Enzymes

Many different reactions take place in biological systems. Experiments have shown that the rate of these reactions when performed outside a living system (ie in vitro ) is much lower than in vivo. In living systems, reactions occur hundreds to millions of times faster than in vitro. This is caused by specific catalysts - enzymes. These often enable the course of such reactions that would otherwise practically not take place in the conditions of the human body (temperature, pH, etc.).

Biological catalysts
A catalyst is a substance that increases the rate of a chemical reaction, but does not change the chemical equilibrium (only shortens the time it takes to achieve it). During the reactions, the enzyme molecule is not consumed.

Enzyme
An enzyme is a specific organic molecule that accelerates reactions in organisms (it acts as a biocatalyst). This enables reactions to take place even at relatively low temperatures, neutral pH and atmospheric pressure, which are normally found in organisms. The vast majority of enzymes are proteins. The exception is some types of RNA molecules - so-called ribozymes.

In addition to the protein component, enzymes can also contain a non-protein component. According to its presence, enzymes can be divided into:


 * simple :
 * contain only the protein part (e.g. hydrolases – pepsin, trypsin , ribonuclease),
 * composite :
 * in addition to the protein part (the so-called apoenzyme, it is ineffective by itself), they also contain a non-protein part - the so-called cofactor . The cofactor together with the apoenzyme forms an active enzyme molecule, the so-called holoenzyme.



Cofactors
A cofactor can be:


 * metal ions: Zn 2+ (e.g. alcohol dehydrogenase), Mn2+ (e.g. arginase), Fe2+, C 2+ , Mg2+ ,
 * organic molecules: they are often derivatives of vitamins.

According to the nature of the binding to the apoenzyme, cofactors are divided into:


 * coenzymes : an organic molecule of a non-protein nature, loosely bound to the apoenzyme molecule - it can be separated from it (e.g. NAD +, NADP + ).


 * FADH2-FBLT.pngprosthetic groups : an organic molecule of a non-protein nature, tightly bound to the apoenzyme molecule (e.g. heme, FAD ).

See the Enzyme Cofactors page for more detailed information .

Multienzyme complex
An enzyme can be made up of a different number of peptide chains. Each chain can contain multiple domains (with the same or different enzyme specificity). If the enzyme contains multiple chains (quaternary structure), we refer to it as a multienzyme complex. Individual subunits usually have different specificities and are non-covalently linked to each other. An example of a multienzyme complex is fatty acid synthase, which catalyzes the synthesis of higher fatty acids in cells.

Zymogens
Some enzymes (e.g. digestive) are created and secreted in their inactive form as so-called zymogens (proenzymes). The reason is the protection of synthesizing cells from being split by the effect of active forms of enzymes. Zymogens are activated only at the point where their activity is required. Activation can, for example, take place as so-called partial proteolysis, during which a precisely defined part of the proenzyme molecule is cleaved off.

Here are two examples of this process:


 * The chief cells of the gastric mucosa secrete the proenzyme pepsinogen . The HCl present in the gastric juice aids in the autoactivation of pepsinogen to active pepsin. The reaction also takes place autocatalytically, when already formed pepsin molecules participate in the splitting of pepsinogen.


 * Like pepsin, trypsin is synthesized in the pancreas as inactive trypsinogen. In the small intestine, the hexapeptide is subsequently cleaved using the enzyme enteropeptidase (formed by the cells of the intestinal mucosa) to form active trypsin.

Isoenzymes and enzyme isoforms
In the organism, there are enzymes called isoenzymes, which catalyze the same reaction, but differ from each other in their physicochemical properties (different affinity to the substrate, K M , sensitivity to inhibitors) and also in their occurrence in tissues. These genetically conditioned differences (a different sequence of DNA nucleotides ), for example, allow a certain regulation of the conditions under which the given reaction will take place in different tissues.

Isoenzymes catalyzing the conversion of glucose to glucose-6-phosphate (phosphorylation of glucose) are illustrative examples - glucokinase (found in hepatocytes and β-cells of the pancreas) and hexokinase (localized in other cells of the body). Glucokinase shows a lower affinity for its substrate – glucose (this is expressed by the so-called K m, for glucokinase it is approximately 10 mmol/l). This means that the enzyme-catalyzed reaction takes place if the blood glucose level reaches a sufficient level (usually after a meal). With normal glycemia (between meals), glucokinase is not very active. The liver thus leaves enough glucose for other tissues that contain hexokinase with a KM valuearound 0.1 mmol/l.

More detailed information can be found on the Embden-Meyerhof-Parnassus track page .

In addition to isoenzymes, enzyme isoforms are also found in the body. These multiple forms of enzymes come from the same gene (same sequence of DNA nucleotides), but differ in different post-translational modifications or alternative splicing. As a result, these enzymes can also catalyze different reactions.

Mechanism of action of enzymes
Enzymes, like other catalysts, work on the principle of reducing the activation energy.

For more detailed information, see What Powers Our Cells .

During the first step, the enzyme-substrate (ES) complex is formed. This reaction is typically very fast and reversible. Subsequently, the substrate is transformed into a product under catalysis by the enzyme. The ES complex thus forms an enzyme-product complex (EP), which disintegrates to release the product. This reaction is slow and irreversible.

The reaction is thus divided into several successive steps, in which one or several transition states ES ( transition states ) arise. The activation energy required for the formation of each intermediate and the subsequent conversion of ES to EP is lower than for the direct conversion of substrate to product, even though the overall ΔG of both reactions is the same.

Interaction of substrate and enzyme
The substrate interacts with the enzyme molecule in a region called the active site (center). It is formed as follows:


 * Enzyme binding site


 * The enzyme binding site is a spatially defined, small part of the enzyme molecule containing precisely distributed functional groups (−SH, −OH, acidic and basic amino acids ), whose position corresponds to the structure of the substrate. Non-bonding interactions (H-bridges, electrostatic and hydrophobic interactions, van der Waals forces) are involved in the binding between the enzyme and the substrate . Covalent bonds occur only exceptionally.


 * A catalytic site


 * The catalytic site contains other groups responsible for the catalytic activity of the enzyme. These groups often come from the cofactor molecule . However, the exact distinction between the binding and catalytic sites is usually problematic.

In addition to the active site, there may also be allosteric sites on the surface of the enzyme, enabling the regulation of enzyme activity due to various effectors (inhibitors or activators).

The original model of the interaction between the substrate molecule and the enzyme (later called the lock and key theory ) created by the German chemist Emil Hermann Fischer at the end of the 19th century assumed that the substrate molecule fits exactly into the enzyme molecule. In the 20th century, this model was modified by the American biochemist Daniel Edward Koshland, Jr., who came up with the claim that the substrate can to some extent induce a conformational change in the site to which it binds (or interact with each other). Therefore, the exact "lock and key" shape is achieved only after binding. It turns out that this induced fit theory describes the interactions between the enzyme and the substrate better than the original model.

Enzyme specificity
Enzyme specificity limits the range of action of a certain enzyme. We distinguish two types of specificity: