You have nerves called motor neurons, these carry a signal from your nervous system, that signal goes to you muscle cells.
When the signal arrives, it triggers a chemical reaction in the muscle cells, where the cells release some ions into the protein structure of the muscle cells. Those ions make the proteins change shape, contracting from long strands into a more condensed shape, which is flexing them.
What you’re asking about is a topic called signal transduction, which is the process through which cells communicate with each other using molecules. The communication molecule (secreted by the nerves) bind with receptors on the outside of the cell, which then causes a cascade of reactions inside the cell. The messenger molecule never actually enters the muscle cells though, it stays outside.
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