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.
