What Is True About Enzymes – The enzyme glucosidase converts the sugar maltose into the disaccharide glucose. Active site residues in red, maltose substrate in black and NAD cofactor in yellow. (PDB: 1OBB)
Zymes (/ ˈɛ n z aɪm z / ) are proteins that act as biological catalysts by speeding up chemical reactions. The molecules that zymes can act on are called substrates, and zymes convert the substrate into different molecules known as products. Almost all metabolic processes in cells require enzymatic catalysis to occur at a high enough rate to sustain life.
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Metabolic pathways depend on the winters that catalyze each step. The study of winters is called zymology, and the field of pseudozyme analysis recognizes that during evolution, some winters have lost their biological catalytic capacity, often reflected in amino acid sequences and “pseudocatalytic” properties. unusual.
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Like all catalysts, winters increase the rate of a reaction by lowering its activation energy. Some winters can cause faster conversion of substrate to product. An extreme example is orotidine 5′-phosphate decarboxylase, which allows reactions that might take millions of years to occur in milliseconds.
Chemically, winters are like all catalysts and do not dissolve in chemical reactions and do not change the equilibrium of the reaction. Winters differ from most other catalysts in their specificity. The activity of winter can be affected by other molecules: an inhibitor is a molecule that reduces the activity of winter, and an activator is a molecule that increases its activity. Many medical drugs and toxins inhibit the enzyme. The activity of winters is greatly reduced outside the optimum temperature and pH, and many (permanent) winters degrade when exposed to high temperatures, losing their structure and catalytic properties.
Some winters are used commercially, for example in the synthesis of antibiotics. Some household products use zymes to speed up chemical reactions: zymes in biological detergents break down proteins, stains or fats in clothes, and zymes in meat tderizer convert protein into smaller molecules, making meat easier to chew.
And the conversion of starch to sugar by plant extracts and saliva is known, but the mechanism by which this occurs is unknown.
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A few decades later, when Louis Pasteur studied the fermentation of sugar into alcohol by yeast, he concluded that this fermentation was the result of a great force inside the yeast cells called “fermts”, which was thought to be, but worked only in living things. He wrote that “alcoholic fermentation is a reaction related to the life and organization of yeast cells, not to cell death or contamination.”
In 1877, Wilhelm Kühne (1837–1900) first used the word zyme, which comes from the Greek word ἔνζυμον, “to leave” or “to leaven,” to describe this process.
The term zyme was later used to refer to non-living substances such as pepsin, and the term fermt was used to refer to chemicals produced by living organisms.
Eduard Buchner submitted his first research paper on yeast extract in 1897. In a series of experiments at the University of Berlin, he found that sugar could be obtained from a yeast extract that had no living cells in the mixture.
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In 1907, he won the Nobel Prize in Chemistry for his “discovery of acellular fermentation.” Following Buchner’s example, enzymes are often named according to their reaction: the suffix -ase is combined with the name of the substrate (eg lactase is the enzyme that breaks down lactose) or with the type of reaction – concepts (eg DNA polymerase.create DNA polymers).
The biochemical identity of winters was still unknown in the early 1900s. Many scientists suggested that winter activity was related to proteins, but others (such as Nobel laureate Richard Wilstatter) said that proteins only carry the actual winters and that individual proteins are not capable of catalysis.
In 1926, James B. Sumner demonstrated that the enzyme urease was a pure protein and synthesized it; He did the same with catalase ferment in 1937. The conclusion that pure proteins could be ferments was shown by John Howard Northrop and Udell Meredith Stanley, who worked on pepsin ferments (1930), trypsin and chymotrypsin. These three scientists won the Nobel Prize in Chemistry in 1946.
The discovery that winters could be crystallized allowed their structures to be solved using X-ray crystallography. This is mainly due to lysozyme, a zyme found in tears, saliva and egg whites, which digests the membranes of some bacteria; The system was solved by a group led by David Chilton Phillips and published in 1965.
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This high-resolution structure of lysozyme marks the beginning of the field of structural biology and efforts to understand how zyms work in atomic-level detail.
Winters can be classified by two main criteria: either their amino acid similarity (and therefore their evolutionary relationship) or their winter activity.
Enzyme activity. The name of winter is usually derived from the substrate or the chemical reaction it performs, with the word ding in -ase.
Examples include lactase, alcohol dehydrogenase, and DNA polymerase. Different zymes that catalyze the same chemical reaction are called isozymes.
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The International Union of Biochemistry and Molecular Biology developed a nomenclature for zymes, EC number (for “Zyme Commission”). Each winter is identified by an “EC” followed by a series of four numbers that represent the degree of winter activity (from very general to very specific). This means that the first number loosely classifies a zyme based on its mechanism, while the other number adds more and more.
These sections are divided into other features such as substrates, products and chemical mechanisms. Winter is fully defined by four names. For example, hexokinase (EC 22.214.171.124) is a transferase (EC 2) that adds a phosphate group (EC 2.7) to a hexose sugar, a molecule with an alcohol group (EC 2.7.1).
Sequence similarity. The EC category does not represent sequence equality. For example, two ligases with the same EC number that regulate the same reaction may have completely different sequences. Regardless of their function, ZIMs, like all other proteins, are classified according to their similarity into several families. These families are documented in dozens in various protein and protein databases such as Pfam.
Winter activity increases initially with temperature (Q10 factor) until the winter structure (daturation) is reached, resulting in the best reaction rate at medium temperature.
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Winters are usually globular proteins, acting alone or in larger complexes. The sequence of amino acids determines the structure that determines the catalytic activity of winter.
Winter’s structure expands (daturates) upon heating or exposure to chemical daturants, and this structural disruption often results in loss of activity.
Overwintering is usually associated with temperatures above the species level; as a result, winters of bacteria living in volcanic environments such as hot springs are consumed by industrial users because of their ability to operate at high temperatures, allowing cyme-catalyzed reactions to operate at very high rates.
Winters are usually much larger than the substrate. The size is 62 amino acid residues, for the monomer of 4-oxalocrotonate tautomerase,
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A small part of its structure (about 2-4 amino acids) is directly involved in catalysis: the catalytic site.
This catalytic site is located close to one or more binding sites that contain substrate residues. The catalytic site and the binding site form the active site of winter. Most of the fermentation systems function to maintain the correct orientation and dynamics of the active site.
In some winters, no amino acid is directly involved in catalysis; instead, zym contains binding and transcription sites for catalytic cofactors.
The winter structure may also contain an allosteric site where binding of a small molecule causes a change that increases or decreases activity.
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There are RNA-based biological enzymes called ribozymes that can work alone or together with proteins. The most common of these is the ribosome, which is a combination of proteins and catalytic RNA units.
Organization of winter structures and examples of lysozyme. Binding sites in blue, catalytic sites in red and peptidoglycan in black. (PDB: 9LYZ)
Winters must bind to the substrate before they can catalyze the chemical reaction. Winters are usually very specific in terms of which substrates they bind to and the chemical reactions involved. Enhancement is achieved by binding a pocket with full shape, charge and hydrophilic/hydrophobic properties to the substrate. Therefore, ZIMs can discriminate the same substrate molecules chemoselectively, regioselectively, and stereospecifically.
Some of the winters showing the highest degree of accuracy are involved in gome copying and expression. Some of these winters have “read check” mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in the first step and checks that the product is correct in the second step.
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This two-step process results in an error rate of less than 1 in 100 million reactions with irreversible mammalian polymerase.
On the other hand, some winters show winter promiscuity, having specific specificity and acting on different physiologically relevant types of substrates. Many winters have relatively little activity that has evolved spontaneously (ie, is neutral), which can be a starting point for the evolutionary selection of new activity.
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