Do Enzymes Increase Activation Energy

A fundamental chore of proteins is to act equally enzymes—catalysts that increment the rate of virtually all the chemical reactions within cells. Although RNAs are capable of catalyzing some reactions, most biological reactions are catalyzed by proteins. In the absence of enzymatic catalysis, most biochemical reactions are and so slow that they would not occur under the mild atmospheric condition of temperature and pressure that are compatible with life. Enzymes accelerate the rates of such reactions by well over a 1000000-fold, so reactions that would have years in the absence of catalysis tin can occur in fractions of seconds if catalyzed by the appropriate enzyme. Cells contain thousands of different enzymes, and their activities make up one's mind which of the many possible chemical reactions really take place within the cell.

The Catalytic Activity of Enzymes

Like all other catalysts, enzymes are characterized by two fundamental properties. Kickoff, they increase the rate of chemic reactions without themselves being consumed or permanently altered by the reaction. Second, they increase reaction rates without altering the chemic equilibrium between reactants and products.

These principles of enzymatic catalysis are illustrated in the following case, in which a molecule acted upon by an enzyme (referred to as a substrate [South]) is converted to a product (P) as the result of the reaction. In the absence of the enzyme, the reaction can be written equally follows:

Image ch2e1.jpg

The chemic equilibrium between Due south and P is adamant by the laws of thermodynamics (as discussed farther in the next section of this affiliate) and is represented by the ratio of the forward and reverse reaction rates (South→P and P→S, respectively). In the presence of the appropriate enzyme, the conversion of S to P is accelerated, but the equilibrium between S and P is unaltered. Therefore, the enzyme must accelerate both the forward and contrary reactions equally. The reaction tin can be written equally follows:

Image ch2e2.jpg

Note that the enzyme (E) is not altered by the reaction, then the chemic equilibrium remains unchanged, adamant solely by the thermodynamic properties of S and P.

The upshot of the enzyme on such a reaction is best illustrated by the energy changes that must occur during the conversion of S to P (Figure 2.22). The equilibrium of the reaction is adamant by the final energy states of S and P, which are unaffected by enzymatic catalysis. In order for the reaction to proceed, nevertheless, the substrate must first be converted to a higher free energy country, called the transition state. The free energy required to reach the transition state (the activation free energy) constitutes a bulwark to the progress of the reaction, limiting the rate of the reaction. Enzymes (and other catalysts) human action by reducing the activation energy, thereby increasing the rate of reaction. The increased rate is the same in both the forward and contrary directions, since both must pass through the aforementioned transition country.

Figure 2.22

Energy diagrams for catalyzed and uncatalyzed reactions. The reaction illustrated is the simple conversion of a substrate S to a product P. Considering the final energy state of P is lower than that of S, the reaction gain from left to right. For the (more...)

The catalytic activeness of enzymes involves the binding of their substrates to class an enzyme-substrate circuitous (ES). The substrate binds to a specific region of the enzyme, called the active site. While bound to the agile site, the substrate is converted into the product of the reaction, which is then released from the enzyme. The enzyme-catalyzed reaction can thus exist written as follows:

Image ch2e3.jpg

Note that E appears unaltered on both sides of the equation, then the equilibrium is unaffected. However, the enzyme provides a surface upon which the reactions converting S to P can occur more than readily. This is a upshot of interactions between the enzyme and substrate that lower the free energy of activation and favor formation of the transition state.

Mechanisms of Enzymatic Catalysis

The binding of a substrate to the active site of an enzyme is a very specific interaction. Active sites are clefts or grooves on the surface of an enzyme, usually equanimous of amino acids from dissimilar parts of the polypeptide concatenation that are brought together in the tertiary structure of the folded poly peptide. Substrates initially bind to the active site past noncovalent interactions, including hydrogen bonds, ionic bonds, and hydrophobic interactions. Once a substrate is leap to the active site of an enzyme, multiple mechanisms tin accelerate its conversion to the product of the reaction.

Although the simple example discussed in the previous section involved simply a unmarried substrate molecule, nearly biochemical reactions involve interactions betwixt two or more than unlike substrates. For example, the formation of a peptide bail involves the joining of two amino acids. For such reactions, the bounden of two or more substrates to the active site in the proper position and orientation accelerates the reaction (Effigy 2.23). The enzyme provides a template upon which the reactants are brought together and properly oriented to favor the formation of the transition land in which they collaborate.

Figure ii.23

Enzymatic catalysis of a reaction betwixt two substrates. The enzyme provides a template upon which the two substrates are brought together in the proper position and orientation to react with each other.

Enzymes accelerate reactions also by altering the conformation of their substrates to approach that of the transition state. The simplest model of enzyme-substrate interaction is the lock-and-key model, in which the substrate fits precisely into the active site (Figure 2.24). In many cases, however, the configurations of both the enzyme and substrate are modified past substrate bounden—a process called induced fit. In such cases the conformation of the substrate is altered so that information technology more closely resembles that of the transition country. The stress produced by such distortion of the substrate can farther facilitate its conversion to the transition country by weakening critical bonds. Moreover, the transition land is stabilized by its tight binding to the enzyme, thereby lowering the required energy of activation.

Figure 2.24

Models of enzyme-substrate interaction. (A) In the lock-and-key model, the substrate fits precisely into the agile site of the enzyme. (B) In the induced-fit model, substrate bounden distorts the conformations of both substrate and enzyme. This distortion (more...)

In add-on to bringing multiple substrates together and distorting the conformation of substrates to approach the transition country, many enzymes participate directly in the catalytic process. In such cases, specific amino acid side chains in the agile site may react with the substrate and form bonds with reaction intermediates. The acidic and basic amino acids are often involved in these catalytic mechanisms, as illustrated in the following discussion of chymotrypsin as an example of enzymatic catalysis.

Chymotrypsin is a member of a family of enzymes (serine proteases) that assimilate proteins by catalyzing the hydrolysis of peptide bonds. The reaction tin can be written as follows:

Image ch2e4.jpg

The different members of the serine protease family (including chymotrypsin, trypsin, elastase, and thrombin) have distinct substrate specificities; they preferentially cleave peptide bonds adjacent to different amino acids. For example, whereas chymotrypsin digests bonds adjacent to hydrophobic amino acids, such as tryptophan and phenylalanine, trypsin digests bonds next to basic amino acids, such every bit lysine and arginine. All the serine proteases, however, are similar in structure and use the same mechanism of catalysis. The active sites of these enzymes contain three critical amino acids—serine, histidine, and aspartate—that drive hydrolysis of the peptide bond. Indeed, these enzymes are called serine proteases because of the key part of the serine residual.

Substrates demark to the serine proteases past insertion of the amino acid adjacent to the cleavage site into a pocket at the active site of the enzyme (Effigy ii.25). The nature of this pocket determines the substrate specificity of the different members of the serine protease family unit. For example, the binding pocket of chymotrypsin contains hydrophobic amino acids that collaborate with the hydrophobic side chains of its preferred substrates. In contrast, the binding pocket of trypsin contains a negatively charged acidic amino acid (aspartate), which is able to course an ionic bond with the lysine or arginine residues of its substrates.

Figure 2.25

Substrate binding by serine proteases. The amino acid side by side to the peptide bond to be cleaved is inserted into a pocket at the active site of the enzyme. In chymotrypsin, the pocket binds hydrophobic amino acids; the binding pocket of trypsin contains (more...)

Substrate bounden positions the peptide bond to be broken adjacent to the active site serine (Effigy ii.26). The proton of this serine is and then transferred to the agile site histidine. The conformation of the active site favors this proton transfer because the histidine interacts with the negatively charged aspartate residual. The serine reacts with the substrate, forming a tetrahedral transition state. The peptide bail is and then cleaved, and the C-terminal portion of the substrate is released from the enzyme. However, the N-terminal peptide remains leap to serine. This situation is resolved when a water molecule (the second substrate) enters the active site and reverses the preceding reactions. The proton of the water molecule is transferred to histidine, and its hydroxyl group is transferred to the peptide, forming a second tetrahedral transition state. The proton is then transferred from histidine back to serine, and the peptide is released from the enzyme, completing the reaction.

Effigy ii.26

Catalytic machinery of chymotrypsin. 3 amino acids at the active site (Ser-195, His-57, and Asp-102) play disquisitional roles in catalysis.

This example illustrates several features of enzymatic catalysis; the specificity of enzyme-substrate interactions, the positioning of different substrate molecules in the active site, and the interest of active-site residues in the germination and stabilization of the transition state. Although the thousands of enzymes in cells catalyze many different types of chemical reactions, the aforementioned basic principles employ to their operation.

Coenzymes

In add-on to binding their substrates, the active sites of many enzymes bind other modest molecules that participate in catalysis. Prosthetic groups are small molecules jump to proteins in which they play critical functional roles. For case, the oxygen carried by myoglobin and hemoglobin is bound to heme, a prosthetic group of these proteins. In many cases metallic ions (such as zinc or fe) are spring to enzymes and play primal roles in the catalytic process. In add-on, various low-molecular-weight organic molecules participate in specific types of enzymatic reactions. These molecules are called coenzymes because they piece of work together with enzymes to enhance reaction rates. In contrast to substrates, coenzymes are not irreversibly contradistinct past the reactions in which they are involved. Rather, they are recycled and tin can participate in multiple enzymatic reactions.

Coenzymes serve as carriers of several types of chemic groups. A prominent example of a coenzyme is nicotinamide adenine dinucleotide (NAD ⁺), which functions as a carrier of electrons in oxidation-reduction reactions (Figure 2.27). NAD⁺ can accept a hydrogen ion (H⁺) and ii electrons (due east^-) from one substrate, forming NADH. NADH can then donate these electrons to a second substrate, re-forming NAD⁺. Thus, NAD⁺ transfers electrons from the first substrate (which becomes oxidized) to the second (which becomes reduced).

Figure 2.27

Function of NAD⁺ in oxidation-reduction reactions. (A) Nicotinamide adenine dinucleotide (NAD⁺) acts as a carrier of electrons in oxidation-reduction reactions past accepting electrons (e^-) to form NADH. (B) For example, NAD⁺ tin accept electrons from ane substrate (more...)

Several other coenzymes likewise deed as electron carriers, and withal others are involved in the transfer of a diversity of additional chemic groups (e.one thousand., carboxyl groups and acyl groups; Table 2.i). The aforementioned coenzymes function together with a variety of different enzymes to catalyze the transfer of specific chemical groups between a wide range of substrates. Many coenzymes are closely related to vitamins, which contribute part or all of the construction of the coenzyme. Vitamins are not required by bacteria such as E. coli but are necessary components of the diets of human and other higher animals, which have lost the ability to synthesize these compounds.

Regulation of Enzyme Activity

An important feature of most enzymes is that their activities are non constant just instead can be modulated. That is, the activities of enzymes can be regulated and then that they function appropriately to meet the varied physiological needs that may arise during the life of the cell.

Ane common type of enzyme regulation is feedback inhibition, in which the product of a metabolic pathway inhibits the activity of an enzyme involved in its synthesis. For example, the amino acid isoleucine is synthesized by a series of reactions starting from the amino acid threonine (Figure 2.28). The start step in the pathway is catalyzed past the enzyme threonine deaminase, which is inhibited by isoleucine, the end product of the pathway. Thus, an adequate amount of isoleucine in the cell inhibits threonine deaminase, blocking further synthesis of isoleucine. If the concentration of isoleucine decreases, feedback inhibition is relieved, threonine deaminase is no longer inhibited, and additional isoleucine is synthesized. By so regulating the activity of threonine deaminase, the cell synthesizes the necessary corporeality of isoleucine only avoids wasting free energy on the synthesis of more isoleucine than is needed.

Effigy ii.28

Feedback inhibition. The offset step in the conversion of threonine to iso-leucine is catalyzed past the enzyme threonine deaminase. The activity of this enzyme is inhibited by isoleucine, the end production of the pathway.

Feedback inhibition is 1 example of allosteric regulation, in which enzyme activeness is controlled by the binding of pocket-sized molecules to regulatory sites on the enzyme (Figure two.29). The term "allosteric regulation" derives from the fact that the regulatory molecules demark not to the catalytic site, but to a singled-out site on the protein (allo= "other" and steric= "site"). Binding of the regulatory molecule changes the conformation of the protein, which in turn alters the shape of the active site and the catalytic activity of the enzyme. In the example of threonine deaminase, bounden of the regulatory molecule (isoleucine) inhibits enzymatic activeness. In other cases regulatory molecules serve as activators, stimulating rather than inhibiting their target enzymes.

Figure 2.29

Allosteric regulation. In this example, enzyme activity is inhibited past the binding of a regulatory molecule to an allosteric site. In the absenteeism of inhibitor, the substrate binds to the active site of the enzyme and the reaction proceeds. The bounden (more...)

The activities of enzymes can also be regulated by their interactions with other proteins and by covalent modifications, such equally the addition of phosphate groups to serine, threonine, or tyrosine residues. Phosphorylation is a peculiarly common machinery for regulating enzyme activity; the add-on of phosphate groups either stimulates or inhibits the activities of many different enzymes (Figure two.xxx). For instance, musculus cells respond to epinephrine (adrenaline) by breaking downward glycogen into glucose, thereby providing a source of free energy for increased muscular activity. The breakdown of glycogen is catalyzed by the enzyme glycogen phosphorylase, which is activated by phosphorylation in response to the binding of epinephrine to a receptor on the surface of the musculus jail cell. Protein phosphorylation plays a primal role in controlling non only metabolic reactions but also many other cellular functions, including cell growth and differentiation.

Effigy 2.xxx

Poly peptide phosphorylation. Some enzymes are regulated by the addition of phosphate groups to the side-chain OH groups of serine (as shown hither), threonine, or tyrosine residues. For example, the enzyme glycogen phosphorylase, which catalyzes the conversion (more...)