Enzyme
An enzyme is a biological macromolecule, usually a protein, that acts as a biological catalyst, accelerating chemical reactions without being consumed in the process. The molecules on which enzymes act are called substrates, which are converted into products. Nearly all metabolic processes within a cell depend on enzyme catalysis to occur at biologically relevant rates. A metabolic pathway is typically composed of a series of enzyme-catalyzed steps. The study of enzymes is known as enzymology, and a related field focuses on pseudoenzymes—proteins that have lost catalytic activity but may retain regulatory or scaffolding functions, often indicated by alterations in their amino acid sequences or unusual 'pseudocatalytic' behavior.
Enzymes are known to catalyze over 5,000 types of biochemical reactions. Other biological catalysts include catalytic RNA molecules, or ribozymes, which are sometimes classified as enzymes despite being composed of RNA rather than protein. More recently, biomolecular condensates have been recognized as a third category of biocatalysts, capable of catalyzing reactions by creating interfaces and gradients—such as ionic gradients—that drive biochemical processes, even when their component proteins are not intrinsically catalytic.
Enzymes increase the reaction rate by lowering a reaction's activation energy, often by factors of millions. A striking example is orotidine 5′-phosphate decarboxylase, which accelerates a reaction that would otherwise take millions of years to occur in milliseconds. Like all catalysts, enzymes do not affect the overall equilibrium of a reaction and are regenerated at the end of each cycle. What distinguishes them is their high specificity, determined by their unique three-dimensional structure, and their sensitivity to factors such as temperature and pH. Enzyme activity can be enhanced by activators or diminished by inhibitors, many of which serve as drugs or poisons. Outside optimal conditions, enzymes may lose their structure through denaturation, leading to loss of function.
Enzymes have widespread practical applications. In industry, they are used to catalyze the production of antibiotics and other complex molecules. In everyday life, enzymes in biological washing powders break down protein, starch, and fat stains, enhancing cleaning performance. Papain and other proteolytic enzymes are used in meat tenderizers to hydrolyze proteins, improving texture and digestibility. Their specificity and efficiency make enzymes indispensable in both biological systems and commercial processes.
Etymology and history
By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified.French chemist Anselme Payen was the first to discover an enzyme, diastase, in 1833. A few decades later, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that this fermentation was caused by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."
In 1877, German physiologist Wilhelm Kühne first used the term enzyme, which comes, to describe this process. The word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms.
Image:Eduardbuchner.jpg|alt=Photograph of Eduard Buchner.|thumb|left|Eduard Buchner
Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose "zymase". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are usually named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate or to the type of reaction.
The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner showed that the enzyme urease was a pure protein and crystallized it; he did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley, who worked on the digestive enzymes pepsin, trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.
The discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This was first done for lysozyme, an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail.
Classification and nomenclature
Enzymes can be classified by two main criteria: either amino acid sequence similarity or enzymatic activity.Enzyme activity. An enzyme's name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Examples are lactase, alcohol dehydrogenase and DNA polymerase. Different enzymes that catalyze the same chemical reaction are called isozymes.
The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers. Each enzyme is described by "EC" followed by a sequence of four numbers which represent the hierarchy of enzymatic activity. That is, the first number broadly classifies the enzyme based on its mechanism while the other digits add more and more specificity.
The top-level classification is:
- EC 1, Oxidoreductases: catalyze oxidation/reduction reactions
- EC 2, Transferases: transfer a functional group
- EC 3, Hydrolases: catalyze the hydrolysis of various bonds
- EC 4, Lyases: cleave various bonds by means other than hydrolysis and oxidation
- EC 5, Isomerases: catalyze isomerization changes within a single molecule
- EC 6, Ligases: join two molecules with covalent bonds.
- EC 7, Translocases: catalyze the movement of ions or molecules across membranes, or their separation within membranes.
Sequence similarity. EC categories do not reflect sequence similarity. For instance, two ligases of the same EC number that catalyze exactly the same reaction can have completely different sequences. Independent of their function, enzymes, like any other proteins, have been classified by their sequence similarity into numerous families. These families have been documented in dozens of different protein and protein family databases such as Pfam.
Non-homologous isofunctional enzymes. Unrelated enzymes that have the same enzymatic activity have been called non-homologous isofunctional enzymes. Horizontal gene transfer may spread these genes to unrelated species, especially bacteria where they can replace endogenous genes of the same function, leading to hon-homologous gene displacement.
Structure
Enzymes are generally globular proteins, acting alone or in larger complexes. The sequence of the amino acids specifies the structure which in turn determines the catalytic activity of the enzyme. Although structure determines function, a novel enzymatic activity cannot yet be predicted from structure alone. Enzyme structures unfold when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity. Enzyme denaturation is normally linked to temperatures above a species' normal level; as a result, enzymes from bacteria living in volcanic environments such as hot springs are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate.Enzymes are usually much larger than their substrates. Sizes range from just 62 amino acid residues, for the monomer of 4-oxalocrotonate tautomerase, to over 2,500 residues in the animal fatty acid synthase. Only a small portion of their structure is directly involved in catalysis: the catalytic site. This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and binding site together compose the enzyme's active site. The remaining majority of the enzyme structure serves to maintain the precise orientation and dynamics of the active site.
In some enzymes, no amino acids are directly involved in catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors. Enzyme structures may also contain allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity.
A small number of RNA-based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these is the ribosome which is a complex of protein and catalytic RNA components.