Introduction
In addition to the synthesis of RNA (Schrader Reference Schrader2009), a cyanomethanol intermediate could also react along a different pathway, leading to the thermodynamically feasible synthesis of polypeptides, the backbone of protein molecules. The cyanomethanol intermediate was postulated as formed, with thermodynamic feasibility, from addition of HCHO and HCN (Schrader Reference Schrader2009). The latter two molecules, in turn, have been calculated as formed from photolysis of a ‘slightly reducing’ atmosphere to which HCN has been added (Mukhin Reference Mukhin1974; Pinto et al. Reference Pinto Joseph, Gladstone and Yung1980; Zahnle Reference Zahnle1986; Ferris Reference Ferris1992; Hennet et al. Reference Hennet, Holm and Engel1992) This synthesis of polypeptides could be regarded as one solution to the ‘chicken and egg’ problem, i.e. which originated first, RNA (Gilbert Reference Gilbert1986; Ferris Reference Ferris2005) or proteins. The present hypothesis has them originating independently from the same molecule.
$$\eqalign{& {\rm Adenosine} \to {\rm RNA} \cr & \quad \quad \uparrow \cr & {\rm Cyanomethanol} \cr & \quad \quad \downarrow \cr & {\rm Polypeptides} \to {\rm Proteins}} $$
Results
Polypeptides from cyanomethanol
The cyanomethanol could reasonably react in one of two ways to yield a polypeptide, as follows.
$$\eqalign{& {\rm N} \equiv {\rm C -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH\; + N} \equiv {\rm C -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH\; + N} \equiv {\rm C -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH} \cr & \quad \quad \quad \quad \quad \quad \quad \quad \quad \quad \quad \downarrow \cr & {\rm N} \equiv {\rm C -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\mathop {\rm C}\limits^\parallel} \limits^{\rm O} {\rm -} \mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\mathop {\rm C}\limits^\parallel} \limits^{\rm O} {\rm -} \mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH}}$$
Here, in the first proposed mechanism, the carbon of the CN in the second molecule from the left detaches from its alpha carbon and unites with the alpha carbon of the molecule to the left, while picking up the O atom. The polymerization is straight addition, with no loss of water molecules.
In mechanism 2, the CN carbon in the second molecule from the left remains attached to the alpha carbon, while the N atom of that molecule detaches and enters the alpha carbon of the first molecule, whose oxygen then moves to the second molecule alpha carbon.
$$\eqalign{& {\rm N} \equiv {\rm C -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH\,} \cdots \,{\rm N} \equiv {\rm C -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH\;} \cdots \;{\rm N} \equiv {\rm C -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH} \cr & \quad \quad \quad \quad \quad \quad \quad \downarrow \cr & {\rm N} \equiv {\rm C -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {\rm C}\limits_{\mathop \parallel \limits_{\rm O}} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {\rm C}\limits_{\mathop \parallel \limits_{\rm O}} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH}}$$
In Tables 1 and 2, the energy required to break all bonds that disappear, and form new bonds that appear, during reaction, is compared for mechanism 1 as compared with mechanism 2. The difference between those disappearing and appearing should be the same in each case. However, the magnitudes of total breaking and forming could be different for each mechanism.
Bond energies of cyanomethanol polymerization for mechanism 1 (kJ mole−1)
The bonds breaking or forming are denoted by a space on each side and the colour red.
Bond energies of cyanomethanol polymerization for mechanism 2 (kJ mole−1)
The bonds breaking or forming are denoted by a space on each side and the colour red.
Thermodynamic feasibility
The total enthalpy change in Tables 1 and 2 are, as expected, the same within the accuracy of the method. Their negative value shows that the reactions are thermodynamically feasible in terms of enthalpy.
Comparing the details of 1 to 2, however, it is seen that stronger bonds must be broken for the reaction to proceed via mechanism 1 than mechanism 2. This implies that the activation energy for mechanism 2 is probably significantly lower than that for 1. Consequently, we assume that mechanism 2 holds true in all cases.
Adsorption to minerals
Background
The soup theory has been the most popular approach to initial formation of biopolymers from small atmospheric molecules (Oparin Reference Oparin and Morgulis1938; Miller Reference Miller1953, Reference Miller1955). This approach however, was, from its inception, considered to have a major flaw of the difficulty of condensation in a medium where hydrolysis is favoured. In fact, the free energy of the reaction of two amino acids to yield a peptide
$${\rm 2RCH}({\rm N}{{\rm H}_2}){\rm COOH} \to {\rm RCH(N}{{\rm H}_{\rm 2}}{\rm )COC}({\rm R}){\rm N}{{\rm H}_{\rm 2}}{\rm COOH }+ {{\rm H}_{\rm 2}}{\rm O}$$
has been estimated as high as 4 kcal per mole in favour of hydrolysis (Martin Reference Martin1998; Rimola et al. Reference Rimola, Ugliengo and Sodupe2004). The excess of water in the medium magnifies this effect.
To help overcome this and other problems in the soup approach, a parallel approach has been developing for over half a century. This approach has the soup in contact with a solid state adsorbent which can possibly catalyse the reactions, provide some protection from degradation from ultraviolet radiation (penetrating an atmosphere that did not as yet contain an ozone layer), and possibly provide chirality by some means. Goldschmidt, in 1945 (Hazen Reference Hazen2006) suggested adsorbing the monomers to right-and left-handed quartz crystals to resolve racemic mixtures into their enantiomers (Goldschmidt Reference Goldschmidt1952). Bernal, in 1949 (Hazen Reference Hazen2006), suggested adsorption to clay minerals which have a large surface area and may act as catalysts for polymerization.
Lahav et al. (Reference Lahav, White and Chang1978) found small amounts of biopolymers, resembling proteins, formed on clay minerals on exposure to amino acids. Ferris & Ertem (Reference Ferris and Ertem1993) brought about synthesis of RNA using clay as a substrate. Hill et al. (Reference Hill, Bohler and Orgel1998) investigated polymerization on rocks and obtained results indicating the reaction proceeded to some extent (Liu & Orgel, Reference Liu and Orgel1998). Schrader (Reference Schrader2009) suggested carrying the concept, of exposure of monomers to solid adsorbents, to an extreme, by avoiding a soup altogether. The monomers were assumed to be carried by raindrops (Zahnle Reference Zahnle1986) onto phosphate containing minerals (Schrader Reference Schrader2009) on Earth, which acted as a chromatographic column with RNA as the final result (Schrader Reference Schrader2009).
In addition to its other advantages, adsorption of monomers or polymers to mineral surfaces holds the possibility of establishing chirality in the adsorbate. Investigation along those lines has centred largely on the possibility of chirality in the substrate mineral, transferring its chirality to the biopolymer, by preferentially adsorbing one or another of the enantiomers from a racemic mixture.
Hazen states ‘Thus, researchers have invoked two broad categories of symmetry-breaking phenomena to explain life's chiral excess (Bonner Reference Bonner1991, Reference Bonner1992, Reference Bonner1995; Palyi et al. Reference Palyi, Zucchi and Caglioti1999). Some authors claim that an important philosophical distinction exists between deterministic models of life's chirality (i.e. that some intrinsic feature of the Universe inevitably leads to preferential selection of left-handed amino acids) versus a chance local selection of left or right (i.e. life might have formed either way through local stochastic processes)’.
In this paper, I accept the stochastic explanation without ruling out the possibility of an intrinsic feature such as, for example, the counter clockwise rotation of objects in the Solar System.
Nevertheless, the traditional theoretical approach to evolution in its biological phase has often been insistence on a stochastic explanation. For example, Mayr (Reference Mayr1982) states that the facts of biological evolution contain five requisites, one of which is that all bio-evolution emanates from a single source (Schrader Reference Schrader and Seckback2006). Another example is the sudden evolutionary appearance of eukaryotes after a billion years or so of prokaryote domination. The origin of this has been attributed to a single-cell change (Lane Reference Lane2011). This of course does not prove that the same principle must be present in chemical evolution, but it certainly must be considered. On this subject, Hazen states ‘Advocates of mineral induced handedness suggest that life's origin was a local molecular event, not dictated by global averages’.
The nearly universal approach that utilizes the method of surface (adsorbent) chirality has been, until the present, to start with completely racemic products and from there on to engage in what is termed ‘symmetry breaking’. For example, Hazen (Reference Hazen2001) and Hazen & Sholl (Reference Hazen and Sholl2003) demonstrated small selective adsorption of D-and L-amino acids on the chiral ‘scalenohedral {214} type crystal faces’. In nature, slight preference for l protein fragments over the d form has been found in the Murchison meteorite. Investigation of these approaches to the role of minerals in aiding the formation of chiral biological molecules is most worthwhile and should be continued.
An innovative variation of the above approaches has been the suggestion of J.V. Smith (Reference Smith1998), who invokes the principle of low dimensionality to propagate L or D forms into biomolecules. He assumes that the monomers are all hydrophobic and require a hydrophobic, or as he states it, an organophilic, mineral surface for adsorption of the monomer. For this purpose, he suggests a molecular sieve called silicalite, who's surfaces consist of Si–O–Si groups which are hydrophobic (Schrader & Yariv Reference Schrader and Yariv1990; Yariv Reference Yariv, Schrader and Loeb1992), i.e. organophilic (Schrader Reference Schrader1968). This sieve contains numerous channels, some of which are tenths of a nanometre in diameter, with hydrophobic walls. He states, without going into details, that monomers adsorbed in these channels should propagate L or D biopolymers.
With respect to the problem of propagation from a single site, he states ‘Although all biochemical life might have developed from a single left-handed chance event that has essentially zero probability in terms of conventional ideas for chemical synthesis, multiple events of high probability are preferred, of which one event may have been the actual trigger.’
The quasi-chiral approach
I present in this paper, an alternative low-dimensional approach which describes molecular adsorption on a mineral surface which can lead to complete L or D chirality for all proteins. Instead of channels such as in zeolite, a crack on a solid mineral surface is sufficient. The mineral surface should have polar groups, such as in phosphate minerals, and the monomers have polar groups, such as CN and OH of cyanomethanol, or NH2 and COOH of glycine.
The ubiquitous chirality of proteins is present in the alpha carbon group of each segment, which in this approach, is already present in the monomer. To explain this, I introduce the concept of the quasi-chiral monomer. The principle of this method, is to start with a non-chiral molecule such as CH2(CN)OH (cyanomethanol), or alternatively HCHNH2COOH (glycine) either one of which on adsorption becomes a quasi-chiral molecule. The reason they can fulfil this function, is that each alpha carbon has two hydrogens that, after adsorption, are no longer equivalent. One H is attached to the surface, while the other projects outward. The polypeptide formed is now quasi-chiral due to non-equivalence of H atoms. Ultimately, after formation of the long-chain polypeptide, each protruding H is replaced by an R group to form a real adsorbed protein where all the alpha carbons have the same chirality. The R groups can be of a wide variety and can be different for each alpha carbon. Equations depicting this phenomenon can be written as follows:
$$\eqalign{& {\rm NC -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH\;} \;{\rm +} \;{\rm NC -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH\;} \;{\rm +} \;{\rm NC -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} {{\rm C}_{\rm \alpha}} {\rm - OH} \cr & \quad \quad \quad \quad \quad \quad \quad \quad \quad \quad \quad \downarrow \cr & {\rm NC -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\mathop {\rm C}\limits^\parallel} \limits^{\rm O} {\rm -} \mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\mathop {\rm C}\limits^\parallel} \limits^{\rm O} {\rm -} \mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm - OH\;}} $$
A detailed look at the adsorption, diagrammatically (Fig. 1), is as follows: The monomer is a tetrahedron, a triangle side of which rests on a surface, with a group or atom in each of the three corners of the triangle and a fourth corner perpendicular to the plane of the surface. A carbon atom is in the middle above the plane of the surface.
Adsorbed cyanomethanol.
Since the surface and its crack, are polar, both the CN and OH groups, which are polar, will be in the triangle adsorbed to the surface crack. Thus, the third corner in the crack of the surface is occupied by an H atom, and the other H atom, its bond described by a dotted line, is perpendicular to the surface. In terms of future reaction then, one H is on the surface relatively inaccessible, while the other protrudes and is accessible. Therefore, the two hydrogens are no longer equivalent. The adsorbed cyanomethanol monomer is then here called quasi-chiral.
In more detail, the following is a possible configuration:
Consider a partially opened book. The interface between the two exposed pages represents a more or less one-dimensional space. Now, cut one of the page segments in half, horizontally. This portrays a crevice in a mineral surface, given diagrammatically in Fig. 2.
Adsorption in crevice.
The two polar groups in cyanomethnol will now adsorb to the bottom of the crevice. The H of the triangle containing the adsorbed polar groups may now be assumed to lean back to the long side of the joined surfaces which form the crevice. The other surface forming the crevice is short, and the H perpendicular to the triangle protrudes, and is available for reaction. Or, alternatively, the bottom of the crevice is regarded as flat, its walls small, and the perpendicular H extends out of the crevice. Ultimately, R (organic) groups replace the protruding H's, and the alpha carbons all remain completely L or D.
The same considerations may be applied to the conventional proposed mechanism of repeated condensation of amino acids, provided that the condensing monomer is glycine and the condensation takes place in a crevice where removal of the H2O product can take place. The equations are as follows:
$$\eqalign{& {\rm H}\mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\rm C}\limits^{\rm O} {\rm - OH\; +} \;{\rm H}\mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\rm C}\limits^{\rm O} {\rm - OH}\;{\rm +} \;{\rm H}\mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\rm C}\limits^{\rm O} {\rm - {\rm O}{\rm H}} \cr & \quad \qquad \vdots \hskip 16em\downarrow \cr &\qquad\quad\vdots\;\,{\rm H}\mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\mathop {\rm C}\limits^\parallel} \limits^{\rm O} {\rm -} \mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\mathop {\rm C}\limits^\parallel} \limits^{\rm O} {\rm -} \mathop {\rm N}\limits_{\rm H} {\rm -} \mathop {{{\rm C}_{\rm \alpha}}} \limits_{\rm H}^{\rm H} {\rm -} \mathop {\mathop {\rm C}\limits^\parallel} \limits^{\rm O} {\rm -} {\rm OH\; + 2}{{\rm H}_{\rm 2}}{\rm O}} $$
The polar groups of the monomer are now COOH of glycine instead of the OH of cyanomethanol and the NH2 of glycine instead of the CN of cyanomethanol.
Conclusions
It is shown that the reaction leading to RNA synthesis via cyanomethanol, can branch off to form polypeptides by the polymerization of cyanomethanol.
The same result can be obtained from condensation of an amino acid provided that the amino acid is glycine.
If the polymerization of cyanomethanol (or condensation of glycine) occurs in a crack on a polar surface, then the resulting polypeptide can be completely chiral in the alpha carbons. This ultimately can lead to chiral proteins in the alpha carbons for any reaction with side chains.
The mechanism subscribes to the approach that life's origin was a local molecular event, in line with the traditional approach of evolutionary theory that requires single source origin. Thus, even for chemical evolution, as well as subsequent biological evolution, many factors must fall into place, spatially and temporally, for it to succeed. A low probability may therefore have to be assigned for its occurrence, even on an Earth-like planet.
Acknowledgements
This paper was presented in part at the 27th Annual Meeting of the Israel Society for Astrobiology and the Study of the Origin of Life, 1 December, 2013. The author thanks Professor Shmuel Yariv and Dr Isaak Lapides for their support.
