ENZYMES: The enzymes mechanism, active site, Lock and Key Model and Induced fit Hypothesis - Chemical catalysis

Topics Included:

• Active Site
• Transition State
• Catalysis
• Lock and Key
• Induced Fit
• Nonproductive Binding
• Entropy
• Chemical Catalysis

Enzymes do two important things:

They recognize very specific substrates, and they perform specific chemical reactions on them at fantastic speeds. The way they accomplish all this can be described by a number of different models, each one of which accounts for some of the behavior that enzymes exhibit. Most enzymes make use of all these different mechanisms of specificity and/or catalysis. In the real world, some or all of these factors go into making a given enzyme work with exquisite specificity and blinding speed.

ACTIVE SITE:

The active site is a specialized region of the enzyme where the enzyme interacts with the substrate. The active site of an enzyme is generally a pocket or cleft that is specialized to recognize specific substrates and catalyze chemical transformations. The interactions between the active site and the substrate occur via the same forces that stabilize protein structure: hydrophobic interactions, electrostatic interactions (charge–charge), hydrogen bonding, and van der Waals interactions. Enzyme active sites do not simply bind substrates; they also provide catalytic groups to facilitate the chemistry and provide specific interactions that stabilize the formation of the transition state for the chemical reaction.

CATALYSIS:

The reaction happens at a faster rate. The catalyst is regenerated. Enzymes do chemistry. Their role is to make and break specific chemical bonds of the substrates at a faster rate and to do it without being consumed in the process. At the end of each catalytic cycle, the enzyme is free to begin again with a new substrate molecule.

Since catalysis is simply making a reaction go faster, it follows that the activation energy of a catalyzed (faster) reaction is lower than the activation energy of an uncatalyzed reaction. It’s possible to say, then, that enzymes work by lowering the activation energy of the reaction they catalyze. This is the same as saying that enzymes work because they work. The question is how they lower the activation energy.

LOCK AND KEY Model:

Specificity model: The correct substrate fits into the active site of the enzyme like a key into a lock. Only the right key fits.

This is the oldest model for how an enzyme works. It makes a nice, easy picture that describes enzyme specificity. Only if the key fits will the lock be opened. It accounts for why the enzyme only works on certain substrates, but it does not tell us why the reaction of the correct substrates happens so fast. It doesn’t tell us the mechanism of the lock.

INDUCED FIT:

The binding of the correct substrate triggers a change in the structure of the enzyme that brings catalytic groups into exactly the right position to facilitate the reaction.

In the induced-fit model, the structure of the enzyme is different depending on whether the substrate is bound or not. The enzyme changes shape (undergoes a conformation change) on binding the substrate. This conformation change converts the enzyme into a new structure in which the substrate and catalytic groups on the enzyme are properly arranged to accelerate the reaction. “Bad” substrates cannot cause this conformation change.

Although water and glucose are chemically similar, hexokinase catalyzes the transfer of phosphate to glucose about 105 times faster than it catalyzes the transfer of phosphate to water. The induced-fit model would argue that the fancy part of the glucose molecule is necessary to induce the enzyme to change its conformation and become an efficient catalyst. Even though the fancy part of the glucose molecule is not directly involved in the chemical reaction, it participates in the enzyme-catalyzed reaction by inducing a change in the structure of the enzyme. Since water doesn’t have this extra appendage, it can’t cause the conformation change and is, therefore, a poor substrate for this enzyme. The induced fit-model would say that in the unreactive conformation of the enzyme, the ATP is 105 times less reactive than when the enzyme is in the reactive conformation.

What the induced-fit model is good at explaining is why bad substrates are bad, but like the lock and key model, it too fails to tell us exactly why good substrates are good. What is it about the “proper” arrangement that makes the chemistry fast?

NONPRODUCTIVE BINDING:

Poor substrates bind to the enzyme in a large number of different ways, only one of which is correct. Good substrates bind only in the proper way.

Again, this model tells us why poor substrates don’t work well. Poor substrates bind more often to the enzyme in the wrong orientation than in the right orientation. Since poor substrates bind in the wrong orientation, the catalytic groups and specific interactions that would accelerate the reaction of the correct substrate come into play in only a very small number of the interactions between the enzyme and a bad substrate. In contrast to the induced-fit model, this model does not require a change in the conformation of the enzyme (Fig. 7-4). In the hexokinase reaction discussed earlier, the nonproductive binding model

would say that only 1 out of 105 water molecules binds to the enzyme in a productive fashion but all the glucose binds in a productive orientation.

ENTROPY:

Organizing a reaction at the active site of an enzyme makes it go faster.

When molecules react, particularly when it’s the reaction between two different molecules or even when it’s a reaction between two parts of the same molecule, they must become more organized. The reason is that the two reacting atoms must approach each other in space. Just finding the appropriate partner is often a tough part of the reaction (biochemistry mimics life once more). Part of the free-energy barrier to a chemical reaction is overcoming unfavorable entropy changes that must accompany the formation of the transition state. By binding two substrates at the same active site, the enzyme organizes the reacting centers.

This reduces the amount of further organization that must occur to reach the transition state for the reaction, making the free energy of activation lower and the reaction faster. Of course, the enzyme must find each of the substrates and organize them at the active site—this is entropically unfavorable too. However, the price paid for organizing the substrates can be taken out of the binding free energy.

CHEMICAL CATALYSIS:

The amino acid side chains and enzymes cofactors provide functional groups that are used to make the reaction go faster by providing new pathways and by making existing pathways faster.

Many chemical reactions can be made to occur faster by the use of appropriately placed catalytic groups. Enzymes, because of their three-dimensional structure, are great at putting just the right group in the right place at the right time. Take the simple reaction of the addition of water to a carbonyl group. We can talk about two factors with this one reaction. The carbonyl group is reactive toward water because the carbonyl group is polarized, the electrons are not shared equally between the carbon and the oxygen. The carbon atom has fewer of them (because oxygen is more electronegative). As the water attacks the carbonyl oxygen, the electrons in the bond being broken, shift to oxygen, giving it a formal negative charge. Putting a positively charged group near the oxygen of the carbonyl group polarizes the carbonyl group and makes the carbonyl more reactive by helping stabilize the development of negative charge on oxygen as the chemical reaction proceeds.

Now let’s look at what we can do with the water. Because it has more negative charge (a higher electron density), _OH is more reactive than HOH. By providing an appropriately placed base to at least partially remove one of the protons from the attacking water molecule, we can increase the reactivity of this water and make the reaction go faster. This is known as acid–base catalysis and is widely used by enzymes to help facilitate the transfer of protons during chemical reactions. Another alternative is for the enzyme to actually form a covalent bond between the enzyme and the substrate. This direct, covalent participation of the enzyme in the chemical reaction is termed covalent catalysis. The enzyme uses one of its functional groups to react with the substrate. This enzyme–substrate bond must form fast, and the intermediates must be reasonably reactive if this kind of catalysis is going to give a rate acceleration.

Reference book: Basic Concepts in Biochemistry (Second edition) by Hiram F. Gilbert, (PhD.), McGraw-Hill