Carbon

Functional Groups

Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. We find them along the “carbon backbone” of macromolecules. Chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen form this carbon backbone. Molecules with other elements in their carbon backbone are substituted hydrocarbons.

The functional groups in a macromolecule are usually attached to the carbon backbone at one or several different places along its chain and/or ring structure. 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.

A functional group can participate in specific chemical reactions. Figure shows some of the important functional groups in biological molecules. They include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in forming molecules like DNA, proteins, carbohydrates, and lipids. We usually classify functional groups as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the nonpolar methyl molecule. Among the hydrophilic functional groups is the carboxyl group in amino acids, some amino acid side chains, and the fatty acids 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 on which it is found. 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.

Table shows the structure and properties of different functional groups. Hydroxyl groups, which consist of OH attached to a carbon chain, are polar. Methyl groups, which consist of three hydrogens attached to a carbon chain, are nonpolar. Carbonyl groups, which consist of an oxygen double bonded to a carbon in the middle of a hydrocarbon chain, are polar. Carboxyl groups, which consist of a carbon with a double bonded oxygen and an OH group attached to a carbon chain, are able to ionize, releasing H+ ions into solution. Carboxyl groups are considered acidic. Amino groups, which consist of two hydrogens attached to a nitrogen, are able to accept H+ ions from solution, forming H3+. Amino groups are considered basic. Phosphate groups consist of a phosphorous with one double bonded oxygen and two OH groups. Another oxygen forms a link from the phosphorous to a carbon chain. Both OH groups in phosphorous can lose a H+ ion, and phosphate groups are considered acidic.
These functional groups are in many different biological molecules. R, also known as R-group, is an abbreviation for any group in which a carbon or hydrogen atom is attached to the rest of the molecule.

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 Figure illustrates.

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