Prokaryotic Cell Structure

Bacterial structures and functions

Bacterial structures are best learned by linking each component to the single function it performs, because examiners test this link directly. The cell wall, made of peptidoglycan in most bacteria, is a rigid layer that withstands high internal osmotic pressure and prevents cell lysis, so a cell that loses its wall bursts in dilute media. Flagella are long helical filaments that rotate to propel the cell, and by changing the direction of rotation they allow chemotaxis, the directed movement toward attractants or away from repellents. Metachromatic granules are cytoplasmic deposits of inorganic polyphosphate, so they act as stores of phosphate and energy reserve, not as orientation devices. Magnetosomes are membrane-enclosed crystals of magnetite or greigite that align the cell along the geomagnetic field, a behaviour called magnetotaxis.

Fimbriae and pili are both hair-like surface appendages, but their roles differ. Fimbriae are short and numerous and mediate adhesion to surfaces and host tissues, whereas conjugative pili are longer and transfer DNA from one cell to another.

Example: a mutant that can swim normally but cannot make a rigid wall will still lyse in water, showing that the wall, not the flagellum, prevents lysis.

Bacterial flagellum structure

A bacterial flagellum has three parts: the filament, a long helical propeller built from flagellin subunits; the hook, a short flexible joint; and the basal body, which is anchored in the cell envelope and houses the rotary motor. Flagellin is exported through the hollow core of the structure and added at the tip, so the flagellum arises from the basal body and grows outward. Typical filaments are several micrometres long and are single helices, not arrays of parallel fibrils.

The basal body consists of a set of rings. The MS ring lies in the cytoplasmic membrane and the C ring lies in the cytoplasm, where it acts as the switch that reverses rotation. In Gram-negative bacteria, the L ring sits in the lipopolysaccharide layer of the outer membrane and the P ring sits in the peptidoglycan layer, and both act as bushings for the rod. The Z ring is different: it is an FtsZ-based structure that organizes septum formation during cell division and is not part of the flagellum.

Key contrast: flagella are motility organs. Conjugation is carried out by pili, not by flagella.

Bacterial inclusion bodies

Inclusion bodies are intracellular deposits that accumulate when a carbon, energy or phosphate source is in excess, and they are commonly classified as membrane-bound or non-membrane-bound. Polyhydroxyalkanoates (PHAs) are polyesters of hydroxy fatty acids, most commonly poly-\beta-hydroxybutyrate, that many bacteria synthesize as carbon and energy reserves. Because they are biodegradable and can be produced by fermentation, PHAs are called microbial plastics. Their petrochemical counterparts, such as polystyrene, polyurethane and polyvinyl chloride, are made by chemical synthesis and are not microbial in origin.

Membrane status is a frequent point of classification. Poly-\beta-hydroxybutyrate granules are coated by a phospholipid monolayer with associated phasin proteins, so they are not free granules. Cyanophycin granules, which are polymers of aspartate and arginine, and polyphosphate (volutin) granules lie free in the cytoplasm with no enclosing layer. Carboxysomes are polyhedral bodies enclosed by a protein shell and are usually treated as bacterial microcompartments rather than as simple granular inclusions, so they do not belong to the non-membrane-bound group in this classification.

Example: a polymer made by chemical polymerization is not a microbial plastic, even if it is used for the same purposes, because the defining feature of a microbial plastic is biological synthesis inside the cell.

E. coli chromosome structure

The Escherichia coli chromosome is a single, circular, double-stranded DNA molecule of about 4.6 \times 10^{6} base pairs. Unlike eukaryotic chromosomes, it is not wrapped around histones. Instead it is compacted within the nucleoid, an irregular region of the cytoplasm that is not bounded by a membrane, through nucleoid-associated proteins such as HU, H-NS and Fis. Replication starts at one origin, oriC, and proceeds bidirectionally, so the chromosome has a single origin and not multiple origins.

The two replication forks move in opposite directions around the circle. If both forks move at the same speed, a locus is copied earlier the closer it lies to oriC along either arc, so the order of replication is set by the shorter distance from the origin. Reading the map in only one direction is a common error, because the counterclockwise fork copies genes just as the clockwise fork does.

Remember the core facts: one circle, one origin, no histones, and a nucleoid rather than a nucleus.

Mycolic acid cell wall

Mycolic acids are very long, \alpha-branched \beta-hydroxy fatty acids found in the cell walls of mycobacteria, Nocardia and related members of the Actinomycetales. They form a waxy, lipid-rich outer layer that is poorly permeable to the crystal violet-iodine complex and to the alcohol decolorizer. As a result, Nocardia species stain unevenly and are not reliably identified by the standard Gram stain, which is why acid-fast staining is used for them.