Prokaryotes: Bacteria, Archaea, and Protists – Structure, Function, and Diversity

Prokaryotes: Bacteria and Archaea

Overview of Prokaryotic Diversity

Prokaryotes, which include Bacteria and Archaea, are among the most ancient and diverse forms of life. They are characterized by the absence of a membrane-bound nucleus and organelles. Prokaryotes play essential roles in ecosystems and have unique adaptations for survival.

• Bacteria and Archaea are distinct domains, each with unique genetic and biochemical traits.

• Prokaryotes are found in nearly every environment on Earth, including extreme habitats.

• Phylogenetic trees show the evolutionary relationships among Bacteria, Archaea, and Eukarya.

• Oldest fossils are cyanobacteria (stromatolites), dating back 3.4–3.5 billion years.

Adaptations of Prokaryotes: Structure & Function

Prokaryotes exhibit a wide range of structural adaptations that allow them to thrive in diverse environments.

• Most prokaryotes are unicellular, though some form colonies.

• Cell size: typically 0.5–5 μm, much smaller than eukaryotic cells (10–100 μm).

• Common shapes:

  1. Cocci – spherical

  2. Bacilli – rod-shaped

  3. Spirilla – spiral-shaped

Cell-Surface Structures

Prokaryotic cells possess specialized surface structures that provide protection and aid in interactions with their environment.

• Cell wall: Maintains cell shape, protects the cell, and prevents bursting in hypotonic environments.

• Bacterial cell walls contain peptidoglycan, a network of sugar polymers cross-linked by polypeptides.

• Archaean cell walls contain polysaccharides and proteins, but lack peptidoglycan. They may have pseudomurein, which is functionally similar but chemically distinct.

• Capsule: A polysaccharide or protein layer outside the cell wall. Functions include:

  • Adherence to surfaces or other cells

  • Protection from dehydration

  • Shielding from immune system attack

General Structure of a Prokaryotic Cell

Typical prokaryotic cells have several key components:

• Cell wall

• Plasma membrane

• Cytoplasm

• Nucleoid region (contains DNA)

• Ribosomes

• Flagella or pili (for movement and genetic exchange)

Bacterial Cell Walls: Gram Stain Classification

The Gram stain is used to classify bacteria based on cell wall composition:

• Gram-positive: Thick peptidoglycan layer; stains purple. More susceptible to antibiotics targeting peptidoglycan.

• Gram-negative: Thin peptidoglycan layer and an outer membrane with toxic lipopolysaccharides; stains pink/red. More resistant to antibiotics.

Gram Stain Procedure:

1. Crystal violet dye & iodine (purple) binds to cell wall.

2. Rinsed in alcohol.

3. Stained with safranin dye (red) binds to DNA.

Cell-Surface Structures: Fimbriae and Pili

Prokaryotes have specialized protein projections for interaction and genetic exchange.

• Fimbriae: Short, hair-like structures that help cells adhere to surfaces or each other.

• Pili (Sex pili): Longer than fimbriae; facilitate DNA exchange between prokaryotes (conjugation).

Motility

Prokaryotes move in response to environmental stimuli using various mechanisms.

• Taxis: Movement toward or away from stimuli.

• Chemotaxis: Movement along a chemical gradient.

• Flagella: Propeller-like structures composed of a motor, hook, and filament. Found in bacteria, archaea, and eukaryotes, but composed of different proteins (homoplasy).

Exaptation: Bacterial flagella evolved from proteins with other functions.

Internal Organization and DNA

Prokaryotes lack complex compartmentalization but may have specialized membranes for metabolic functions.

• Nucleoid region: Area where the circular chromosome is located; not membrane-bound.

• Plasmids: Small, circular DNA molecules outside the main chromosome; often carry genes for antibiotic resistance or other functions.

Reproduction & Adaptation

Prokaryotes reproduce rapidly and adapt quickly to environmental changes.

• Binary fission: Asexual reproduction by cell division; can occur every 1–3 hours, or as fast as 20 minutes in some species.

• Endospore: A dormant, tough, and non-reproductive structure produced by some bacteria; allows survival in harsh conditions.

Genetic Diversity in Prokaryotes

Genetic variation in prokaryotes arises from several mechanisms:

• Mutation: Random changes in DNA sequence.

• Rapid reproduction: Increases the chance of mutations.

• Genetic recombination: Combining DNA from two sources via:

  1. Transformation: Uptake of external DNA from the environment.

  2. Transduction: Movement of genes between bacteria by bacteriophages (viruses).

  3. Conjugation: Direct transfer of DNA between prokaryotic cells via sex pili.

• Horizontal gene transfer: Movement of genes among individuals from different species.

Genetic Diversity: F Factor and Plasmids

The F (fertility) factor is a plasmid or chromosomal segment that enables DNA transfer during conjugation.

• Cells with F plasmid (F+) are DNA donors; F- cells are recipients.

• F factor can be transferred during conjugation.

• If F factor is in the chromosome, the recipient becomes a recombinant bacterium with DNA from two sources.

Diversity of Nutritional & Metabolic Adaptations

Prokaryotes are metabolically diverse and can be classified by how they obtain energy and carbon.

• Phototrophs: Obtain energy from light.

• Chemotrophs: Obtain energy from chemicals.

• Autotrophs: Use CO2 as a carbon source.

• Heterotrophs: Require organic nutrients for carbon.

Mode	Energy Source	Carbon Source	Types of Organisms
Photoautotroph	Light	CO2, HCO3-	Photosynthetic prokaryotes (cyanobacteria), plants, algae
Chemoautotroph	Inorganic chemicals (e.g., H2S, NH3)	CO2, HCO3-	Unique to certain prokaryotes (e.g., Sulfolobus)
Photoheterotroph	Light	Organic compounds	Unique to certain aquatic and salt-loving prokaryotes
Chemoheterotroph	Organic compounds	Organic compounds	Many prokaryotes (e.g., Clostridium), fungi, animals, some plants

Diversity of Nutritional & Metabolic Adaptations: Chemosynthesis

Hydrothermal vent communities depend on chemoautotrophic bacteria for energy. These bacteria fix inorganic carbon using chemical energy from the oxidation of reduced compounds.

Oxygen and Nitrogen in Metabolism

Prokaryotes vary in their oxygen requirements and nitrogen metabolism.

• Obligate anaerobes: Poisoned by O2; use fermentation or anaerobic respiration.

• Obligate aerobes: Require O2 for cellular respiration.

• Facultative anaerobes: Can survive with or without O2.

• Nitrogen fixation: Conversion of atmospheric nitrogen (N2) to ammonia (NH3), essential for amino acids and nucleic acids.

Metabolic Cooperation

Prokaryotic cells can cooperate metabolically to utilize resources more efficiently.

• Example: Anabaena cyanobacteria form heterocysts (specialized cells) for nitrogen fixation, while other cells perform photosynthesis.

Prokaryotes in the Biosphere

Prokaryotes are crucial for ecosystem function and nutrient cycling.

• Recycle chemical elements between living and nonliving components.

• Increase availability of nitrogen, phosphorus, and potassium for plant growth.

• Function as decomposers, breaking down dead organisms and waste.

Ecological Interactions

Prokaryotes engage in various ecological relationships with other organisms.

• Symbiosis: Close ecological relationship between two species (host and symbiont).

• Types of symbiosis:

  1. Mutualism: Both organisms benefit (e.g., gut bacteria in humans).

  2. Commensalism: One benefits, the other is neither harmed nor helped (e.g., E. coli in intestines).

  3. Parasitism: Parasite harms but does not kill host (e.g., Lyme disease bacteria).

• Pathogens: Disease-causing parasites; prokaryotes cause about half of all human diseases.

Pathogenic Prokaryotes

Some prokaryotes cause disease by releasing toxins.

• Exotoxins: Secreted proteins that cause disease even if the producing bacteria are not present.

• Endotoxins: Released only when bacteria die and their cell walls break down.

• Horizontal gene transfer can spread virulence genes.

• Some pathogenic bacteria are potential weapons of bioterrorism (e.g., Bacillus anthracis).

Prokaryotes in Research and Technology

Prokaryotes are important tools in biotechnology and environmental science.

• E. coli is used in gene cloning.

• Agrobacterium tumefaciens is used to produce transgenic plants.

• Bioremediation: Use of organisms to remove pollutants from the environment; engineered prokaryotes can produce vitamins, antibiotics, hormones, and ethanol from waste biomass.

Protists

Introduction to Protists

Protists are a diverse group of mostly unicellular eukaryotes that do not fit into the plant, animal, or fungal kingdoms. They exhibit a wide range of morphologies and life strategies.

• Protists are monophyletic, meaning they share a common ancestor.

• Include organisms such as algae, amoebas, and protozoa.

• Play important roles in aquatic ecosystems as primary producers and consumers.