Transport and transporters
TO DO: compare to http://wiki.geneontology.org/index.php/Transporter_terms_standard_definitions
Process: Transport and Localization
This area of the biological process ontology covers the processes involved in positioning a substance or cellular entity and maintaining it in that location. Terms and Structure
The processes that influence the location of a substance or entity in or outside the cell fall under the general term localization. Localization is split into two parts; there is the establishment of localization, which covers transport and/or autonomous movement of substances or cellular components, as well as orienting a protein or organelle. The maintenance of localization covers sequestering and active retrieval processes.
The structure to represent the localization of a substance or entity is shown below.
x localization [p] establishment of x localization [i] establishment of x orientation [i] x movement [i] x transport [i] x export [i] x import [i] x secretion [p] maintenance of x localization [i] sequestering of x
Standard Definitions
Note that not all localization terms have standard definitions at present; as a guide to term usage, x movement should be used to refer to the change in position of entities that can propel themselves, whilst x intended for substances that are moved by another entity. Storage, retention or sequestration are represented by the term sequestering of x.
- x localization: The processes by which x (where x is a substance or cellular entity, such as a protein complex or organelle) is transported to, and maintained in, a specific location.
- establishment of x localization: The directed movement of x to a specific location.
- maintenance of x localization: The processes by which x is maintained in a location and prevented from moving elsewhere.
- x secretion: The regulated release of x from a cell or group of cells.
- x transport: The directed movement of x into, out of or within a cell, or between cells.
- x export: The directed movement of x out of a cell or organelle.
- x import: The directed movement of x into a cell or organelle.
- establishment of x orientation: The processes that set the alignment of x relative to other cellular structures.
Function: Transporter activity
Terms and Structure
[i]transmembrane transporter activity [i]active transporter activity [i]primary active transporter activity [i]decarboxylation-driven active transporter activity [i]light-driven active transporter activity [i]methyl transfer-driven active transporter activity [i]oxidoreduction-driven active transporter activity [i]ATPase-coupled transmembrane transporter activity [i]secondary active transporter activity [i]antiporter activity [i]symporter activity [i]uniporter activity
[i]transmembrane transporter activity [i]passive transmembrane transporter activity [i]channel activity [i]gated channel activity [i]dephosphorylation-gated channel activity [i]ion gated channel activity [i]ligand-gated channel activity [i]mechanically gated channel activity [i]phosphorylation-gated channel activity [i]voltage-gated channel activity
[i]transporter activity [i]substrate-specific transporter activity [i]substrate-specific transmembrane transporter activity [i]transmembrane transporter activity [i]substrate-specific transmembrane transporter activity
[i]transmembrane transporter activity [i]efflux transmembrane transporter activity [i]uptake transmembrane transporter activity
Transporter Standard Definitions
Active Transporters
- X transmembrane transporter activity: Catalysis of the transfer of X from one side of the membrane to the other. X is [insert description].
- X uptake transmembrane transporter activity: Catalysis of the transfer of X from the outside of a cell to the inside of a cell across a membrane. X is [insert description].
- X efflux transmembrane transporter activity: Catalysis of the transfer of X from the inside of a cell to the outside of the cell across a membrane. X is [insert description].
- active transmembrane X transporter activity: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction. X is [insert description].
- primary active transmembrane X transporter activity: Catalysis of the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a primary energy source. Primary energy sources known to be coupled to transport are chemical, electrical and solar sources. X is [insert description].
- decarboxylation-driven active transmembrane X transporter activity: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by decarboxylation of a cytoplasmic substrate. X is [insert description].
- light-driven active transmembrane X transporter activity: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by light. X is [insert description].
- methyl transfer-driven active transmembrane X transporter activity: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a methyl transfer reaction. X is [insert description].
- oxidoreduction-driven active transmembrane X transporter activity: Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by an exothermic flow of electrons from a reduced substrate to an oxidized substrate. X is [insert description].
- secondary active transmembrane X transporter activity: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Chemiosmotic sources of energy include uniport, symport or antiport. X is [insert description].
- X:solute antiporter activity: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a antiport mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. X is [insert description].
- X:solute symporter activity: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a symport mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. X is [insert description].
- X uniporter activity: Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a uniport mechanism which is independent of the movement of any other molecular species. X is [insert description].
In secondary active transporter defs include a reaction where possible. For example:
Catalysis of the reaction: sugar(out) + H+(out) = sugar(in) + H+(in). Catalysis of the reaction: solute(out) + H+(out) = solute(in) + H+(in).
Passive Transporters
- passive transmembrane X transporter activity: Catalysis of the transfer of X from one side of the membrane to the other, down the solute's concentration gradient. X is [insert description].
- X channel activity: Catalysis of facilitated diffusion of X (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
- gated X channel activity: Catalysis of the transmembrane transfer of X by a channel that opens in response to a specific stimulus.
- dephosphorylation-gated X channel activity: Catalysis of the transmembrane transfer of X by a channel that opens in response to dephosphorylation of one of its constituent parts.
ion-gated X channel activity: Catalysis of the transmembrane transfer of X by a channel that opens in response to a specific ion stimulus.
- ligand-gated X channel activity: Catalysis of the transmembrane transfer of X by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
- mechanically-gated X channel activity: Catalysis of the transmembrane transfer of X by a channel that opens in response to a mechanical stress.
phosphorylation-gated X channel activity: Catalysis of the transmembrane transfer of X by a channel that opens in response to phosphorylation of one of its constituent parts.
- voltage-gated X channel activity: Catalysis of the transmembrane transfer of X by a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
- X channel activity: Catalysis of facilitated diffusion of X (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
- x gated y channel activity: Catalysis of the transmembrane transfer of y by a channel that opens in response to stimulus by x. Transport by a channel involves catalysis of facilitated diffusion of a solute (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel, without evidence for a carrier-mediated mechanism.
Other standard definitions
- L-amino acid: L-Y is the levorotatory isomer of [insert systematic name].
- D-amino acid: D-Y is the dextrorotatory isomer of [insert systematic name].
- constitutive activity: This activity is constitutive and therfore always present, regardless of demand.
- inducible activity: This activity is inducible and therefore only present when there is demand.
- high affinity: In high affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.
- low affinity: In low affinity transport the transporter is able to bind the solute only if it is present at very high concentrations.