BioNumbers


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What is the size of the cell?



Cell / ComponentSizeVolume
Diameter of a hydrogen atom0.1 nm
Amino Acid0.8 nm
Diameter of a DNA Alpha helix2 nm
Globular Protein4 nm
Microfilaments6 nm
Thickness cell membranes10 nm
Ribosome11 nm
Microtubule25 nm
Nuclear pore50 nm
Large Virus100 nm
Small bacteria such as Mycoplasma150-250 nm
Centriole200 nm
Lysosomes200 - 500 nm
Peroxisomes200 - 500 nm
Giant virus (mimivirus)400 nm
General size for Prokaryotes1 - 10 Ám
Diameter of human nerve cell process1 Ám
E. coli (bacteria)2 Ám6 - 9.8 10-16 L
Mitochondrion3 Ám
Length of chloroplast5 Ám
The nucleus3 - 10 Ám
Yeast nucleus 7 10-15 L
Drosophila cell nucleus 2.5 10-13 L
Human red blood cell9 Ám
Most Eukaryotic animal cells10 - 30 Ám
Most Eukaryotic plant cells10 - 100 Ám
Small Amoeba90 Ám
Human Egg100 Ám
Megakaryocyteup to 160 Ám
giant bacterium Thiomargaritaup to 500 Ám
Large Amoebaup to 800 Ám
Diameter of the squid giant nerve cell1 mm
Source: wikibooks




How long is the genome? How many genes are there?

OrganismLength of the genomeNumber of genes
Human mitochondrial DNA16 kb
Lambda virus48.5 kb
D. melanogaster (fruit fly) chromosome 41.75 Mb
S. pombe (yeast) chromosome III3.5 Mb
E. coli genome4.6 Mb4300
S. pombe chromosome II4.6 Mb
S. pombe chromosome I5.7 Mb
S. pombe genome13.8 Mb
S. cerevisiae12.5 Mb6000
Neurospora crassa39.5 Mb10000
Mus musculus (mouse) chromosome 1145 Mb
Human chromosome 2090 Mb
C. elegans (nematode) genome100 Mb19000
D. melanogaster genome165 Mb13500-17000
Human chromosome 6225 Mb
Oryza sativa (rice) genome441 Mb
Musa sp. (banana) genome873 Mb
Spinacia oleracea (spinach) genome989 Mb
Gallus gallus (chicken) genome1,200 Mb
Zea mays (corn) genome2,500 Mb
Homo sapiens (human) genome3,000 Mb20000-25000
Nicotiana tabacum (tobacco) genome4,434 Mb
Avena sativa (oat) genome11,315 Mb
Triticum aestivum (wheat) genome15,966 Mb
Lilium longiflorum (Easter lily) genome90,000 Mb
Fritillaria assyriaca (butterfly) genome124,900 Mb
Protopterus aethiopicus (lungfish) genome139,000 Mb
Source: David W. Brooks (UNL univ.)
See also: Genome Sizes

GeneGene length
E. coli (bacteria) alanine transfer RNA 1B gene76 bp
E. coli ferredoxin gene333 bp
B. subtilis (bacteria) glutathione peroxidase gene480 bp
B. subtilis ATP synthase (subunit a) gene732 bp
E. coli biotin synthetase gene1038 bp
Human beta-globin gene1.5 kb
Human insulin gene1.7 kb
E. coli beta-galactosidase gene3.5 kb
Human adenovirus 235.9 kb
Human thyroglobulin gene300 kb
Source: David W. Brooks (UNL univ.)




What is the duration of the cell cycle?


Cell typeCell cycle durationCell life time
Early embryo cells (shortly after fertilization)30 min
Budding yeast cells1.5-3h
Intestinal epithelial cells12h
Mammalian fibroblasts in culture20h
Human liver cells1 year
Source: A course on cell cycle

Cell typeG1 phase durationS phase durationG2 phase durationM phase durationTotal duration
Typical rapidely proliferating mammalian cell10-12h5-8h3-4h1-2h20-24h
Source: NCBI: The Eukaryotic Cell Cycle

Human cells that last a life time (from birth - and even before - to death)
  • cerebral cortex neurons
  • heart muscle cells
  • cells in the inner portion of the crystalline lens of the eyes.
Source: USAtoday: Cells that last a lifetime




How many molecules are there in a cell?


Type of moleculeTotal number of molecules in one cellNumber of different moleculesNumber of copies of each molecule
RNA (abundant)48 000412000
RNA (interm.)150 000500300
RNA (rare)165 0001100015
Proteins10^101000015
Source: Alberts, "Molecular Biology of the Cell"


ConcentrationExamples / OrganismTypical rateReference
Intracellular concentration of proteinsS. cerevesiae: metabolites de la glycolyse (Pyruvate, ATP, etc)from 100 ÁM to 5 mMAlbers et al, 2002
Intracellular concentration of proteinsE. coli: beta-galactosidase~20 copies/cells (40 nM)Kennell & Riezman,1977
Intracellular concentration of RNAE. coli: beta-galactosidase1 - 1000 copies/cells (1nm - 1ÁM)Savageau,1999
Nuclear concentration of transcriptionnal factorsS. cerevesiae: Gal4 (glucose)Less than 10 copies per cellJohnston, 1987





What are typical transcription and translation rates?

The rate of transcription in mammalian cells is of the order of 1000 nucleotides/minute (Hargrove et al. 1991). Therefore, a mRNA of 1 kb is produced every minute. If we consider a cellular volume of 10 10-12 L and a concentration of 10nM, this corresponds to a transcription rate of about 0.1 nM/h.

The rate of translation (protein synthesis) is of the order of 140 amino acids/minute (Lewin, 1997). Therefore, a protein of 1000 aa is produced every 10 minutes. If we consider a cellular volume of 10 10-12 L and a concentration of 10nM, this corresponds to a translation rate of about 0.01 nM/h.

ProcessTypical rate
RNA elongation (mammals)30 nucl/sec
Protein synthesis (mammals)30 nucl/sec = 10 aa/sec
DNA replication (bacteria)100 nucl/sec
Transcription (bacteria)30-85 nucl/sec
Traduction (bacteria)50 nucl/sec = 18 aa/sec
Sources: Alberts, "Molecular Biology of the Cell" + Rawn, "Biochemistry"




ProcessExamples / OrganismTypical rateReference
TranscriptionMammals0.025-25 nM h-1Hargrove et al. 1991
TranscriptionE. coli0.01-0.03 nM h-1Mathews & Durbin, 1990
TranscriptionE. coli0.03-0.2 nM h-1Vogel & Jensen, 1995
TranscriptionEukaryots50 bp sec-1Louis et al,2003; Hargrove et al. 1991; Jackson et al. 2000
TranscriptionBacteria~50 bp sec-1Lewin, 1997
Protein synthesisMammals (blood red cells)0.01 nM h-1Lewin, 1997
Protein synthesisBacteria0.09 nM h-1Lewin, 1997
Protein synthesisE. coli0.05-0.1 nM h-1Ehrenberg and Kurland, 1988
Protein synthesisEukaryots2 aa.sec-1Louis et al,2003; Alberts, 1994;Lewin, 1997; Jackson et al. 2000
Protein synthesisE. coli8 - 33 aa.sec-1Manor et al.,1969; Kennell and Riezman, 1977; Talkad et al,1976





What are typical mRNA and protein half-life times?




BiomoleculeOrganismTypical half-life timeCorresponding kinetic rateReference
RNABacteria40 sec - 20 min2 - 60 h-1Santillan & Mackey, 2001; Kushner,1996
RNAEukaryotsa few minutes - tens of minutes1 - 50 h-1Hargrove & Schmidt, 1989
RNAMammals0.5-3 h0.2 - 1.4 h-1Hargrove et al. 1991
RNABacteria1.5 - 2 min20 - 30 h-1Leive & Kollin, 1967; Blundell & Kennell, 1974
ProteinBacteria3 - 20 h0.03 - 0.2 h-1Mandelstam, 1957; Rotman & Speigelman, 1954
ProteinEukaryotsA few minutessome - some tens h-1Hargrove & Schmidt, 1989
ProteinMammals0.4 - 3 h0.2 - 2 h-1Hargrove et al. 1991
ProteinEukaryots < 0.1 - 2 h0.3 - 7 h-1Carillo et al., 1995
ProteinMammals / Drosophila2 - 3 min10 - 20 h-1Rechsteiner, 1988





What are typical kinetic rates?




EnzymeSubstrateKM (μM)
ChymotrypsinAcetyl-L-tryptophonamide5000
LysozymeHexa-N-acetylglucosamine6
Beta-galactosidaseLactose4000
Threonine deaminaseThreonine5000
Carbonic anhydraseCO28000
PenicillinaseBenzylpenicillin50
Pyruvate carboxylasePyruvate400
Arginine-tRNA synthetaseArginine tRNA+ATP3
Source: Kirschner, Harvard


Source: Kirschner, Harvard




What are typical protein-DNA binding/unbinding rates?




DNA-ProteinsOrganismDimerisation constantReference
LacIE. coli0.1-1E-03 nMSetty et al. 2003 ; Wong et al.,1997; Oehler et al.,1990
Repressor cI - operator complexLambda phage3 nMHasty et al.,2001; Ackers et al.,1982; Ptashne M et al.,1980; Johnson AD et al.,1981; Johnson AD et al.,1980
Dpn-Dpn/D-boxesDrosophila2.6 nMLouis et al.,2003; Winston et al.,1999
Tryptophan repressor-operator complexE. coli2.6 nMSantillan et al., 2001 (Appendix B); Klig et al., 1987
Gal4-Gal80 (glucose)S. cerevisiae2.4 nMParthun et al.,1990
Protein-gene ???Eucaryotes~1 nMBerg et al, 2002
Estrogen receptor-consensus sequenceVertebrates0.5 nMPeale FV et al.,1988
Gcn4p-HIS3 regulatory sequenceYeast0.1 nMHope and Struhl, 1985





What are typical protein association/dissociation rates?




ProteinsOrganismDimerisation constantReference
Repressor ?Lambda phage5E-04 - 5E-01 nM-1Keller, 1995
C-Jun/C-Fos (ZIP proteins)Eukaryots1 nMLouis et al.,2003 (Appendix), Heuer et al. 1996
Simulation(?)Simulations (?)on-rate: 0.5 - 5e+06 M-1.sec-1 (1.8 - 18 nM-1.h-1)Louis et al.,2003 (Appendix); Northrup and Erickson, 1992
NF-kappaB; p65 - TBP (2 transcriptional factors)Humanon-rate: 2.3e+06 M-1.sec-1 (8.3 nM-1.h-1)Louis et al.,2003 (Appendix); Paal et al., 1997
????off-rate: 8e-04 sec-1 (28.8 h-1)Louis et al.,2003 (Appendix); Paal et al., 1997
Anthranilate synthase (enzyme) - TryptophaneE. colion-rate: 1.76e-02 ÁM-1.min-1 (1e-03 nM-1.h-1)Santillan et al., 2001 (Appendix B); Caligiuri et al.,1991
Anthranilate synthase (enzyme) - TryptophaneE. colioff-rate: 7.2e-02 min-1 (4.3 h-1)Santillan et al., 2001 (Appendix B); Caligiuri et al.,1991
Anthranilate synthase (enzyme) - TryptophaneE. coli4e+3 nMSantillan et al., 2001 (Appendix B); Caligiuri et al.,1991
represseur tryptophane - tryptophane (co-represseur)E. colion-rate: 9.9e+06 M-1.s-1 (36 nM-1.h-1)Santillan et al., 2001 (Appendix B); Schmitt et al., 1995
represseur tryptophane - tryptophane (co-represseur)E. colioff-rate: 2e+03 s-1 (7.2e+06 h-1)Santillan et al., 2001 (Appendix B); Schmitt et al., 1995
represseur tryptophane - tryptophane (co-represseur)E. coli2e+5 nMSantillan et al., 2001 (Appendix B); Schmitt et al., 1995
LacI - IPTG (artificial inducer)E. coli1.3e+03 nMSetty et al.,2003; Gilbert and Muller-Hill, 1967
CI-CI (heterodimer)Lambda phage20 nMHasty et al.,2001; Ackers et al., 1982





What are typical transport rates and diffusion constants?


ProcessExamples / OrganismTypical timeCorresponding kinetic rateReference
Transport of RNA into the cytoplasmEucaryotes~20 min~0.3 h-1Lewin, 1997
Nuclear transport rateSV40 large T antigen 0.3 h-1Wagner et al, 1990


MoleculeCell contextDiffusion rate (μm2/s)Reference
H2O In water2100Stein, 1990
H2ONucleus of chicken erythrocyte230Garcia-Perez 1999
CO2In water1880Fridlyand, 1996 (Maxarei 1980)
Protein (GFP)In water87Elowitz 1999 (Swaminathan 1997)
Protein (GFP)In eukaryotic cell (CHO) cytoplasm27Elowitz 1999 (Swaminathan 1997)
Protein (GFP)Rat liver mitochondria25 (20-30)Elowitz 1999 (Partikian 1998)
Protein (GFP)E. coli cytoplasm7.7▒2.5Elowitz 1999
Fluorescent dye (Carboxy-fluorescein)Aqueous solution487▒22Kramer, 2007
Fluorescent dye (Carboxy-fluorescein)A. thaliana cell wall32▒14Kramer, 2007
Fluorescent dye (Carboxy-fluorescein)A. thaliana mature root epidermis2.5▒0.7Kramer, 2007
Transcription factor (LacI)One dimensional movement along DNA in vitro (Equivalent to 4?105 bp2s-1. In vivo apparent 1D diffusion coefficient is an order of magnitude higher due to 3D diffusion)0.04Elf et al, 2007
Morphogen (Bicoid) Cytoplasm of Drosophila embryo0.3▒0.1 Gregor 2007
Morphogen (Wingless)Wing imaginal disk of Drosophila0.05 (0.02-0.08) Kicheva 2007
Source: Milo, Weismann





Many thanks to Wassim Abou-JaoudÚ and to Jean-Christophe Leloup for their contribution
Didier Gonze - Created 6/9/2009 - Updated: 24/1/2011 - [Home]