Metabolism

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:

The general structure of metabolic process terms is this:

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:

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:

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:

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:

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