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Enzyme

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Definition

noun

plural: enzymes

en·zyme, [ˈɛnzaɪm]

(biochemistry) A catalyst or a chemical produced by cells to generally speed up specific chemical reaction without changing the chemical reaction at the end of the reaction


Details

Overview

An enzyme is a molecule that can be synthesized biologically or chemically (synthetically). Its major function is to act as a catalyst that speeds up a particular chemical reaction without changing the chemical reaction at the end of the reaction. Enzyme is usually a protein molecule with a characteristic sequence of amino acids that fold to produce a specific three-dimensional structure, which gives the molecule unique properties. Proteins are one of the major biomolecules; the others are carbohydrates (especially, polysaccharides), lipids, and nucleic acids. Enzymes that are proteins in nature are composed of polymers of amino acids. The amino acids are joined together by peptide bonds. The type and the sequence of amino acids in an enzyme protein are specified by the DNA in the cell that produces them. While not all enzymes are proteins, not all proteins are enzymes as well. A protein may be classified based on its form and main functions: it can be a globular protein like most enzymes, fibrous protein which are for structural role, such as collagen, keratin, etc.; and membrane proteins that serve as receptors or channels for polar or charged molecule to pass through the cell membrane.


Enzymes that are not proteinaceous in nature are exemplified by ribozymes. A ribozyme is an enzyme made of RNA rather than a protein. Example of a ribozyme is the ribosome, which is a complex of protein and catalytic RNA units.


Characteristics

Enzymes are often globular. They may occur singly or as a subunit in a complex. They are often larger than their substrates although only a small portion would be directly involved in catalysis. This site involved in catalysis is referred to as the catalytic site. Another site in an enzyme structure is the binding site through which the substrate reacts or binds to. The catalytic site and the binding site make up the enzyme's active site. The allosteric site of the enzyme refers to the site where another molecule can bind to causing the enzyme to change its conformation, which then leads to its increase or decrease its activity. There are two major types of molecules that modulate enzyme activity: (1) inhibitors and (2) activators. Inhibitors are molecules that inhibit or decrease enzymatic activity. Activators are molecules that stimulate or increase enzymatic activity. Others that can affect the activity of enzymes are the denaturants. Exposure to temperature and pH beyond the optimal conditions lead to the denaturation of the enzyme. Denaturation causes the enzyme to lose its structure and catalytic properties. The structure of the enzyme is crucial to its function. The specificity of an enzyme is based on its unique 3D structure.



Types

Enzymes are usually classified and named according to the reaction they catalyze. The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers. They are as follows:


Common biological reactions

Biosynthesis

The production of enzyme by way of protein synthesis involves amino acid synthesis, transcription, and translation. In amino acid synthesis, there is a set of biochemical processes that produce amino acids from carbon sources like glucose. Within the cells, enzyme is generated by transcription and translation processes. Transcription is the process by which mRNA template, encoding the sequence of amino acids in the form of a trinucleotide code, is transcribed from DNA to provide a template for translation. Translation is the process in which amino acids are linked together in a specific order according to the rules specified by the genetic code. It occurs in the cytoplasm where the ribosomes are located. It consists of four phases: (1) activation (the amino acid is covalently bonded to the tRNA), (2) initiation (the small subunit of the ribosome binds to 5' end of mRNA with the help of initiation factors), (3) elongation (the next aminoacyl-tRNA in line binds to the ribosome along with GTP and an elongation factor), and (4) termination (the A site of the ribosome faces a stop codon). The newly formed proteinaceous structure will undergo further processes, e.g. post-translational modification and folding.


Catalysis

Similar to any catalyst, an enzyme would be able to speed up a chemical reaction without altering the equilibrium of a reaction. It means that a catalyst is not consumed in a reaction. Nevertheless, an enzyme differs from non-biological catalysts in being much more specific. Before an enzyme can catalyze a reaction, it must bind to its substrate first. According to the induced fit model suggested by Daniel Koshland in 1958, the enzyme undergoes reshaping as it interacts with its substrate while the substrate may also change shape slightly so that they eventually fit into each other. The enzyme speeds up a biological process by lowering the activation energy. It does so (1) by stabilizing the transition state, (2) by providing an alternative pathway, and/or (3) by destabilizing the substrate ground state.


Some enzymes require non-protein molecules called cofactors for their catalytic activities. The cofactor may be organic or inorganic. Cofactors bind usually to the active site of the enzyme. When the cofactor is unbound, the enzyme is referred to as apoenzyme; When bound, the enzyme is referred to as a holoenzyme (however, holoenzyme also refers to an enzyme containing multiple protein subunits).


A coenzyme is a molecule that transports chemical groups (e.g. hydride ion, phosphate group, acetyl group, methyl group, formul group, etc.) from one enzyme to another. Examples of coenzymes are NADH, NADPH, ATP, FMN (flavin mononucleotide), FAD (flavin adenine dinucleotide), TPP (thiamine pyrophosphate), and THF (tetrahydrofolate).


Biological functions

Enzymes are biological catalysts. They speed up chemical reactions. Almost all of the metabolic processes use enzymes to accelerate the conversion of substrates into products. Enzymes speed up the reaction rate about a million times faster over a process without an enzyme.



Supplementary

Etymology

  • German enzym, Medieval Greek enzūmos, (leavened)

Derived term(s)


Further reading

See also



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