Enzyme Active Site and Substrate Specificity
Enzymes catalyze chemical reactions by lowering activation energy barriers and converting substrate molecules to products.
Describe models of substrate binding to an enzyme’s active site.
- The enzyme ‘s active site binds to the substrate.
- Increasing the temperature generally increases the rate of a reaction, but dramatic changes in temperature and pH can denature an enzyme, thereby abolishing its action as a catalyst.
- The induced fit model states an substrate binds to an active site and both change shape slightly, creating an ideal fit for catalysis.
- When an enzyme binds its substrate it forms an enzyme-substrate complex.
- Enzymes promote chemical reactions by bringing substrates together in an optimal orientation, thus creating an ideal chemical environment for the reaction to occur.
- The enzyme will always return to its original state at the completion of the reaction.
- substrate: A reactant in a chemical reaction is called a substrate when acted upon by an enzyme.
- induced fit: Proposes that the initial interaction between enzyme and substrate is relatively weak, but that these weak interactions rapidly induce conformational changes in the enzyme that strengthen binding.
- active site: The active site is the part of an enzyme to which substrates bind and where a reaction is catalyzed.
Enzyme Active Site and Substrate Specificity
Enzymes bind with chemical reactants called substrates. There may be one or more substrates for each type of enzyme, depending on the particular chemical reaction. In some reactions, a single-reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products.
The enzyme’s active site binds to the substrate. Since enzymes are proteins, this site is composed of a unique combination of amino acid residues (side chains or R groups). Each amino acid residue can be large or small; weakly acidic or basic; hydrophilic or hydrophobic; and positively-charged, negatively-charged, or neutral. The positions, sequences, structures, and properties of these residues create a very specific chemical environment within the active site. A specific chemical substrate matches this site like a jigsaw puzzle piece and makes the enzyme specific to its substrate.
Active Sites and Environmental Conditions
Environmental conditions can affect an enzyme’s active site and, therefore, the rate at which a chemical reaction can proceed. Increasing the environmental temperature generally increases reaction rates because the molecules are moving more quickly and are more likely to come into contact with each other.
However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the enzyme and change its shape. If the enzyme changes shape, the active site may no longer bind to the appropriate substrate and the rate of reaction will decrease. Dramatic changes to the temperature and pH will eventually cause enzymes to denature.
Induced Fit and Enzyme Function
For many years, scientists thought that enzyme-substrate binding took place in a simple “lock-and-key” fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view called induced fit. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the substrate. This dynamic binding maximizes the enzyme’s ability to catalyze its reaction.
When an enzyme binds its substrate, it forms an enzyme-substrate complex. This complex lowers the activation energy of the reaction and promotes its rapid progression by providing certain ions or chemical groups that actually form covalent bonds with molecules as a necessary step of the reaction process. Enzymes also promote chemical reactions by bringing substrates together in an optimal orientation, lining up the atoms and bonds of one molecule with the atoms and bonds of the other molecule. This can contort the substrate molecules and facilitate bond-breaking. The active site of an enzyme also creates an ideal environment, such as a slightly acidic or non-polar environment, for the reaction to occur. The enzyme will always return to its original state at the completion of the reaction. One of the important properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done catalyzing a reaction, it releases its products (substrates).
Control of Metabolism Through Enzyme Regulation
Cells regulate their biochemical processes by inhibiting or activating enzymes.
Explain the effect of an enzyme on chemical equilibrium
- In competitive inhibition, an inhibitor molecule competes with a substrate by binding to the enzyme ‘s active site so the substrate is blocked.
- In noncompetitive inhibition (also known as allosteric inhibition), an inhibitor binds to an allosteric site; the substrate can still bind to the enzyme, but the enzyme is no longer in optimal position to catalyze the reaction.
- Allosteric inhibitors induce a conformational change that changes the shape of the active site and reduces the affinity of the enzyme’s active site for its substrate.
- Allosteric activators induce a conformational change that changes the shape of the active site and increases the affinity of the enzyme’s active site for its substrate.
- Feedback inhibition involves the use of a reaction product to regulate its own further production.
- Inorganic cofactors and organic coenzymes promote optimal enzyme orientation and function.
- Vitamins act as coenzymes (or precursors to coenzymes) and are necessary for enzymes to function.
- coenzyme: An organic molecule that is necessary for an enzyme to function.
- allosteric site: A site other than the active site on an enzyme.
- cofactor: An inorganic molecule that is necessary for an enzyme to function.
Control of Metabolism Through Enzyme Regulation
Cellular needs and conditions vary from cell to cell and change within individual cells over time. For example, a stomach cell requires a different amount of energy than a skin cell, fat storage cell, blood cell, or nerve cell. The same stomach cell may also need more energy immediately after a meal and less energy between meals.
A cell’s function is encapsulated by the chemical reactions it can carry out. Enzymes lower the activation energies of chemical reactions; in cells, they promote those reactions that are specific to the cell’s function. Because enzymes ultimately determine which chemical reactions a cell can carry out and the rate at which they can proceed, they are key to cell functionality.
Competitive and Noncompetitive Inhibition
The cell uses specific molecules to regulate enzymes in order to promote or inhibit certain chemical reactions. Sometimes it is necessary to inhibit an enzyme to reduce a reaction rate, and there is more than one way for this inhibition to occur. In competitive inhibition, an inhibitor molecule is similar enough to a substrate that it can bind to the enzyme’s active site to stop it from binding to the substrate. It “competes” with the substrate to bind to the enzyme.
In noncompetitive inhibition, an inhibitor molecule binds to the enzyme at a location other than the active site (an allosteric site). The substrate can still bind to the enzyme, but the inhibitor changes the shape of the enzyme so it is no longer in optimal position to catalyze the reaction.
Allosteric Inhibition and Activation
In noncompetitive allosteric inhibition, inhibitor molecules bind to an enzyme at the allosteric site. Their binding induces a conformational change that reduces the affinity of the enzyme’s active site for its substrate. The binding of this allosteric inhibitor changes the conformation of the enzyme and its active site, so the substrate is not able to bind. This prevents the enzyme from lowering the activation energy of the reaction, and the reaction rate is reduced.
However, allosteric inhibitors are not the only molecules that bind to allosteric sites. Allosteric activators can increase reaction rates. They bind to an allosteric site which induces a conformational change that increases the affinity of the enzyme’s active site for its substrate. This increases the reaction rate.
Cofactors and Coenzymes
Many enzymes only work if bound to non-protein helper molecules called cofactors and coenzymes. Binding to these molecules promotes optimal conformation and function for their respective enzymes. These molecules bind temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds.
Cofactors are inorganic ions such as iron (Fe2+) and magnesium (Mg2+). For example, DNA polymerase requires a zinc ion (Zn2+) to build DNA molecules. Coenzymes are organic helper molecules with a basic atomic structure made up of carbon and hydrogen. The most common coenzymes are dietary vitamins. Vitamin C is a coenzyme for multiple enzymes that take part in building collagen, an important component of connective tissue. Pyruvate dehydrogenase is a complex of several enzymes that requires one cofactor and five different organic coenzymes to catalyze its chemical reaction. The availability of various cofactors and coenzymes regulates enzyme function.
In eukaryotic cells, molecules such as enzymes are usually compartmentalized into different organelles. This organization contributes to enzyme regulation because certain cellular processes are contained in separate organelles. For example, the enzymes involved in the later stages of cellular respiration carry out reactions exclusively in the mitochondria. The enzymes involved in the digestion of cellular debris and foreign materials are located within lysosomes.
Feedback Inhibition in Metabolic Pathways
Feedback inhibition is when a reaction product is used to regulate its own further production. Cells have evolved to use feedback inhibition to regulate enzyme activity in metabolism, by using the products of the enzymatic reactions to inhibit further enzyme activity. Metabolic reactions, such as anabolic and catabolic processes, must proceed according to the demands of the cell. In order to maintain chemical equilibrium and meet the needs of the cell, some metabolic products inhibit the enzymes in the chemical pathway while some reactants activate them.
The production of both amino acids and nucleotides is controlled through feedback inhibition. For an example of feedback inhibition, consider ATP. It is the product of the catabolic metabolism of sugar (cellular respiration), but it also acts as an allosteric regulator for the same enzymes that produced it. ATP is an unstable molecule that can spontaneously dissociate into ADP; if too much ATP were present, most of it would go to waste. This feedback inhibition prevents the production of additional ATP if it is already abundant. However, while ATP is an inhibitor, ADP is an allosteric activator. When levels of ADP are high compared to ATP levels, ADP triggers the catabolism of sugar to produce more ATP.