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Aspects of Physical Chemistry Read chapter Read first chapter

2013 | OriginalPaper | Chapter

9. Life: The Physical Underpinnings of Replication

Authors : Rebecca Turk-MacLeod, Ulrich Gerland, Irene Chen

Published in: Astrochemistry and Astrobiology

Publisher: Springer Berlin Heidelberg

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Abstract

Replication is a fundamental process that is critical to life as we know it. While replication today is carried out by complex biochemical machineries that have been evolving for billions of years, it must have originated with relatively small molecules in simple systems. Here we explore this concept, focusing on the physicochemical characteristics and prebiotic potential of two classes of biological macromolecules: nucleic acids and lipids. We discuss the informational and catalytic capabilities of DNA and RNA, the thermodynamic limits of information transfer, the structure and function of lipid membranes, and the formation and maintenance of primitive ‘protocells’.

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previous chapter Life, Metabolism and Energy
next chapter Physical Chemistry: Extending the Boundaries
Footnotes
1
One important mode of altruism, reciprocal altruism (e.g., in the Prisoner’s dilemma), can evolve under certain conditions, such as repeated interactions. However, the first replicases were unlikely to have a mechanism to decide whether or not to cooperate, so reciprocal altruism will not be considered further here.
 
2
It actually takes a pair of replicases to start an autocatalytic cycle of replication. The second replicase might have been encapsulated in the same vesicle by chance, or may have been generated via templated non-enzymatic polymerization.
 
Literature
1.
2.
3.
4.
Benner SA, Hutter D (2002) Phosphates, DNA, and the search for nonterrean life: a second generation model for genetic molecules. Bioorg Chem 30:62–80. doi:10.​1006/​bioo.​2001.​1232
5.
6.
7.
Woese CR, Dugre DH, Dugre SA et al (1966) On the fundamental nature and evolution of the genetic code. Cold Spring Harb Symp Quant Biol 31:723–736
8.
9.
Kruger K, Grabowski PJ, Zaug AJ et al (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31:147–157. doi:10.​1016/​0092-8674(82)90414-7
10.
11.
12.
13.
14.
15.
Cech TR (1992) In: Frangsmyr T, Malmstrom BG (eds) Nobel lectures, chemistry 1981–1990. World Scientific Publishing Co., Singapore
16.
Carothers JM, Oestreich SC, Davis JH, Szostak JW (2004) Informational complexity and functional activity of RNA structures. J Am Chem Soc 126:5130–5137. doi:10.​1021/​ja031504a
17.
18.
19.
20.
21.
22.
23.
24.
Jencks WP (1969) Catalysis in chemistry and enzymology. McGraw Hill, New York
25.
Joyce GF (1987) Nonenzymatic template-directed synthesis of informational macromolecules. Cold Spring Harb Symp Quant Biol 52:41–51
26.
Zielinski WS, Orgel LE (1985) Oligomerization of activated derivatives of 3′-amino-3′-deoxyguanosine on poly(C) and poly(dC) templates. Nucleic Acids Res 13:2469–2484. doi:10.​1093/​nar/​13.​7.​2469
27.
Leu K, Obermayer B, Rajamani S, Gerland U, Chen IA (2011) The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA. Nucleic Acids Res 39:8135–8147. doi:10.​1093/​nar/​gkr525
28.
Li X, Liu DR (2004) DNA-templated organic synthesis: nature’s strategy for controlling chemical reactivity applied to synthetic molecules. Angew Chem Int Ed Engl 43:4848–4870. doi:10.​1002/​anie.​200400656
29.
Weber AL, Orgel LE (1978) The formation of peptides from the 2′(3′)-glycyl ester of a nucleotide. J Mol Evol 11:189–198. doi:10.​1007/​BF01734480
30.
Weber AL, Orgel LE (1980) Poly(U)-directed peptide-bond formation from the 2′(3′)-glycyl esters of adenosine derivatives. J Mol Evol 16:1–10. doi:10.​1007/​BF01732065
31.
32.
Tamura K, Schimmel P (2003) Peptide synthesis with a template-like RNA guide and aminoacyl phosphate adaptors. Proc Natl Acad Sci USA 100:8666–8669. doi:10.​1073/​pnas.​1432909100
33.
34.
35.
Joshi PC, Aldersley MF, Delano JW, Ferris JP (2009) Mechanism of montmorillonite catalysis in the formation of RNA oligomers. J Am Chem Soc 131:13369–13374. doi:10.​1021/​ja9036516
36.
Turk RM, Illangasekare M, Yarus M (2011) Catalyzed and spontaneous reactions on ribozyme ribose. J Am Chem Soc 133:6044–6050. doi:10.​1021/​ja200275h
37.
38.
Hilvert D, Carpenter SH, Nared KD, Auditor MT (1988) Catalysis of concerted reactions by antibodies: the Claisen rearrangement. Proc Natl Acad Sci USA 85:4953–4955. doi:10.​1073/​pnas.​85.​14.​4953
39.
40.
41.
Eigen M (1971) Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58:465–523
42.
43.
44.
Nowak MA, Schuster P (1989) Error thresholds of replication in finite populations. Mutation frequencies and the onset of Muller’s ratchet. J Theor Biol 137:375–395. doi:10.​1016/​S0022-5193(89)80036-0
45.
46.
47.
48.
Schuster P (2006) In: Klussmann S (ed) The aptamer handbook. Weinheim, Wiley-VCH
49.
50.
Hopfield JJ (1974) Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci USA 71:4135–4139. doi:10.​1073/​pnas.​71.​10.​4135
51.
Ninio J (1974) A semi-quantitative treatment of missense and nonsense suppression in the strA and ram ribosomal mutants of Escherichia coli. Evaluation of some molecular parameters of translation in vivo. J Mol Biol 84:297–313. doi:10.​1016/​0022-2836(74)90586-5
52.
53.
Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 83:9373–9377. doi:10.​1073/​pnas.​83.​24.​9373
54.
Mathews DH, Sabina J, Zuker M, Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288:911–940. doi:10.​1006/​jmbi.​1999.​2700
55.
56.
Schink S, Renner S, Alim K, Arnaut V, Simmel FC, Gerland U (2012) Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides. Biophys J 102:85–95. doi:10.​1016/​j.​bpj.​2011.​11.​4011
57.
58.
Alcock J (1993) Animal behavior: an evolutionary approach. Sinauer Associates, Inc., Sunderland
59.
60.
Hamilton WD (1975) In: Fox R (ed) Biosocial anthropology. Wiley, New York
61.
Sober E, Wilson DS (1998) Unto others: the evolution and psychology of unselfish behavior. Harvard University Press, Cambridge
62.
63.
Wilson DS (1975) A theory of group selection. Proc Natl Acad Sci USA 72:143–146
64.
Price GR (1972) Extension of covariance selection mathematics. Ann Hum Genet 35:485–490
65.
66.
Rissing SW, Pollock GB, Higgins MR et al (1989) Foraging specialization without relatedness or dominance among co-founding ant queens. Nature 338:420. doi:10.​1038/​338420a0
67.
Goodnight CJ, Stevens L (1997) Experimental studies of group selection: what do they tell us about group selection in nature? Am Nat 150(Suppl 1):S59–S79. doi:10.​1086/​286050
68.
69.
Buss LW (1987) The evolution of individuality. Princeton University Press, Princeton
70.
Gould SJ (2002) The structure of evolutionary theory. Harvard University Press, Cambridge
71.
Lewontin RC (1970) Units of selection. Annu Rev Ecol Syst 1:1–18
72.
Smith JM, Szathmary E (1995) The major transitions in evolution. W.H Freeman, Oxford
73.
74.
Cavalier-Smith T (2001) Obcells as proto-organisms: membrane heredity, lithophosphorylation, and the origins of the genetic code, the first cells, and photosynthesis. J Mol Evol 53:555–595. doi:10.​1007/​s002390010245
75.
76.
Matsuura T, Yamaguchi M, Ko-Mitamura EP et al (2002) Importance of compartment formation for a self-encoding system. Proc Natl Acad Sci USA 99:7514–7517. doi:10.​1073/​pnas.​062710399
77.
78.
Szabó P, Scheuring I, Czárán T, Szathmáry E (2002) In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity. Nature 420:340–343. doi:10.​1038/​nature01187
79.
Gebicki JM, Hicks M (1973) Ufasomes are stable particles surrounded by unsaturated fatty acid membranes. Nature 243:232–234. doi:10.​1038/​243232a0
80.
Allen WV, Ponnamperuma C (1967) A possible prebiotic synthesis of monocarboxylic acids. Curr Mod Biol 1:24–28
81.
Yuen GU, Lawless JG, Edelson EH (1981) Quantification of monocarboxylic acids from a spark discharge synthesis. J Mol Evol 17:43–47. doi:10.​1007/​BF01792423
82.
McCollom TM, Ritter G, Simoneit BR (1999) Lipid synthesis under hydrothermal conditions by Fischer-Tropsch-type reactions. Orig Life Evol Biosph 29:153–166. doi:10.​1023/​A:​1006592502746
83.
Rushdi AI, Simoneit BR (2001) Lipid formation by aqueous Fischer-Tropsch-type synthesis over a temperature range of 100 to 400 degrees C. Orig Life Evol Biosph 31:103–118. doi:10.​1023/​A:​1006702503954
84.
Lawless JG, Yuen GU (1979) Quantification of monocarboxylic acids in the Murchison carbonaceous meteorite. Nature 282:396. doi:10.​1038/​282396a0
85.
Naraoka H, Shimoyama A, Harada K (1999) Molecular distribution of monocarboxylic acids in Asuka carbonaceous chondrites from Antarctica. Orig Life Evol Biosph 29:187–201. doi:10.​1023/​A:​1006547127028
86.
Yuen G, Blair N, Des Marais DJ, Chang S (1984) Carbon isotope composition of low molecular weight hydrocarbons and monocarboxylic acids from Murchison meteorite. Nature 307:252–254. doi:10.​1038/​307252a0
87.
Yuen GU, Kvenvolden KA (1973) Monocarboxylic acids in Murray and Murchison carbonaceous meteorites. Nature 246:301. doi:10.​1038/​246301a0
88.
Deamer DW (1985) Boundary structures are formed by organic components of the Murchison carbonaceous chondrite. Nature 317:792. doi:10.​1038/​317792a0
89.
Deamer DW, Pashley RM (1989) Amphiphilic components of the Murchison carbonaceous chondrite: surface properties and membrane formation. Orig Life Evol Biosph 19:21–38. doi:10.​1007/​BF01808285
90.
Cistola DP, Hamilton JA, Jackson D, Small DM (1988) Ionization and phase behavior of fatty acids in water: application of the Gibbs phase rule. Biochemistry 27:1881–1888. doi:10.​1021/​bi00406a013
91.
Small DM (1986) In: Small DM (ed) The physical chemistry of lipids: from alkanes to phospholipids. Plenum Press, New York
92.
Apel CL, Deamer DW, Mautner MN (2002) Self-assembled vesicles of monocarboxylic acids and alcohols: conditions for stability and for the encapsulation of biopolymers. Biochim Biophys Acta – Biomembranes 1559:1–9. doi:10.​1016/​S0005-2736(01)00400-X
93.
Walde P, Goto A, Monnard P-A et al (1994) Oparin’s reactions revisited: enzymatic synthesis of poly(adenylic acid) in micelles and self-reproducing vesicles. J Am Chem Soc 116:7541–7547. doi:10.​1021/​ja00096a010
94.
95.
Hunter RJ (2001) Foundations of colloid science, 2nd edn. Oxford University Press, New York
96.
Blandamer MJ, Cullis PM, Soldi LG et al (1995) Thermodynamics of micellar systems: comparison of mass action and phase equilibrium models for the calculation of standard Gibbs energies of micelle formation. Adv Colloid Interface Sci 58:171–209. doi:10.​1016/​0001-8686(95)00252-L
97.
Israelachvili JN, Mitchell DJ, Ninham BW (1976) Theory of self-assembly of hydrocarbon amphiphiles into micelles and bilayers. J Chem Soc, Faraday Trans 2 72:1525–1568. doi:10.​1039/​F29767201525
98.
99.
100.
101.
Blöchliger E, Blocher M, Walde P, Luisi PL (1998) Matrix effect in the size distribution of fatty acid vesicles. J Phys Chem B 102:10383–10390. doi:10.​1021/​jp981234w
102.
Berclaz N, Blöchliger E, Müller M, Luisi PL (2001) Matrix effect of vesicle formation as investigated by cryotransmission electron microscopy. J Phys Chem B 105:1065–1071. doi:10.​1021/​jp002151u
103.
104.
Angelini TE, Liang H, Wriggers W, Wong GCL (2003) Like-charge attraction between polyelectrolytes induced by counterion charge density waves. Proc Natl Acad Sci USA 100:8634–8637. doi:10.​1073/​pnas.​1533355100
105.
106.
107.
108.
109.
110.
111.
Hanczyc MM, Fujikawa SM, Szostak JW (2003) Experimental models of primitive cellular compartments: encapsulation, growth, and division. Science 302:618–622. doi:10.​1126/​science.​1089904
112.
113.
114.
Berclaz N, Müller M, Walde P, Luisi PL (2001) Growth and transformation of vesicles studied by ferritin labeling and cryotransmission electron microscopy. J Phys Chem B 105:1056–1064. doi:10.​1021/​jp001298i
115.
116.
Bartlett JH, Kromhout RA (1952) The Donnan equilibrium. Bull Math Biophys 14:385–391
117.
Tinoco I, Sauer K, Wang JC, Puglisi JD (2002) Physical chemistry: principles and applications in biological sciences, 4th edn. Prentice Hall, Upper Saddle River
118.
119.
120.
121.
Shoemaker SD, Vanderlick TK (2002) Stress-induced leakage from phospholipid vesicles: effect of membrane composition. Ind Eng Chem Res 41:324–329. doi:10.​1021/​ie010049t
122.
123.
Budin I, Szostak JW (2011) Physical effects underlying the transition from primitive to modern cell membranes. Proc Natl Acad Sci USA 108:5249–5254. doi:10.​1073/​pnas.​1100498108
Deamer DW, Fleischacker GR (eds) (1994) Origins of life: the central concepts. Jones and Bartlett Publishers, Boston
Deamer D, Szostak JW (eds) (2010) The origins of life. Cold Spring Harbor Laboratory Press, New York
Gesteland RF, Atkins JF (eds) (1993) The RNA world, 3rd edn. Cold Spring Harbor Laboratory Press, New York
Jencks WP (1969) Catalysis in chemistry and enzymology. McGraw Hill, New York
Saenger W (1984) Principles of nucleic acid structure. Springer, New York
Metadata
Title
Life: The Physical Underpinnings of Replication
Authors
Rebecca Turk-MacLeod
Ulrich Gerland
Irene Chen
Copyright Year
2013
Publisher
Springer Berlin Heidelberg
Book
Astrochemistry and Astrobiology

Print ISBN: 978-3-642-31729-3

Electronic ISBN: 978-3-642-31730-9

Copyright Year: 2013

DOI
https://doi.org/10.1007/978-3-642-31730-9_9

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