Saturday, October 15, 2005

What's a Ribosome?

A Ribosome is an enzyme.In most books it's describe as a huge machinery that has a specific function o mapping mRNA into proteins and many creationists use this complicated design (much like a turing machine) as a proof of existence of a "designer".

However if we think it out differently we can see a ribosome as an enzyme that has no specificity (see previous article on enzymes and specificity) and whose function is to create peptidic bonds. This enzyme however has two mobile parts, the first one is a domain that allows for a "mobile specificity" that is provided by RNA molecules that can be of 4 types as well as a two other domains that allow for the entry of tRNAs and also peptides (the growing chain of protein).

The ribosome then catalyzes the reactions where there's a match between the "mobile specificity" and the tRNA anticodon, when this happens the aminoacid bonded to the tRNA is transferred to the poly-peptide chain and a conformational change causes the mRNA chain to be displaced and a new codon is presented to the ribosome.

This complex behavior could be simplified as an enzyme that could only catalyze peptide bond reaction formations and then allowed for some degree of specificity that later became more complex as codons were inserted as well as the mechanism of using a mRNA string that would lead to the catalyzing reaction to become irreversible.

A good way to prove this theory would be to prove that a ribosome would have catalytic capabilities even if it had only one of its parts (the top part with the tRNA input for instance) and this could be simulated using 3-D lattice grids.

Tuesday, October 11, 2005

On reversibility of reactions and life

Irreversible reactions are those that either liberate energy as they happen or require energy in order to happen (this depends on the amount of Gibbs free energy difference of substrates and products).

An organism would try and do most of its work by using reversible reactions because these not only do not consume energy but also will not waste energy that could be used for more important tasks. In fact most of the irreversible energy freeing reactions happen in the glycolytic and cytric acid cycle where the free energy can readily be stored in the form of nucleotide triphosphates and other well known carriers of life. The reactions that are irreversible and consume energy are coupled to reactions that are irreversible and free energy (ATP dephosphorilation into ADP) and happen in situations where they are needed for the construction of polimers required for the cell's survival (DNA,RNA,etc.) or for the early steps of pathways that will later return the energy consumed (glycolysis for instance).

An important point to keep in mind however is that the control exerced by the organism in within the irreversible reactions and if all the reactions were reversible the organism would not be able to decrease its entropy and increase its environment's entropy and it could be no more complex than any thermodinamically closed system.

On the origins of Glycolysis

Glycolysis requires in its first steps the consumption of 2 molecules of ATP for each molecule of Glycosis to be digested. However such a metabolic pathway could not have emerged as so since it first requires consumption of energy that would be replaced only in later steps that might no exist yet.
Thus the evolution of glycolysis must have been in the inverse order of intake of Gycosis: in the beginning the cells or any previous forms of life used the molecules that were at the most energetic side of glycolysis and as evolution and natural selection acted, ways of converting more abundant species into the ones that could provide energy were developed (as enzymes that could catalyze these reactions).

On bacteria treatment

The approach used to erradicate bacteria, infections by parasytes such as T. cruzi/brucei and cancerous cells is to attack the targetted cells with radiation or drugs in order to kill them all despite thendeath also of host's cells. This approach however does not work on an heterogeneous population that will in fact loose the weakest (in relation to the drug attack) individuals and have them replaced by others more suitable to handle the drug attack. This process works exactly as natural selection and will lead to pathogens more and more resistant. However a reverse approach could be taken: A great abundance of nutrients would lead to an increase in the population where resistant pathogens would have to compete with the non-resistant ones that should have some sort of metabolic advantage since they don't have to carry the burden of the mechanisms that allow them to resist to the drugs. In this case after some generations the resistant pathogens should have lost all their resistant members and a drug attack would be more efficient. So a strategy could be to overfeed the pathogen and use a brutal drug attack as late as possible (as late as the pacient can survive the dru shock treatment).

On origin of life and need of DNA for a starter

The origin of life doesn't need a system enclosed by membranes in fact it would require a system as open as possible so the probability of different chemical species meet would be greater. The origin might be of multiple different molecules being interchanged by each other in equilibrium however the presence of some of them could act as catalysts (although weak) and this process might have lead to the eventual formation of chains where the substance A catalyzed the transformation of B into C (and vice versa) and the substance C catalyzed the convertion of a substance D into A and as long as B and D are abundant there will be an increase in the amount of A and C: an autocatalytic system that can be the precursor of life itself.

The system is easier to create when there are many more susbtances in the pool so the probability of making a closed chain becomes bigger and eventually the system becomes autocatalytic. The existence of membranes might have appeared later when the control of the input and output of substances into the system became more important than the diversisty of substances available (we can imagine that there's an equilibrium between a too big number of different substances are now required to stay together and that would be scattered away without the presence of some physical limitation (after all the membranes are catalysts as well since they keep the metabolites whithin a closed region of space)).

So life might have started before the advent of DNA or RNA or any other form of information storage system as predicted by Shroedinger. An information carrier might have appeared only after a mapping code started to be used in order to better control the metabolism, in fact the advent of a mapping system in only an extension of the process of adding intermediates into a chain reaction in order to provide autocatalysis.

Enzymes: evolution of catalysis and specificity

Enzymes probably didn't "appear" in nature as specific as they are today, in fact the first enzymes should be very general (break ester or peptide bonds, etc.) and then as a need of more control of the reactions, these enzymes have been duplicated and each of these copies specialized in order to account to specific metabolites (cross between substrates and products) that define a unique (or almost unique) reaction.

This process could proceed an then we would reach a situation where we will have more than one enzyme for each reaction (isoenzymes) that will have different control in different types of cells.

In order to prove this hypothesis one could create a simulator with a control system (enzyme sysnthesis and degradation) with both general and specific enzymes and show the differences between the control of metabolism in these two systems