An atom is the fundamental unit of chemical matter. The nucleus is an atom's center of mass and center of positive charge. The nucleus contains positively charged protons, shown in white, and uncharged neutrons, shown in blue. A cloud of negatively charged particles called electrons surrounds the nucleus.

All atoms of a given element have the same number of protons, but the number of neutrons can vary. Isotopes are atoms of the same element with different numbers of neutrons in their nuclei. Here we see three isotopes of carbon. They all have 6 protons, since they're all carbon atoms.

Atoms are electrically neutral, so they have the same number of negatively charged electrons as positively charged protons. The atom on the left has 6 neutrons, the atom in the middle has 7 neutrons, and the atom on the right has 8 neutrons. The atomic mass is the sum of the number of protons and neutrons, given in atomic mass units or a-m-u’s.

Isotopes are often named according to their atomic mass. The most common or stable isotope, such as carbon-12, is frequently known by its element name.

Atoms of some elements readily gain or lose electrons. An ion is a charged species that results from the gain or loss of electrons from a neutral atom or molecule.

Let's look at a sodium atom. It has 11 protons and 12 neutrons in its nucleus, and 11 electrons outside the nucleus. Sodium is one of several atoms that easily donates an electron. This leaves just 10 electrons, but since there are still 11 protons, sodium has a plus one charge. This charge means it's a sodium ion.

Certain other elements tend to gain electrons. Here we see a fluorine atom which accepts an electron to become the negatively charged fluoride ion. Atoms and ions rarely exist in isolation in nature, because they tend to combine through chemical bonding.

A chemical bond is an attractive force between two or more atoms or ions that holds them together. One type of bond is called a covalent bond. A covalent bond is a bond where the electrons are shared between atoms. Carbon atoms tend to share electrons with other atoms, such as with four hydrogen atoms in the diagram we see here. Atoms like sodium and fluorine don't share their electrons. Instead, they combine using ionic bonds. An ionic bond is a chemical bond formed by the attraction between positive and negative ions.

As mentioned earlier, atoms rarely exist in isolation in nature, with the except of certain gases like helium or neon. Instead, most elements exist as molecules or compounds. A molecule is a group of at least two covalently bonded atoms. The atoms can be the same, as in the oxygen molecule, or they can be different, as in the water molecule. A molecular formula is an expression indicating the number of each type of atom in one molecule of a substance.

Here we see that an oxygen molecule contains two oxygen atoms, while a water molecule contains two hydrogen atoms and one oxygen atom. When there's only one atom of a given element, we leave off the subscript one. A compound is a substance composed of two or more elements combined in fixed proportions. This means that the oxygen molecule is not a compound, since it only contains atom of one element, but the water molecule is a compound because it contains atoms of the elements hydrogen and oxygen.

Most molecules exist in one of three phases, solid, liquid, or gas, depending on the temperature and pressure. Molecules in the solid phase are tightly packed and interact strongly with one another. Molecules in the liquid phase interact with one another, but are free to move around. Molecules in the gas phase are far apart and have few interactions with one another. The interactions between water molecules in the solid and liquid phases are called hydrogen bonds. A hydrogen bond is a weak to moderate attractive force between a hydrogen atom bonded to oxygen, nitrogen, or fluorine, and an oxygen, nitrogen or fluorine atom on another molecule. Keep in mind that this is a bond between molecules, rather than within a molecule.

Now that we know something about molecules and compounds, let's take a closer look at the molecules that give rise to sickle cell anemia. DNA is a complex molecule, and we'll learn a lot more about it later in the course. Here we see two molecules found in DNA. The molecule on the left is thymine, found in normal hemoglobin DNA. At a certain position in the hemoglobin gene, the sickle cell gene has adenine, shown on the right, instead of thymine. These two molecules differ only by a hydrogen atom, a couple of oxygen atoms, and three nitrogen atoms. Yet these relatively small differences have a huge impact on the function of the hemoglobin molecules encoded by the two genes. In fact, for some people, the difference is truly a matter of life and death!

We'll come back to this example later in the course when we study the conversion of genes to proteins. But now you've learned enough chemistry to understand the cause of sickle cell anemia at the molecular level.

Copyright 2006 The Regents of the University of California and Monterey Institute for Technology and Education