Atoms are the smallest pieces of matter; they are made of particles (protons and electrons). When atoms are grouped together, these groups are called molecules (the smallest pieces of compounds).

You probably think of atoms, molecules, and particles as all being extremely small pieces of matter. This is not exactly accurate; while atoms are matter—the smallest pieces of matter you can find—molecules are the smallest bits of compounds. And particles aren’t matter, but the building blocks of it.

For example, copper is an element. A copper atom is the smallest piece of copper that exists. Hydrogen is also an element; two hydrogen atoms and one oxygen atom combine to form a molecule of water, which is a compound.

While atoms are the tiniest bits of matter, they are made of the sub-atomic building blocks of matter—protons and electrons—revolving around a nucleus. The “atomic number” of an element, as seen on a periodic chart, refers to the number of protons contained in one atom of that element.

 

Material in the world is mostly made up of combinations of elements, particular substances that each have a unique set of properties.  The smallest bit of an element is an atom - go to anything smaller, and it isn't that element anymore.  Atoms do have parts, though, and the parts act to produce the element's properties.  Atoms can also combine in ways that produce whole new properties:  atoms in these relationships are called molecules, which are the smallest bits of compounds.  Water is a compound with two hydrogen atoms and one oxygen atom in each molecule.

In the middle of each atom is a nucleus (which, unfortunately, has the same name as the much-bigger middle of one type of cell - don't get them confused!), a tiny dense body of two different types of atomic particles.  When people calculate the mass of an atom, each particle in the nucleus has a single atomic unit (AU) of mass.  The two different types each "weigh" one unit, and the mass of all of the nuclear particles is added to get the atomic mass or weight.  Mass and weight are different things, but the difference doesn't mean that much when atoms are being discussed.

One type of atomic particle is the proton.  Each carries a single positive electrical charge, giving the nucleus a charge equal to all of the protons in there.  The number of protons also determines which element the atom belongs to, and that number is called the atomic number.  A special force is required to keep all of those protons from flying away from each other, and that force is stabilized by the other atomic particle, the neutron.  Neutrons have no charge, because they contain a positive proton and a negative electron kind of "smooshed together."  Atoms of one element may have different numbers of neutrons, different atomic weights, and different nuclear stabilities;  atoms of the same element but having different weights are called isotopes.  Isotopes may be unstable and can "pop" to a more stable form (called "decaying") through a loss of energy or of whole pieces of the nucleus - the lost bits are types of radiation, and those isotopes are considered to be radioactive.

 

Molecules are made up of atoms held together in various ways.  The connections between the atoms are called bonds, and the new arrangement of electrons changes the properties that the atoms had by themselves.  Molecules have formulas, which show the atoms (by element abbreviations) and numbers, such as H2O for water.  There are three types of bonds that figure into biological chemistry.