Cell Biology by the Numbers

Table of Contents......Page 8
Detailed Table of Contents......Page 9
List of Estimates......Page 13
Preface......Page 16
Acknowledgments......Page 20
WHY WE SHOULD CARE ABOUT THE NUMBERS......Page 24
THE BIONUMBERS RESOURCE......Page 27
HOW TO MAKE BACK-OF-THE-ENVELOPE CALCULATIONS......Page 28
Big numbers at your disposal......Page 30
Rules of thumb......Page 31
RIGOROUS RULES FOR SLOPPY CALCULATIONS......Page 33
THE GEOGRAPHY OF THE CELL......Page 37
Chapter 1: Size and Geometry......Page 46
How big are viruses?......Page 48
How big is an E. coli cell and what is its mass?......Page 52
How big is a budding yeast cell?......Page 55
How big is a human cell?......Page 57
How big is a photoreceptor?......Page 60
What is the range of cell sizes and shapes?......Page 64
How big are nuclei?......Page 67
How big is the endoplasmic reticulum of cells?......Page 71
How big are mitochondria?......Page 75
How big are chloroplasts?......Page 77
How big is a synapse?......Page 80
How big are biochemical nuts and bolts?......Page 83
Which is bigger, mRNA or the protein it codes for?......Page 86
How big is the “average” protein?......Page 88
How big are the molecular machines
of the central dogma?......Page 93
What is the thickness of the cell membrane?......Page 97
How big are the cell’s filaments?......Page 100
Chapter 2: Concentrations and Absolute Numbers......Page 108
What is the elemental composition of a cell?......Page 111
What is the mass density of cells?......Page 114
What are environmental O2 and CO2
concentrations?......Page 117
What quantities of nutrients need to be supplied in growth media?......Page 123
What is the concentration of bacterial cells in a saturated culture?......Page 127
What is the pH of a cell?......Page 130
What are the concentrations of different
ions in cells?......Page 134
What are the concentrations of free metabolites in cells?......Page 137
What lipids are most abundant in membranes?......Page 142
How many proteins are in a cell?......Page 147
What are the most abundant proteins in a cell?......Page 151
How much cell-to-cell variability exists in protein expression?......Page 155
What are the concentrations of cytoskeletal
molecules?......Page 158
How many mRNAs are in a cell?......Page 163
What is the protein-to-mRNA ratio?......Page 167
What is the macromolecular composition
of the cell?......Page 171
What are the copy numbers of transcription
factors?......Page 175
What are the absolute numbers of signaling
proteins?......Page 178
How many rhodopsin molecules are in a rod cell?......Page 185
How many ribosomes are in a cell?......Page 190
Chapter 3: Energies and Forces......Page 196
What is the thermal energy scale and how
is it relevant to biology?......Page 197
What is the energy of a hydrogen bond?......Page 202
What is the energy scale associated with the
hydrophobic effect?......Page 206
How much energy is carried by photons used in photosynthesis?......Page 208
What is the entropy cost when two molecules form a complex?......Page 212
How much force is applied by cytoskeletal
filaments?......Page 215
What are the physical limits for detection by cells?......Page 218
How much energy is released in ATP hydrolysis?......Page 225
What is the energy in transfer of a
phosphate group?......Page 228
What is the free energy released upon
combustion of sugar?......Page 231
What is the redox potential of a cell?......Page 232
What is the electric potential difference across membranes?......Page 239
What is the power consumption of a cell?......Page 242
How does metabolic rate scale with size?......Page 247
Chapter 4: Rates and Durations......Page 252
What are the time scales for diffusion in cells?......Page 254
How many reactions do enzymes carry out each second?......Page 258
How does temperature affect rates
and affinities?......Page 263
What are the rates of membrane transporters?......Page 266
How many ions pass through an ion
channel per second?......Page 269
What is the turnover time of metabolites?......Page 271
Which is faster: transcription or translation?......Page 274
What is the maturation time for fluorescent
proteins?......Page 280
How fast do proteasomes degrade proteins?......Page 284
How fast do RNAs and proteins degrade?......Page 287
How fast are electrical signals propagated in cells?......Page 292
What is the frequency of rotary molecular motors?......Page 297
What are the rates of cytoskeleton assembly
and disassembly?......Page 301
How fast do molecular motors move on
cytoskeletal filaments?......Page 306
How fast do cells move?......Page 311
How long does it take cells to copy their genomes?......Page 315
How long do the different stages of the
cell cycle take?......Page 318
How quickly do different cells in the body replace themselves?......Page 321
Chapter 5: Information and Errors......Page 326
How big are genomes?......Page 327
How many chromosomes are found in different organisms?......Page 330
How many genes are in a genome?......Page 334
How genetically similar are two random people?......Page 338
What is the mutation rate during genome
replication?......Page 340
What is the error rate in transcription
and translation?......Page 346
What is the rate of recombination?......Page 349
Chapter 6: A Quantitative Miscellany......Page 356
HOW MANY CELLS ARE THERE IN AN ORGANISM?......Page 357
HOW MANY CHROMOSOME REPLICATIONS OCCUR PER GENERATION?......Page 362
HOW MANY RIBOSOMAL RNA GENE COPIES ARE IN THE GENOME?......Page 365
WHAT IS THE PERMEABILITY OF THE CELL MEMBRANE?......Page 369
HOW MANY PHOTONS DOES IT TAKE TO MAKE A CYANOBACTERIUM?......Page 373
HOW MANY VIRIONS RESULT FROM A SINGLE VIRAL INFECTION?......Page 375
EPILOGUE......Page 378
INDEX......Page 382