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The active site is a groove or pocket on the enzyme surface, into which the substrate here, a glucose molecule binds and undergoes reaction. Enzymes exhibit four fundamental characteristics. First, enzymes do not make a reaction occur that would not occur on its own, they just make it happen much faster. Second, the enzyme molecule is not permanently altered by the reaction. It may be changed transiently, but the enzyme at the end of the reaction is the same molecule it was at the beginning.

Therefore, a single enzyme molecule can be used over and over to catalyze the same reaction. Third, an enzyme can catalyze both the forward and the reverse reaction. One direction may be more favorable than the other, but the unfavorable direction of the reaction can occur. Fourth, enzymes are highly specific for the substrates they bind, meaning they catalyze only one reaction. Take a look at Figure 2. The forward reaction from glucose to the top of the energy hill to carbon dioxide and water at the base is energetically favorable, as indicated by the "downhill" position of the products.

Because energy is released, the forward reaction sequence is called exergonic. Conversely, to synthesize glucose from CO 2 and H 2 O requires energy input to surmount the energy hill and drive the reaction in reverse; therefore, glucose synthesis is called endergonic. Figure 2. An energy profile for the glucose reaction.

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An enzyme green enhances the reaction rate by lowering the amount of activation energy required to boost the reactants to the transition state at the summit of the energy barrier. Every biochemical reaction involves both bond breaking and bond forming. The reactant molecules or substrates must absorb enough energy from their surroundings to start the reaction by breaking bonds in the reactant molecules. This initial energy investment is called the activation energy. The activation energy is represented by the uphill portion of the graph with the energy content of the reactants increasing.

It is the height of this hilltop that is lowered by enzymes.

15.3 Digestive System Processes

At the top of the energetic hill, the reactants are in an unstable condition known as the transition state. At this fleeting moment, the molecules are energized and poised for the reaction to occur. As the molecules settle into their new bonding arrangements, energy is released to the surroundings the downhill portion of the curve. At the summit of the energy hill, the reaction can occur in either the forward or the reverse direction. Look again at Figure 2. The products CO 2 and H 2 O can form spontaneously or through a series of enzyme-catalyzed reactions in the cell.

What enzymes do to accelerate reactions is to lower the energy activation barrier green to allow the transition state to be reached more rapidly. What is so special about the active site that allows it to accomplish this goal? Several mechanisms are involved. Proximity Effect. Substrate molecules collide infrequently when their concentrations are low. The active site brings the reactants together for collision. The effective concentration of the reactants is increased significantly at the active site and favors transition state formation.

Orientation Effect. Substrate collisions in solution are random and are less likely to be the specific orientation that promotes the approach to the transition state. The amino acids that form the active site play a significant role in orienting the substrate. Substrate interaction with these specific amino acid side chains promotes strain such that some of the bonds are easier to break and thus the new bonds can form. Promotion of Acid-Base Reactions.

Cell signalling: kinases & phosphorylation

For many enzymes, the amino acids that form the active site have functional side chains that are poised to donate or accept hydrogen ions from the substrate. The loss or the addition of a portion H can destabilize the covalent bonds in the substrate to make it easier for the bonds to break. Hydrolysis and electron transfers also work by this mechanism. Exclusion of Water. Most active sites are sequestered and somewhat hydrophobic to exclude water. This nonpolar environment can lower the activation energy for certain reactions. In addition, substrate binding to the enzyme is mediated by many weak noncovalent interactions.

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The presence of water with the substrate can actually disrupt these interactions in many cases. Enzymes can use one or more of these mechanisms to produce the strain that is required to convert substrates to their transition state. Enzymes speed the rate of a reaction by lowering the amount of activation energy required to reach the transition state, which is always the most difficult step in a reaction.

The first ideas about substrate binding to the active site of an enzyme were based on a lock and key model, with the active site being the keyhole and the substrate being the key. When the right substrate entered the active site, catalysis occurred because the substrate was perfectly complementary to the active site. This model described some enzymes, but not all.

For others, binding leads to conformational, or shape changes, in the enzyme active site to enhance the bond breakage and formation required to reach the transition state. In both models, the active site provides the tightest fit for the transition state, and the substrate is drawn into the transition state configuration as a result. Temperature and pH. Enzymes are sensitive to their environmental conditions. Up to a point, the rate of the reaction will increase as a function of temperature because the substrates will collide more frequently with the enzyme active site.

At extremes of pH or temperature, either high or low, the native structure of the enzyme will be compromised, and the molecule will become inactive see Figure 3. Note that there is a sharp decrease in the temperature optimum for typical human enzymes at approximately 40 degrees Celsius degrees Fahrenheit. At temperatures greater than 40 Figure 3. Temperature and pH profiles. Each enzyme has an optimal pH and temperature that favor the native conformation for maximum activity.

The enzyme in essence falls apart, and the active site is no longer able to function. In contrast, the optimal temperature for enzymes of the thermophilic bacteria extremophiles that live in hot springs is quite high at 70 degrees Celsius degrees Fahrenheit , a temperature that would instantly scald skin. Enzymes also show a pH range at which they are most active see Figure 3. The pH effect results because of critical amino acids at the active site of the enzyme that participate in substrate binding and catalysis. The ionic or electric charge on the active site amino acids can enhance and stabilize interactions with the substrate.

In addition, the ability of the substrate and enzyme to donate or receive an H is affected by pH. The pH optimum differs for different enzymes. For example, pepsin is a digestive enzyme in the stomach, and its pH optimum is pH 2. In contrast, trypsin is a digestive enzyme that works in the small intestine where the environment is much less acidic.

Its pH optimum is pH 8. Cofactors and Coenzymes. Many enzymes require additional factors for catalytic activity.


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The cofactors are inorganic such as the metal atoms, zinc, iron, and copper. Organic molecules that function to assist an enzyme are referred to as coenzymes. Vitamins are the precursors of many essential coenzymes. Cofactors and coenzymes may remain at the active site of the enzyme in the absence of the substrate, or they may be present transiently during catalysis.

Allosteric Inhibitors and Activators. In addition to the active site where the substrate binds, an enzyme may have separate sites, called allosteric sites, where specific molecules can bind to increase or decrease the activity of the enzyme. The allosteric inhibitors and activators bind the enzyme through weak, noncovalent interactions and exert their effects by changing the conformation of the enzyme, a change that is transmitted to the active site.

Typically, the allosteric modulators regulate enzyme activity by affecting substrate binding at the active site. Although biochemical reactions are controlled in part by the specificity of substrate biding and by allosteric regulation, the human body could not function if all enzymes were present together and all operating maximally with no regulation. There are over known enzymes, each of which is involved with one specific chemical reaction.

Enzymes are substrate specific. The enzyme peptidase which breaks peptide bonds in proteins will not work on starch which is broken down by human-produced amylase in the mouth. Enzymes are proteins. The functioning of the enzyme is determined by the shape of the protein. The arrangement of molecules on the enzyme produces an area known as the active site within which the specific substrate s will "fit".

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It recognizes, confines and orients the substrate in a particular direction. Space filling model of an enzyme working on glucose. Note the shape change in the enzyme indicated by the red arrows after glucose has fit into the binding or active site. The induced fit hypothesis suggests that the binding of the substrate to the enzyme alters the structure of the enzyme, placing some strain on the substrate and further facilitating the reaction. Cofactors are nonproteins essential for enzyme activity. Coenzymes are nonprotein organic molecules bound to enzymes near the active site.

NAD nicotinamide adenine dinucleotide. A cartoonish view of the formation of an enzyme-substrate complex. Enzymatic pathways form as a result of the common occurrence of a series of dependent chemical reactions. In one example, the end product depends on the successful completion of five reactions, each mediated by a specific enzyme. The enzymes in a series can be located adjacent to each other in an organelle or in the membrane of an organelle , thus speeding the reaction process. Also, intermediate products tend not to accumulate, making the process more efficient.

By removing intermediates and by inference end products from the reactive pathway, equilibrium the tendency of reactions to reverse when concentrations of the products build up to a certain level effects are minimized, since equilibrium is not attained, and so the reactions will proceed in the "preferred" direction. Negative feedback and a metabolic pathway. The production of the end product G in sufficient quantity to fill the square feedback slot in the enzyme will turn off this pathway between step C and D.

Temperature : Increases in temperature will speed up the rate of nonenzyme mediated reactions, and so temperature increase speeds up enzyme mediated reactions, but only to a point. When heated too much, enzymes since they are proteins dependent on their shape become denatured. When the temperature drops, the enzyme regains its shape. Thermolabile enzymes, such as those responsible for the color distribution in Siamese cats and color camouflage of the Arctic fox, work better or work at all at lower temperatures.

Concentration of substrate and product also control the rate of reaction, providing a biofeedback mechanism. Activation , as in the case of chymotrypsin, protects a cell from the hazards or damage the enzyme might cause. Changes in pH will also denature the enzyme by changing the shape of the enzyme. Enzymes are also adapted to operate at a specific pH or pH range. Plot of enzyme activity as a function of pH for several enzymes. Note that each enzyme has a range of pH at which it is active as well as an optimal pH at which it is most active.

Allosteric Interactions may allow an enzyme to be temporarily inactivated. Binding of an allosteric effector changes the shape of the enzyme, inactivating it while the effector is still bound. Such a mechanism is commonly employed in feedback inhibition. Often one of the products, either an end or near-end product act as an allosteric effector, blocking or shunting the pathway.


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  • Action of an allosteric inhibitor as a negative control on the action of an enzyme. Competitive Inhibition works by the competition of the regulatory compound and substrate for the binding site. If enough regulatory compound molecules bind to enough enzymes, the pathway is shut down or at least slowed down.