Final answer:
A cell's operational programming is stored in its chromosomes, which contain genes that code for various protein and RNA products, directing all cellular activities.
Step-by-step explanation:
A cell's operational "programming" is stored in its chromosomes, which are discrete DNA structures. Chromosomes are the substance of eukaryotic cells where DNA forms a complex with histone proteins to create chromatin. A significant aspect of this DNA is organized into genes, which can code for protein products or RNA products. The collection of all a cell's genetic material is referred to as its genome, and this genome serves as the operational blueprint that directs all cellular activities. Therefore, the correct answer to the question is option 1: chromosomes.