The Origin of Life
What is life?
“Matter with delusions of self-importance” – Schrodinger
Anthropocentric view
Defining it as a “congruence” between abiotic chemistry and biochemistry
Must fulfill the requirements of:
Driving Force – a method of capturing carbon
Metabolism through catalysis
Method of heredity and replication
Integrity – establish cell boundaries
Excretion – waste disposal
A way of storing and releasing energy
Examine a number of theories and their strength by how many of the requirements
they fulfil – though the strongest theory to date is that life originated from alkaline
hydrothermal vents
Initial Theories
Primordial Soup
Proposed by JBS Haldane (1929) – UV radiation supplied energy to synthesise methane,
ammonia and hydrogen sulphide into organic macromolecules, which were react further
to produce viral particles then the first cells, which were heterotrophic fermenters. It
also implied that the RNA was the inventor of the basic chemistry of life.
Stanley Miller’s famous laboratory experiment in 1953 lent support to synthesis of
organic from inorganic
But there are many problems with this theory
Polymerisation of nucleotides required both energy and high concentration – neither
the soup seemed to possess
Primordial soup was stuck in thermodynamic equilibrium – had no external source of
energy to drive further chemical reactions
UV radiation was both creative and destructive
Incompatibility with current biochemistry – most reactions in cells are driven by
metalloproteins – enzymes with mineral clusters or metal centres (Ni, S, Fe)
These mineral clusters have striking similarity to minerals such as greigite – implying
more ancient roots than RNA
Fermentation is also not a primitive process – a complex disproportionation, most simple
glycolytic fermentation requires the combined use of 12 enzymes by the Embden –
Meyerhoff pathway
Could not have evolved as a functional unit without external energy in primordial oceans
Phylogenetics – there are few “pure fermenters” in early branches of tree
Most fermenters retain some component of chemiosmosis – notably proton-motive
ATPases
Archaea and Bacteria have different gene sequences and enzyme crystal structures
involved in fermentation – implied that fermentation has evolved twice – LUCA was not
,a fermenter
Wachterhauser’s “black smokers” – 1970’s
To challenge the soup theory – suggested that life originated from volcanic deep sea
vents
Though posed more problems than soup theory: was not in equilibrium with sea water
(1200oC), though too hot (3500oC), low in H2, too acidic (pH 1-2), life depending on
reaction of H2S or H2 – all O2 derived from photosynthesis, too much sulphur, 2-D
chemistry
Breakthrough: “Lost City” 2000
Alkaline hydrothermal vents – formed by serpentinitsation – a geochemical process
where olivine is hydroxylated to serpentine
Conditions – 150 -200oC, pH 9 – 11, rich in H2 (mM), oceans provided CO2 (3.8 Gya,
concentration 1000 fold higher than they are today) delicate porous structure
composed of micropores, feathery aragonite (CaCO3) walls allow thermal currents to
circulate, contained methane, acetate, formate
How requirements are fulfilled
1) Carbon Capture (Fixation – convert to organic compounds) and Energy
Metabolism
LUCA was not a fermenter – chemiosmosis
probably universal and fundamental
(phylogeny – spread out in tree of life)
Vents have natural proton gradients –
similar to that between biological
membranes (200mV) – higher H+ outside
due to acidic oceans (high in CO2)
Proton gradients are ubiquitous – needed
for photosynthesis and oxidative
phosphorylation
Proton gradients can drive carbon and
energy metabolism in vents – could be enough to drive beginnings of anabolic
biochemistry, leading to RNA world in the vent
- Beginnings of natural selection in vent systems could ultimately lead from an
RNA world to DNA, proteins and natural selection
- Can lead to formation of “protocells”
Origin of life likely sparked from the direct hydrogenation of CO 2, forming methane
or acetate possibly through the acetyl coA pathway
, All modern autotrophs fix CO2 using
hydrogen directly/indirectly (water/ e-
donors H2S)
Synthesis of cell biomass is exergonic in
alkaline hydrothermal conditions (temp. etc.)
– nucleotides, amines fatty acids etc,
(Amend and McCollom, 2009) but reduction
of carbon dioxide by hydrogen has a
significant endothermic barrier (despite
being an exothermic reaction)
BUT methanogens and acetogens can do this!
- Only 5 known primary pathways of carbon
fixation/assimilation – all of them use ATP
(except the acetyl coA pathway (Wood-
Ljundahl) – pathway of direct reaction of
hydrogen with CO2 (Electron transfer Reduction of CO2 and H2 to methane or acetate
from hydrogen to carbon dioxide) is exergonic overall but requires overcoming a
thermondynamic barrier.
- This pathway is found in ancient
Achieved by reducing low-potential ferredoxins
prokaryotes – methanogens (archaea) with help of flavin-based bifurcation
and acetogens (bacteria) + possibly LUCA Flavin-based electron bifurcation couples
- In both methanogens and acetogens, endergonic reduction of ferredoxin using
electrons derived from H2 to the exergonic
steps of carbon reduction catalysed by
reduction of high potential acceptor
metalloenzymes with mineral clusters The membrane potential generated is used for
containing Fe, S, Ni at centres ATP synthesis (via ATP synthase) and carbon
- Most species have a single ion coupling assimilation.
site and lack quinones, cytochromes
- Electron flux to methane and acetate is used purely to generate methane
potential, which is harnessed for both carbon assimilation, ATP synthesis via
acetyl coA pathway
- As alkaline vents already possess ion gradients across thin organic walls –
methanogenesis and acetogenesis in fact reconstitute what alkaline vents
provide for free
Many methanogens grow from mildly exergonic reaction = 4H2 + CO2 CH4 +
2H2O (generate ATP via chemiosmotic coupling)
- Make ~ 1mol methane per 1.3g of cells (Thauer et al., 2008) – flux of hydrogen
and carbon dioxide to the products that sustains cells is about 40x greater by
mass than yield
- Methanogens turn over ~50-55 billion ATP molecules per division, 50-100x each
cell’s mass (figures for cells with evolutionarily refined enzymes)
- Before advent of enzymes, flux through life’s initial main energy-releasing
reaction by necessity was less specifically channelled toward cell material, for
RNA-like bases to form spontaneously via prebiotic chemistry – biochemistry
required much more carbon energy flux than modern cells
Formation of methane/acetate releases energy (Releases energy while generating
What is life?
“Matter with delusions of self-importance” – Schrodinger
Anthropocentric view
Defining it as a “congruence” between abiotic chemistry and biochemistry
Must fulfill the requirements of:
Driving Force – a method of capturing carbon
Metabolism through catalysis
Method of heredity and replication
Integrity – establish cell boundaries
Excretion – waste disposal
A way of storing and releasing energy
Examine a number of theories and their strength by how many of the requirements
they fulfil – though the strongest theory to date is that life originated from alkaline
hydrothermal vents
Initial Theories
Primordial Soup
Proposed by JBS Haldane (1929) – UV radiation supplied energy to synthesise methane,
ammonia and hydrogen sulphide into organic macromolecules, which were react further
to produce viral particles then the first cells, which were heterotrophic fermenters. It
also implied that the RNA was the inventor of the basic chemistry of life.
Stanley Miller’s famous laboratory experiment in 1953 lent support to synthesis of
organic from inorganic
But there are many problems with this theory
Polymerisation of nucleotides required both energy and high concentration – neither
the soup seemed to possess
Primordial soup was stuck in thermodynamic equilibrium – had no external source of
energy to drive further chemical reactions
UV radiation was both creative and destructive
Incompatibility with current biochemistry – most reactions in cells are driven by
metalloproteins – enzymes with mineral clusters or metal centres (Ni, S, Fe)
These mineral clusters have striking similarity to minerals such as greigite – implying
more ancient roots than RNA
Fermentation is also not a primitive process – a complex disproportionation, most simple
glycolytic fermentation requires the combined use of 12 enzymes by the Embden –
Meyerhoff pathway
Could not have evolved as a functional unit without external energy in primordial oceans
Phylogenetics – there are few “pure fermenters” in early branches of tree
Most fermenters retain some component of chemiosmosis – notably proton-motive
ATPases
Archaea and Bacteria have different gene sequences and enzyme crystal structures
involved in fermentation – implied that fermentation has evolved twice – LUCA was not
,a fermenter
Wachterhauser’s “black smokers” – 1970’s
To challenge the soup theory – suggested that life originated from volcanic deep sea
vents
Though posed more problems than soup theory: was not in equilibrium with sea water
(1200oC), though too hot (3500oC), low in H2, too acidic (pH 1-2), life depending on
reaction of H2S or H2 – all O2 derived from photosynthesis, too much sulphur, 2-D
chemistry
Breakthrough: “Lost City” 2000
Alkaline hydrothermal vents – formed by serpentinitsation – a geochemical process
where olivine is hydroxylated to serpentine
Conditions – 150 -200oC, pH 9 – 11, rich in H2 (mM), oceans provided CO2 (3.8 Gya,
concentration 1000 fold higher than they are today) delicate porous structure
composed of micropores, feathery aragonite (CaCO3) walls allow thermal currents to
circulate, contained methane, acetate, formate
How requirements are fulfilled
1) Carbon Capture (Fixation – convert to organic compounds) and Energy
Metabolism
LUCA was not a fermenter – chemiosmosis
probably universal and fundamental
(phylogeny – spread out in tree of life)
Vents have natural proton gradients –
similar to that between biological
membranes (200mV) – higher H+ outside
due to acidic oceans (high in CO2)
Proton gradients are ubiquitous – needed
for photosynthesis and oxidative
phosphorylation
Proton gradients can drive carbon and
energy metabolism in vents – could be enough to drive beginnings of anabolic
biochemistry, leading to RNA world in the vent
- Beginnings of natural selection in vent systems could ultimately lead from an
RNA world to DNA, proteins and natural selection
- Can lead to formation of “protocells”
Origin of life likely sparked from the direct hydrogenation of CO 2, forming methane
or acetate possibly through the acetyl coA pathway
, All modern autotrophs fix CO2 using
hydrogen directly/indirectly (water/ e-
donors H2S)
Synthesis of cell biomass is exergonic in
alkaline hydrothermal conditions (temp. etc.)
– nucleotides, amines fatty acids etc,
(Amend and McCollom, 2009) but reduction
of carbon dioxide by hydrogen has a
significant endothermic barrier (despite
being an exothermic reaction)
BUT methanogens and acetogens can do this!
- Only 5 known primary pathways of carbon
fixation/assimilation – all of them use ATP
(except the acetyl coA pathway (Wood-
Ljundahl) – pathway of direct reaction of
hydrogen with CO2 (Electron transfer Reduction of CO2 and H2 to methane or acetate
from hydrogen to carbon dioxide) is exergonic overall but requires overcoming a
thermondynamic barrier.
- This pathway is found in ancient
Achieved by reducing low-potential ferredoxins
prokaryotes – methanogens (archaea) with help of flavin-based bifurcation
and acetogens (bacteria) + possibly LUCA Flavin-based electron bifurcation couples
- In both methanogens and acetogens, endergonic reduction of ferredoxin using
electrons derived from H2 to the exergonic
steps of carbon reduction catalysed by
reduction of high potential acceptor
metalloenzymes with mineral clusters The membrane potential generated is used for
containing Fe, S, Ni at centres ATP synthesis (via ATP synthase) and carbon
- Most species have a single ion coupling assimilation.
site and lack quinones, cytochromes
- Electron flux to methane and acetate is used purely to generate methane
potential, which is harnessed for both carbon assimilation, ATP synthesis via
acetyl coA pathway
- As alkaline vents already possess ion gradients across thin organic walls –
methanogenesis and acetogenesis in fact reconstitute what alkaline vents
provide for free
Many methanogens grow from mildly exergonic reaction = 4H2 + CO2 CH4 +
2H2O (generate ATP via chemiosmotic coupling)
- Make ~ 1mol methane per 1.3g of cells (Thauer et al., 2008) – flux of hydrogen
and carbon dioxide to the products that sustains cells is about 40x greater by
mass than yield
- Methanogens turn over ~50-55 billion ATP molecules per division, 50-100x each
cell’s mass (figures for cells with evolutionarily refined enzymes)
- Before advent of enzymes, flux through life’s initial main energy-releasing
reaction by necessity was less specifically channelled toward cell material, for
RNA-like bases to form spontaneously via prebiotic chemistry – biochemistry
required much more carbon energy flux than modern cells
Formation of methane/acetate releases energy (Releases energy while generating
