Enzymes
Enzymes are one of the key types of polypeptides and are crucial
to life on earth. All living organisms use enzymes to make, modify,
and chop up the polymers discussed here. Enzymes are the catalysts
that do specific jobs. In fact, oftentimes each enzyme does only
one type of job or makes only one kind of molecule. This means
that there have to be lots of different enzymes, all made of different
combinations of amino acids joined in unique ways in polypeptides,
to do all the jobs that any living organism needs done. We know
that every creature on earth has hundreds or even thousands of
different enzymes to do all the jobs that it requires. What's
really strange is that each one of the enzymes has to be made
by other enzymes. This leads to very complicated control mechanisms:
we don't have the faintest idea (in most cases) how nature decides
what enzymes need to be made and when, or how the enzymes are
turned on and off. We are beginning to figure this out, and the
study of such systems is an important part of biochemistry and
biology.
Riding Down the Silk Road
One of the unique polypeptides that we used very early for its
superb properties was silk. Silk was discovered by the Chinese
long before the birth of Christ. Silk is made by tiny caterpillars
trying to spin cocoons for their transformation into moths. We
steal the silk from the caterpillars which leaves them in limbo,
pretty much. The silk is spun into fibers.
Bundles of very thin individual polymers joined together to be
stronger. This is the way we also make rope, using weak individual
strands bound together in such a way that the total is both flexible
and strong. The structure of silk molecules is unusual for a
polypeptide. It possesses lots of the unsubstituted amino acid,
glycine. Glycine segments are able to form flat extended chains
that can pack together nice and tightly. This gives silk its
unique strength and shiny flexibility. Silk has such unique properties,
especially in hot wet climates, that it dominated trade for centuries
in east Asia. The silk trade between Japan and China controlled
the economics of civilizations in that region for longer than
either country cares to admit. Even in America, silk was important
before World War II for use in silk stockings. When silk was
used for parachute cord, women in America got very upset. This
resulted in chemical companies synthesizing artificial silk, nylon,
to make nylon stockings so that women's feet could stay warm and
the men could go back to fighting their wars.
Another key difference between polypeptides and nylons is the
way they are made. We humans make nylons in tons per day in huge
chemical plants where simple molecules are joined together in
large quantities to give products that we need or want. Nature
is much more careful and concise in how she does things. For
a living organism to make an enzyme, another enzyme or active
species must be involved. The synthesis always involves a template,
or recording, of how the individual amino acids are to be joined
together to give the final polymer. This template, or map is
a messenger RNA (mRNA). The message it carries, of course, is
how the peptide-making enzyme involved should make the polypeptide.
Each amino acid is brought to the enzyme by a carrier molecule
and is activated for incorporation by a whole cascade family of
reaction steps. The enzyme adds a single amino acid, one at a
time, as indicated by the mRNA. This is a slow and tedious process
and takes a long time. Sometimes the enzyme gets frustrated,
waiting for the right amino acid to come along, and slaps a wrong
one on instead. To compensate this the enzyme is made to back
up occasionally to check its work. If it has made a mistake,
it has a process for clipping out the wrong amino acid and inserting
the right one. We humans never do this. If we make a mistake,
we simply grind it up and throw it away.
Our Feeble Capabilities
We are beginning to understand how nature puts these molecules
together and we've figured out how to do it ourselves. However,
we're not very good at it and can't make very large molecules
vary efficiently. The reason is, if we make a mistake, it ruins
the whole molecule and we don't know how to fix it. The kind
of machine that's used to make synthetic analogs of polypeptides
is called a "peptide synthesizer". Such a machine is
built around tiny polymer beads that we attach to the first amino
acid which we want to put in our polypeptide chain. (This is
called the Merrifield Synthesis Approach. The use of polymer
beads was a great creative idea, and Robert Merrifield won the
Nobel Prize for it back in 1984.) We than take an activated
amino acid, similar to what nature uses, and attach it by forming
an amide bond. We repeat this process over and over again, trying
to get this reaction to go every time on every molecule on every
bead. Sometimes, we are not so lucky and we miss and amino acid.
This means that some of the polypeptides have units missing.
This always leads to mixtures of good product and bad product,
in which the good product may be the minor component. This gets
worse the bigger the polypeptide we are trying to make, and is
one of the major problems we have with how we make polypeptides.
If we could just figure out how to back up and check each one
of our additions, and then correct the mistakes that are there,
maybe we could do as good a job as nature. Maybe.
You're probably asking why we would want to do such a bad job
of making synthetic analogs of what nature does so well. (If you
aren't, just play along anyway.) There are lots of reasons, one
of which is to figure out just how nature does it. Another is
to figure out why peptides and enzymes work the way that they
do. It's not always clear to us mere mortals why a given sequence
of amino acids causes a polypeptide to assume a certain shape
or structure. These structures are key to how the polypeptides
do whatever job nature has devised for them. Sometimes, when
we see the way nature puts these molecules together, we can make
synthetic analogs that do the same thing but are easier to make.
This has led to the development of new drugs and to treatments
for some genetic diseases.
Nature also does things differently than us by synthesizing polypeptides
in water. Most of our syntheses, in fact, don't use water. We
synthesize our polyamides in toxic organic solvents. This leads
us to a problem: what do we do with the organic solvents when
we're through? Sometimes we burn the, but more and more we try
to recycle these materials. Not only are they getting more expensive
to buy in the first place (compared to cheap water which is everywhere,
or almost everywhere) but we must be responsible for their recycle,
purification, and final disposal. An example of how nature uses
water in this way, and one which we still haven't figured out is
the production of spider silk. Spiders spin their webs from solutions
of polypeptides in water. These solutions are squeezed through
the spider's tiny spinneret and elongated quickly to form the
spider webs which we've all seen and sometimes gotten tangled
in. What's really weird is that, once these spider webs form,
they are no longer soluble in water. If we could just figure
out how spiders first make spider silk in water and then spin
their webs from it, we could make nylon the same way. This might
save us a lot of waste disposal problems, and money. This is
one area of basic research where we need lots and lots of help;
maybe you can think of something we could try.
If you have an idea, let us know about it on the form below!
Another family of polysaccharides includes starch and cellulose.
Starch
is a high molecular weight polysaccharide. Foods like bread, corn, and
potatoes are full of starch. Starch may
have as many as 10,000 sugar units all linked together. The way these
units link up, all in a linear arrangement or with some of them
forming branches, determines what kind of starch or polysaccharide
it is (more about this later). Another very important member
of the polysaccharide family is cellulose.
This is the main polymer that makes up plants and trees. Wood is
primarily cellulose This
polymer is different than starch. (Click here
to find out more.) Starch is soluble n hot water and can easily
be made into useful objects. Cellulose, on the other hand, is
highly crystalline
and almost totally insoluble in anything. Cotton is a form of
cellulose that we use in most of our clothes. The fact that it
is insoluble in hot water is important. Were it otherwise our
clothes would dissolve when we washed them. Cellulose also has
the neat property that when you wet it and run a hot iron over
it, it smoothes out and flattens down. This makes our cotton
clothes look nice (at least for a little while) but still allows
them to clean up easily when we wash them.
Another member of the polysaccharides is chitin. It makes up the shells
of crawfish, shrimp, crabs, lobsters, and other crustaceans. It is hard,
insoluble…and yet
somehow flexible. We haven't figured out how to make synthetic polymers
that have this neat combination of properties. We also haven't
figured out how to do much with chitin, although we do use cellulose
for a lot of chemical applications and to make paper, wooden
houses, wooden shoes, and the like. There's a lot of research
underway to use chitin for different stuff, and maybe someday
we'll make clothes or plastic out of it. This is an area of research
that its important since it uses natural polymers that come from
renewable resources or waste products. (Do you know how many
shrimp lose their shells every year for us?)
