Prokaryotes

Core Concepts

Bacteria versus Archaea

Both are prokaryotic, but molecular evidence places them in separate domains:

Archaea were once thought to exist only in extreme environments, but they are now known to be abundant in moderate environments, including the ocean and the human gut. Methanogens (methane-producing archaea) are important in the carbon cycle and in the digestive tracts of ruminants.

Prokaryotic cell structure

• Plasma membrane: Houses ETC components in many prokaryotes. Nucleoid: DNA region; not membrane-bound. Ribosomes: 70S (antibiotic target). Cell wall: Contains peptidoglycan in bacteria. Gram-positive: thick peptidoglycan (purple). Gram-negative: thin layer + outer LPS membrane (pink). Capsule: Sticky outer layer (adhesion, immune evasion). Pili: Adhesion + conjugation (sex pilus). Flagella: Rotating protein filaments (different from eukaryotic 9+2).

Prokaryotic reproduction and genetic diversity

Prokaryotes reproduce by binary fission — the cell grows, the chromosome replicates, and the cell divides into two genetically identical daughter cells. However, prokaryotes have several mechanisms for generating genetic diversity without sexual reproduction:

• Mutation: Spontaneous changes in DNA sequence. With short generation times and large population sizes, mutations accumulate rapidly, providing variation for natural selection.

• Transformation: Uptake of free DNA from the environment. This DNA may be incorporated into the recipient's genome by homologous recombination.

• Transduction: Transfer of bacterial DNA by bacteriophages (viruses that infect bacteria). During the viral life cycle, bacterial DNA can be accidentally packaged into viral capsids and delivered to a new host cell.

• Conjugation: Direct transfer of DNA between bacterial cells through a sex pilus. The donor cell typically contains an F plasmid (fertility plasmid) that encodes the machinery for conjugation. Conjugation can transfer plasmids or chromosomal DNA.

These processes enable rapid evolution, including the spread of antibiotic resistance genes.

Metabolic diversity

Prokaryotes exhibit metabolic diversity far exceeding that of eukaryotes:

Energy source: Phototrophs (light) or chemotrophs (chemicals). Carbon source: Autotrophs (CO2) or heterotrophs (organic molecules). Four modes: photoautotrophs (light + CO2), chemoautotrophs (chemicals + CO2; unique to prokaryotes), photoheterotrophs, chemoheterotrophs (most organisms).

Oxygen requirements: Obligate aerobes (require O2), obligate anaerobes (poisoned by O2), facultative anaerobes (use O2 when available), aerotolerant anaerobes (tolerate but don't use O2).

Ecological roles: Prokaryotes are essential decomposers; they fix nitrogen (N2 → NH3; only prokaryotes), nitrify, denitrify, and photosynthesize (cyanobacteria). Many form symbioses — mutualistic (gut microbiota, legume nodules), commensal, or parasitic.

The human microbiota: Trillions of prokaryotes in/on the body — aiding digestion, producing vitamins, training the immune system, and protecting against pathogens. Antibiotic disruption has significant health consequences.

Pathogenic bacteria: A small fraction are pathogens. Disease mechanisms: exotoxins (secreted proteins), endotoxins (LPS from Gram-negative outer membrane), direct tissue damage, excessive immune activation.

Antibiotic resistance: Bacteria survive treatment through mutation or horizontal gene transfer of resistance genes. Mechanisms: enzymatic destruction (beta-lactamase), target alteration, efflux pumps, reduced permeability. Resistance is evolution by natural selection in real time — antibiotics kill susceptible bacteria, resistant ones survive and multiply. Overuse accelerates this process.

ELI Example

Prokaryotes are a city's plumbing — invisible, essential, breaking down waste and converting materials. When plumbing fails (pathogen), you notice. Antibiotics are targeted pipe cleaners. Resistant bacteria survive, multiply, and spread — evolution on a timescale we can watch.

Do Not Confuse

Lab Link

In the laboratory, bacteria are observed using oil-immersion microscopy (100× objective). The Gram stain differentiates Gram-positive (purple) from Gram-negative (pink) bacteria based on cell wall structure. Students observe bacterial morphology — cocci (spherical), bacilli (rod-shaped), spirilla (spiral) — and arrangements (chains, clusters). Aseptic technique is critical to avoid contamination. Inhibition-zone assays (e.g., testing the effectiveness of different antibiotics or disinfectants) demonstrate the principles of antimicrobial action and resistance conceptually.

High-Yield Memory Anchors

• Prokaryotes = Bacteria + Archaea. No nucleus, 70S ribosomes, mostly unicellular.

• Genetic diversity: mutation + transformation + transduction + conjugation.

• Metabolic modes: photo/chemo + auto/hetero. Only prokaryotes are chemoautotrophs.

• Most prokaryotes are NOT pathogens. Microbiota = essential for health.

• Antibiotic resistance = evolution by natural selection, accelerated by antibiotic overuse.

Quick Check

Q1 (Foundational): List three structural features that distinguish prokaryotic cells from eukaryotic cells.

Q2 (Application): A patient has a bacterial infection. The doctor prescribes an antibiotic, but after a week, the infection persists. When the bacteria are cultured, most are now resistant to the antibiotic. Explain how this resistance likely arose and spread in the bacterial population.

Q3 (Comparison/Reasoning): Compare the mechanisms of transformation, transduction, and conjugation in prokaryotes. Which mechanism involves direct cell-to-cell contact?

Quick Check Answers

A1: (1) Prokaryotes lack a membrane-bound nucleus (DNA in nucleoid region). (2) Prokaryotes lack membrane-bound organelles (no mitochondria, ER, Golgi). (3) Prokaryotic ribosomes are 70S (vs. 80S in eukaryotes). (Also acceptable: cell wall composition, typically smaller size, circular chromosome, binary fission.)

A2: The antibiotic treatment acted as a strong selective pressure. In the initial bacterial population, a small number of cells likely already carried a mutation or had acquired a gene conferring resistance (from prior transformation, transduction, or conjugation). The antibiotic killed the susceptible bacteria. The resistant bacteria survived and reproduced by binary fission, producing a population dominated by resistant cells. The resistance gene may have also spread to other bacteria through horizontal gene transfer (conjugation, transduction, or transformation) during the infection. This is evolution by natural selection operating on a rapid timescale.

A3: Transformation: uptake of free DNA from the environment. Transduction: transfer of DNA by a bacteriophage (virus) that accidentally packages bacterial DNA. Conjugation: direct transfer of DNA through a sex pilus — requires cell-to-cell contact. Only conjugation involves direct physical contact between bacterial cells.

Chapter Summary

Prokaryotes: Bacteria + Archaea. No nucleus; 70S ribosomes; binary fission. Genetic diversity: mutation, transformation, transduction, conjugation. Extraordinary metabolic diversity (photo/chemo, auto/hetero). Essential ecological roles: decomposers, nitrogen fixers, microbiota. Few are pathogens. Antibiotic resistance = evolution by natural selection.

Common Mistakes

Mistake: "All bacteria cause disease."

Reality: The vast majority of bacteria are harmless or beneficial. They are essential for digestion, vitamin production, nutrient cycling, and ecosystem function. Only a small fraction are human pathogens.

Mistake: "Prokaryotes are primitive, simple life forms."

Reality: Prokaryotes are structurally simpler than eukaryotes but biochemically sophisticated. Their metabolic diversity far exceeds that of eukaryotes. They have been evolving for over 3.5 billion years and are exquisitely adapted to their niches.

Mistake: "Antibiotics work against viruses."

Reality: Antibiotics target bacteria, not viruses. They do nothing for viral infections like the common cold, influenza, or COVID-19. Using antibiotics for viral infections contributes to resistance without any benefit. Antiviral drugs (a different class) target viruses.