Prebiotic Chemistry and Chemical Evolution of Nucleic Acids PDF
Preview Prebiotic Chemistry and Chemical Evolution of Nucleic Acids
Nucleic Acids and Molecular Biology 35 César Menor-Salván E ditor Prebiotic Chemistry and Chemical Evolution of Nucleic Acids Nucleic Acids and Molecular Biology Volume 35 Serieseditor AllenW.Nicholson Philadelphia,PA19122,USA Moreinformationaboutthisseriesathttp://www.springer.com/series/881 César Menor-Salván Editor Prebiotic Chemistry and Chemical Evolution of Nucleic Acids Editor CésarMenor-Salván NSF-NASACenterforChemicalEvolution SchoolofChemistryandBiochemistry GeorgiaInstituteofTechnology Atlanta,GA,USA UnidaddeBioquímicayBiologíaMolecular,Dept.BiologiadeSistemas UniversidaddeAlcala Madrid,Spain ISSN0933-1891 ISSN1869-2486 (electronic) NucleicAcidsandMolecularBiology ISBN978-3-319-93583-6 ISBN978-3-319-93584-3 (eBook) https://doi.org/10.1007/978-3-319-93584-3 LibraryofCongressControlNumber:2018949306 ©SpringerInternationalPublishingAG,partofSpringerNature2018 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. 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Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface Thisbookhasbeenpreparedwiththeaimtoguidethereaderintothecurrentideas upon chemical evolution of nucleic acids, i.e., all the chemical processes that occurred immediately before the emergence of Life, toward the formation, self- assembly, selection, and supramolecular organization of nucleic acids, and which, ultimately, allowed the emergence of a system capable of Darwinian evolution. Althoughthe bigquestion standingbehind ishow life emerged inageochemically plausibleenvironmentfromchemicallysimpleprecursors,thismonographdoesnot intend to offer an answer to that question, which, perhaps, is one of the most persistent, elusive, and interesting questions of human thought. We focused it on theoriginandearly,abioticevolutionofnucleicacids.Todiscussthat,werecruiteda group of influential scientists in topics covering from the geochemistry and miner- alogy of phosphate and the prebiotic origin of small molecules to the chemical evolution of nucleic acid polymers and the emergence of complex systems. The bookiswritteninsuchawaythatitprovidesaperspectiveonthelatestknowledgein thistopicforgeneralreaderswithagoodbackgroundinGeneralChemistry,aswell asforeducatedexpertsinallfieldswithinAstrobiologyandOriginsofLifeStudies. ThebookbeginswitharemembranceofStanleyMiller,oneofthepioneersofthe experimental Prebiotic Chemistry. The following six chapters are devoted to the chemical origin of building blocks of nucleic acids (nucleobases and nucleosides) and its organization, the influence of the geochemistry and mineralogy in the prebiotic chemistry of nucleic acids, the origin of organic phosphate, and the fate ofnucleicacidsinthelow-temperaturehydrothermalsystems;inthefollowingtwo chapters, two relevant questions upon the early, abiotic chemical evolution of nucleic acid polymers are discussed; the final two chapters introduce the reader intosomeconceptsupontheemergenceofcomplexityinprebioticevolution. To prepare a monograph is a challenging but, in my opinion, a necessary task. After one century of scientific quest for the origins of life, we have accumulated enoughdataandideastocreatemonographsandtextbooksonthetopic.Thebooks pavethewayfromthedataandobservationsaccountedinthescientificjournalsto the culture and knowledge. Books present in a tangible form a process that we scientistsperforminsideourheads.Amonographisagoodopportunityandaspace v vi Preface of freedom to present the ideas, models, and theories of experts without the usual constraints ofregularpapers.Thatisexactlywhatwe tried inthisbook: thereader will finda valuable,firsthand account of theresearch and ideas of thecontributing authors,inamorediscursiveformatthanthecorsetedpapers.Ithinkitisimportant tonotethattherearenocompetingideasortheoriesaroundtheChemicalEvolution and Origins of Life. Competition is an illusion created by human egos, but in the study of chemical evolution, as Prof. Nicholas V. Hud once said, our role as prebioticchemistsistoprovidechemicalandgeologicallyplausiblemodelscenar- ios for conditions and molecules that allow the robust formation of proto-biopoly- mers.Thereareseveralpossiblemodelscenariosthatcouldpossiblyhaveledtothe emergenceoflife,andwehavenowaytoknowwhatorhowmanyofthesepossible scenarios, reactions, andchemical pathways havebeenactiveduringtheorigins of life epoch, around 4 billion years ago on Earth. Prebiotic Chemistry and Chemical Evolution is in constant feedback with fields as Geology and Space Sciences. Precisely, the advance in space science is testing and validating the robustness of ourproposedmodelsand,maybeinthenearfuture,spaceexplorationwillfindareal environment in which Chemical Evolution is active, giving us definite answers to ourquestions.Untilthatmomentousevent,allmodelsandreactionswithinprebiotic chemistry that are plausible from the point of view of geochemistry and geology shouldbeconsideredandaccountedforfuturereference.Hence,thepreparationof scientific books, in my opinion, is a responsibility with the future students and readers interested in this topic and an indicator of the maturation of the scientific field.Tofulfillthisresponsibilityisnotaneasytask,however,inthecontextofour system of science. Nowadays, top-notch scientists are immersed in a hyper- competitivesysteminwhichthepriorityisthepublicationofpapersinhighimpact factor journals, nearly followed by the writing of grant proposals, the fulfilling of endless bureaucracy, and, in most cases, teaching responsibilities. Hence, in an unbalanced system that does not encourage the communication of science and the generationofknowledge(justthegenerationofpapers),theyhaveverylittlesupport and even less time available to write books or monograph chapters. Given this context,Ihopethereader willappreciate, asIdo,thegenerousandlaudableeffort investedbytheauthorsinthepreparationofthisbook. WhenProf.AllenW.Nicholson,fromTempleUniversityatPhiladelphia,invited andencouragedmetoeditabookdevotedtotheprebioticchemistryofnucleicacids, I realized that it would not be easy to completely cover the models that should be represented in a book on that topic, in part for the reasons explained above. I apologizeifthereaderfeelsthatsometopicsareunderrepresented.Iappreciatethe supportandpatienceuntilfinalizationofthebook,proofreading,andformattingof SabineSchwarzandAnandVenkatachalam,fromSpringerNature,andthestaffof SPi Global. My special thanks go to my colleagues, friends, and the staff of the Center for Chemical Evolution and the Georgia Institute of Technology, without whomthisbookwouldnothaveexisted. Atlanta,GA CésarMenor-Salván July2018 Outline Theoriginoflifeisoneofthebigquestionsofhumanknowledgeandachallenging topic for scientific research. Chemical evolution can be defined as all the chemical processes and interactions conducive to self-assembly and supramolecular organi- zation,leadingtoanincreaseincomplexityandtheultimateemergenceoflife.This volumeaddressestheformationofandinitialeventsinthechemicalevolutionofthe nucleicacids,includingthegeochemicalrootsofreactioncomponents.Thevolume presentsareviewoftheseminalworkofStanleyMiller,andhowthedevelopmentof organic chemistry in the nineteenth century led to the development of the field of prebioticchemistry,representingthefrontierbetweenorganicchemistry,geochem- istry, and biochemistry. Also covered are current topics on the organization of the nucleic acids: the origin of the nucleobases and nucleosides, phosphorylation and polymerizationreactions,andtheself-assemblyandsupramolecularorganizationin thecontextoflife’sorigins. Keywords Origins of life (cid:129) Evolution (cid:129) RNA-world (cid:129) Nucleotide synthesis (cid:129) Chemistryofpurinesandpyrimidines(cid:129)Phosphorylation vii Stanley L. Miller: A Personal Retrospective I met Stanley Miller in 1965 when I was a first-year graduate student in the DepartmentofChemistryattheUniversityofCaliforniaatSanDiego(UCSD). At thattime,Iwasinterestedinthestructureofsupercooledwaterandwastryingtouse X-raycrystallographytodetermineifwaterhadanincreasingicelikestructurewhen itwassupercooledtolowerandlower temperaturesbelowitsfreezing point.Iwas usingtheX-rayequipmentinthelaboratoryofaUCSDchemistryProfessorJoseph Krautwhohadallowedmetheuseofhisinstrumentation,between10pmand8am. BecauseittookawhiletogetX-rayimagesofonesample,Ioftenwonderedaround looking at what some of the professors had posted on their doors and walls. I was surprisedtofindachemistryprofessorwhowasalsoworkingatthoselatehours.The professorwasStanleyMiller,andweeventuallystruckupmanyconversations(this wasattimestoughbecauseStanleywasthenaheavychain-smoker). Although I remembered reading something about Stanley Miller making amino acids inan experiment simulatingthe early Earth, I did notknow exactly how and when hedidthisexperiment.Stanleyshowedmetheapparatus andhowitworked and gave mesome of his papers to read. Stanley was also interested in what I was doingandwhatIhadfound.AfterexplainingmyprojectandsayingIwasfindingit very frustrating and challenging to carry out the measurements, he offered his advice. Although my project was interesting, I would probably not get my PhD untilIwas40yearsold.Beingonly22atthetime,hiscommentwasnotencouraging tosaytheleast. Asmyfrustrationswithmyprojectincreased,Ibecamemoreandmoreintrigued by the experiments Stanley had done and was continuing to do. I was especially captivatedwhenhementionedhowlittlewasactuallyknownabouttheconditionson the abiotic Earth and that the field was ripe for some new ideas and novel experiments. ThemoreIthoughtaboutthesecommentsthemoreinterestingtheybecame.Istill remember my excitement fantasizing about what the Earth was like over 4 billion yearsago.IwenttothelibraryandusedChemicalAbstracts(thiswaswellbeforethe InternetandGoogleScholar)andtriedtoreadeverythingIcouldfindabouttheearly ix x StanleyL.Miller:APersonalRetrospective Earth,whichatthattimewasasubjectmoreintherealmofgeologists.IreadHarold Urey’s book The Planets: Their Origin and Development (1952) which impressed me about how important chemistry was in trying to understand the history of our planet.UreywasalsoamemberofchemistryfacultyatUCSD,andIalsotalkedwith him about theearly Earth’s chemistry. One thing I remember about our discussion was Urey’s use of thermodynamics and equilibrium constants to constrain the mixture of gases that could have been present in the early atmosphere, especially ifhydrogenwaspresent.ImentionedthistoStanley,whoinresponsesaidthatthere could be thermodynamic equilibrium constants for organic reactions that could be used to place further constraints on concentrations of reduced species in the atmo- sphere, especially ammonia. We discussed the reactions involved in amino acid formationinhisexperiments,andStanleyhintedthatmaybeIshouldlookintothis.I jumpedatthechance. So I went back to the library to read about any equilibrium reactions involving organic compounds, especially parts of the Strecker Reaction that had Stanley had proposedasthepathwaybywhichaminoandhydroxylacidswereproducedinhis experiments.Thefirststepwasthereactionofanaldehydeorketonewithhydrogen cyanide and ammonia to produce the corresponding amino and hydroxyl nitriles. Thiswasareversiblereaction,whichwasconstrainedatleastforaminoacidsbythe concentrationsofthethreereactioncomponents.Constrainingallthesecomponents was complex and unlikely to yield anything useful because the number of combi- nationsoftheconcentrationsofthethreeconstituentswasimpossiblyhuge. I thought maybe finding out how the various amino acids used in biology were discoveredmightyieldsomeinterestinginsights.Iagainwentbacktothelibraryand to begin a search of the various reactions by which amino acids had been first synthesized. Searching Chemical Abstracts for reactions that might be relevant, I began compiling a list of possible reactions. One in particular caught my eye: the apparentequilibriumbetweenasparticacid,fumaricacid,andammonia. A report in 1926 (Dessaignes 1850) showed that aspartic acid decomposed by deaminationtofumaricacidandammoniainthepresenceofbacteria.Thereaction was reversible, and equilibrium between all three species was attained. When I showed this to Stanley, he immediately suggested that maybe the equilibrium couldbeusedtoconstraintheamountofammoniaontheearlyEarth.Theproblem wasthatitwasnotknownhowrapidlythedeaminationreactiontookplaceatEarth’s environmental temperatures,andwhether equilibriumcould beestablishedwithout the presence of bacteria. Stanley and I discussed the several possible experimental scenarios to determine the rate of deamination at various temperatures. Finally, he saidpicktheoneyouthinkisbestandtestitout. ThiswasoneofthehallmarksofmygraduatestudentrelationshipwithStanley: discussideasandthenIwouldbebasicallyonmyownwithplanningandsettingup experiments as well as finding analytical methods to measure the extent of any reaction. Thiswasavaluablelessonforme.ItgavemeindependencetodowhatIwanted andtothinkonmyown.AsIstartedsettingupexperimentsandanalyticalmethodsI
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