Study Guide: Bacteria and Archaea (Chapter 27)

Bacteria and Archaea: Diversity, Structure, and Function

Overview of the Tree of Life

The tree of life represents the evolutionary relationships among all living organisms, divided into three domains: Bacteria, Archaea, and Eukarya. Prokaryotes (Bacteria and Archaea) are the most ancient and abundant forms of life, thriving in diverse environments.

Characteristic	Bacteria	Archaea	Eukarya
Nuclear envelope	Absent	Absent	Present
Membrane-enclosed organelles	Absent	Absent	Present
Peptidoglycan in cell wall	Present	Absent	Absent
Membrane lipids	Unbranched hydrocarbons	Some branched hydrocarbons	Unbranched hydrocarbons
RNA polymerase	One kind	Several kinds	Several kinds
Initiator amino acid for protein synthesis	Formyl-methionine	Methionine	Methionine
Introns in genes	Very rare	Present in some genes	Present in many genes
Response to antibiotics	Growth usually inhibited	Growth not inhibited	Growth not inhibited
Histones associated with DNA	Absent	Present in some species	Present
Circular chromosome	Present	Present	Absent
Growth at temperatures >100°C	Some species	Some species	Not present

Structural and Functional Adaptations of Prokaryotes

Prokaryotes exhibit a variety of shapes and adaptations that contribute to their success. Most are unicellular and much smaller than eukaryotic cells. The three most common shapes are:

• Cocci (spherical)

• Bacilli (rod-shaped)

• Spirilli (spiral-shaped)

The cell wall is a critical structure, maintaining cell shape, protecting the cell, and preventing lysis in hypotonic environments. Bacterial cell walls contain peptidoglycan, while archaeal cell walls lack peptidoglycan and instead contain polysaccharides and proteins.

Gram Staining

• Gram-positive bacteria: Thick peptidoglycan layer, stain purple.

• Gram-negative bacteria: Thin peptidoglycan layer, outer membrane with lipopolysaccharides, stain pink.

Many antibiotics target peptidoglycan, making Gram-positive bacteria more susceptible.

Additional Cell Surface Structures

• Capsule: Sticky layer for adherence and protection from the immune system.

• Fimbriae: Hair-like appendages for attachment to surfaces or other cells.

• Pili: Longer appendages for DNA exchange (conjugation).

Endospores

Some prokaryotes form metabolically inactive endospores that can survive harsh conditions for centuries.

Internal Organization

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

Genetic Material

• Most prokaryotes have a single, circular chromosome located in the nucleoid region.

• They may also have small, independently replicating DNA molecules called plasmids.

Reproduction and Genetic Diversity

Prokaryotes reproduce rapidly by binary fission, leading to short generation times and high population growth. Genetic diversity arises from:

• Rapid reproduction

• Mutation

• Genetic recombination (transformation, transduction, conjugation)

Conjugation and Plasmids

Conjugation involves the transfer of DNA between cells via a pilus. The F factor is required for pilus formation and DNA transfer.

Antibiotic Resistance

R plasmids carry genes for antibiotic resistance, which can be transferred between bacteria, leading to the spread of resistant strains.

Nutritional and Metabolic Adaptations

Prokaryotes are classified by their energy and carbon sources:

• Photoautotrophs: Light as energy, CO2 as carbon source

• Chemoautotrophs: Inorganic chemicals as energy, CO2 as carbon source

• Photoheterotrophs: Light as energy, organic compounds as carbon source

• Chemoheterotrophs: Organic compounds as energy and carbon source

Oxygen and Nitrogen in Metabolism

• Obligate aerobes: Require O2 for cellular respiration

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

• Facultative anaerobes: Can use O2 or not

• Nitrogen fixation: Conversion of N2 to NH3 by some prokaryotes

Metabolic Cooperation

Prokaryotes cooperate metabolically, forming biofilms or exchanging metabolites. In cyanobacteria, specialized cells called heterocysts fix nitrogen while others perform photosynthesis.

Prokaryotic Diversity: Major Groups

Prokaryotes are divided into two domains: Bacteria and Archaea. Bacteria include several major groups:

• Proteobacteria: Diverse, includes five subgroups (Alpha, Beta, Gamma, Delta, Epsilon)

• Chlamydias: Intracellular parasites

• Spirochetes: Helical, some are pathogens

• Cyanobacteria: Photosynthetic, oxygen-generating

• Gram-positive bacteria: Includes many decomposers and pathogens

Proteobacteria Subgroups

• Alpha: Includes Rhizobium (nitrogen-fixing in legumes)

• 

• Beta: Includes Nitrosomonas (ammonia to nitrite conversion)

• 

• Gamma: Includes Thiomargarita namibiensis, Escherichia coli, pathogens

• 

• Delta: Includes myxobacteria (fruiting bodies), Bdellovibrio

• 

• Epsilon: Includes Helicobacter pylori (causes ulcers)

• 

Other Bacterial Groups

• Chlamydias: Intracellular animal cell parasites

• 

• Spirochetes: Helical, includes pathogens like Leptospira

• 

• Cyanobacteria: Filamentous, photosynthetic, likely ancestors of chloroplasts

• 

• Gram-positive bacteria: Includes decomposers, pathogens (e.g., Bacillus anthracis, Clostridium botulinum)

• 

Archaea

Archaea share traits with both bacteria and eukaryotes. Many are extremophiles:

• Extreme halophiles: Thrive in highly saline environments

• 

• Extreme thermophiles: Thrive in very hot environments

• Methanogens: Produce methane, strict anaerobes

• 

Ecological Roles of Prokaryotes

Prokaryotes are essential for life, playing major roles in recycling nutrients, decomposing organic matter, and converting molecules for use by other organisms. They form symbiotic relationships:

• Mutualism: Both partners benefit

• Commensalism: One benefits, other unaffected

• Parasitism: One benefits, other harmed (pathogens)

Prokaryotes and Human Health

Prokaryotes can be both beneficial and harmful to humans. The human gut contains hundreds of bacterial species, many of which aid digestion. Pathogenic bacteria cause diseases by releasing toxins:

• Exotoxins: Secreted, cause disease even if bacteria are absent

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

Horizontal gene transfer can spread virulence genes, making some strains more dangerous.

Prokaryotes in Research and Technology

Prokaryotes are used in biotechnology, gene cloning, and bioremediation. The CRISPR-Cas system, derived from prokaryotes, is a powerful tool for gene editing.