Reading: Functional Groups

Functional groups are groups of atoms that occur within organic molecules and confer specific chemical properties to those molecules. When functional groups are shown, the organic molecule is sometimes denoted as “R.” Functional groups are found along the “carbon backbone” of macromolecules which is formed by chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen. Molecules with other elements in their carbon backbone are substituted hydrocarbons. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms.

Properties of Functional Groups

A functional group can participate in specific chemical reactions. Some of the important functional groups in biological molecules include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl groups. These groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids.

Classifying Functional Groups

Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity. An example of a hydrophobic group is the non-polar methane molecule. Among the hydrophilic functional groups is the carboxyl group found in amino acids, some amino acid side chains, and the fatty acid heads that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H+) from the COOH group resulting in the negatively charged COO group; this contributes to the hydrophilic nature of whatever molecule it is found on. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.

Functional Group Structure[1] Properties General Features
Hydroxyl OH attached to a carbon chain Polar

Characterized by presence of H and O

Simple structure

Methyl three hydrogens attached to a carbon chain Nonpolar

Characterized by presence of H and C

Simple structure

Carbonyl an oxygen double bonded to a carbon in the middle of a hydrocarbon chain Polar

Characterizied by central C and O

Bound to 2 organic side groups

Carboxyl a carbon with a double bonded oxygen and an OH group attached to a carbon chain Charged, ionized to release H+. Since carboxyl groups can release H+ ions into a solution, they are considered acidic.

Characterized by central C bound to O and OH


Amino two hydrogens attached to a nitrogen Charged, accepts H+ to form NH3+. Since amino groups can remove H+ from solution, they are considered basic.

 Characterized by presence of N

Branched structure

Phosphate a phosphorous with one double bonded oxygen and two OH groups Charged, ionizes to release H+. Since phosphate groups can release H+ ions inot soultion,

 Characterized by presence of P

Complex structure

Sulfhydryl SH attached to a carbon chain Polar

 Characterized by presence of S

Simple branched structure

Hydrogen Bonds between Functional Groups

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate, as illustrated in Figure 1.

Molecular models show hydrogen bonding between thymine and adenine, and between cytosine and guanine. These four DNA bases are organic molecules containing carbon, nitrogen, oxygen, and hydrogen in complex ring structures. Hydrogen bonds between the bases hold them together.

Figure 1. Hydrogen bonds connect two strands of DNA together to create the double-helix structure.

Section Summary

The unique properties of carbon make it a central part of biological molecules. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function. Carbon has four electrons in its outermost shell and can form four bonds. Carbon and hydrogen can form hydrocarbon chains or rings. Functional groups are groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.

Check Your Understanding

Answer the question(s) below to see how well you understand the topics covered in the previous section. This short quiz does not count toward your grade in the class, and you can retake it an unlimited number of times.

Use this quiz to check your understanding and decide whether to (1) study the previous section further or (2) move on to the next section.

  1. R stands in for an organic molecule