Which nutrient is the most difficult to break down and, thus, is generally used last for energy in the body?

The best answer is proteins.

Explanation:

In starvation , the body uses  protein to make energy only as a last resort.  It usually prefers fats, after carbohydrates, because it is much more worthwhile to make energy from fats. One gram of fat produces 37.7 kilojoules compared to 16.7 kilojoules per gram of  protein.

Structurally, proteins are the most complex macromolecules. A single protein may be comprised of hundreds of amino acids. Proteins are considered the most important macromolecules after nucleic acids.

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