Enzymatic Processes in Ecology

Enzymatic processes are very important in ecology. As already stated, most of the biological reactions could not occur or could occur only after a very long time without the catalytic action of enzymes, even if the AG0 of the reaction is negative, that is, the reactions are spontaneous. For instance, glucose reacts with oxygen to produce carbon dioxide and water: the AG0 is highly negative and the glucose is almost completely consumed in the reaction. Nevertheless, if we dissolve the glucose in water saturated with oxygen, the reaction could not start for a very long time because of the stability of the molecule of glucose, that is, because of the high activation energy needed to break the molecule.

On the contrary, in an aqueous cellular environment, glucose reacts fast through a series of enzymatic reactions that permit not only to foster the primitive reaction, but also to use the energy released during the reaction to build other molecules needed by the cells (e.g., ATP).

Therefore enzymes are fundamental to most of the biological processes of ecological importance: for instance, they allow the digestion of food and the assimilation of elemental nutrients, and they contribute to the defense and in general to the metabolism of the organism.

Hereinafter, some examples of enzymes fundamental to ecology are briefly described. They are selected from all because they are linked to three important processes. As we know, ecosystems can be characterized by the fluxes between the different compartments of three different currencies: mass, energy, and information. The three processes are related to these three currencies: photosynthesis, synthesis of ATP, and replication of DNA.

One of the most important processes in ecology related to mass transfer is primary production: it constitutes the basis for all trophic network and hence for the development of life. A part of some chemotroph organisms, most of the primary producers are phototroph, that is, they fix inorganic carbon into new biomass by photosynthesis. This complex reaction is composed of several intermediate stages: the carbon fixation usually occurs by carboxylation of ribulose-1,5-bisphosphate, to produce two molecules of 3-phosphoglycerate (3GP), that are successively transformed in glucose. The carboxylation is fostered by (RuBisCO, which is the most abundant enzyme in the planet.

The turnover number of this enzyme is very low, especially compared to the average of other enzymes; indeed, RuBisCO is able to fix only few carbon dioxide molecules per second, resulting as the limiting factor in the photosynthesis reaction (at least in normal conditions).

As suggested by the name, RuBisCO is able to foster two different, and in some way opposite, reactions: the carboxylation and the oxygenation of the ribulose-1,5-bisphosphate. The latter reaction produces only one molecule of 3GP and does not fix any inorganic carbon, binding into the active site a molecule of oxygen, that in fact acts as a competitive inhibitor for carboxylation.

As any other competitive inhibitor (see section titled 'Enzymatic Kinetics'), the presence of oxygen slows down the main reaction but it does not affect the maximum rate that can still be achieved with the high concentration of main substrate (in this case CO2). For instance, many phytoplankton taxa have adapted to this competition developing some carbon-concentrating mechanisms in order to increase the internal concentration of inorganic carbon (as carbon dioxide or carbonic acid) and to support carboxylation. The specificity factor for this enzyme varies by an order of magnitude in different phytoplankton taxa and it can be observed that taxa with lower specificity factor of RuBisCO, that is, where oxygenation can occur more frequently, have greater capability to concentrate inorganic carbon.

Another strategy to enhance carboxylation is to increase the maximum rate increasing the total amount of enzyme available, and this could explain why this protein is so abundant. Another important process related to mass fluxes in the ecosystems is mineralization of organic matter by microbial community. The well-known mass conservation principle implies that all elements cycle in the ecosphere through different pathways. Organic matter cycles from inorganic compounds that are fixed by primary producers, to the different levels of consumers through the trophic network; the dead organic matter is degraded and finally mineralized into inorganic compounds: in this way, the cycle can start again and new live organisms can be born and grow. The mineralization of organic matter is executed by enzymatic process via a multistage process, whose ultimate steps are executed by microorganisms that use organic matter as substrate in order to complete their metabolic processes (i.e., to grow). The dynamics of mineralization can hence be described with the kinetics equation for bacterial growth, known as the Monod equation (see section titled 'Enzymatic Kinetics').

Energy in the cells is transported and stored by ATP molecules: they consist of a molecule of adenosine and three phosphate groups. The chemical bonds between the phosphate groups are extremely rich in energy, that can be released when ATP loses one or more of them (e.g., the transformation from ATP to ADP releases about 10kcal mol-1). ATP synthesis is catalyzed by the ATP phospho-hydrolase (H+-transporting), commonly named ATP synthase: this enzyme is present in bacteria membrane, in plants (where the synthesis occurs in the chloroplast during photosynthesis), and in animal cells (in the mito-condria where respiration occurs). The structure and mechanisms are almost same in spite ofthe big differences between the metabolism of all these organisms. The enzyme is composed of two parts connected by an irregular shaft: one (called F1) with the active sites that catalyze the reaction, and the other (called F0) that acts as a proton pump in order to provide the protons needed for the ATP synthesis.

Each active site may have three different conformations:

• a loose conformation, when it binds substrates (ADP

• a tight conformation, when catalysis occurs; and

• an open conformation when ATP is released.

The shift between a conformation and the following is driven by the rotation of the shaft, forced by the proton flux through F0. In the F1 part, there are three active sites that are always in different conformations, making the ATP synthesis a continuous process.

The same enzyme is also able to catalyze the reverse reaction of hydrolysis of ATP: this process, catalyzed in the F0 part of the enzyme, is used for instance by some bacteria that consume ATP generated by fermentation in order to provide protons to drive substrate accumulation, maintaining ionic balance.

One of the elements that carries most of the information in an ecosystem is DNA. The DNA is a long polymer of nucleotides with the structure of a double helix where all the information necessary to the survival and development of the cell, and organisms, is concentrated. During the cell duplication process, which is at the basis of the growth of organisms or of population of monocellular organisms, all the information need to be transmitted to the offspring cells: this is achieved through a complete replication of the DNA in two identical copies, that afterward split in the two offspring cells. Synthetically the replication process can be resumed in three principal steps: initiation, when the process starts and the double helix is unwound; elongation, when the new strands are synthesized; and finally termination, when DNA is totally duplicated and need to be separated in the two new double helixes. This whole process is not spontaneous, but it requires several enzymes able to catalyze every single step. The most important ones are topoisomerase, which begins the unwinding of DNA; helicase, which completes the unwinding and splits the DNA helix; the DNA polymerase, which polymerizes the nucleotides to replicate the strands; and the DNA ligase, which connects the fragments of DNA (called the Okazaki fragments) formed in the replication of one strand of DNA. DNA polymerase adds nucleotides to a primer (a DNA or RNA basis) and then moves along the strand to add another nucleotide or break away from the strand. There are several types of DNA polymerases, which differ for function and ability: some are also able to check and correct mistakes that occurred in the replication, while others can only elongate the new chain of nucleotides. Furthermore, some types of polymerases can add only a few nucleotides before they break away and are replaced by other poly-merases, while some others are able to polymerize thousands of nucleotides.

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