Biochemistry, protein enzymes (2023)


Every day, trillions of chemical reactions take place in our body, thanks to which the necessary metabolic processes take place. Enzymes are proteins that act on substrate molecules and reduce the activation energy required for a chemical reaction to occur, stabilizing the transition state. This stabilization accelerates the rate of reactions and causes them to occur at a physiologically significant rate. Enzymes bind substrates at key sites on their structure, called active sites. They are typically highly specific and only bind to certain substrates in certain reactions. Without enzymes, most metabolic reactions would take much longer and would not be fast enough to support life.


There are six main categories of enzymes: oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. Each category carries out a general type of reaction, but catalyzes many different specific reactions within its own category. Some enzymes, called apoenzymes, are inactive until they are attached to a cofactor that activates the enzyme. The cofactor can be metal ions (eg Zn) or organic compounds that bind to the enzyme covalently or non-covalently. The cofactor and apoenzyme complex is called a holoenzyme. Enzymes are proteins consisting of amino acids linked together in one or more polypeptide chains. This sequence of amino acids in a polypeptide chain is called the primary structure. This, in turn, determines the three-dimensional structure of the enzyme, including the shape of the active site. The secondary structure of a protein describes the localized structures of the polypeptide chain, for example, α helices or β sheets.

The complete three-dimensional assembly of a polypeptide chain into a protein subunit is known as its tertiary structure. A protein can consist of one (monomer) or more subunits (eg a dimer). The three-dimensional arrangement of subunits is called a quaternary structure. The structure of the subunit is determined by the sequence and characterization of the amino acids in the polypeptide chain. The active site is the groove or cleft in the enzyme where the substrate binds, facilitating the catalyzed chemical reaction. Enzymes are typically specific because the conformation of amino acids in the active site stabilizes substrate-specific binding. The active site usually occupies a relatively small portion of the entire enzyme and is usually filled with free water when not binding to a substrate.[1][2]

molecular level

There are two different models of substrate binding to the active site of the enzyme. The first model, called the lock and key model, assumes that the shape and chemical composition of the substrate complement the shape and chemical composition of the active site of the enzyme. This means that when the substrate enters the active site, it fits perfectly and the two come together to form an enzyme-substrate complex. The second model is called the induced fit model and assumes that the enzyme and substrate initially do not have exactly complementary shape/chemistry or alignment, but rather that this correspondence is induced at the active site by substrate binding. Substrate binding to the enzyme is generally stabilized by local molecular interactions with amino acid residues in the polypeptide chain. There are four common mechanisms by which most of these interactions arise and change the active site to form an enzyme-substrate complex: covalent catalysis, general acid-base catalysis, approximate catalysis, and metal ion catalysis.

  1. Covalent catalysis occurs when one or more amino acids in the active site form a transient covalent bond with a substrate. This reaction usually takes the form of an intermediate through nucleophilic attack of catalytic residues, which helps to stabilize subsequent transition states.

  2. General acid-base catalysis occurs when a molecule other than water acts as a proton donor or acceptor. Water can be one of the proton donors or acceptors in the reaction, but it cannot be the only one. This feature can sometimes help make catalytic residues better nucleophiles, making them easier to attack substrate amino acids.

  3. Catalysis roughly occurs when two different substrates work together at the active site to form an enzyme-substrate complex. A common example of this is water entering the active site to donate or accept a proton after the substrate has already bound, creating better nucleophiles that can make and break bonds more easily.

  4. Metal ion catalysis involves the participation of a metal ion in the active site of the enzyme, which can help make the attacking moiety a better nucleophile and stabilize any negative charge in the active site.

Enzymes can be a single subunit or consist of multiple subunits. The subunits of an enzyme with multiple subunits can sometimes work together in a mechanism called "cooperativity", where one subunit influences the other to produce either a positive activity-enhancing effect or a negative inhibitory effect. Due to the cooperation between the subunits, the enzyme can assume the T or R state. The T state, or "tight" state, results in less affinity for substrate binding than the enzyme in its normal state. The R state, or "relaxed" state, results in higher affinity and greater substrate binding by the enzyme as a whole. There are also two different models for the relationship between these two states of an enzyme with multiple subunits. The agreed model states that when an enzyme is in the T state, if one subunit transitions to the R state, then all other subunits will transition to the R state at the same time, resulting in increased binding and affinity for other effectors. This model is also reversible, as if all the subunits were in the R state and the effector dissociated, then they would all move towards the T state. On the other hand, the sequential model states that when an effector binds to one of the subunits , effector affinity subunit residues increase, but not all of them necessarily change from one state to another. They are just more willing to change.[3][4][5][6]



The initial step is when the enzyme binds to the substrate to form the enzyme-substrate complex [ES] (reaction 1). Increasing the [S] substrate concentration will in turn increase the reaction rate until the maximum rate is reached. Once the ES is formed, a product is formed that dissociates from the enzyme and the enzyme is then ready to repeat the catalysis steps.

Enzymes do not change or change the equilibrium of a given reaction, but instead affect the free energy needed to start the conversion, which affects the rate of reaction. The energetic obstacle that must be overcome for progress to respond is called activation energy; this is the highest energy in the reaction diagram. This is the most unstable conformation of the substrate in the reaction. Enzymes generally do not add energy to the reaction, but they lower the energy of the transition state, requiring less activation energy.

Inhibitors are regulators that bind to an enzyme and inhibit its functionality. There are three types of models in which an inhibitor can bind to an enzyme: competitive, non-competitive and non-competitive inhibition.

  1. Competitive inhibition occurs when an inhibitor binds to the enzyme's active site where the substrate would normally bind, thereby preventing substrate binding. In the case of enzymes subject to Michaelis-Menten kinetics, this results in the reaction having the same maximum rate but lower affinity for the binding substrate.

  2. Non-competitive inhibition occurs when an inhibitor binds to a site on the enzyme other than the active site, but results in a reduced ability of the substrate to bind to the active site. In this model, the substrate is still able to bind, but the active site is less efficient. Maximum velocity under non-competitive inhibition decreases, but substrate affinity remains the same.

  3. Non-competitive inhibition (also called anti-competitive inhibition) occurs when the inhibitor binds only to the enzyme substrate (ES in reaction 1). This reaction usually occurs when two or more reactants or products are involved in the reaction. In non-competitive inhibition, both maximum binding rate and affinity decrease.

A different type of inhibition occurs with allosteric enzymes. They can bind to a molecule called an allosteric effector, which will affect the Vmax of the catalytic reaction or the binding affinity of the substrate.[7][8][9]

clinical significance

Knowledge about enzymes is essential in medicine for diagnosing many diseases. In clinical trials, enzymes can act as markers to identify disease states in the body. Doctors can often determine what type of disease a patient has and which organ has been damaged by characterizing the enzymes released into the circulation. Enzymes can also be a component of tissue biopsies and provide detailed diagnostic information.[10]



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Wagner T, Boyko A, Alzari PM, Bunik VI, Bellinzoni M. Conformational transitions at the active site of mycobacterial 2-oxoglutarate dehydrogenase after binding of 2-oxoglutarate phosphonate analogues: from the Michaelis-like complex to ThDP adducts.J Biological Structure.October 1, 2019;208(2):182-190.[PubMed: 31476368]


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Vo NNQ, Nomura Y, Muranaka T, Fukushima EO. Structure-activity relationships of pentacyclic triterpenoids as inhibitors of cyclooxygenase and lipoxygenase enzymes.J Nat Prod.December 27, 2019;82(12):3311-3320.[PubMed: 31774676]


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Disclosure:Theodore Lewis declares that he has no adequate financial relationship with ineligible companies.

Disclosure:William Stone declares that he has no adequate financial relationship with ineligible companies.


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