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2-Oxoglutarate is the conjugate-base form of a five-carbon dicarboxylic keto acid, also called alpha-ketoglutarate. Its ketone carbon is adjacent to a carboxylate group.

In the citric acid cycle, isocitrate is oxidatively decarboxylated to 2-Oxoglutarate, which is then converted to succinyl-CoA. Through transamination, the same carbon skeleton connects with glutamic acid, linking energy metabolism and nitrogen metabolism.^[ref]

Alpha-ketoglutarate is another name for 2-Oxoglutarate, a five-carbon dicarboxylate containing a ketone adjacent to a carboxylate group. The names describe the same carbon skeleton using two positional naming conventions.

Alpha-ketoglutarate links the citric acid cycle with amino acid metabolism: transamination interconverts its carbon skeleton with that of glutamic acid. Its oxidative decarboxylation yields succinyl-CoA and carbon dioxide.^[ref]

Gamma-carboxyglutamic acid is a derivative of glutamic acid with an additional carboxyl group attached at the gamma carbon of the side chain. Its side chain can be written $-\mathrm{C}{\mathrm{H}}_2-\mathrm{CH}(\mathrm{COOH}{)}_2$ in the fully protonated representation. The extra carboxyl group changes the ion-binding properties of the corresponding gamma-carboxyglutamate residue within a protein.

In 1974, J. Stenflo and colleagues identified this unusual amino acid in prothrombin. Anomalous electrophoresis behaviour led to analysis by nuclear magnetic resonance and mass spectrometry, connecting a chemical modification with the special properties of this clotting protein.^[ref]

An illuminating comparison is to count the side-chain acid groups: glutamic acid has one, while gamma-carboxyglutamic acid has two. Their ionized forms provide additional negatively charged oxygen donors for calcium ions. The arrangement of several modified residues in a folded Gla domain gives the protein its calcium-binding architecture; an isolated modified amino acid is only one component of that structure.^[ref]

Glutamate is an anionic form of glutamic acid, with one fewer proton. The acid and anion are different chemical species.

Glutamic acid is an amino acid with a second carboxylic acid group in its side chain. Near physiological pH, this side chain is mostly deprotonated, giving glutamate.

Transamination connects the glutamate carbon skeleton with 2-Oxoglutarate. This allows amino groups to be transferred between carbon skeletons, making glutamate central to nitrogen metabolism as well as a constituent of proteins.

The RGD motif is the three-amino acid sequence arginine–glycine–aspartic acid, abbreviated R–G–D in one-letter notation. In fibronectin, this sequence contributes to cell adhesion and recognition by integrins. A protein primary structure can therefore contain a short recognizable region whose activity depends on its molecular presentation.

The originating 1984 experiment measured attachment-promoting activity of synthetic fragments from fibronectin. Its reported active sequence was the four-residue peptide RGDS, with serine following the RGD motif. The three-letter name of the core and the four-residue experimental fragment must be kept distinct.^[ref]

For an original sequence example, the invented five-residue string ARGDS contains the RGD motif at positions 2–4; ARGES does not. The two strings have equal length, but substituting glutamic acid for aspartic acid changes their local sequence. This inspection identifies a motif, not an experimentally established attachment activity. A folded protein, a surface-presented peptide and a soluble peptide present different physical contexts; the activity of one preparation does not specify every function of full-length fibronectin.