In this biology series, we’ve introduced some aspects of biotechnology, but the field goes
much deeper than the handful of techniques most people are aware of. Beyond feats of ingenuity,
like engineering bacteria that produce insulin in mass quantities to treat
diabetics, synthetic biology has tremendous application in the realm of materials science.
For those who are unfamiliar, materials science is precisely what it sounds like.
It is the science behind the manufacturing of all the different materials we interact with
every day. Take a look around you. Consider any appliances that are nearby.
Look at the screen on your computer or smartphone. The materials required to
make these objects were not plucked from a tree, they were developed by humans,
and materials science is an interdisciplinary field spanning chemistry, physics, and engineering
which has made this possible. In short, for the past few centuries we have been learning
how to do chemistry to invent new materials, with ever-increasing success and creativity.
An example of this can be found in the petrochemical industry.
Petrochemicals are substances obtained from the refinement of petroleum.
We have all heard this word before, but what does it mean? Petroleum, sometimes called crude oil,
is a mixture of liquid hydrocarbons that is present in certain rock strata. It is organic
matter, the remnants of ancient living organisms like bacteria and algae, which once dead, sank to
the sea floor and was buried with other sediments, transforming slowly over millions of years
into what we know of as oil, essentially just a soup of hydrocarbons sequestered deep underground.
We can extract this oil from the ground with drilling machines,
and then employ a refining process which separates the different organic compounds that are present,
each having different uses. Of course everyone knows about one major application for petroleum,
and that is gasoline. We use oil to make gas for our cars and other vehicles. But what is
less commonly discussed is that components of crude oil are used as a starting material
in manufacturing synthetic fabrics, plastics, and many other materials. It may come as a surprise,
but nearly everything in our modern world is derived from this process to some degree,
from electronics to clothing, cars, houses, and much more. In truth,
the petrochemical industry is comfortably the largest materials industry on Earth,
processing nearly a hundred million barrels of oil per day, and worth trillions of dollars per year.
The majority of this output is associated with the production of fuels, but the production of
plastics from petroleum is still a half a trillion dollar industry that is continuing to grow.
Of course there are tremendous environmental and political ramifications associated with the
acquisition of oil and its usage, all of which is hugely important to discuss. But that discussion
will be left for future playlists in environmental science and political science. In this tutorial,
we are simply going to discuss the process by which such materials have traditionally been
produced, and the ways in which biotechnology is beginning to revolutionize this industry.
Now, as we mentioned, it has been common practice for well over a century at this point
to take crude oil, refine it, and then use its components to engage in chemical manufacturing,
which just means doing chemical reactions on an industrial scale. There are many challenges
associated with this approach. It can be difficult to get certain reactions to proceed on such a
massive scale as they would in a regular chemistry lab. Some such reactions have toxic byproducts.
In the cases where stereochemistry is relevant, these processes are typically not enantiospecific,
so we get racemic mixtures instead of precise stereoisomers, thereby limiting utility.
And as most of us are aware, large quantities of carbon dioxide are released in the excavation,
manufacturing, and usage of petroleum products, which has serious environmental ramifications.
But in recent decades, an elegant solution to all of these problems has been identified. If
we understand that oil is ultimately a biological product, then it follows that we should be able
to make oil products biologically, and indeed we can. As we know, nature also does chemistry,
and within a living organism, the bulk of this responsibility is performed by enzymes.
Enzymes each catalyze a highly specific chemical reaction or set of reactions,
and they do so with a high degree of efficiency, and enantioselectivity. Living organisms employ
thousands of enzymes in complex interconnected networks to transform simple, readily available
starting materials into a variety of compounds with biological utility. As we know, plants use
enzymes and energy from sunlight to convert carbon dioxide and water into complex carbohydrates. Then
other organisms with different enzymes use those carbohydrates and oxygen to generate a variety
of other products, releasing carbon dioxide in the process, thereby creating a cycle of synthesis and
breakdown between these interconnected chemical factories. And although each individual enzyme is
far from versatile, typically able to do only one thing, they do that thing extremely well.
So enzymes seem to be a slam dunk as far as promoting efficient chemical reactions.
And fortunately, biotechnology is now in a state where we can produce and utilize enzymes with
relative ease. Just the way that we can engineer microorganisms which produce proteins like insulin
for medical purposes, we can engineer them to make any kind of enzyme we want, and these enzymes can
perform desirable chemistry for us. However, this approach provides challenges of its own. There are
a finite number of enzymes that exist, and again, they facilitate very specific transformations. In
other words, individual enzymes can only carry out certain reactions on a small number of substrates,
so they can’t perform every single reaction we can think of. Therefore, if we have a particular
target molecule in mind, it is far from trivial to identify a series of enzymes that will take some
readily available starting material and induce the ultra-specific series of transformations
that will yield our target molecule. Nevertheless, this is the incredible
task that synthetic biologists have set their sights upon. And although their science is
groundbreaking in many ways, it should be noted that it actually builds upon ancient practices.
For thousands of years, we have utilized microorganisms like yeast in order to
make alcoholic beverages, including beer and wine. These organisms take plant-based sugars,
and through anaerobic respiration, which we learned about in a previous tutorial, they produce
energy for themselves, while generating ethanol as a byproduct, the alcohol that we commonly refer to
as simply alcohol. These organisms perform this chemistry using enzymes. For the longest time,
we had no clue what we were actually doing on the molecular level in perfecting the brewing process.
We just knew that if we mix these things together in a low-oxygen environment,
we get a wonderful beverage. But thanks to the incredible advancements in the biological
sciences that took place in the 20th century, we now know precisely what these organisms are doing,
step by step, to convert sugar into ethanol. We know which enzymes they are utilizing,
and we know precisely what each enzyme does. So with this newfound understanding, we are learning
how to employ this type of process to get nature to make the substances that we want instead,
using not just the enzymes found in yeast, but an exponentially expanding catalog
of every known enzyme, compiled from a wide array of biological organisms and cellular functions.
Now, as we learn what reaction each of these enzymes is capable of catalyzing, it then
becomes possible to piece together synthetic strategies. Consider any synthetic pathway we
could employ in the laboratory, broken down into a series of steps, each of which involves a specific
transformation. These transformations could include oxidation, reduction, proton transfer,
elimination, virtually any of the reactions we learned in the organic chemistry series. Then, for
each step, instead of identifying reagents that would promote the reaction in a laboratory flask,
we try to identify a class of enzymes that could conduct the reaction. This class can include
experimentally validated enzymes known to conduct similar reactions, as well as any of the thousands
of homologous enzymes from tens of thousands of species, some of which may also be able
to carry out the reaction, with the eventual goal of selecting the best candidate for the reaction.
Let’s say it’s a five-step synthesis. If we can determine a sequence of five enzymes that
will catalyze those five transformations, we have generated a potentially viable strategy
for the production of a compound. Now the question is, how do we get the
enzymes? Well again, we can use nature. Enzymes are proteins, just like insulin, so the strategy
here will be identical to that of biosynthetic insulin production. Whatever the gene is which
encodes the enzyme of interest, we can synthesize the gene ourselves, place it in a DNA plasmid,
insert the plasmid into a microorganism, and the gene will be expressed just like any other,
generating the foreign enzyme within the microorganism. Now let’s say we synthesize the
genes for all five of these enzymes that together correspond to the pathway of interest. We can put
all five of them in a plasmid, insert that, and the microorganism will make all five enzymes.
Then we just feed the microorganism some cheap feedstock such as plant-based agricultural waste,
and it’s off to the races. This feedstock provides the energy and raw materials for the various
biosynthetic pathways that naturally occur in that organism, and somewhere within those pathways
lies an intermediate that can be funneled into our novel pathway to generate the target molecule.
Furthermore, the microorganism will reproduce at an exponential rate,
so before long we will have trillions of cells each acting as a little factory, with
the foreign enzymes inside, doing all the work we need them to do to get the product we want.
With each year that passes, our understanding of biological metabolic processes grows.
Our catalog of enzymes expands by leaps and bounds, each of which represents a
potential tool in our toolkit for conducting chemistry purely through biological processes.
The benefits of this technique are as varied as they are powerful. First there
is the environmental impact. By employing this approach to produce plastics and other materials,
petroleum as a starting material is obsolete. This significantly reduces the amount of oil we
require, and therefore the amount of carbon we dig out of the ground to be released into the
atmosphere. We can instead use cheap and non-toxic raw plant material to feed microorganisms,
whether that is wood pulp or agricultural waste. Those plants have removed carbon dioxide from the
atmosphere, so rather than pulling sequestered carbon out of the ground and releasing it, we
sequester carbon from the atmosphere and harness it in the manufacturing process. So even though
materials production constitutes only a fraction of oil usage, it still makes an enormous impact.
The next advantage is apparent in examining the process itself. Large-scale process chemistry
is very complex, with huge industrial machinery, expensive chemicals and solvents, and many other
challenges. This type of biosynthesis, by contrast, is quite similar to the process of
brewing beer, apart from the fairly complex task of isolating and purifying the finished product.
Of course there is an incredible amount of work to be done up front in identifying the enzymes,
manufacturing the plasmids, engineering the microorganism, optimizing the growth
conditions for the microorganism, and so forth. But once all of that is done,
that strain is placed in a vat with raw plant materials, and the whole thing just goes on
its own. No expensive machinery. No isolating and purifying each intermediate along the way.
It can literally be done all at once in a relatively simple vessel, with purification of
the product from the fermentation broth occurring all the way at the very end of the whole process.
Beyond this, while traditional chemistry may require dramatically different processes and
equipment for one product with respect to another, with biosynthesis the equipment
is always the same, that one same vessel. The end result of all this innovation means being able to
transform raw plant matter from agricultural waste into plastic. You can’t get any greener than that.
Without a doubt, it would seem that this approach is poised to revolutionize the production of
important materials, and by extension the world. With the general concepts behind this process now
understood, let’s move forward and get a little bit more specific with the details.