Key Numbers in Biology.PDF

SnapShot:Key Numbers in BiologyUri Moran,1 Rob Phillips,2 and Ron Milo11Weizmann Institute of Science,Rehovot,Israel;2California Institute of Technology,Pasadena,CA,USASee online version for legend and references.1262 Cell 141,June 25,2010 2010 Elsevier Inc.DOI 10.1016/j.cell.2010.06.0191262.e1 Cell 141,June 25,2010 2010 Elsevier Inc.DOI 10.1016/j.cell.2010.06.019SnapShot:Key Numbers in BiologyUri Moran,1 Rob Phillips,2 and Ron Milo11Weizmann Institute of Science,Rehovot,Israel;2California Institute of Technology,Pasadena,CA,USABiology is becoming increasingly quantitative.Taking stock of key numbers in cell and molecular biology enables back-of-the-envelope calculations that test and sharpen our understanding of cellular processes.Further,such calculations provide a quantitative context for the torrent of data from new experimental techniques.However,such useful numbers are scattered in the vast biological literature in a way that often leads to a frustrating literature-mining ordeal.Here,we have collected a set of basic numbers in biology that we find extremely useful for obtaining an order of magnitude feel for the molecular processes in cells.Several examples(see below)show how to combine these numbers to think about biological questions.The values should be considered rules of thumb rather than definitive values as variety is the spice of life and variability is ever present in biology.This compilation is based on the BioNumbers wiki project(http:/www.BioNumbers.org)where these and the values of several thousand other biological properties are provided together with their experimental context and references to the primary literature.Is There Enough Time to Replicate the Genome?The bacterium Escherichia coli has a genome of roughly 5 million base pairs(bp)and a replication rate in the range of 2001000 bp/s.These numbers imply that it should take the two replisomes at least 2500 s to replicate the genome,a number that is much larger than the maximal division rate of?20 min.How can this be?It turns out that,under ideal conditions,E.coli uses nested replication forks that begin to replicate the DNA for the granddaughter and great granddaughter cells before the daughter cells have even completed replication.How Many Mutations in a 5 ml Culture of Bacteria?Using the 109/bp mutation rate of E.coli per replication and a genome size of?107(both strands),we predict?102 mutations per genome replication.In a 5 ml saturated culture(optical density?2.0)of E.coli,there are about 109 to 1010 cells.The final doubling of this culture requires the replication of?109 cells,thus even this last cell division event would be responsible for?107 single base pair substitutions.If the culture started with a single bacterium,every single nonlethal base pair substitution in the E.coli genome is likely to be represented in the culture.How Long to Reach Confluence?In a 96 multiwell plate,each well has a diameter of 5 mm(i.e.,an area of 20 mm2=2 107 m2).Given that the diameter of a HeLa cell is 25 m(i.e.,500 m2 area),it takes roughly 40,000 cells to reach confluence.Starting with a single cell(obtained by cell sorting rather than cell splitting)with a generation time of about 1 day,the time to reach confluence is about 2 weeks.How“Dense”Is a Saturated E.coli Culture?A saturated E.coli culture has about 109 cells/ml.Given that each cell is about 1012 grams,we get a cell concentration of about 1 mg/ml or about 1 part in a thousand of the mass(or volume).The mean spacing between the cells is roughly 10 m(which is not as dense as the concentration of bacteria in the gut of the termite where densities are typically a factor of ten higher).How Many Carbon Atoms Are in a Cell?A cell with a volume of 1 m3 and a density of about 1 g/ml has a total mass of 1012 grams.From the formula C4H7O2N1 and the weights of the elements,we derive a carbon con-tent of about 12 4/(12 4+7+2 16+14)=48/101 or about one half of the dry mass.With 30%dry mass(70%water),we obtain?1013 gm of carbon.Next we transformed the number of molecules using Avogadros constant:6 1023 1013/12=5 109 carbon atoms per cell.To verify this,we have done the calculation in a different way:assuming there are about 3 106 proteins,each one consisting of about 300 amino acids,we get a total of?109 amino acids.An amino acid has about five carbon atoms,so we arrive at a similar value.Both estimates depend linearly on the cell volume,which can vary significantly based on growth conditions.How Far Can Macromolecules Move by Diffusion?It takes about 10 s on average for a protein to traverse a HeLa cell.An axon 1 mm long is about 100 times longer than a HeLa cell,and as the diffusion time scales as the square of the distance it would take 105 seconds or?2 days for a molecule to travel this distance by diffusion.This demonstrates the necessity of mechanisms other than diffusion for moving molecules long distances.A molecular motor moving at a rate of?1 m/s will take a“reasonable”time(?15 min)to traverse an axon 1 mm in length.AcknowledgmentsWe thank Uri Alon,Niv Antonovsky,Danny Ben-Zvi,David Cahen,Erez Dekel,Idan Efroni,Avigdor Eldar,Yuval Eshed,Nir Friedman,Hernan Garcia,Paul Jorgensen,Michal Kenan-Eichler,Jane Kondev,Marc Kirschner,Daniel Koster,Avi Levy,Michal Lieberman,Debbie Marks,Elliot Meyerowitz,Elad Noor,Chris Sander,Dave Savage,Moselio Schaechter,Maya Schuldiner,Eran Segal,Daniel Segre,Benny Shilo,Guy Shinar,Alex Sigal,Rotem Sorek,Mike Springer,Bodo Stern,Arbel Tadmor,Julie Theriot,Rebecca Ward,Detlef Weigel,Jon Widom,and Tali Wiesel for help in preparing this SnapShot.RefeRencesAlon,U.(2006).An Introduction to Systems Biology:Design Principles of Biological Circuits(New York:Chapman&Hall/CRC).Altman,P.L.,and Katz,D.S.D.(1978).Biology Data Book(New York:John Wiley&Sons Inc.).Burton,R.F.(2000).Physiology by Numbers(Cambridge,UK:Cambridge University Press).Goldreich,P.,Mahajan,S.,and Phinney,S.(1999).Order-of-magnitude physics:Understanding the world with dimensional analysis,educated guesswork,and white lies(http:/www.inference.phy.cam.ac.uk/sanjoy/oom/book-a4.pdf).Harte,J.(1988).Consider a Spherical Cow:A Course in Environmental Problem Solving(Mill Valley,CA:University Science Books).Milo,R.,Jorgensen,P.,Moran,U.,Weber,G.,and Springer,M.(2010).BioNumbers the database of key numbers in molecular and cell biology.Nucleic Acids Res.38,D750D753.Neidhardt,F.C.,Ingraham,J.L.,and Schaechter,M.(1990).Physiology of the Bacterial Cell:A Molecular Approach(Sunderland,MA:Sinauer Associates).Phillips,R.,and Milo,R.(2009).A feeling for the numbers in biology.Proc.Natl.Acad.Sci.USA 106,2146521471.Phillips,R.,Kondev,J.,and Theriot,J.(2008).Physical Biology of the Cell(London:Garland Science).Weinstein,L.,and Adam,J.A.(2008).Guesstimation:Solving the Worlds Problems on the Back of a Cocktail Napkin(Princeton,NJ:Princeton University Press).