A lecture note on the modern theory on the origin of life on Earth. A basic introductory knowledge on biology class.
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when moement is with the gradient from high to low concentration it is still facilitated b! carrier proteins.The cell membrane also enables a cell to maintain a stable p7 necessar! for en!me actiit! and faourable concentrations of arious minerals (such as not too much sodium). This requires transport channels (>pumps/) that specificall! moe h!drogen ions (protons) under the control of the cell. These pumps are highl! selectie.%2Transport across membranes is so important that B*2#32O of all genes in most genomes encode membrane proteinsD. %% The smallest 4nown genome of a free5liing organism organism that of the parasite parasite Mycoplasma genitalium, codes for *& transporter transporterss%*amongst its 8* protein5coding genes.A pure lipid membrane would not allow een the passie moement of the positiel!5charged ions of mineral nutrients such as calcium, potassium, magnesium, iron, manganese etc. or the negatiel!5charged ions such as phosphate, sulfate etc. into the cell and the! are all essential for life. A pure5lipid membrane would repel such charged ions which dissole in water not lipid. ndeed a simple fat membrane would preent the moement of water itself (tr! mixing a lipid li4e olie oil with water)M "embrane transporters would appear to be essential for a iable liing cell. n the %9*2s the idea that life began with soap! bubbles (fat globules) was popular (1parin/s >coacerate/ h!pothesis) but this pre5dated an! 4nowledge of what life entailed in terms of <;A and protein s!nthesis or what membranes hae to do. The ideas were naPe in the extreme but the! still get an airing toda! in QouTube ideos showing bubbles of lipid een diiding as if this were releant to explaining the origin of life (see: elf5made cells, 1f course notM) notM). Fig"re 0( The chiralit! of t!pical amino acids. >/ represents the carbon5h!drogen side5chain of the amino acid which aries in length. K@73 ma4es alanine for example. e( H%n!e!ne'' 1#&ir%li23
Amino acids sugars and man! other biochemicals being 35dimensional can usuall! be in two forms that are mirror images of one anotherH li4e !our right and left hand are mirror images of each other. This is called handedness or chirality (Cigure (Cigure ').;ow liing things are based on biochemicals that are pure in terms of their chiralit! (homochiral): left5handed amino acids and right5 handed sugars for example. 7ere/s the rub: chemistr! witho without ut en!me en!mess (li4e (li4e the "iller# "iller#$re $re!! experi experimen ment) t) when when it does does an!thin an!thing g produc produces es mixtur mixtures es of amino amino acids that are both right5and left5handed. t is li4ewise with the chemical s!nthesis of sugars (with the formate reaction for example).%31rigin5of5li 1rigin5of5life fe researchers researchers hae batt battle led d with with this this prob proble lem m and and all all sort sortss of pote potent ntia iall solutions hae been suggested but the problem remains unsoled.% =en =en gett gettin ing g 99O 99O puri purit! t! whic which h woul would d require some totall! artificial unli4el! mechanism for >nature/ to create doesn/t cut it. +ife needs %22O pure left5handed amino acids. The reason for this is that placing a right5 handed amino acid in a protein in place of a left5handed one results in the protein haing a different 35dimensional shape. ;one can be tolerated to get the t!pe of proteins needed for life. W&% %re &e )ini)") re4"ire)en' for % #ell o li$e?
A minimal free5liing cell that can manufacture i ts components using chemicals and energ! obtained from its surrounding enironment and reproduce itself must hae:A cell membrane. This separates the cell from the enironment. t must be capable of maintaining a different chemical enironment inside the cell compared to outside (as aboe). ithout this life/s chemical processes are not possible.A wa! of storing the information or specifications that instructs a cell how to ma4e another cell and how to operate moment b! moment. The onl! 4nown means of doing this is DNA and an! proposals for it to be something else (such as RNA) hae not been shown to be iable-and then there has still to be a wa! of changing from the other s!stem to <;A which is the basis of all 4nown life. %' A wa! of reading the information in (*) to ma4e the cell/s components and also control the amount produced and the timing of production. The maIor components are proteins which are strings (pol!mers) of hundreds to thousands of some *2 different amino acids. The onl! 4nown (or een conceiable) conceiable) wa! of ma4ing the cell/s proteins from the <;A specifications inoles oer %22 proteins and other complex co-factors. In$ol$e! %re
nano5machines such as RNA polymerase (smallest 4nown t!pe has R'22 amino acids) gyrases which twistSuntwist the <;A spiral to enable it to be >read/ (again these are er! large proteins) ribosomes sub5cellular >factories/ where proteins are manufactured and at least *2 transfer-RNA moleculesH these select the right amino acid to be placed in the order specified on the <;A (all cells that we 4now of hae at least &% because most amino acids are specified b! more than one <;A three5letter code). The transfer5;As hae sophisticated mechanisms for ma4ing sure the right amino acid is selected according selected according to the <;A code. There are also mechanisms to ma4e sure that the proteins made are folded three5dimensionall! in the correct wa! that inolechaperones to protect the proteins from mis5folding plus chaperonin folding >machines/ in which the proteins are helped to fold correctl!). All cells hae these. hewM And that/s Iust the basics. A greatl! simplified animation of protein s!nthesis which includes the action of ;A pol!merase ribosomes transfer5;As chaperonins and chaperones. All liing cells hae this s!stem of protein s!nthesis.A means of manufacturing the cell/s biochemical needs from the simpler chemicals in the enironment. This includes a wa! of ma4ing AT AT the uniersal energ! currenc! of life. All liing cells toda! hae AT AT synthase a phenomenall! complex and efficient electric rotar! motor to ma4e AT0 AT0 (or in reerse to create electric currents that drie other reactions and moement both inside and outside the cell).A means of cop!ing the information and passing it on to offspring (reproduction). A recent simulation of one cell diision of the simplest 4nown free5liing bacterium (which >onl!/ has '*' genes) required %*8 des4top computers wor4ing together for %2 hours.%&This gies some indication of what needs to happen for the first liing cell to li!e" An An interesting proIect began some !ears ago to ascertain what could be the minimal cell that could operate in a free5liing mannerH that is not dependent on another another liing organism. organism. 7oweer 7oweer it did hae aailable a nutrient5ri nutrient5rich ch medium medium that proided a wealth wealth of complex organic compounds such that the cell did not hae to s!nthesie man! of its needed biochemicals. This minimal cell is is now 4nown to need oer 22 protein and ;A components%6 and of course that means that its <;A needs to be loaded up with the specifications for ma4ing these. That is the <;A needs to hae oer 22 >genes/. e will come bac4 to this later. Pol2)er for)%ion 1-ol2)eri'%ion3
+ife is not Iust composed of amino acids or sugars but it is loaded with polymers which are strings or chains of simpler compounds Ioined together. A pol!saccharide is a pol!mer of sugars. A protein is a pol!mer of amino acids and <;A and
;A are pol!mers of nucleotides. 0ol!saccharides are the simplest where the lin4s in the chain are normall! the same sugar compound such as glucose (ma4ing starch in plants or gl!cogen in animals). 0roteins are much more complex being chains of amino acids where each lin4 in the chain can be one of *2 different amino acids. And there are four different lin4s in <;A and ;A.;ow water water is is an essential ingredient of liing cellsH t!pical bacteria are about 6'O water. ?eing the >uniersal solent/ water is a necessar! carrier for the arious components of cellsH it is the milieu in which it all happens. The origin of life is a matter of programming, not just chemistry.
7ere is a huge problem for origin5of5life scenarios: when amino acids are Ioined together for example a water molecule is released. This means that in the presence of water the reaction is pushed in the wrong direction bac4wardsH that is proteins will fall apart not build unless the water is actiel! remoed. A cell oercomes this b! protecting the reaction site from water (inside ribosomes) and proiding energ! to drie this and the pol!mer formation. Thus the formation of proteins of more than a few amino acids is a huge problem for all origin5of5life scenarios (and adding more time does not sole the problemH the! Iust fall apart more).0ol!mer formation also requires that the ingredients (monomers) that are Ioined together are bi-functional"That simpl! means that the amino acids for ma4ing proteins (or sugars for ma4ing pol!saccharides) hae at least two actie sites that will allow another amino acid (or sugar) to be Ioined to each end. A protein5forming amino acid will hae at least one amino group (5;7*) and one carbox!l group (5@117) with the amino group of one amino acid Ioining to the carbox!l group of another thus growing the chain. A compound with onl! one actie site ( mono-functional ) would terminate the formation of the chain. The problem for origin5of5life scenarios is that an! proposed chemical reactions that produce some amino acids also produce mono5functional ones that terminate protein formation.%8;ucleic acids such as <;A and ;A are based on a sugar5pol!mer bac4bone. Again the presence of some sugars that are mono5functional would terminate the formation of these and the presence of water also dries this reaction in the wrong direction as well (to fall apart). T&e origin of life i' % )%er of -rogr%))ing5 no 6"' #&e)i'r2
The aboe information would be sufficient to eliminate notions of the naturalistic origin of life but we hae not coered the most important problem which is the origin of the programming. +ife is not based Iust on pol!mers but pol!mers with specific arrangements of the subunitsH spec specif ific ic arr arrange angeme ment ntss of amino mino acid acidss to ma4e ma4e func functi tion onal al proteinsSen!mes and specific arrangements of nucleic acid bases to ma4e ma4e functio functional nal <;A and ;A.A ;A.Ass astrob astrobiol iologi ogist st 0aul 0aul
cause.** f we thin4 of other coding s!stems such as the "orse code or a written alphabetical language where s!mbols were inented to represent the sounds of speech such coded s!stems onl! arise from intelligence. t is an arbitrar! conention that >a/ is usuall! pronounced as in >cat/ in =nglishH nothing about the shape of the letter indicates how it should be pronounced. +i4ewise there is Iust no conceiable possibilit! of explaining the <;A coding s!stem from the laws of ph!s ph!sic icss and and chem chemis istr! tr! beca becaus use e ther there e is no ph!sic ph!sical al or chem chemic ical al rela relatition onsh ship ip betw betwee een n the the code code and and what hat is coded.Curthermore if the origin of an! <;A code were not a big enough problem the <;A code turns out to be of the man! millions possible Bat or er! close to a global optimum for error minimiation: the best of all possible codes.D*3 This error minimiation in the code is possible because there are potentiall! & >codons/ * for *2 amino acids so that nearl! all amino acids hae more than one codon (a few common amino acids such as leucine hae six). *' These multiple codons are sometimes called >redundant/ often ta4en to mean >extra to needed/ or >superfluous/. 7oweer the extra codons are optimied such that the most li4el! single5letter mista4es (mutations) in the coding are more li4el! not to change the amino acid or at least to change it to a chemicall! similar one (thus being less disruptie to the structure of the protein manufacture manufactured).Th d).The e extra codons are also inoled in sophisticate sophisticated d control control of the amount amount of protein s!nthesied s!nthesied through through >translatio >translation n leel control/. This control s!stem operates operates in bacteria bacteria and higher organisms. organisms.*&There is no wa! that a coding s!stem can deelop in successie stages to be optimied. f a wor4able coding s!stem did come into existence no change in the code can occur because the code and the decoding s!stem (reading machiner!) hae to change at the same time an incredibl! improbable li4elihood. o the optimied code cannot be explained except as another incredible flu4e of >nature/ right at the supposed beginning of life. No 6"' % #o!ing '2'e)5 ," infor)%ion
;ot onl! does the origin of the coded information storing s!stem need to be explained the information or specifications for proteins etc. stored on the <;A has also to be explained. eisiting the simplest cell cell deried b! 4noc4ing out genes from a
iable free5liing microbe to see which ones were >essential/ this minimal cell needs oer 22 protein and ;A components. pecifications for all these hae to be encoded on the <;A otherwise this h!pothetical cell cannot manufacture them or reproduce itself to ma4e another cell. t would ta4e a large boo4 to print this information coded in the four >letters/ of the <;A.As per the 0aul eoled/ into this simplest cell need to demonstrate the route from their h!pothetical simpler start to the first liing cell. =nthusiasts for abiogenesis often appeal to >billions of !ears/ as a hand5waing approach to soling the problems but this proides no mechanism. eactions that are going in the wrong direction are not going to reerse and go in the correct direction b! adding more time. Life %l'o nee!' error7#orre#ing '2'e)'
"olecular biolog! has reealed that cells are phenomenall! complex and sophisticated een the simplest ones. The information as stated is stored on the <;A. 7oweer <;A is a er! unstable molecule. 1ne report sa!s:There is a general belief that <;A is >roc4 solid/-extremel! stableD sa!s ?randt =ichman associate professor of biological sciences at Wanderbilt Wanderbilt who directed the proIect. BActuall! <;A is highl! reactie. 1n a good da! about one million bases in the <;A in a human cell are damaged. damaged.*6Therefore all cells must hae s!stems for correcting faults that deelop in the structure of the <;A or in the coded information. ithout these error5correcting s!stems the number of errors in the <;A sequence accu accumu mula late te and and resu resultlt in the the demi demise se of the the cell cell (>er (>erro rorr cata catast stro roph phe/ e/). ). This This feat featur ure e of all all liin liing g cell cellss adds adds yet >impossible// to origin of life scenarios.A scenarios.An! n! information information that happened to arise on a theoretical <;A molecule molecule in a another >impossible primordial soup would hae to be reproduced accuratel! or the information would be lost due to cop!ing errors and chemical damage. ithout an alread! functioning repair mechanism the information would be degraded quic4l!. 7oweer the instructions to build this repair machiner! are encoded on the er! molecule it repairs another icious circle for origin of life scenarios.*8hen scientists discoered bacteria that lie in extreme conditions such as around h!drothermal ents in the sea the! were heralded as >primitie life/ because some origin5of5life researchers had proposed that life might hae started in such places. 7oweer these >extremophiles/ as the! hae been called (>li4ing extremes/) hae quite sophisticated error5 correcting s!stems for their <;A. Cor example Deinococcus radiodurans is a bacterium that can withstand extreme doses of ioniing radiation that would 4ill !ou or me or other bacteria. t does sustain <;A damage where the <;A is fractured into man! pieces. 7oweer about &2 genes are actiated to repair the brea4s and reconstruct the genome in the hours following the damage.*97!drothermal ents are hot inhospitable places and the <;A of microbes that lie there is continuall! being damaged such that the microbes must hae sophisticated error5protecting and correcting s!stems to surie. The! are not at all simple and do not proide an! sort of iable model for explaining the origin of life. 32"oreoer all bacteria not Iust the >extremophiles/ must hae sophisticated error5correcting s!stems that inole man! genes and when the error correction is inactiated b! mutations the bacteria become non5iable. This proides !et another problem for the origin of life. Origin of life '#en%rio'
"ost effort has gone into a >proteins first/ approach whereb! proteins supposedl! formed first and the <;A sequences to ma4e the needed proteins and the ;As necessar! to ma4e proteins from the sequences of <;A came later. 7oweer other than the problem of getting the correct set of opticall! pure amino acids and the problem of pol!merisation to ma4e the protein chains of amino acids few proteins can act as templates to ma4e copies of themseles.3* Also a fundamental problem is that there is no mechanism for creating the <;A sequence for a protein from the protein itself as pointed out b! information theorist 7ubert Qoc4e!. Qoc4e!.33 RNA fir'?
n the %982s some ;A molecules were discoered that hae the abilit! to catal!se some chemical reactionsH these were dubbed >ribo!mes/ (from ribonucleic acid enzymes). This finding stimulated a lot of excitement and so a lot of effort has gone into ;A5first scenarios or the >;A world/. At least there are en!mes that can generate <;A code from ;A codeH that is if !ou could get the ;A !ou might be able to imagine a scenario for getting the <;A. 7oweer the en!me complexes that can ma4e a <;A cop! of an ;A sequence are phenomenall! complex and themseles would neer arise b! natural processes. And there are man! other seemingl! insurmountable problems with the ;A5first scenarios %9 of which hae been enumerated b! @airns5mith.3 Curthermore ;A is much less stable than <;A which itself is er! unstable as documented aboe.The multiplicit! of scenarios proposed reinforces the conclusion that researchers reall! hae little idea how life could hae >made itself/. There is no iable h!pothesis as to how life could start off simpler and step5 wise progress to become an actual liing cell. ;eo5climb mount impossible/ but this cannot help een h!potheticall! until there is a iable self5reproducing entit! a4a a cell the minimum requirements for which set out earlier (>hat are the minimum requirements for a cell to lie,/). Life fro) o"er '-%#e?
Crancis @ric4 co5discoerer of the <;A double helix structure is a well54nown proponent of >life from space/.3' 7e proposed that aliens sent life to earth 4nown as >directed panspermia/. Another form of this idea simpl! >panspermia/ is that life arose somewhere else in the unierse and came to earth as microbes on meteorites or cometsH =arth was >seeded/ with life in this manner. =ither ersion of panspermia effectiel! puts the matter be!ond the reach of science. About the onl! element of panspermia that is testable is the abilit! of microbes to surie riding onSin a meteorite to earth. And this has been tested and found wantingH microbes don/t surie.3& A lot of the impetus for the search for extra5terrestrial intelligence (=T =T)) and extra5solar planets comes planets comes from a desire to find eidence that life might hae
formed >out there/. ?ut een allowing the whole unierse as a laborator! does not sole the problemH life would neer form as the following section reinforces. i4imedia commonsS?oo!abaoo4a Pro,%,ili2 #%l#"l%ion' for &e origin of life
"an! attempts attempts hae been made to calculate calculate the probabilit! of the formation formation of life from chemicals chemicals but all of them inole ma4ing simplif!ing assumptions that ma4e the origin of life een possible (i.e. probabilit! J 2)."athematician ir Cred 7o!le stated in arious wa!s the extreme improbabilit! of life forming or een getting a single functional biopol!mer such as a protein. 7o!le said B;ow imagine %2'2 blind persons ed: standing shoulder to shoulder the! would more than fill our entire planetar! s!stemU each with a scrambled ubi4 cube and tr! to conceie of the chance of them all simultaneousl! arriing at the soled form. Qou then hae the chance of arriing b! random shuffling of Iust one of the man! biopol!mers on which life depends. The notion that not onl! the biopol!mers but the operating program of a liing cell could be arried at b! chance in a primordial soup here on earth is eidentl! nonsense of a high order. +ife must plainl! be a cosmic phenomenon.D36ndeed we can calculate the probabilit! of getting Iust one small protein of %'2 amino acids in length assuming that onl! the correct amino acids are present and assuming that the! will Ioin together in the right manner (pol!merie). The number of possible arrangements of %'2 amino acids gien *2 different ones is (*2) %'2. 1r the probabilit! of getting it right with one tr! is about % in %2%9'. +est someone protest that not eer! amino acid has to be in the exact order this is onl! a small protein and onl! one of seeral hundred proteins needed man! of which are much larger and the <;A sequence has to arise as well seriousl! compounding the problem. ndeed there are proteins that will not function at all with een a small alteration to their sequence.38 At that time 7o!le argued that life must therefore hae come from outer space. +ater he realied that een gien the unierse as a laborator! life would not form an!where b! the unguided (non5intelligent) processes of ph!sics and chemistr!:BThe li4elihood of the formation of life from inanimate matter is one to a number with 2222 naughts after it … t is big enough to bur! elementar! >elementar! logical operations/) operations/) that could hae occurred in the unierse since the supposed big bang (%3.6 billion !ears) has been calculated at no more than %2%*2 b! "T researcher eth +lo!d.2 This sets an upper limit on the number of experiments that are theoreticall! possible. This limit means that an eent with a probabilit! of % in %2 2222 would ne!er happen" ;ot een our one small protein of %'2 amino acids would form.7oweer bioph!sicist 7arold "orowit% came up with a much lower probabilit! of % in %2%2222222222. This was the chance of a minimalist bacterium being assembled from a broth of all the basic building bloc4s (e.g. theoreticall! obtained b! heating a brew of liing bacteria to 4ill them and brea4 them down to their basic constituents).As an atheist "orowit argued that therefore life was not a result of chance and posited that there must be some propert! of aailable energ! that dries the formation of entities that can use it (a4a >life/). This sounds much li4e the idea of Faia which attributes pantheistic m!stical properties to the unierse."ore recentl! the atheist philosopher Thomas ;agel proposed something similar to account for the origin of life and mind.* An!thing but beliee in a supernatural designer it would appear.The appear.The different probabilities calculated arise from the difficult! of calculating such probabilities and the differing assumptions that are made. f we ma4e calculations using assumptions that are most faourable to abiogenesis and the result is still ridiculousl! improbable then it is a more powerful argument than using more realistic assumptions that result in an een more improbable result for the materialist (because the materialist can tr! to argue against some of the assumptions with the latter approach).7oweer all calculations of the probabilit! of the chemical origin of life ma4e unrealistic assumptions in faour of it happening otherwise the probabilit! would be ero. Cor example "orowit/s broth of all the ingredients of a liing cell cannot exist because the chemical components will react with each other in wa!s that will render them unaailable for forming the complex pol!mers of a liing cell as explained aboe.7igh profile information theorist 7ubert Qoc4e! ($@ ?er4ele!) realied this problem: BThe origin of life b! chance in a primeal soup is impossible in probabilit! in the same wa! that a perpetual motion machine is in probabilit!. The extremel! small probabilities calculated in this chapter are not discouraging to true belieers … howeerU A practical person must conclude that life didn/t happen b! chance.D 3;ote that in his calculations Qoc4e! generousl! granted that the raw materials were aailable in a primeal soup. ?ut in the preious chapter of his boo4 Qoc4e! showed showed that a primeal soup could neer hae existed existed so belief in it is an act of >faith/. >faith/. 7e later concluded concluded Bthe primeal soup paradigm is self5deception based on the ideolog! of its champions.D More %!)i''ion'
;ote that Qoc4e! is not the onl! high5profile academic to spea4 plainl! on this issue: BAn!one who tells !ou that he or she 4nows how life started on earth some 3. billion !ears ago is a fool or a 4nae. ;obod! 4nows.D-0rofessor tuart Gauffman origin of life researcher $niersit! of @algar! @anada.'B…we must concede that there are presentl! no detailed
?en tein: Bo !ou hae no idea how it started,D ichard
+ife did not arise b! ph!sics and chemistr! without intelligence intelligence.. The intelligence intelligence needed to create life een the simplest life is far greater than that of human humansH sH we are are stil stilll scra scratc tchi hing ng arou around nd tr!i tr!ing ng to understand full! how the simplest life forms wor4. There is much !et to be learned of een the simplest bacterium. ndeed as we learn more the >problem/ of the origin of life gets more difficultH a solution does not get nearer it gets further awa!. ?ut the real problem is this: the origin of life screams at us that there is a super-intelligent designer of life and that is Iust not acceptable to the secular mind of toda!. T&e origin of life8 % #rii4"e of #"rren '#ienifi# )o!el' by Aw Aw Swee-Eng
0rofound adances in the fields of molecular biolog! in recent !ears hae enabled the elucidation of cell structure and function in detail preiousl! unimaginable. The unexpected leels of complexit! reealed at the molecular leel hae further strained strained the concept concept of the random assembl! of a self5replicat self5replicating ing s!stem. At the same time the recent discoer! of fossil algae and stromatolites (primitie colonies of c!anobacteria) from as earl! as the 0recambrian hae reduced the time for deelopment of the first cell as much as tenfold. Together with implications of this for the oxidatie state of the primitie atmosphere these deelopments will force researchers to rethin4 man! fundamental ideas pertaining to current models of the origin of life on =arth. The eidence for the nature of the primitie atmosphere is examined and the possibilit! of ribonucleic ribonucleic acid (;A) as the first self5replicating self5replicating molecule is ealuated. The focus is then on <;A proteins and the first cells. T&e e%rl2 %)o'-&ere
The nature of the atmosphere under which life arose is of great interest. The high ox!gen content of the =arth/s atmosphere is unique among the planets of the olar !stem and could hae been tied up with the composition of the core and its crust. t has to be said that none of the h!potheses of core formation of the =arth suries quantitatie scrutin!. The gross features of mantle geochemistr! such as its redox state (Ce1) and its iron#sulphur s!stems apparentl! do not agree with experimental data.%* There are outstanding questions relating to the formation and rec!cling of the Archaean crust.3 Fig"re *( implified apparatus for abiotic s!nthesis of organic compounds
as perfor performed med origin originall! all! b! "iller "iller and $re!. $re!. ?! ar!i ar!ing ng the mixture mixture of gases including using olcanic gases of toda! experimenters hae been able to produce man! t!pes of organic compounds.nteresting organic molecules such as sugars and amino acids can be formed from laborator! >atmospheres/ of different proportions of @1* 7*1 ; * ;73 7* @7 7* and @1. This happens onl! in the absence of free 1 *. 1x!gen is highl! reactie brea4ing chemical bonds b! remoing electrons from them. A reducing gas (7* @7 or @1) is therefore thought to be essential for the successful s!nthesis of prebiotic organic molecules.t has been generall! accepted that at about %.' Fa *iga annum K billion !ears agoU the ox!gen content of the air rose at least %'5fold. (;ote that eolutionar!Suniformitarian >ages/ are onl! used here for argument/s sa4e.) ?efore this the ox!gen had been reduced b! Ce() in sea water and deposited in enormous bands as oxides or h!droxides on the shallow sea floors floors.. The source source of the ferrous ferrous iron iron was was h!drot h!drother hermal mal ents ents in the compan! of reducing gases such as h!drogen sulphide (7*).n %993 iddel iddel and his team team cultur cultured ed non5su non5sulph lphur ur bacter bacteria ia from from marine marine and freshwater muds. These anox!genic photos!nthetic bacteria use ferrous iron as the electron donor to drie @1* fixation. fixation. t was a signal discoer! discoer! that ox!gen5independent biological iron oxidation was possible before the eolution eolution of ox!gen5relea ox!gen5releasing sing photos!nthe photos!nthesis. sis. Xuantitatie Xuantitatie calculations calculations support the possibilit! of generating such massie iron oxide deposits dating from Archaean and =arl! 0roterooic times 3.'#%.8 Fa. Fa.n %99* 7an and unnegar made a discoer! which impinged on discussions of ox!gen ox!gen eolution eolution during during the 0recambrian. 0recambrian. To eer!one/s eer!one/s surprise the! report reported ed the spiral spiral algal algal fossil fossil *rypania within within banded banded iron formations formations (?Cs) in "ichigan $A. Algae require ox!gen so their existence at this Iuncture shows banded iron formations do not necessaril! indicate global anoxic conditions. conditions.'ndeed as earl! as %982 two reports appeared on the discoer! of stromatolites in the 3.#3.' Fa arrawoona Froup sediments from the 0ilbara ?loc4 Australia. &6 imilar remains were also discoered in Eimbabwe8 and outh Africa.9t is fair to conclude that the =arth/s earl! atmosphere before 3.' Fa could hae significant quantities of ox!gen. This should discourage the sort of h!pothesising on abiotic monomer and pol!mer s!ntheses so often assumed to hae occurred in Archaean times. obert iding sa!s that the *rypania discoer!B … could spell the end of ?C5dominated models of ox!gen build5up in the earl! atmosphere … The cat reall! will be put among the pigeons howeer if furtherU fossil discoeries extend the eu4ar!ote record bac4 much be!ond **22 million !ears ago into what is still widel! perceied to hae been an essentiall! anaerobic world.D%2 S#en%rio' for -re,iolog2
A number of of reised textboo4s on molecular biolog! came out in %99#%99' which while cone!ing the standard arguments for origin5of5life h!potheses are cautious in their affirmation. ightl! so because adances in the field hae uncoered exquisite details of intracellular processes. These challenge superficial explanations that their origin and subsequent refinement were fed b! randomness. After mentioning the famous simulation b! "iller and $re! of prebiotic s!nthesis of organic compounds (Cigure %) Woet and Woet handle the riddle of the formation of biological monomers with a caeat. The! write:BGeep in mind howeer that there are alid scientific obIections to this scenario as well as to the seeral others that hae been seriousl! entertained so that we are far from certain as to how life arose.D %%The text of Molecular $ell #iology in in its second edition was well indexed on the eolution of cells describing the "iller experiment in detail. %*The third edition has dropped dropped the chapter chapter on eolution eolution of cells found in the second edition.%3 imilarl! tr!er/s fourth edition of his textboo4 on bioche biochemis mistr! tr! ma4es ma4es no mention mention of the abioti abioticc s!nthe s!nthesis sis of organi organicc molecu molecules. les.%B
A pillar of Bprebiological eolutionD has been the long period of time supposedl! aailable for the emergence of BprotocellsD whose deelopment in turn profoundl! altered the climate of the planet and its geolog!. Cor an estimated age of the =arth of *%** .& Fa this seemed initiall! to pose no problem. 7oweer the discoer! of stromatolites in estern Australia *% and in *3* *3 outh Africa upset the timetable seerel!. seerel!. The finding of algal filaments filaments dated at onl! slightl! slightl! more than % Fa !ounger than the =arth itself restricted the time required for the eolution of the liing cell. ari passu the list of processes thought to *'*& occur abioticall! has been shrin4ing.*' =en the origin of the huge banded iron formations of the Archaean can now be *6 attributed to microorganisms microorganisms and aup and Walentine hae suggested that bolide impacts hae at interals of %2 ' to %26 !ears periodicall! erased more than one origin of life. *8 According to this scenario ten or more extinct extinc t bioclades could hae preceded the @ambrian. A bioclade is a group of life forms descended from a single eent of life origin. .* Fa has been gien as the date of the oldest roc4s which is ostensibl! consistent with the cooling and degassing of an actie molten =arth that is said to be .& Fa old. *9 According to the isotopic carbon record in sedimentar! roc4s 3.8 Fa would date the origin origin of life.32Cred 7o!le the @ambridge astronomer and ph!sicist made some sobering calculations on the origin of the cell.3% The probabilit! of forming the *222 or so en!mes needed b! a cell lies in the realm of % in %2 2222. This ma4es the conceptual leap from een the most complex BsoupD to the simplest cell in the time aailable (that is about '22 "a) so dramatic that it requires some suspension of rationalit! in order to accept it. mall wonder that latterl! it is being touted that life ma! hae ta4en far less time to appear.@arl agan has opined:Bf %22 million !ears is enough for the origin of life on the earth could %222 !ears be enough for it (to appear) on Titan,D3* A ri,on"#lei# %#i! 1RNA3 9orl!
;A is a linear pol!mer of ribonucleotides usuall! single stranded. =ach ribonucleotide monomer contains the sugar ribose lin4ed with a phosphate group and one of four bases: adenine guanine c!tosine or uracil. ;A appears in both pro4ar!otic and eu4ar!otic cells as messen messenger ger ;A ;A (m;A (m;A) ) transf transfer er ;A ;A (t;A) (t;A) and riboso ribosomal mal ;A (r;A) (r;A) which which are inoled in protein s!nthesis with <;A the source of information. ome iruses howeer contain genomes of ;A. The nuclei of eu4ar!otic cells carr! two other t!pes of ;AH heterogeneous nuclear ;A (hn;A or pre5m;A) and small nuclear ;A (sn;A).n recent literature there is much excitement oer the discoer! that there are ;As that can catal!se specific biochemical reactions. These are the ribo!mes that is ;A with with en!matic 33 functions. ;A can do this this surpri surprisin sing g feat feat b! foldin folding g its linear linear chains chains to approp appropria riate te secondar! and tertiar! structures thereb! conferring BdomainD t!pe catal!tic structures as seen in protein en!mes. Fig"re .( The molecular molecular structures structures of deox!ribonu deox!ribonucleic cleic acid (<;A) and ribonucleic ribonucleic acid (;A) are built using the nitrogenous bases adenine and guanine (purines) and th!mine c!tosine and uracil (p!rimidines) which are the BlettersD of the genetic code. That ;A can act as a template and also now exhibits catal!tic actiit! fuelled h!potheses for the eolution of an B;A worldD. worldD. 3 n this scenario ;A is the primar! pol!mer of life that replicates itself. <;A and proteins were later refinements. o the first genes were short strands of ;A that reproduced themseles perhaps on cla! surfaces. This conIecture is strengthened b! the fact that in cells toda! there are segments of some eu4ar!otic pre5r;As which can cleae themseles off and Ioin the two cut ends together to reform the mature r;A. n %98* Thomas @ech and his colleagues at the $niersit! of @olorado discoered this can can ta4e ta4e plac place e in the the abse absenc nce e of prot protei ein n in the the cili ciliat ated ed prot proto ooa oan n Tetrahymena thermophila.3' Vust as remar4able are the small nuclear ;As (sn;As) which complex with protein to form small nuclear ribonucleoproteins (sn;0sH pronounced BsnurpsD). 0articles calle called d spli splice ceos osome omess con coner ertt pre5 pre5m m;A ;A to m;A m;A..3& 1the 1therr ribo ribo! !mes mes incl includ ude e the the hammerhead ariet! and ;Ase 0 which generates the ' Z ends of t;As. The former are found found in certai certain n plant plant iruse iruses. s. 1rigin 1rigin5of 5of5li 5life fe theori theories es see prebio prebiotic tic signif significa icance nce in these these >estig >estigial ial// post5t post5tran ransla slatio tional nal mechani mechanisms sms.Th .Thoug ough h attrac attracti tie e there there are seera seerall seriou seriouss obIections to the notion that life began with ;A:0entose sugars constituents of ;A and <;A can be s!nthesised in the formose reaction gien the presence of formaldeh!de (7@71). The products are a melange of sugars of arious carbon lengths which are opticall! left5 and right5handed (d and l). ith few exceptions sugars found in biological s!stems are of the d t!peH for instance [5d5ribose of ;A which is alwa!s produced in small quantities abioticall! abioticall!.7! .7!droc!a droc!anic nic acid (7@;) (7@;) undergoes undergoes pol!merisat pol!merisation ion to form diaminomaleo diaminomaleonitril nitrile e which which is on the pathwa pathwa!! to produc producing ing adenin adenine e h!pox h!poxant anthine hine guanin guanine e xanthi xanthine ne and diaminopurin diaminopurine. e. These are purines: purines: there is difficult! difficult! in producing producing p!rimidines p!rimidines (c!tosine (c!tosine 3638 th!mine and uracil) in comparable quantities36 (see Cigure 3).;either preformed purines nor p!rimidines hae been successfull! lin4ed to ribose b! organic chemists. An attempt to ma4e purine nucleosides resulted in a Bdi!ing arra! of related compoundsD.39 This is expected if sugars and bases were randoml! coupled. The prebiotic production of numerous isomers and closel! related molecules hinders the li4elihood li4elihood of forming forming desirable desirable mononucleosi mononucleosides. des. Curthermore unless ribose and the purine bases form nucleosides rapidl! the! would be degraded quite quic4l!. P"rine %n! P2ri)i!ine N"#leoi!e Bio'2n&e'i'
0urine ribonucleotides (for example A"0 F"0) are s!nthesised from scratch b! liing s!stems in wa!s not remotel! connected with the laborator! models. The purine ring s!stem is built up stepwise from an intermediate 'Z5phosphoribos!l5%5 p!rophosph p!rophosphate ate (000) (000) to a larger larger molecule molecule inosine monophosphat monophosphate e ("0). ("0). This inoles a pathwa! pathwa! comprising comprising %% reacti reactions ons.Th .The e bios! bios!nthe nthesis sis of p!rimi p!rimidin dines es is less less comple complex x but again again the proces processs is elegan elegantl! tl! dissimi dissimilar lar to thein !itro chemistr! with some of the en!mes on the pathwa! exercising regulator! functions.The purine and p!rimidine bios!ntheti bios!ntheticc pathwa!s pathwa!s are finel! tuned and defects such as en!me deficiencies deficiencies their mutant forms or loss of feedbac4 feedbac4 inhibition cause diseases in man.uppose that we alread! hae mononucleosides-purines (or p!rimidines) lin4ed to ribose. 7eating these in a mixture of urea ammonium chloride and h!drated calcium phosphate has been shown to produce mono5 di5 and c!clic phosphates of the mononucleoside. The subsequent chemistr! would !ield a rich (or untid! depending on how it is iewed) racemic mixture of d5 and l5oligonucleotides in all sorts of combinations and permutations. nternal c!clisation reactions would destro! much of these oligonucleotides. 2uppose further that we hae a parent strand of ;A in a chirall!5mix chirall!5mixed ed pool of actiated actiated monoribonucleotid monoribonucleotides. es. ?! base5pairin base5pairing g the strand correctl! correctl! aligns on itself the incoming incoming monomeric units in matching sequence. 0hosphodiester bonds are spontaneousl! forged. The chief obstacles to efficient
and faithful cop!ing appear to be threefold.%d5mononucleotides and l5mononucleotides hinder each other/s pol!merisation on an ;A template.hort chains of nucleotides tend to fold bac4 on themseles to form double helical atson5@ric4 segments.;ewl! formed strands separate with difficult! from their parent ;A strands. The process grinds to a halt.$sing actiated monomers-both nucleotides and amino acids-Cerris and his co5wor4ers could form oligomers up to '' monomers long on mineral surfaces. uch surfaces bind monomers of one charge (negatie in these experiments) and strength of binding increases with chain length.
The presumed rise of ox!gen leels in a primitie reducing atmosphere formerl! attributed to the eolution of photos!nthesis can be explained b! ox!gen5independent biological iron oxidation. ecent inestigations indicate that the =arth/s atmosphere was neer as reducing as preiousl! thought. ecent discoer! of fossil stromatolites and algae from the 0recambrian has reduced the time for eolution of the first cell ten5fold.The atmosphere of 3.' billion !ears ago could hae contained significant quantities of ox!gen. $nder oxidising conditions the formation of organic compounds and their pol!merisation do not occur. ?iological homochiralit! of sugars and amino acids remains an enigma.7!potheses of ribonucleic acids (;As) as the initial self5replica self5replicating ting molecule molecule hae serious serious unresoled unresoled difficultie difficulties.=xtr s.=xtrapolat apolating ing results results of in !itro s!nthesis sis of purine puriness and !itro s!nthe p!rimidines should ta4e into account that bios!nthesis utilises different reaction pathwa!s. O&er O-ion'
Attention switched to other molecules that can carr! information and replicate themseles. n %99% a team of
+i4e ;A deox!ribonucleic acid (<;A) is a linear pol!mer of nucleotides. =ach nucleotide consists of a pentose sugar a nitrogenous base and a phosphate group. The sugar#phosphate lin4ages form an external bac4bone with the bases stic4ing in and h!drogen5bonding with complementar! bases of the opposite sugar#phosphate bac4bone ipper5fashion producing the famous double helix structure of <;A. The helix can ta4e on alternate forms in which it twists to alter the compactness of its spiral and bends to change its oerall shape. The pac4ing of <;A in a microscopicall! isible chromosome represents a %22225fold shortening of its actual l ength. +ittle is 4nown of the structure of <;A in the natural state within the cell. @learl! it is d!namic and b! assuming different forms <;A controls arious biological processes such as replication transcription and recombination. This is a fruitful area for research. T&e S2n&e'i' of ;7!7Ri,o'e
The abiotic origin of <;A is beset with problems similar to those seen with ;A. 8 The s!nthesis of deox!ribose forms the nub. e hae alread! mentioned the difficult s!nthesis of een small amounts of [5d5ribose for the in !itro production of no!o from deox!ribose ;A. ;A. Curthe Curthermo rmore re we might might hae hae expect expected ed deox!r deox!ribon ibonucl ucleot eotide idess to be bios!n bios!nthe thesis sised ed de no!o deox!ribose precursors. precursors. n real life howeer <;A components (the deox!ribon deox!ribonucleot ucleotides ides dA<0 dA<0 d@<0 d@<0 dF<0 and d$<0) d$<0) are s!nthesised from their corresponding ri,on"#leoi!e' b! the reduction of the @* Zposition. The en!mes that do this are named ribonucleotide reductases. There are three main classes of reductases. All replace the * Z517 group of ribose ia 9'2 some elegant free radical mechanisms. mechanisms.9 The class anaerobic Escherichia coli reductase reductase is thought to be the most closel! related to the common reductase ancestor from which the three main classes are presumed to hae eoled. t has been proposed that the pristine reductase en!me similar to present5da! class en!mes arose before the adent of photos!nthesis and therefore before the appearance of ox!gen.;ow the E" coli class en!me mentioned aboe can be induced b! culturing the bacteria under anaerobic conditions. This en!me is an Ce5 protein that in its actie form contains an o<2gen7'en'ii$e gl2#2l free radical. radical.'% This poses a conundrum: the surial and continual eolution of an ox!gen5 sensitie en!me when ox!gen appeared. 1n the other hand the class reductases re4"ire ox!gen for free radical gene genera ratition on.. ure urel! l! the! the! coul could d not not hae hae eol eole ed d and and oper operat ated ed in the the anae anaero robi bicc firs firstt cell cell in an ox!g ox!gen en5fr 5free ee enironment.'* "oreoer one of the most remar4able aspects of this E" coli ribonucleotide class reductase is its abilit! to maintain its highl! reactie free radical state for a long period. nterestingl! this is achieed in !i!o b! inern%ll2 gener%e! o<2gen. Cour proteins hae to be in place: Clain oxidoreductase which releases superoxide ion (1*#) uperoxide dismutase to rapidl! conert this destructie radical to 7*1* and 1* A catalase to disproportionate disproportionate 7*1* to 7*1 and 1* and A fourth fourth protein thioredoxin that functions as a reductant. The ox!gen oxidises Ce and a deepl! buried t!ros!l residue (T!r%**). 7erein lies a difficult!. The reductases are complex protein reaction centres acting in tandem on each other and on the *Z517 group of ribose. These must all hae co5 ,efore DNA %n! %long 9i& 9i& RNA. @ould eoled ,efore @ould this this be seriou seriousl! sl! contem contempla plated ted for a metabo metabolic licall! all! naie ;A BprogenoteD, T&e origin' of !eo<2ri,o'e %n! of DNA &erefore re)%in "n'ol$e! )2'erie'(
=en if the <;A molecule were assembled abioticall! there is the instabilit! and deca! of the pol!mer b! h!drol!sis of the gl!cos!l bonds and the h!drol!tic deamination of the bases. bases.'3 =ach human cell turns oer *222#%2222 <;A purine bases eer! da! owing to h!drol!tic depurination and subsequent repair. Fenetic information can be stored stabl! onl! because a batter! of <;A repair en!mes scan the <;A and replace the damaged nucleotides. ithout these en!mes it would be inconceiabl inconceiable e how primitie cells 4ept abreast abreast of the constant high5leel high5leel damage b! the enironment enironment and b! endogenous endogenous reactions. f unrepaired cell death would result. ndeed the spontaneous errors resulting from intrinsic <;A instabilit! are usuall! man! times more dangerous than chance inIuries from enironmental causes.' The en!mes of the <;A repair s!stem are a marel in themseles and hae been rightfull! recognised as such.''eports of the culture of #acillus sphaericus from spores presered in amber for oer B*' million !earsD does not tall! with what is 4nown of the ph!sico5 chemical properties of <;A.'& Se$er%l DNA P%r%!o
The total amount of <;A in the haploid genome is its @5alue. ntuitiel! we would expect that there should be a relationship between the complexit! of an organism and the amount of its <;A. The failure to consistentl! correlate the total amount of <;A in a genome with the genetic and morphological complexit! of the organism is called the @5alue paradox.'6 This paradox paradox manifests itself in three wa!s."an! plant species hae from two to ten times more <;A per cell than the human cell. Among the ertebrates with the greatest amount of <;A are the amphibians. alamander cells contain %2#%22 times more <;A than mammalian cells. t is hard to ma4e sense of the existence of such maIor redundancies in organisms eolutionaril! less complex than man.There is also considerable intragroup ariation in <;A content where morpholog! does not ar! much. Cor example the broad bean contains about three to four times as much <;A per cell as the 4idne! bean. Wariations of up to %22 times are found among insects and among amphibians. n other words cellular <;A content does not correlate with ph!logen!.+arge stretches of <;A in the genome sa! of humans appear to hae no demonstrable function. This will be discussed later. Inron' %n! e
1nce the genes of unrelated cells were studied it became clear that the molecular genetics of higher organisms are different from those of bacteria. The principles uncoered in pro4ar!otes cannot simpl! be applied to eu4ar!otes. Cor one thing the precursor ;A found in the nucleus called heterogeneous nuclear ;A (hn;A) was far greater in amount than the m;A that emerged from the nucleus into the c!toplasm. t was discoered that the linear hn;A molecule contained excess ;A which was cut out and the m;A was then constructed from splicing together the in5between pieces. An editing process had ta4en place.'8 The logical inference from this finding was that the genomic <;A from which the hn;A was transcribed must be similarl! constructed. The notion of the co5linear relationship between a segment of <;A and the protein for which it codes is not true at least for higher organisms.The word BintronD was used to describe such a noncoding region of a structural gene. The! separate the BexonsD which encode the amino acids of the protein. '9 Cor instance the human [5globin gene comprises in linear sequence three exons separated b! two introns within a total length of %&22 nucleotides. ntrons are abundant in higher eu4ar!otes uncommon in lower eu4ar!otes and rare in pro4ar!otic structural genes. Wariations in the length of the genes are primaril! determined b! the lengths of the introns. ince the discoer! of intronsSexons the intricate processes of nuclear m;A splicing hae been elegantl! elucidated. Among these are the remar4able self5splicing introns&2 and the equall! reolutionar! finding that indiidual nucleotides can be inserted into ;A after transcription altering them remar4abl!.&% The ineitable questions emerged. hat role does haing genes in pieces sere, 7ow hae such interrupted genes BeoledD oer time,1ne h!pothesis points out that exons usuall! encode for a part of the protein that folds to form a domain. hat constitutes a domain has been a matter of controers!. ?! dispersing indiidual exons of a protein among introns it is reasoned that brea4ing <;A and reIoining and recombining different exons is that much easier. This process of shuffling exonsSdomains is presumed to hae created new proteins with multi5domain structures. This is thought to be a more efficient wa! for a cell to create proteins rather than through random <;A mutations. 7ere is a means of duplicating modif!ing assembling and reassembling units with modular functions into larger structures. According to this h!pothesis this is the reason wh! introns hae suried through time. eeral queries ma! be raised. Cirst exon shuffling as a deice to speed up eolution eolution is logicall! logicall! tied up with a subsidiar! assumption assumption that possessing possessing similar domains qualifies qualifies proteins proteins for biochemical biochemical 4inship which is to sa! sa! these proteins are alleged to bear the mar4s of descent descent from a common ancestral ancestral protein. protein.&* ?ut the construction of ph!logenetic trees relies on unstable molecular cloc4s and other genetic mechanisms largel! un4nown&3 and as discussed below should be approached with caution.?iochemical 4inship aside would not domains exercising similar function be structurall! ali4e such as we see between sa! the catal!tic domains of the two serine proteases ch!motr!psin and tissue plasminogen actiator,econd ;A splicing is an accurate and complex procedure comparable in complexit! to protein s!nthesis and initiation of transcription. t is carried out b! a '2 to &2 ribonucleoprotein made up of small nuclear ribonucleoproteins (sn;0s) as well as other proteins. Vust as the ribosome is built up in the process of translation the spliceosome components assemble in an orderl! manner on the intron to be spliced before the initial cleaage of the ' Z splice site. The splicing must be carried out precisel! Ioining the 'Z end of the preceding exon to the 3 Zend of that following. A frameshift of een one nucleotide would change the resulting m;A message. The inescapable conclusion is that these interloc4ing components must hae BeoledD together as an imperfect splicing mechanism is worse than none.Third were the original protein5coding units seamless that is uninterrupted b! introns, And were the introns bits of Bselfish <;AD that later insinuated themseles into the hosts/ structural genes, hat purpose then the subsequent eolution of a multi5step complicated splicing machiner! to remoe the introns, &#&9 ould not simpl! eliminating the introns ma4e better sense for selectie adantage,Courth and most importantl! transport of m;A from the nucleus to the c!toplasm is coupled to splicing and !oe' no o##"r "nil %ll &e '-li#ing i' #o)-lee( 7ow does the ;A enter the c!toplasm for translation during the eolution of the splicing mechanism, This would hae disrupted protein s!nthesis and would be powerfull! selected against. against.62#6* h! is splicing in all its ariants so rampant toda!,The problem would arise too were introns abundant in cells without nuclear membranes-the pro4ar!otes. "attic4 wrote:Bf introns were introduced into a procar!otic cell/s genes there would be no opportunit! to remoe them before protein is made and the result would be BnonsenseD non5functional proteins.D63This is essentiall! correct because spliceosomes would be needed for their remoal but again begs the question on the iabilit! of the transitional phases.The relationships between exons and protein domains remain to be wor4ed out. here introns came from and how the! were integrated into the genome is a m!ster! to eolutionists.6 T&o'e o$erl%--ing #o!e'
"essenger ;As generall! contain onl! one reading frame which is dictated b! the position of the initiation codon. This correct reading frame translates the nucleotide code into a functional protein. tarting at an A$F codon translation continues in triplets to a termination codon. The starting point can be altered b! a mutation usuall! resulting from insertion or deletion of a single nucleotide to gie an alternate reading frame. A frameshift error results in the s!nthesis of a pol!peptide that does not resemble the normal product. T!picall! it will be inactie and because stop codons are abundant in the alternatie frames shorter than the natie protein.ome organisms store information in their <;A in the form of
oerlapping codes. The oerlapping codes are still triplet but hae different initiation points. n other words the same stretch of <;A carries the information for producing two proteins of entirel! different amino acid sequence. This discoer! is trul! startl startling ing becaus because e the possib possibili ilit! t! that that genes genes might might oerla oerlap p in differ different ent readin reading g frames frames impose imposess seere seere eolut eolution ionar! ar! constraints. A faourable mutation in one frame must be faourable in the other. A termination codon in the second frame would be fatal to the organism as a whole. o the two oerlapping genes hae to eole in parallel. Qoc4e! considered the problem from the point of iew of information theor! applied to biolog! itself a enture fraught with caeats. 6' n his opinion information theor! shows that transcription from two or een three reading frames in a <;A or ;A sequence is possible proided the total informational content to be transcribed does not exceed the full informational capacit! of the <;A or ;A sequence. This interesting bit of information is a necessar! but not a sufficient explanation for the origin of oerlapping codes. The pac4ing of information for s!nthesising additional essential proteins through weaing such information into a pre5 existing nucleotide sequence is little short of miraculous assuming that chance is the author."ost of the 4nown examples of 6&66 such programmed frameshifts occur in iral genes.6& The notorious hepatitis ? irus has four open reading frames on the long strand of its <;A to produce four different proteins. n a stri4ing demonstration of sheer econom! it turns out that each reading frame oerlaps % le%' one o&er fr%)e. And the code for the pol!merase en!me oerlaps the other three. 68 t is true that programmed frameshifts are not common but the! hae been found across a wide spectrum of organisms. Qeast 6982 and E" coli also practise frameshifting. frameshifting.69 The mechanisms b! which the! wor4 seem to inole Bshift!D messages in the m;A where the ribosomes ma! read four nucleotides as one amino acid and then continue reading triplets. 1r it ma! bac4 up one base before reading triplets in the new frame. Bhift! t;AsD are also implicated. 8%#83 T&e non7"ni$er'%l #o!e
=en the code/s uniersalit!-a strong argument for the h!pothesis that life on =arth eoled onl! once-has a large number of BexceptionsD. These are usuall! credited to later eolutionar! deelopments as the following quote from a paper b! Vu4es and his colleagues shows. @ommenting on the dearth of molecular studies on Bthe more than %2 million species of organisms now liing on =arth all of which are deried from a single pool of the ancestorD the! continue:B … nonuniersal codes hae been discoered at a relatiel! high incidence. @odon $FA Trp has been found in seen "!coplasma species and related bacteriaH at least two 4inds of nonuniersal code are independentl! used in ciliated protooansH the same code change was found in two different organismic lines ciliated protooans and unicellular green algaeH a !east line uses a still different code. All nonplant mitochondria that hae been examined use nonuniersal codes which are more or less characteristic for each line. t is remar4able that mitochondria from one species use more than two nonuniersal codonsH six in !easts four or fie in man! inertebrates and four in ertebrates. Thus nonuniersal codes are widel! distributed in arious groups of organisms and organelles. … The nonuniersal codes are not randoml! produced but are deried from the uniersal code as a result of a series of nondisruptie changes.D8 All this Iust means that h!potheses of the origin of the genetic code based on our understanding of the nature of the <;A its transcription and translation hae to be substantiall! reised. T&e 'ilen )%6ori2
t is now agreed that an! theor! on the origin of <;A must ta4e into account that the genomes of multicellular organisms are characterised b! high intron content. "attic4 has proposed that introns haing a high sequence complexit! be regarded as informational ;A (i;A).8' =ach chromosome is increasingl! being iewed as a complex Binformational organelleD. At least some now regard the idea that there is BIun4D or BuselessD <;A as untenable 8& but the logical extensions are not usuall! followed through.An unanswered question concerns the enormous amount of <;A in most eu4ar!otic genomes which appears to sere no useful purpose. ntrons contribute to this excess. The highl! consered nature of the sequences in introns points to the possibilit! that the! hae sered important function(s) from the time of their first appearance in their hosts/ genomes. Cor instance mouse and human T5cell receptor genes show 6% per cent homolog! oer their entire %22 4b length een though less than six per cent of that length encodes the receptor protein. 86ecent ecent studies studies describe describe finding a 8889 88 ;A regulator of gene expression originating from the introns of another m;A. This small ;A binds to the so5called 3Z untranslate untranslated d region region (3Z$T) which lies at the end of each gene/s m;A once again confounding the notion of Bfunctionle BfunctionlessD ssD ;A.ntro ;A.ntron5cont n5containing aining genes hae !et another another intriguing intriguing propert! propert! uncoered uncoered in %99* b! 0eng and his co5 wor4ers wor4ers in ?oston. ?oston. The! introduced introduced a new quantitatie quantitatie method to displa! correlations correlations in the sequence of nucleotides. nucleotides. To their surprise the! discoered that the nucleotide sequence in intron5containing genes is correlated oer remar4able ranges of thousands of base pairs apart. Their results are based on a statistical assessment of * iral bacterial !east and mammalian sequences. This means that a particular nucleotide at one site would somehow influence which nucleotide would locate at a remotel! distant site. This long5range dependence indicates an intricate self5similarit! that is reminiscent of fractal d!namics.92 n addition there are hints of % l%ng"%ge 'r"#"re a4in to that seen with ordinar! languages in the lengths of non5protein coding <;A. Their findings support the possibilit! that noncoding regions of <;A ma! carr! biological information. The two standard linguistic tests applied were those of Feorge Eipf and @laude hannon. The coding regions of the genes returned negatie results for both tests.9%
As with the d5sugars of carboh!drates so with the amino acids from which proteins are made. The! are t!picall! l (left5 rotati rotating) ng) in optica opticall actii actiit! t!.. d5amin d5amino o acids acids are found found in bacter bacterial ial produc products ts and peptid peptide e antibi antibioti otics cs but the! are not incorporate incorporated d into proteins ia the ribosomal ribosomal protein s!nthesising s!nthesising s!stem.The s!stem.The almost total dominance dominance of one chiral form in present life forms is an enigma. Wital processes such as protein bios!nthesis ligand5receptor actiit! substrate binding en!matic catal!sis and antigen#antibod! interaction depend on the present chemical5handedness. Cisun and ain hae proided proided another example of monochiral utilit! b! examining examining proton transfer along the h!drogen5bonded h!drogen5bonded chain formed b! amino acids. acids.9 After all membrane proteins are structured to enable such transfers to ta4e place as a means of regulating proton concentrations. The amino acids the! examined were l5t!rosine l5serine and l5threonine. hat would happen the! as4ed if a long sequence sequence of such 175bearing 175bearing acids were interrupted interrupted b! an unnatural d isomer, isomer, Their anal!ses reealed that it suppressed transfer through the h!drogen5bonded networ4. The authors point out the generall! disruptie effects that deforming natural pol!mers with d5amino acids would hae on dierse biological phenomena such as information charge energ! and mass exchanges.The eolutionar! explanation for left5handed amino acids is simpl! that a common ancestor b! sheer coincidence happened to hae this mirror image. ell5worn explanations such as the anisotropic effects of refracted light are conincing onl! to those who propose them. B@hiral fieldsD that could effect a critical prebiotic transition to one chiral chiral species hae been wor4ed out on paper .9' The trouble is that so far there there has been no success for the apparentl! apparentl! simple problem of tipping the experimental scales to faour one of two isomers.The problem of chiralit! is crucial to the origin of life. Cor
"uch thought has been gien to suggesting pathwa!s as to how a pol!peptide chain freshl! made folds into its unique shape.%2* ?ut biological s!stems are inherentl! complicated and so are their components. Toda! the concept that proteins can self5assemble has been modified to incorporate the astonishing part pla!ed b! accessor! proteins called #&%-erone' first identified in E" coli .%23#%26 @haperones are found in all t!pes of cells and in eer! cellular compartment. The! bind to target proteins to facilitate proper folding preent or reerse improper associations and protect their accidental degradation. 1f special interest is a subset of chaperones called chaperonins. The! are large barrel5shaped pol!meric proteins present in bacteria mitochondria chloroplasts and eu4ar!otes. The! enfold protein chains in a cait! a protected micro5enironment to allow their guest molecules opportunit! to fold correctl!. @haperones utilise the energ! of AT0 h!drol!sis to bind and release their charges. The! are also inoled in man! macromolecular assembl! processes including the assembl! of nucleosomes protein transport in bacteria assembl! of bacterial pili binding of transcription factors and ribosome assembl! assembl! in eu4ar!otes. eu4ar!otes. A subset of molecular molecular chaperones has een been implicated implicated in signal transduction. transduction. This follows upon the discoer! that steroid hormone receptors which are c!toplasmic proteins combine not onl! with their respectie hormones hormones but also require chaperones chaperones in order to form functioning functioning rec!cling complexes. complexes.%28 uch structural arrangements must be highl! consered seeing that these chaperones are found in similar macromolecular complexes in organisms as dierse as mammals and !easts.%29 This is supposed to attest to their great antiquit! (if eolution is true) because properl! folded proteins are absolutel! essential for a cell/s iabilit!.+odish and his co5authors express their opinion:BColding of proteins in itro is inefficientH onl! a minorit! undergo complete folding within a few minutes. @learl! proteins must fold correctl! and efficientl! in io otherwise cells would waste much energ! in the s!nthesis of non5functional proteins and in the degradation of misfolded and unfolded proteins.D %%27ow did cellular proteins aoid being tied up into 4in4s indiiduall! and aggregates corporatel! before chaperones came on the scene, f chaperones help other proteins fold what mechanism helps chaperones to fold, And chaperones are themseles complex proteins. A well5studied chaperonin @pn&2 has a %%%%%* unique structure consisting of fourteen identical subunits of a &2 4
The existence of chaperones influences the endos!mbiont h!pothesis of the origin of eu4ar!otes. This h!pothesis proposes that chloroplasts and mitochondria began as free5liing aerobic pro4ar!ote ancestors which were engulfed b! and formed a %%%%' mutuall! adantageous relationship with an ancient large anaerobic pro4ar!ote with a nucleus.%% These endos!mbionts became the organelles mentioned which then apparentl! lost man! of their own genes to the nuclei of their hosts. ;ow the timeframe of ox!gen leels in the primitie =arth is extremel! controersial in the face of conflicting palaeobiological eidence. eidence.%%& ;eertheless how a stable relationship between ingested aerobic inaders and an anaerobic or aerotolerant host was possible and wh! some genes and not others should be transferred to the host/s nucleus is not clear.An idea of how man! genes were BlostD to the host nucleus ma! be gleaned from the fact that the c!tosol s!nthesises for the mitochondri mitochondria a the following following proteins: proteins: ribosomal ribosomal proteins proteins <;A replication replication en!mes en!mes aminoac!l5t aminoac!l5t;A ;A s!nthases s!nthases ;A pol!merase pol!merase soluble en!mes en!mes of the citric acid c!cle and so on.%%6 t is clear that since proteins proteins are made at two separate sites nuclear5code nuclear5coded d proteins must be imported imported into mitochondria mitochondria and chloroplasts chloroplasts.. This is not made eas! b! the fact that imported proteins hae to cross subcompartments to get into both organelles as the organelles possess double membranes: two subcompartments in the case of mitochondria three for chloroplasts because of the th!la4oid membrane.7ere is where chaperones are needed to bind the pol!peptide chains Iust as the! emerge through special pores into the mitochondrial matrix. matrix. Assistance Assistance with protein protein folding is gien b! !et other chaperones near at hand. hand.%%8 A similar process operates in the importing of proteins into the chloroplast. As plant cells hae both chloroplasts and mitochondria two different 4inds of signal peptides are also required to send proteins to the correct addresses.%%9 The er! complicated transport arrangements described force us to quer! how the! arose and what selectie adantages there could be for original endos!mbionts to share genomes with the nucleus of the host cell. As if this is not difficult enough a further logical and logistical problem is
