the chemistry of life’origins: ii. from the building blocks to life
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The chemistry of life’origins: II. From the building blocks to life. CHONS + H 2 O. . Robots or catalysts. . RNA world Viruses?. . Cells, i.e. RNA proteins membranes. Clays? . Polymer formation in water - PowerPoint PPT PresentationTRANSCRIPT
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The chemistry of life’origins:
II. From the building blocks to life
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CHONS+ H2O
Robots orcatalysts
RNA world
Viruses?
Cells, i.e.RNA
proteins membranes
Clays?
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Polymer formation in water
Formally, the formation of a biopolymer consists to eliminate water moleculesbetween monomer units. However, the formation of either polyamino acids or
polynucleotides from their monomers is not energetically favored.In water, energy is required to link 2 amino acids. For example, the free energy for the condensation of alanine and glycine to form the dipeptide alanyl-glycine
in water is 4.13 Kcal/mol at 37°C and pH 7:
H-Ala-OH + H-Gly-OH H-Ala-Gly-OH + H2O G0 = 4.13 Kcal
The thermodynamic barrier is very large for the formation of a long chainpolyamino acid.
For example, 1 M solutions in each of the 20 protein amino acids would yield at equilibrium a 10-99 M concentration for a 12 000 Dalton protein.
To yield one protein at equilibrium, the volume of the solution would have to be 1050 times the volume of the Earth!
So energy input was necessary to make polynucleotides and polyamino acids in the primitive oceans.
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NH
O
O
OCH3
C
CH3
NH2 COOH
H
Alanine NCA
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Glu-SEtGlu-SET &
bicarbonate
Glu-oligomers obtained in the presence of bicarbonate via the intermediate formation of a carbamate –OOC-NH-CHR-CO-SET and probably a Leuch’s
anhydride.
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13.8014.304.2030.624.2ZnS
00005.801.890.5FeS
7019.41.93.41.454.512.4CdS
02.6006.540.1038.2Clay
6.208.800.67.668.18.7Blank
4-SEt4-OH3-SEt3-OH2-SEt2-OHDKP1-SEt
Polymerization of H-Leu-SEt in the presence of different mineral surfaces(15 days, pH 8, 25 C)
n H–Leu–S–C2H5 H–Leun–S–C2H5 + nHS–C2H5
H–Leun–S–C2H5 + H2O H–Leun–OH + HS–C2H5
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13.931.311.301.7728.73.52.6Wet/dry
00001.93.41.454.512.425 C
7-OH6-OH5-OH4-OH3-OH2-SEt2-OHDKP1-SEt
Polymerization of H-Leu-SEt in the presence of CdS using wet/dry cycles (12 hr at 25 C / 12 hr at 80 C for 2 weeks, pH 8).
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Rainbow submarine hydrothermal system
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n H–Leu–S–C2H5 H–Leun–S–C2H5 + nHS–C2H5
H–Leun–S–C2H5 + H2O H–Leun–OH + HS–C2H5
Polymerization of amino thioesters on hydrothermal sediments
control
1
2
DKP
3
4
>4
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Flow reactor simulating a submarine hydrothermal system
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The β-sheet structure of alternating hydrophilic / hydrophobic peptides
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Formation of double layer β-sheets of alternating hydrophobic/hydrophilic polypeptides, driven by hydrophobic clustering of side-chains.
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β-sheets are more stable than α-helices
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The hydrophobic amino acid must be strongly hydrophobic
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Poly(Leu50, Lys50) which exhibits random coil, α- and β-geometries, develops
more β-structures with increasing temperature.
20 °C 60 °C
α 58% 34%
β 27% 51%
random 16% 15%
Higher temperatures favor β-sheet structures
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The β-sheet structure of alternating hydrophilic / hydrophobic peptides
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Percentage of β-sheets with increasing L-enantiomers
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77%L 84%L
86%L 92%L
95%L 99%L
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The alternating polypeptide poly(Glu-Leu) is randomly coiled in water.
It adopts:
-a β-sheet structure in the presence of traces of CaCl2
but
- an α–helix in the presence of FeCl3.
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Even more interestingly, poly(Glu-Leu) is also capable of extracting cations from insoluble minerals and adopts an ordered conformation:
-a β-sheet structure in the presence of CdS
- an α–helix in the presence of molybdenum
Peptides with 10-amino acids are long enough to significantly adsorbonto the mineral surface.
Montmorillonite adsorbs the peptide but does not induce any conformational change.
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Control
+ poly(Leu-Lys)
Poly(Leu-Lys) catalyses the cleavage of RNA phosphodiester bonds, providing
a rate enhancement of 185, compared to the control.
The decapeptide is long enough to exhibit the catalytic activity.
Poly(Pro-Leu-Lys-Leu-Lys) andpoly(D,L Leu - D,L Lys) are inactive
(rate enhancement of 11 and 17, resp.).
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CONCLUSION
Stable short β-sheet forming peptides were probably abundant in the primitive oceans
Doing what?
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CHONS+ H2O
Robots orcatalysts
RNA worldViruses?
Cells, i.e.RNA
proteins membranes
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Heterocyclic base (adenine)
Sugar (ribose)
Phosphate
A nucleotide, the basic constituent of RNA
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RNA ribose (peak 8) is poorly formed from formaldehyde
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Chemical self-replication works beautifully with preformed RNA strands
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Are clays of any help?
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With CDI
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O
BASE
OOH
OO
O
P
-
OBASE
OHO
O
O-
O P
RNA Pyranosyl-RNA, p-RNA
P-RNA:• base pairs more strongly than RNA
• the twist of the helices is less important• self-organisation and stereoselective polymerisation
of p-ATCG tetramers
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O
BASE
O
O
O-
O
P
OBASE
OHO
O
O-
O P
RNA Threose-RNA, TNA
TNA:• is more stable to hydrolysis than RNA
• forms TNA-TNA double helices• forms TNA-RNA hybrid duplexes with RNA
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N
NH
BASE
O
O
Peptide nucleic acid, PNA
PNA:• has a 2-aminoethyl glycine backbone
• forms PNA-PNA double helices• forms PNA-RNA hybrid double helices
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CHONS+ H2O
Robots orcatalysts
RNA worldViruses?
Cells, i.e.RNA
proteins membranes
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Catalysis
Autocatalysis
Self-replication: autocatalysis + selection of bifunctional elements
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Autocatalytic growth of micelles: primitive life?
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A self-replicating peptide?Reza Ghadiri showed that the 32-residue α-helical peptide autocatalytically templates its own synthesis by accelerating the amide bond condensation
of 15- and 17-residue fragments.The 32-residue peptide replicator is capable of efficiently amplifying homochiral
products from a racemic mixture of peptides fragments
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Catalysis
Autocatalysis
Self-replication: autocatalysis + selection of bifunctional elements
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Cross-inhibition in template-directed polymerisation of activated L,D nucleotides
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Autocatalytic growth of Glu-oligomers on short α-helices withan active ester of Glu in benzene
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Autocatalytic growth of Glu-oligomers on short α-helices
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Catalysis
Autocatalysis
Self-replication: autocatalysis + selection of bifunctional elements
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Possible steps ahead
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Self-replication by surface-controlled growth and fracture
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That’s all for today, folks!
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Stereoselection via glycine crystals
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Magnetochirality (with 7.5 Tesla!)