Atoms are the building blocks of molecules. Atoms interact with each other to form a variety of molecules, which show different chemical and physical properties. Here I will use the carbon atom as an example to show some important concepts (not all) you should know. Keep in mind that we use a symbol to represent each atom (strictly speaking, a chemical symbol represents an element). For example, the chemical symbol for carbon element is C. Chemical symbols for all elements can be found in the Periodic Table
(1) Atom is not the smallest particle.
The atom consists of protons, neutrons, and electrons, all of which are smaller than the atom. From a size perspective, the radius of a neutral atom is between 30 - 300 x 10-12 m. For a C atom, its radius is 1.7 x 10-12 m ( 170 pm, or 1.7 Å), the radius of a proton is 0.8775 x 10-15 m, and the radius of a neutron is about 0.8 x 10-15 m, whereas an electron is very small and its size is believed to less than 10-18m
(2) Each atom has its unique set of protons, neutrons and electrons.
For each neutral C atom, it has 6 protons, 6 neutrons, and 6 electrons. Protons and neutrons form the nucleus, whereas electrons are moving around the nucleus. The number of protons and neutrons in some atoms may not be the same. For example sodium has 11 protons, 12 neutrons and 11 electrons. Keep in mind that the number of protons in an atom will not change in neutral form or in ionic forms.
Protons are positively charged (+), electrons are negatively charged (-), and neutrons are charge neutral (which means their charge is zero). Each proton has a charge of +1, and each electron has a charge of -1. When an atom gains or loses electrons, the net charge of the atom will be the sum of charges from protons and electrons. For example, sodium has 11 protons and 11 electrons. When it loses one electron, the net charge will be +11 + (-10) = +1, which means the resulting atom is positively charged and the charge is +1, we write it as Na+, we call it sodium ion, and it is a cation (a positively charged atom). Similarly, a chlorine atom has 17 protons and 17 electrons. After it gains one electron, the resulting atom will have +17 + (-18) = -1 charge, we write it as Cl-, we call it chloride ion (you see the naming is a little bit different from cations), and it is an anion (a negatively charged atom). Some atoms can lose or gain more than one electron. For example, Ca loses two electrons to form Ca2+ ion and S gains two electrons to form S2-.
(3) Electrons are lightweight particles.
A proton has a mass of 1.67 x 10-27 kg, and a neutron has a mass of 1.67 x 10-27 kg, but an electron has a mass of 9.11 x 10-31 kg. A proton (or a neutron) is about 1833 times (=1.67 x 10-27 kg/9.11 x 10-31 kg) heavier than an electron. For this reason, when we consider the mass of an atom (or a molecule), we do not consider the mass of electrons.
(4) mass number = # of protons + # of nutrons
For example, if a C atom has 6 protons and 6 neutrons, then its mass number will be 6 + 6 = 12. We normally write this number on the top-left corner of its chemical symbol along with the # of protons like this,
126C. If a C atom has 6 protons and 7 neutrons, then its mass number will be 6 + 7 = 13. We normally write this number on the top-left corner of its chemical symbol along with the # of protons, 136C. These two types of C atoms are isotopes.
(5) amu is the mass unit for atoms
Because the masses of protons and neutrons are so small, it is not very convenient to use kg as their mass units, therefore, we define the mass of 1/12 of a carbon atom that has 6 protons and 6 neutrons as 1 amu, which, if expressed in kg, will be 1.66054 x 10-27 kg. Since the mass of a proton is about 1.67262 x 10-27 kg, it is equivalent to 1.007277 amu. Similarly, the amu of a neutron is 1.008665 amu. For approximation, we can say the amu for a proton and a neutron is 1 amu. Because an atom typically has many protons and neutrons, the amu for an atom will be the sum of the amu of protons and neutrons. For example, the sodium atom has 11 protons and 12 neutrons, its amu will be 11 amu + 12 amu = 23 amu. In other words, amu is a different mass unit for atoms.
(6) Each element has its isotopes.
In nature, all C atoms, no matter where you got them, have the same number of protons (because that determines their identities). But the number of neutrons in C atoms may be different. It was found that some C atoms have 2 neutrons, and some have 3, 4, 5, 6,7,8.....16, 22 neutrons. Therefore, you can say there are 22 types of C atoms, but most are short-lived and only two (the ones with 6 and 7 neutrons) are very stable. That is the reason why we often only talk about two isotopes of C.
Even more, 98.99% of them are the ones with 6 neutrons, and 1.11% are the ones with 7 neutrons. These percentages are called abundances. In other words, the distribution percentage of isotopes in nature is constant. Isotopes will have different masses because they have different numbers of neutrons. The mass you see from the periodic table is the average of them. For example, in nature, 98.99% of carbon has a mass of 12 amu (126C), and 1.11% has a mass of 13.003355 amu (136C), therefore the average mass of C will be 12 amu x 98.89% + 13.003355 amu x 1.11% = 12.01 amu, which is the mass number you see on the Periodic Table.
Another example is O. It has three isotopes. The abundance and amu for each are 168O, 99.759%, 15.99491 amu, 178O, 0.037%, 16.99913 amu, 188O, 0.204%, 17.99916 amu, its average mass will be
0.99759 x 15.99491 amu + 0.00037 x 16.99913 amu + 0.00204 x 17.99916 amu = 15.999 amu.
(7) Atoms combine to make molecules.
For example, two O atoms come together to form an oxygen molecule, O2. We put "2" as a subscript to indicate there are two oxygen atoms in one oxygen molecule. From a composition perspective, because the oxygen molecule is made of two same kind of atoms, so, the oxygen molecule is an element. On another side, one O and two H atoms can combine to produce a water molecule, H2O. Because this molecule is made of two different atoms (H and O), therefore, water is a compound. As a convention, if there is only one atom in a molecule, we do not put "1" as a subscript. We do not write water molecule as H2O1