Transport and transporters

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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]ATPase-coupled transmembrane 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]pyrophosphate hydrolysis-driven proton 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.



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