Some Philosphy of the Enzyme

This is a quick blurb on thoughts I managed to have while watching a lecture video on enzymes. It portrays some of the philosophy behind why enzymes exist, enzyme reactions, and what an enzyme is. This reading is not specifically at a layman’s level, I did not invest the time to write out explanations about every term or concept, although I did try to explain a little bit here and there, it assumes at least advanced high school biology or first-year undergrad (enzyme) biology or biochemistry and most efficiently, at least an undergrad degree in biology or related to fully understand the full abstract concept I am trying to portray. Or maybe some very astute intellects or philosophically educated people might be able to parse my argument. But I think maybe everyone can learn something from this reading.

Enzymes are proteins which are built in such a way as to increase the effectiveness of chemical reactions which would not take place under normal conditions.

Some biochemical reactions can take up to 1015 years to proceed, longer than the age of the universe. This means they are simply not favorable, they just don’t happen under normal conditions. It’s like trying to get a pig to fly -it just doesn’t happen.
An enzyme would be analogous to giving a pig some wings, or allow it to levitate so that it may experience flight.

Two molecules with a low, or negligible, reaction rate may not react and form a new product or two new product molecules. If a reaction rate is 1015 years, this means that it would take 1015 years for this specific reaction to happen, and that this is caused by the random conformations and interactions that happen, and between all the probabilities of ionic charge placement, physical spatial placement, flexion speed and angle of the interaction would all be at the highest possible probability for a reaction to take place, and that this probability is something like 10-15 %. It’s not impossible for this reaction to take place, but it takes so many perfect conditions lining up for it to happen. These conditions allow for the highest energy conformation to overcome the energy barrier required to initiate the reaction (just as a match doesn’t light up by itself, it must have energy input by mechanical arm movement, a flick of the wrist, and the friction created by rubbing the match on a surface). Here the conditions between two molecules I have described above all line up to give it the necessary energy to overcome this barrier and react.

Figure: reaction progress where the x-axis is time, and the y-axis is amount of energy required to overcome the change from starting (reactant) molecules to product molecules. Here, Ea stands for energy of activation, and we see that an enzyme catalyzed reaction lowers the barrier for reaction to proceed. Think of the two lines like hills one must push up a large boulder, the red steeper hill (no enzyme) is harder than the enzyme hill (purple).

It takes a lot of energy to make an enzyme. ATP is used in the process of transcription (RNA making), translation (RNA to protein making), and further, building the amino acids for the protein, breaking down proteins from food, and folding the protein (enzyme) into its native conformational shape. When a protein is folded, it contains energy in its bonds and its tertiary and quaternary conformations. The ionic interactions and hydrophobic interactions work to fold the protein, and it adopts its shape when it reaches a stable energy conformation. When this conformation is met, it is basically a ‘bank’ or investment of energy, in which it contains polarized ionic interactions ready for use.

These ionic interactions interact with the molecule of choice and fold it or bend it in a way which wouldn’t be favorable normally (which it wouldn’t do on its own). It also interacts with the other molecule of choice to line up to conditions to make it favorable to interact. This reaction with a rate of 1015 years now takes seconds or milliseconds. An enzyme is a catalyst which is stored energy in a specific manner to allow the low probability conditions to have a high probability by specifically lining up the angle of interaction between the two, folding the proteins in a specific manner by using the charges the enzyme contains as a source of energy. This is how it overcomes the initial activation barrier.

So, philosophically speaking, an enzyme is stored energy with a specific function of creating the favorable conditions for two molecules to perform a low probability reaction. Enzymes are available because they perform this function -they are required for life. They are mediators of chemical reactions and is why they only appear in specific places, such as in specific compartments within biological organisms. This is to assure that the two molecules won’t’ react spontaneously all the time, and only react under those specific conditions (in the biological compartments required for life).

The universe has made it so that the reactants can be pooled into a biological compartment and reacted to form products (with usually specific function). The reactants are the molecules required to form the product, and the high energy of activation is required so as they not react outside of the compartment containing the enzyme. This allows specific reactions to take place in specific places, and the reactants to not be available everywhere. The products are readily available because they do not spontaneously degrade or react into something new.

But why would an enzyme be purposefully created to do this? To think of a biological organism evolving from the primordial pool of life, and to be set up in such a way that is compartmentalized and contains genes to code for enzymes which react specifically compartmentalized molecules for use in the greater chain of energy and metabolism of the organism is mind-blowing. It’s almost beyond intellectual limit. An enzyme, in this evolutionary analysis, is simply a chance set of (DNA) codons aligned in a specific manner to allow for the translation and construction of proteins from mRNA transcripts which are enzymes required to initiate obscure or difficult reactions to gain specific products to perform specific functions in vivo.

Nature is astounding in this manner, but within the evolutionary description, it is all just a series of probabilistic coincidences.

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