Prokaryotes: Bacteria & Archaea – Structure, Classification, and Biology

Topic 3: Prokaryotes (Bacteria & Archaea)

Introduction

Prokaryotes are single-celled organisms that lack a membrane-bound nucleus and organelles. They are divided into two major domains: Bacteria and Archaea. Understanding their classification, structure, metabolism, reproduction, and ecological roles is fundamental to biology and biochemistry.

History of Classification

Development of Biological Classification Systems

Biological classification has evolved over time, reflecting advances in our understanding of life's diversity. Early systems grouped all life into a few kingdoms, but molecular data led to the current three-domain system.

Scientist	Year	System	Domains/Kingdoms
Linnaeus	1735	2 kingdoms	Animalia, Plantae
Haeckel	1866	3 kingdoms	Protista, Plantae, Animalia
Chatton	1925	2 empires	Prokaryota, Eukaryota
Whittaker	1969	5 kingdoms	Monera, Protista, Plantae, Fungi, Animalia
Woese et al.	1990	3 domains	Bacteria, Archaea, Eukarya

Additional info: The three-domain system is now widely accepted, based on genetic and molecular evidence.

Three-Domain Hypothesis

Currently Accepted Tree of Life

The three-domain hypothesis divides all life into Bacteria, Archaea, and Eukarya. This model is based on differences in ribosomal RNA sequences and other molecular data.

• Bacteria: Most diverse and numerous domain; includes most known prokaryotes.

• Archaea: Often found in extreme environments; genetically distinct from bacteria.

• Eukarya: Includes all eukaryotic organisms (plants, animals, fungi, protists).

Defining Features of Prokaryotes

What is a Prokaryotic Cell?

• No membrane-bound nucleus: Genetic material is in a single, circular DNA molecule in the cytoplasm.

• No membrane-bound organelles: Lacks mitochondria, endoplasmic reticulum, etc.

• Haploid: Usually only one copy of each gene.

• Cell wall: Most have a rigid cell wall (composition varies between Bacteria and Archaea).

Comparison: Bacteria vs. Archaea

Cellular Feature	Bacteria	Archaea
RNA polymerase	One type (5 subunits)	One type (13 subunits; similar to eukaryotes)
Peptidoglycan in cell wall	Present	Absent
First amino acid in translation	Formylmethionine	Methionine
Histones associated with DNA	No	Yes

Cell Structure and Morphology

Shapes and Cell Walls

• Shapes: Common shapes include cocci (spherical), bacilli (rod-shaped), and spirilla (spiral).

• Cell Walls: Bacterial cell walls contain peptidoglycan; archaeal cell walls are diverse and lack peptidoglycan.

• Gram Staining: Bacteria are classified as Gram-positive (thick peptidoglycan layer) or Gram-negative (thin peptidoglycan, outer membrane).

Additional info: Gram staining is a key diagnostic tool in microbiology.

Metabolism in Prokaryotes

Overview of Metabolic Diversity

Prokaryotes exhibit remarkable metabolic diversity, allowing them to inhabit a wide range of environments.

• Energy sources: Light (phototrophs) or chemicals (chemotrophs).

• Electron donors: Organic (organotrophs) or inorganic (lithotrophs).

• Carbon sources: CO2 (autotrophs) or organic compounds (heterotrophs).

Energy Source	Electron Donor	Carbon Source	Example
Light	Inorganic	CO2	Cyanobacteria (photoautotrophs)
Chemicals	Organic	Organic	Most bacteria (chemoorganoheterotrophs)
Chemicals	Inorganic	CO2	Nitrifying bacteria (chemolithoautotrophs)

Cellular Respiration and Electron Transport

• Aerobic respiration: Uses oxygen as the final electron acceptor.

• Anaerobic respiration: Uses other molecules (e.g., nitrate, sulfate) as electron acceptors.

• Fermentation: Energy production without an electron transport chain.

Equation for aerobic respiration:

$C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{energy (ATP)}$

Reproduction in Prokaryotes

Binary Fission

• Binary fission: Asexual reproduction where a cell divides into two genetically identical daughter cells.

• Rapid population growth under favorable conditions.

Lateral (Horizontal) Gene Transfer

Mechanisms of Gene Transfer

• Transformation: Uptake of free DNA from the environment.

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

• Conjugation: Direct transfer of DNA between cells via a pilus.

Additional info: Lateral gene transfer increases genetic diversity and complicates phylogenetic analysis.

Interactions with Other Organisms

Microbiome

• Definition: The collection of all microorganisms living in association with a host organism.

• Essential for digestion, immunity, and overall health in humans and other animals.

• Microbiomes are highly specific to individuals and body locations.

Symbiosis and Ecological Roles

• Nitrogen fixation: Conversion of atmospheric nitrogen (N2) to ammonia (NH3), making nitrogen available to plants.

• Bioremediation: Use of bacteria and archaea to degrade environmental pollutants.

• Pathogenicity: Some prokaryotes cause diseases in humans, animals, and plants.

Major Lineages of Prokaryotes

Domain Bacteria

• Proteobacteria: Includes many medically and ecologically important species (e.g., Escherichia coli).

• Firmicutes: Includes Bacillus and Clostridium species; some cause disease.

• Actinobacteria: Important for soil health and antibiotic production.

• Cyanobacteria: Photosynthetic bacteria; important for oxygen production.

Domain Archaea

• Thaumarchaeota, Crenarchaeota, Korarchaeota, Euryarchaeota: Major archaeal lineages, often found in extreme environments.

• Extremophiles: Archaea that thrive in high temperature, salinity, or acidity.

• Methanogens: Produce methane as a metabolic byproduct.

Summary Table: Key Differences Between Bacteria and Archaea

Feature	Bacteria	Archaea
Cell wall	Peptidoglycan	No peptidoglycan; diverse composition
Membrane lipids	Ester-linked	Ether-linked
RNA polymerase	Simple	Complex (similar to eukaryotes)
Habitat	Wide range	Often extreme environments

Conclusion

Prokaryotes are fundamental to life on Earth, displaying immense diversity in structure, metabolism, and ecological roles. Their study provides insights into evolution, biotechnology, and the functioning of ecosystems.