Energy in Biological Systems

182 Pages·1991·25.936 MB·English

by  C. A. Smith, E. J. Wood

Energy in
BIOLOGICAL
SYSTEMS
MolecLAlar aVid Cell
...- -...
BIOCHEMISTRY
Energyin
BIOLOGICAL
SYSTEMS
SMITH AND WOOD
[C1J
SPRINGER-SCIENCE+BUSINESS MEDIA, B.V.
First edition 1991
© Springer Science+Business Media Dordrecht 1991
OriginalIy published by Chapman & HalI in 1991
Typeset in 10/11 Y2pt Palatino by EJS Chemical Composition,
Midsomer Norton, Bath, Avon
ISBN 978-0-412-40770-3
Apart from any fair dealing for the purposes of research or private study,
or criticism orreview, as permitted under the UK Copyright Designs and
Patents Act, 1988, this publication may not be reproduced, stored,
or transmitted, in any form or by any means, without the prior permission
in writing of the publishers, or in the case of reprographic reproduction
only in accordance with the terms of the licences issued by the Copyright
Licensing Agency in the UK, or in accordance with the terms of licences
issued by the appropriate Reproduction Rights Organization outside
the UK. Enquiries conceming reproduction outside the terms stated
here should be sent to the publishers at the UK address printed on
thispage.
The publisher makes no representation, express or implied, with regard
to the accuracy of the information contained in this book and cannot
accept any legal responsibility or liability for any errors or omissions that
maybemade.
British Library Cataloguing in Publication Data
Energy in biological systems. -(Molecular and cell biochemistry)
1. Smith, C. II. Wood, E.J. III. Series
574.5
ISBN 978-0-412-40770-3 ISBN 978-94-011-3124-7 (eBook)
DOI 10.1007/978-94-011-3124-7
Library of Congress Cataloging-in-Publication Data
Available
Copy Editors: Sara Firman and Judith Ockenden
Sub-editor: Simon Armstrong
Production Controller: Marian Saville
Layout Designer: Geoffrey Wadsley (after an original design by Julia Denny)
IlIustrators: Capricom Graphics
Cover design: Amanda Barragry
Contents
Editors' foreword vii
Contributors viii
Preface ix
Abbreviations x
Greek alphabet xii
1 Energy and life 1
1.1 Introduction 1
1.2 Thermodynamics 2
1.3 Free energy, enthalpy and entropy 3
1.4 The biochemistry of adenosine triphosphate (ATP) 11
1.5 Overview 15
Answers to exercises 15
Questions 16
2 An overview of bioenergetics 18
2.1 Introduction 18
2.2 Organization of metabolism 20
2.3 What is catabolism for? 26
2.4 Acquiring energy from the environment 33
2.5 Strategies for generating ATP and NADPH in catabolism 40
2.6 Overview 44
Answers to exercises 44
Questions 45
3 Electron transport 47
3.1 Introduction 47
3.2 Electron transport 48
3.3 Oxidative phosphorylation 56
3.4 Synthesis of AIP 61
3.5 Photosynthesis 65
3.6 The mechanism of ATP synthesis 70
3.7 Overview 72
Answers to exercises 73
Questions 73
4 The tricarboxylic acid cycle 75
4.1 Introduction 75
4.2 How the cycle was elucidated 76
4.3 Some biochemical details 84
4.4 The TCA cycle in relation to other cellular processes 91
4.5 Overview 98
Answers to exercises 98
Questions 99
7
L
Contents v
5 Glycolysis 101
5.1 Introduction 101
5.2 Early history of the study of glucose metabolism 101
5.3 The Embden-Meyerhof pathway 104
5.4 Biological significance of the glycolytic pathway 107
5.5 Glycogen and other polysaccharides 110
5.6 Other monosaccharides 115
5.7 The pentose phosphate pathway 116
5.8 Overview 122
Answers to exercises 123
Questions 123
6 Lipids: breakdown of fatty acids; brown fat; ruminant metabolism 125
6.1 Introduction 125
6.2 Triacylglycerols as energy reserves 125
6.3 Oxidation of fatty acids 126
6.4 Thermogenesis 129
6.5 Ruminant metabolism 133
6.6 Overview 137
Answers to exercises 137
Questions 138
7 Amino acid catabolism 139
7.1 Introduction 139
7.2 Protein degradation 139
7.3 Removal of nitrogen from amino acids 141
7.4 Essential amino acids 144
7.5 Carbon chain catabolism 146
7.6 Interconversion of amino acids and transamination 150
7.7 Pathways for nitrogen excretion 155
7.8 Biosynthesis of urea 156
7.9 Overview 160
Answers to exercises 160
Questions 160
Answers to questions 162
Glossary 167
Index 169
/ vi Contents /
'--------------'
Editors'
Foreword
This book is one of a series of brief fundamental·· texts for junior
undergraduates and diploma students in biological science. The series,
Molecular and Cell Biochemistry, covers the whole of modem biochemistry,
integrating animal, plant and microbial topics. The intention is to give the
series special appeal to the many students who read biochemistry for only
part of their course and who are looking for an all-encompassing and
stimulating approach. Although all books in the series bear a distinct family
likeness, each stands on its own as an independent text.
Many students, particularly those with less numerate backgrounds, find
elements of their biochemistry courses daunting, and one of our principal
concerns is to offer books which present the facts in a palatable style. Each
chapter is prefaced by a list of learning objectives, with short summaries and
revision aids at the ends of chapters. The text itself is informal, and the
incorporation of marginal notes and information boxes to accompany the
main text give a tutorial flavour, complementing and supporting the main
narrative. The marginal notes and boxes relate facts in the text to applicable
examples in everyday life, in industry, in other life sciences and in medicine,
and provide a variety of other educational devices to assist, support, and
reinforce learning. References are annotated to guide students towards
effective and relevant additional reading.
Although students must start by learning the basic vocabulary of a subject,
it is more important subsequently to promote understanding and the ability to
solve problems than to present the facts alone. The provision of imaginative
problems, examples, short answer questions and other exercises are designed
to encourage such a problem-solving attitude.
A major challenge to both teacher and student is the pace at which
biochemistry and molecular biology are advancing at the present time. For the
teacher and textbook writer the challenge is to select, distill, highlight and
exemplify, tasks which require a broad base of knowledge and indefatigable
reading of the literature. For the student the challenge is not to be
overwhelmed, to understand and ultimately to pass the examination! It is
hoped that the present series will help by offering major aspects of
biochemistry in digestible portions.
This vast corpus of accumulated knowledge is essentially valueless unless
it can be used. Thus these texts carry frequent, simple exercises and problems.
It is expected that students will be able to test their acquisition of knowledge
but also be able to use this knowledge to solve problems. We believe that only
in this way can students become familiar and comfortable with their
knowledge. The fact that it is useful to them will mean that it is retained,
beyond the last examination, into their future careers.
This series was written by lecturers in universities and polytechnics who
have many years of experience in teaching, and who are also familiar with
current developments through their research interests. They are, in addition,
familiar with the difficulties and pressures faced by present-day students in
7
/
Editors' foreword vii
the biological sciences area. The editors are grateful for the co-operation of all
their authors in undergoing criticism and in meeting requests to re-write (and
sometimes re-write again), shorten or extend what they originally wrote.
They are also happy to record their grateful thanks to those many individuals
who very willingly supplied illustrative material promptly and generously.
These include many colleagues as well as total strangers whose response was
positive and unstinting. Special thanks must go to the assessors who very
carefully read the chapters and made valuable suggestions which gave rise to
a more readable text. Grateful thanks are also due to the team at Chapman &
Hall who saw the project through with good grace in spite, sometimes, of
everything. These include Dominic Recaldin, Commissioning Editor,
Jacqueline Curthoys, formerly Development Editor, Simon Armstrong,
Sub-editor, and Marian Saville, Production Controller.
Finally, though, it is the editors themselves who must take the
responsibility for errors and omissions, and for areas where the text is still not
as clear as students deserve.
Contributors DR P.S. AGUTTER Department of Biological Sciences, Napier College
of Commerce, Edinburgh, UK. Chapters 4 and 5.
DR J. ARONSON Department of Molecular and Cellular Biology, University
of Arizona, Tucson, Arizona, USA. Chapter 7.
DR J.J. GAFFNEY Department of Biological Sciences, Manchester Polytechnic,
Manchester, UK. Chapters 3 and 6.
PROFESSOR J.J.A. HEFFRON Department of Biochemistry, University
College, Cork, The Republic of Ireland. Chapter 1.
DR S. SHAW Department of Biological Sciences, Manchester Polytechnic,
Manchester, UK. Chapter 2.
DR c.A. SMITH Department of Biological Sciences, Manchester Polytechnic,
Manchester, UK. Chapters 5 and 6.
/ viii Contributors /
L_- _____- ----'
Preface
The generation of biologically usable energy by oxidative processes, including
electron transport, is a major area of importance to all life forms. It is a
complex area and one that is still rather poorly understood despite many
person-years of research and the accumulation of a plethora of data. For both
student and teacher this presents problems. Many students, for example, find
the idea of thermodynamics intrinsically difficult and are resistant to it as well
as being poorly equipped mathematically to appreciate fully the concepts
involved. Many teachers, too, are sceptical of the value of the rigorous
application of classical thermodynamics to biological systems and may be less
than enthusiastic in their teaching of it as a result. However, it has to be said
that without a knowledge of energy relationships, the catabolic and anabolic
pathways of metabolism are virtually meaningless.
The initial chapters of this book, therefore, offer a simple approach to, and
an explanation of, relevant thermodynamic principles in familiar terms, and
provide a basis for the rest of the material in the book. The next chapter gives
the basic information required for understanding the ways in which
biologically usable energy in the form of ATP is produced via oxidative
pathways. It aims to give a clear and concise explanation of the structure and
function of the coenzymes, and an up-to-date account, in simple terms, of
how the transduction of oxidative energy is achieved in organelles such as the
mitochondria. The pathways and mechanisms described form the metabolic
hub into which reducing equivalents are fed from the breakdown of all food
and storage materials. The four final chapters then describe these catabolic
pathways-the TeA cycle, and carbohydrate, lipid and amino acid break
down-in detail.
Athough this approach is the reverse of that taken in many textbooks, it is
our aim to show students where they are going or where pathways lead. In
our experience, students all too often 'start at the top' with little idea of why
glucose, or a fatty acid, or amino acid, is undergoing catabolism in the first
place. Therefore, an initial understanding of 'the final common pathway' of
catabolism and energy production helps them orient their study of the vast
numbers of catabolic routes.
In a number of cases we have attempted to give metabolism a new slant
by discussing the pathways from a historical standpoint. We tend to forget
rather too easily the years of painstaking pioneering work by dedicated
biochemists, who produced brilliant advances without the help of the
sophisticated equipment, automated devices and computers that are
regarded as the sine qua non these days. The aim of this is to emphasise that it
is the original, experimental scientific approach that is important in making
advances rather than the number of pounds spent on sophisticaed
equipment.
We have also tried to stress the importance of linking chemical detail to
biological function. From a student's point of view, nothing is worse than
perceiving metabolic pathways as series of complex reactions to be learned by
rote, without any comprehension of what they are. Hopefully, our approach
will encourage students to take a step back and understand, rather than learn
by heart because there might be a question in the examination!
The area of bioenergetics is poorly served by student texts: we hope that the
present volume goes some way towards providing an accessible and
enjoyable introduction to it.
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Preface ix
Abbreviations
A adenine (alanine)
ACP acyl carrier protein
ACTH adrenal corticotrophic hormone
ADP adenosine diphosphate
Ala,A alanine
AMP adenosine monophosphate
cAMP adenosine 3' ,5'-cyclic monophosphate
Arg,R arginine
Asn,N asparagine
Asp,D aspartic acid
ATP adenosine triphosphate
ATPase adenosine triphosphatase
C cytosine (cysteine)
CDP cytidine diphosphate
CMP cytidine monophosphate
CTP cytidine triphosphate
CoA,CoASH coenzyme A
CoQ,Q coenzyme Q, ubiquinone
Cys,C cypteine
d- 2-deoxy-
D aspartic acid
d-Rib 2- deoxyribose
DNA deoxyribonucleic acid
cDNA complementary DNA
e- electron
E glutamic acid
E oxidation-reduction potential
F phenylalanine
F the Faraday (9.648 x 104 coulomb mol-l)
FAD flavin adenine dinucleotide
Fd ferredoxin
fMet N-formyl methionine
FMN flavin mononucleotide
Fru fructose
g gram
g acceleration due to gravity
G guanine (glycine)
G free energy
Gal galactose
G1c glucose
/
/ x Abbreviations
Gln,Q glutamine
Glu, E glutamic acid
Gly,G glycine
GDP guanosine diphosphate
GMP guanosine monophosphate
GTP guanosine triphosphate
H histidine
H enthalpy
Hb haemoglobin
His,H histidine
Hyp hydroxyproline (HOPro)
I isoleucine
IgG immunoglobulin G
IgM immunoglobulin M
He, I isoleucine
ITP inosine triphosphate
Joule
K degrees absolute (Kelvin)
K lysine
L leucine
Leu,L leucine
lux naturaliogarithm ofx = 2.3031oglOx
Lys,K lysine
M methioine
Mn relative molecular mass, molecular weight
Man mannose
Mb myoglobin
Met,M methionine
N asparagine
N Avogadro's number (6.022 x 1023)
N any nucleotide base (e. g. in NTP for nucleotide
triphosphate)
nicotinamide adenine dinucleotide
nicotinamide adenine dinucleotide phosphate
P proline
Pi inorganic phosphate
PPi inorganic pyrophosphate
Phe,F phenylalanine
Pro,P proline
Q coenzyme Q, ubiquinone
Q glutamine
R arginine
R the gas constant (8.314J K-I mol-I)
Rib ribose
RNA ribonucleic acid
mRNA messenger RNA
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Abbreviations xi