Enzymes are molecules, specifically proteins, that help speed up biochemical reactions by interacting with the ingredients (reactants and products) without changing them permanently. This facilitation process is known as catalysis, and correspondingly, enzymes themselves are identified as catalysts.
Enzymes, like a lot of players in the microbiology world, can have long and cumbersome names, almost all of which end in "-ase." But if you are familiar with the formal system within which enzymes are named, you can unravel a lot of mysteries about a given enzyme's function without knowing precisely what reaction that enzyme catalyzes.
What Is a Catalyst?
Colloquially, a catalyst is any entity that improves the flow, efficiency or effectiveness of a given endeavor. If you are a basketball coach and you know that putting a given popular player in the game will fire up the crowd and the team in general, then you are leveraging the presence of a catalyst.
Human catalysts make things happen, and they tend to make people around them look maximally proficient as well. In the same way, biological catalysts can make certain biochemical processes appear almost automatic, when in fact these processes would stumble and stagger along toward a non-assured conclusion in the absence of the enzyme – which, at least as often as not, doesn't even get written into the formula for the chemical reaction in which it participates, because by definition a catalyst is unchanged from its original form at the end of the reaction.
Enzyme: Definition and Discovery
By the late 1870s, it had become established that something in yeast could cause sources of sugar to morph into alcoholic beverages far more quickly than might occur spontaneously, and that the same principle of fermentation applied to the aging of cheese. Left alone under the right conditions, some kinds of rotting fruit can eventually result in the formation of ethyl alcohol; adding yeast, however, not only speeds up fermentation, but also introduces both predictability and a measure of control into the entire chemical reaction.
"Enzyme" is from the Greek for "with yeast." As used today, it refers to biological catalysts within organisms, or substances that are produced both by and for the benefit of a living system.
The main function of all enzymes is to catalyze the metabolic processes that occur within a cell. A more formal enzyme definition specifies that enzyme must not only act on reactions within a living cell, but have been created by an organism – the same one or a different one – as well.
Individual enzymes can be described in terms of their specificity. This is a measure of how exclusive an enzyme's relationship is with its substrate or substrates. Substrates are the molecules to which enzymes bind, usually the reactants. When an enzyme binds only to one substrate in one reaction, this implies absolute specificity. When it can bind to a number of different but chemically similar substrates, the enzyme has group specificity.
How well enzymes work – that is, how much they are able to affect the reactions they target compared to neutral conditions – depends on a number of factors. These include temperature and acidity, which affect the stability of all proteins, not just enzymes. As you would expect, increasing the amount of substrate can increase the rate of the reaction, as long as the enzyme is not "saturated" already; conversely, adding enzymes can speed up a reaction at a given level of substrate, and can allow more substrate to be added without running up against a production ceiling.
The rate of substrate disappearance (and reactant appearance) in reactions in which enzymes are involved is not linear, but rather tends to slow down as the reaction nears completion. This is represented on a graph of concentration versus time by a downward slope that becomes more gradual as time passes.
Almost any list of enzymes featuring the best-known and best-studied ones is almost certain to feature catalysts in glycolysis, the citric acid (i.e., Krebs or tricarboxylic acid) cycle or both. These processes, each of which consist of multiple individual reactions, involve the breakdown of glucose to pyruvate in the cell cytoplasm and the conversion of pyruvate to a rotating series of intermediates that ultimately allow aerobic respiration to occur.
Two enzymes involved in the early portion of glycolysis are glucose-6-phosphatase and phosphofructokinase, whereas citrate synthase is a major player in the citric acid cycle. Can you predict what these enzymes might do based on their names? If not, try again in about five minutes.
The name of an enzyme may not roll off the tongue with ease, but such is the cost of embracing chemistry. Most of the names consist of two words, with the first identifying the substrate on which the enzyme acts and the second signaling the type of reaction involved (more on this second attribute in the next section).
Although an overwhelming number of enzyme names end in "-ase," a number of important and well-studied ones do not. Any list of enzymes pertaining to human digestion will include trypsin and pepsin. The enzyme suffix "-ase," however, by itself signifies nothing more than the fact that the protein in question is, in fact, an enzyme, and it does not address functional details.
There are six major classes of enzymes, separated into categories on the basis of their function. Most of these classes include sub-classes as well. Their names are helpful in determining what they do, but only if you known some Greek or Latin.
- Oxidoreductases are enzymes that participate in reactions in which the substrate is either oxidized (i.e., loses electrons) or reduced (i.e., gains electrons). Examples include enzymes ending in dehydrogenase, oxidase, peroxidase and reductase. Lactate dehydrogenase, which catalyzes the interconversion of lactate and pyruvate in fermentation, belongs in the oxidoreducatase class.
- Transferases, as suggested by the name, transfer functional groups, rather than just electrons or single atoms, from one molecule to another. Kinases, which add phosphate groups to molecules (e.g., the addition of a phosphate group to fructose-6-phosphate in glycolysis) are examples.
- Hydrolases catalyze hydrolysis reactions, in which a water molecule ("hydro-") is used to cleave apart a larger molecule ("-lase") to break it into smaller ones. Phosphatases, which are the functional opposites of kinases, do this by removing phosphate groups; proteases, peptidases and nucleases, which break down protein-rich molecules, are a second subtype.
- Lyases create double bonds in a molecule by removing a group from a carbon atom. (In the reverse reaction, a group is added to one of the carbon atoms in the double bond to transform it into a single bond.) Enzymes ending in decarboxylase, hydratase, synthase and lyase itself are examples.
- Isomerases catalyze isomerization reactions, which are rearrangements of a molecule to create an isomer, a molecule with the same number and kinds of atoms (that is, the same chemical formula) but a different shape. Thus, they are a kind of transferase, but instead of moving groups between molecules, they do so within molecules. Isomerase, mutase and racemase enzymes fall into this class.
- Ligases catalyze the formation of a bond through the process of ATP hydrolysis, rather than by moving an atom or a group from one place to another. Carboxylase synthetase is an example of a ligase enzyme.
- Indiana University: Six Classes of Enzymes
- University of Guelph: Enzymes as Catalysts
- Queen Mary University of London: Enzyme Nomenclature
- NCBI Bookshelf: The Cell: A Molecular Approach (2nd Edition): The Central Role of Enzymes as Biological Catalysts
- Prince Georges Community College: Exploring the Molecules of Life: Enzymes