Identifying Functional Groups
Reactive atoms such as oxygen, nitrogen and phosphorus are present in many organic molecules. Because the chemical behavior of many reactive atoms or groups of atoms is well characterized, the presence and position of specific functional groups on an organic molecule can be used to predict the chemical behavior of that biomolecule. Functional groups are a set of commonly found groups of atoms covalently bonded to carbon in organic molecules. The unique functional groups present on a biomolecule determine reactivity, solubility, and other physical properties that lead to its biological role in living organisms. Understanding how common functional groups affect chemical reactivity improves our ability to understand the chemical behavior and cellular roles of all biomolecules.
In structural models depicting functional groups, a common convention is using a capital R to represent the rest, or remainder, of a molecule. R often represents a simple hydrocarbon chain, but can represent more complex organic arrangements when they are not relevant to the topic of discussion. As a general rule, the dash in R― indicates a single covalent bond between the functional group and a carbon atom located in the remainder of the molecule.
Alcohols are biomolecules that contain at least one hydroxyl group (R―OH). The simplest of all oxygen-containing functional groups, hydroxyl groups add polarity to organic molecules because of the strong electronegative nature of oxygen atoms. Therefore, unless the remainder of an organic molecule is very large and nonpolar, most alcohols dissolve in water by forming hydrogen bonds.
Similarly, carbonyl groups in aldehydes and ketones usually increase polarity and reactivity of organic molecules. The shorthand structural model for a carbonyl is >C=O, where > represents two covalent bonds extending from the “carbonyl carbon” to two other atoms. Biomolecules containing carbonyls tend to be somewhat volatile, stimulating human senses with strong odors, both pleasant and unpleasant.
Although it may be confusing, carbonyl and carboxyl functional groups (R―COOH) have similar names for a reason. A carboxyl group contains both a carbonyl group and a hydroxyl group, bonded to the same carbon atom. The name carboxyl derives from combining these two terms, carbonyl + hydroxyl = carboxyl.
With two oxygen atoms in this functional group, organic molecules containing carboxyl groups are often highly polar and reactive, although size and other functional groups present in an organic molecule are important in determining polarity and solubility. Traditionally, organic compounds containing carboxyl groups have been called carboxylic acids because of the tendency to release hydrogen ions into a solution (lowering pH). Structural models of organic molecules containing carboxyl groups are sometimes shown in the ionized form after release of a hydrogen ion (R―COO–).
Amines are organic molecules containing an amino group (R―NH2). In general, amino groups increase polarity and reactivity of an organic molecule and readily form hydrogen bonds with water and other polar molecules. Like free ammonia (NH3), amines are weakly basic and bind to hydrogenions in solution (raising pH). Structural models of organic molecules containing amino groups are sometimes shown in the ionized form after binding a hydrogen ion (R―NH3+).
On the opposite end of the spectrum, phosphate groups (R―PO42–) are highly acidic, almost exclusively existing in an ionized state in solutions by releasing two hydrogen ions. With four electronegative oxygen atoms, phosphate groups are highly reactive, and transfer of a phosphate group from one molecule to another delivers energy to chemical reactions. ATP, the main energy carrier in cells, is composed of three phosphate groups bonded in succession. The release of a phosphate group from ATP provides energy for many biologically important chemical reactions.
How to Spot Functional Groups
Use this activity to review key characteristics of several biologically important functional groups.
Identifying Functional Groups
This activity tests your ability to identify functional groups on molecular structures.
The billions of complex biomolecules that collectively compose a living cell are classified into four macromolecule groups: carbohydrates, proteins, lipids, and nucleic acids. From providing cell structure and protection to catalyzing vital chemical reactions, each macromolecule group plays a vital role in maintaining and propagating life.
Additionally, many macromolecules are involved in regulating and promoting the synthesis and breakdown of other macromolecules. Carbohydrates and lipids store energy needed to drive synthesis reactions. Nucleic acids store and transmit information that directs which macromolecules to synthesize, while protein and nucleic acid enzymes catalyze chemical reactions in both synthesis and degradation of macromolecules. The sum of all chemical reactions synthesizing and breaking down macromolecules in living organisms is collectively referred to as an organism’s metabolism.
Although biomolecules share a carbon backbone, the specific set of functional groups in any given macromolecule group specifies its chemical behavior and role in living cells. Different functional groups make each macromolecule structurally and functionally unique, yet all four groups share common traits. Understanding the commonalities between the four macromolecule groups helps to highlight the differences in structure and function.
At the base of most complex organic molecules is a monomer, a smaller organic molecule that often plays its own functional roles in living organisms. Although each type of monomer is structurally different, a common type of chemical reaction creates covalent bonds between monomers. As two monomers are connected, a two-unit chain, or dimer, forms. Monomers covalently bonded to one another in longer chains are polymers. A chemical reaction is a change in the chemical bonds of one or more molecules. The original molecules are reactants, and the molecules formed by the reaction are products. A chemical equation, such as the one shown above, depicts an arrow pointing from reactants to products to indicate the direction of change.
The chemical reactions that form covalent bonds between monomers are collectively called dehydration synthesis reactions. In this type of reaction, a water molecule is released as a product, effectively dehydrating the reactants as a larger biomolecule is synthesized. Dehydration synthesis is also called a condensation reaction due to the removal of water (condensation = water “condenses” out). In each of the four macromolecule groups, the specific chemical bonds formed by dehydration synthesis involve unique atom pairs and three-dimensional positions, affecting the structure and function of each biomolecule differently.
The opposite chemical reaction occurs when polymers are separated into individual monomers. Hydrolysis reactions incorporate the atoms from a water molecule into each monomer as the chemical bond between the monomers is broken (hydrolysis = water “loosens” the bond). In hydrolysis reactions, water participates in the chemical reaction as a reactant. A cell’s collective metabolism results from the balance between these reciprocal reactions. Cells use dehydration synthesis reactions to build the functional biomolecules that support life. When biomolecules are damaged or no longer needed, cells use hydrolysis reactions to degrade the polymers and frequently recycle the monomers to form new biomolecules.
Building and Breaking Biomolecules
This activity tests your ability to identify the reactants and products in dehydration synthesis and hydrolysis reactions.