Based on current experimental and theoretical evidence, we can conclude that the proto-biotic life chemistry in general (not only on Earth) develops in a liquid from one or several exothermic molecules (precursors) by selection-evolution via two parallel prebiotic random polymerization processes from basic compounds to catalyzers (enzymes) and synthesizers (polymer molecules which carry out template-based enzyme synthesis based on their sequence, i.e. genetic code) fed by an energy cycle. In terrestrial life chemistry, vesicle-based chemistry is a precondition for a full life-cycle with bio-matter production and proliferation (see Chap. 2.8.4). Therefore it is plausible to assume that in general there is a third class of polymers (layer-builders) produced by the life chemistry, which form a membrane and a self-dividing vesicle.

In extrapolation of these basics, we can say that life in general has 6 principal features (Figure 1):

- synthesis of biological matter (including basic compounds) in a liquid (terrestrial: water H₂O) catalyzed by enzymes (terrestrial: proteins), where basic compounds (terrestrial: 20 amino acids, 4 nucleobases A, U, G, C) are synthesized from anorganic precursors (terrestrial primary: HCN, H₂S)

- use of an energy cycle with a continuous energy flow against entropic decay (terrestrial primary cycle: Wächtershäuser’s iron-sulfur cycle, terrestrial secondary cycle: photo-synthesis)

- life chemistry based on catalyzer enzymes (terrestrial: peptides) and synthesizers (genes, terrestrial: poly-nucleobases) built from basic compounds, and running within a cell-membrane, where synthesizers are more stable than enzymes; synthesizers serve as a pattern for enzyme structure, catalyze the enzyme synthesis, and preserve and copy the pattern

- spontaneous emergence of a proto-lifecycle, which starts reproduction and evolution through selection

- replication with copying of genes, and cell division within a fixed time interval (terrestrial: ca. 1000 s)

- evolution by mutation and adaptation to the environment with the goal of survival

We can formulate some boundary conditions for life:

• The only common element, which supports a large variety of molecules, and polymers, is carbon.

Terrestrial life is based on carbon chemistry, and presumably the same is true for most forms of life in the universe.

• The fluid carrier medium in terrestrial life is water, and water is the only common molecule with a fluid phase around T = 300 K.

• Biological carbon chemistry has activation energies in the range (25 kJ/mol, 130 kJ/mol), corresponding to per-molecule energy range (0.25 eV, 1.3 eV).

• Star light as an energy source has an approximate energy range

( E ( λ = 0.5   μ m ) = 2.5   eV , E ( λ = 1   μ m ) = 1.2   eV ), with E ( λ ) = h c λ , center wavelength λ = 0.5   μ m for sun-like stars, center wavelength λ ≈ 1   μ m for Red Dwarves, which is feasible as energy source for carbon chemistry.

• The thermal energy E t h ( T ) = k B T needed to overcome the activation energy in carbon chemistry is approximately (2σ above mean) E t h , c e 2 = E a , m i n , where E a , m i n = 0.25   eV for carbon chemistry, i.e. E t h , c = 0.034   eV , with corresponding minimum temperature T c = 390   K , which lies within the water fluidity temperature range.

We can extrapolate general features of the four life-functional molecular families.

• Precursors, solvents, energy cycle molecules

These molecules are synthesized in space, or belong to the primeval molecules on planets. Among them, there is at least one molecule, which is exothermic (supplies energy), and one which is the (fluid) solvent.

In terrestrial biology, precursors are: HCN, H₂S, H₂, CO, H₃PO₄, and the solvent is of course water H₂O. Among these, HCN is the energy supplier and HCN + H₂O are the atom suppliers, and determine the characteristic atom content ratio ( H : C : N : O ) = ( 3 : 1 : 1 : 1 ) in basic amino acids and nucleobases.

The energy cycle molecules participate in the basic energy cycle reaction, in the terrestrial biology they are: H₂S, FeS which form the fundamental pyrite reaction F e S + H 2 S → F e S 2 + 2 H + + 2 e − .

• Enzymes

The enzymes are the catalyzers, which control the life synthesis reactions. They are chains consisting of basic molecules bound by one kind of chemical bond.

In terrestrial biology, they are peptides, which are linear chains of amino acids bound by the amino-bond with energy 8 - 16 kJ/mol.

• Synthesizers

The synthesizers are the coding molecules for the enzymes, they are more stable than the enzymes, and therefore are ring molecules (rings are normally more stable than their linear counterparts). Their diameter is smaller than the length of the linear enzymes by a factor 1/2 to 1/3. Therefore they form codons from 1, 2 or 3, which translate into one enzyme (1-bit, 2-bit, 3-bit code).

In terrestrial biology, they are poly-nucleobases (PNB’s), which are linear chains of nucleobases

complementary adenine Ade, guanine Gua: 5-ring + 6-ring

complementary thymine Thy, uracil Ura: 6-ring.

PNB’s are linked by hydrogen-bonds, in RNA by phosphodiester-bonds.

• Layer-bilders

These molecules form the protective semi-permeable membrane of the life vesicle (biological cell).

The membrane controls the influx and outflux of molecules, and the vesicle is capable of self-recreation.

In terrestrial biology, they are phospho-lipids, namely in the proto-cell glycerol-phosphate.

• Reaction network

Enzymes, synthesizers, and phospho-lipids are all synthesized in the life self-supporting reaction network catalyzed by enzymes.

Precursors, solvent, and energy cycle molecules are supplied outside the vesicle and enter resp. leave it through the membrane.

Alternative life-models

Carbon-nitrogen-hydrogen chemistry in water (terrestrial model)

T = 0˚C...150˚C (P = 1 - 100 bar)

activation energy range: (25 kJ/mol, 130 kJ/mol), per molecule (0.25 eV, 1.3 eV)

basic materials: H C N + F e S + H 2 S + H 3 P O 4

enzyme polymers: peptides,

synthesizers (genes): poly-nucleins

solvent: water

energy cycle: F e S + H 2 S , photosynthesis

location: water-carrying planets in habitable zone, in contact with mineral rock

This is the terrestrial life model, mainly dealt with in this paper. The spontaneous emergence of a proto-lifecycle is proved numerically based on chemical reaction data, and partly supported by direct observation (see Chap. 2.8.3, Chap. 3.2).

The proto-lifecycle runs with

- 3 amino acids Gly, Pro. Cys

- 2 nucleobases Gua, Cyt

- 5 peptides (enzymes) Gly2, Gly3, Pro, Pro2, GlyPro

- 1 lipid Gly1ph

- 5 PNB’s (genes) Gua2, Gua3, Cyt2, Cyt, GuaCyt

- 5 PNA’s GlyGua2, GlyGua3, ProCyt2, ProCyt, GlyGuaProCyt2

Carbon-hydrogen-oxygen chemistry in water

T = 0˚C...150˚C (P = 1 - 100 bar)

activation energy range: (25 kJ/mol, 130 kJ/mol), per molecule (0.25 eV, 1.3 eV)

basic materials: C O 2 + C H 4 + N H 3 , no iron or sulfur

enzyme polymers: poly-vinyl-alcohols, poly-ethylene-glycols, poly-acryl-amide

synthesizers (genes): aliphatic amines

solvent: water

energy cycle: photosynthesis, C O + H 2 O

location: water-carrying planets in habitable zone, no contact with minerals

This is a tentative life model for water environments without minerals, iron, and sulfur.

Aliphatic amines like tetra-methyl-ethylene-diamine function as catalyzers for poly-acryl-amides.

Carbon-hydrogen-nitrogen chemistry fluid hydrocarbons

T = 0˚C...300˚C (P = 1 - 100 bar)

basic materials: C H 4 + H 2 S + N H 3 , no oxygen

enzyme polymers: hydrocarbon linear-branched polymers with substitutions N, S

synthesizers (genes): polycyclic aromatic hydrocarbons (PAH) with substitutions N, S

solvent: fluid hydrocarbons

energy cycle: photosynthesis

location: waterless planets in habitable zone with dense atmosphere with hydrocarbons and nitrogen

This is a hypothetic life model based on hydrocarbon solvent, where the spontaneous emergence of proto-lifecycle with proto-genes from PAH’s and enzymes from poly-hydro-carbons with N and S substitutions is still to be proved.

This model is arguably the only viable alternative to water-based life models, it supports also temperatures up to 300˚C.

PAH’s are known to be common in the cosmic matter, and they are also rather stable and can function as catalyzers for hydrocarbons. PAH’s can polymerize under UV radiation [4] .

Silicon chemistry in molten rock

T = 1000˚C...1500˚C

basic materials: S i O 2 + A l 2 O 3 + M g O

polymers: polysilicates

solvent: molten silicates

energy cycle: radiation

location: hot Earth planets

The temperatures in this model are far outside the life-favorable range, therefore it is very probably no viable model for life.

Carbon + salts compounds in liquid ammonia

reactions probably too slow for life evolution

T = −78...−33˚C (P = 1 bar)

T = −77 C...98˚C (P = 60 bar)

solvent: liquid ammonia

basic materials: hydrocarbons, salts, organic metal complexes, organic carbon compounds C-H-N

polymers: complex hydrocarbons with oxyl-, amino- and metal-radicals

energy cycle: carbon-hydrogen chemistry?

location: Titan-like planets

The temperatures in this model are far below the life-favorable range, therefore it is very probably no viable model for life.

Carbon compounds in liquid ethane-methane

reactions probably too slow for life evolution

T = −183... −89˚C (P = 1 bar)

solvent: liquid ethane-methane

energy cycle: photosynthesis? tidal heating?

basic materials: organic carbon compounds C-H-N

polymers: complex hydrocarbons with oxyl-, amino-radicals

membrane (computer-modeled in February 2015): acrylonitrile similar to a phospholipid bilayer

location: Titan-like planets

The temperatures in this model are far below the life-favorable range, therefore it is very probably no viable model for life.

In the case of the terrestrial life, the process took place probably from the precursor molecules {HCN, H₂} in water via prebiotic synthesis of amino acids and nucleobases under UV-radiation, and then parallel polymerization to catalyzers (poly-peptide enzymes) and synthesizers (peptide-nucleotides PNA) fed by the pyrite energy cycle (see Figure 2 “random prebiotic chemistry”).

The polymers poly-peptides and PNA are not very stable, especially in acidic water and temperatures around boiling point 100˚C, so they must be continually reproduced in order to survive [5] [6] : that is where the Darwinian evolution mechanism sets in. The amino acids and nucleobases also degrade, although at higher temperatures (T > 185˚C), so they, too, must be replenished [7] . On the other hand, the enzymes are continuously in contact with precursors molecules and with the energy cycle, so they degrade relatively quickly, so they must be reproduced as quickly. Simple copying is not as efficient as replication based on a stable pattern molecule: this is the role of the synthesizers (PNA).

The evolution selects a coupling between peptides and PNA-segments (genes), where the PNA-segments build-up the corresponding peptide from amino acids, and in turn each of the peptides catalyzes one of the required metabolic processes: synthesis of required amino acids and nucleobases from precursors, the energy cycle, synthesis of phospholipids and the build-up of the protective membrane.

The result for the proto-life cycle (Chap. 3.2) is a model1 3-bit binary (G/C) 5 × 2 genetic code (Gua-Cyt nucleobase pair) stored in the PNA (Leu-Gua and His-Cyt), coding for Gly and Pro amino acid sequences, which in turn catalyze the synthesis of 5 needed amino acids (Gly, Pro, Leu, His, Cys), nucleobases (Cyt, Gua) and phospholipid glycerol-phosphate, and the catalysis of the energy cycle via Cys with SH-radical (see Figure 3 “proto-life chemistry”).

This model is of course at first only a plausible scenario, but it is supported by the known prebiotic HCN-chemistry able to produce all amino acids, all nucleobases, phospholipids and sugars [8] [9] . Furthermore, the binary genetic code

has been shown to be the probable original mechanism of PNA-RNA-coding and protein synthesis [10] [11] . Then, one can show by enzyme calculations, that Gly-Pro-peptides indeed act as enzymes in the synthesis of amino acids and nucleobases from (HCN, H₂O, H₂) (see Chap. 2.2, Chap. 2.4, Chap. 2.5 and [12] ). Finally, digital simulation based on a simplified model of the HCN chemistry shows that molecular evolution selects indeed a binary genetic code like the one proposed in [10] [11] .

A general consequence of the validity of this scenario is that the elementary enzymes (amino acids) and elementary synthesizers (nucleobases) are selected by evolution based on the precursor chemistry, i.e. here of the HCN-water chemistry, and not vice versa.

The present stage of terrestrial life evolution (chap. 3.5) represents the DNA-cell (bacteria, archaea, eukaryotes), which uses the full DNA genetic code with 20 amino acids, and corresponding 20 aaRNA’s for peptide synthesis, 4 nucleotides: cytosine, thymine, adenine, guanine (thymine replaces uracil in RNA-coding). The pairs A-G and C-T are complementary in the DNA-double-helix. The self-sustainable energy cycle is mostly the photosynthesis (plants, cyanobacteria). The self-sustainable energy cycle is mostly photosynthesis (plants, cyanobacteria).

In principle, it is possible with methods of quantum chemistry (e.g. Hartree-Fock calculation) to calculate the chemical evolution in time of a given mixture of molecules in liquid solution, given the initial concentration, and physical conditions (temperature, pressure, external flow of matter, energy supply by radiation and spark discharge), and based solely on the structure of initially given and of emerging molecules. In reality, in order to calculate a realistic scenario in this way, the needed computational power exceeds by far the performance of today’s supercomputers.

There are two kinds of data, which are needed for a structure-based numerical simulation of chemical evolution.

First, we need the molecular formation energy H_f (molecular energy for short) for a given molecule, as a function of its bond structure. H_f is required for the calculation of the reaction energy ΔE of a given reaction A + B   ( k + → )   C + Δ E .

Second, we need the reaction rate d C ( t ) d t for such a reaction as a function of the bond structure of the reacting molecules A and B (here C(t) denotes the concentration of the compound C).

Enzymes (in terrestrial life peptides) are the key element of life in general. They accelerate specific reactions 10⁴ - 10⁶ fold and, coupled with synthesizers (PNA/RNA), they enable the reproduction and survival of all life molecules, including themselves.

The specific action of an enzyme with a single substrate (precursor molecules) can be explained using a lock-and-key analogy. In this analogy, the lock is the enzyme and the key is the substrate. Only the correctly sized key (substrate) fits into the key hole (active site) of the lock (enzyme).

Below, we present the mathematical formulation of the action of an enzyme: the substrate (with site bonds E_n) allocates along the enzyme (with site bonds E ′ n ), the substrate sites are bound to the substrate sites with bond energy F_n. The substrate bonds are then weighted with local density p_n, and the resulting mean bond energy E b c = ∑ n p n E n is considerably lower than the original mean bond energy E b m = ∑ n E n / N : this is threshold-reducing action of an enzyme, illustrated in the graphics below Figure 4 [19] .

Initially assuming a well-mixed distribution of enzymes and substrate of equal concentration, we view the “lock” as constantly-spaced enzyme molecules of density profile r n = r ( x n + Δ x / 2 ) , x_n = nΔx, Δx small, with density values r_n.

The substrate (or “key”) molecules are particle pairs having a local density profile p_n = p(x_n) at positions x_n = nΔx. Each enzyme-substrate “complex” locally lowers the activation energy of the reaction so that overall activation energy is maximally lowered when all key particles are closest (Kullback-Leibler-distance) to the corresponding lock particles. The KL-distance is a r_n-weighted Boltzmann entropy of the profile p_n, which makes it a plausible ansatz from the viewpoint of thermodynamics.

The enzyme KL-model is formulated as follows.

Minimization problem:

H K L ( p ∥ r ) = ∑ n = 1 N p n ln [ p n r n ] = min (6)

∑ n p n = 1 , constraint: normalization substrate, with bond energies E_n, ∑ n E n = E b , E_b is the molecular energy of the substrate.

Enzyme density values r_n are normalized ∑ n r n = 1 , with bond energies E ′ n and the molecular energy ∑ n E ′ n = E ′ b , and r n = E ′ n E ′ b , E ′ b is the molecular energy of the enzyme.

With Lagrange-multipliers we get the minimization problem

∑ n = 1 N p n ln ( p n r n ) − Λ 1 ( ∑ n = 1 N p n − 1 ) = min

Differentiation ∂ p n and ∂ Λ 1 gives N + 1 equations for N + 1 variables {p_n, Λ₁}

1 + ln ( p n r n ) − Λ 1 = 0 and ∑ n = 1 N p n = 1

we get 1 − ∑ n = 1 N − 1 p n = p N and Λ 1 = 1 + ln ( p N r N ) as 2 equations for p_N and Λ₁ and p n = r n exp ( Λ 1 − 1 )

In this case, differentiation yields the (approximate) local minimum p_i = r_i with min = 0, numerical minimization yields global minimum with negative values, the solution has one large value p_i0 close to 1, at the index of the smallest r_i ( r i 0 = min ( r i ) ), and the rest of the p_i is small. The enzyme coupling “selects” the weakest bond and preserves it, and attenuates the energy of the other bonds: this is the catalyzer mechanism.

Example lock-and-key theory

We illustrate the Kullback-Leidler enzyme model by calculation of a concrete example: the prebiotic synthesis of glycine from HCN, water and hydrogen catalyzed by diglycine [12]

2 H C N + 2 H 2 O + 2 H → d i g l y c i n e g l y c i n e + N H 3 , where g l y c i n e = O H   −   C O   −   C H 2   −   N H 2 and d i g l y c i n e = O H   −   C O   −   C H 2   −   N H   −   C O   −   C H 2   −   N H 2

We formulate the substrate-enzyme interaction pattern in the input as follows

H O H   H C N   H H   H 2 O   H C N substrate 2 H C N + 2 H 2 O + 2 H

O H   C   =   O   H C H   N H   C   =   O   H C H   H N H enzyme diglycine

with substrate bond energies in kJ/mol (H1HO is HH bond in water)

E_in = {H1HO, H1HO, CH, C3N, HH, H1HO, H1HO, CH, C3N} {143.694, 143.694, 143.694, 165.472, 658.049, 143.694, 931.529, 143.694, 143.694, 143.694, 143.694, 165.472, 658.049}

enzyme bond energies in kJ/mol

E ′ i n = {C2O, C2O, CH, CH, NH, C2O, C2O, CH, CH, NH, NH} {110.436, 110.436, 165.472, 165.472, 381.609, 110.436, 110.436, 165.472, 165.472, 381.609, 381.609}

The KL-weights are

p_in = {0.000751014, 0.990651, 0.00112518, 0.00112514, 0.0025965, 0.000750763, 0.000750619, 0.00112519, 0.00112512}

enzyme density values r i n = E ′ i n / ∑ n E ′ i n , {0.0743559, 0.0743559, 0.111411, 0.111411, 0.256934, 0.0743559, 0.0743559, 0.111411, 0.111411}

We formulate the substrate-enzyme interaction pattern in the output correspondingly

O H   C   =   O   H C H   N H   −   C   =   O   C H 2   −   N H 2 enzyme diglycine

O H   C   =   O   H C H   N H 2   N H 3 g l y c i n e = O H   −   C O   −   C H 2   −   N H 2 + N H 3

E_on = {OH, CO, C2O, CC, CH, CH, CN, NH, NH, NH, NH, NH} {257.109, 290.849, 110.436, 157.643, 165.472, 165.472, 35.7925, 381.609, 381.609, 381.609, 381.609, 381.609}

E ′ o n = {OH, CO, C2O, CC, CH, CH, CN, NH, C2O, CH, CH, NH} {257.109, 290.849, 110.436, 157.643, 165.472, 165.472, 35.7925, 381.609, 110.436, 165.472, 165.472, 381.609}

enzyme density values r o n = E ′ o n / ∑ n E ′ o n , {0.107695, 0.121828, 0.0462586, 0.066032, 0.0693113, 0.0693113, 0.0149924, 0.159845, 0.0462586, 0.0693113, 0.0693113, 0.159845}

The KL-weights are

p_on = {0.000213839, 0.000242668, 0.000090888, 0.000129961, 0.00013647, 0.00013647, 0.998051, 0.000317807, 0.0000907091, 0.00013647, 0.00013647, 0.000317807}

The mean bond energies original and original activation energy are

E i b m = ( ∑ n E i n ) / n i = 350.37

E o b m = ( ∑ n E o n ) / n o = 257.57

E a = E o b m − E i b m = 92.80

The mean bond energies catalyzed, and catalyzed activation energy are

E ′ i b m = ( ∑ n p i n E i n ) / n i = 11.10

E ′ o b m = ( ∑ n p o n E o n ) / n o = 2.79

E ′ a = E ′ o b m − E ′ i b m = 8.31

so the original activation energy is E a = 92.80 , and the catalyzed activation energy is E ′ a = 8.31 , and the attenuation ratio is f a = E a E ′ a = 11.17 .

The calculation of biochemical reaction rates from 2.3.2 is described below in Figure 5.

The calculation of lock-and-key enzyme model from 2.4 is described below in Figure 6.

We present here three prebiotic reactions of the HCN-chemistry, which generate important amino acids and nucleobases of the proto-life scenario described in the following section [20] . These reactions have been carried out in the lab by Patel et al. [8] and Das et al. [9] .

Cytosine reaction [8]

Glycine reaction [9] , including energy output in kJ/mol (negative = released)

Proline reaction [8]

We present here a plausible scenario of terrestrial proto-life based on the HCN-chemistry according to the Patel-Das model [8] [9] , the binary genetic proto-code proposed by Carter-Wills [10] and Rodriguez et al. [11] , and the pyrite (iron-sulfur) energy cycle proposed by Wächtershäuser [21] .

There are several basic features of the terrestrial life chemistry, which support this scenario

- the basic components, amino acids and nucleobases, have roughly the composition scheme C_xN_xH_2xO₂, which corresponds to the precursor input xHCN + 2H₂O + xH of the HCN chemistry with hydrogen provided by the energy cycle.

- the maximum activation energy E_a of the spontaneous HCN-chemistry is 40 kJ/mol [8] , which fits very well with the reaction energy ΔE = 41 kJ/mol of the iron-sulfur-cycle, the iron-sulfur-cycle and the reverse acetogenesis, both involving sulfur, are the two main non-photogenetic energy cycles (apart from the Wood-Ljungdahl cycle) used in the terrestrial life chemistry.

- both basic component families can be traced back to fundamental components.

For the amino acids, it is the special group C of amino acids, set apart from the remaining groups A (electrically charged side chain), B (polar uncharged side chain) and D (hydrophobic side chain). The special group C consists of the simplest linear amino acid glycine, the simplest ring-amino-acid proline with its penta-ring and the simplest sulfur-amino acid cysteine: these are the 3 components of the model1-proto-code.

For the nucleobases it is cytosine, the hexa-ring nucleobase, and the coupled nucleobase guanine, which is a double hexa-penta-ring molecule, these are the 2 nucleobases of the model1 proto-code.

The model2 proto-code consists of max-4-bit-codons (guanine Gua or cytosine Cyt) coding for 2 amino acids (glycine Gly or proline Pro). It is a 1-1 code, i.e. a gene has only one codon, so there is no need for several steps of “sequencer” tRNA’s as in the full DNA-code, the peptide synthesis in the proto-life-cycle is a 1-step process. The codon = gene e.g. GG for Gly is represented by the corresponding poly-nucleobase PNB GuaGua, which “grabs” the corresponding amino acids (in this case Gly) via H-bonds (consuming energy) and forms the corresponding “stacked” poly-nucleic-acid (PNA), which after completion spontaneously splits-off the complete peptide (releasing energy).

The enzymes are Gly-Pro-sequences, which catalyze the synthesis of the 8 needed compounds (5 amino acids Gly, Pro, Leu, His, Cys, 2 nucleobases Gua, Cyt, 1 phospholipid glycerol-1-phosphate) from the precursors (hydrogen cyanide HCN, H₂O, H, hydrogen sulfide H₂S, phosphoric acid H₃PO₄).

The model1 proto-code is a simpler version with max-3-bit codons, where the 2 additional amino acids Leu and His in the PNA are replaced by the enzyme-building amino acids Gly and Pro.

This is a minimalistic version of a proto-code: at least 2 amino acids are needed as elements of enzymes (here Gly, Pro), a third (here Cys) containing sulfur is needed for catalyzing the energy cycle and stabilizing the lipid membrane.

Glycine is the simplest amino acid and is a linear molecule with 2 carbon-nodes (COOH-head and C-node with a NH₂-radical), the corresponding nucleobase guanine is a double penta-hexa-ring with 5 C- and 4 N-nodes.

Proline consists of the COOH-head and a penta-ring with 4 C-nodes and one N-node, the corresponding nucleobase cytosine is a hexa-ring with 4 C-nodes and 2 N-nodes.

Therefore, it is obvious that enzymes, which catalyze linear molecules like glycine must contain glycine, and those which catalyze ring-molecules like proline or the nucleobases must contain proline.

During catalysis, the precursors align along the enzyme, so the enzyme must have at least as many nodes (C, N) as the resulting compound. The precursors for the ring-parts of the compound align along the ring-part of the enzyme. The precursor sequence is contiguous.

The alignment rules are:

● HCN binds to HCH or HCN

● water OH-H binds to CO

● HH resp. 2HH binds to NH or OH or (if none is available) to CO

The reactions of the model1-proto-code fall into 9 categories (Table 1, Table 2)

1) Catalyzed synthesis of basic compounds and energy reaction (pyrite reaction)

The basic compounds (amino acids and nucleobases) are synthesized from precursors HCN, H₂O, H₂, H₂S, catalyzed by enzymes controlled by the corresponding genes.

Example: (ΔE reaction energy, E_a original activation energy, E_c catalyzed activation energy, n_B number of bonds)

Direct glycine synthesis catalyzed by GlyGly:

2 H C N + 2 H 2 O + H 2 → G l y ( C O O H   −   C H 2 N H 2 ) + N H 3 , enzyme GlyGly, ΔE = 223 kJ/mol, E_a = 94.8 kJ/mol, E_c = 7.6 kJ/mol, n_B = 25

A key role plays the pyrite reaction, as energy provider, but foremost as the source of hydrogen for the synthesis of basic compounds:

F e S + H 2 S → F e S 2 + H 2 , enzyme Cys, ΔE = 41 kJ/mol, E_a = 160.6 kJ/mol, E_c = 0.02 kJ/mol, n_B = 16

The pyrite reaction has a low energy output, but a high activation energy, so it runs practically only with catalysis (uncatalyzed reaction time is t r = t 0 exp ( E a k T ) = 3.45 × 10 − 9 × 1.37 × 10 21 = 5.32 × 10 12   s = 1.69 × 10 5   a ).

The synthesis reactions have high reaction energy (ΔE = 100...1200 kJ/mol), high activation energy (E_a = 100...200 kJ/mol), and do not run in water without enzymes.

The “self-catalyzing” synthesis of proline via cytosine (ring) has a very low activation energy

C y t ( C 4 H 5 N 3 O 3 ) + H C N + 6 H 2 → P r o ( C 5 H 9 N O 2 ) + H 2 O + 2 N H 3 , ΔE = 582.9 kJ/mol, E_a = 21.7 kJ/mol, n_B = 16

The basic compounds synthesis reactions are all exothermic, and have high activation energy E_a = 92...145 kJ/mol (using cytosine-proline synthesis). when running without catalysis, the maximum reaction time is (Gua)

t r = t 0 exp ( E a k T ) = 0.99 × 10 − 9 × 1.59 × 10 19 = 1.57 × 10 10   s = 0.50 × 10 3   a

Apart from amino acid and nucleobase synthesis, the third important basic compounds are the phospholipids, which form the proto-membrane, here the synthesis of the lipid precursor glycerol-1-phosphate Glyc1ph from the basic precursor phosphoric acid H₃PO₄, catalyzed by triglycine GlyGlyGly 3 H C N + 2 H 2 O + 4 H 2 + H 3 P O 4 → G l y c 1 p h + 3 N H 3 , ΔE = 395.5 kJ/mol, E_a = 139.5 kJ/mol, E_c = 6.6 kJ/mol, n_B = 27.

2) Nucleobase polymerization

Nucleobases form stacks bound by H-bonds (poly-nucleobase = PNB), these reactions are spontaneous, strongly exothermic (ΔE ~600 kJ/mol) and have low activation energy (E_a = 5…10 kJ/mol).

C y t + C y t → C y t C y t ( 3 H − ) CytCyt is bound by 3 H-bonds, ΔE = 491 kJ/mol, E_a = 5 kJ/mol

3) Simple PNA formation

Simple peptide-nucleic-acid (PNA) form from an amino acid and a nucleobase

Gly + Gua → GlyGua + H 2 O , ΔE = 339 kJ/mol, E_a = 14 kJ/mol

Pro + Cyt → ProCyt + H 2 O , ΔE = −44.3 kJ/mol, E_a = 12.6 kJ/mol

These reactions are low exo- or low endothermic and have low activation energy.

4) Direct PNA polymerization

Simple PNA’s form chains

GlyGua + GlyGua → GlyGuaGlyGua ( 6H − ) , ΔE = 126 kJ/mol, E_a = 3 kJ/mol

5) PNA formation from amino acids and nucleobases

Two amino acids and a simple pNB form a PNA

Gly + Gly + GuaGua → GlyGuaGlyGua ( + 2H − ) + 2H 2 O , ΔE = 468 kJ/mol, E_a = 10 kJ/mol

These reactions are mostly endothermic and have a low activation energy.

6) Peptide forming

GlyGuaGlyGua + 2H 2 O → GuaGua ( + 4H − ) + GlyGly + H 2 O , ΔE = 682 kJ/mol, E_a = 11.3 kJ/mol

A peptide “breaks-off” from a PNA-stack, the reactions are exothermic and have low activation energy.

The sequence type2 → type5 → type6 is the PNA-controlled peptide synthesis, in contrast to type9, the spontaneous peptide synthesis (see below). This sequence is exothermic (the endothermic reactions type5 use the energy from the preceding reaction type2), whereas the reactions of type9 are endothermic, and their activation energy E_a is mostly lower than the corresponding E_a in type 9.

7) Diverse synthesis and energy cycles

The HCN chemistry as the basis for the proto-code reactions depends on a sufficient supply of HCN. As discussed in ( [2] Chap. 3.4), there is evidence of the presence of HCN, along with methane CH₄ and ammonia NH₃ in the early Earth atmosphere. But there are also cyanide synthesis reactions, which could produce HCN under volcanic pools or in hydrothermal vents.

CO 2 + NH 3 + H 2 → HCN + 2H 2 O , ΔE = −90.9 kJ/mol, E_a = 74.2 kJ/mol

CO 2 + NH 3 + SH 2 → HCN + 2H 2 O + S , ΔE = −111.5 kJ/mol, E_a = 6.5 kJ/mol

They have as reducing component H₂ or SH₂, which are supplied by the pyrite reaction.

They are both endothermic, so they depend upon energy supply, e.g. from the pyrite reaction.

Their activation energy E_a is relatively low, especially for the SH₂-reaction: this one can run purely thermally, without enzymes.

There is the synthesis of the proto-sugar glyceraldehyde Gle, a precursor of ribose needed for RNA:

Gly + H 2 O → Gle ( HCO   −   HCOH   −   H 2 COH ) + NH 3 , ΔE = 346.2 kJ/mol, E_a = 14 kJ/mol

As for energy cycles, there is the mentioned pyrite reaction

FeS + H 2 S → FeS 2 + H 2 , ΔE = 41 kJ/mol, E_a = 160.6 kJ/mol

but also the CO₂-reduction by hydrogen, which was present in the prebiotic Earth atmosphere

CO 2 + H 2 → CO + H 2 O , ΔE = 90.1 kJ/mol, E_a = 115.8 kJ/mol

and oxidation of carbon monoxide CO in water, which is still used by methanogen bacteria [23]

CO + H 2 O → HCOOH , ΔE = 548.8 kJ/mol, E_a = 33.3 kJ/mol

8) Decay of basic compounds

Under present biotic conditions on Earth, the basic compounds are long-lived, amino acids decompose in water thermally at temperature T > 185˚C at neutral pH, nucleobases have in water a half-life of 20 - 200 days at 100˚C, and they degrade at 250C at neutral pH [24] .

The decay via hydrolysis of the basic compounds functions via break-off of the C = O radical, which all of them contain, with the formation of formic acid. All decays are endothermic (run only with energy input), and have a low activation energy.

A typical decay reaction is the hydrolysis of glycine:

Gly ( COOH   −   CH 2 NH 2 ) + H 2 O → OH   −   CH 2 NH 2 + HCOOH , ΔE = −335.9 kJ/mol, E_a = 9.0 kJ/mol

9) Direct peptide polymerization

These are the direct merging reactions of amino acids into peptides, without the interaction of PNA’s (see peptide formation):

Gly + Gly → GlyGly + H 2 O , ΔE = −117.7 kJ/mol, E_a = 64.8 kJ/mol

Pro + Pro → ProPro + H 2 O , ΔE = −1097.7 kJ/mol, E_a = 27.9 kJ/mol

These reactions are endothermic, with moderate activation energy, they run spontaneously only at high temperature and with a multiple energy input from the energy reaction ( Δ E ( Gly + Gly → GlyGly + H 2 O ) ≈ 3 E ( FeS + H 2 S → FeS 2 + H 2 ) = 123   kJ / mol ), i.e. very slowly even with a catalyzed energy reaction.

The opposite reactions like

GlyGly + H 2 O → Gly + Gly

are exothermic decay reactions of peptides with a decomposition temperature T_d, where t 0 exp ( E a / k T d ) = 1   s , so for t 0 ≈ 10 − 9   s we get approximately for Gly: k T d = E a / log ( 10 9 ) and T d = 350   K = 77 ˚ C , which is in good agreement with the known decomposition temperature of poly-peptides (75˚C - 85˚C).

Therefore the PNA-controlled peptide formation sequence type2 → type5 → type6 is really necessary for the molecular evolution of life from the HCN-HCN-chemistry.

On the other hand, in the prebiotic chemistry on Earth there was a seed concentration of amino acids from meteorites (rough estimation for the concentration c = 10⁻⁶), but no polymers, i.e. no enzymes, and therefore no organic catalysis. In the initial prebiotic period before the onset of the model1 proto-code life cycle, peptide polymerization was spontaneous, with the support of an energy cycle: Cys-catalyzed pyrite reaction of H₂S, CO₂-reduction or CO-oxidation.

With seed-concentration for the basic compounds of c = 10⁻⁶, and remaining concentration from [23] given below, we get the energy production of the 3 energy cycles [12]

E p ( H 2 S ) = 0.0045   kJ / s ⋅ mol , E p ( CO 2 ) = 5.3 × 10 − 7 kJ / s ⋅ mol , E p ( CO ) = 0.00062   kJ / s ⋅ mol ,

and using this, for the effective build-up time of G l y + G l y → G l y G l y + H 2 O with the H₂S-pyrite reaction

t c ( 2 Gly ) = t r ( 2 Gly ) c ( Gly ) Δ E ( 2 Gly ) t r ( 2 Gly ) 1 E p = 1.0 × 10 9   s = 31.7   a with the effective reaction time t r = t 0 exp ( E a k T ) .

The result of the simulation is a completely realistic scenario of the origin of terrestrial life based on HCN and H₂S as precursors, and the H₂S energy cycle. It consists of two phases:

Phase1 (scenario2) is the enrichment of amino acids, nucleobases and peptides in a hydrothermal pool with amplification factors of 25 to 8000 and a time constant of 500s, the process is guided by thermal convection and proceeds via spontaneous peptide polymerization, which needs considerable energy taken from the more powerful CO-energy cycle.

Phase2 (scenario3) is the build-up of a genuine self-catalytic life-proto-cycle in a self-assembling lipid membrane.

The underlying genetic code is a proto-code with 3 amino acids (Gly, Pro, Cys) and 2 nucleobases (Gua, Cyt) with 5 proto-genes (GG, GGG, CC, C, GC) coding for 5 peptides (Gly2, Gly3, Pro2, Pro, GlyPro), which catalyze the synthesis of 5 basic components (Gly, Cys, Pro, Cyt, Gua). The peptide synthesis is carried out by peptide-nucleid-acids (PNA’s) generated in the proto-cycle, which correspond to the modern RNA-transferases. The process is guided by diffusion, and the calculation shows, that there is a periodic instability, i.e. a collapse-division time of the proto-cell of roughly 1000 s, which is about the same as the cell-division cycle time in modern bacteria. The PNB-proto-genes remain stable in the cycle and play the role of information carriers.

The process described above uses precise reactions and proto-code.

On the other hand, it is unrealistic that the proto-code described above is the only alternative. The PNA building is a spontaneous process, which is not very accurate. There will be other PNA’s, which will produce other similar peptides. Those peptides will survive, if they can at least partly catalyze a basic reaction,

That means, there will be not one gene PNB = GuaGua with the corresponding PNA = (GlyGua)₂ for glycine synthesis, but a family of genes (quasi-gene in the terminology of Manfred Eigen). The set of quasi-genes forms a quasi-species, where the variable genes adapt to the changing environment.

The evolution leads to an increasing number of more and more complex genes and peptides, where the catalysis is more and more specific: the quasi-species evolves into a genuine species.

Considering all this, we get the following life-origin quasi-species scenario (Figure 13(a), Figure 13(b)).

Complete genesis of proto-life cycle reaction scenario

phase1: red, phase2: black

In phase1, there are additional spontaneous polymerization reactions fed by the additional energy cycle, which are replaced by peptide-catalyzed reactions in phase2.

Complete genesis of proto-life cycle model

phase1: red, phase2: black

Here is included in red the phase1 open hydrothermal pool, whose reactions yield the enrichment in basic compounds and peptides necessary for the start of phase2.

We have the following Table 6 of genetic proto-code (model1) of the proto-lifecycle, discussed in full in Chap. 3.2.

The model1 binary proto-life-cycle uses a binary 1-1-code, i.e. a 2-letter-code (G, C) with 1 codon per gene. It has 2 coding amino acids (Gly for G, Pro for C) and 3 precursors (HCN, H₂S, H₂).

HCN has a relatively low molecular energy (=free enthalpy H_f) of |H_f| = 551.9, so the life-cycle needs energy only for PNA-building, which is supplied by the pyrite energy cycle (ΔE = 41 kJ/mole), whereas the basic-compound-synthesis runs exothermally without energy input.

HCN forms by electric discharge or UV-light from CO₂ and NH₃, and is also destroyed by UV-light, so it was only available early in the Earth history. Later (after ~100 My) the life-cycle had to adapt to other, more stable precursors. The

most plausible and least energy-consuming alternative is (CO, NH₃, H₂S, H₂), where the energy needed for the basic-compound-synthesis is in the range 140 - 400 kJ/mol, and can be supplied by multiple pyrite energy cycle (or single CO energy cycle).

The synthesis of the 2 basic amino acids (Gly, Pro) and the 2 nucleobases (Gua, Cyt) runs according to the scheme ( [16] p. 94)

2CO + NH 3 + H 2 → Gly ( C 2 H 5 NO 2 ) , ΔE = −139 kJ/mole (endothermal)

5CO + NH 3 + 6H 2 → Pro ( C 5 H 9 NO 2 ) + 3H 2 O , ΔE = −163.3 kJ/mol

4CO + 3NH 3 + H 2 → Cyt ( C 4 H 5 N 3 O ) + 3H 2 O , ΔE = −340.5 kJ/mol

5CO + 5NH 3 → Gua ( C 5 H 5 N 5 O ) + 4H 2 O + H 2 , ΔE = −400 kJ/mol

Model3 proto-PNA code

In order to produce enzymes for these reactions in addition to the existing ones, more coding amino acids and a larger code with 4 nucleobases is needed. A minimalistic version is model3: the extended model1 proto-PNA ternary code with 4 letters (G, C, A, U), 2-bit-codons, 12 coding amino acids and 4 nucleobases, and 1 codon per gene (1-1-code).

We start with the PNA 2-bit code (Table 7)

We take model 2 with (Gly, Pro, Cys, His, Leu) as a basic configuration, and the code of model1 includes the enzymes.

The coding is the same as in the RNA-code except, when modified because of a nucleobase instead of an amino acid: Gua (GC) replaces Ala, Cyt (CG) replaces

Arg. Furthermore, we replace Tyr/Stop (UA) by Uracil Ura, and we replace Asn/Lys (AA) by Adenine Ade (the two U-A-codons with A at the end).

For the enzymes, we accept the extended correspondence from model1

G↔Gly, C↔Pro, A↔His, U↔Leu

In case of double-coding like Asp/Glu (GA) or Asn/Lys (AG), we take the simpler (=older) amino acid.

The nucleobase-pairing rule in PNA is G↔G, C↔C, A↔U.

Now we have the following code table Table 8.

Now, we have 4 basic-enzyme-coding amino acids (Gly, Pro, His, Leu), plus 8 enzyme-coding amino acids (Cys, Phe, Ile, Val, Ser, Thr, Asp, Asn), plus 4 nucleobases (Gua, Cyt, Ura, Ade).

This code is a plausible configuration, not a calculated solution, as in model1. Still, it can be regarded as a “basic” code within the quasi-species of the 2-bit ternary 1-1 PNA-proto-code.

The compounds in the reaction network are:

- 12 amino acids (Gly, Pro, His, Leu, Cys, Phe, Ile, Val, Ser, Thr, Asp, Asn)

- 4 nucleobases (Gua, Cyt, Ura, Ade)

- 16 peptides (enzymes) (Gly2, LeuGly, Pro2, ProGly2, ..., GlyHis, HisGly)

- 1 lipid Gly1ph

- 16 poly-nucleobases PNB’s (genes) (GG, UG, CC, CG, ..., AA, GA, AG)

- 16 poly-nucleobase-aminoacids PNA’s

GlyGua2, LeuAdeGlyGua, ProCyt2, ProCytGlyGua2,

GlyGuaProCyt, ProCytHisUra, ProCytLeuAde

LeuAde2, HisUraLeuAde, GlyGuaLeuAde, LeuAdeProCyt, HisUraProCyt,

LeuAdeHisUra, HisUra2, GlyGuaHisUra, HisUraGlyGua

The precursors are CO, NH₃, H₂S, H₃PO₄

The energy cycle: pyrite reaction F e S + H 2 S → F e S 2 + 2 H + + 2 e −

We have the following model3 scenario Figure 14.

The model3: the extended model1 proto-PNA ternary code with 4 letters (G, C, A, U), 2-bit-codons, 8 coding amino acids and 4 nucleobases, and 1 codon per gene (1-1-code).

A plausible transition from model3 proto-PNA code to the proto-RNA code of LUCA proceeds by full use of the 3-bit-code, by increasing the number of amino acids to 20, and by extending the 1-codon genes to multi-codon genes with the introduction of start- and stop-codons.

Furthermore, the PNB-PNA synthesis is replaced by tRNA-synthesis with one tRNA for every amino acid, with the addition of 20 codons coding for the 20 tRNA’s.

The PNB’s are replaced by a single RNA-strand with the supporting skeleton of ribose and phosphate radicals, which makes the RNA much more stable than its fore-runner PNB’s. The RNA is exactly copied by the enzyme RNA-polymerase (which is coded in a dedicated gene). Now, the RNA carries fixed genes, and is not a collection of quasi-genes like the PNB’s.

LUCA was living in hydrothermal vents and/or hot volcanic pools.

LUCA’s environmental conditions were: T ~80˚C, pH = 9, intermediate pressure.

LUCA used as energy cycle the acetogenesis (Wood-Ljungdahl)

H 2 + C O 2 → f o r m a t e → C H 3   p r o t e i n C O → → a c e t y l C o A → a c e t a t e + A T P

The precursors were: H₂, CO₂, NH₃, H₂S, PO 4 3 − ion

Now, we have the following reaction scenario Figure 15.

Scenario2 Chap. 2.8 is the full proto-life cycle from the reaction table in Chap. 2.7, in the physical environment of a hydrothermal vent. It serves as an amplifier process for all involved molecule classes amino acids, nucleobases, peptides, poly-nuclein-acids PNA, lipids), which are distributed in surroundings by thermal convection, keeping the concentration of bio-molecules in the thermal boundary layer stable and relatively low.

Scenario2 starts with enriched concentrations (init2) of c = 10⁻⁴ = 100 ppm for basic compounds, c = 10⁻⁶ = 1 ppm for peptides, and c = 0.01 for precursors.

The reaction network consists of spontaneous and peptide-catalyzed basic-compound-synthesis, with the H2S (pyrite) energy cycle and the CO energy cycle, then the PNA-controlled peptide synthesis, and direct PNA-polymerization.

The PNA-controlled peptide synthesis works also without the initial presence of peptides (i.e. initial peptide concentration c = 0), whereas the direct peptide polymerization requires high rates of CO energy cycle to counteract the reverse reaction (direct peptide decay).

The results of the enrichment reactions are given in the following Table 9.

This can be formulated concisely in the following scheme:

time constant: about 500 s

Yaman & Harvey [28] calculate minimal reaction time for amino acid synthesis catalyzed by dinucleotide t r ( E a = 20   kcal / mol ) = exp ( E a / k T )   1   ns ≈ 200   s .

The proto-code consists of binary 3-bit-codons (guanine Gua or cytosine Cyt) coding for 2 amino acids (glycine Gly or proline Pro). The enzymes are Gly-Pro-sequences, which catalyze the synthesis of the 6 needed compounds (3 amino acids Gly, Pro, Cys, 2 nucleobases Gua, Cyt, 1 phospholipid glycerol-1-phosphate) from the precursors (hydrogen cyanide HCN, H₂O, H, hydrogen sulfide H₂S, phosphoric acid H₃PO₄).

The simplified model1 proto-code with 5 proto-genes for 6 compounds (enthalpy values from [22] ) and 2 PNA’s for 3 amino acids, 1 lipid and 2 nucleobases is now as follows (Table 10, Figure 17).

The scenario (=scenario3 Chap. 2.8) of the PNA proto-cell is the full proto-life cycle, confined in the interior of a lipid vesicle. As was reported in ( [2] Chap. 3.4), amino acids within a lipid membrane stabilize the lipid layer, and the lipids

serve under certain conditions as catalyzer for peptide polymerization. Precursor molecules enter the vesicle via osmosis, but bio-molecules are enclosed in it, and are not carried away by convection, there is diffusion only within the vesicle. Therefore the concentration of bio-molecules can increase until it reaches a critical level, and the system becomes unstable, the vesicle divides and proliferation takes place. The reaction cycle now has all attributes of life (Figure 18(a)):

- synthesis of basic compounds from precursors (“food”) using an energy cycle

- self-regulation by catalysis through peptides-enzymes

- PNA-gene-controlled enzyme production from amino acids

- proliferation through bio-matter production and vesicle division.

The compounds in the reaction network are:

- 3 amino acids Gly, Pro. Cys

- 2 nucleobases Gua, Cyt

- 5 peptides (enzymes) Gly2, Gly3, Pro, Pro2, GlyPro

- 1 lipid Gly1ph

- 5 PNB’s (genes) Gua2, Gua3, Cyt2, Cyt, GuaCyt

- 5 PNA’s GlyGua2, GlyGua3, ProCyt2, ProCyt, GlyGuaProCyt2

The precursors are HCN, H₂S, H₃PO₄

The energy cycle: pyrite reaction F e S + H 2 S → F e S 2 + 2 H + + 2 e −

This scenario3 reaches significantly higher concentrations than scenario2, because the bio-molecules cannot leave the vesicle. Only precursor molecules can pass the membrane, for them the boundary condition c = c₀ is valid at the membrane.

The PNB’s become now the proto-genes, which are stable in the cycle.

The basic components synthesis runs under catalytic peptide control, the pyrite energy cycle is catalyzed by Cys, PNA building from amino acids and PNB’s takes energy from the energy cycle, the PNA’s split into peptides and PNB’s releasing energy, and the cycle runs anew.

The pyrite energy reaction delivers energy and H₂ at the membrane, catalyzed by Cys, the insoluble FeS₂ falls out in colloidal form.

The current of precursors through the membrane is governed by osmosis:

∂ c ( t , x 1 ) ∂ t = f v m ( c ( t , x 1 ) − c 0 )

and within the vesicle there is diffusion for all molecules

∂ c ( x , t ) ∂ t = f v d ∂ 2 c ( x , t ) ∂ x 2

If f_vd = 0, i.e. without diffusion, the system reaches an equilibrium, and there is a solution for all times.

The diffusion introduces a definite critical time t_c, where the system becomes unstable, i.e. where the solution of the differential equations ceases to exist: the vesicle divides, separates into two, and the reaction cycle starts again. This critical time depends on the system parameters and the initial concentration, and has values around 1000s, which agrees well with the observed division periods of self-reproducing lipid-amino-acid vesicles and also of bacteria.

Yaman & Harvey [28] presented a simplified proto-genetic code with 9 two-letter codons from (A, G, C) for 5 amino acids and 3 precursors, which runs purely abiotically by catalysis with the corresponding dinucleotide (Table 11).

With only two letters (G, C) and 4 codons, it reduces to the table that matches the model1 table for the entries CC and GG, whereas the entries CG and GC catalyze indirectly arginine resp. alanine, which does not participate directly in the proto-lifecycle of model1.

After ~100 My, the life-cycle had to adapt to other, more stable precursors than HCN.

The most plausible and least energy-consuming alternative precursors (CO, NH₃, H₂S, H₂).

We have the following model3 code in Table 12.

We have here a full 2-bit code for aminoacids + nucleobases, specifically, we have 4 basic-enzyme-coding amino acids (Gly, Pro, His, Leu), plus 8 enzyme-coding amino acids (Cys, Phe, Ile, Val, Ser, Thr, Asp, Asn), plus 4 nucleobases (Gua, Cyt, Ura, Ade) (Figure 18(b)).

This code is a plausible configuration, not a calculated solution, as in model1. Still, it can be regarded as a “basic” code within the quasi-species of the 2-bit ternary 1-1 RNA-proto-code.

The model3 is the extended model1 proto-PNA ternary code with 4 letters (G, C, A, U), 2-bit-codons, 8 coding amino acids and 4 nucleobases, and 1 codon per gene (1-1-code).

A plausible transition from model3 proto-PNA code to the proto-RNA code of LUCA proceeds by full use of the 2-bit-code, by increasing the number of amino acids to 20, and by extending the 1-codon genes to multi-codon genes with the introduction of start- and stop-codons.

Furthermore, the PNB-PNA synthesis is replaced by tRNA-synthesis with one tRNA for every amino acid, with the addition of 20 genes coding for the 20 tRNA’s.

The PNB’s are replaced by a single RNA-strand with the supporting skeleton of ribose and phosphate radicals, which makes the RNA much more stable than its fore-runner PNB’s. The RNA is exactly copied by the enzyme RNA-polymerase (which is coded in a dedicated gene). Now, the RNA carries fixed genes, and is not a collection of quasi-genes like the PNB’s.

The full RNA code is shown in 1.1.

The precursors are CO₂, NH₃, H₂, H₂S, H₃PO₄

The energy cycle is the aceto-genesis from H₂ and CO₂

H 2 + C O 2 → f o r m a t e → C H 3   p r o t e i n C O → → a c e t y l C o A → a c e t a t e + A T P

The biosynthetic reaction network consists of ≈150 basic reactions, from which 95% were exergonic [29] . The four key reactions are acetogenesis (Wood-Ljungdal), gluconeogenesis, reverse citric acid cycle, pentose phosphate pathway. From the 26 key intermediate cofactors the most important 7 are: ATP, GTP, THF, NAD, NADP, CoA, SAM.

Now, we have the following reaction scenario (Figure 19).

The DNA-cell (bacteria, archaea, eukaryotes) uses the full DNA genetic code (Table 13) with 20 amino acids, and corresponding 20 aaRNA’s for peptide synthesis,

4 nucleotides: cytosine, thymine, adenine, guanine (thymine replaces uracil in RNA-coding). The pairs A-G and C-T are complementary in the DNA-double-helix.

The cell membrane consists of ester and ether lipids (bacteria, eukaryotes) or diether lipids (archaea).

The (self-sustainable) energy cycle is widely diverse:

- reverse acetogenesis with sulfate reduction (sulfur bacteria)

- Wood-Ljungdahl aceto-genesis (archaea and bacteria in hydrothermal vents and volcanic pools)

- methanogenesis from carbon dioxide and hydrogen (archaea)

- photosynthesis (cyanobacteria)