Title: Origin of life, primary pump scenario :
1COST Action D 27
Origin of life, primary pump scenario
catalysis and concentration in this coevolutive
process. Pr Auguste Commeyras University of
Montpellier 2 -CNRS IBMM UMR-5247 Dr R. Pascal
group (DSBC)
NORDITA/Stockholm 25/29 February 2008
2The Birth of life
- Panspermia being far to be proved, life is born
on our planet. This also means that life could
have appeared on another one. - Geological sciences locate the birth of life
between 3.9 and 3.6 billion years before present
time on our planet, which was still young (Earth
is indeed 4.55 billion years old). - Two converging approaches are used to study the
extraordinary mechanism which gave birth to life
- The approach of the biologists who try to take
back up the time and to go from the living beings
towards the inert matter, -
- the approach of the chemists who follow the
direction of time and study the way used by inert
material to become a living beings.
3The different groups of chemists working about
the origin of life can be classified within
- GENETICISTS
- METABOLISTS
- COMPARTIMENTALISTS
- COEVOLUTIONNISTS
- For coevolutionnists, all molecules and
macromolecules essential to life were born almost
at the same time, and under the influence of
unique and permanent driving force. - For coevolutionnists the emergence of
Homochirality can be seen as a step of this
approach. I mean a consequence of the dynamic of
the system. - We are coevolutionnist.
4During many years on this field we look for
- 1/ A credible INITIAL ENERGETIC SYSTEM,
-
- 2/ A Â PERMANENTÂ energetic system, since it is
probable that life could be born via trial and
error approaches under a permanent energy
pressure. - 3/ Understanding the  CONSEQUENCES of the
permanent energy pressure by following the
evolution of the system. - 4/ Natural and credible processes of
 CONCENTRATION since it seems obvious that the
concentration of organic compounds must have been
increased in order to favor organic reactions. -
- 5/ Â SIMPLE WAYSÂ , material and time savings,
to make credible the accomplishment of the
complex process of life emergence.
5A coevolutive scenario could be described as
follow
6Coevolutive scenario for the emergence of life.
SUN Permanent driving force
EARTH Peculiar planet on which a chemical system
maintained out of equilibrium push to the
simultaneous emergence of
Essential molecules
predisposed molecules
nucleotides triphosphates
etc
peptides
Fatty acids
RNA
which drives to the birth of genetic code, to
the compartimentalisation, and beyond, to a
"Darwinian" system
7To have been able to go in so different
directions, the prebiotic reactions must have
been multi-directional, that means not
robust. In prebiotic chemistry the prevalent
postulate was the robustness of the reactions
and, for many years, we were not convinced by
this postulate. We became enthusiastic when we
heard about the formal contestation of the
 robustness of the prebiotic postulate from
Albert Eschenmoser work.
8Indeed, Albert Eschenmoser rejected this
postulate at the end of 2006, and he even
considered that the  non robust reactions have
better potentialities than the  robustÂ
reactions in chemical evolution. Albert
Eschenmoser wrote
- The less robust chemical reactions in a given
environment are, the more sensitive and
responsive to a catalytic acceleration, and the
higher will be their chances to become assisted
by catalysts that may be present or be emerging
in the environment.
Albert Eschenmoser (Conference COST D27 Barcelona
dec 2006)CHEMISTRY BIODIVERSITY Vol. 4
(2007) PP 554-573
9Emergence of different families of molecules in
the global scenario
10Coevolutive scenario for the emergence of life.
SUN Permanent driving force
EARTH Peculiar planet on which a chemical system
maintained out of equilibrium push to
simultaneous emergence of
Essential molecules
predisposed molecules
nucleotides triphosphates
etc
peptides
Fatty acids
RNA
which drives to the birth of genetic code, to
the compartimentalisation, and beyond, to a
"Darwinian" system
11Essential molecules
- The emergence of essential molecules HCN, RCHO,
HNCO, NO, HCCH, HCC-CN - is well documented, see for instance the
information given by the NASA. -
- http//jpldataeval.jpl.nasa.gov/download.html
- and the 2 following NASA slides,
12http//jpldataeval.jpl.nasa.gov/download.html
13(No Transcript)
14The emergence of these essential molecules is not
described further in this presentation
15Predisposed molecules
16Coevolutive scenario for the emergence of life.
SUN Permanent driving force
EARTH Peculiar planet on which a chemical system
maintained out of equilibrium push to
simultaneous emergence of
Essential molecules
predisposed molecules
nucleotides triphosphates
etc
peptides
Fatty acids
RNA
which drives to the birth of genetic code, to
the compartimentalisation, and beyond, to a
"Darwinian" system
17Predisposed molecules
- As predisposed molecules we can list,
aminoacides, nucleosides, nucleotides - The discussion about the synthesis of
a-aminoacids allows us to introduce the idea of a
catalyst system already present in the potential
prebiotic environnement.
18What is now accepted is that from essential
molecules (HCN, RCHO,NH3), a-aminoacids comes
from hydrolysis of a-aminonitrile (IV). (see
below) This hydrolysis is catalysed either by
carbonyl compounds (via a-aminoalcoolate (VIII)
or carbonic anhydride (via carbamate(X)). The
rate ratio between these two pathways is at least
1000 in favor of the catalysis by carbonic
anhydride.
a-aminoacids catalysed By Carbonic anhydride
19In the primitive atmosphere the pressure of CO2
was high (between 10 and 70 bar). The pH of the
primitive ocean was about 6. So the concentration
of carbamate was high (pka of Carbamic acid being
5.8).
From the carbamate the mechanism for the
formation of hydantoïne is the following
The global catalysis of this reaction is showed
in the next slide.
 Rousset, Laspéras, Taillades, Commeyras
(1980). Tetrahedron, 36 2649-2661.
20See the animation of the synthesis of
aminoacids and peptides in possible prebiotic
conditions.
21(No Transcript)
22This work exemplifies the postulate of Albert
Eschenmoser.The synthesis of a-aminoacid (and
beyond peptides) were assisted by a catalyst (the
CO2), already present in the environment.
- The less robust chemical reactions in a given
environment are, the more sensitive and
responsive to a catalytic acceleration, and the
higher will be their chances to become assisted
by catalysts that may be present or be emerging
in the environment.
Albert Eschenmoser (Conference COST D27 Barcelona
dec 2006)CHEMISTRY BIODIVERSITY Vol. 4
(2007) PP 554-573
23Coevolutive scenario for the emergence of life.
SUN Permanent driving force
EARTH Peculiar planet on which a chemical system
maintained out of equilibrium push to
simultaneous emergence of
Essential molecules
predisposed molecules
nucleotides triphosphates
etc
peptides
Fatty acids
RNA
which drives to the birth of genetic code, to
the compartimentalisation, and beyond, to a
"Darwinian" system
24With the synthesis of peptides I want to discuss
the first example of a need of concentration.
25Synthesis of peptides and the need of
concentration.
- When we have a look on the estimated
concentration of organic molecules in the early
ocean (0,4 mg.L-1 ltClt 400 mg.L-1 Chyba 1992 and
Chronin 1993), it becomes obvious that the
organic molecules were too diluted and thus
unable to react together. So that, a process of
concentration was necessary to allow chemical
reactivity. - In the primary pump scenario (next slide), our
first idea was to use natural evaporation in
order to increase the concentration of organic
molecules and to make them reactive. - Such idea of concentration by natural
evaporation was introduced by Darwin and strongly
supported by Stanley Miller in the drying lagoon
scenario. Nevertheless, in drying lagoon scenario
nothing was noticed on the mode of activation of
molecules.
26Atmosphere
Primary Pompe
pH1,5
Beach
Ocean
Commeyras, Collet, Plasson, et al, 2002, Polymer
International. 51, 661-665.
27Synthesis of peptides and the need of
concentration.
- In the primary pump scenario the activation of
a-amino acids is known. - This activation through the system NO/O2 produces
N-carboxyanhydride (NCA) and an equivalent amount
of HNO2. - Consequently during the formation of NCA the pH
decreases from 6 (pH of the primitive ocean) to
1.5. - If the NCA stayed at this pH 1.5, it will never
give peptides but a-aminoacids through hydrolysis
within few hours. - To produce peptides NCA must be poured in a water
solution at pH 4. - And a such rapid inversion of pH (from 1.5 to gt
4) can not be managed in a lagoon, but only on a
unique place on earth, that is to say on the
beach because of the tide. - Since primitive ocean was buffered at pH 6
(H2CO3/HCO3Na) its beach appeared to be the
appropriate place to run the primary pump with
natural concentration and fast pH inversion.
28Let see the animation of this primary pump
working.
29(No Transcript)
30Coevolutive scenario for the emergence of life.
SUN Permanent driving force
EARTH Peculiar planet on which a chemical system
maintained out of equilibrium push to
simultaneous emergence of
Essential molecules
predisposed molecules
nucleotides triphosphates
etc
peptides
Fatty acids
RNA
which drives to the birth of genetic code, to
the compartimentalisation, and beyond, to a
"Darwinian" system
31To be realistic, a scenario about the emergence
of life must take into account the emergence of
precursors of RNA, RNA strands, and to have in
addition the same environment as others
prebiological materials.
Nucleotides triphosphates
32The first information in this field was given by
Raphaël Plasson. During his PHD Raphaël Plasson
has observed a small perturbation in the curve of
hydrolysis of NCA in phosphate buffer between pH
5 and pH 7 (pH of the early ocean)
33That means that in the primary pump the NCA share
their energy.
- Jean-Philippe Biron and Robert Pascal showed
that this perturbation in the curve of hydrolysis
is due to the nucleophilic attack of inorganic
phosphate on the NCA, leading to an aminoacyl
phosphate. - J A C S 2004, 126, 9198-9199
34(No Transcript)
35The second information was given by John
Sutherland. J.S. showed that Cytidine Mono
Phosphate (CMP) is formed in only two steps in a
good yield, at 20C, neutral pH, and few hours,
from essential molecules.
We can expect that these results will be soon
extended by J.S. to the others nucleotides, AMP,
GMP, UMP.
36The third information was obtained by our group.
Aminoacyl phosphate, in presence of AMP, gives
ATP.
ATP is characterized by emission of photons in
presence of luciferase
37By extrapolation, all NTP (ATP, GTP,CTP, UTP)
could have been formed on the beach, in the
primary pump scenario.
38second example of concentration
- In the primary pump scenario all NTP are formed
daily but probably with low yield. - In water NTP are hydrolyzed.
- So their concentration cannot increase. And if
NTP are leaved too diluted, RNA cannot be formed. - Concentration step is required.
- Which step ? for example avoiding ATP hydrolysis
in water.
If dATP/dt kf kh ATP , the concentration
limit of ATP in the solution depends of its
constant of hydrolysis (kh).
39Anna Kovalova in our group recently demonstrated
that
- the stability of ATP in water is dramatically
increased in the presence of peptides.
at 60C 30 is hydrolyzed In 3 days
3 days
4 h
1 day
At 30C or less, ATP (and probably NTP) seems
completely stable in presence of peptides. So NTP
which has been produced daily in this scenario
could have been concentrated.
40In the primary pump scenario, the reactional
pathway to go from the atmosphere to energetic
molecules (NCA, NTP) is very short. Maximum 20
different reactions.
All these reactions are very fast geologically
speaking (few hours), they are produced in the
same conditions, in the same area and these
reactions are repeated every day. In this
scenario nature daily constructed dices (all NCA
and all NTP) and daily played with them.
Dendritic peptides are formed under kinetic and
thermodynamic control by the primary pump. They
accumulated, and progressively evolved until
homochirality.
NTP are loaded continuously in these dendritic
peptides in continuous evolution. and when good
catalytic activity appeared, RNA were formed. But
RNA were not the only sink of ATP
41Today conclusion The primary pump scenario
seems to follow the coevolutionist way
- 1/ In this global scenario the primary pump as
INITIAL and PERMANENT ENERGETIC SYSTEM is
proposed. This primary pump which shares its
energy to form NTP becomes the true driving force
of the emergent system. - 2/ Every day, the Primary pump build starting
dices (all NCA and all NTP), from which
respectively peptides and RNA could be formed. - 3/ The kinetic and thermodynamic laws, play with
theses dices, and improve the complexity of the
system by the technique "trial - error " due to
the permanent energy pressure. - 5/ A Â CONSEQUENCEÂ of such a dynamic system,
could be the emergence of homochirality L (by
chance) of peptides, and homochirality D (by
selection) of RNA. - 6/ The ways of  CONCENTRATION used are simple
and natural. -
- 7/ The PATHWAYSÂ used are short, thrifty in
material (everything is recycled) and time
saving. -
- 8/ The chemical reactions used are not robust,
some of them are assisted by catalysts present in
the environment, others are assisted by catalyst
emerging in the environment.
42Thanks to Albert EschenmoserThanks to you.