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Self-Organizing Bio-structures. NB2-2009 L. Duroux. Overall goal. Give an insight of self-organizing processes in nature and how these designs inspired humans to create nano-sized objects
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Self-Organizing Bio-structures NB2-2009 L. Duroux
Overall goal • Give an insight of self-organizing processes in nature and how these designs inspired humans to create nano-sized objects • Lectures focuses on self-organization/self-assembly of bio-structures: molecules to supra-molecular assemblies
SO & physics Diffusion-limited Aggregation Snowflake Benard Convection Cells Sand Dune
SO & chemistry micelle DNA keratin & collagen Simplex virus
SO & Biology Slime mold Nautilus Daisy Zebra
SO & Nanotechnology Liquid crystals Dendrimers Bacterio-rhodopsin DNA tiles
Supramolecular Chemistry • Jean-Marie LEHN (Nobel Chemistry, 1987) • Chemistry beyond molecules Supermolecules • Organization, intermolecular non-covalent bonds, different (better) properties than parts
Lecture Plan • Pre-biotic chemistry (Ch. 2 & 3) • The formation of macromolecular sequences (Ch. 4) • Self-Organization in Biological systems (Ch. 5) • Supra-molecular Chemistry • Self-Assembly of Nucleic Acids • DNA in Nanotechnologies • Self-Assembly of Polypeptides • Proteins in Nanotechnologies • Viruses • Membranes
Supporting Material • Text Book: “The Emergence of life” by Pier L. Luigi (ISBN: 0-521-82117-7) • Text Book: “Supramolecular Chemistry –Fundamentals and Applications, Advanced Textbook” by Ariga and Kunitake (ISBN: 10 3-540-01298-2) • Selected review articles on specialized topics
Other Readings (specific topics) • Self-Assembled Nanostructures, by J. Zhang et al,2002, 340 p.,Hardcover ISBN: 978-0-306-47299-2 • Self-Assembling Peptide Systems in Biology, Medicine and Engineering, by A. Aggeli et al, 2001, 372 p., HardcoverISBN: 978-0-7923-7090-1 • Self-Assembly in Supramolecular Systems, by L F Lindoy & I M Atkinson, 2000, 234p., Hardcover ISBN 0 85404 512 0
Lecture 1 From Pre-Biotic Chemistry to Macromolecular Assemblies
A scale of Molecular Complexity towards Life CELLS METABOLIC NETWORKS POLYMER COMPLEXES MACROMOLECULES BIOMONOMERS MOLECULES ATOMS
Formation of organic molecules “building blocks” Organic synthesis in reducing atmosphere
Synthesis of Adenine from cyanide • Nitriles: highly polar group (dipole: 3.9 Debye) • Reaction: substitution (Ca), addition on triple bond • Condensation catalyzed by heat (in aqueous medium) 1.16Å 890kJ/mol
Synthesis of Pyrimidine bases CH4 + N2 spark
Synthesis of Aldoses C=O 1.24Å 735kJ/mol • Aldehydes/ketones: permanent or induced dipole (O2 electronegativity) • Tautomery and H mobility on Ca Nucleophilic additions on Ca
Peptide bonds formation Catalytic activity
The “Pyrite” hypothesis • In hydrothermal sources • Reduction of atm. CO2 and N2 • Autotrophic Final product: pyruvate • Self-organized, coupled chemical reactions: metabolism from the start!
Deep-sea vents biota • Reducing conditions in deep-sea vents: Fe chemistry, temperature >350degC: • FeS + H2S FeS2 + 2H+ + 2e- • Extreme thermophiles ribosomal RNA: most primitive organisms known to date!
Exo-Biological sources • Space dust: 40000 tons/year OR 8 ng/cm2 • Murchinson meteorite: 4.6 bY, amino acids, purines, pyrimidines, carbox. Ac., polyols… • Carbon as a result from H2 and He “burning” (fusion) in stars
What was found or not in meteorites or comets dust • Found: diverse simple organic molecules, membrane-forming aliphatic molecules • Not found: polypeptides, mononucleotides
The question of “chemical selection” • Why do Miller’s amino acids form (a-enantiomers)? • a-amino-acids are more thermodynamically stable than b-amino-acids • BUT: many molecules under kinetic controls catalysts, i.e. enzymes! • Enzymes first? How possible? • How can selection (in Darwinian terms) be applied to prebiotic chemistry?
The example of D-ribose in RNA/DNA Why D-ribose instead of D-ribulose ?
Reasons for pre-biotic selection • Contingency • A chemical pathway is determined by the co-occurrence of precursors in time and space • Determinism • Nature has “chosen” a path that leads to further developments/evolution (according to the laws n Physics and Chemistry)
The Deterministic hypothesis • Would a “wrong” thermodynamically stable chemical lead to a dead-end in evolution OR to an equally good alternative? • Hypothesis tested by Eschenmoser et al. (1986): • D-furanose vs D-pyranose as the “sugar” for DNA (homo-RNA)
Eschenmoser’s homo- and allo-DNA Eschenmoser, 1999. Science, 284:2118-2124
Stability of homo-DNA duplexes Greater stability due to higher rigidity of pyranose ring: pre-oganisation into helical structure
Other alternatives to D-ribose • Other “potentially natural” oses could give alternative DNA with similar Tm • Nature only selected D-ribose… a matter of contingency or determinism?
On the origin of Molecular Asymmetry • Why only one type of chirality in families of molecules (L-form of amino-acids, D-form for sugars)? • Why only one type of chirality and stereoregularity in natural polymer chains? • Any thermodynamic reason? Only subtle differences in free energy between two forms (10-10 J). • In chemistry, often racemic mixtures are obtained!
Molecular asymmetry • See animation
Crystals as ”symmetry breakers” • Achiral or racemic mixtures generally give crystals with faces of opposite handedness: equal probability to interface medium • The face of the crystal at interface with medium will induce racemisation of the solution (glycine crystals)
Complementarity in homochirality • Would life be possible with D-amino acids? • Maybe, but only with L-sugars… • Example: topoisomerase with D-amino-acids incapable to recognise right-handed DNA! • If enzymes catalyzed sugars synthesis…
In Summary • Thermodynamic control: gives an initial set of favorable products, essentially monomers • Kinetic control: responsible for the diversification (hence life), in particular polymers • Sequence of 129aa of lysozyme not because most stable combination! • Symmetry can be broken, but how does asymmetry propagate?
