book.bionumbers.orgCell Biology by the Numbers

-- Toggle navigation -- Cell biology by the numbers -- The Path to Biological Numeracy Preface Why We Should Care About the Numbers How to make back-of-the-envelope calculations Order-of-Magnitude Biology Toolkit Rigorous Rules for Sloppy Calculations The Geography of the Cell I: Size and Geometry Cells Size and Geometry Introduction How big are viruses ? How big is an E. coli cell and what is its mass? How big is a budding yeast cell? How big is a human cell? How big is a photoreceptor ? What is the range of cell sizes and shapes ? Organelles How big are nuclei ? How big is the endoplasmic reticulum of cells? How big are mitochondria ? How big are chloroplasts ? How big is a synapse ? Cellular Building Blocks How big are biochemical nuts and bolts ? Which is bigger, mRNA or the protein it codes for? How big is the “average” protein ? How big are the molecular machines of the central dogma? What is the thickness of the cell membrane ? How big are the cell’s filaments ? II: Concentrations and Absolute Numbers Making a cell Concentrations and Absolute Numbers – Introduction What is the elemental composition of a cell? What is the density of cells? What are environmental O2 and CO2 concentrations? What quantities of nutrients need to be supplied in growth media ? What is the concentration of bacterial cells in a saturated culture? Cell census What is the pH of a cell? What are the concentrations of different ions in cells? What are the concentrations of free metabolites in cells? What lipids are most abundant in membranes? How many proteins are in a cell? What are the most abundant proteins in a cell? How much cell-to-cell variability exists in protein expression? What are the concentrations of cytoskeletal molecules? How many mRNAs are in a cell? What is the protein to mRNA ratio? What is the macromolecular composition of the cell? Machines and signals What are the copy numbers of transcription factors ? What are the absolute numbers of signaling proteins ? How many rhodopsin molecules are in a rod cell? How many ribosomes are in a cell? III: Energies and Forces Biology meets physics Energies and Forces – Introduction What is the thermal energy scale and how is it relevant to biology? What is the energy of a hydrogen bond ? What is the energy scale associated with the hydrophobic effect ? How much energy is carried by photons used in photosynthesis ? What is the entropy cost when two molecules form a complex? How much force is applied by cytoskeletal filaments ? What are the physical limits for detection by cells? Energy currencies and budgets How much energy is released in ATP hydrolysis ? What is the energy in transfer of a phosphate group ? What is the free energy released upon combustion of sugar ? What is the redox potential of a cell? What is the electric potential difference across membranes? What is the power consumption of a cell? How does metabolic rate scale with size? IV: Rates and Duration Time scales for small molecules Rates and Durations – Introduction What are the time scales for diffusion in cells? How many reactions do enzymes carry out each second? How does temperature affect rates and affinities ? What are the rates of membrane transporters ? How many ions pass through an ion channel per second? What is the turnover time of metabolites? Central dogma What is faster, transcription or translation ? What is the maturation time for fluorescent proteins? How fast do proteasomes degrade proteins? How fast do RNAs and proteins degrade? Cellular dynamics How fast are electrical signals propagated in cells? What is the frequency of rotary molecular motors ? What are the rates of cytoskeleton assembly and disassembly? How fast do molecular motors move on cytoskeletal filaments? How fast do cells move ? Cell life cycle How long does it take cells to copy their genomes? How long do the different stages of the cell cycle take? How quickly do different cells in the body replace themselves? V: Information & Errors Genome Information & Errors – Introduction How big are genomes ? How many chromosomes are found in different organisms? How many genes are in a genome? How genetically similar are two random people? Mutations What is the mutation rate during genome replication? What is the error rate in transcription and translation? What is the rate of recombination ? VI: A Quantitative Miscellany A Quantitative Miscellany – Introduction How many cells are there in an organism ? How many chromosome replications occur per generation? How many ribosomal RNA gene copies are in the genome? What is the permeability of the cell membrane? How many photons does it take to make a cyanobacterium ? How many virions result from a single viral infection? Epilogue Vignettes that reveal how numbers serve as a sixth sense to understanding our cells Reader Mode whet your appetite > How big is the endoplasmic reticulum of cells? > How big is an E. coli cell and what is its mass? > How genetically similar are two random people? 2 24 -- Purchase Draft Download About us About Us Preface Help improve by sending Ron & Rob your feedback...