Size
Atoms are so unbelievably small it helps to imagine them with an analogy. Think about the last time you went to a baseball stadium and try to remember how big it was. If the nucleus of an atom were the size of a fly on the grass, the atom as a whole would be about the size of the stadium. Yet the proton at the center of a hydrogen atom constitutes some 99.9995 percent of the atom's total mass.
Larger Atoms
The proportions are very similar for larger atoms. Take the helium atom, for example, which contains two protons, two neutrons and two electrons. Again, the nucleus is over 99.999 percent of the total mass. The actual mass of an electron is 9.109 x 10^-31 kilograms, while the mass of a proton is 1.673 x 10^-27 kilograms --- several orders of magnitude greater. The mass of a neutron is slightly greater than the mass of a proton.
Measurements
The mass of these subatomic particles is so small it may seem incredible that humans are able to measure it. You can't measure the mass of an electron or proton with an ordinary scale, but you can use other tricks instead. Since both particles are charged, when they move through a magnetic field the field exerts a force on them. You can use the amount of deflection and the known charge of both particles to calculate their mass.
Oil Drop Experiment
The mass of the electron was originally calculated using a somewhat different approach. J. J. Thomson, the scientist who discovered electrons, found their mass-to-charge ratio, but scientists still needed to know their charge to find their mass. Another scientist named Robert Millikan determined the charge through the oil-drop experiment. He designed a device where a fine mist of charged oil droplets would fall into an electric field. By adjusting the strength of the field, he could find the point at which it exactly counterbalanced the force of gravity for a given droplet, and with this information he could calculate the droplet's charge. He found that all droplets had charges that were multiples of a single number: 1.602 x 10^-19 Coulombs, the charge of a single electron.