Table Of ContentC CELL BIOLOGY
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Very little in our human experience is truly comparable to the immensely
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crowded and bustling interior of a cell. Biological numeracy provides a new kind L
of understanding of the cellular world. This book brings together up-to-date
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quantitative data from the vast biological literature and uses the powerful tool of I b y t h e n u m b e r s
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“back of the envelope” estimates to reveal fresh perspectives and insights from
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numbers commonly encountered in cell biology. Readers gain a feeling for the
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sizes, concentrations, energies, and rates that characterize the lives of cells—
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thereby shedding new light on the microscopic realm.
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Rob Phillips, Ron Milo, and Nigel Orme
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Ron Milo is an Associate Professor in the Department of Plant and Environmental N
Sciences at the Weizmann Institute of Science in Israel. He created the BioNumbers M
database when he was a Systems Biology Fellow at Harvard Medical School. I
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Rob Phillips is the Fred and Nancy Morris Professor of Biophysics and Biology at &
the California Institute of Technology. He is co-author of the widely used book R
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Physical Biology of the Cell and a director and long-standing faculty member of the
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Physiology Course at the Marine Biological Laboratory.
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I Ron Milo
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Rob Phillips
ISBN 978-0-8153-4537-4
illustrated by
Nigel Orme
9 780815 345374
CellBiologyByTheNumbers COVER ART3.indd 1 18/09/2015 16:09
CELL BIOLOGY
by the numbers
CELL BIOLOGY
by the numbers
Ron Milo
Rob Phillips
illustrated by
Nigel Orme
Garland Science
Vice President: Denise Schanck
Senior Editor: Summers Scholl
Senior Editorial Assistant: Katie Laurentiev
Production Editor: Natasha Wolfe
Cover Designer and Illustrator: Nigel Orme
Copyeditor: John Murdzek
Typesetting: Cenveo, Inc.
Proofreader: Elephant Editorial Services
Indexer: Bill Johncocks
Chapter Opening Images:
Chapter 1: Courtesy of Shutterstock.com
Chapter 2: Courtesy of Mark van Coller
Chapter 3: Courtesy of George Karbus
Chapter 4: Courtesy of Clark Little Photography
Chapter 5: Courtesy of Sean Davey
Chapter 6: Courtesy of Shutterstock.com
© 2016 by Garland Science, Taylor & Francis Group, LLC
This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted
with permission, and sources are indicated. A wide variety of references are listed. Reasonable efforts have been made
to publish reliable data and information, but the author and the publisher cannot assume responsibility for the validity
of all materials or for the consequences of their use. All rights reserved. No part of this publication may be reproduced,
stored in a retrieval system or transmitted in any form or by any means—graphic, electronic, or mechanical, including
photocopying, recording, taping, or information storage and retrieval systems—without permission of the copyright
holder.
ISBN 978-0-8153-4537-4
The Library of Congress Cataloging-in-Publication data:
Milo, Ron, author.
Cell biology by the numbers / Ron Milo, Rob Phillips.
p. ; cm.
ISBN 978-0-8153-4537-4
[DNLM: 1. Cells–ultrastructure. 2. Cellular Structures. 3. Data Interpretation,
Statistical. QU 350]
QH585.5.D38
572—dc23
2015033337
Published by Garland Science, Taylor & Francis Group, LLC, an informa business,
270 Madison Avenue, New York NY 10016, USA, and 2 Park Square, Milton Park,
Abingdon, OX14 4RN, UK.
Printed in the United States of America
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Visit our website at http://www.garlandscience.com
This book is dedicated to our parents,
Ada & Igal and Lee & Bob.
vii
Table of Contents
List of Estimates xii
Preface xv
Acknowledgments xix
The Path to Biological Numeracy xxiii
Chapter 1: Size and Geometry 3
Cells and Viruses 5
Organelles 24
Cellular building blocks 40
Chapter 2: Concentrations and Absolute Numbers 65
Making a cell 68
Cell census 87
Machines and signals 132
Chapter 3: Energies and Forces 153
Biology meets physics 154
Energy currencies and budgets 182
Chapter 4: Rates and Durations 209
Time scales for small molecules 211
The central dogma 231
Cellular dynamics 249
LIfe cycle of cells 272
Chapter 5: Information and Errors 283
Genome 284
Mutations and errors 297
Chapter 6: A Quantitative Miscellany 313
Epilogue 335
Index 339
viii
Detailed Table of Contents
List of Estimates xii
Preface xv
Acknowledgments xiii
The Path to Biological Numeracy xxiii
Why We Should Care About the Numbers xxiii
The BioNumbers Resource xxvi
How to Make Back-of-the-Envelope Calculations xxvii
Order-of-Magnitude Biology Toolkit xxix
Rigorous Rules for Sloppy Calculations xxxii
The Geography of the Cell xxxvi
Chapter 1: Size and Geometry 3
Cells and viruses
How big are viruses? 5
How big is an E. coli cell and what is its mass? 9
How big is a budding yeast cell? 12
How big is a human cell? 14
How big is a photoreceptor? 17
What is the range of cell sizes and shapes? 21
Organelles
How big are nuclei? 24
How big is the endoplasmic reticulum of cells? 28
How big are mitochondria? 32
How big are chloroplasts? 34
How big is a synapse? 37
Cellular building blocks
How big are biochemical nuts and bolts? 40
Which is bigger, mRNA or the protein it codes for? 43
How big is the “average” protein? 45
How big are the molecular machines
of the central dogma? 50
What is the thickness of the cell membrane? 54
How big are the cell’s filaments? 57
ix
Chapter 2: Concentrations and Absolute Numbers 65
Making a cell
What is the elemental composition of a cell? 68
What is the mass density of cells? 71
What are environmental O and CO concentrations? 74
2 2
What quantities of nutrients need to be supplied in growth
media? 80
What is the concentration of bacterial cells in
a saturated culture? 84
Cell census
What is the pH of a cell? 87
What are the concentrations of different
ions in cells? 91
What are the concentrations of free metabolites in cells? 94
What lipids are most abundant in membranes? 99
How many proteins are in a cell? 104
What are the most abundant proteins in a cell? 108
How much cell-to-cell variability exists
in protein expression? 112
What are the concentrations of cytoskeletal
molecules? 115
How many mRNAs are in a cell? 120
What is the protein-to-mRNA ratio? 124
What is the macromolecular composition of the cell? 128
Machines and signals
What are the copy numbers of transcription factors? 132
What are the absolute numbers of signaling proteins? 135
How many rhodopsin molecules are in a rod cell? 142
How many ribosomes are in a cell? 147
Chapter 3: Energies and Forces 153
Biology meets physics
What is the thermal energy scale and how is
it relevant to biology? 154
What is the energy of a hydrogen bond? 159
What is the energy scale associated with
the hydrophobic effect? 163
How much energy is carried by photons used
in photosynthesis? 165
What is the entropy cost when two molecules
form a complex? 169
How much force is applied by cytoskeletal filaments? 172
What are the physical limits for detection by cells? 175
