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Protein metabolism involves the synthesis of amino acids and proteins and the breakdown of proteins. Dietary proteins are an essential source of amino acids necessary for protein synthesis, as the body is not able to synthesize all twenty amino acids. The breakdown of dietary proteins into amino acids begins in the stomach with the secretion of pepsin and hydrochloric acid, which promote protein denaturation and breakdown into smaller polypeptides and individual amino acids. Other enzymes secreted by the pancreas, like trypsin and chymotrypsin also participate in protein breakdown. The amino acids can then be transported into cells, and used to synthesize protein, or can be further broken down to remove the amino group by deamination. During deamination, the amino group gets broken down into ammonia, which is excreted, and the carbon skeleton, which has several fates. The carbon skeleton of the ketogenic amino acids produce acetyl-CoA and other derivatives, which can enter the citric acid cycle, or produce fatty acids; while the glucogenic amino acids produce pyruvate and other carbon intermediates which can be converted to glucose, or converted to fatty acids or glycogen for storage.

Purine and pyrimidine nucleotides are the subunits of nucleic acids, DNA and RNA, and are the precursors of nucleotide cofactors, such as NAD. Nucleotide metabolism involves the synthesis and degradation of nucleotides, which are formed from a phosphate, pentose sugar (ribose or 2-deoxyribose), and a nitrogenous base (a purine or pyrimidine). Two major pathways are involved in the synthesis of nucleotides, the de novo pathway and the salvage pathway. Nucleotides are synthesized by the de novo pathway using amino acids, CO2, and tetrahydrofolate. The salvage pathway interconverts nucleosides and nucleotides and recycles purine and pyrimidine bases released as by-products from the breakdown of nucleotides and cofactors during cellular metabolism. The salvage pathway uses a smaller amount of energy than the de novo synthesis pathway.