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Energy Flows, Metabolism and Translation
Energy Flows, Metabolism and Translation
Review
metabolites and biopolymers are generally not thermo- biological energy quantum, is needed to support life
dynamically stable [21] and, depending on the [23]. The relevance of a minimal quantum of free
conditions, can be converted into inorganic carbon, energy in biology has been debated and it has been
CH4 or CO2. As a result, driving the system towards proposed that in certain environments, this need can
equilibrium (for instance, by heating and then increas- be overcome by the cooperation of different forms of
ing the rates of irreversible processes) will not life based on complementary metabolisms [24]. But
ultimately give a complex mixture of organic molecules complex associations of different species based on
as products. Then, for both thermodynamic and different metabolisms are unlikely for emerging living
dynamic reasons, self-organization in biomolecular forms so that the existence of a minimum early bio-
systems requires a flow of energy [13,14]. In real irre- chemical energy quantum remains relevant in this
versible systems, energy flows from sub-systems having context [11]. In fact, the formation of one adenosine
high potential towards those of low potential and is triphosphate (ATP) molecule from a proton gradient
usually released as heat and radiated at low frequen- is in principle capable of taking advantage of a mini-
cies. As the life form that we know on the Earth is mum amount of energy corresponding to ca one-
mostly based on carbon chemistry and covalent third of the free energy content of ATP (i.e. ca
bonds, the amount of free energy needed to induce 20 kJ mol21 as more than three proton translocations
self-organization in chemical systems very likely are needed to build one ATP from adenosine di-
approaches the order of magnitude needed to destabi- phosphate (ADP) and inorganic phosphate). This
lize covalent bonds (representing at least a significant amount has been called a biological minimal quantum
fraction of the corresponding bonding free energy, e.g. of energy [23]; it is related to the requirement for a dis-
350 kJ mol21 for a C – C bond). This value is consistent crete minimum value in energy delivered by unit event
with the free energy potential of many high-energy bio- below which function is not possible. As far as early
chemical metabolites, 50– 70 kJ mol21 [11], meaning biochemical pathways are concerned, it is then reason-
that energy must have been brought about at a molecu- able to consider that the minimum amount of energy
lar scale by carriers capable of delivering quanta possible to integrate in the metabolism was much
of energy in the corresponding range to trigger the higher for less evolved organisms.
emergence of life (scheme 1).1
This free energy requirement is fulfilled by electro-
magnetic radiations with wavelengths close to the (b) Energy and carbon metabolism
range of visible light emitted by the Sun, a blackbody The indication that aldehydes are essential com-
heated at ca 6000 K. But, as previously mentioned ponents for the origin of life, unambiguous from
by others [17], a repeated absorption of photons by their role in the formose reaction [25] or in the for-
early biological systems seems impracticable, though mation of amino acids [26], can also be appreciated
more or less direct mechanisms can be responsible by an analysis of potential carbon metabolisms
for the photochemical generation of high-energy mole- [27,28]. Actually, the first attempt to introduce ther-
cules. As a matter of fact, ions, atoms or radicals can modynamic data in the discussion of possible early
be generated by photolysis, and recombination may carbon metabolisms has been made by Urey [29];
lead to activated molecules with a sufficient lifetime the corresponding data are quoted in the top left
(isolated in a free energy well by high enough kinetic part of table 1. The first conclusion inferred from
barriers) so that they can reach the ground or a those data is the instability of organics in the presence
location in which a more complex chemistry can take of oxygen (second column), which is the driving force
place [11]. Considering a range of lifetimes from 1 s for the respiratory metabolism of contemporary living
to 1 year leads to 85 – 120 kJ mol21 height for the kin- organisms. But, under anoxic condition, organic mol-
etic barrier, which also matches the above-deduced ecules become much less unstable. This is consistent
amount corresponding to a fraction of the free with the formation of organics in the reduced environ-
energy of a covalent bond. ments found in the interstellar medium, on other
bodies of the solar system (Titan) or even in hydro-
thermal systems present in mid-ocean ridges.
(a) The energy quality requirements for life Considering only one-carbon derivatives (CO2,
In any discussion of metabolisms available for the formic acid, formaldehyde, methanol and methane),
origin of life, it is essential to take into account that as in the original work of Urey, leads to the conclusion
a consequence of the second law is that free energy that methanogenesis is the easiest pathway for the
requirements cannot be fully understood at a macro- autotrophic generation of energy from inorganic
scopic—extensive—scale, but are associated with sources. Though it requires (directly or indirectly)
discrete chemical events occurring at a molecular the reduction of carbon dioxide in four steps, only
scale. As a matter of fact, providing a determined the last two are strongly exergonic, leaving unresolved
amount of energy either as a single energy carrier or the question of the formation of significant amounts of
as an identical quantity shared by a huge number of formaldehyde (and sugars). But expanding Urey’s
molecules is not equivalent. Moreover, this non-equiv- work by taking into account a more complex carbon
alence corresponds actually to an entropy production chemistry, including carbohydrate ( – CHOH – ),
that is precisely what is needed for compensating the aliphatic ( – CH2 – ) carbons, as well as graphite (inor-
loss of entropy associated with self-organization. It ganic carbon) (table 1), it appears that several other
has then been suggested that a minimal amount of processes are capable of providing energy to the
free energy per chemical event, called the minimum metabolism. A chemistry based on exergonic reactions
Phil. Trans. R. Soc. B (2011)
2952 R. Pascal & L. Boiteau Review. Energy flows
Table 1. Standard free energy of reactions (DrG8 in kJ mol21) of simple carbon derivatives susceptible to giving rise to early
metabolisms. Values in parentheses are published by Urey in 1952 [29].
can be built from carbohydrates (–CHOH–)n, whereas metabolites and free energy simultaneously. Before
inorganic carbon and hydrocarbons appear to constitute examining the possibility that the anabolism of auto-
thermodynamic ends (no exergonic reaction possible trophic early living organisms may also have coupled
except hydrogenation under strongly reducing condi- the thermodynamically unfavourable formation of
tions). Although they behave as energetic biomolecules important biochemical constituents with the con-
through respiratory metabolism, lipids made of aliphatic sumption of chemical energy sources, we can
hydrocarbons (–CH2 –)n are non-reactive end-products emphasize that this mere observation is consistent
in anoxic environments, which is consistent with the with the heterotrophic hypothesis [8,9]. The metab-
long-term stability of oil as well as coal in sediments. olism of early living entities could then have been
In addition to this nature of waste in an energy producing dependent on the transformation of high-energy
pathway, fatty acids present the strong advantage of self- organic molecules formed in the environment that
aggregating into lipid bilayers and constitute boundaries could be converted into metabolic end-products,
for early living entities [30,31], whereas carbonization or through processes able, at the same time, to provide
methanogenesis leads to products that are useless for the amount of energy needed for the metabolism.
living organisms. The potency of carbohydrate trans- The class of molecules formed in this way includes
formations has already been emphasized in the low-molecular weight reactants with double or triple
literature [24,27,28,32] and is clearly shown in table 1, bonds (formaldehyde, hydrogen cyanide, cyanic acid,
as well as the difficulty in their synthesis, strongly favour- urea, cyanamide, cyanoacetylene, etc.) that have
able starting from formaldehyde only. The need of been observed in the interstellar medium [35]. For
abundant abiotic sources of formaldehyde, or an equiv- instance, it has been demonstrated for years that mol-
alent capable of generating carbohydrates, may then be ecules of this kind can sustain a very rich prebiotic
considered as an energetic constraint on the origin of chemistry leading to the formation of building blocks
life, which is consistent with an atmospheric or extra- such as sugars [25] and amino acids [26]. But a
terrestrial delivery to the early Earth [33]. The fact much more sophisticated chemistry has been observed
that carbonyl carbon is reduced more easily than it from these intermediates: they are additionally able to
is formed from oxidized precursors (table 1) confirms activate phosphate [36], to phosphorylate nucleosides
that the formation of substantial amounts of formal- and activate nucleotides [37], or even to directly drive
dehyde and formose products by reduction of CO2 the formation of activated nucleotides [38]. Although,
requires very selective pathways that may be accessible they are found in interstellar media, it is unlikely that
to living organisms having developed very specific high-energy intermediates survived for long periods
catalysts, but may be difficult for early life in the environ- in the parent bodies of meteorites, so that their
ment of hydrothermal systems. This inadequacy is source has to be found close to the location where
also consistent with the well-known high kinetic reactiv- life emerged. Photolysis, lightning in reducing [39]
ity of the carbonyl group [34], which is the basis of or neutral atmospheres [20], or impacts [18] have
many organic synthesis routes but which also increases been proposed as likely processes for the formation
the susceptibility of this group to reducing agents of high-energy intermediates. Activated species built
including hydride. in this way result from the recombination of atoms,
ions and radicals transiently formed during events
occurring during short timescales followed by associat-
(c) Heterotrophy ive processes leading to metastable molecules [40]
The line of reasoning developed above suggests that with lifetimes sufficient to reach locations where self-
the most important organic constituents of the first organization can take place [11]. Ultraviolet light is
living entities were not formed from CO2 by a direct in principle sufficient to break most components of
reduction that could hardly provide biochemical the atmosphere although many reactions require
Phil. Trans. R. Soc. B (2011)
Review. Energy flows R. Pascal & L. Boiteau 2953
O R1 O
O– H3N
N N
H H
O R2
Kpep O R1 O
H
N
±H2O N N
H H
O R2
Scheme 3. Formation of a peptide bond from two peptide segments.
which can reach the diffusion limit in aqueous solution concentration from ATP unless a specific stabilization
[48] and are potentially capable of being concerted [49] is present as in the active site of aaRS. But the develop-
with electron transfers, which may be used to get energy ment of the translation machinery required the
from transient conformational states of membrane pro- availability of a source of energy capable of promoting
teins involved in the electron transfer cascade. A second the formation of aa-tRNA (or any of its precursors as
one may be related to the possibility of adaptation of a for example aminoacylated RNA mini-helices [56]).
wide range of redox potentials to the generation of a The fact that the free energy content of aa-AMP is far
single universal energy currency, namely ATP, which beyond that of ATP by as much as ca 37 kJ mol21 [55]
can then be used to bring about energy in a diversity suggests that ATP was not the early activating agent
of endergonic metabolic transformations. Both oxi- for amino acids [50]. A first explanation may be that
dative phosphorylation and photophosphorylation can ATP was settled as a universal currency, whereas
then be considered as unlikely systems to get energy tRNA amino-acid esters formed in a completely inde-
for primitive cells. pendent way and had already been selected as
intermediates. A pathway leading from ATP to aa-
tRNA via aa-AMP may have afterwards improved this
3. FREE ENERGY REQUIREMENTS FOR THE
system as a result of an unexpected event in evolution
EMERGENCE OF TRANSLATION
(exaptation), for example through catalytic promiscuity.
(a) Bioenergetics of peptide formation
Otherwise, the aaRS function may have emerged as
The formation of an amide bond from a peptide seg-
ribozymes in an RNA world with both an adenylation
ment with a free C-terminal carboxylic acid and the
N-terminal amine of a second one (scheme 3) is not domain capable of catalysing the formation of aa-
very far from thermodynamic equilibrium (Kpep AMP (the thermodynamically favourable reverse reac-
tion of pyrophosphate with adenylate to give ATP is
0.1 M21) at moderate pH [50].
not spontaneous in water) while stabilizing this inter-
Therefore, in water and under physiological con-
mediate and abilities in the aminoacylation reaction.
ditions, moderately activated esters such as aminoacyl-
Additionally, these catalysts should have to hinder
transfer RNAs (aa-tRNA, DG80 ¼ 235 kJ mol21 [51])
are fully adapted to peptide biosynthesis provided that the spontaneous reaction with carbon dioxide known
the aminolysis step (peptide bond formation) can take to consume aminoacyl adenylates and related mixed
anhydrides [57]. The alternative is to consider that
advantage of a catalyst capable of approximating reac-
adenylates (or similar mixed anhydrides formed from
tants, a role of entropy trap fulfilled by the ribosome
nucleotides) were formed abiotically and available for
[52]. But, aa-tRNAs are not the only intermediates of
early living organisms; in this view, the role of ATP in
protein biosynthesis as amino acids are universally acti-
adenylate formation must have emerged later [57].
vated as adenylates (aa-AMP) before aminoacylation of
tRNA. The development of aminoacyl-tRNA synthe- This view is supported by the fact that amino acid N-
tases (aaRS) was one of the first processes needed to carboxy anhydrides (NCA, scheme 4) can be abiotically
formed [50,58,59] and have been shown to spontaneou-
establish an RNA–protein world and the corresponding
sly react to give mixed anhydride with phosphate
genes are among the most conserved ones [53].
and nucleotides [60,61] with no need of enzyme at
neutral pH.
(b) A driving force for the evolution of It is important to notice that as soon as NCA are con-
translation? sidered as prebiotically relevant, peptides must have
Harry Noller [54] pointed out that finding a driving been formed spontaneously as NCA polymerize easily.
force supporting a scenario for the development of Living organisms depending only on RNA for genetic
translation in an RNA world is not easy. The emergence continuity and lacking encoded proteins (in agreement
of enzymes that stabilize the intermediates of the trans- with the RNA world hypothesis) would only have to
lation process is especially puzzling in this discussion as improve this process to take advantage of the formation
translation could not develop from pre-existing folded of non-coded random peptides, without the need of
proteins. For instance, understanding why adenylates specifically built machinery. It must be emphasized
have been selected as intermediates cannot be easily that, like aa-AMP, the large majority of carboxy-acti-
understood as the equilibrium for their formation vated amino acids, including thioesters, would have
from the ATP in solution is highly unfavourable ([aa- been converted into NCA (scheme 4) [62] because of
AMP][PPi]/[ATP][AA] ¼ 3.5 1027 [55]), and they the reaction of the amino group with CO2 as a result
would not be formed in significant equilibrium of the abundance of CO2 and bicarbonate on the early
Phil. Trans. R. Soc. B (2011)
Review. Energy flows R. Pascal & L. Boiteau 2955
O
OH
R1
NH2 activating agent
CO2
O O R1
CO2 H
X O fast N
R1 R1 N
H
NH2 N O O
H
O
OH
R1 CO2 fast slow
HN X
O O O
O P O R2
R1 OH
NH2
Scheme 4. NCA can be formed starting from sufficiently activated amino acid derivatives including mixed anhydrides with
phosphate and nucleotides. Peptide formation from a carboxy activated amino acid usually takes place through the interme-
diacy of NCA.
O B
O
O B O O
O NH2
O P
O B O O
O HO R1
NCA O OH
O OH O P O
O P O O
OH H 2N B
O O O
R1
O O
P
O O
Scheme 5. Intramolecular aminoacyl transfer from nucleotide phosphate mixed anhydrides occurring from mixed anhydrides
of 30 -phosphorylated nucleosides. Spontaneous aminoacylation of nucleotides by NCA is taking place as well as cyclization.
Earth [63]. Moreover, additional experiments [57] have peptide precursors is to consider that their initial role
shown that aa-AMP like other amino acid phosphate- lay in the conversion of the free energy available
mixed anhydrides do not give rise to efficient peptide from amino acid chemistry as NCA into a form
chain formation except in the presence of carbon diox- useful for nucleic acid chemistry. The spontaneous
ide demonstrating that peptides are mainly formed reactions of NCA in aqueous solution leading both
through the intermediacy of NCA, which removes to phosphate-mixed anhydride and aminoacylated
any evolutionary advantage of adenylates as peptide esters (scheme 5) constitute a chemical substratum
precursors. Actually, living organisms have probably from which an early translation apparatus may have
developed mechanisms to avoid the formation of NCA evolved through selective recognition of amino acid
in the cell in order to prevent uncontrolled aminoacyla- side-chains by RNA and ribosomal activity may have
tion of proteins so that NCA have presently no identified developed. Independent of this process, any activated
role in cells. Finally, NCA have also demonstrated form of nucleotides (mixed anhydrides, pyrophos-
abilities in aminoacylating nucleotides by reaction with phates, or triphosphates) may have been useful for
a 30 -phosphorylated end [60] (scheme 5). RNA replication and polymerization, providing a selec-
tive advantage to the NCA-driven pathway in an RNA
world. Afterwards, the selective advantage of translated
4. A SCENARIO FOR THE EMERGENCE proteins may have driven evolution, and the develop-
OF BOTH AMINOACYLATION AND ADENOSINE ment of protein enzymes capable of sequestrating and
TRIPHOSPHATE stabilizing adenylates would have been a key impro-
An appealing scenario to explain the selection of aden- vement as well as their interconversion into more
ylates by evolution in spite of their ineffectiveness as stable phosphoanhydrides having an increased lifetime
Phil. Trans. R. Soc. B (2011)
2956 R. Pascal & L. Boiteau Review. Energy flows
RNA world:
evolution
ribozyme-mediated mixed anhydride stabilization.
Catalysis of phosphoanhydride formation.
Selectivity in peptide formation.
PPi RNA3
ppp-RNA1 aa-p-RNA1 aa-O 2¢,3¢
ribozyme primitive ribosomal activity
RNA–protein world:
evolution
Scheme 6. A scenario for the evolution of amino acid activation pathway starting from an NCA-driven nucleotide activation
towards an ATP-driven protein formation.
inducing the possibility of free energy exchanges high-energy mixed anhydrides were involved early,
between different metabolic pathways (scheme 6). which suggests that the driving force for the emergence
of translation was the delivery of energy from amino
acid chemistry to nucleotide chemistry. This role of
5. CONCLUSIONS amino acid derivatives cannot be deduced from present
Considering thermodynamics constraints leads to a biochemical pathways but provides an explanation both
better understanding of the driving forces by which of the emergence of ATP as a universal biochemical
life may have arisen or evolved during its early steps. currency and of translation.
The most important one is the need for an energy This work was supported by EPOV interdisciplinary
flow continuously compensating for the loss of entropy programme of the CNRS and COST action CM0703.
associated with self-organization, which requires the
input of low-entropy energy sources (light for instance)
and high-entropy energy (heat or radiation at long NOTE
wavelengths) flowing out of the system. Natural selec- 1
The occurrence of very specific enzyme catalysts capable of enhan-
tion may arise in those systems as soon as structures cing reaction rates with proficiencies that can exceed factors of 1019
that are capable of self-reproduction emerge, so that [22] by stabilizing transition states and unstable intermediates con-
the ones that replicate faster from precursors and ceals the need of such amounts of free energy in contemporary
energy tend to predominate owing to their kinetic biochemistry, which was not the case in prebiotic chemical systems
as catalytic efficiencies were probably limited.
behaviour, and as soon as their variability is not limited.
The consequences of the need for an energy flow have
been discussed with respect to carbon metabolism
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