chemistry and evolution at the origin of life › ~pks › presentation › madrid.pdf · chemistry...
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![Page 1: Chemistry and Evolution at the Origin of Life › ~pks › Presentation › madrid.pdf · Chemistry and Evolution at the Origin of Life Visions and Reality Peter Schuster Institut](https://reader033.vdocument.in/reader033/viewer/2022042404/5f1a8468db21903bf312379d/html5/thumbnails/1.jpg)
Chemistry and Evolution at the Origin of Life
Visions and Reality
Peter SchusterInstitut für Theoretische Chemie und Molekulare
Strukturbiologie der Universität Wien
Madrid, Astrobiology Meeting 30.11.2001
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From prebiotic chemistryto the first cellularorganisms
World of c laysP rogramable c atalystsSe lf-reproducing mineralsSur face catalysis ?Reprod uction in thre e dimensions ?
Template che mistryTe mplate induced reactionsLigati on, complemen tary synthesis,molec ular copying, autocatalysisRN A precursors ?Origin of the first RN A molecules ?Ster eochemical pu rity, chirality ?Nat ure of molecu lar templates ? Non instru cted polymers
Condensation , polymerizatio n,agg regationR andom oligop eptides, proten oids,l ipid membrane s, carbohydrat es, ...Con densation ag ent ?Pol ymerization m echanism ?
E xtraterrestria l organicmolecul esHydro gen cyanide, f ormaldehyde,ami no acids, hydr oxi acids,...Mete rorites,comets , dust clouds Simulation experimentsHydrogencya nide, amino ac idshydroxiaci ds, purine base sMiller-Urey, F ischer-Tropsc h, ...Pri mordial atmo sphere ? H eating during condensation ?
?? ?? ???? ?? ?? ???? ???? ????
Sulfur b ased chemistr ySurfacecata lysis on pyrite sHydrot hermal vents
RNA WorldLigatio n, cleavage, ed iting,replication , selection, opt imization Reactions w ith nucleotide templatesR NA catalysis
Su lfur metabolis m ?Hea t gradients at deep sea volc Organi c molecules
World of clays
Programable catalysts
Self-reproducing minerals
Surface catalysis ?
Reproduction in three dimensions ?
Template chemistry
Template induced reactions
Ligation, complementary synthesis,molecular copying, autocatalysis
RNA precursors ?
Origin of the first RNA molecules ?
Stereochemical purity, chirality ?
Nature of molecular templates ?Non instructed polymers
Condensation, polymerization,aggregation
Random oligopeptides, protenoids,lipid membranes, carbohydrates, ...
Condensation agent ?
Polymerization mechanism ?
Extraterrestrial organicmolecules
Hydrogen cyanide, formaldehyde,amino acids, hydroxi acids,...
Meterorites, comets, dust clouds
Simulation experiments
Hydrogen cyanide, amino acidshydroxi acids, purine bases
Miller-Urey, Fischer-Tropsch, ...
Primordial atmosphere ? Heating during condensation?
???? ???? ???? ???? ???? ????
Sulfur based chemistry
Surface catalysis on pyritesHydrothermal vents
RNA World
Ligation, cleavage, editing,replication, selection, optimization
Reactions with nucleotide templatesRNA catalysis
Sulfur metabolism ?
Heat gradients at deep sea volcanos ?
Organic molecules
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Origins of reactive organic molecules
Extraterrestrial organicmolecules
Hydrogen cyanide, formaldehyde,amino acids, hydroxi acids,...
Meterorites, comets, dust clouds
Heating during condensation?
Simulation experiments
Hydrogen cyanide, amino acidshydroxi acids, purine bases
Miller-Urey, Fischer-Tropsch, ...
Primordial atmosphere ?
Sulfur based chemistry
Surface catalysis on pyritesHydrothermal vents
Sulfur metabolism ?
Heat gradients at deep sea volcanos ?
Organic molecules
![Page 4: Chemistry and Evolution at the Origin of Life › ~pks › Presentation › madrid.pdf · Chemistry and Evolution at the Origin of Life Visions and Reality Peter Schuster Institut](https://reader033.vdocument.in/reader033/viewer/2022042404/5f1a8468db21903bf312379d/html5/thumbnails/4.jpg)
World of clays
Programable catalysts
Self-reproducing minerals
Surface catalysis ?Reproduction in three dimensions ?
Template chemistry
Template induced reactions
Ligation, complementary synthesis,molecular copying, autocatalysis
RNA precursors ?
Origin of the first RNA molecules ?
Stereochemical purity, chirality ?
Nature of molecular templates ?
Non instructed polymers
Condensation, polymerization,aggregation
Random oligopeptides, protenoids,lipid membranes, carbohydrates, ...
Condensation agent ?Polymerization mechanism ?
From small organic molecules to instructed polymers
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???? ???? ???? ???? ???? ????
RNA World
Ligation, cleavage, editing,replication, selection, optimization
Reactions with nucleotide templatesRNA catalysis
From an RNA world to the first living organisms
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Three-dimensional structure ofphenylalanyl-transfer-RNA
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OCH2
OHO
O
PO
O
O
N1
OCH2
OHO
PO
O
O
N2
OCH2
OHO
PO
O
O
N3
OCH2
OHO
PO
O
O
N4
N A U G Ck = , , ,
3' - end
5' - end
Na
Na
Na
Na
The chemical formula of RNA consisting of nucleobases, ribose rings, phosphate groups, and sodium counterions
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2
Association
Ligation
Complex dissociationAutocatalytic formation ofa hexanucleotide template from two trinucleotides
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Hydrogen bonds
Hydrogen bonding between nucleotide bases is theprinciple of template action of RNA and DNA
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G
G
G
G
C
C
C G
C
C
G
C
C
G
C
C
G
C
C
G
C
C
C
C
G
G
G
G
G
C
G
C
Plus Strand
Plus Strand
Minus Strand
Plus Strand
Plus Strand
Minus Strand
3'
3'
3'
3'
3'
5'
5'
5'
3'
3'
5'
5'
5'+
Complex Dissociation
Synthesis
Synthesis
Complementary replication as the simplest copying mechanism of RNA
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G
G
G
C
C
C
G
C
C
G
C
C
C
G
C
C
C
G
C
G
G
G
G
C
Plus Strand
Plus Strand
Minus Strand
Plus Strand
3'
3'
3'
3'
5'
3'
5'
5'
5'
Point Mutation
Insertion
Deletion
GAA AA UCCCG
GAAUCC A CGA
GAA AAUCCCGUCCCG
GAAUCCA
Mutations represent the mechanism of variation in nucleic acids
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SpaceSequence
Con
cent
ratio
n
Master Sequence
The molecular quasispecies
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U
U
U
U
U
G
G
G
G
G
G G
G
G
G
G
G G
G
G
G
G
A
A
A
A
A
A
A
A
A
A
C
C
C C
C C
C
C
C
C
C C
C
C
C
Cleavage site
The "hammerhead" ribozyme
OH
OH
OH
ppp
5'
5'
3'
3'
The smallest knowncatalytically activeRNA molecules
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Association
Ligation
Complex dissociation
E N T + +
E N
2 T
E
N
=
=
Ar- -CO-S-Bn
H N- -CO-NH
RMKQLEEKVYELLSKVA
CLEYEVARLKKLGE2 2
Ar- -CO-NHRMKQLEEKVYELLSKV LEYEVARLKKLVEGE 2
T
=
Ligation Site
Ar
Bn
=
=
4-Acetamidobenzoyl-
Benzyl-
Autocatalytic formation of a oligopetide template from twotwo precursor oligopeptides
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L5
L5
R1
R1
M2
M2
K3
K3
Q4
Q4
E7E7
E6
E6
LEKK
29
22
15
8
KKEL
8
15
22
29
LLL
12
19
26
VVVV
9
16
23
30LEK
13
20
27
ECRE
11
18
25
32
Y10
A24G31
SYK
14
21
28
ER
E
32
25
11
KEL
27
20
13V30V23V16V9
GAAY
31
24
17
10
SYK
14
21
28
LLL
26
19
12
Color code for amino acid residues
hydrophobic
hydrophilic, neutral
positively charged
indifferent
negatively charged
The a-helix wheel illustrating template action of oligopeptides by means of hydrophobic interaction
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The three-dimensional structure of a short B-DNA double helix
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Three-dimensional structure of thecomplex between the regulatoryprotein cro-repressor and the bindingsite on l-phage B-DNA
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++
Replication:DNA 2 DNA→
Tran
scrip
tion:
DN
A
RN
A→
Metabolism
Food
Waste
Nucleotides
Amino Acids
Lipids
Carbohydrates
Small Molecules
Translation: RNA Protein→
ProteinmRNA
Ribosom
Information processing and metabolism in the DNA-RNA-protein world
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Stock Solution Reaction Mixture
The flowreactor as a device for studies of evolution in vitro and in silico
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0 250 500 750 1000 1250
Time
0
10
20
30
40
50A
vera
ge d
ista
nce
of th
e po
pula
tion
from
targ
etMajor changes in phenotypes
Num
ber
of p
heno
type
s in
the
rela
y se
ries
Evolution in silico in the flow reactor
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Genotype Space
Fitn
ess
Start of Walk
End of Walk
Random Drift Periods
Adaptive Periods
Evolution in genotype space sketched as a non-descending walk in a fitness landscape
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yes
Selection Cycle
no
GeneticDiversity
Desired Properties? ? ?
Selection
Amplification
Diversification
Selection cycle used inapplied molecular evolutionto design molecules withpredefined properties
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Retention of binders Elution of binders
Chr
omat
ogra
phic
col
umn
The SELEX technique for the evolutionary design of aptamers
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Stage I:Independent CompetingReplicators
Stage II:Functionally CoupledReplicators
Stage III:
New Unit of Selection
Stage IV = I:Independent CompetingUnits
Parasite
Parasite
The hypercycle model of major evolutionary transitions
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Coworkers
Walter Fontana, Santa Fe Institute, NM
Christian Reidys, Christian Forst, Los Alamos National Laboratory, NM
Peter Stadler, Universität Wien, AT,Ivo L.Hofacker
Christoph Flamm
Bärbel Stadler, Andreas Wernitznig, Universität Wien, AT,Stefanie Widder, Ulrike Mückstein, Stefan Wuchty
Ulrike Göbel, Institut für Molekulare Biotechnologie, Jena, GE,Walter Grüner, Stefan Kopp, Jaqueline Weber