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Protein was an organic chemical compound. It was a food source for many types of life forms.
Primordial soup, which the Seventh Doctor noted that life sprung from, consisted of sugars, proteins, and amino acids. (TV: Ghost Light) As a result, many species consisted partially of protein (TV: The Stones of Blood, The Haunting of Villa Diodati, et al.) or needed to consume proteins to survive (TV: The Seeds of Doom, The Waters of Mars, et al.)
Types of proteins included globulin, which was found in blood. (TV: The Stones of Blood) DNA that did not code for a protein was classed as "non-coding". (TV: School Reunion)
When the Thirteenth Doctor tasted the powdery remains of a bony hand in order to determine its origin, she stated that it was human, protein and collagen. (TV: The Haunting of Villa Diodati)
Krynoids required animal proteins while young. (TV: The Seeds of Doom)
The Nestene Consciousness got its food source from protein planets until they were destroyed in the Last Great Time War. (TV: Rose)
To battle the effects of cyanide, the Tenth Doctor needed, among other things, some sort of protein, which he got from a jar of walnuts. (TV: The Unicorn and the Wasp)
The Third Doctor told Jo Grant, who was eating an apple for breakfast, that she should be eating protein, which apples did not have much of. (TV: The Green Death)
In the 21st century, the T-Mat was used to send a shipment of synthetic protein from New York City to Moscow. (TV: The Seeds of Death)
The crew of Bowie Base One had protein packs as part of their diet. (TV: The Waters of Mars)
The methane refineries on Delta III produced compressed protein which was transported to Delta Magna. (TV: The Power of Kroll)
The crew of Sanctuary Base 6 had protein supplements such as Protein One, Two and Three. (TV: The Impossible Planet)
On Necros, Davros produced protein from the bodies preserved in Tranquil Repose and sold it across the galaxy as food. After Davros was arrested by the Renegade Daleks, the Sixth Doctor suggested that the inhabitants cultivate the weed plant for protein. (TV: Revelation of the Daleks)
Daleks fed on protein, occasionally harvesting it from their victims. Each Dalek was equipped with internal feeding tubes leading to an organic refuse disposal. While miniaturised inside a Dalek, the Twelfth Doctor revealed this process to Clara Oswald and a Combined Galactic Resistance squad after one of their own had been "hoovered" by a Dalek antibody, grimly pointing out that his remains constituted the top layer of the pool of liquified protein they had landed in. (TV: Into the Dalek)