Dictionary > Enzyme

Enzyme


Reviewed by: Todd Smith, PhD


Definition

noun
plural: enzymes
en·zyme, ˈɛnzaɪm
(biochemistry) A biomolecule that acts as catalyst to speed up specific chemical reactions. Enzymes are either proteins or RNA (ribozymes) molecules.

Overview

An enzyme is a biomolecule that can be synthesized biologically (naturally occurring) or through other processes (synthetically). Its major function is to act as a catalyst that speeds up a particular chemical reaction without itself being changed in the process. Enzymes are commonly protein molecules 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 encoded by the DNA in the cell that produces them. While not all enzymes are proteins, not all proteins are enzymes as well. Enzymes that are not proteinaceous in nature are exemplified by ribozymes. A ribozyme is an enzyme made of RNA rather than a protein. An example of a ribozyme is in 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. While large relative to their substrates, only a small portion of an enzyme is 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 in 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 (chaotropic agents). 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 reactions they catalyze. The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers. They are as follows:

  • EC 1 Oxidoreductases: catalyze oxidation/reduction reactions
  • EC 2 Transferases: transfer a functional group (e.g. a methyl or phosphate 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

Common biological reactions

The production of enzymes by way of protein synthesis involves transcription and translation. Within the cells, an 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 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.

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, 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.

Etymology

  • German enzym, Medieval Greek enzūmos, (leavened)

Related terms:

See also


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