Lyase

Transcription

So today, we're going to talk about enzymes and all the different kinds of reactions that enzymes can catalyze. But before we do that, let's review the idea that enzymes make biochemical reactions go faster. And if you look at a reaction coordinate diagram, you'd notice that enzymes speed up reactions by lowering their activation energy. Now, enzymes are generally named for their reactions, which is convenient because it makes it a lot easier to remember what an enzyme does if someone gives you its name. And a great example of this is that one of the enzymes involved in DNA replication is called DNA polymerase, which is named as such because it acts on DNA and specifically makes polymers of DNA. Now, the suffix "ase" is usually just one that you find at the end of most enzyme names. Now, another great example is that the enzyme that catalyzes the first step of glycolysis, which you may remember is the reaction between glucose and ATP to form glucose-6-phosphate and ADP, is called hexokinase. And "hexo" refers to the number 6, which is a reference to glucose being a six-carbon sugar. And "kinase" is a term referring to enzymes that add phosphate functional groups to different substrates. So overall, hexokinase adds phosphates to six-carbon sugars like glucose. Now generally, every enzyme has a very specific name that gives insight into the specific reaction that that enzyme can catalyze. So we can actually divide most enzymes into six different categories based off the kinds of reactions that they catalyze. Now, our first group is the transferase group. And the basic reaction that transferases catalyze are ones where you move some functional group, X, from molecule B to molecule A. And a great example of one of these reactions occurs during protein translation, where amino acids bound to tRNA molecules are transferred over to the growing polypeptide chain. So in this case, A refers to our amino acid chain, B refers to our tRNA, and X refers to this lysine residue, which is being transferred from B to A. And this reaction in particular is catalyzed by an enzyme called peptidyl transferase, which is an appropriate name since it is a transferase involved in making peptides. Next we have the ligase group, which catalyzes reactions between two molecules, A and B, that are combining to form a complex between the two, or AB. And an example of a reaction using a ligase that you might be familiar with occurs during DNA replication, where two strands of DNA are being joined together. So in this reaction, A and B represent the two separated DNA polymers, which are being joined to form a single strand. And this reaction in particular is catalyzed by an enzyme called DNA ligase, which is named since it's a ligase that works on DNA strands. Now our third group as the oxidoreductase group, which is a little different from the others since it actually includes two different types of reactions. And these reactions involve transferring electrons from either molecule B to molecule A or from molecule A to molecule B. Now, we say that an oxidase is directly involved in oxidizing or taking electrons away from a molecule, while a reductase is involved in reducing or giving electrons to a molecule. And we call these enzymes oxidoreductases together because they can usually catalyze both the forward and reverse reactions, which is why I used equilibrium arrows here instead of just a normal single-headed arrow. Now a great example of an oxidation reduction reaction occurs during lactic acid fermentation, where electrons are either passed from NADH to pyruvate or from lactic acid to NAD. Now, this reaction is catalyzed by an enzyme called lactate dehydrogenase. Remember that the word "dehydrogenase" refers to the removal of a hydride functional group. And that's the same as saying the removal of electrons, since hydrides are basically just hydrogen atoms with two electrons on them instead of just one. Now, this enzyme is given its name since it's able to remove a hydride, or remove electrons, from a molecule of lactic acid. Next, we have the isomerase group. And enzymes in this group are typically involved in reactions where a molecule, like molecule A, is being converted to one of its isomers. And an example of this type of a reaction is the conversion of glucose-6-phostate to fructose-6-phosphate, which is one of the steps of glycolysis that you may remember. Now, this reaction is catalyzed by an enzyme called phosphoglucose isomerase, which is appropriately named since it creates isomers of glucose molecules that are phosphorylated. Now, our next category is the hydrolase category. And hydrolases use water to cleave a molecule, like molecule A, into two other molecules, B and C. And a great example of one of these reactions is the hydrolysis reaction that can occur to peptide bonds. And if we have this lysine-alanine dipeptide here, it could be reacted with water to form two individual amino acids that are no longer bound. And this particular hydrolysis reaction can be catalyzed by a class of enzymes that we call serine hydrolases, which some people call serine proteases. And they are named this way because they are hydrolases that use a serine residue as the key catalytic amino acid that is responsible for breaking the peptide bond. Now, our last category is a little more complicated than the others. And it's the lyase group. Now, lyases catalyze the dissociation of a molecule, like molecule A, into molecule B and C, without using water like hydrolases would, and without using oxidation or reduction like an oxidoreductase would. And one example of a reaction catalyzed by a lyase is the cleavage of argininosuccinate into arginine and succinate. And this reaction takes place during the urea cycle, which you also might be familiar with. Now this specific reaction is catalyzed by an enzyme called argininosuccinate lyase, which is appropriately named because it is a lyase that catalyzes the breakdown of an argininosuccinate molecule. Now, it's important to recognize that since lyases don't use water or oxidation to break a bond, they need to generate either a double bond between two atoms or a ring structure in a molecule in order to work. So what did we learn? Well, first we learned that enzymes are sometimes named for their reactions. And next we learned about the six different types of enzymes. We have transferases, which transfer functional groups from one molecule to another; ligases, which ligate or join two molecules together; oxidoreductases, which move electrons between molecules; isomerases, which convert a molecule from one isomer to another; hydrolases, which break bonds using water; and lyases, which break bonds without using water and without using oxidation.