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Microbial Biochemistry . G.N. Cohen Microbial Biochemistry Second Edition Prof. G.N. Cohen Institut Pasteur rue du Docteur Roux 28 75724 Paris France [email protected] ISBN 978-90-481-9436-0 e-ISBN 978-90-481-9437-7 DOI 10.1007/978-90-481-9437-7 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2010938472 # Springer Science+Business Media B.V. 2011 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Foreword This book originates from almost 60 years of living in the company of micro- organisms, mainly with Escherichia coli. My scientific life has taken place almost exclusively at the Institut Pasteur in Paris, where many concepts of modern molecular biology were born or developed. The present work emphasizes the interest of microbial physiology, biochemistry and genetics. It takes into account the considerable advances which have been made in the field in the last 30 years by the introduction of gene cloning and sequencing and by the exponential development of physical methods such as X-ray crystallog- raphy of proteins. The younger generation of biochemists is legitimately interested in the problems raised by differentiation and development in higher organisms, and also in neuros- ciences. It is however my feeling that the study of prokaryotes will remain for a long time the best introduction to general biology. A particular emphasis has been given to particular systems which have been extensively studied from historical, physiological, enzymological, structural, genetic and evolutionary points of view: I present my apologies to those who may find that this choice is too personal and reflects too much my personal interest in subjects in which I have either a personal contribution or where important results have been obtained by some of my best friends. I am grateful to the Philippe Foundation for the help it has given to me and to many of my students for many years. My thanks are due to my wife, Louisette Cohen for her patience and help, not only while this book was written, but also during our near 70 years common life. This work is a tribute to the memory of my beloved colleagues, my mentor Jacques Monod, and the late Harold Amos, Dean B. Cowie, Michael Doudoroff, Ben Nisman, Earl R. Stadtman, Roger Y. Stanier, Germaine Stanier, Huguette and Kissel Szulmajster. Paris, France G.N. Cohen v . Contents 1 Bacterial Growth ..............................................................1 The Lag Phase ..................................................................1 The Exponential Phase..........................................................1 Linear Growth...................................................................2 The Yield of Growth............................................................3 Variation of the Growth Rate at Limiting Carbon Source Concentrations ..................................................................4 Continuous Growth: The Chemostat ...........................................5 Advantages of the Continuous Exponential Culture ...........................7 Diauxic Growth .................................................................7 Selected References........................................................... 10 2 The Outer Membrane of Gram-negative Bacteria and the Cytoplasmic Membrane ........................................... 11 The Outer Membrane of Gram-Negative Bacteria .. ......................... 11 The Cytoplasmic Membrane.................................................. 12 Energy Generation ............................................................ 13 ATP Synthase .............................................................. 13 Subunit Composition of the ATP Synthase .................................. 14 ATP Synthesis in Archaea .................................................... 16 Selected References........................................................... 16 3 Peptidoglycan Synthesis and Cell Division ................................ 17 General Structure ............................................................. 17 Assembly of the Peptidoglycan Unit ......................................... 18 The Membrane Steps ......................................................... 19 Assembly of the Murein Sacculus ............................................ 20 Penicillin Sensitivity .......................................................... 20 Cell Division . ................................................................. 21 Selected References........................................................... 22 vii viii Contents 4 Cellular Permeability ....................................................... 23 Accumulation, Crypticity, and Selective Permeability....................... 24 b-Galactoside Permease....................................................... 25 Accumulation in Induced Cells: Kinetics and Specificity ................. 26 The Induced Synthesis of Galactoside Permease . ......................... 29 Functional Significance of Galactoside Permease: Specific Crypticity ... 30 Functional Relationships of Permease: Induction ......................... 32 Genetic Relationships of Galactosidase and Galactoside Permease... ................................................................. 32 Galactoside Permease as Protein........................................... 33 Periplasmic Binding Proteins and ATP Binding Cassettes................... 36 Phosphotransferases: The PTS System ....................................... 39 TRAP Transporters ........................................................... 41 A Few Well-identified Cases of Specific Cellular Permeability ............. 42 Amino Acid Permeases .................................................... 42 Peptide Permeases.......................................................... 43 Porins.......................................................................... 45 Iron Uptake... ................................................................. 47 Conclusion ... ................................................................. 48 Selected References........................................................... 48 5 Allosteric Enzymes .......................................................... 51 Allosteric Inhibition and Activation .......................................... 54 An Alternative Model......................................................... 61 Conclusion ... ................................................................. 62 Selected References........................................................... 62 6 Glycolysis, Gluconeogenesis and Glycogen Synthesis .................... 63 Glycogen Degradation ........................................................ 63 Glycolysis ..................................................................... 63 Hexokinase ................................................................. 65 Glucose 6-Phosphate Isomerase............................................ 65 Phosphofructokinase ....................................................... 66 Fructose 1,6-Bisphosphate Aldolase ....................................... 68 Triose Phosphate Isomerase................................................ 68 Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH).................. 68 Phosphoglycerate Kinase................................................... 69 Phosphoglyceromutase ..................................................... 69 Enolase ..................................................................... 69 Pyruvate Kinase ............................................................ 70 Gluconeogenesis .............................................................. 70 Fructose Bisphosphatase in Microorganisms ................................. 70 Glycogen Synthesis ........................................................... 71 Glycogen Synthase ......................................................... 71 Contents ix Control of Glycogen Biosynthesis ............................................ 72 Branching Enzyme ............................................................ 72 7 The Pentose Phosphate and Entner–Doudoroff Pathways ............... 73 The Pentose Phosphate Pathway.............................................. 73 The Enzymes of the Oxidative Phase......................................... 73 Glucose 6-Phosphate Dehydrogenase...................................... 73 6-Phosphogluconolactonase ................................................ 74 6-Phosphogluconate Dehydrogenase (Decarboxylating) .................. 74 Ribose Phosphate Isomerase ............................................... 74 The Enzymes of the Non-oxidative Phase.................................... 74 Transketolase ............................................................... 75 Transaldolase ............................................................... 76 Ribulose-5-Phosphate-3-Epimerase........................................ 76 Regulation of the Pentose Phosphate Pathway ............................... 77 The Entner–Doudoroff Pathway ........................................... 77 8 The Tricarboxylic Acid Cycle and the Glyoxylate Bypass
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