Journal of Biosciences

, Volume 39, Issue 1, pp 13–27 | Cite as

Biochemistry and evolutionary biology: Two disciplines that need each other

  • Athel Cornish-Bowden
  • Juli Peretó
  • María Luz Cárdenas


Biochemical information has been crucial for the development of evolutionary biology. On the one hand, the sequence information now appearing is producing a huge increase in the amount of data available for phylogenetic analysis; on the other hand, and perhaps more fundamentally, it allows understanding of the mechanisms that make evolution possible. Less well recognized, but just as important, understanding evolutionary biology is essential for understanding many details of biochemistry that would otherwise be mysterious, such as why the structures of NAD and other coenzymes are far more complicated than their functions would seem to require. Courses of biochemistry should thus pay attention to the essential role of evolution in selecting the molecules of life.


Biochemistry biological design evolution LUCA NAD RNA world 



ACB and MLC acknowledge the support of the Centre National de la Recherche Scientifique. JP acknowledges the intellectual motivation of many students during more than 20 years of teaching evolutionary biochemistry and origins of life at the University of Valencia, as well as the financial support for his research on symbiosis to the Spanish Mineco (grant BFU2012-39816-C02-01). The impetus for writing this article came from three sessions at the IUBMB-FEBS-SEBBM Congress in Seville in 2012, and we thank the organizers for facilitating our participation in these.


  1. Anonymous 1754 Pensées sur l’interprétation de la NatureGoogle Scholar
  2. Benner SA 2009 Life, the Universe and the scientific method (Gainesville, FL: The Ffame Press)Google Scholar
  3. Berg JM, Tymoczko JL and Stryer L 2012 Biochemistry (San Francisco: W. H. Freeman)Google Scholar
  4. Blackmond DG 2011 The origin of biological homochirality. Philos. Trans. R. Soc. Lond. B Biol. Sci. 36 2878–2884CrossRefGoogle Scholar
  5. Blount ZD, Barrick JE, Davidson CJ and Lenski RE 2012 Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489 513–518PubMedCentralPubMedCrossRefGoogle Scholar
  6. Buckling A, Maclean RC, Brockhurst M A and Colegrave N 2009 The Beagle in a bottle. Nature 457 824–829PubMedCrossRefGoogle Scholar
  7. Cárdenas ML 2013 Michaelis and Menten and the long road to the discovery of cooperativity. FEBS Lett. 587 2767–2771PubMedCrossRefGoogle Scholar
  8. Cárdenas ML, Cornish-Bowden A and Ureta T 1998 Evolution and regulatory role of the hexokinases. Biochim. Biophys. Acta 1401 242–264PubMedCrossRefGoogle Scholar
  9. Cornish-Bowden A 1976 The effect of natural selection on enzymic catalysis. J. Mol. Biol. 101 1–9PubMedCrossRefGoogle Scholar
  10. Cornish-Bowden A 1985 The amino-acid sequences of the copper-zinc superoxide dismutases from swordfish and Photobacter leiognathi confirm the predictions made from the compositions. Eur. J. Biochem. 151 333–335PubMedCrossRefGoogle Scholar
  11. Cornish-Bowden A 2002 Enthalpy–entropy compensation: a phantom phenomenon. J. Biosci. 27 121–126PubMedCrossRefGoogle Scholar
  12. Cornish-Bowden A 2012 Enthalpy–entropy compensation as deduced from measurements of temperature dependence; in Protein-ligand interactions (ed) H Gohlke (Weinheim: Wiley–Blackwell) pp 33–43CrossRefGoogle Scholar
  13. Cornish-Bowden A 2013 The origins of enzyme kinetics. FEBS Lett. 587 2725–2730PubMedCrossRefGoogle Scholar
  14. Cornish-Bowden A and Cárdenas ML 2001 Information transfer in metabolic pathways: effects of irreversible steps in computer models. Eur. J. Biochem. 268 6616–6624PubMedCrossRefGoogle Scholar
  15. Cornish-Bowden A and Nanjundiah V 2006 The basis of dominance; in The biology of genetic dominance (ed) RA Veitia (Georgetown, Texas: Landes Bioscience) pp 1–16Google Scholar
  16. Crick FHC 1958 On protein synthesis. Symp. Soc. Exp. Biol. 12 138–163PubMedGoogle Scholar
  17. Daeschler EB, Shubin NH and Jenkins FA Jr 2006 Devonian tetrapod-like fish and the evolution of the tetrapod body plan. Nature 440 764–771PubMedCrossRefGoogle Scholar
  18. Dallinger DH 1878 On the life-history of a minute septic organism: with an account of experiments made to determine its thermal death point. Proc. R. Soc. Lond. 27 332–350CrossRefGoogle Scholar
  19. Dean AM and Thornton JW 2007 Mechanistic approaches to the study of evolution: the functional synthesis. Nat. Rev. Genet. 8 675–688PubMedCentralPubMedCrossRefGoogle Scholar
  20. Deichmann U, Schuster S, Mazat, J-P and Cornish-Bowden A 2014 Commemorating the 1913 Michaelis–Menten paper Die Kinetik der Invertinwirkung: three perspectives. FEBS J. 281 435–463PubMedCrossRefGoogle Scholar
  21. Demeshkina N, Jenner L, Westhof E, Yusupov M and Yusupova G 2013 New structural insights into the decoding mechanism: translation infidelity via a G · U pair with Watson–Crick geometry. FEBS Lett. 587 1848–1857PubMedCrossRefGoogle Scholar
  22. Dobzhansky T 1973 Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach. 35 125–129CrossRefGoogle Scholar
  23. Doolittle RF and Blombäck B 1964 Amino-acid sequence investigations of fibrinopeptides from various mammals: evolutionary implications. Nature 202 147–152PubMedCrossRefGoogle Scholar
  24. Ducluzeau AL, van Lis R, Duval S, Schoepp-Cothenet B, Russell MJ and Nitschke W 2009 Was nitric oxide the first deep electron sink? Trends Biochem. Sci. 34 9–15Google Scholar
  25. Fell D 1997 Understanding the control of metabolism (London: Portland Press)Google Scholar
  26. Fersht AR and Kaethner MM 1976 Enzyme hyper-specificity – rejection of threonine by valyl-transfer-RNA synthetase by mis-acylation and hydrolytic editing. Biochemistry 15 3342–3346PubMedCrossRefGoogle Scholar
  27. Fisher RA 1934 The possible modification of the response of the wild type to recurrent mutations. Am. Nat. 62 115–126CrossRefGoogle Scholar
  28. Fitch WM and Margoliash E 1967 Construction of phylogenetic trees. Science 155 279–284PubMedCrossRefGoogle Scholar
  29. Friedmann HC 2004 From ‘butyribacterium’ to ‘E. coli’ – An essay on unity in biochemistry. Perspect. Biol. Med. 47 47–66PubMedCrossRefGoogle Scholar
  30. Galilei G 1638 Discorsi e dimostrazioni matematiche intorno a due nuove scienze attenenti alla mecanica e i movimenti locali (Leyden: Elzevir)Google Scholar
  31. Geoffroy St Hilaire É 1830 Principes de philosophie zoologique: discutés en mars 1830 au sein de l’Académie royale des sciences (Paris: Pichon et Didier)CrossRefGoogle Scholar
  32. Guijarro A and Yus M 2009 The origin of chirality in the molecules of life (Cambridge: RSC Publishing)Google Scholar
  33. Gunja-Smith Z, Marshall JJ, Mercier C, Smith EE and Whelan WJ 1970 Revision of the Meyer–Bernfeld model of glycogen and amylopectin. FEBS Lett. 12 101–104PubMedCrossRefGoogle Scholar
  34. Gutfreund H 1995 Kinetics for the Life Sciences (Cambridge: Cambridge University Press)CrossRefGoogle Scholar
  35. Hochachka PW and Somero GN 1984 Biochemical adaptation (Princeton, NJ: Princeton University Press)Google Scholar
  36. Hofmeyr JHS and Cornish-Bowden A 2000 Regulating the cellular economy of supply and demand. FEBS Lett. 476 47–51PubMedCrossRefGoogle Scholar
  37. Jacob F 1977 Evolution and tinkering. Science 196 1161–1166PubMedCrossRefGoogle Scholar
  38. Kacser H and Burns JA 1981 The molecular basis of dominance. Genetics 97 639–666PubMedCentralPubMedGoogle Scholar
  39. Kacser H, Burns JA and Fell DA 1995 The control of flux. Biochem. Soc. Trans. 23 341–366PubMedGoogle Scholar
  40. Kawecki TJ, Lenski RE, Ebert D, Hollis B, Olivieri I and Whitlock MC 2012 Experimental evolution. Trends Ecol. Evol. 27 547–560PubMedCrossRefGoogle Scholar
  41. Kimura M 1983 The neutral theory of molecular evolution (Cambridge: Cambridge University Press)CrossRefGoogle Scholar
  42. Kluyver AJ and Donker HJL 1925 The unity in the chemistry of the fermentative sugar dissimilation processes of microbes. Proc. K. Ned. Akad. Wet. 28 297–313Google Scholar
  43. Knowles JR 1991 Enzyme catalysis – not different, just better. Nature 350 121–124PubMedCrossRefGoogle Scholar
  44. Kohn JA, Deshpande K and Ortlund EA 2012 Deciphering modern glucocorticoid cross-pharmacology using ancestral corticosteroid receptors. J. Biol. Chem. 287 16267–16275Google Scholar
  45. Kolkman JA and Stemmer WPC 2001 Directed evolution of proteins by exon shuffling. Nat. Biotechnol. 19 423–428PubMedCrossRefGoogle Scholar
  46. Lawen A and Zocher R 1990 Cyclosporin synthetase: the most complex peptide synthesizing multienzyme polypeptide so far described. J. Biol. Chem. 265 11355–11360PubMedGoogle Scholar
  47. Lewin R 1987 Bones of contention: Controversies in the search for human origins (New York: Simon and Schuster)Google Scholar
  48. Lomako J, Lomako WM and Whelan WJ 1988 A self-glucosylating protein is the primer for rabbit muscle glycogen biosynthesis. FASEB J. 2 3097–3103PubMedGoogle Scholar
  49. McBrearty S and Jablonski NG 2005 First fossil chimpanzee. Nature 437 105–108PubMedCrossRefGoogle Scholar
  50. Mayr E 1961 Cause and effect in biology. Science 134 1501–1506PubMedCrossRefGoogle Scholar
  51. Mays PK, McAnulty RJ, Campa JS and Laurent GJ 1991 Age-related changes in collagen synthesis and degradation in rat tissues. Importance of degradation of newly synthesized collagen in regulating collagen production. Biochem. J. 276 307–313PubMedCentralPubMedGoogle Scholar
  52. Meléndez R, Meléndez-Hevia E and Cascante M 1997 How did glycogen structure evolve to satisfy the requirement for rapid mobilization of glucose? A problem of physical constraints in structure building J. Mol. Evol. 45 446–455PubMedCrossRefGoogle Scholar
  53. Meléndez-Hevia E and de Paz-Lugo P 2008 Branch-point stoichiometry can generate weak links in metabolism: the case of glycine biosynthesis. J. Biosci. 33 771–780PubMedCrossRefGoogle Scholar
  54. Meléndez-Hevia E, de Paz-Lugo P, Cornish-Bowden A and Cárdenas ML 2009 A weak link in metabolism: the metabolic capacity for glycine biosynthesis does not satisfy the need for collagen synthesis. J. Biosci. 34 853–872PubMedCrossRefGoogle Scholar
  55. Meyer KH and Bernfeld P 1940 Research on starch. V Amylopectin Helv. Chim. Acta 23 875–885CrossRefGoogle Scholar
  56. Michaelis L and Menten ML 1913 Kinetik der Invertinwirkung. Biochem. Z. 49 333–369Google Scholar
  57. Monod J, Changeux JP and Jacob F 1963 Allosteric proteins and cellular control systems. J. Mol. Biol. 6 306–329PubMedCrossRefGoogle Scholar
  58. Oba T, Andachi Y, Muto A and Osawa S 1991 CGG – an unassigned or nonsense codon in Mycoplasma capricolum. Proc. Natl. Acad. Sci. USA 88 921–925PubMedCentralPubMedCrossRefGoogle Scholar
  59. Ohta T 1973 Slightly deleterious mutant substitutions in evolution. Nature 246 96–98PubMedCrossRefGoogle Scholar
  60. Ohta T and Gillespie JH 1996 Development of neutral and nearly neutral theories. Theor. Popul. Biol. 49 128–142PubMedCrossRefGoogle Scholar
  61. Penny D, Foulds LR and Hendy MD 1982 Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature 297 197–200PubMedCrossRefGoogle Scholar
  62. Peretó J 2011 The origin and evolution of metabolisms; in Origins and evolution of life: an astrobiological perspective (ed.) M Gargaud, P López-García and H Martin (Cambridge: Cambridge University Press) pp 270–287CrossRefGoogle Scholar
  63. Pizzarello S and Lahav M 2010 On the emergence of biochemical homochirality: an elusive beginning. Orig. Life Evol. Biosph. 40 1–2PubMedCrossRefGoogle Scholar
  64. Pizzarello S and Shock E 2010 The organic composition of carbonaceous meteorites: the evolutionary story ahead of biochemistry. Cold Spring Harb. Perspect. Biol. 2 a002105PubMedCentralPubMedCrossRefGoogle Scholar
  65. Raymond J and Blankenship RE 2004 Biosynthetic pathways, gene replacement and the antiquity of life Geobiology 2 199–203CrossRefGoogle Scholar
  66. Raymond J and Segrè D 2006 The effect of oxygen on biochemical networks and the evolution of complex life. Science 311 1764–1767PubMedCrossRefGoogle Scholar
  67. Sarich VM and Wilson AC 1967 Rates of albumin evolution in primates. Proc. Natl. Acad. Sci. USA 58 142–148PubMedCentralPubMedCrossRefGoogle Scholar
  68. Stott R 2012 Darwin’s ghosts: In search of the first evolutionists (London: Bloomsbury)Google Scholar
  69. Szathmáry E 2003 Why are there four letters in the genetic alphabet? Nat. Rev. Genet. 4 995–1001PubMedCrossRefGoogle Scholar
  70. Tawfik DS 2010 Messy biology and the origins of evolutionary innovations. Nat. Chem. Biol. 6 692–696PubMedGoogle Scholar
  71. Thompson DW 1945 On growth and form (Cambridge: Cambridge University Press)Google Scholar
  72. Ureta T 2011 Origen y Evolución de Proteinas y Enzimas (Santiago, Chile: Editorial Universitaria)Google Scholar
  73. Valdecasas AG, Boto L and Correas AM 2013 There is no common ground between science and religion. J. Biosci. 38 181–187PubMedCrossRefGoogle Scholar
  74. Woese CR and Fox GE 1977 Phylogenetic structure of the prokaryote domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74 5088–5090PubMedCentralPubMedCrossRefGoogle Scholar
  75. Woese CR and Goldenfeld N 2009 How the microbial world saved evolution from the Scylla of molecular biology and the Charybdis of the modern synthesis. Microb. Mol. Biol. Revs. 73 14–21CrossRefGoogle Scholar
  76. Wright S 1934 Fisher’s theory of dominance. Am. Nat. 63 274–279CrossRefGoogle Scholar
  77. Yang Z, Chen F, Alvarado JB and Benner SA 2011 Amplification, mutation, and sequencing of a six-letter synthetic genetic system. J. Am. Chem. Soc. 133 15105–15112PubMedCentralPubMedCrossRefGoogle Scholar
  78. Zuckerkandl E and Pauling L 1962 Molecular disease, evolution, and genetic heterogeneity; in Horizons in biochemistry (ed) M Kasha and Pullman B (New York: Academic Press) pp 189–225Google Scholar
  79. Zuckerkandl E and Pauling L 1965 Evolutionary divergence and convergence of proteins; in Evolving genes and proteins (ed) V Bryson and HJ Vogel (New York: Academic Press) pp 97–166Google Scholar

Copyright information

© Indian Academy of Sciences 2014

Authors and Affiliations

  • Athel Cornish-Bowden
    • 1
  • Juli Peretó
    • 2
  • María Luz Cárdenas
    • 1
  1. 1.Unité de Bioénergétique et Ingénierie des Protéines, Centre National de la Recherche Scientifique, Aix-Marseille UniversitéMarseille Cedex 20France
  2. 2.Departament de Bioquímica i Biologia Molecular, Institut Cavanilles de Biodiversitat i Biologia EvolutivaUniversitat de ValènciaValenciaSpain

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