For almost 100 years after this, most scientists thought of atoms as solid structures, until in 1897 J.J.Thompson discovered that atoms contained even smaller particles called electrons. So the modified atomic structure now had electrons embedded in an atom, like M&Ms in icecream.
It was therefore a shock in 1906 when Rutherford and Gieger announced that when they fired alpha particles at a thin sheet of gold foil, most of the alpha particles passed straight through it, but a few bounced back. As Rutherford said "It was almost as if you fired an artillery shell at a piece of tissue paper and it came back and hit you!" The alpha particles were detected by flashes of light on a screen.
This experiment showed that most of an atom is empty space, but there is a very small, dense nucleus in the center which has almost all the mass of the entire atom. Later Rutherford discovered positively charged protons in the nucleus of the atom. Rutherford was well-known for his interesting phrases, like this one:
"All science is either physics or stamp-collecting!"
So finally in the 1930s the modern model of the atom was in place: a dense nucleus containing protons and neutrons, with electrons orbiting near the outside of the atom. Most diagrams such as the one below give a very inaccurate view of an atom:
In reality, electrons are much further away from the nucleus than you would expect. If the nucleus was represented by a golf ball, the whole atom would be three miles wide! So now Rutherford's experiment makes sense: a typical alpha particle would pass straight through an atom, with only a very occasional one bouncing off the tiny nucleus.
Each chemical element has a set number of protons in its nucleus. For example, carbon is the only element with 6 protons per atom. The number of protons is called atomic number of the element. In an atom, the number of electrons is the same as the number of protons, so every carbon atom has 6 protons and 6 electrons. However the number of neutrons can vary from one atom to another. Atoms of the same element with different numbers of neutrons are called isotopes.
Remember that most of the weight of an atom is in its nucleus (protons and neutrons). The mass number or atomic weight of an element tells you the total number of protons + neutrons in the element. For example, this diagram shows the nucleus of a Beryllium atom. The red "P" tells you the number of protons and the neutrons are shown by the purple "N".
Notice that the 4 electrons are in two layers, or energy levels. The first energy level can hold a maximum of 2 electrons, the second can hold a maximum of 8 electrons.
So, for example, an atom of sodium, with a total of 11 electrons looks like this: