self-organizing bio-structures nb2-2009 l. duroux
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Overall goalOverall goal
Give an insight of self-organizing Give an insight of self-organizing processes in nature and how these processes in nature and how these designs inspired humans to create designs inspired humans to create nano-sized objectsnano-sized objects
Lectures focuses on self-Lectures focuses on self-organization/self-assembly of bio-organization/self-assembly of bio-structures: molecules to supra-structures: molecules to supra-molecular assembliesmolecular assemblies
Supramolecular Supramolecular ChemistryChemistry
Jean-Marie LEHN (Nobel Chemistry, Jean-Marie LEHN (Nobel Chemistry, 1987)1987)
Chemistry beyond molecules Chemistry beyond molecules SupermoleculesSupermolecules
Organization, intermolecular non-Organization, intermolecular non-covalent bonds, different (better) covalent bonds, different (better) properties than partsproperties than parts
Lecture PlanLecture Plan
1.1. Pre-biotic chemistry (Ch. 2 & 3)Pre-biotic chemistry (Ch. 2 & 3)2.2. The formation of macromolecular The formation of macromolecular
sequences (Ch. 4)sequences (Ch. 4)3.3. Self-Organization in Biological systems (Ch. Self-Organization in Biological systems (Ch.
5)5)4.4. Supra-molecular ChemistrySupra-molecular Chemistry5.5. Self-Assembly of Nucleic AcidsSelf-Assembly of Nucleic Acids6.6. DNA in NanotechnologiesDNA in Nanotechnologies7.7. Self-Assembly of PolypeptidesSelf-Assembly of Polypeptides8.8. Proteins in NanotechnologiesProteins in Nanotechnologies9.9. VirusesViruses10.10. MembranesMembranes
Supporting MaterialSupporting Material
Text Book: “The Emergence of life” by Text Book: “The Emergence of life” by Pier L. Luigi Pier L. Luigi (ISBN: 0-521-82117-7)(ISBN: 0-521-82117-7)
Text Book: “Text Book: “Supramolecular Chemistry –Fundamentals and Applications, Advanced Textbook” by Ariga and Kunitake (ISBN: 10 3-540-01298-2)
Selected review articles on specialized Selected review articles on specialized topicstopics
Other Readings (specific Other Readings (specific topics)topics)
Self-Assembled Nanostructures, Self-Assembled Nanostructures, by J. Zhang by J. Zhang
et alet al,, 20022002, 340 p.,, 340 p., Hardcover ISBN: 978-0-306-47299-2Hardcover ISBN: 978-0-306-47299-2
Self-Assembling Peptide Systems in Biology, Self-Assembling Peptide Systems in Biology, Medicine and Engineering, Medicine and Engineering, by A. Aggeli et al, by A. Aggeli et al, 20012001, 372 p., , 372 p., HardcoverHardcoverISBN: 978-0-7923-7090-1ISBN: 978-0-7923-7090-1
Self-Assembly in Supramolecular SystemsSelf-Assembly in Supramolecular Systems, , by L F Lindoy & I M Atkinson, by L F Lindoy & I M Atkinson, 20002000, 234p., , 234p., Hardcover Hardcover ISBNISBN 0 85404 512 0 0 85404 512 0
Lecture 1Lecture 1
From Pre-Biotic Chemistry to From Pre-Biotic Chemistry to Macromolecular AssembliesMacromolecular Assemblies
A scale of Molecular Complexity towards Life
CELLS METABOLIC NETWORKS POLYMER COMPLEXES MACROMOLECULES BIOMONOMERS MOLECULES ATOMS
Formation of organic Formation of organic molecules “building molecules “building
blocks”blocks”Organic synthesis in reducing Organic synthesis in reducing
atmosphereatmosphere
Synthesis of Adenine from Synthesis of Adenine from cyanidecyanide
•Nitriles: highly polar group (dipole: 3.9 Debye)
•Reaction: substitution (C), addition on triple bond
•Condensation catalyzed by heat (in aqueous medium)
1.16Å890kJ/mol
Synthesis of AldosesSynthesis of Aldoses
Aldehydes/ketones: permanent or induced Aldehydes/ketones: permanent or induced dipole (Odipole (O22 electronegativity) electronegativity)
Tautomery and H mobility on CTautomery and H mobility on C Nucleophilic additions on CNucleophilic additions on C
C=O1.24Å735kJ/mol
The “Pyrite” hypothesisThe “Pyrite” hypothesis
In hydrothermal In hydrothermal sourcessources
Reduction of atm. Reduction of atm. COCO22 and N and N22
Autotrophic Autotrophic Final Final product: pyruvateproduct: pyruvate
Self-organized, Self-organized, coupled chemical coupled chemical reactions: reactions: metabolism from the metabolism from the start!start!
Deep-sea vents biotaDeep-sea vents biota
Reducing conditions in deep-sea Reducing conditions in deep-sea vents: Fe chemistry, temperature vents: Fe chemistry, temperature >350degC:>350degC: FeS + HFeS + H22S S FeS FeS22 + 2H + 2H++ + 2e + 2e--
Extreme thermophiles ribosomal Extreme thermophiles ribosomal RNA: most primitive organisms RNA: most primitive organisms known to date!known to date!
Exo-Biological sourcesExo-Biological sources
Space dust: 40000 tons/year OR 8 Space dust: 40000 tons/year OR 8 ng/cmng/cm22
Murchinson meteorite: 4.6 bY, amino Murchinson meteorite: 4.6 bY, amino acids, purines, pyrimidines, carbox. Ac., acids, purines, pyrimidines, carbox. Ac., polyols…polyols…
Carbon as a result from HCarbon as a result from H22 and He and He “burning” (fusion) in stars “burning” (fusion) in stars
What was found or not in What was found or not in meteorites or comets dustmeteorites or comets dust
Found: diverse simple organic Found: diverse simple organic molecules, membrane-forming molecules, membrane-forming aliphatic moleculesaliphatic molecules
Not found: polypeptides, Not found: polypeptides, mononucleotidesmononucleotides
The question of “chemical The question of “chemical selection”selection”
Why do Miller’s amino acids form (Why do Miller’s amino acids form (--enantiomers)?enantiomers)? -amino-acids are more thermodynamically -amino-acids are more thermodynamically
stable than stable than -amino-acids-amino-acids BUT: many molecules under kinetic controls BUT: many molecules under kinetic controls
catalysts, catalysts, i.e.i.e. enzymes! enzymes!
Enzymes first? How possible?Enzymes first? How possible?
How can selection (in Darwinian terms) How can selection (in Darwinian terms) be applied to prebiotic chemistry?be applied to prebiotic chemistry?
The example of D-ribose in The example of D-ribose in RNA/DNARNA/DNA
Why D-ribose instead of D-ribulose ?
Reasons for pre-biotic Reasons for pre-biotic selectionselection
ContingencyContingency A chemical pathway is determined by the A chemical pathway is determined by the
co-occurrence of precursors in time and co-occurrence of precursors in time and spacespace
DeterminismDeterminism Nature has “chosen” a path that leads to Nature has “chosen” a path that leads to
further developments/evolution further developments/evolution (according to the laws n Physics and (according to the laws n Physics and Chemistry)Chemistry)
The Deterministic The Deterministic hypothesishypothesis
Would a “wrong” thermodynamically Would a “wrong” thermodynamically stable chemical lead to a dead-end in stable chemical lead to a dead-end in evolution OR to an equally good evolution OR to an equally good alternative?alternative?
Hypothesis tested by Eschenmoser Hypothesis tested by Eschenmoser et al. (1986):et al. (1986): D-furanose D-furanose vsvs D-pyranose as the D-pyranose as the
“sugar” for DNA (homo-RNA)“sugar” for DNA (homo-RNA)
Eschenmoser’s homo- and Eschenmoser’s homo- and allo-DNAallo-DNA
Eschenmoser, 1999. Science, 284:2118-2124
Stability of homo-DNA Stability of homo-DNA duplexesduplexes
Greater stability due to higher rigidity of pyranose ring: pre-oganisation into helical structure
Other alternatives to D-Other alternatives to D-riboseribose
Other “potentially natural” oses Other “potentially natural” oses could give alternative DNA with could give alternative DNA with similar Tmsimilar Tm
Nature only selected D-ribose… a Nature only selected D-ribose… a matter of contingency or matter of contingency or determinism?determinism?
On the origin of Molecular On the origin of Molecular AsymmetryAsymmetry
Why only one type of chirality in families of Why only one type of chirality in families of molecules (L-form of amino-acids, D-form for molecules (L-form of amino-acids, D-form for sugars)?sugars)?
Why only one type of chirality and stereoregularity Why only one type of chirality and stereoregularity in natural polymer chains?in natural polymer chains?
Any thermodynamic reason? Only subtle Any thermodynamic reason? Only subtle differences in free energy between two forms (10differences in free energy between two forms (10-10-10 J).J).
In chemistry, often racemic mixtures are obtained!In chemistry, often racemic mixtures are obtained!
Crystals as ”symmetry Crystals as ”symmetry breakers” breakers”
Achiral or racemic mixtures Achiral or racemic mixtures generally give crystals with faces of generally give crystals with faces of opposite handedness: equal opposite handedness: equal probability to interface medium probability to interface medium
The face of the crystal at interface The face of the crystal at interface with medium will induce with medium will induce racemisation of the solution (glycine racemisation of the solution (glycine crystals)crystals)
Complementarity in Complementarity in homochiralityhomochirality
Would life be possible with D-amino Would life be possible with D-amino acids?acids? Maybe, but only with L-sugars…Maybe, but only with L-sugars…
Example: topoisomerase with D-amino-Example: topoisomerase with D-amino-acids incapable to recognise right-acids incapable to recognise right-handed DNA!handed DNA!
If enzymes catalyzed sugars synthesis…If enzymes catalyzed sugars synthesis…
In SummaryIn Summary
Thermodynamic control: gives an initial set Thermodynamic control: gives an initial set of favorable products, essentially monomersof favorable products, essentially monomers
Kinetic control: responsible for the Kinetic control: responsible for the diversification (hence life), in particular diversification (hence life), in particular polymerspolymers Sequence of 129aa of lysozyme not because Sequence of 129aa of lysozyme not because
most stable combination!most stable combination!
Symmetry can be broken, but how does Symmetry can be broken, but how does asymmetry propagate? asymmetry propagate?