Cell Biology by the Numbers

Description

How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation? Cell Biology by the Numbers explores these questions―and dozens of others―providing a richly illustrated and handy reference for students and researchers in molecular and cell biology, chemistry, and biophysics. The book features question-driven vignettes and "back of the envelope" calculations that investigate some of the key numbers in cell biology. Readers will learn about the sizes, concentrations, rates, energies, and other numbers that describe and drive the living world. 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