Like archeans, eubacteria are prokaryotes, meaning their cells do not have nuclei in which their DNA is stored. This distinguishes both groups from the eukaryotes, whose DNA is contained in a nucleus. Despite this structural resemblance, the Eubacteria are not closely related to the Archaea, as shown by analysis of their RNA (see below).
Eubacteria are enclosed by a cell wall. The wall is made of cross-linked chains of peptidoglycan, a polymer that combines both amino acid and sugar chains. The network structure gives the wall the strength it needs to maintain its size and shape in the face of changing chemical and osmotic differences outside the cell. Penicillin and related antibiotics prevent bacterial cell growth by inactivating an enzyme that builds the cell wall. Penicillin-resistant bacteria contain an enzyme that chemically modifies penicillin, making it ineffective.
Some types of bacteria have an additional layer outside the cell wall. This layer is made from lipopolysaccharide (LPS), a combination of lipids and sugars. There are several consequences to possessing this outer layer. Of least import to the bacteria but significant for researchers, this layer prevents them from retaining a particular dye (called Gram stain) that is used to classify bacteria. Bacteria that have this LPS layer are called Gram-negative, in contrast to Gram-positive bacteria, which do not have an outer LPS layer and which do retain the stain. Of more importance to both the bacteria and the organisms they infect is that one portion of the LPS layer, called endotoxin, is particularly toxic to humans and other mammals. Endotoxin is partly to blame for the damage done by infection from Salmonella and other Gram-negative species.
Within the cell wall is the plasma membrane, which, like the eukaryotic plasma membrane, is a phospholipid bilayer studded with proteins. Embedded in the membrane and extending to the outside may be flagella, which are whiplike protein filaments. Powered by molecular motors at their base, these spin rapidly, propelling the bacterium through its environment.
Within the plasma membrane is the bacterial cytoplasm. Unlike eukaryotes, bacteria do not have any membrane-bound organelles, such as mitochondria or chloroplasts. In fact, these two organelles are believed to have evolved from eubacteria that took up residence inside an ancestral eukaryote.
Bacterial cells take on one of several common shapes, which until recently were used as a basis of classification. Bacilli are rod shaped; cocci are spherical; and spirilli are spiral or wavyshaped. After division, bacterial cells may remain linked, and these form a variety of other shapes, from clusters to filaments to tight coils.