In biochemistry, an ion pump is a protein embedded in a membrane that...well...does exactly what it says on the tin. Water soluble ions (such as sodium or even silver) are selectively transported across the otherwise impermeable membrane or against a concentration gradient. This has a number of uses, such as transforming energy from a gradient to ATP (the proton pump) or maintaining a physiological concentration of some ion.

For example, calcium is a common "messenger" in the cell whose concentration is carefully regulated. Pumps in various membranes (the plasma membrane and the mitochondrial membrane) are 'switched' on or off to kick start a 'calcium wave' that sweeps across the cell. Indeed, the whole process of neuron's transmitting information is based on altering the concentration of two ions (sodium and potassium) across the cells outer membrane. The charge difference is what is transmitted, which is controlled by the ion pumps.