Bacteria and Archaea: Structure, Function, and Diversity of Prokaryotes

Bacteria and Archaea

Introduction to Prokaryotes

Prokaryotes are a structurally and metabolically diverse group of single-celled organisms that have dominated the biosphere for over 3.5 billion years. They are found in nearly every environment on Earth, including extreme habitats where few other organisms can survive.

• Prokaryotes include both Bacteria and Archaea.

• They are essential to life on Earth, with only a minority being pathogenic.

• Prokaryotes are more numerous than all humans who have ever lived.

Ecological Importance of Prokaryotes

• Prokaryotes recycle carbon and other elements between organic matter, soil, and atmosphere.

• They form symbiotic relationships with eukaryotes (e.g., gut bacteria producing vitamins).

• Endosymbiotic theory: Mitochondria and chloroplasts evolved from prokaryotes living inside larger host cells.

Classification of Prokaryotes

Modern Classification

Molecular evidence has revealed two major branches of prokaryote evolution, leading to the domains Bacteria and Archaea. These are no longer grouped as a single kingdom.

• Bacteria: Most familiar prokaryotes, with cell walls containing peptidoglycan.

• Archaea: Often inhabit extreme environments; cell walls lack peptidoglycan and have unique biochemical traits.

Characteristics of Prokaryotes

Cell Structure and Morphology

• Most are unicellular, though some form colonies.

• Common shapes: Cocci (spheres), Bacilli (rods), Spirilli (helices).

• Cell size: 1–5 μm in diameter (smaller than most eukaryotic cells).

• Lack a nucleus; DNA is in a nucleoid region.

• Nearly all have a cell wall external to the plasma membrane.

Cell Wall Composition: Gram Stain

The Gram stain differentiates bacteria based on cell wall structure:

Type	Cell Wall Structure	Gram Stain Result
Gram-positive	Thick peptidoglycan layer	Purple
Gram-negative	Thin peptidoglycan, outer membrane with lipopolysaccharides	Pink/red

Surface Structures

• Capsule: Sticky protective layer outside the cell wall.

• Fimbriae (attachment pili): Surface appendages for adherence to surfaces or other cells.

• Sex pili: Specialized fimbriae for DNA transfer during conjugation.

Motility

• Flagella: Most common structure for movement (taxis).

• Spirochetes: Move via internal helical filaments (corkscrew motion).

• Some secrete slimy threads to glide along surfaces.

Endospores

• Resistant cells formed by some bacteria (e.g., Bacillus anthracis).

• Endospores can survive harsh conditions for long periods.

Genetics and Genomes

• Prokaryotes have smaller, simpler genomes than eukaryotes.

• DNA is usually a single circular chromosome in the nucleoid region.

• Plasmids: Small rings of DNA with a few genes, often for antibiotic resistance or special functions.

Reproduction and Genetic Variation

• Reproduce asexually by binary fission.

• Mutation is the main source of genetic variation.

• High mutation rates due to rapid reproduction (e.g., E. coli can produce 8 × 106 mutations per day across all genes).

Genetic Recombination Mechanisms

• Transformation: Uptake of DNA from the environment.

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

• Transduction: Transfer of DNA by bacteriophages (viruses that infect bacteria).

Conjugation Process Table

Step	Description
1	F+ cell (donor) forms mating bridge with F- cell (recipient)
2	One strand of F plasmid DNA breaks and enters recipient
3	Both cells synthesize complementary DNA strands
4	Recipient becomes recombinant F+ cell

Transduction Process Table

Step	Description
1	Phage infects donor cell
2	Phage DNA and proteins synthesized
3	Fragment of donor DNA packaged in phage
4	Phage infects recipient cell
5	Recombination creates recombinant cell

Metabolic Diversity

Prokaryotes are classified by how they obtain energy and carbon:

• Phototrophs: Use light as energy source.

• Chemotrophs: Obtain energy from chemicals.

• Autotrophs: Use CO2 as carbon source.

• Heterotrophs: Require organic nutrients as carbon source.

Metabolic Types Table

Type	Energy Source	Carbon Source
Photoautotroph	Light	CO2
Chemoautotroph	Inorganic chemicals	CO2
Photoheterotroph	Light	Organic compounds
Chemoheterotroph	Organic compounds	Organic compounds

Oxygen and Nitrogen Metabolism

• Obligate aerobes: Require O2 for cellular respiration.

• Facultative anaerobes: Use O2 if present, or fermentation/anaerobic respiration if not.

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

• Nitrogen fixation: Some prokaryotes (e.g., Rhizobium) convert atmospheric N2 to ammonia (NH3), making nitrogen available to plants.

Major Clades of Bacteria

• Proteobacteria: Diverse group including phototrophs, chemotrophs, and heterotrophs; some are pathogenic.

• Chlamydias: Parasites that live within animal cells.

• Spirochetes: Helical heterotrophs; some cause diseases like syphilis and Lyme disease.

• Cyanobacteria: Photoautotrophs that generate O2; ancestors of plant chloroplasts.

• Gram-positive bacteria: Includes soil decomposers (actinomycetes), pathogens (e.g., Bacillus anthracis), and mycoplasmas.

Summary Table: Bacteria vs. Archaea

Feature	Bacteria	Archaea
Cell Wall	Contains peptidoglycan	No peptidoglycan; may have polysaccharides/proteins
Habitat	Wide range, including moderate environments	Often extreme environments (e.g., hot springs, salt lakes)
Membrane Lipids	Ester-linked	Ether-linked
Gene Expression	Unique to bacteria	Some similarities to eukaryotes

Additional info: These notes synthesize and expand upon the provided slides, adding definitions, tables, and context for clarity and completeness for General Biology students.