Enzymes: A Primer

Hello, everyone! I hope you had an excellent weekend! Today I’ve been studying some biochemistry, and I thought, “I can’t seem to hammer down some of the details. You know what would be a good idea?” So here I am, writing happily about enzyme mechanics. Sorry in advanced if it’s a little haphazard and rushed; I’m about to have to go to physics, so I’m trying to get this done. All right! Let’s get down to business!

どうぞ


If you’ve studied much biology, you’ve learned pretty well what an enzyme is. As the catalysts of biological reactions, they’re the reason that your body can do things such as, you know, break down sugar for ATP, regulate your blood glucose levels, build complex molecules that you need to live, and so on. You know, no biggie.

Their usefulness is uncontested. Numerous times in my studies of biology-related things, I’ve heard professors and other scientists admit that to replicate the chemical reactions that enzymes carry out in our bodies at rates of millions of times a second is oftentimes nearly impossible. However, if you’re like me, you professor probably did a lot of hand-waving when it came to how they actually work. “Oh, you know, they, liek, lower reaction energy, ‘n stuff.” Thanks. That’s certainly specific.

Well, it turns out the reason that they weren’t being explicit is probably because it’s some difficult stuff to really get a handle on. Enzymes come in a wide variety, and they do a lot of things. Luckily, in an attempt to be systematic, scientists have already divided them up. First, though, let’s talk about what they all have in common.

First of all, enzymes increase the velocity of a reaction. That means exactly what it sounds like; when you put an enzyme into a reaction, it speeds things up. Why is that? Well, in brief, enzymes lower activation energy. What that practically means is that enzymes lower the energy required to make the reaction proceed by using pathways that are lower energy than would occur without the enzymes.

Secondly, enzymes are very specific; they will differentiate between isomers (3-phosphoglycerate versus 2-phosphoglycerate, for example) or make only specific isomers (glucose-6-phosphate instead of glucose-1-phosphate). That’s a good thing, too, since our body usually only wants one specific isomer of a molecule to work with (can I get a BODY, Y U ONLY WANT D-SUGARS?).

We’ll go into detail about mechanisms in a bit, but first, there are a few things to take note of: firstly, enzymes lower activation energy, but they don’t change the overall free energy change of the reaction. That makes sense, if you think about what free energy describes. Since free energy is essentially a description of the energy difference between the product molecules and the reactant molecules, and the enzyme starts with the same reactants and makes the same products, the same free energy change occurs in a reaction, regardless of whether it’s catalyzed.

This leads to a second point: enzymes make a reaction reach equilibrium faster, but they don’t change the position of equilibrium. If reactants are more abundant than products at equilibrium when the reaction isn’t catalyzed, they still will be when it is catalyzed.

Finally, enzymes catalyze forward and reverse reactions at equal rates; if an enzyme speeds up the formation of a product by 10000 times, let’s say, it will also speed up the reformation of reactants by that much, meaning that the ratios of the rates won’t change.

Phew, thank goodness that’s over. Now, let’s look at the categories, shall we?

Class 1: Oxidoreductases

These do exactly what they sound like they should; they catalyze redox reactions, or reactions in which electrons are gained or lost by the substrate. This is an important function, since, as my professor says, electrons are the “gold of the cell.” A good example of this enzyme at work is found in the sixth reaction of glycolysis; glyceraldehyde-3-phosphate (a phosphorylated sugar that comes from breaking down glucose after a number of steps) is turned into 3-phosphoglycerate using an oxidoreductase, and a molecule called NAD+ picks up hydride (a proton and two electrons) to become NADH. Alcohol dehydrogenase is another important enzyme—it turns ethanol into acetaldehyde by removing electrons (and two protons), which detoxes cells from alcohol.

Class 2: Transferases

Also appropriately named, these transfer groups from one molecule to another. This class is also extremely important for a number of reasons, not the least of which being that it includes a subclass of enzymes called “kinases” which transfer inorganic phosphate between molecules. (You know, phosphate. As in adenosine triphosphate. As in ATP.) A good example of a kinase at work in glycolysis is in the last step (step ten), wherein pyruvate kinase transfers phosphate from phosphoenolpyruvate to ADP to make pyruvate and ATP. This is an important step, since it’s the step where you finally generate net ATP in glycolysis!

Class 3: Hydrolases

Hydrolases break bonds using water. (Who would have thought, right?) They come in a lot of varieties, but phosphatases, which are hydrolases, perform the opposite function of kinases—they remove phosphate groups. For example, in the last reaction of gluconeogenesis, the process by which pyruvate is made into glucose (kind of the opposite of glycolysis, eh?), glucose-6-phosphate is made into glucose by a hydrolase (glucose-6-phosphatase) that cleaves the phosphoester bond between glucose and the phosphate with water.

Class 4: Lyases

These are easy to confuse with hydrolases, and their name doesn’t really tell you precisely what they do. Luckily, they’re pretty common! Lyases do one of three things: catalyze the removal of groups by breaking a single bond (without water), form double bonds by removing water, or add water to a multiple bond to make a single bond. It’s important to note that lyases that use water aren’t hydrolases because they’re only reducing bond order with water, not breaking the bonds between groups. Lyases crop up several times in glycolysis (yes, that’s where all my examples are coming from—I have to know it, okay?). For example, in step 4 of glycolysis, fructose-1,6-bisphosphate is split into two pieces, glyceraldehyde-3-phosphate (which then gets oxidized by the enzyme in my Class 1 example) and dihydroxyacetone-phosphate, by a lyase called aldolase.

Class 5: Isomerases

This is where that whole “stereospecific” thing really becomes an issue. Isomerases (you guessed it!) take one isomer of a molecule and turn it into another. That means they can turn glucose-6-phosphate into fructose-6-phosphate, D-ribose into D-arabinose, etc. These crop up all over the place in glycolysis, especially as reactions in equilibrium (they don’t take or make energy). A good example is in step 5; the diydroxyacetone-phosphate generated by the lyase in the example above is then turned into another glyceraldehyde-3-phosphate by triose phosphate isomerase.

Class 6: Ligases

Ligases perform the important function of forming bonds between molecules. A lot of times, these require ATP to do their magic. For example, in gluconeogenesis, a ligase called pyruvate carboxylase does about what you’d expect, and puts a carboxylate group on a molecule of pyruvate so it can eventually be made into glucose.

Phew! That was a lot of information, yeah? I thought so too. Sadly, that’s hardly the half of it. There’s still a lot to learn in this vein, especially when it comes to the reactions of glycolysis and gluconeogenesis. First, though, we still have to talk about enzyme mechanics.


Questions? Comments? There’s a lovely little text box down there! See it? I know you see it~!

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