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Example Weekly Reflection: Enzyme Lab

Wil Franklin's picture


I've been thinking about a lab activity on catalase enzyme and struggling to find an interesting and compelling reason why students need to know about the idea of enzymes and the subtler points about enzyme kinetics.  To put a fine point on it, I want a very particular problem or question that cannot be answered fully without the understanding of enzymes.  What follows in my latest train of thought.




Energy and matter is well defined and highly predictable with the exception of black holes and the beginning of time.  In fact, energy is coupled with matter by Einstein's  E = MC2.  Radiant electromagnetic energy can be described and predicted by wave and particle models, while heat and matter can be easily understood in terms of entropy or the second law of thermodynamics.  Simply put, the second law says, energy and matter abhors gradients.  All gradients of differential matter and energy in space tend to fall apart - gradients disappear. Stars, planets, solar systems, galaxies temporarily resist this tendency, but all eventually succumb as the universe moves to a big homogenous mixed up soup. This is what is meant by the second law that states entropy in an open system will always increase (systems always increase in chaos and decrease in order/structure).

Living systems and systems with life in it are a little different. Yes, here too, on whole entropy always increases (gradients disappear), but "somehow" life uses this falling apart of gradients to make, maintain and remake gradients.  Perhaps, life might be described by a particular organization of matter in space where energy does not adhere to it's normal predictable patterns.  Life is tiny spaces where entropy decreases - order increases.



So, what is this "somehow"? How does life resist the laws of physics? Science begins to make sense of this dilemma with the concept of enzymes. Enzymes are a proteinaceous molecular catalyst with a twist.  Catalyst in general facilate the falling apart of matter that is not inclined to do so.  But unlike a simple catalyst, enzymes use energy to restructure matter such that some of the energy released is used to decrease entropy that would have other wise gone to waste - read, entropy increases if that matter falls apart in the absence of enyzmes. (This is a gross simplification, the subtleties are reserved for a more in depth study of enzymes, beginning with a footnote below). Why do enzymes do this?  It is not for science to say. Suffice it to say, enzymes do and ever since they started doing so, they have become more sophisticated at persisting, until through evolution (read lots of time) little replicating cells of interacting enzymes were formed. These bags of enzymes further enhance the entropy decreasing properties of this space and eventually go on to form interconnected ecosystems of energy flow and matter cycling.  The biosphere of our planet earth is just one big complex of structures that siphon off some of the energy that normally increases entropy to cordon off a space where entropy instead, decreases.  The biosphere is an elaborate system that resists and reverses (temporarily?) entropy.  And all this is possible because of the trick of enzymes.  The properties and processes of enzyme influence the flow of energy through individuals (metabolism) and as such through ecosystems as well.


Here's a question: How can we know that a population of organisms needs food/energy and what is the most efficient food to supply if we could and wish to keep it growing?  Specifically, in a several separate populations of yeast living off different energy sources, which populations are going hungry and which food should we supply if we care to keep the population healthy and growing?


Footnote: Enzymes only speed up reactions that would otherwise happen or could possibly happen, that is to say are energetically feasible according to the laws of physics that are being discussed above. Thus, it would seem that enzymes do not create, maintain or remake gradients but rather just speed up the inevitable falling apart of them.  But there is a subtle point that turns out to be significant to this discussion.  Some enzymes can catalyze reaction that for all practical purposes would not happen, thus creating species of molecules that would not exist. This is particular true when we expand to large populations and multiple, coupled enzymatic reactions. Simple probability states that the probability of any consecutive events is the product of each of those events individually.  Thus an extremely rare energetic transformation that must occur before another extremely rare reaction and on and on would thus be near impossible.  However, in the presence of a large populations of enzymes that make these events much more likely by adding a bit of energy to help jump start the reaction, the series of contingent events that would otherwise be nearly impossible (effectively so rare that it doesn't ever occur) now comes into existence.  Furthermore, enzymatic reaction that increase the likelihood of these reactions also tend to build up the new species in concentrations that would not otherwise occur in nature, effectively creating a gradient and increasing the likelihood that more of these types of reaction can occur - all simple probability.