Prebiotic Chemistry and Chemical Evolution of Nucleic Acids

300 Pages·2018·9.9 MB·English

by  César Menor-Salván

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
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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