Self Assembly

I. What is self-assembly?

Self-Assembly is the process by which a system of non-living chemical components became organized into a living, biological system. For self-assembly to occur, there must be a change in a system from a more disorganized state to a more "ordered" or "organized" condition that exhibits some form of structure.

The overall process of self-assembly is not yet understood, indeed, if it were, a gemeral understanding of the origins of life would be achieved. Self-assembly has a range of generic meanings not related specifically to the origins of life, particularly in the study of self-organizing molecular systems research in physical chemistry. In this sence its meaning has to to with the ability of a system of chemical reactants to spontaneously form more "ordered" macromolecular structures.

II. The overall process of self-assembly

A. What are the minimal requirements for a proto-biological system?

1. Minimal protocell structure

  1. Protocell: A membrane-enclosed vesicle capable of exhibiting some of the qualities found in living cells.
  2. [minimum protocell] "... an entity thermodynamically separated from the environment and able to replicate using available nutrient molecules and energy sources." (Morowitz, Heinz & Deamer 1988, 281).

2. Growth and reproduction: A number of purely physical systems exhibit this sort of behavior ­ a soap bubble grows to a large size and then splits into two as the larger form becomes "unstable". These are physical systems that exhibit discrete forms of thermodynamically defined stability, there is a "tendency" for such systems to exist in those forms or configurations which exhibit the lowest level of free energy.

3. Use of energy and energy flow: We have a sense that there must be the utilization of chemical bond energy in order for even a protobiological system to exist

4. Ability to evolve: this is a combination of growth and reproduction combined with a system permitting the accumulation of mutations or changes

B. What are steps involved in getting to such a system?

1. Getting to the minimal lipid-bounded protocell systems

  1. Solutions of lipids spontaneously through self-assembly to form vesicles. This occurs as the vesicular form is the most thermodynamically stable state for these structures.
  2. Wetting and drying cycles of the lipid vesicles (liposomes) cause them to break apart and re-form.
  3. Reformed liposomes will accumulate solutes and other molecules that persist during the drying phase.

2. Primitive energetics and energy transfer

  1. Growth of the liposomes occurs if there is a mechanism whereby new lipid molecules are added to the vesicle wall.
  2. Primitive metabolism could have been the internal chemistry that caused monomeric wall precursors to be assembled internally and added to the wall.
  3. Photochemically-driven energy sources, most likely to be membrane-bound.
  4. Internally-captured enzymes or ribozymes perform autocatylic reactions.

Proteinoid Microspheres: A different view of the same thing

Research on proteinoid microspheres represented the life work of Sidney Fox. Mixtures of amino acids heated and then wetted can spontaneously re-organize into spherical balls with protein-like walls. More photos of microspheres can be seen here. Read a transcript of a lecture given by Professor Fox about his audiences with Pope John Paul II.

3. Early informational mechanisms

  1. RNA as both enzyme and informational molecule
  2. Non-nucleic acid templates for information transfer
  3. The duplications in the code ­ do they indicate the possibility of a reduced number of aa's in an early system?

    4. Combining the above components, is there a unique order that must be followed; can we, at least, set the sequence of events?

    5. Genetic takeover concept, could a protobiological system have been constructed differently?

    1. Before autotrophy - what were the components of biological systems prior to the evolution of chemo or photosynthesis? Is this even possible?
    2. Before oxygen -- which metabolic pathways evolved prior to the development of O2 gas?
    3. Are there other ordered sequences in biochemical pathways such that we can recognize an unambiguous order to the acquisition of metabolism?

    III. Order out of Chaos: Theoretical considerations

    A. Spenser: Evolution proceeds from the homogeneous to the heterogeneous

    1. e.g. differentiation of the earth during its formation and early history
    2. apparent description of evolution as more species are created, the overall ecology becomes more complex

    B. Terms:

    • Random vs. non-random
    • Ordered states vs. chaotic states
    • Simple vs. complex

    IV. Energy and Entropy: Thermodynamics

    A. Entropy and order: physicists can describe systems in terms of their overall handling of energy. How do biological systems fit into this way of describing nature?

    "Following Sherrington (1940) you can think of the environment for life as a stream, with organisms as eddies in the stream that are locally moving against the entropy trend. On the surface of the Earth the main motive stream is the stream of photons from the Sun. Sooner or later the energy that arrives on the Earth will be reradiated into space in a more degraded form. But between this arrival and this departure the gigantic eddies of the weather and the water cycle are driven continuously. Much more intricate are the convolutions inserted by life on Earth between the absorption of sunlight in green leaves and the reradiation of that energy, eventually, into space." (Cairns-Smith 1982)

    1. Entropy is defined as the amount of heat (kilocalories) contained a system divided by its absolute teperature in Kelvin: S = Q /T.
    2. The second law of thermdynamics states that in any system that experiences a change or exchange in energy, the entropy in the resultant system must be greater than or equal to zero, δS=δQ/T≥0. One way of describing this has been to state that over time, the universe becomes more disordered or "run down", or more "randomized". The second law, therefore seems to violate what we see happening with in biological systems that appear to create more ordered systems over time. And the chemistry of the evolutionary process involves the exchange of energy in a system, so it is subject to the second law. We get around this problem by defining the "system" that is subject to the second law as including the Sun and Earth - thus, the energy arriving from the sun and its interaction with Earth's (biological) surface results in an overall entropy increase, even though, locally, on the Earth's surface, biology causes an apparent decrease in entropy.

    B. Non-equilibrium studies

    V. Chemical principles that relate to behavior

    A. Colloidal chemistry

    • Examples: Paint, milk
    • Forces
      • Van der Waals: particle charge distribution
      • Electrostatic:

    B. Ionized macromolecules

    1. (Westheimer 1987) Phosphate is responsible for attaching to biomolecules and ionizing them
    2. Ionized molecules are more easily kept inside a lipid bilayer and this may be a physiological requirement for any biosynthetic pathway (Davis 1958),

    VI. Extant studies of self-assembly

    A. Physical Systems: There are many studies in material science whereby physiochemical conditions in a particular setup in the laboratory lead to apparent "order" from random or "disordered" systems. In these examples, the notion of on ordered state vary from experimenter to experimenter, but in general researchers are impressed when atoms and molecules organize themselves into macromolecular structures that are recognizably different from their source structure. Whether such examples of ordered states have any bearing whatsoever on the origins of life remains to be seen, but the study of such physical systems may eventually lead to more general understanding of physiochemical processes that were important in abiogenesis.

    1. Colloidal rods and spheres constructed from silica gel (SiO2 • H2O)
    2. Fullerenes, C60 Buckminsterfullerines or buckey balls are highly stable version of carbon with only carbon to carbon balls. They can be formed as part of soot formation from a carbon arc. This one is from "".
    3. dendrites, branched fractal structures appear during the growth of Mn-Oxides on surfaces.

    B. Toward biologically meaningful systems

    1. Oparin's coacervates
      1. Coacervation = "the spontaneous separation of a continuous one phase aqueous solution of a highly hydrated polymer into two aqueous phases of differing concentration" (paraphrased from Lehninger).
      2. Capture of smaller molecules to generate both substrate and catylist.
      3. If the catylized reaction produces reactants that are incorporated into the wall of the coacervate, then it will expand (grow).
      4. Genetics comes later.
    2. Sidney Fox and his proteinoids
      1. 2Ám in diameter, this is small, but about the size of most eubacteria.
      2. stable at pH=3 to 7
      3. can be double-walled (bilayered) and they respond to osmotic change indicates they function as semipermiable membranes
      4. they can bud (hence grow) spontaneously


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    18 October 2007