Binding site
Encyclopedia
In biochemistry
, a binding site is a region on a protein
, DNA
, or RNA
to which specific other molecules and ions—in this context collectively called ligands
—form a chemical bond
.
Binding sites also exist on antibodies
as specifically coded regions that bind antigens
based upon their structure.
The term saturation refers to the fraction of total binding sites that are occupied at any given time.
When more than one type of ligand can bind to a binding site, competition
ensues.
An equilibrium
exists between unbound ligands and bound ligands.
Binding sites also exhibit chemical specificity
, a measure of the types of ligands that will bond, and affinity
, which is a measure of the strength of the chemical bond.
Binding sites are often an important component of the functional characterization of biomolecules
. For example, the characterization the binding site of a substrate
to an enzyme
is essential to model the reaction mechanism
responsible for the chemical change from substrate to product
.
A more specific type of binding site is the transcription factor binding site
, present on DNA.
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
, a binding site is a region on a protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
, DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
, or RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
to which specific other molecules and ions—in this context collectively called ligands
Ligand (biochemistry)
In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In a narrower sense, it is a signal triggering molecule, binding to a site on a target protein.The binding occurs by intermolecular forces, such as ionic bonds, hydrogen...
—form a chemical bond
Chemical bond
A chemical bond is an attraction between atoms that allows the formation of chemical substances that contain two or more atoms. The bond is caused by the electromagnetic force attraction between opposite charges, either between electrons and nuclei, or as the result of a dipole attraction...
.
Binding sites also exist on antibodies
Antibody
An antibody, also known as an immunoglobulin, is a large Y-shaped protein used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, termed an antigen...
as specifically coded regions that bind antigens
Antigen
An antigen is a foreign molecule that, when introduced into the body, triggers the production of an antibody by the immune system. The immune system will then kill or neutralize the antigen that is recognized as a foreign and potentially harmful invader. These invaders can be molecules such as...
based upon their structure.
The term saturation refers to the fraction of total binding sites that are occupied at any given time.
When more than one type of ligand can bind to a binding site, competition
Competition
Competition is a contest between individuals, groups, animals, etc. for territory, a niche, or a location of resources. It arises whenever two and only two strive for a goal which cannot be shared. Competition occurs naturally between living organisms which co-exist in the same environment. For...
ensues.
An equilibrium
Chemical equilibrium
In a chemical reaction, chemical equilibrium is the state in which the concentrations of the reactants and products have not yet changed with time. It occurs only in reversible reactions, and not in irreversible reactions. Usually, this state results when the forward reaction proceeds at the same...
exists between unbound ligands and bound ligands.
Binding sites also exhibit chemical specificity
Chemical specificity
Chemical specificity is the ability of a protein's binding site to bind specific ligands. The fewer ligands a protein can bind, the greater its specificity....
, a measure of the types of ligands that will bond, and affinity
Chemical affinity
In chemical physics and physical chemistry, chemical affinity is the electronic property by which dissimilar chemical species are capable of forming chemical compounds...
, which is a measure of the strength of the chemical bond.
Binding sites are often an important component of the functional characterization of biomolecules
Biomolecule
A biomolecule is any molecule that is produced by a living organism, including large polymeric molecules such as proteins, polysaccharides, lipids, and nucleic acids as well as small molecules such as primary metabolites, secondary metabolites, and natural products...
. For example, the characterization the binding site of a substrate
Substrate
Substrate may mean:*Substrate , Natural stone, masonry surface, ceramic and porcelain tiles*Substrate , the material used in the bottom of an aquarium*Substrate , the material used in the bottom of a vivarium or terrarium...
to an enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
is essential to model the reaction mechanism
Reaction mechanism
In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs.Although only the net chemical change is directly observable for most chemical reactions, experiments can often be designed that suggest the possible sequence of steps in...
responsible for the chemical change from substrate to product
Product (chemistry)
Product are formed during chemical reactions as reagents are consumed. Products have lower energy than the reagents and are produced during the reaction according to the second law of thermodynamics. The released energy comes from changes in chemical bonds between atoms in reagent molecules and...
.
A more specific type of binding site is the transcription factor binding site
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
, present on DNA.