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Ivan Kushkevych
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BACTERIAL
PHYSIOLOGY AND BIOCHEMISTRY
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Progress in Biochemistry and Biotechnology
BACTERIAL
PHYSIOLOGY AND BIOCHEMISTRY
Ivan Kushkevych
Department of Experimental Biology,
Faculty of Science, Masaryk University,
Brno, Czech Republic
Edited by
Josef Jampílek
Academic Press is an imprint of Elsevier
125 London Wall, London EC2Y 5AS, United Kingdom
525 B Street, Suite 1650, San Diego, CA 92101, United States
50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States
The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom
No part of this publication may be reproduced or transmitted in any form or by any means,
electronic or mechanical, including photocopying, recording, or any information storage and
retrieval system, without permission in writing from the publisher. Details on how to seek
permission, further information about the Publisher’s permissions policies and our
arrangements with organizations such as the Copyright Clearance Center and the Copyright
Licensing Agency, can be found at our website: www.elsevier.com/permissions.
This book and the individual contributions contained in it are protected under copyright by the
Publisher (other than as may be noted herein).
Notices
Knowledge and best practice in this field are constantly changing. As new research and
experience broaden our understanding, changes in research methods, professional practices, or
medical treatment may become necessary.
Practitioners and researchers must always rely on their own experience and knowledge in
evaluating and using any information, methods, compounds, or experiments described herein.
In using such information or methods they should be mindful of their own safety and the safety
of others, including parties for whom they have a professional responsibility.
To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors,
assume any liability for any injury and/or damage to persons or property as a matter of products
liability, negligence or otherwise, or from any use or operation of any methods, products,
instructions, or ideas contained in the material herein.
ISBN: 978-0-443-18738-4
ACKNOWLEDGEMENTS...................................................................................................... ix
ABBREVIATIONS.................................................................................................................. xi
FOREWORD.......................................................................................................................... xiii
vi
contents
5.5.2. Anaerobic respiration................................................................. 199
5.5.2.1. Nitrate reduction and denitrification...........................199
5.5.2.2. Sulfate reduction (desulfurization)............................. 202
5.5.2.3. Carbon (IV) oxide reduction to methane....................208
5.5.3. Aerobic respiration in chemolithotrophic bacteria..................... 210
5.5.3.1. Oxidation of ammonia................................................ 211
5.5.3.2. Oxidation of reduced sulfur compounds..................... 213
5.5.3.3. Oxidation of iron compounds.....................................216
5.5.3.4. Oxidation of hydrogen................................................217
5.5.3.5. Oxidation of methane.................................................. 218
5.5.4. Aerobic respiration in chemoorganotrophic bacteria................. 218
5.5.4.1. Incomplete oxidation of substrate...............................219
5.5.4.2. Complete oxidation of substrate.................................220
5.5.4.3. Oxidation of saccharides and polysaccharides...........225
5.5.4.4. Oxidation of lipids......................................................227
5.5.4.5. Oxidation of hydrocarbons.........................................229
5.5.5. Catabolism of nitrogenous compounds...................................... 233
5.5.5.1. Dissimilation of proteins and amino acids.................. 233
5.5.5.1.1. Anaerobic degradation
(amino acid fermentation).......................... 233
5.5.5.1.2. Aerobic (oxidative) catabolism
of amino acids............................................240
5.5.6. Catabolism of heterocyclic compounds..................................... 246
5.5.6.1. Fermentation of heterocyclic compounds................... 246
5.5.6.2. Oxidation of heterocyclic compounds........................249
5.6. Processes of anabolism (biosynthesis)..................................................251
5.6.1. Biosynthesis of saccharides....................................................... 251
5.6.2. Biosynthesis of lipids.................................................................259
5.6.3. Consumption of CO2 by heterotrophic bacteria.........................265
5.6.4. Fixation of molecular nitrogen...................................................268
5.6.5. Biosynthesis of amino acids.......................................................269
5.6.6. Biosynthesis of nucleotides........................................................278
5.6.7. Biosynthesis of nucleic acids..................................................... 282
5.6.8. Biosynthesis of proteins.............................................................285
5.7. Regulation of metabolism process........................................................291
5.7.1. Regulation of enzyme synthesis................................................. 292
5.7.2. Regulation of enzymatic activity...............................................297
5.7.3. Specifics of regulation mechanisms...........................................298
5.7.4. Regulation of energetic metabolism...........................................300
vii
contents
5.8. Metabolism of phototrophic bacteria.................................................... 301
5.8.1. Photolithotrophs......................................................................... 301
5.8.2. Photoorganotrophs..................................................................... 305
RECOMMENDED REFERENCES.......................................................................................361
INDEX ...................................................................................................................................363
viii
ACKNOWLEDGEMENTS
Scientific reviewers:
Prof. PharmDr. Josef Jampílek, Ph.D., Professor of Medicinal Chemistry, Department of Chemical Biology,
Faculty of Science, Palacky University Olomouc, Slechtitelu 27, 783 71 Olomouc, Czech Republic;
Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava,
Ilkovicova 6, 842 15 Bratislava, Slovakia
Prof. Lorenzo Drago, Ph.D., Professor of Clinical Microbiology, Department of Biomedical Sciences for
Health, University of Milan, 20133 Milan, Italy
Prof. Aidan Coffey, Ph.D., Professor of Microbiology, Department of Biological Sciences, Cork Institute
of Technology, Bishopstown, Cork, Ireland
This educational book contains the modern knowledge of bacterial physiology and biochemistry.
The book includes seven chapters that describe the subject of bacterial physiology, chemical composition,
functional cell structures, nutrition, growth, and the processes of cell differentiation. Special attention
is paid to the bacterial metabolism, including the processes of catabolism and anabolism. The energy
of biochemical reactions, carriers of hydrogen, the role of ATP in the bacterial cells, and types of
phosphorylation are also discussed. The physiological role of bacteria in ecosystems, intercellular and
internal population interactions, quorum-sensing regulation of gene expression, and luminescent bacteria
and bioluminescence are described. The effect of environmental factors on bacteria, including physical
and chemical factors, and their mechanisms are presented. The description of chemotherapeutics and
antibiotics and mechanisms of their action is also provided. This book can be helpful for bachelor and
master students who study General Microbiology, Medical Microbiology, Veterinary Microbiology, and
Molecular Biology, for microbiologists, biochemists, biologists, experts in the cell and molecular biology,
and for readers interested in the study of bacterial physiology and biochemistry.
Acknowledgments: The author sincerely thanks Igor Starunko from Ivan Franko National Univer-
sity of Lviv (Ukraine) for his help and the technical preparation of the illustrative material and layout of
the book. The author also expresses special thanks to the scientific editor, Prof. Josef Jampílek, as well as
the reviewers, Prof. Lorenzo Drago and Prof. Aidan Coffey, for their time and help, critical comments,
and recommendations during preparation of this book.
Ivan Kushkevych
ix
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chapter 1. introduction into bacterial physiology and biochemistry
ABBREVIATIONS
xii
FOREWORD
xiv
chapter 1. introduction into bacterial physiology and biochemistry
CHAPTER 1
I n this chapter, the studies of bacterial physiology and biochemistry and their
main goals are characterized. Bacteria in the phylogeny of living organisms and
diversity of cell shapes are described. Special attention is paid to the comparison of
cell structures and their metabolic properties in different organisms, including bacteria,
archaea, and eukaryotes. Moreover, main features of bacterial evolution and methods
of modern bacterial physiology and biochemistry are presented.
Ribosomes:
Size 70S 70S 80S
Sensitivity to chloramphenicol and Positive Negative Negative
kanamycin
Metabolism:
Similar ATPase Absent Present Present
Methanogenesis Absent Present Absent
Fixation of nitrogen Present Present Absent
Photosynthesis with participation
of chlorophyll Present Absent Present
Chemolithotrophs Present Present Absent
2
chapter 1. introduction into bacterial physiology and biochemistry
Thermotoga Diplomonads
Aquifex
Archaea are highly specialized prokaryotic organisms, and although they are simi-
lar to bacteria in the structural organization, they have a number of fundamental diffe
rences. The most important feature of the archaea is the specificity of their ribosomal
and transport RNA; their ribosomes differ in shape. Differences were also found in
other components of the protein synthesis system. Archaea do not have fatty acids and
polyhydric alcohols as part of membrane lipids and usually have from 20 to 40 carbon
atoms. The lipid layer of the membrane is formed by a monomolecular layer, which,
obviously, gives its strength. Externally, archaea often have surface layers formed in
a certain way by structured and regularly packed protein or glycoprotein molecules of
the correct and sometimes strange form. The structure of the cell wall of the archaea may
include peptides and polysaccharides. Some archaea are characterized by processes that
are not intrinsic to other organisms. For example, some representatives of this group
of prokaryotes form methane (methanogens) in their process of life. Most archaeas are
extremophiles, that is, they develop under extreme conditions, at high temperatures
(+90 °C) or in saturated saline solutions. Acidophilic archaea grow in the environment,
4
chapter 1. introduction into bacterial physiology and biochemistry
where the pH is as low as in the concentrated sulfuric acid. There are autotrophic forms
of archaea that do not require organic food but are satisfied with the energy obtained
through oxidation–reduction reactions, with the involvement of inorganic molecules.
Bacteria that differ in their morphological and physiological properties are an
extremely diverse group of prokaryotic microorganisms. They can be spherical, cylin-
drical, spiral, and pleomorphic (Fig. 1.3).
Diplobacilli
Streptococci
Streptobacilli
Tetrad
Sarcina
Coccobacilli
Staphylococci
Spiral shapes
Fig. 1.3. Basic shapes of bacterial cells: spherical (coccus, cocci), rods (bacteria, bacillus), and spirals.
5
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qualifications of a popular teacher. He would not have aspired to
finished eloquence of style: to the eloquence of gesture and of
manner, he was still more a stranger. But there is an eloquence of
physiognomy, which Mr. Rittenhouse most eminently possessed.
The modesty and amenity of his manner would have effected much,
whether his audience had been a class of philosophers, or an
assembly of ladies. Of his own discoveries, and opinions, and
theories, he would have always spoken with that sweet and modest
reserve, for which he was ever distinguished. He would have dwelt
with the most generous and ample enthusiasm upon the great
discoveries of Newton; and if, at any time, he could have forgotten
that impartial conduct, which it is the duty of the historian of a
science to observe, it would have been when he might have had
occasion to defend the theories of that great man, against the
objections of succeeding and minor philosophers.
Not fifteen days before his death, he had finished the perusal of a
German translation of Rousseau’s beautiful letters on Botany, which I
had put into his hands.
Mr. Rittenhouse, like Newton and many other men of great talents,
employed much of his time in the perusal of works on the subject of
natural and revealed religion. This was, I think, more especially the
case in the latter part of his life. Among other books which I could
mention, I well recollect that he read the Thoughts of the celebrated
French philosopher Pascall: and he acknowledged, that he read
them with pleasure. But that pleasure, he observed to me, was
diminished, when he learned, what was often the state of Pascall’s
mind:—a state of melancholy and gloom: and sometimes even of
mental derangement. At the time of his death, the American
Philosopher was engaged in the perusal of Mosheim’s Ecclesiastical
History: and he had just before finished the perusal of the
Meditations of the Emperor Marcus Antoninus; that excellent work,
replete with the sublimest morality, and with much of a sublime
religion.
About three weeks before his death, I had put into his hands the
first volume of Dr. Ferguson’s Elements of Moral and Political
Science. I took the liberty of particularly directing his attention to the
last chapter of the volume: the chapter on the future state. He read it
with so much satisfaction, that he afterwards sent it to his elder
daughter, with a request that she would peruse it.
Letter from Lady Juliana Penn to the Rev. Peter Miller, Ephrata.
Sir,
I did not receive the precious stone, you were so goad to send me,
till yesterday. I am most extremely obliged to you for it. It deserves to
be particularly distinguished on its own, as well as the giver’s
account. I shall keep it with a grateful remembrance of my
obligations to you.
Juliana Penn.
Sir,
Go. Washington.
A1. The reader will find a very learned and interesting dissertation
on the astronomy of these and other nations of antiquity, in Lalande’s
Astronomie, liv. ii. W. B.
A2. Our orator might well pass on, without noticing more
particularly the fabulous annals of the Chaldeans. They assigned to
the reigns of their ten dynasties, 432 thousand years: and Lalande
observes, that this number, 432, augmented by two or by four
noughts, frequently occurs in antiquity. This prodigious number of
years expresses, according to the notions of the inhabitants of India,
the duration of the life of a symbolical cow: in the first age, this cow,
serving as a vehicle for innocence and virtue, advances with a firm
step upon the earth, supported by her four feet; in the second, or
silver age, she becomes somewhat enfeebled, and walks on only
three feet; during the brazen, or third age, she is reduced to the
necessity of walking on two; finally, during the iron age, she drags
herself along; and, after having lost, successively, all her legs, she
recovers them in the succeeding period, all of them being
reproduced in the same order.
Mr. Lalande remarks, that these four ages have a relation to the
numbers 4, 3, 2, 1, which seem to announce some other thing than
an historical division. Therefore, to give this fabulous duration of the
world some semblance of truth. Mr. Bailly[A2a] rejects, in the first
place, the fourth age, of which, at present, (that is, when Lalande
wrote,) only 4887 years have passed: the residue of this duration
could not be considered by Bailly as any thing more than a reverie:
and as for the three first ages, he takes the years for days; in order
to shew, that, in reality, they reckoned by days, before they
computed by solar years. By these means, Bailly has reduced the
pretensions of the people of India to 12,000 years; and he identifies
this calculation for the Indians with that of the Persians, who give,
likewise, 12,000 years for the duration of the world. The accordance
thus produced in the two chronologies, seemed to Bailly to
strengthen the authenticity of the recital; and makes it appear, that
these notions prevailed alike among the Egyptians and the Chinese.
Such are the data, such the calculations, and such the reasoning
of Mr. Bailly, on this subject.
But, although Mr. Lalande has noticed the retrograde series of the
progressive numbers (1,) 2, 3, 4, in the Asiatic account of the age of
the world, a kind of mysterious constitution of the amount of the
years, in the several ages which make up the entire sum of its
duration, seems to have escaped the observation of that acute
philosopher; and probably the same circumstance passed also
unnoticed by Mr. Bailly: it may be considered as a species of
chronological abracadabra, engendered in the prolific brain of some
eastern philosopher: the following is the circumstance here meant. It
will be perceived, in the first place, that the arrangement of the
numerical figures, in making up the years allotted to the fourth age of
the world, is apparently artificial, and therefore, probably, altogether
arbitrary. It will then be seen, that the number of years in the third
age is double the amount of those in the fourth; that those in the
second is made up by adding together the years in the fourth and
third ages; and, that those in the first age are constituted by an
addition of the number of years in the fourth and second ages. This
being the fact, it does not seem to bear out Mr. Bailly, in his
hypothesis, and the calculations founded on it. W. B.
A2a. Mr. Bailly was the author of a History of Ancient and modern Astronomy.
His Essay on the Theory of Jupiter’s Satellites, which is said to be a valuable
treatise, was published in the year 1766. Both works are in the French language,
and were printed in France.
A3. Lalande observes that Mr. Bailly has gone back, in his
astronomical researches, to the first traditions of an antedeluvian
people, among whom there remained scarcely any traces of such
knowledge; and that he has presented us, in his work, with ingenious
conjectures and probabilities; or, more properly, appearances of
truth, (“vraisemblables,”) written with many charms of extensive
information. But, according to Mr. Lalande himself, all the ancient
astronomy down to the time of Chiron, which was about fourteen
centuries before the Christian era, may with probability be reduced to
the examining of the rising of some stars at different times of the
year, and the phases of the moon; since, long after that period, as
this great astronomer remarks, the Chaldeans and Egyptians yet
knew nothing of either the duration or the inequalities of the
planetary movements. W. B.
A7. Friar Bacon is said to have been almost the only astronomer
of his age; he informs us that there were then but four persons in
Europe who had made any considerable proficiency in the
mathematics.
This astronomer, who was greatly celebrated in his time, was the
first, according to Lalande, who calculated good Almanacks; which
he had composed for thirty successive years; viz. from 1476 to 1506.
In these (which were all published at Nuremberg in 1474, two years
before his death,) he announced the daily longitudes of the planets,
their latitudes, their aspects, and foretold all the eclipses of the sun
and moon; and these ephemerides were received with uncommon
interest by all nations. After noticing these, Lalande mentions the
ephemerides which are published annually at Bologna, Vienna,
Berlin, and Milan; but he pronounces the Nautical Almanack, of
London, to be the most perfect ephemeris that was ever published.
Regiomontanus compiled several other works, which greatly
promoted his reputation, He died in 1476, at the age of forty years.
W. B.
A11. “Certain it is,” says the learned and pious Dr. Samuel Clarke
(in his Discourse on the Evidences of Nat. and Rev. Religion,) “and
this is a great deal to say, that the generality, even of the meanest
and most vulgar and ignorant people,” (among Christians,) “have
truer and worthier notions of God, more just and right apprehensions
concerning his attributes and perfections, deeper sense of the
difference of good and evil, a greater regard to moral obligations and
to the plain and more necessary duties of life, and a more firm and
universal expectation of a future state of rewards and punishments,
than, in any heathen country, any considerable number of men were
found to have had.”
A14. Thales, who died about five centuries and an half before the
Christian era, in the ninety-sixth year of his age,[A14a] first taught the
Greeks the cause of eclipses, He knew the spherical form of the
earth; he distinguished the zones of the earth by the mean of the
tropicks and the polar circles; and he treated of an oblique circle or
zodiac, of a meridian which intersects all these circles in extending
north and south, and of the magnitude of the apparent diameter of
the sun.
A14a. But, according to Dufresnoy, he was born in the first year of the 35th
Olympiad, and died the first year of the 52d, those periods corresponding,
respectively, with the years 640 and 572, B. C.: and if so, he lived only sixty-eight
years.