I think the origin of metabolites comes from the assembly of simple organic molecules, or the disassembly of complex organic molecules which are facilitated/catalyzed by the enzymes/proteins which are expressed from their corresponding DNA and mRNA segments.

Also, I think the origin of the metabolites is separate from the "DNA--> mRNA --> protein" because the proteins that are expressed from its corresponding DNA and mRNA segments are responsible for facilitating/catalyzing the assembly of simple biomolecules to complex biomolecules, and vise versa.

Hope this helps.

They are the result of enzymatic synthesis or degradation and can be anything and everything from byproducts or waste products (ethanol, urea), intermediates (NADH), or products (ATP). There is handy chart that is useful in elucidating a very limited overview of just a few of the myriad processes which function either primarily or solely on the manipulation of metabolites:

http://biochemical-pathways.com/#/map/1