Professor Dave here, let's learn about enzymes.
We now know that proteins are polymers of amino acids, and since
there are 20 amino acids in the body, and each protein has hundreds of amino acids,
there are a mind-boggling number of possibilities for primary protein
structure. This is how proteins can be so diverse and serve so many functions in
the body. One type of protein is called an enzyme. An enzyme is a protein that
serves some catalytic function in the body. Remember that a catalyst is
something that lowers the activation energy of a reaction, and enzymes
catalyze biochemical reactions. These are critical molecules for living organisms
because nature can't do chemistry like we do chemistry in the lab. In the lab we
can throw anything we want into a flask and heat it up,
cool it, down use strong acids and bases, or any number of strange exotic
compounds. But inside your body,
nature has to do chemistry at body temperature and neutral pH, only with the
materials at hand and using only the reactions it has stumbled upon by blind
chance over the past few billion years. Thus the enzyme evolved. An enzyme takes
a chemical reaction that would be nearly impossible inside the body and makes it
up to a trillion times more favorable, such that it is feasible to occur on a
normal biological time scale. So how do they work? Well every enzyme has a
specific substrate, and the enzyme recognizes its substrate with extremely
high specificity, so it's kind of like a lock and key, where a specific molecule
is the key that activates the enzyme's function. There is a specific area on the
enzyme that the substrate will bind to which is called the active site.
The substrate will bind to the active site because it has just the right shape and
composition to do so,
meaning it is the right size but it also has functional
groups that make favorable electrostatic interactions with certain key residues
in the active site of the enzyme, whether those are van der Waals interactions,
hydrogen bonds, or any other interaction of this type. The substrate might fit
into the active site as is or it might cause an induced fit, where the enzyme
changes shape slightly once the substrate is inside. But either way, once
the substrate is inside the active site and binding has occurred, a number of
things might happen.
One possibility is that the enzyme causes the substrate to bend in a
particular way, which it will do in order to make certain interactions with the
enzyme, and when in this bent configuration some of the bonds become
weaker and easier to break. This is one way the enzyme qualifies as a catalyst.
The molecule would have a hard time breaking apart on its own but in the
conformation induced by the enzyme, the activation barrier associated with the
reaction is much smaller, so many enzymes have the task of breaking down large
molecules like the ones we eat to form the tiny components that we can use to
build our own biomaterial. Once the enzyme catalyzes the reaction, the
reaction proceeds, the altered substrate leaves, and the enzyme can then go and
catalyze another reaction. Enzymatic activity is always stereospecific,
meaning that if a substrate can exist as two mirror images, only one of those forms
will fit into the active site of the enzyme. Most enzymes have names that end
in "ase" so you'll know an enzyme when you hear one. The rest of the name usually
has to do with what the enzyme operates on. For example, the enzyme lactase breaks
down lactose, the sugar found in milk, into two smaller sugars. We will learn
about these types of molecules next. It is a deficiency in lactase that causes
lactose intolerance in some people, because without enough of this enzyme it
is very difficult to digest lactose, as nothing is present to break it down once ingested.
But breaking down molecules into pieces isn't the only thing that enzymes can do.
Let's look at the categories. We already mentioned enzymes that break down
molecules, and those could be a hydrolase, which catalyzes the hydrolysis of a
chemical bond, which effectively separates a molecule into two pieces, or
a lyase, which also cleaves covalent bonds, but by means other than hydrolysis.
An enzyme with the opposite function, a ligase, is an enzyme that joins two
molecules together. A transferase is an enzyme that transfers a functional group
from one molecule to another, an isomerase catalyzes a spatial
rearrangement of the substrate, and an oxidoreductase is an enzyme that
transfers electrons from one molecule to another. Sometimes when an enzyme
operates on its substrate, they will temporarily become covalently linked.
This can happen if a residue in the active site has a nucleophilic group
like the hydroxyl group on serine, which can react with an electron-deficient
atom in the substrate, kind of like an SN2 reaction. Sometimes an enzyme simply
does acid-base catalysis, meaning it either donates a proton or accepts a
proton from some functional group on the substrate to make it more reactive.
An example of this is when a residue in the active site is acidic, like lysine, which
if protonated at the amino group, can donate this additional proton.
Sometimes in order to function, an enzyme requires certain cofactors or coenzymes. This is
some other thing that must also bind to the enzyme before it can operate on the substrate.
Cofactors are things like metal ions, where as coenzymes are actual
organic molecules like vitamins.
That's why we need to get all our vitamins, so that our enzymes can
function properly. So you can see that there is a great variety of enzymatic
activity, and all of it is biologically crucial. Certain enzymes break large
molecules down into the small components we need for other enzymes to then build
up all the biomolecules in our bodies, which is constantly happening
in every cell in our bodies. We will come back to enzymes later but for now let's
move on to some other biomolecules.
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