Metabolic Process

Terms and structure

The process of metabolism includes both biosynthetic and catabolic processes. We also distinguish between metabolism that occurs at the level of a multicellular organism (organismal metabolism) and metabolism that occurs at the level of the cell (cellular metabolism). These subclasses also apply to biosynthesis and catabolism.

Metabolic processes can be described as being organismal when they occur in more than one cell type. An example of this is C4 photosynthesis, a type of carbohydrate biosynthesis achieved with the involvement of two cell types, bundle sheath cells and mesophyll cells. Metabolic processes that are restricted to a single cell or cell type are described as cellular metabolism. The vast majority of metabolic processes are cellular, so unless a corresponding organismal metabolism occurs, we do not add "cellular" to the term name.

For example, during digestion, carbohydrate catabolism occurs first in the mouth, by salivary amylase, and then in the stomach. This process would be described as organismal carbohydrate catabolic process. However, carbohydrate catabolic processes also occurs within a single cell, e.g. glycolysis, so we also need a cellular carbohydrate catabolic process term:

  • metabolic process
    • [i] catabolic process
      • [i] carbohydrate catabolic process
        • [i] cellular carbohydrate catabolic process
        • [i] organismal carbohydrate catabolic process
      • [i] cellular catabolic process
        • [i] cellular carbohydrate catabolic process
      • [i] organismal catabolic process
        • [i] organismal carbohydrate catabolic process

The general structure of metabolic process terms is this:

  • substance metabolic process
    • [i] cellular substance metabolic process
      • [i] cellular substance biosynthetic process
      • [i] cellular substance catabolic process
    • [i] organismal substance metabolic process
      • [i] organismal substance biosynthetic process
      • [i] organismal substance catabolic process
    • [i] substance biosynthetic process
      • [i] cellular substance biosynthetic process
      • [i] organismal substance biosynthetic process
    • [i] substance catabolic process
      • [i] cellular substance catabolic process
      • [i] organismal substance catabolic process

However, remember that most types of metabolism are children of cellular metabolic process (or cellular biosynthetic process, cellular catabolic process), and do not have the modifier 'cellular'.

For example, where substance A and substance B metabolic process are cellular processes:

  • metabolic process
    • [i] cellular metabolic process
      • [i] substance A metabolic process
        • [i] substance A biosynthetic process
        • [i] substance A catabolic process
      • [i] substance B metabolic process
        • [i] substance B biosynthetic process
        • [i] substance B catabolic process
      • [i] cellular biosynthetic process
        • [i] substance A biosynthetic process
        • [i] substance B biosynthetic process
      • [i] cellular catabolic process
        • [i] substance A catabolic process
        • [i] substance B catabolic process

Standard Definitions

substance metabolic process
The chemical reactions and pathways involving substance, [description of substance].
substance biosynthetic process
The chemical reactions and pathways resulting in the formation of substance, [description of substance].
substance catabolic process
The chemical reactions and pathways resulting in the breakdown of substance, [description of substance].
substance fermentation
The enzymatic conversion of substance to simpler components, resulting in energy in the form of adenosine triphosphate (ATP).

Other standard metabolic processes

Salvage and de novo biosynthesis

Biosynthesis can be further split up into those processes that create a substance from scratch and those that use derivatives of the substance. The ontology structure is as follows:

  • metabolic process
    • [i] biosynthetic process
      • [i] 'de novo' biosynthetic process
      • [i] salvage
    • [i] catabolic process

substance salvage
Any process that produces substance from derivatives of it, without de novo synthesis.
substance 'de novo' biosynthetic process
The chemical reactions and pathways resulting in the formation of substance from simpler precursors.

Standard Synonyms

The following synonyms should be added to metabolic process terms unless the synonym does not make sense or it has a specialised meaning that conflicts with the intended usage.
substance metabolic process
exact: substance metabolism
substance biosynthetic process
exact: substance anabolism
exact: substance biosynthesis
exact: substance formation
exact: substance synthesis
substance catabolic process
exact: substance breakdown
exact: substance catabolism
exact: substance degradation
substance salvage
exact: substance salvage pathway
substance 'de novo' biosynthetic process
exact: 'de novo' substance anabolism
exact: 'de novo' substance biosynthesis
exact: 'de novo' substance formation
exact: 'de novo' substance synthesis

Qualifiers

The following qualifiers can be used with metabolic process, biosynthetic process and catabolic process terms. The examples given use the metabolic process term but the standard definitions for biosynthetic process and catabolic process can be substituted into the definition in its place.
cellular substance metabolic process
The chemical reactions and pathways involving substance, as carried out by individual cells.
organismal substance metabolic process
The chemical reactions and pathways involving substance, occurring at the tissue, organ, or organismal level of a multicellular organism.
aerobic substance metabolic process
The chemical reactions and pathways involving substance in the presence of oxygen.
anaerobic substance metabolic process
The chemical reactions and pathways involving substance in the absence of oxygen.
X-dependent substance metabolic process
The chemical reactions and pathways involving substance, requiring the presence of X.
X-independent substance metabolic process
The chemical reactions and pathways involving substance, independent of X.
More complex metabolic process terms to represent specific processes can be constructed by adding one or more of the following suffixes to a term name and altering the definition as appropriate.
substance A biosynthetic process from substance B
The chemical reactions and pathways resulting in the formation of substance A from other compounds, including substance B.
substance A catabolic process to substance B
The chemical reactions and pathways resulting in the breakdown of substance A into other compounds, including substance B. Can also be used with fermentation terms.
substance A catabolic process via substance C
The chemical reactions and pathways resulting in the breakdown of substance A into other compounds, via the intermediate substance C. Can also be used with biosynthetic process and fermentation terms.
substance A catabolic process, using enzyme
The chemical reactions and pathways resulting in the breakdown of substance A, catalyzed by enzyme. Can also be used with biosynthetic process and fermentation terms.
substance A catabolic process, X pathway
The chemical reactions and pathways resulting in the breakdown of substance A, by the X pathway. Can also be used with biosynthetic process and fermentation terms.
substance A catabolic process, X cycle
The chemical reactions and pathways resulting in the breakdown of substance A in the X cycle. Can also be used with biosynthetic process and fermentation terms.
substance A catabolic process, by biochemical process
The chemical reactions and pathways resulting in the breakdown of substance A, by biochemical process. Can also be used with biosynthetic process and fermentation terms.
For example:
L-lysine catabolic process to glutarate, by acetylation
The chemical reactions and pathways resulting in the breakdown of L-lysine into other compounds, including glutarate, by acetylation.
glucose biosynthetic process from tryptophan via maltose and cystathione, using sucrose invertase
The chemical reactions and pathways resulting in the formation of glucose from other compounds, including tryptophan, via the intermediates maltose and cystathione, catalyzed by sucrose invertase.

Different pathways or processes leading to the same product

Where there are several biosynthetic pathways leading to the same product, we list each of them as a subclass of a general pathway.

For example, we have:

  • glucose catabolic process ; GO:0006007
    • [i] glycolysis ; GO:0006096
    • [i] pentose-phosphate shunt ; GO:0006098

It is straightforward to name well-known pathways (e.g. glycolysis and the pentose-phosphate pathway are two ways to accomplish glucose catabolic process), but harder for nameless minor pathways. Minor pathways should be named by referring to start and end products, and intermediates if further distinguishing is required.

For example:

  • L-arabinose catabolism ; GO:0019572
    • [i] L-arabinose catabolism to 2-oxoglutarate ; GO:0019570
    • [i] L-arabinose catabolism to xylulose 5-phosphate ; GO:0019569