Chapter 20: The Diversity of Prokaryotes and Viruses – Study Notes

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This section introduces the prokaryotic domains, Archaea and Bacteria, and their fundamental characteristics and differences.

Prokaryotes are single-celled organisms lacking membrane-bound organelles and a nucleus.
They are the most abundant group on Earth, present in diverse environments including the human body (the "microbiome").
Prokaryotes are typically very small (0.2–10 micrometers), much smaller than eukaryotic cells (10–100 micrometers).
Three common shapes due to rigid cell walls:
- Spherical (cocci): e.g., Streptococcus pyogenes, Staphylococcus aureus
- Rod-like (bacilli): e.g., Bacillus subtilis
- Corkscrew-shaped (vibrio): e.g., Vibrio cholerae
Bacterial cell structure includes: pilus, capsule, cell wall, plasma membrane, nucleoid (DNA), cytoplasm, ribosomes, and flagellum.
Bacteria vs. Archaea:
- Bacteria have cell walls made of peptidoglycan; Archaea have an S-layer made of proteins.
- Differences also exist in plasma membrane structure, ribosomal RNA, and enzymes for RNA synthesis.

Feature	Archaea	Bacteria
Cell Wall Composition	No peptidoglycan; S-layer (protein)	Peptidoglycan present
Membrane Lipids	Branched hydrocarbons	Unbranched hydrocarbons
Histone Proteins	Present	Absent
Introns in Genes	Present in some	Absent
RNA Polymerase	Several types	One type
Initiator Amino Acid	Methionine	Formylmethionine
Ribosomal RNA	More similar to eukaryotes	More distant from eukaryotes

Classification within domains is now based on DNA sequence data, not just morphology or biochemistry.
Systematists recognize about 30 major bacterial groups and 5 archaeal groups; evolutionary relationships are still being studied.

Prokaryotes thrive due to their adaptability, motility, and diverse metabolic strategies.

Motility: Many prokaryotes move using flagella, which differ structurally from eukaryotic flagella.
- Bacterial flagella are solid, made of flagellin, and rotate via a wheel-and-axle mechanism.
- Archaeal flagella (archaella) are thinner and made of different proteins.
Quorum Sensing: Prokaryotes communicate via signaling molecules (AHLs) to coordinate behaviors like toxin production, bioluminescence, and biofilm formation.
Biofilms: Aggregates of prokaryotes surrounded by sticky slime, protecting them from antibiotics and disinfectants. Example: dental plaque.
Endospores: Some bacteria (e.g., Bacillus, Clostridium) form resistant spores to survive harsh conditions.
- Endospores contain DNA and enzymes in a thick coat; metabolism ceases until conditions improve.
- Can survive boiling, radiation, and desiccation.
Metabolic Diversity:
- Chemoheterotrophs: Use organic molecules for energy and carbon.
- Chemoautotrophs (lithotrophs): Use inorganic molecules (e.g., H2, S, NH3) for energy.
- Photoautotrophs: Use light energy and CO2 for photosynthesis.
Reproduction:
- Most prokaryotes reproduce by binary fission, producing genetically identical cells.
- Rapid reproduction allows for quick evolution via mutations.
- Horizontal gene transfer (e.g., conjugation via sex pili) increases genetic diversity.

Type	Energy Source	Carbon Source	Example
Chemoheterotroph	Chemical (organic)	Organic	E. coli
Chemoautotroph	Chemical (inorganic)	CO2	Thiobacillus
Photoautotroph	Light	CO2	Cyanobacteria

Prokaryotes play essential roles in ecosystems and human health, but can also cause disease.

Symbiotic relationships:
- Mutualistic: Both host and microbe benefit (e.g., E. coli in human gut produces vitamin K).
- Parasitic: Microbe benefits, host is harmed (e.g., pathogenic E. coli, Vibrio cholerae).
- Commensal: Microbe benefits, host is unaffected.
Nutrient cycling:
- Bacteria decompose organic matter, recycling nutrients.
- Nitrogen-fixing bacteria (e.g., Rhizobium) convert atmospheric N2 to ammonia for plants.
Bioremediation: Use of bacteria to clean up pollutants (e.g., oil spills).
Pathogenic bacteria: Cause diseases such as tetanus (Clostridium tetani), botulism (Clostridium botulinum), plague (Yersinia pestis), Lyme disease (Borrelia burgdorferi), cholera (Vibrio cholerae).
Emerging and re-emerging diseases: Bacterial and viral diseases can reappear or newly emerge (e.g., SARS-CoV-2, Zika virus).

This section describes non-living infectious agents: viruses, viroids, and prions.

Viruses:
- Acellular, non-living entities with DNA or RNA surrounded by a protein coat (capsid).
- Cannot metabolize or respond to stimuli; require host cells to reproduce (obligate parasites).
- Viral shapes: helical, icosahedral, complex.
- Some viruses have an envelope derived from host cell membrane, with glycoproteins for host specificity.
- Examples: HIV (causes AIDS), herpes viruses, bacteriophages (infect bacteria).
Viroids:
- Small, circular RNA molecules without a protein coat.
- Cause plant diseases (e.g., potato spindle tuber disease).
- No known animal viroids.
Prions:
- Infectious proteins, misfolded versions of normal neuronal proteins (PrP).
- Cause neurodegenerative diseases (e.g., mad cow disease, kuru).
- Prions can induce misfolding in normal proteins, leading to disease.
Viral infections are difficult to treat; antibiotics are ineffective, and antiviral drugs may have limited success due to rapid viral evolution.

Agent	Genetic Material	Protein Coat	Host Range	Example Disease
Virus	DNA or RNA	Present	Plants, animals, bacteria	AIDS, influenza
Viroid	RNA	Absent	Plants	Potato spindle tuber
Prion	None	Absent	Animals	Mad cow disease

Binary fission equation: (where is final cell number, is initial cell number, is number of generations)
Photosynthesis equation (for cyanobacteria):
Nitrogen fixation equation: