Structural Biochemistry/Enzyme Terms

Structural Biochemistry Enzyme Terms

• ENZYME: Enzymes are the catalysts of biological systems and are remarkable molecular devices that determine the patterns of chemical transformations. Nearly all known enzymes are proteins, have great catalytic power, and high specificity for the transition state. Enzymes do not change the thermodynamics of a reaction they just accelerate the reactions or adjust the kinetics.
• SUBSTRATE: Enzymes are highly specific both in the type of reaction they can catalyze and in their choice of reactants. The reactants that enzymes bind with are called substrates.
• COFACTOR: Often times the catalytic activity of an enzyme is due to the presence of small molecules called cofactors. Cofactors are divided into two groups: 1) metal ions and 2) small organic molecules like vitamins called coenzymes.
• APOENZYME: An enzyme that requires a cofactor and is currently lacking its cofactor is called an apoenzyme.
• HOLOENZYME: An enzyme that is catalytically active is called a holoenzyme if that enzyme is a complete apoenzyme plus its needed cofactor.
• COENZYME: Coenzymes are a type of cofactor and are small organic molecules like vitamins that can be either tightly or loosely bound to an enzyme. Tightly bound coenzymes are called prosthetic groups.
• PROSTHETIC GROUP: Prosthetic groups are coenzymes that are tightly bound to an enzyme.
• TRANSITION STATE: The transition state of a chemical reaction is the intermediate stage between a substrate or reactant and the product. The transition state has a higher free energy that the initial substrate stage and the final product stage.
• FREE ENERGY OF ACTIVATION: The rate of a reaction depends on the free energy of activation or delta G of the transition state, which largely unrelated to the normal delta G of a reaction. The enzyme will help to lower this free energy of activation by helping to stabilize the transition state thereby increasing the rate of the reaction and the likelihood that products will form.
• FREE ENERGY: Free energy is given the symbol G. The free energy difference or delta G is the determinate of whether a reaction will proceed spontaneously or will require an input of free energy to drive the reaction to completion. If delta G is negative the reaction is exergonic and spontaneous. If delta D is positive the reaction endergonic and will not proceed spontaneously.
• ACTIVE SITE: The active site of an enzyme is the region that binds the substrate or substrates and the cofactor if present. It also contains the residues that directly participate in the making and breaking of bonds. The residues of the active site are called the catalytic groups. The active site is typically a cleft or crevice, takes up a relatively small part of the total volume of the enzyme, have unique microenvironments, and bind to substrates with weak interactions.
• INDUCED FIT: Induced fit is where the active site on an enzyme will assume a shape that is complementary to that of the substrate only after the substrate is bound. This is a dynamic recognition and is contrary to the key and lock model of enzyme-substrate binding.
• SEQUENTIAL REACTION: In a sequential reaction all the substrates must bind to the enzyme before any product is released. Sequential reactions come in two types: 1) ordered, where the substrates bind to the enzyme in a defined sequence, and 2) random, where the order of the substrates binding and the order of the products released does not matter as long as all substrates bind before any product is released.
• KINETICS: The study of the rates of chemical reactions is called kinetics and the specific study of the rates of enzyme-catalyzed reactions is called enzyme kinetics.
• DOUBLE-DISPLACEMENT REACTION: In the double displacement reaction or ping-pong reaction, one or more of the products are released before all the substrates bind to the enzyme. The key feature in a double displacement reaction is the existence of a substituted enzyme intermediate, in which the enzyme is temporarily modified.
• ALLOSTERIC ENZYME: Allosteric enzymes consist of multiple subunits and multiple active sites and do not obey Michaelis-Menten kinetics. Allosteric enzymes instead display sigmoidal plots of reaction velocity versus substrate concentration. An example of an allosteric enzyme is hemoglobin, where the subunits act cooperatively.
• COMPETITIVE INHIBITION: Competitive inhibition is a type of reversible inhibition where an enzyme can either bind to the substrate like normal or bind to the inhibitor but cannot bind to both the substrate and the inhibitor. A competitive inhibitor diminishes the rate of catalysis by reducing the proportion of enzyme molecules bound to a substrate. This type of inhibition does not affect the rate of reaction, so the V-max does not change. However, the K-m of the reaction increases because the inhibitor is competing with the substrate for the active site. A competitive inhibitor can be overcome with an increased concentration of substrate in the system.
• UNCOMPETITIVE INHIBITION: An uncompetitive inhibitor is distinguished by the fact that the inhibitor binds only to the enzyme-substrate complex. After the inhibitor binds to the enzyme-substrate complex, it greatly lengthens the time it takes for catalysis to occur. As a result, V-max decreases. Since the inhibitor will only bind to the enzyme-substrate complex, the K-m actually decreases.
• NONCOMPETITIVE INHIBITION: A type of inhibition where the inhibitor binds to a site that is not the active site of an enzyme. After binding to the enzyme, the inhibitor causes a conformational change in the enzyme, hampering its ability to perform catalysis. Because of this, the V-max of the reaction decreases. Since the inhibitor does not affect the affinity of the enzyme for its substrate, K-m remains unchanged.
• MIXED INHIBITION: In mixed inhibition a more complex pattern of inhibition is utilized where a single inhibitor both hinders the binding of a substrate and decreases the turnover number of the enzyme.
• Lock and Key – A mechanism used to explain enzymatic activity. It states that each enzyme has a shape that matches a particular substrate and that the fit is similar to that of a lock and a key. In this mechanism, the enzyme does not change shape. This mechanism has proven to be INCORRECT.
• Michaelis-Menten – A model of enzyme kinetics that specifically describes the rates of irreversible enzymatic reactions. It only applies for the steady-state phase of reactions.
• K-m – The Michaelis constant. It is also known as the affinity constant because it describes the affinity of an enzymatic active site for its substrate. The lower the affinity constant, the greater the affinity an enzyme has for its substrate.
• Feedback inhibition – A type of inhibition in which a product of an enzymatic pathway inhibits the first enzyme of that pathway.
• Cooperative activity of active sites – A property that allows the state of one active site to affect the state of all the other active sites in an enzyme. For example, in a cooperative enzyme, the binding of substrate to one active site will make all of the other active sites more likely to bind to substrates.
• R-state – One of two states that enzymes may have. This is called the relaxed state because the active sites of the enzyme have a great affinity for their substrate.
• T-state – One of two states that enzymes may have. This is called the tense state because the active sites of the enzyme have a low affinity for their substrate.
• Isoenzymes – Isoenzymes are two enzymes that have different amino acid sequences yet perform the same function.
• Burst Phase – The burst phase of a reaction occurs near the beginning of the reaction. At this time, there is no product and a great amount of enzyme and substrate. The rate of reaction at this point is very great and Michaelis-Menten kinetics does not apply to this phase.
• Steady-State Phase – The second phase of a reaction where there is a measurable amount of product. At this point, Michaelis-Menten kinetics can be applied.
• Activation Energy- A threshold that must be crossed in order to facilitate a chemical reaction. here are three ways to reach the activation energy: by raising the temperture of the system, increasing the concentration of reactions, or by using an enzyme or catalyst.

References

Berg, Jeremy M., Tymoczko, John L., and Stryer, Lubert. Biochemistry. 6th ed. New York, N.Y.: W.H. Freeman and Company, 2007.