on their book and wish it every success.
November 1976
Preface to the second edition
It is eleven years since the appearance of the first edition of Biochemistry and Oral Biology
during which time there have been many notable advances not only in biochemistry and
molecular biology but also in dental science. This has meant that large parts of the book have had
to be rewritten or extensively revised. The text follows the same general pattern as the first
edition but some of the material has been rearranged and a completely new chapter 'The
prevention of plaque-induced diseases' has been added. The team of authors has been
strengthened by the inclusion of John McGivan who is responsible for Chapter 16
(Bioenergetics) and for rewriting the chapters on the control of metabolism. He also revised the
chapters on enzymes and amino acid metabolism. The updating of other parts of the book would
have been impossible without the help of various friends and former colleagues mostly in the
Department of Biochemistry at Bristol. The chapters on nucleic acids and protein synthesis have
been rewritten and that on mutations, evolution and inherited disease revised by Dr L. Hall.
Invaluable help with other sections of the book was given as follows: Chapter 1 -Dr W. Wälder,
Chapter 15-Dr M. J. A. Tanner, Chapters 17 and 18-Dr T. Hopkirk, Chapter 25-
Dr M. Luscombe. Dr H. C. Watson provided the computerized diagrams from which Figures 5.5
and 5.6 were drawn and Dr Hilary Muirhead those for Figures 5.7c and d. Dr E. H. Batten
provided Figure 26.1. Others whose help is gratefully acknowledged are Professor O. T. G.
Jones and Dr J. Williams. Finally we would like to thank Mrs Brenda Fowler, Mrs Rosemary
Musgrave and Miss Karen Short for help with the typing.
A.S.C. andJ.E.E.
May, 1988
Note I would like to record the fact that owing to increased pressure of administrative work,
the editing of the greater part of this second edition (other than the chapters for which I was
originally responsible) was undertaken by Anne Cole during her retirement.
J.E.E.
vii
Preface to the first edition
While many books cater for the biochemical needs of science and medical students, no modern
introductory biochemistry text appears to be available that meets the specific requirements of
those whose main interest is dentistry. We feel that there is a need for a book which, while
explaining the basic principles of biochemistry, also includes topics that are of specifically dental
interest. Also relevant are subjects, such as nutrition, that were once considered as areas of
'physiological chemistry' but which now, despite their importance, tend to be neglected as far as
basic science courses for dentists and doctors are concerned.
The plan of our book proceeds from the structural basis of biochemistry, via metabolism and
its control towards an increasing degree of specialization on dental topics-soft tissues, hard
tissues and the biology of the mouth. Thus, after a preliminary look at the aims of biochemistry,
some basic chemical facts and the role of water, comes Section 2 on Molecular Architecture.
Section 3, concerning Nutrition, includes a discussion of fluoride, giving the main facts on which
arguments for or against a policy of water fluoridation are based. Section 4, Molecular
Organization and Interactions, starts with Chapters on general principles of metabolism and the
biochemical organization of the cell and ends with an outline of biochemical individuality and
the molecular basis of inherited disease. The last subject is rarely dealt with in textbooks of
biochemistry, though it is of obvious importance to clinicians.
Once the basic metabolic pathways have been considered, the book continues with Section 5,
Control Processes, which covers regulatory mechanisms operating within the cell and also the
hormones responsible for integrating the body's various component systems. Section 6 on Soft
Tissues contains chapters on body fluids, epithelium and connective tissue and deal swith areas
rarely covered in detail in textbooks of biochemistry.
The two final sections are specifically concerned with aspects of Oral Biology. Section 7 on the
Calcified Tissues, which includes chapters on calcium and phosphorus metabolism, biological
apatite, mineralized tissues and the mineralization process, helps to bridge the gap between
chemistry and dental histology. Finally in Section 8, Biology of the Mouth, consideration is
given to biochemical aspects of saliva, the oral flora and the formation and properties of dental
plaque. A chapter on plaque diseases completes this survey of dental biochemistry.
Throughout the book we have tried to avoid undue detail and excessive numbers of formulae
and equations, and also to show how biochemistry is relevant not only to dentistry but also to
many wider aspects of life today.
ix
x Preface to first edition
In most instances SI units are used, although, when dealing with energy, at this time of
transition it was thought helpful to give values in both joules and calories. For very small
measurements of length, nanometres are nearly always used despite the fact that X-ray
crystallographers understandably continue to prefer Angstroms. The one instance where we
have intentionally used units other than SI is for pressure. It seems to us that millimetres of
mercury are, for most people, a more meaningful method of expression than pascals. For
concentrations of material we have sometimes preferred mg or g per 100 ml to molar
concentrations. This is either a matter of common usage, as with blood glucose concentrations,
or because the exact composition of such mixtures as plasma proteins is unknown. A table of
units is given on page ix.
January, 1977 A.S.C. AND J.E.E.
Units
Table of units used
Physical quantity Unit Symbol
Volume litre 1
Length metre m
angstrom Â*(1Â = 04 nm)
Mass gram g
Time second s
Energy joule J
calorie cal*
Pressure millimetres of mmHg*
mercury
* Not SI units.
Prefixes for multiples and submultiples of units
Multiple Prefix Symbol
IO6 mega M
103 kilo k
1(T3 milli m
1(T6 micro μ
io-9 nano n
io-12 pico P
Amounts and concentrations
Amounts of material are usually expressed as moles which are equivalent to the molecular
(or atomic) weight of the substance in grams.
Concentrations are expressed in terms of molarity, i.e. the number of moles present in 1 litre
of the solution or g (mg) Γ1 (decilitres).
xiii
Section 1
Some preliminary considerations
Chapter 1
Introduction
The scope of biochemistry
The aims of biochemistry are to describe the nature of living forms and living processes in terms
of chemistry and physics. Biochemists believe that the existence and activities of living
organisms can be explained on the basis of the interaction of their component molecules. These
may be divided very broadly into two groups, namely small molecules and macromolecules.
The main types of macromolecule are proteins, nucleic acids and polysaccharides, all of which
are long, chain-like molecules built up from a large number of linked subunits. These bio-
polymers tend to associate into still larger complexes with other molecules which may or may not
be of the same type. The small molecules act not only as the building units from which macro-
molecules are synthesized but also as sources of energy, messengers and regulators. Macro-
molecules are the essential basis of the elaborate structures in and around which the life
processes occur; they also control and regulate these processes. Thus macromolecules are
responsible for the energy exchanges and chemical reactions that comprise metabolism, for the
irritability which enables the organism to respond to changes in its environment, for mobility and
for reproduction.
Since molecules do not function alone but by interaction with other molecules, living
processes require specific arrangements of molecules and 'life' resolves itself into a question of
molecular organization.
This organization is based on certain general principles, e.g.:
1. That biological molecules have been 'selected' for specific functions.
2. That biological events always tend to happen in a manner that will lead to an overall decrease
in free energy.
3. That biological systems are open, dynamic and self-ordering.
In the higher forms of life biological organization falls into a series of levels arranged in a
discontinuous order. At each level there appear to be units of a fairly definite size which become
associated to form a unit at the next level, and as each successive level of organization is achieved
new properties emerge. The levels may be listed as follows:
(a) Small molecules
(b) Macromolecules
1
2 Chapter 1 : Introduction- The scope of biochemistry
(c) Subcellular structures
(d) Cells
(e) Tissues
(/) Organs
(g) Organisms
(A) Societies.
For the most part, biochemical studies are concentrated at the levels of molecules, subcellular
structures and cells, but, in order to explain iife' in chemical and physicochemical terms every
level of organization must be studied and it is where discontinuities exist that the most
challenging problems occur. For example, how do cells differentiate? What makes cells of the
same and different types associate to form tissues? Why do cells, organs and organisms grow to
a certain size and then stop growing? Why are partially constructed subcellular components, e.g.
mitochondria, membranes, cilia etc., never seen within cells? Such structures are either present
in their completed form or not present at all. This suggests that assembly of the components into
the single appropriate configuration depends on the existence of a precise set of conditions
under which they fall into their proper place in the right numbers and orientation for the
assembly of the complete structure.
Biological organization therefore seems to require the provision of a suitable environment
where the individual molecules can interact in such a way that they become specifically
orientated. The mitotic spindle is formed in just this way since it appears spontaneously in
response to a set of critically determined environmental conditions. Another example is seen in
the formation of collagen fibres, where a self-ordered fabric is produced by the mutual
interaction of collagen molecules (Chapter 27). Furthermore molecular organization depends
on appropriate molecular architecture since, for molecules to interact, they must be suitably
designed. In fact, natural selection has ensured that biological macromolecules are uniquely
fitted for their functional role. The simplest function o fa macromolecule is perhaps the storage
of energy. A substance which fulfils this role in the animal world is glycogen, a biopolymer of
glucose. To serve its purpose the structure of glycogen does not need to be very precisely defined
provided that it can be degraded rapidly when extra energy is required. It is significant,
therefore, that the molecular weight of glycogen is variable and that it possesses a highly
branched structure, which means that the molecule is vulnerable to enzymic attack at many
points simultaneously (Figure 7.2).
Proteins, the most ubiquitous of the biological macromolecules, perform an enormous variety
of functions, and have structures which are not only complicated but also highly specific. They
are composed of a large but definite number o famino acid units selected from twenty or so
different types joined together in a specific sequence. Although the protein molecules are linear
and unbranched the properties of their amino acid side chains are such that highly specific
interactions occur. These take place between different protein molecules so that they are able to
associate to form sheets and bundles and also between different parts of the same molecule so
that it may assume an elaborately folded configuration. As a consequence, protein molecules
have well-defined geometrical shapes, and as a result of ionization effects they also have
characteristic patterns of electric charge. Such patterns are believed to play an important part in
their interaction with other molecules.
Proteins fulfil both structural and metabolic functions within the organism. The requirements
for structural proteins are that they should be insoluble, chemically stable and possess a rigid
structure capable of orientation. The long chain-like molecules of structural proteins are usually
only slightly folded and have specific bonding sites so that the molecule scan join together both
in series and in parallel to form molecular aggregations with great tensile strength and varying
