Elements, Compounds, Atoms, and Ions for AP Biology

By — McGraw-Hill Professional
Updated on Oct 24, 2011

Practice problems for these concepts can be found at:  Chemistry Review Questions for AP Biology


By definition, matter is anything that has mass and takes up space; an element is defined as matter in its simplest form; an atom is the smallest form of an element that still displays its particular properties. (Terms boldfaced in text are listed in Glossary at the end of the book.) For example, sodium (Na) is an element mentioned often in Human Physiology. The element sodium can exist as an atom of sodium, in which it is a neutral particle containing an equal number of protons and electrons. It can also exist as an ion, which is an atom that has a positive or negative charge. Ions such as sodium that take on a positive charge are called cations, and are composed of more protons than electrons. Ions with a negative charge are called anions, and are composed of more electrons than protons.

Elements can be combined to form compounds. The two major types of compounds you need to be familiar with are organic and inorganic compounds. Organic compounds contain carbon and usually hydrogen; inorganic compounds do not. Some of you are probably skeptical, at this point, as to whether any of what I have said thus far matters for this exam. Bear with me because it does. You will deal with many important organic compounds later on in this book, including carbohydrates, proteins, lipids, and nucleic acids.

I would like to cover a topic that many find confusing and therefore ignore in preparing for this exam. This is the subject of functional groups. These poorly understood groups are responsible for the chemical properties of organic compounds. They should not intimidate you, nor should you spend a million hours trying to memorize them in full detail. You should remember one or two examples of each group and be able to identify the functional groups on sight, as you are often asked to do so on the AP exam.

The following is a list of the functional groups you should study for this exam:

  1. Amino group. An amino group has the following formula:
  2. The symbol R stands for "rest of the compound" to which this NH2 group is attached. One example of a compound containing an amino group is an amino acid. Compounds containing amino groups are generally referred to as amines. Amino groups act as bases and can pick up protons from acids.

  3. Carbonyl group. This group contains two structures:
  4. If the C=O is at the end of a chain, it is an aldehyde. Otherwise, it is a ketone. (Note: In aldehydes, there is an H at the end; there is no H in the word ketone.) A carbonyl group makes a compound hydrophilic and polar. Hydrophilic means water-loving, reacting well with water. A polar molecule is one that has an unequal distribution of charge, which creates a positive side and a negative side to the molecule.

  5. Carboxyl group. This group has the following formula:
  6. A carboxyl group is a carbonyl group that has a hydroxide in one of the R spots and a carbon chain in the other. This functional group shows up along with amino groups in amino acids. Carboxyl groups act as acids because they are able to donate protons to basic compounds. Compounds containing carboxyl groups are known as carboxylic acids.

  7. Hydroxyl group. This group has the simplest formula of the bunch:
  8. A hydroxyl group is present in compounds known as alcohols. Like carbonyl groups, hydroxyl groups are polar and hydrophillic.

  9. Phosphate group. This group has the following formula:
  10. Phosphate groups are vital components of molecules that serve as cellular energy sources: ATP, ADP, and GTP. Like carboxyl groups, phosphate groups are acidic molecules.

  11. Sulfhydryl group. This group also has a simple formula:
  12. This functional group does not show up much on the exam, but you should recognize it when it does. This group is present in the amino acids methionine and cysteine and assists in structure stabilization in many proteins.

Practice problems for these concepts can be found at:  Chemistry Review Questions for AP Biology

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