This overview is intentionally general and brief because this is content that is normally covered and thus general knowledge for any biology teacher. It is provided in this unit more as a supply of general content. This will be helpful to refer to when discussing making connections between other biology content strands and enzymes as well as when discussing teaching enzymes through bioremediation.
Importance and Production
Most enzymes are proteins that facilitate reactions. They are large molecules that fall into the general category of macromolecules. Enzymes act on substrates to create products. A reaction may be the combining substrate units to create a product or the breakdown of a substrate molecule into products. This action occurs within cells to support many different cellular processes. Enzymes may be releasing energy, building energy storage molecules, translating DNA, building proteins, as well as other functions. Although the reactions that enzymes facilitate will eventually happen spontaneously, enzymes make reactions happen at rates high enough to support life. Reaction rates are in the tens of thousands per second, allowing cells to do work and consequently support life.
The human body requires tens of thousands of different enzymes to function, each with specific functions. Functions will be discussed later in this unit. Even a simple bacterium, such as Escherichia coli, requires thousands of enzymes to live its unicellular existence.
Importance and Production: Coding
The majority of discovered enzymes are proteins. Cellular function is regulated by enzymes that are produced in house by the cell itself. When considering a multi-cellular organism, cells of different tissues may have markedly different enzymes from one another in order to perform their tissue specific function. This can be useful when determining the function of different cells. The instructions for making the requisite enzymes are coded into the DNA of the cell. Each different type of enzyme is produced by the cell's translation of a specific genetic code of DNA into a protein product. Translation of DNA is also carried out by enzymes. DNA code provides the specific sequence of amino acids needed to produce a specific product protein. DNA code is universal to all organisms. The sequence of DNA that codes for a given amino acid is the same no matter the organism. All organisms use the same genetic language to translate their DNA.
Importance and Production: Production
Enzymes are produced using amino acid building blocks. The DNA code sequence will dictate the type and sequence of amino acids thus dictating the enzyme produced by a given code. The process of translation of genetic code into protein product is performed out by organelles called ribosomes. The ribosomes are either free in the cytoplasm of the cell or embedded in the membrane of the endoplasmic reticulum. Depending on the function of the enzyme or activity of the cell enzymes may be produced for immediate use. Enzymes may also be produced and stored for later use.
Structure of Enzymes
Structure of Enzymes: Enzymes are Proteins
Most enzymes are proteins but not all proteins are enzymes. Proteins are made of any combination of the twenty amino acids. Protein structure is dictated by combination, number, and sequence of the amino acids that constitute it as coded by DNA. Some proteins, and hence enzymes, are combinations of multiple proteins folded together to form a single structure. Although enzymes do perform work, they are simply just macromolecules and must not be thought of as living or even as organelles. The action of the enzyme is to facilitate a reaction. In general an enzyme contains or creates an ideal micro-environment for a specific reaction to occur, this micro-environment is called the active site of the enzyme.
Structure of Enzymes: Structure Leads to Function
The final structure of an enzyme allows for binding of a specific substrate(s) in order to catalyze a reaction. The structure of importance is the active site wherein the substrate(s) bind. This active site will facilitate the reaction by providing the conditions to catalyze a specific reaction. Enzyme action may be to break a substrate down into smaller parts (catabolic reactions) or to bind two substrates together to form a single molecular product (anabolic reactions). Commonly the binding of the substrate to the active site will change the shape of the enzyme or the substrate resulting in the breaking of bonds or forming of new bonds. The enzyme provides the conditions for the reaction to take place by having a very specific shape that will stress the bonds of a single substrate, resulting in separation into products or aligning two substrates in such a way that they will bond forming a single product.
Structure of Enzymes: Active Sites
Active sites are specific to the substrates and as the name implies, this is where the enzymatic reaction takes place. It is popular to describe the active site and substrate relationship as that of a lock and key. Although this is not longer the accepted model it is still a functional way to present the concept within a high school classroom. In this model, the active site is thought of as a lock and the substrate as a key. Therefore each key will only fit in a single lock. This analogy also assumes that the both lock and key are static and rigid. This model helps create a visual first for the students to frame their view of enzymes. Note that the model is imperfect because enzymes and substrates are not rigid and inflexible. Some enzyme active sites will bend and stress the bonds of a bonded substrate in order to break bonds. In contrast some enzyme-substrate relationships rely on the manipulation of substrates in order to create bonds. Other active sites function as being true micro-environments for the substrates. It may be the case that the active site has a pH or temperature that differs from the surrounding medium. This condition is ideal for the reaction, thus facilitating the reaction in an otherwise non-reactive environment for the substrate.
Structure of Enzymes: Multienzyme Complexes
Reactions are not necessarily independent and reaction events are often steps in complex processes that require multiple enzymes. Enzymes can be found in complexes comprised of multiple copies of the several different enzymes that all perform a specific task that is part of a reaction sequence. This results in more efficient processes for the cell. In essence this is an aggregate of macromolecules, a complex that catalyze a reaction sequence using proximity to increase efficiency.
Enzymes cause reactions to happen at rates fast enough to support life; therefore, the control of the activity of the enzyme can regulate the functions of the cell. Regulation can be fostered by directly inhibiting or activating an enzyme. Enzyme rates are also affected by temperature and pH. Cells must regulate their enzymes but it is not always the case that the cell has any control of the conditions that it is exposed to. As we learn more about enzyme regulation we can begin to see the importance of understanding what affects enzymatic rate.
Regulation: Temperature and pH
Enzymes have specific ranges of temperature and pH that they will function in. Optimal ranges of pH are specific to enzymes. Understanding the relationship between temperature and reaction rate is more intuitive. If one considers kinetic energy as it relates to movement of particles it makes sense, that within limits, higher temperatures correlate with higher reaction rates. This is due to higher kinetic energy and an increase of molecular movement and thus collision. The more the substrate and enzymes are moving the more likely it is that they come in contact with the each other. Often, the upper limit of the relationship between temperature and increased reaction rate, is dictated by the temperature threshold of the enzyme. At this point the enzymatic rate will cease to increase and will sharply decline. Enzymes, being proteins, are denatured by when exposed to extreme temperatures. Denaturation will result in a shape change for the enzyme, thus loss of structure equals loss of function.
Temperature and pH are an indirect way that enzymes are regulated. Indirect because often is the case that the temperature or pH that a given enzyme is subjected to is being manipulated by an extracellular event. This can be an interesting quest for a high school biology class to help gain understanding about how important homeostasis is to the human body and why it is so dangerous for the body to have to operate outside of its normal temperature range, i.e., when the body experiences fever.
Decreasing or stopping the function of an enzyme is called inhibition. Think of an enzyme being naturally active in order to regulate the action it must be inhibited. As an analogy this would be a car with not gas pedal and only a brake pedal. The car will constantly run automatically unless the brake is applied to stop it. Many enzymes can be regulated in this way. Consider an enzymatic pathway that results in a product that is needed in finite amounts. The product in this case may also be the inhibitor. The way this would work is that when the product is in excess of what the cell needs it is will bind to the inhibition site, preventing further production of a molecule that is not needed. It may also be the case that the inhibitor molecule is produced via different pathway in response to a trigger. Whatever the case is, the enzymatic activity is being regulated by a negative control.
The enzyme may have a binding site that allows an inhibitor molecule to bind causing a shape change in the enzyme and resulting in a deformation of the enzyme's active site. In this case, while the inhibitor is bound to the enzyme, the deformed active site is rendered inoperable. Upon release of the inhibitor the active site regains shape and may begin catalyzing reactions again. Another inhibition method may involve the binding of an inhibitor molecule to the active site. The active site will thus be occupied by the inhibitor effectively blocking the substrate.
Enzymes may also exist in a non-active form unless an activator molecule binds them to activate them. As analogy, this car would have only a gas pedal and will naturally be stationary unless activated by applying the gas pedal. This is a positive regulation of an enzyme, wherein the binding results in activity. Enzymes that are regulated by activators will have a binding site for the activator. When the activation molecule is bound to the enzyme the enzyme becomes functional.
Consider that a cell may not need all of its enzymes to be functioning at all times. Cells may only need certain enzymes when the cell is exposed to a certain conditions. When certain conditions are met the cell may quickly turn on or off the enzymes as a response. It is important to stress that enzyme rates are controlled by cells and that these rates may be controlled via different strategies. Furthermore cellular function is controlled by manipulation of enzymatic rates.