Enzymes Are Composed Of What Organic Molecule

Enzymes Are Composed Of What Organic Molecule – In this article, you will learn about the functions, mechanics and types of one of the most important biomolecules: enzymes.

Enzymes are a group of biomolecules responsible for catalyzing chemical reactions in cells. Enzymes make life possible because they enable many of the most important biochemical changes in cells. In fact, without enzymes, important processes such as cellular respiration, photosynthesis and protein synthesis would not occur. In fact, the use of enzymes allows them to be used in important research methods, such as molecular cloning and PCR.

Enzymes Are Composed Of What Organic Molecule

Most enzymes are proteins. These enzymes are made of amino acids linked together by peptides, like all proteins. Like all proteins, enzymes can change under extreme conditions. However, there are many enzymes made of ribonucleic acid (RNA), which biochemists call “ribozymes”. Interestingly, most enzymes consist mainly of amino acids, but they can have other binding units of metal cations or organic compounds that play an important role in enzyme activity. Biochemists call organic compounds that do not contain protein “artificial compounds.”

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In addition to synthetic groups, enzymes may also require molecules to participate in the reaction other than the main reactant, called “cosubstrates”. In general, biochemists use the term “cofactor” to include cosubstrates, artificial groups, and metal cations used by enzymes.

Enzymes, as a group, have many types of structure, and biochemists have observed enzymes in different shapes and sizes. This diversity reflects the wide variety of functions that enzymes serve, due to the large number of chemicals necessary for life.

As mentioned before, enzymes play an important role in catalysis. In other words, enzymes make it easier for a slow, rate-determining reaction, which speeds up the overall reaction chain. How enzymes serve this purpose is directly related to their structure.

All enzymes have an important structure called the active site, to which their desired reactants bind. Bacteria often build enzymes to carry out a single reaction, meaning that the active site of the enzyme only needs to bind the reactants of its reaction and nothing else. For this reason, the active site of the enzyme generally has a high substrate value, which means that only its reactants are able to bind to the active site. “Substrate” is the technical term biochemists use to describe the desired molecule that binds to the enzyme.

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Also, since part of the enzyme molecule is derived from the chemical composition of its active site, the enzyme molecule must bind in a specific way. The chemical groups of the substrate must interact with those of the active site to bind the enzyme.

Since the active sites bind only certain structural molecules, this allows the enzymes to be specific for certain stereoisomers of chiral substrates.

Once the substrate fills the active site, the conformation of the enzyme, or its chemical structure, changes. This changes the substrates to more easily allow the desired reaction to occur.

In general, reactions catalyzed by enzymes involve the breaking and formation of chemical bonds. To do this, enzyme modification usually involves enzyme units separating parts of the molecule to break bonds and joining other parts to form bonds.

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As mentioned earlier, enzymes speed up reactions by moving substrates for maximum reaction. Chemists understand this phenomenon by looking at the “transition state” of a reaction. However, rather than being an isolated molecule, a transition state represents a step that is necessary between a product and a reactant that exists at the same time.

All reactions have a rate of change, and the chemistry of this state measures its rate. Because of their short-lived nature, transition states have much higher energy and less stability than their products and reactants. Therefore, even if a reaction involves the release of energy from the reactants to the products, the reactants still need to absorb some energy for the reaction to begin. Chemists generally show this using an energy diagram, where reactants must climb a mountain of energy to reach a transition point, before lowering the energy to form products.

Energy diagram of a chemical reaction. The vertical distance between the reactants and the surface of the red peak represents the energy required to create the transition state. source

This is where enzymes come in. The structure of the active site of the enzyme is designed to stabilize the transition state. Usually, the enzyme does this to protect the most active and unstable groups with complementary groups in the active site.

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Charges (red and blue) and non-polar, hydrophobic chemical groups (orange) of the active site correspond to those of the transition state, which provides stability.

By stabilizing the transition state, the enzyme decreases its overall strength. This then lowers the energy barrier of the reaction, allowing it to proceed at a faster rate. As mentioned before, this catalysis allows important biochemical changes to occur at a rate sufficient for life to exist. The steady-state approximation is applicable to many enzyme-catalyzed reactions.

Enzymes represent a diverse group of proteins, due to the different types of biochemical reactions they produce in living organisms. Biochemists use the suffix “-ase” to refer to enzymes. The most important enzymes fall into one of these six broad categories:

The oxidoreductase reaction, where the carbonyl compound can be oxidized to carboxylic acid or reduced to alcohol or methyl, depending on the type of oxidoreductase.

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Generic ligase reaction, where a bond is formed between two molecules, resulting from the energy released by the conversion of ATP to ADP The structure of the zyme and the example of lysozyme. Binding sites in blue, auxiliary site in red and peptidoglycan substrate in black. (PDB: 9LYZ)

In biology and biochemistry, the active site is the site of a zyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the binding site, and residues that influence the reaction of that substrate, the auxiliary site. Although the active site occupies only ~10–20% of the zyme volume,

It is the most important component that directly influences the chemical reaction. It usually contains three to four amino acids, while other amino acids in the protein are necessary to maintain the high structure of the zymes.

Each active site is optimized to bind to a specific substrate and induce a specific reaction, resulting in higher levels. This specificity is determined by the arrangement of amino acids in the active site and the structure of the substrates. Sometimes zymes also need to associate with other cofactors to do their job. The active site is usually the groove or pocket of the zyme which may be located in a deep groove in the zyme,

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Or between interfaces of multimeric zymes. An active site can activate a reaction repeatedly since the residue is not changed in the d of the reaction (it can change during the reaction, but it is renewed by d).

This process is achieved by lowering the energy of the reaction process, so many substrates have the energy to react.

Usually, the zyme molecule has only two active sites, and the active sites correspond to one type of substrate. The active site has a binding site that binds to the substrate and directs it for catalysis. The orientation of the substrate and the close proximity between it and the active site is so important that in some cases the zyme can still work well, even if all the other parts have been changed and lost their function.

In principle, the interaction between the active site and the substrate is non-covalent and transitive. There are four important types of interactions that hold the substrate in a defined way and form the zyme-substrate complex (ES complex): hydrogen bonds, van der Waals interactions, hydrophobic interactions and energetic interactions.

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The distribution of charges on the substrate and the active site must be balanced, meaning that all positive and negative charges must cancel. Otherwise, there will be repulsive forces pushing them. The active site usually contains non-polar amino acids, although sometimes polar amino acids may also occur.

Binding of the substrate to the binding site requires at least three contact points to achieve stereo-, regio-, and antioselectivity. For example, an alcohol dehydrogase that catalyzes the transfer of a hydride from ethanol to NAD + interacts with the methyl group of the substrate, the hydroxyl group and the pro-(R) hydrog will be removed during the reaction.

To use their work, the zymes need to take their correct proteins (natural folds) and tertiary structure. To maintain this defined three-dimensional structure, proteins rely on a variety of interactions between amino acid residues. If these interactions are interfered with, for example, with extreme values ​​of pH, high temperature or high concentration of ions, this will cause the zyme to become dated and lose its catalytic activity.

It is believed that the strong compatibility between the active site and the substrate molecule increases the efficiency of the reaction. If the tightness of the active site of DNA polymerase and its substrate is increased, the reliability, which means that the correct rate of DNA replication also increases.

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There are three proposed types of how zymes interact with their specific substrate: the key and the key model, the

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