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Nov 15, 2013 (3 years and 8 months ago)

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Darwin,
Chemistry and
the Origin of
Life

Andy Pratt

Department of Chemistry



Darwinian natural selection and the
generation of complexity


Cells as historical artifacts


Molecular fossils


A model for the origin of life based on
molecular selection


Some simple experiments involving
biomimetic phosphate chemistry

OVERVIEW


http://itech.dickinson.edu/chemistry

The complex
products of
natural selection

Darwin, Chemistry and the Origin of Life

TAKING DARWIN SERIOUSLY

Cells are archaeological sites

The fossils are chemical:

metabolites and metabolic processes

http://itech.dickinson.edu/chemistry

The complex
products of
natural selection

http://itech.dickinson.edu/chemistry

The complex
products of
natural selection

Darwin, Chemistry and the Origin of Life

Genomes & Chinese whispers:

The insights of Pauling and Zuckerkandl

“Jack, the next card wins”

“Jack, the next car wins”

“Jack, the neck scar twin”

“Jack, the next Darwin?”

Darwin, Chemistry and the Origin of Life



Darwinian natural selection provides a
mechanism for generating complexity


Inspiration to chemical creativity

TAKING DARWIN SERIOUSLY



But how did something as complex as a
cell arise?


When did chemistry become biology?


The role of the selection of chemical
process in the origin of life, two examples:


Catalysis and Solubility

ORIGINS OF METABOLISM

Time (Mya)

0

1000

4000

2000

3000

Features


Anaerobic environment


Rich in Iron and Sulfur


Constant input of redox energy


Carbon fixed into organic molecules


Compartments for evolution


A contemporary fit



Hydrothermal vent systems


Mike Russell and others

HYDROTHERMAL VENT SYSTEMS

http://uwnews.washington.edu/

Anaerobic carbon fixation

Wood
-
Ljungdahl pathway
-

ACS / CODH

Likely original anaerobic carbon fixation

Wood
-
Ljungdahl pathway
-

ACS / CODH

Likely original anaerobic carbon fixation

Hegg,
Acc. Chem. Res
. 2004
, 37
, 775

ACS

CODH

Biogeochemistry and element fixation

BIOMIMETIC CARBON FIXATION

Carbon fixation:

the reductive acetyl CoA pathway

CH
3
-
B
12

+ CO

+ HSCoA

CH
3
COSCoA

CO dehydrogenase

Acetyl CoA synthase

CH
3
SH

+ CO

CH
3
COSCH
3

+

CH
3
COOH

NiS, FeS,

H
2
O,100
o
C

Huber & Wächtershäuser,
Science
, 1997,
276
, 245

Seravalli, Kumar,


& Ragsdale

Biochemistry,

2002,
41
, 1807

S
F
e
S
F
e
F
e
S
X
F
e
S
N
i
HYDROTHERMAL VENT BIOGEOCHEMISTRY?

Russell & Martin,

TiBS,
2004
,
29
,
358

BIOGEOCHEMISTRY
EMERGES?


BIOMIMETIC Fe(Ni)S CATALYSIS:


Huber & Wächtershäuser
,
Science
, 1997,
276
, 245


Cody
et al
.,
Science
, 2000,

289,
1337


D
ö
rr
et al
, Ang. Chem. Int. Edn. Engl
.
2003,
42
, 1540


W
ä
chtersh
ä
user etc
Tet Lett
.,
2003
,

44
, 1695


Minerals
to
Enzymes

IN PRINCIPLE, MIKE RUSSELL’S
MOUND PROVIDES:



On going chemical input and redox gradient for
energy and metabolite flux



Catalytic surfaces to mediate electron
-
transfer and
other protobiochemical processes



Compartmentalisation in microporous material



Concentration of proto
-
metabolites via surface
adsorption

Surfaces and solutions?

Evolution of chemistry of metabolism?

IRON SULFIDE MICROCOMPARTMENTS

Russell & Martin,
Phil Trans RS (B),
2003
,
358
,
59

“The most important thing in life is death”
-

Monod

FEATURES OF LIFE


Ongoing redox energy input


Occurs in discrete aqueous environments (cells)


Darwinian selection

KEY EARLY DISCOVERIES OF METABOLISM


Reductive fixation of carbon generates BOTH
organic molecules AND dehydrating power in water


Selective production of condensation polymers
which are
kinetically stable
, but
thermodynamically
unstable

PROTEINS + WATER

DNA/RNA + WATER

POLYSACCHARIDES + WATER

AMINO ACIDS

NUCLEOTIDES

SUGARS

“The most important thing in life is death”
-

Monod

FEATURES OF LIFE

PROTEINS + WATER

DNA/RNA + WATER

POLYSACCHARIDES + WATER

AMINO ACIDS

NUCLEOTIDES

SUGARS

ATP

KINETIC vs THERMODYNAMIC STABILITY

Molecular evolution:

Molecules survive if formed faster than they degrade

Kinetic stability + catalysis

ATP as the harnessing of dehydrating power

PROTEINS + WATER

DNA/RNA + WATER

POLYSACCHARIDES + WATER

AMINO ACIDS

NUCLEOTIDES

SUGARS

SURFACES: CONCENTRATION & CATALYSIS
POLYPHOSPHATE ACCUMULATION

Susie Meade
& Ico de Zwart


Phosphate species concentrate via precipitation


Mineral catalysis of biomimetic phosphoryl transfer


Surface accumulation of polyphosphates

COMPETITIVE PHOSPHATE SURFACE BINDING

Glycerol
-
2
-
phosphate vs Pyrophosphate

Glycerol
-
2
-
phosphate vs Pyrophosphate

COMPETITIVE PHOSPHATE SURFACE BINDING

Glycerol
-
2
-
phosphate vs Pyrophosphate

Experiments repeated with other phosphate species


e.g.
Glycerol
-
2
-
phosphate vs Phosphate


Adenosine
-
5’
-
monophosphate (AMP)

vs Pyrophosphate

COMPETITIVE PHOSPHATE SURFACE BINDING


SELECTIVE “METABOLITE” RELEASE


Selection for organic phosphates in solution


Homeostatic backdrop of sparingly soluble phosphates

COMPETITIVE PHOSPHATE SURFACE BINDING

EVOLVING SOLUTION METABOLISM



Mineral surface chemistry can proliferate until
the local redox gradient is dissipated


Protometabolism will ‘die’ unless it becomes
mobile


Selection of solubilized autocatalytic networks
which colonize new compartments


ORIGIN OF MOLECULAR EVOLUTION AND
METABOLISM

EVOLVING SELECTION


Selection processes:


Molecules made faster than they are lost,
e.g.

by decomposition or dilution


Catalytic chemistry is reproduced in a new
compartment before redox gradient exhausted


Selection favours:


Increased autocatalytic efficiency


Manipulation of solubility equilibria


Dynamic solubility equilibria allows
reproduction and homeostasis


Encapsulation of cohorts of catalytic centres

P
i

Fe
2+

Fe
3+

Fe
2+

Fe
2+

P
i

P
i

Fe
3+

P
i

EVOLVING TO AN INTEGRATED
SOLUTION METABOLISM


Sparingly soluble salts


Dynamic ion exchange


Homeostasis

Control of solubility via:


Redox


Organic ligands for phosphate (
e.g.

organic
derivatives) and Fe
2+
(peptides)

Competitive equilibria (
e.g.

S
2
-
)


Feedback loops


Micellar encapsulation

S
2
-

S
2
-

S
2
-

S
2
-

P
i

Fe
2+

S
2
-

Fe
2+

Fe
2+

Fe
2+

Fe
2+

P
i

P
i

S
2
-

S
2
-

S
2
-

S
2
-

S
2
-

Many thanks to


Ico de Zwart

Susie Meade

Marie Squire

Ward Robinson

Mike Russell
(NASA)

and

Evolving catalysis by the mineral surface


FeS is deposited as Mackinawite

Figure: Russell & Hall,
GSA Memoir

198

(2006), 1

Mackinawite, Greigite and the

Origin of Molecular evolution?

Fig: Rickard & Luther,
Chemical Reviews
, 2007,
107
, 514
-
62

Electron
-
transfer
co
-
factor

Mackinawite & Greigite

Fig: Rickard & Luther,
Chemical Reviews
, 2007,
107
, 514
-
62

Greigite

Fig: Rickard & Luther,
Chemical Reviews
, 2007,
107
, 514
-
62

Fe
II/III

Fe
II

Mackinawite, Greigite and the

Origin of Molecular evolution?

Fe
2+
(aq)

S
2
-
(aq)

Mackinawite (FeS)

Pyruvate

Amino acids

Peptides

Organic ligands

Greigite (Fe
3
S
4
)

CO
2

CH
3
COSR

AcP
i

PP
i

P
i

P
i

THE INVENTION OF METABOLISM


Electron transfer slow without catalysis

Fe
2+


S
2
-

CO
2

Organics

+ Fe
3+


Iron sulfides provide generic catalysis


Ligands & Fe
3+

provide feedback loop


Reproduction with variation and selection


CO
2
: weak electron acceptor


FeS: electron donor

Protein FeS
Clusters

Rao & Holm

Chem. Rev.


2004,
104
, 527

Complexity of Life:
a

product of



Reproduction



Variation



Selection

“Nothing in Biology Makes Sense

Except in the Light of Evolution”

Theodore Dobhzhansky


Life is a process not an entity


Cells are historical documents

CHEMICAL FUNDAMENTALS OF LIFE


Thermochemical gradient


Kinetic barrier to dissipation


CATALYSIS

Energy


Feedback loops


AUTOCATALYSIS


SELECTION

for enhanced catalysis


EVOLUTION

of autocatalytic loops


REPLICATION

of autocatalysis with
VARIATION

and
SELECTION

LIFE

is a
PROCESS
, not an
ENTITY

Based on
REPLICATION

of
METABOLIC

INFORMATION

with
VARIATION

&
SELECTION

CHEMICAL FUNDAMENTALS OF LIFE

Energy


METABOLIC EVOLUTION

The greatest improvement in the
productive powers of labour, and the
greater part of the skill, dexterity,
and judgment with which it is any
where directed, or applied, seem to
have been the effects of the division
of labour.


An Inquiry into the Nature and Causes of the
Wealth of Nations
,
Adam Smith

CHEMICAL FUNDAMENTALS OF LIFE

Energy


METABOLIC EVOLUTION


At start: inefficient
GENERIC

catalysts


REPLICATION

with
VARIATION

and
SELECTION



diversified, more
effective catalysts


Need
LOCALIZATION
(compartments)

Ongoing & later issues:


Evolving
COMPLEXITY

of interlocked
autocatalytic cycles


Benefit of
REPLICATION FIDELITY



HOMEOSTASIS

Greigite mimics diverse Fe
4
S
4

clusters

Feedback loop:

C
-
fixation induces mineral change;

creates better catalyst; increases C
-
fixation rate