Prebiotic Proteins

Nutrient Content high in protein, prebiotic fiber, antioxidant vitamins A and C, B vitamins, dietary minerals Phytochemical Content high in carotenoids (alpha- and beta-carotene, beta-cryptoxanthin, lutein, violaxanthin), polyphenols (quercetin, gallic acid, gallotannins, rhamnetin, cyanidin and xanthone glycosides, including mangiferin, mainly in skin)... 

High Nutrient Content protein, prebiotic fiber, antioxidant A-C-E vitamins (diminished by heating), B vitamins, dietary minerals High Phytochemical Content carotenoids (beta-cryptoxanthin, beta-carotene) polyphenols (anthocyanins, particularly delphinidin and cyanidin glycosides and rutinosides, catechins, proanthocyanidins, chlorogenic acid, quercetin, hydroxycinnamic acid)... 

High Nutrient Content protein, prebiotic fiber, antioxidant A-C-E vitamins, B vitamins, dietary minerals... 

The predominance of L-amino acids in biological systems is one of life s most intriguing features. Prebiotic syntheses of amino acids would be expected to produce equal amounts of L- and D-enantiomers. Some kind of enantiomeric selection process must have intervened to select L-amino acids over their D-connterparts as the constituents of proteins. Was it random chance that chose L- over D-isomers ... 

Molybdenum hexafluoride. 3,1412 Molybdenum-iron-sulfur complexes, 4,241 Molybdenum oxide amino acid formation prebiotic systems, 6, 872 Molybdenum storage protein microorganisms, 6, 681 Molybdenum telluride, 3, 1431 Molybdenum tetraalkoxides physical properties, 2, 347 Molybdenum tribromide, 3,1330 Molybdenum trichloride, 3,1330 Molybdenum trifluoride, 3, 1330 Molybdenum trihalides, 3, 1330 bond lengths, 3, 1330 magnetic moments, 3,1330 preparation, 3,1330 properties, 3, 1330 structure, 3,1330 Molybdenum triiodide, 3,1330 Molybdenum trioxide complexes, 3, 1379 Molybdenum triselenide, 3, 143)... 

Several institutes throughout the world immediately began to carry out experiments on prebiotic chemistry. At this point, we need to realize that the prebiotic synthesis of protein building blocks is only a first step towards solving the biogenesis problem. Put simply, it is a method for making bricks which will later be used in building a multi-storey office block ... 

This interpretation of the experimental results is not accepted by Clifford Matthews, who has for many years defended the following hypothesis the prebiotic proteins (or peptides) are formed from HCN by polymerisation reactions and not from single a-amino acids (see Chap. 5). The necessary preconditions for polycondensation of amino acids—high temperatures, acidic conditions and the absence of water—were not present on primeval Earth. 

If prebiotic peptides and/or proteins were in fact initially formed in aqueous solution (the hypothesis of biogenesis in the primeval ocean ), the energy problems referred to above would have needed to be solved in order for peptide synthesis to occur. As discussed in Sect. 5.3, there is some initial experimental evidence indicating that the formation of peptide bonds in aqueous media is possible. An important criterion for the evolutionary development of biomolecules is their stability in the aqueous phase. The half-life of a peptide bond in pure water at room temperature is about seven years. The stability of the peptide bond towards cleavage by aggressive compounds was studied by Synge (1945). The following relative hydrolysis rates were determined experimentally, with the relative rate of hydrolysis for the dipeptide Gly-Gly set equal to unity ... 

When derivatives of amino acids are formed, their zwitterionic character is destroyed, a process which requires the supply of energy. We shall first discuss chemical activation, as it is important for the understanding of hypotheses dealing with prebiotic protein formation. In the case of amino acids which are activated at the carbonyl group, the amino group remains unsubstituted. The derivatives are able to react with nucleophilic residues (Y) ... 

Important prebiotic sequences, for example, the linking up of amino acids to form proteins, involve acylation reactions (see Sects. 5.1 and 5.2). Condensation agents are often not very efficient in aqueous phases condensation reactions may involve drastic conditions, such as high temperatures or an acidic environment. Activated amino acids, for example, thioester derivatives, can be considered as starting... 

Calculation of the internal cell potential is a very complicated matter because the electrochemistry of all of the species within the protocell would have to be balanced subject to their composition quotient Q, after which the standard free energy would have to be established from tabulations. The transport of Na+ would also change this balance, along with the ionic strength of the solution and the stability of the proteins or prebiotic molecules within the protocell. Such non-equilibrium thermodynamics forms the basis of the protocell metabolism. The construction... 

Several factors indicate that the amino acids detected in all of these carbonaceous chondrites are indigenous and that they must have originated abiotically. First, the presence of protein and non-protein amino acids, with approximately equal quantities of D and L enantiomers points to a nonbiological origin and precludes terrestrial contamination. In addition, the non-extractable fraction of the Murchison is significantly heavier in 13C than terrestrial samples. Finally, the relative abundances of some compounds detected resemble those of products formed in prebiotic synthesis experiments. The aliphatic hydrocarbons are randomly distributed in chain length, and the C2, C3, and C4 amino acids have the highest concentrations (i.e., the most easily synthesized amino acids with the least number of possible structures are most abundant) [4]. 

These model experiments involving e.e. amplification of amino adds during polymerization admittedly need prebiotically unrealistic substrates as well as carefully contrived experimental conditions. Nevertheless, it is noteworthy that both secondary structures of proteins, a-helices, and P-sheets have been found capable of acting stereoselectively to provide e.e. enhancements during these model polymerizations. 

Of the four major classes of biochemicals (carbohydrates, proteins, nucleic acids and lipids), experiments have shown that the first three classes could have arisen through prebiotic chemistry. Although the biosynthesis of many natural products can be traced back to acetate (e.g. fatty acids, terpenes and polyketide biosynthesis) or amino acids (e.g. alkaloid biosynthesis), there are many whose biosynthetic origins are either obscure or result from a complex combination of pathways (Fig. 2). 

Why then is there this popularity of the prebiotic RNA world There are three reasons that come to mind. One is the already mentioned great success of the RNA world at large, which, by inference, gives confidence in the power of RNA. Another reason is that from self-rephcating and mutating ribozymes, one can conceive in paper a route to DNA and proteins - and then one has the whole story. A third reason is the lack of a good competitive model - namely the fact that there is no alternative mechanism that is supported experimentally. 

Having highlighted some of the data and issues about the prebiotic chemistry of low-molecular-weight compounds, let s now turn to the functional long chains -mostly proteins and nucleic acids. The first part of this chapter is devoted to the prehiotic chemistry of hiopolymers, the second part, which will necessarily be more speculative, to ideas of conceiving the very origin of macromolecular sequences. 

In the case of proteins or nucleic acids we do not have two, but several comonomers furthermore we are not dealing with the simple case of radical polymerization, but with the more complex polycondensation. Very little is known about the kinetics of the copolymerization of polycondensates - for example analysis of ta and re has not been done systematically for amino acids. However, a few general points can still be made on the basis of the general principles of copolymerization. One has been already mentioned that the initial composition of amino acids in the prebiotic soup may not correspond to the amino-acid composition in the chain. Thus, the fact that one given amino acid has a very small frequency of occurrence in protein chains may not necessarily mean that this amino acid was not present under prebiotic conditions the low frequency in the chains can simply be the result of the kinetics of polycondensation. Conversely, the presence of preferred residues or short sequences in protein chains might be due to the interplay of kinetic parameters, and have little to do with the initial biological constraints. 

In principle, it is not fair, or course, to approach a problem of prebiotic chemistry by using sophisticated techniques of present-day molecular biology, such as phage display. However in this case the particular research question was not the origin of life, but rather the question given a vast library of random polypeptide chains, what is the folding frequency The criterion utilized for determining whether a protein is folded or not was based on resistance to the hydrolytic power of proteases, with... 

There is another general lesson that we can learn from these experiments. If our proteins are the product of contingency, most probably the pathway to their prebiotic synthesis cannot be reproduced in the laboratory. This is indeed the bottle neck in the bottom-up approach to the origin of life. 

We have learned previously that the synthesis of exactly our proteins on Earth is doomed by conhngency - we cannot hope to hnd out the exact condihons that deternuned the hnal sequence of a given protein or a nucleic acid from our Earth. Once this biher assertion is accepted, we should at least attempt experiments that show that the prebiotic synthesis of some specihc sequence in many identical copies is possible. Also, it is perhaps surprising that there has been so little reported in the... 

The conclusion is that membranous vesicles readily form a variety of amphiphilic molecules that would have been available in the early Earth environment, along with hundreds of other organic species. It is likely that during the chemical evolution leading to the first catalytic and replicating molecules, the ancestors of today s proteins and nucleic acids, membranous vesicles were available in the prebiotic environment, and ready to provide a home for the first forms of cellular life. 

The RNA cells eventually have to evolve into protein/DNA cells. And this is a long and certainly not easy pathway. However, this is the beauty of the prebiotic RNA world that at least on paper, a possible pathway leading to DNA and proteins can be conceived. One ideal pathway showing the transition from the RNA to the DNA cell is illustrated in the Figure 11.4. 

Bujdak, J., Eder, A., Yongyai, Y., Faybikova, K., and Rode, B. M. (1995). Peptide chain elongation a possible role of montmorillonite in prebiotic synthesis of protein precursors. Orig. Life Evol. Biosph., 5,431 1. 

---