Friday, January 20, 2006

Universal mechanism of catalytic action and stability of charged polymers

I have explained in two earlier postings (this and this) the idea that dark N-H-atoms could naturally serve as names of bio-molecules, and that molecules labelled by conjugate names could play the role of lock and key in catalytic action. This would mean that the emergence of symbolic representations and "molecular sex" between conjugate named molecules distinguishes bio-chemistry from the ordinary chemistry. Below some further remarks related to this idea.

1. Basic observations

The basic observations are following.

  1. Since fine structure constant for the interactions of dark electrons with proton (and any other charge) is scaled down by 1/hbar factor the effective charge of proton plus dark N-electron system is 1-N/λk and positive except for full shell of electrons with N=λk.

  2. The fusion of N-H-atom and its conjugate must liberate proton and decay of λk-atom requires that proton is feeded to the system.

2. A universal model for a catalytic action

The previous observations lead to a detailed model for bio-catalytic action.

  1. N-hydrogen atoms have effective charge 1-N/λk for N< λkso that the binding regions of catalysts and reacting molecules should carry effective fractional surface charge which is always positive: this is a testable prediction.

  2. Catalyst in general has several names: one for each reactant molecule. Catalytic action involving the formation of reactants-catalyst complex by fusion of N-H-atoms and their conjugates necessarily involves a temporary liberation of protons, one for each letter of each name of the catalyst.
  3. The generation of λk-H-atom in the fusion of letter and conjugate letter should correlate with the formation of hydrogen bonds between catalyst and substrate.
  4. The liberated protons could drop to a larger space-time sheet and liberate metabolic energy quanta kicking the complex formed by the reacting molecules over the potential wall separating it from the outcome of the reaction. In the transition to the final state the surplus energy would be liberated and kick a protons back to the original space-time sheet and λk-atom would decay to N-atom and its conjugate. Also metabolism could kick the dropped protons back to the system so that the catalyst would not be stuck to the product of the reaction.

3. How to understand the stability of charged bio-polymers?

The fact that the names of bio-molecules carry positive effective charge relates in an interesting manner to the problem of how charged bio-polymers can be stable (I am grateful for Dale Trenary for pointing me the problem and for interesting discussions). For instance, DNA carries a charge of -2 units per nucleotide due to the phosphate backbone. The models trying to explain the stability involve effective binding of counter ions to the polyelectrolyte so that the resulting system has a lower charge density.

The simulations of DNA condensation by Stevens however predict that counter ion charge should satisfy z> 2 in the case of DNA. The problem is of course that protons with z=1 are the natural counter ions. The positive surface charge defined by the dark N-H-atoms attached to the nucleotides of DNA strand could explain the stability. In the case of DNA double strand the combination of names and conjugate names liberates one proton per nucleotide and stability could be guaranteed by these, possibly dark, protons residing at a larger space-time sheet.

For more details see the chapter Crop circles and life at parallel space-time sheets: part I of "Genes, Memes, Qualia,...", where a brief overview about living systems as ordinary matter quantum controlled by dark matter is given. If you are too afraid that you neighbor spots you in the middle of act of reading something about crop circles, you might prefer the end of the chapter Many-Sheeted DNA.

Matti Pitkanen


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