Structure of Prokaryotes

Core Concepts

Cell shapes and arrangements

Most bacteria come in a few basic shapes: cocci (spheres), bacilli (rods), spirilla (rigid spirals), spirochetes (flexible corkscrews), and vibrios (curved rods). Cells also grow in characteristic arrangements reflecting how they divide: diplo- (pairs), strepto- (chains), staphylo- (clusters), and palisades (side-by-side rows). Shape and arrangement are quick diagnostic hints, not proof of identity — identification requires staining, biochemistry, or molecular tests.

The cell envelope: membrane, wall, and capsule

The plasma membrane is a phospholipid bilayer controlling what enters and leaves; because prokaryotes lack mitochondria, electron transport for energy generation occurs at this membrane. Outside it sits the cell wall, providing mechanical support and osmotic protection — without it, the cell would swell and burst in dilute environments. In most bacteria the wall is built of peptidoglycan, a mesh of sugar chains (NAM and NAG) cross-linked by short peptides. The amount and arrangement of peptidoglycan define the two great clinical classes:

• Gram-positive bacteria have a thick peptidoglycan layer plus teichoic acids. They stain purple because the thick mesh traps crystal violet even after decolorization.
• Gram-negative bacteria have a thin peptidoglycan layer sandwiched between the plasma membrane and an outer membrane — a second bilayer with porins (channels) and lipopolysaccharide (LPS) on its outer face. LPS is an endotoxin: when Gram-negative cells die and lyse, LPS is released and can trigger fever and, in severe cases, septic shock. These bacteria stain pink because the thin wall cannot retain crystal violet.

Wall architecture predicts antibiotic susceptibility: many cell-wall–targeting antibiotics work best against Gram-positive bacteria, which lack the outer-membrane barrier. Some bacteria don't fit the pattern: acid-fast bacteria such as Mycobacterium tuberculosis have waxy mycolic acids in the wall, resist the Gram stain, and need the acid-fast stain instead. Archaea generally lack peptidoglycan, using other wall polymers or protein layers — another reason peptidoglycan-targeting drugs don't affect them.

Outside the wall, many bacteria secrete a glycocalyx — a sugar-and-protein coat. Firm and organized, it is a capsule; loose and diffuse, a slime layer. Capsules are major virulence factors: they help bacteria adhere and resist phagocytosis (a slippery capsule is hard for immune cells to grab), and they contribute to biofilm formation on teeth, catheters, and implants.

Appendages: flagella, pili, and fimbriae

Flagella are long whiplike structures that rotate like propellers to move the cell through liquid. A bacterial flagellum has three parts — a basal body (motor, embedded in the envelope), a hook, and a long filament of the protein flagellin — and rotation is powered by the proton gradient across the membrane. Flagella enable chemotaxis: the cell runs and tumbles, biasing movement toward attractants (nutrients) and away from repellents.

Pili are shorter, straighter protein tubes. Conjugation pili connect two cells so DNA — often a plasmid — can transfer from donor to recipient: a major route of horizontal gene transfer and of the spread of antibiotic-resistance genes. Fimbriae are numerous, very short adhesion filaments that work like Velcro, letting the cell attach to host tissues and surfaces — often the first step of infection and biofilm formation. Distinguish by function: flagella move, fimbriae stick, pili connect.

Inside the cell: nucleoid, plasmids, ribosomes, inclusions, and endospores

The nucleoid holds the main chromosome, typically a single circular DNA molecule. Many bacteria also carry plasmids: small circular DNA molecules replicating independently of the chromosome. Plasmids are not essential for everyday survival but often carry useful genes — antibiotic resistance, toxin production, metabolic abilities — and they are the usual cargo of conjugation, a key engine of bacterial evolution and of the global antibiotic-resistance problem.

Ribosomes synthesize proteins. Prokaryotic ribosomes are 70S (50S + 30S subunits), distinct from eukaryotic cytoplasmic 80S ribosomes; antibiotics such as tetracyclines and aminoglycosides target the 70S ribosome, inhibiting bacterial protein synthesis far more than human — a classic example of selective toxicity. Inclusions are storage granules: glycogen and other carbon reserves, polyphosphate, sulfur, or gas vesicles that give some aquatic cells buoyancy.

The most dramatic internal structure is the endospore — a dormant, highly resistant body formed inside certain Gram-positive bacteria (Bacillus and Clostridium) when conditions turn hostile (starvation, heat, drying). During sporulation, the cell copies its DNA, wraps one copy in a tough coat enriched with dipicolinic acid, and lyses, releasing the spore. The endospore contains almost no water, is metabolically inert, and can survive boiling, drying, radiation, and many disinfectants for years. When conditions improve, germination returns it to an active vegetative cell — which is why botulism spores in improperly canned food, tetanus spores in soil and wounds, and anthrax spores persist so stubbornly, and why autoclaving (heat plus pressure) is the standard for destroying them in healthcare and lab settings. An endospore is a survival structure, not a reproductive one: one cell makes one spore, which becomes one cell again.

Common Confusions