Simple proteins and protein complexes contain only amino acids. In contrast, many other proteins, called conjugated proteins, covalently bond with non-protein moieties.

Nucleoproteins are protein complexes that contain nucleic acids, categorized as deoxyribonucleoproteins (DNPs) or ribonucleoproteins (RNPs) respectively. The nucleosome is a typical example of a DNP where nuclear DNA is associated with histone proteins. The major antigen for the Covid-19 virus SARS-CoV is an RNP that is critical for virus genome replication.

Glycoproteins are conjugated proteins typically located on the surface of cells. Their short carbohydrate chain consists of sugar residues that project outwards from the cell. The carbohydrate domain is essential for cell-cell adhesion, cellular recognition, and signal transduction.

Lipoproteins are protein conjugates with a protein shell over a lipid core that contains cholesterol, triglycerides, or both. Mammalian lipoproteins facilitate the mass transfer of insoluble lipids between their synthesis sites in the liver to other cells. There are several types of lipoproteins categorized by their densities. When the amount of one or more lipoproteins becomes too high, a fraction of the complex becomes insoluble. The insoluble lipoproteins can deposit and block the coronary artery, leading to stroke or heart attack.

Some other conjugated protein types include phosphoproteins, hemoproteins, flavoproteins, metalloproteins, phytochromes, cytochromes, and opsins. Hemoglobin, responsible for oxygen transport in blood vessels, is a conjugate protein that contains iron in its heme prosthetic group.