3.01 Enzymes

Toxins and poisons are often irreversible enzyme inhibitors.

- An example is sarin, a nerve gas. In 2017, sarin was used in a chemical attack in Syria, killing about 100 people and injuring hundreds more. This small molecule binds covalently to the R group on the amino acid serine, which is found in the active site of acetylcholinesterase, an enzyme important in the nervous system. - Other examples include the pesticides DDT and parathion, inhibitors of key enzymes in the nervous system. -For instance, penicillin blocks the active site of an enzyme that many bacteria use to make cell walls.

Enzymes can only hasten reactions that would eventually occur anyway, but this enables the cell to have a dynamic metabolism, routing chemicals smoothly through metabolic pathways.

Also, enzymes are very specific for the reactions they catalyze, so they determine which chemical processes will be going on in the cell at any given time.

The shape that best fits the substrate isn't necessarily the one with the lowest energy, but during the very short time the enzyme takes on this shape, its active site can bind to the substrate. The active site itself is also not a rigid receptacle for the substrate.

As the substrate enters the active site, the enzyme changes shape slightly due to interactions between the substrate's chemical groups and chemical groups on the side chains of the amino acids that form the active site

here is a limit to how fast the reaction can be pushed by adding more substrate to a fixed concentration of enzyme.

At some point, the concentration of substrate will be high enough that all enzyme molecules will have their active sites engaged.

The activation of the reactants is represented by the uphill portion of the graph, in which the free-energy content of the reactant molecules is increasing.

At the summit, when energy equivalent to Ea has been absorbed, the reactants are in the transition state: They are activated, and their bonds can be broken. As the atoms then settle into their new, more stable bonding arrangements, energy is released to the surroundings. This corresponds to the downhill part of the curve, which shows the loss of free energy by the molecules. The overall decrease in free energy means that Ea is repaid with dividends, as the formation of new bonds releases more energy than was invested in the breaking of old bonds.

As soon as the product exits an active site, another substrate molecule enters.

At this substrate concentration, the enzyme is said to be saturated, and the rate of the reaction is determined by the speed at which the active site converts substrate to product.

When an enzyme population is saturated, the only way to increase the rate of product formation is to add more enzyme.

Cells often increase the rate of a reaction by producing more enzyme molecules.

enzyme inhibitors

Certain chemicals selectively inhibit the action of specific enzymes. Sometimes the inhibitor attaches to the enzyme by covalent bonds, in which case the inhibition is usually irreversible.

Most vitamins are important in nutrition because they act as coenzymes or raw materials from which coenzymes are made.

Cofactors function in various ways, but in all cases where they are used, they perform a crucial chemical function in catalysis.

Learning Objectives

Describe the properties of enzymes. Explain how enzymes affect the rate of biological reactions.

Describe the properties of enzymes.

Enzymes are macromolecules that act as catalysts to speed up reactions without being consumed by the reaction. Enzymes are usually proteins and regulate the pathways of metabolism. The active site of an enzyme is the specific region where substrate molecules will bind. For an enzyme-mediated chemical reaction to occur, the substrate must be compatible with the active site of the enzyme. Enzymes catalyze biological processes by lowering the activation energy needed for chemical reactions to occur.

Introduction

Enzymes are special proteins that increase the rate of a reaction by decreasing the amount of energy needed to get a reaction started. Enzymes are biological catalysts, molecules that increase the speed of a reaction without being used up in the reaction. For example, a wrench is a tool that loosens or tightens bolts. Just as the shape of the wrench determines the types of bolts it can tighten, the shape of an enzyme determines what reaction it can speed up within a cell. Also, a wrench is not changed or destroyed after its use, just as an enzyme remains intact after its use in a reaction. Enzymes are sensitive to temperature and pH like other proteins, so they can only speed up reactions when the conditions are right.

Enzyme Structures

Enzymes come in all shapes and sizes. Since they are proteins, they are made from a combination of 20 different amino acids. This means there is a large variety of enzymes in our body that work daily to catalyze all types of chemical reactions.

Enzyme Catalysis

Enzymes have specific structures and functions that help regulate biological processes. The enzyme active site is where specific substrates will bind. The enzyme-mediated reaction can only occur if the shape and charge of the substrate is compatible with the active site of the enzyme. Sometimes enzymes and substrates are described as matching locks and keys that form unique bonds with one another to catalyze reactions. But a lock and key model is not the right "fit." It is the induced fit model that more accurately describes how enzymes and substrates bond together.

A spontaneous chemical reaction occurs without any requirement for outside energy, but it may occur so slowly that it is imperceptible.

For example, even though the hydrolysis of sucrose (table sugar) to glucose and fructose is exergonic, occurring spontaneously with a release of free energy , a solution of sucrose dissolved in sterile water will sit for years at room temperature with no appreciable hydrolysis. However, if we add a small amount of the enzyme sucrase to the solution, then all the sucrose may be hydrolyzed within seconds

Most enzyme names end in -ase.

For example, the enzyme sucrase catalyzes the hydrolysis of the disaccharide sucrose into its two monosaccharides, glucose and fructose

Every chemical reaction between molecules involves both bond breaking and bond forming.

For example, the hydrolysis of sucrose involves breaking the bond between glucose and fructose and one of the bonds of a water molecule and then forming two new bonds, as shown previously in the diagram of the sucrose hydrolysis reaction.

In most cases, however, is so high and the transition state is reached so rarely that the reaction will hardly proceed at all. In these cases, the reaction will occur at a noticeable rate only if energy is provided, usually as heat.

For example, the reaction of gasoline and oxygen is exergonic and will occur spontaneously, but energy is required for the molecules to reach the transition state and react. Only when the spark plugs fire in an automobile engine can there be the explosive release of energy that pushes the pistons. Without a spark, a mixture of gasoline hydrocarbons and oxygen will not react because the barrier is too high.

The reaction catalyzed by each enzyme is very specific; an enzyme can recognize its specific substrate even among closely related compounds.

For instance, sucrase will act only on sucrose and will not bind to other disaccharides, such as maltose.

However, the activation energy provides a barrier that determines the rate of the reaction. The reactants must absorb enough energy to reach the top of the activation energy barrier before the reaction can occur.

For some reactions, is modest enough that even at room temperature there is sufficient thermal energy for many of the reactant molecules to reach the transition state in a short time.

Citing enzyme inhibitors that are metabolic poisons may give the impression that enzyme inhibition is generally abnormal and harmful.

In fact, molecules naturally present in the cell often regulate enzyme activity by acting as inhibitors. Such regulation—selective inhibition—is essential to the control of cellular metabolism

Catalysis in the Enzymes Active site

In most enzymatic reactions, the substrate is held in the active site by so-called weak interactions, such as hydrogen bonds and ionic bonds.

Enzymes use a variety of mechanisms that lower activation energy and speed up a reaction

In reactions involving two or more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them. As the active site of an enzyme clutches the bound substrates, the enzyme may stretch the substrate molecules toward their transition state form, stressing and bending critical chemical bonds that must be broken during the reaction. Because is proportional to the difficulty of breaking the bonds, distorting the substrate helps it approach the transition state and thus reduces the amount of free energy that must be absorbed to achieve that state. The active site may also provide a microenvironment more conducive to a certain reaction than the solution itself would be without the enzyme. For example, if the active site has amino acids with acidic R groups, it may provide a pocket of low pH in an otherwise neutral cell. Here, an acidic amino acid may facilitate transfer to the substrate as a key step in catalyzing the reaction. Amino acids in the active site may directly participate in the reaction. Sometimes this process involves brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme. Subsequent steps restore the side chains to their original states, so that the active site is the same after the reaction as it was before.

A permanent change in a gene, known as a mutation, can result in a protein with one or more changed amino acids.

In the case of an enzyme, if the changed amino acids are in the active site or some other crucial region, the altered enzyme might have a novel activity or might bind to a different substrate.

cofactors

Many enzymes require nonprotein helpers for catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by the amino acids in proteins.

how enzymes speed up reactions

Proteins, DNA, and other complex cellular molecules are rich in free energy and have the potential to decompose spontaneously; that is, the laws of thermodynamics favor their breakdown.

What accounts for this molecular recognition

Recall that most enzymes are proteins, and proteins are macromolecules with unique three-dimensional configurations. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence.

Describe the factors that affect enzyme activity.

Some factors that can affect the functions of enzymes include pH, temperature, and chemical inhibitors. When enzymes reach a certain temperature range or pH, they become denatured due to disruptions in chemical bonds and weak interactions that stabilize the shape of the enzymes. There are also chemicals that can inhibit the enzymatic activity by binding to an enzyme. A competitive inhibitor binds to the active site of the enzyme and blocks substrates from binding. A noncompetitive inhibitor binds to another part of the enzyme, which causes the enzyme's shape to change. The substrate will no longer be able to bind effectively. Examples of enzyme inhibitors include toxins, poisons, and antibiotics.

Many enzyme inhibitors, however, bind to the enzyme by weak interactions, and when this occurs, the inhibition is reversible.

Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site

Activation energy is often supplied by heat in the form of thermal energy that the reactant molecules absorb from the surroundings.

The absorption of thermal energy accelerates the reactant molecules, so they collide more often and more forcefully. It also agitates the atoms within the molecules, making the breakage of bonds more likely. When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition known as the transition state.

These molecules only persist because at temperatures typical for cells, few molecules can make it over the hump of activation energy.

The barriers for selected reactions must occasionally be surmounted, however, for cells to carry out the processes needed for life.

Enduring Understanding

The highly complex organization of living systems requires constant input of energy and the exchange of macromolecules.

free energy of activation, or activation energy

The initial investment of energy for starting a reaction—the energy required to contort the reactant molecules so the bonds can break; We can think of activation energy as the amount of energy needed to push the reactants to the top of an energy barrier, or "uphill", so that the "downhill" part of the reaction can begin.

Most metabolic reactions are reversible, and an enzyme can catalyze either the forward or the reverse reaction, depending on which direction has a negative change in g. This in turn depends mainly on the relative concentrations of reactants and products.

The net effect is always in the direction of equilibrium.

Just as each enzyme has an optimal temperature, it also has a pH at which it is most active.

The optimal pH 6-8 values for most enzymes fall in the range of but there are exceptions. - For example, pepsin, a digestive enzyme in the human stomach, works best at a very low pH. Such an acidic environment denatures most enzymes, but pepsin is adapted to maintain its functional three-dimensional structure in the acidic environment of the stomach. - In contrast, trypsin, a digestive enzyme residing in the more alkaline environment of the human intestine, would be denatured in the stomach

substrate

The reactant an enzyme acts on

Essential Knowledge

The structure of enzymes includes the active site that specifically interacts with substrate molecules. For an enzyme-mediated chemical reaction to occur, the shape and charge of the substrate must be compatible with the active site of the enzyme. The structure and function of enzymes contribute to the regulation of biological processes.

Above that temperature, however, the speed of the enzymatic reaction drops sharply.

The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures.

Effects of Temperature and pH

The three-dimensional structures of proteins are sensitive to their environment. As a consequence, each enzyme works better under some conditions than under other conditions, because these optimal conditions favor the most active shape for the enzyme

Enzymes, like other catalysts, emerge from the reaction in their original form.

Therefore, very small amounts of enzyme can have a huge metabolic impact by functioning over and over again in catalytic cycles

Changing one molecule into another generally involves contorting the starting molecule into a highly unstable state before the reaction can proceed.

This contortion can be compared to the bending of a metal key ring when you pry it open to add a new key. The key ring is highly unstable in its opened form but returns to a stable state once the key is threaded all the way onto the ring. To reach the contorted state where bonds can change, reactant molecules must absorb energy from their surroundings. When the new bonds of the product molecules form, energy is released as heat, and the molecules return to stable shapes with lower energy than the contorted state.

Under environmental conditions where the new function benefits the organism, natural selection would tend to favor the mutated form of the gene, causing it to persist in the population.

This simplified model is generally accepted as the main way in which the multitude of different enzymes arose over the past few billion years of life's history.

This shape change makes the active site fit even more snugly around the substrate

This tightening of the binding after initial contact—called induced fit—is like a clasping handshake. Induced fit brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction.

Temperature and pH are environmental factors important in the activity of an enzyme

Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when the molecules move rapidly.

Only a restricted region of the enzyme molecule actually binds to the substrate. This region, known as the active site, is typically a pocket or groove on the surface of the enzyme where catalysis occurs

Usually, the active site is formed by only a few of the enzyme's amino acids, with the rest of the protein molecule providing a framework that determines the shape of the active site. The specificity of an enzyme is attributed to a complementary fit between the shape of its active site and the shape of the substrate, like that seen in the binding of a signaling molecule to a receptor protein

The enzyme binds to its substrate (or substrates, when there are two or more reactants), forming an enzyme-substrate complex.

While enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate to the product (or products) of the reaction.

Each enzyme has an optimal temperature at which its reaction rate is greatest.

Without denaturing the enzyme, this temperature allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules.

enzyme

a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction.

effect of local conditions on enzyme activity

affected by general environmental factors, such as temperature and pH. It can also be affected by chemicals that specifically influence that enzyme.

An enzyme catalyzes a reaction by lowering the barrier Ea(Figure 6.13), enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.

an enzyme cannot change the for a reaction; it cannot make an endergonic reaction exergonic.

Without regulation by enzymes,

chemical traffic through the pathways of metabolism would become terribly congested because many chemical reactions would take such a long time.

The R groups of a few of the amino acids that make up the active site catalyze the

conversion of substrate to product, and the product departs from the active site

noncompetitive inhibitors

do not directly compete with the substrate to bind to the enzyme at the active site. Instead, they impede enzymatic reactions by binding to another part of the enzyme. This interaction causes the enzyme molecule to change its shape in such a way that the active site becomes much less effective at catalyzing the conversion of substrate to product

An enzyme is not a stiff structure locked into a given shape.

enzymes (and other proteins) seem to "dance" between subtly different shapes in a dynamic equilibrium, with slight differences in free energy for each "pose."

These adjuncts, called cofactors, may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate.

he cofactors of some enzymes are inorganic, such as the metal atoms zinc, iron, and copper in ionic form.

coenzyme

if the cofactor is an organic molecule

Heat can increase the rate of a reaction by allowing reactants to attain the transition state more often, but this would not work well in biological systems.

irst, high temperature denatures proteins and kills cells. Second, heat would speed up all reactions, not just those that are needed. Instead of heat, organisms carry out catalysis, the process by which a catalyst selectively speeds up a reaction.

evolution of enzymes

most enzymes are proteins, and proteins are encoded by genes. Thus far, biochemists have identified more than 4,000 different enzymes in various species, most likely a very small fraction of all enzymes

competitive inhibitors

reduce the productivity of enzymes by blocking substrates from entering active sites. This kind of inhibition can be overcome by increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the sites.

The enzyme is then free to take another substrate molecule into its active site.

the entire cycle happens so fast that a single enzyme molecule typically acts on about 1,000 substrate molecules per second, and some enzymes are even faster.

The rate at which a particular amount of enzyme converts substrate to product is partly a function of the initial concentration of the substrate:

the more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules.