What Are Prokaryotes?

A prokaryote is a unicellular organism with no nucleus. Prokaryotes are the most ancient organisms on Earth and appear in the fossil record around 3.5 billion years ago. Prokaryotes are very abundant and found in all environments, including air, water, and soil, and in and on the human body. In fact, prokaryotic cells in the human body outnumber eukaryotic cells. Prokaryotes are split into two domains—Bacteria and Archaea—that differ from each other in a few important ways. The domain Bacteria contains organisms that are pathogenic, which means they cause disease in humans, as well as organisms that are non-pathogenic and do not cause harm. Some bacteria are industrially useful for making important products used in medicine, such as insulin, antibiotics, and enzymes. Despite being similar in size and shape, Archaea are not bacteria. In fact, Archaea are more closely related to eukaryotic cells. Organisms in the domain Archaea are not known to cause infection in humans and are not susceptible to any known antibiotics. They tend to live in extreme environments such as hot springs (Methanococcales) and salt lakes (Halobacteriales), but they can be found in many regular environments, and some are also found in and on the human body. One example is Methanobacteriales, hydrogen-consuming, methane-producing, microbes found in the human gastrointestinal tract.

Bacteria and Archaea come in a few basic shapes. A coccus (plural, cocci) is a bacterium with a round or spherical shape. Cocci can exist as single cells or can remain attached to each other after cell division. Streptococcus pneumoniae, a common cause of pneumonia, occurs as a diplococcus, or pair of cells. Other coccus bacteria exist as long chains (such as Streptococcus pyogenes), or grapelike clusters of cells, such as Staphylococcus aureus, a common cause of skin infections. A bacillus (plural, bacilli) is a rod-shaped bacterium. Bacilliform bacteria, as they are also called, can occur as single cells or as branching chains of cells. Examples of bacilliform bacteria include some major bacterial causes of food poisoning, such as Escherichia coli and the Salmonella genus. A spirilla is a spiral, curved, or corkscrew shaped bacteria, such as Helicobacter pylori, which causes peptic ulcers, and Campylobacter jejuni, a common cause of food poisoning. Less common shapes include the vibrio, or comma-shaped bacterium, such as Vibrio cholerae, which causes the deadly diarrheal illness cholera, and Vibrio vulnificus, which can cause dangerous skin infections and primary septicemia. Some Archaea can come in unusual shapes, such as Haloquadratum, an archaeon with flat, square-shaped cells that thrives in high salt environments.

Although prokaryotes lack a nucleus, they sequester their DNA in a compartment of the cytoplasm called the nucleoid. Prokaryotic DNA exists as a single, free-floating, closed-loop chromosome. A chromosome is a structure that contains DNA, the genetic material that is passed from one generation to the next. DNA gets transcribed or copied into messenger ribonucleic acids (mRNA) that are then translated on ribosomes (through the assembly of amino acids) into bacterial proteins. A ribosome is a structure composed of RNA and is itself an enzyme that constructs new proteins based on the instructions initially encoded by DNA and delivered by the transcribed mRNA molecules. Ribosomes are found throughout the cytoplasm in bacteria. Bacteria can also contain a plasmid, which is a small, circular piece of bacterial DNA that replicates on its own and can be transferred between cells. Plasmids carry genes that are important for survival. Antibiotic resistance can be spread through transfer of plasmids between bacteria. Plasmid transfer between cells is performed using a pilus (plural, pili), a short, hairlike projection found on the surface of some bacteria that helps cells stick together. Longer pili can transfer DNA from cell to cell.

Other external structures include fimbriae, which are short protein tubes on the surface of cells that allow bacteria to attach to surfaces and to other cells to form colonies. A flagellum (plural, flagella) is a threadlike tail that allows some cells to move. Cells can have a single flagellum or multiple flagella in various arrangements. Flagella are powered by a proton motor and rotate like a corkscrew to propel the cell forward. The cell membrane is the structure that encloses the cell and consists of the phospholipid bilayer.

Many bacteria secrete glycocalyx (also called pericellular membrane), an extracellular layer of polysaccharides and glycoprotein that coats the cell membrane. The glycocalyx layer is called a capsule when it is thick and viscous. When the glycocalyx is thin and fluid, it is called a slime layer. Both capsules and slime layers protect the cell from being ingested by other cells. Additionally, the slime layer aids in the formation of biofilms, or communities of bacteria living together in a gel-like matrix, such as the plaque that forms on teeth.

Only a few bacteria are able to produce an endospore, a toughened, condensed form of cell that can withstand harsh environmental conditions such as radiation, high heat, extreme cold, lack of nutrients or water, and disinfectants. Endospores are often produced in response to nutrient depletion and can survive for many years, reactivating under a change in conditions. Bacillus anthracis, the causative agent of anthrax, and Clostridium botulinum, the causative agent of botulism, are both capable of producing endospores, and can be found in soils globally. In B. anthracis the endospore itself is the pathogen. In C. botulinum the endospore allows the species to withstand high heat when food is being prepared. When the temperature decreases, endospores become vegetative bacteria, producing toxins that cause botulism.

The bacterial cell wall encloses the cell membrane and is composed of a mesh-like protein layer. The cell wall gives the cell structure and prevents it from bursting in response to cytoplasmic osmotic pressure. It is made of peptidoglycan, a substance forming the cell wall of many bacteria that is made up of glycosaminoglycan (sugar) chains interlinked with short peptides (amino acids). Understanding the cell wall has practical applications such as developing antibiotics like penicillin that kill bacteria by preventing the interlinking of peptidoglycan, causing the cells to swell and burst.

Bacterial cell walls come in two varieties that differ essentially based on thickness of the peptidoglycan layer. Different species of bacteria can be classified using a technique called Gram staining, a method of staining used to differentiate types of bacteria based on cell wall structure. The technique is named for the Danish bacteriologist Hans Christian Gram (1853–1938), who invented it. A purple stain known as crystal violet is applied to bacterial cells and then washed out using a decolorizing agent, followed by the application of a red counterstain known as safranin. Bacteria with a thick cell wall that is made of many layers of peptidoglycan will retain the purple stain after the washing step and will appear purple under the microscope. These bacterial cells are called gram-positive. By contrast, gram-negative bacteria have a cell wall that is made of only a thin layer of peptidoglycan, and the purple stain can be washed out. Gram-negative bacteria appear pink under the microscope after the application of the counterstain. These cell wall differences affect susceptibility to antibiotics; gram-negative bacteria are typically more tolerant to antibiotics because of the difficulty of crossing the outer membrane. In Archaea, the cell wall is not made of peptidoglycan. Instead, the cell walls of Archaea are made of a protein called pseudopeptidoglycan (pseudomurein). Though pseudopeptidoglycan shares a similar function to peptidoglycan, it has a different chemical composition.