Enzymes are referred to as biological catalysts because they will enhance the rate of reactions. So the enzymes are synthesized in our living cells, which are low molecular weight proteins.
The majority of enzymes in our body are proteins, with certain exceptions. Some of the RNA is also a somatic activity; an example is Ribose. Today, we will learn about the mechanism of enzyme action and how enzymes work. Let’s start our lecture.
How Do Enzymes Work?
Enzymes are proteins that act as biological catalysts, facilitating chemical reactions in living organisms. They work by lowering the activation energy required for a reaction to occur. Here’s a general overview of how enzymes work:
Substrate Binding: Enzymes have a specific three-dimensional structure with a region called the active site. The substrate, the molecule or molecules upon which the enzyme acts, binds to the active site through precise molecular interactions such as hydrogen bonding, electrostatic interactions, and hydrophobic interactions.
Enzyme-Substrate Complex Formation: When the substrate binds to the active site, it forms an enzyme-substrate complex. This complex is stabilized by weak interactions, allowing the enzyme to hold the substrate in a specific orientation conducive to the chemical reaction.
Catalytic Reaction: Once the enzyme-substrate complex is formed, the enzyme can catalyze the conversion of the substrate into the desired products. Enzymes can accelerate reactions by providing an alternative reaction pathway with lower activation energy. They achieve this through several mechanisms:
a. Strain or Stress: Enzymes can induce strain on the bonds within the substrate, making them more reactive and prone to breaking or forming new bonds.
b. Proximity and Orientation: Enzymes bring the reacting molecules (substrates) close together, increasing the chance of successful collision and reaction. They also orient the substrates in a specific configuration that favors the formation of the desired products.
c. Active Site Chemistry: The active site of an enzyme contains specific amino acid residues that participate in the chemical reaction. These residues can act as acids, bases, or catalysts, facilitating the transfer of protons or electrons between the substrate molecules, stabilizing reaction intermediates, or promoting specific chemical transformations.
Product Formation and Release: After the catalytic reaction, the enzyme facilitates the release of the products. The products have a lower affinity for the active site than the substrate, allowing them to be released, thus regenerating the active enzyme for further catalysis.
Enzyme Regulation: Enzyme activity can be regulated to meet the organism’s needs. This regulation can occur through various mechanisms, such as feedback inhibition, allosteric regulation, covalent modification, or changes in enzyme concentration.
Almost every biochemical reaction is catalyzed by an enzyme-like all other catalysts enzymes, increasing chemical reactions without being consumed or permanently altered. However, they differ from ordinary chemical catalysts in:
- Higher catalytic power (Higher reaction rates).
- Greater reaction specificity.
- Milder reaction conditions.
- Capacity for regulation.
Few non-biological catalysts have all these properties. However, the catalytic mechanism employed by enzymes is identical to those used by chemical catalysts. Enzymes are better designers and are biologically relevant conditions, and catalyze reactions are slow.
Mechanism of enzyme action: Lock & Key Hypothesis
What are the lock and key hypotheses? It is related to the relationship between substrate and enzyme. The substrate can be referred to as a key. The enzyme’s active site can be called lock and thus key and lock mechanisms.
It indicates that the substrate has a complementary shape with the enzymes’ active site. It means only a specific substrate can fit it. They are specific reactions because only a particular substrate can bind to the active site. Not any substrate can bind to any active site.
The lock and key model is the induced fit model that describes how our binding occurs more correctly. The substrate fits precisely and correctly into the active side to complement their complementary shapes in the lock and key model.
It moves into the active side when they fit, forming those non-covalent interactions. Our induced fit model shows that the enzyme’s active site does not complement our substrate. Still, when the binding takes place, the enzyme conforms to the structure of that substrate. So the enzyme’s active site changes shape ever so slightly.
The enzyme’s active site shape is not exactly complimentary with the induced fit model. However, upon binding the substrate to the active site, the binding causes the active site to complement the substrates. The induced-fit model tells us it is when the binding occurs at the active site of that enzyme.
So the substrate becomes complementary to the active side, and the active site becomes complementary to that particular substrate. The induced-fit model correctly describes the binding between the enzyme and the substrate’s active site.
The catalytic activity of enzymes involves their binding or substrates to form an enzyme-substrate complex. The substrate binds to a specific enzyme region called its active site. The substrate is converted into the reaction product, releasing it from the enzyme.
A peak denotes the transition state. The difference between the ground state’s energy levels and the transition state is called Gibbs free activation energy. Or simply the activation energy Delta G denotes it.
Here are 5 methods to describe the mechanism of the enzyme.
Non-covalent interactions
Let us study non-covalent interactions between enzyme and substrate, like non-covalent bonds, hydrogen bonds, and hydrophobic, ionic interactions. These interactions are accompanied by a release of free energy called binding energy.
This binding energy contributes to specificity as well as to catalysis. This binding energy ultimately derives much of the catalytic power of enzymes. As it is a significant source of free energy used by enzymes to lower the activation energies of reactions as per the equation,
V= k [S] = kT/h [S] e^-∆G/RT
About 5.7 kilojoules per mole must lower g to accelerate the first-order reaction by a factor of 10 under conditions commonly found in cells. The energy from forming a weak interaction is generally estimated to be 4 to 30 kilojoules per mole.
Therefore, many such interactions’ overall binding energy level is sufficient to lower activation energies by 6,200 kilojoules per mole. The same binding energy that provides energy for catalysis also gives an enzyme.
We have all these different types of enzymes found inside our bodies. They decrease the reaction’s activation energy, but how exactly is that achieved, and what are some mechanisms? What are some enzymes’ methods to achieve this decrease in activation energy?
Covalent catalysis
Many enzymes contain active sites with catalytic residues that form covalent bonds with the substrate molecule. They also keep that molecule in place for the time being until that reaction takes place.
The enzyme is never used or depleted, or changed in any reaction. We have to break that bond, and that’s exactly why we call this bond a temporary or a transient covalent bond. For example, some enzymes include trypsin, chymotrypsin, and other digestive enzymes.
In this reaction, in the first step, this molecule forms a bond between the oxygen and this carbon kicking off this terminal amino acid to form the following temporary, transient acyl intermediate molecule. At the end of the reaction, this bond is broken.
It forms the bond to keep this group attached to the active site so that another substrate can move in and grab this group. So the bacterial enzyme glycol peptide transpeptidase utilizes covalent catalysis. Chymotrypsin is an important digestive enzyme that exists inside the digestive system.
Catalysis by proximity
By collision theory, two substrate molecules about to react must collide. They must collide with enough energy and with the proper orientation.
When we form the product molecule when the collision occurs with the proper orientation and the right amount of energy, do we form a product molecule? They bring the substrate molecules into the tiny space, creating a microenvironment for that reaction.
So inside the active site, they create a microenvironment that brings those substrate molecules nearby but also orients those subject molecules in the proper orientation.
- Many biological reactions involve two or more substrate molecules. It implies that for a reaction to take place. They must be close enough and must also have the proper orientation.
- Active sites provide a microenvironment that brings the substrate close enough for collisions to occur at a high frequency. The active sites may also orient the molecules properly for that bond to form and form those products.
Acid-base catalysis
Many residues are involved, or specific residues are found in active sites that transfer an H ion. One specific residue is the histidine amino acid. So the histidine molecule has a relatively close pH to the normal physiological pH. Active sites may contain residues such as histidine that can transfer hydrogen ions. If a hydrogen ion transfers from one molecule to another, it creates a strong nucleophile. That strong nucleophile might be needed in that particular biological reaction.
The active site may activate a nucleophile required in that catalysis by transferring the hydrogen ion. Also, It can stabilize different groups that might be found inside the activities containing charges. The transfer of hydrogen ions can increase the electrostatic interactions within that active site. It can, in turn, stabilize things like the transition state inside that chemical reaction.
Example: One particular example of an enzyme that uses acid-base catalysis is chymotrypsin. Inside the chymotrypsin active site, serine residue acts as a nucleophile.
The hydrogen ion from the oxygen of serine must take away. The hydrogen atom is transferred onto the nitrogen. The histidine side chain delocalizes the positive charge among these different atoms. But this one now contains a full negative charge.
Metal-ion catalysis
The mechanism by which enzymes can decrease the activation energy and increase reaction rates is called metal ion catalysis. Example: myoglobin and hemoglobin. These proteins use metal atoms, and enzymes utilize metal as cofactors.
What’s so special about these metal atoms? Metal atoms can lose electrons very quickly, and by losing electrons, they gain a positive charge. So they are deficient in electrons. They have a positive charge, interacting with molecules inside the active site. They can stabilize the transition states and the intermediate molecules formed within that active site.
Example: A zinc metal atom is used to form a strong nucleophile. The hydroxide nucleophile and metal atom can hold that substrate molecule in place.
So, in the same way, we can use covalent catalysis to orient that substrate and hold it in place. We can also use the positive charge of these metal atoms to bring the substrate molecules in the proper orientation and hold them inside the active site so that reaction can occur at a reasonably high rate.
Enzymes are the biological catalysts that speed up the rates of all reactions inside our cells. I hope you will understand the working principle and mechanism of enzymes properly. If you have any questions, please ask me in the comment section.
References:
Stryer L, Berg JM, Tymoczko JL. Biochemistry (5th ed.). San Francisco: W.H. Freeman.
Murphy JM, Farhan H, Eyers PA. “Bio-Zombie: the rise of pseudoenzymes in biology.” Biochem Soc Trans.
Radzicka A, Wolfenden. “A proficient enzyme.” Science. 267 (5194): 90–931.
Callahan BP, Miller BG. “OMP decarboxylase—An enigma persists.” Bioorganic Chemistry.
Williams HS. A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences. Harper and Brothers.
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