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PREBIOTIC CHEMISTRY
Biophysic course WS 2006, Rome.
1.Science confronting the origin of life on Earth.
1.2.: Prebiotic chemistry
SOME MAIN ASSUMPTIONS OF PRESENT
DAY RESEARCH ON THE ORIGIN OF LIFE
1. Life originated from inanimate matter as a spontaneous and continous increase of molecular complexity. LIFE
Chemical continuity principle - no transcendental
principle.
2. The chemical process(es) to transition to life can be
reproduced in the laboratory with the presently
available chemical techniques and chemicals.
inanimate
3. And this can be implemented in a reasonable
matter
(hours or max. days) experimental time span once you know the right combination of prebiotic compounds
and theconditions.
4. Since there is no documentation on how things really
happened, there is no obligatory research pathway.
Lightnings_SV3.avi
Water
vapor
Electrodes
discharge sparks
("lightning
simulation")
CH4
H2O
NH3
H2
Molecule
Formic acid
Glycine
Alanine
Lactic acid
Acetic acid
Condenser
Stopcocks
for testing
of samples
Sarcosine
Out
Succinic acid
Urea
Cold water
inlet
Heated water
("ocean")
Condensed liquid
with complex
molecules
Glutamic acid
Aspartic acid
1
10
100 1000
Yield in micromoles
Chemistry of HCN, precursor of purines
Ferris & Orgel 1996, 1967
2 HCN
CN
HN
HCN
NC
NH2
NC
NC
NH2
NC
NH2
HCN
Synthesis of purines
Oró, 1960
CN
H2N
H2N
NC
H2N
CN
diaminomaleonitrile
N
adenine
H2N
HCN
N
H
N
N
H
diaminopurin
O
N
HN
N
-
NCO
(CN)2
O
N
N
H2N
N
H2N
N
H
NH2
N
H
H2O
(CN)2
NH2
N
N
4-amino-imidazole-5-carbonitrile
HCN
N
O
N
H
hypoxantine
N
HN
H2N
O
N
guanine
N
H
N
HN
H2N
NH
N
H
xanthine
Synthesis of sugar phosphates
Eschenmoser 1988, 1990
NH2
CN
hv
H
N
CN
H3PO4 / H2O
65° C
ca. 50%
O
O P O
OH
+
NH3
OH
OH2
CN
80° C
ca.45%
2-
O3PO
OH
Activation of aminoacids by the N-carboxyanhydride
and their condensation.
Why do aminoacid form in Miller‘
experiment?
Why this...and not that?....
They form because there are the most
stable of the possible compounds- due
to processes under thermodynamic
control
OTHER SOURCES OF ORGANICS
a considerable enrichment of prebiotic moieties may
have come from submarine vents and other
hydrothermal sources (see for example Miller and
Bada, 1988; Holm and Andersson, in Brack, 1998;
Stetter, in Brack, 1998).
One should start from the 1979 discovery of deep-sea
vents with black smokers which are associated with
an extraordinary abundance of the most
phylogenetically primitive organisms on Earth.
OTHER SURCES OF ORGANICS
The present amount of space dust falling on Earth
amounts to ca. 40,000 tons per year, which sounds
impressive. This, spread over all Earth surface,
corresponds to only 8 × 10-9 g/cm2 per year
(Love and Brownlee, 1993), and the percentage of organics
may be tiny (Miller, 1998; Oro et al., 2002).
On the other hand, accumulation over billions of
years can bring to a considerable amount of matter.
OTHER SOURCES OF ORGANICS
aminoacids are present in meteorites (Epstein et al., 1987;
Pizzarello et al., 1994; Pizzarello and Cronin, 2000;
Pizzarello and Weber, 2004). In this regard, of particular
interest is the report about -methyl aminoacids, which
have been found in the L enantiomeric excess in
Murchnson and Murray meteorites (Cronin and
Pizzarello, 1997).
These compounds are particularly resistant
to racemization,
Major Sources (in kg/yr) of Prebiotic Organic Compounds in the Early Earth (from Oro et
al., 2002)
Terrestrial Sources
UV Photolysis1
Electric Discharge2
Shocks from
impacts3
Hydrothermal
Vents4
kg/yr*
3 × 108
3 × 107
4 × 102
1 × 108
Extraterrestrial
Sources5
IDP’s
Comets
Total
2 × 108
1 × 1011
1011
Assumes intermediate atmosphere, defined as [H2] /
[CO2] = 0.1.
·
IDP= interplanetary dust.
1
Synthesis of the Miller-Urey type.
2
Such as that caused by lightning interacting with a
volcanic discharge.
3
An
estimate
for
compounds
created
from
the
interaction between infalling objects and the Earth’s
atmosphere.
4
Based on present-day estimates for total organic
matter in hydrothermal vent effluent.
5
Conservative estimate based on possible cumulative input calculated assuming
flux of 1022 kg of cometary material during first Ga (109 years) of Earth’s history. If
comets contain on the order of 15 wt% organic material, and if ≈ 10% of this
material survives, it will comprise approximately 1011 kg yr-1 average flux via
comets during the first 109 years.
·
PREBIOTIC CHEMISTRY HAS
REACHED
CONSIDERABLE SUCCESS ..... BUT
Even if the chemist would have
access to all prebiotic bio-monomers
he would NOT have
the solution to the origin of life
THE CORE OF THE PROBLEM:
LIFE AS WE KNOW IT IS DETERMINED BY
SPECIFIC MACROMOLECULAR SEQUENCES
LIKE NUCLEIC ACIDS AND PROTEINS
CO
NH
C H CO
NH
CH
R1
X
CO
NH
CH
R2
Y
Z
R3
P
Y
O
P
O
O
Rib
Base1
O
P
O
Rib
Base2
O
P
O
Rib
Base3
SCHEMATIC REPRESENTATION OF THE
THREE-DIMENSIONAL STRUCTURE OF I gG
antigenbinding
site
Fab-unit
Fc-unit
Fab-unit
antigenbinding
site
carbohydrate
residue
Each amino acid residue is represented by a small circle. The H chains are red
and the L chains blue. A carbohydrate residue is yellow.
E. W. Silverton, et al. Proc. Nat. Acad. Sci. 74
(1977); p. 142.
A-DNA
B-DNA
Z-DNA
The macromolecules of life
are not there
because they are more stable
than their billions of constitutional isomers
They–and/or their precursorsare the products of statistics and contingency
in the polymerization processes
and
evolution
On the importance of being a copolymer
(
Calculate:
CO
CH
)n
NH
Ri
How many different macromolecules
can you build, when
n = 60 and i = 1 - 20
60
20 x 20 x 20 x .....
evolution
N = 2060
~
1070
!!!
energetics
In nature there are only 1012 - 1014 proteins
space of the proteins
present in nature 10 10
(radius ca. 1 atom)
radius of the
universe
space of all
possible proteins
10130
(20100)
Cast the dice again and........
And you will get a different set
of macromolecules
that do not necessarily support life
QUESTIONS:
HOW AND WHY „OUR“ PROTEINS
HAVE BEEN SELECTED?
ARE THE PROTEINS OF LIFE THE ONLY
ONES THAT COULD BE FORMEDAND GAVE ORIGIN
TO LIFE BY A DETERMINISTIC
(OBLIGATORY)
SERIES OF EVENTS
OR
ARE THEY THE PRODUCT OF
CONTINGENCY(CHANCE)
AND LIFE IS ALSO A PRODUCT OF
CONTINGENCY?
PROJECT RANDOM POLYPEPTIDES:
MAKE A VASTE LIBRARY OF RANDOM
DE NOVO PROTEINS
ASK THE QUESTION: HOW MANY OF
THEM WILL BE
FOLDED?
Folding is the prerequisiste for any
intelligent function by proteins
PHAGEMID VECTOR SYSTEM
IN PHAGE DISPLAY
Helper Phage
Modified Phage
gene 3
fusion protein
Plasmidic
DNA
ss DNA
gene 3
fusion
STRATEGY FOR THE ISOLATION
OF FOLDED PEPTIDES
mAB
TAG
Thrombin Cleavage Site
Random Peptide (50mer)
pIII
Phage
ANALYSIS OF THE PEPTIDE
PHAGE LIBRARY
Library
1.98 x 109 clones
180 clones were randomly selected
44% correct insert (79 clones)
73 clones tested for thrombin stability
% of the73 clones of the phage library
DISTRIBUTION OF THE PEPTIDE
LIBRARY WITH RESPECT TO
THROMBIN DIGESTION
30.00
“Stable”
25.00
“Unstable”
20.00
15.00
10.00
5.00
0.00
0-10
10-20
20-30
30-40
40-50
50-60
60-70
% digestion categories
70-80
80-90
90-100