PREBIOTIC CHEMISTRY

Biophysic course WS 2006, Rome.

1.Science confronting the origin of life on Earth.

1.2.: Prebiotic chemistry

2.2. The chemical process(es) to transition to life can beThe chemical process(es) to transition to life can bereproduced in the laboratory with the presentlyreproduced in the laboratory with the presentlyavailable chemical techniques and chemicals.available chemical techniques and chemicals.

3.3. And this can be implemented in a reasonableAnd this can be implemented in a reasonable(hours or max. days) experimental time span -(hours or max. days) experimental time span -once you know the right combination of prebiotic compoundsonce you know the right combination of prebiotic compoundsand theconditions.and theconditions.

LIFELIFE

inanimateinanimate mattermatter

1.1. Life originated from inanimate matter as a spontan-Life originated from inanimate matter as a spontan-

eous and continous increase of molecular complexity.eous and continous increase of molecular complexity.Chemical continuity principle - no transcendentalChemical continuity principle - no transcendentalprinciple.principle.

SOME MAIN ASSUMPTIONS OF PRESENTSOME MAIN ASSUMPTIONS OF PRESENTDAY RESEARCH ON THE ORIGIN OF LIFEDAY RESEARCH ON THE ORIGIN OF LIFESOME MAIN ASSUMPTIONS OF PRESENTSOME MAIN ASSUMPTIONS OF PRESENTDAY RESEARCH ON THE ORIGIN OF LIFEDAY RESEARCH ON THE ORIGIN OF LIFE

4.4. Since there is no documentation on how things reallySince there is no documentation on how things reallyhappened, there is no obligatory research pathway.happened, there is no obligatory research pathway.

Lightnings_SV3.avi

Electrodesdischarge sparks("lightningsimulation")

Watervapor

Stopcocksfor testingof samples

Heated water("ocean")

Condensed liquidwith complexmolecules

Cold waterinlet

Out

Condenser

CH4H2ONH3H2

Glutamic acidAspartic acid

Urea

Succinic acid

Sarcosine

Acetic acid

Lactic acidAlanine

GlycineFormic acid

Molecule

1 10 100 1000Yield in micromoles

NHCN

NH2

NC

NC

NH2

NH2

NC

NC

2 HCNHCN HCN

Chemistry of HCN, precursor of purines

Ferris & Orgel 1996, 1967

Chemistry of HCN, precursor of purines

Ferris & Orgel 1996, 1967

NH2

NH2

CN

CN

N

NH

NH2

NCN

NH

NH2

NH2

O

N

N NH

N

NH2

N

N NH

N

NH2

NH2

HN

N NH

N

O

HN

N NH

N

O

NH2

HN

NH NH

N

O

NH2

diaminomaleonitrile 4-amino-imidazole-5-carbonitrile

adenine diaminopurin hypoxantine guanine xanthine

H2O

HCN (CN)2 (CN)2HCN NCO-

Synthesis of purinesOró, 1960

Synthesis of purinesOró, 1960

NH2

CN

NH

CNO3PO OH

OH

2-O P O

OH

NH3O

CN

+

H3PO4 / H2O OH2hv

65° Cca. 50%

80° Cca.45%

Synthesis of sugar phosphates

Eschenmoser 1988, 1990

Synthesis of sugar phosphates

Eschenmoser 1988, 1990

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 ORGANICSa 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 ORGANICSThe 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 ORGANICSaminoacids 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 kg/yr*

UV Photolysis1

Electric Discharge2

Shocks from impacts3

Hydrothermal Vents4

3 × 108

3 × 107

4 × 102

1 × 108

Extraterrestrial Sources5

 

IDP’s Comets

2 × 108

1 × 1011

Total 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.

 

Even if the chemist would have access to all prebiotic bio-monomers

he would NOT have the solution to the origin of life

PREBIOTIC CHEMISTRY HAS REACHEDCONSIDERABLE SUCCESS ..... BUT

LIFE AS WE KNOW IT IS DETERMINED BY SPECIFIC MACROMOLECULAR SEQUENCESLIKE NUCLEIC ACIDS AND PROTEINS

THE CORE OF THE PROBLEM:

CCOO NN HH CC HH

RR11 RR22 RR33

CCOO NN HH CC HH CC OO NN HH CC HH

XX YY ZZ PP YY

PP

OO

RRiibbOO PPOO OO RRiibb PPOO OO RRiibb

OO BBaassee11 BBaassee22 BBaassee33

antigen-binding

siteantigen-binding

site

carbohydrateresidue

Fab-unit Fab-unit

Fc-unit

SCHEMATIC REPRESENTATION OF THETHREE-DIMENSIONAL STRUCTURE OF IgG

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 therebecause they are more stable than their billions of constitutional isomers

They–and/or their precursors-are the products of statistics and contingencyin the polymerization processesand evolution

On the importance of being a copolymer

CO CH NH

Ri

n( )

Calculate: How many different macromoleculescan you build, whenn = 60 and i = 1 - 20

60

20 x 20 x 20 x ..... N = 2060 ~ 1070 !!!

evolution energetics

In nature there are only 1012 - 1014 proteins

radius of the universe

space of allpossible proteins 10130

(20100)

space of the proteins present in nature 1010 (radius ca. 1 atom)

Cast the dice again and........

And you will get a different set of macromoleculesthat 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 FORMED- AND GAVE ORIGINTO LIFE BY A DETERMINISTIC (OBLIGATORY)SERIES OF EVENTSORARE 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

PlasmidicDNA

Modified Phage

gene 3fusion protein

gene 3fusion

ss DNA

Helper Phage

PHAGEMID VECTOR SYSTEM IN PHAGE DISPLAY

Random Peptide (50mer)

TAG

mAB

Thrombin Cleavage Site

pIIIPhage

STRATEGY FOR THE ISOLATION OF FOLDED PEPTIDES

44% correct insert (79 clones)

Library1.98 x 109 clones

180 clones were randomly selected

73 clones tested for thrombin stability

ANALYSIS OF THE PEPTIDE PHAGE LIBRARY

0.00

5.00

10.00

15.00

20.00

25.00

30.00

0-10 10-20 20-30 30-40 40-50 50-60 60-70 70-80 80-90 90-100

“Stable” “Unstable”

% o

f the

73 c

lone

s of

the

phag

e lib

rary

% digestion categories

DISTRIBUTION OF THE PEPTIDE LIBRARY WITH RESPECT TO THROMBIN DIGESTION