5.2 Bacteria, Archaea, and Viruses
Key Takeaways
- Bacteria are prokaryotes with peptidoglycan cell walls; Gram-positive bacteria retain crystal violet because of a thick peptidoglycan layer, while Gram-negative bacteria appear pink due to an outer lipopolysaccharide membrane.
- Bacteria exchange genetic material by three horizontal-transfer mechanisms: **conjugation** (pilus-mediated DNA transfer), **transformation** (uptake of naked environmental DNA), and **transduction** (phage-mediated DNA transfer).
- Archaea are extremophiles that thrive in harsh environments and include **thermophiles**, **halophiles**, and **methanogens**; their membranes use ether-linked isoprenoid lipids and their walls lack true peptidoglycan.
- Viruses are acellular, obligate intracellular parasites consisting of a protein capsid plus a DNA or RNA genome; lytic cycles destroy host cells immediately while lysogenic cycles integrate viral DNA into the host genome.
- Prions are misfolded proteins that induce normal proteins to misfold (no nucleic acid), and viroids are naked RNA molecules that infect plants - both challenge classical definitions of life.
Bacteria: The Original Cellular Life
Bacteria are single-celled prokaryotes that have populated Earth for at least 3.5 billion years. They lack a nucleus and membrane-bound organelles; their DNA sits in a region called the nucleoid, often supplemented by small circular plasmids that carry accessory genes (such as antibiotic-resistance genes).
Cell Wall and Gram Staining
Bacterial cell walls contain peptidoglycan - a polymer of sugars (NAG and NAM) cross-linked by short peptides. The Gram stain divides bacteria into two groups based on wall structure:
| Feature | Gram-Positive | Gram-Negative |
|---|---|---|
| Peptidoglycan layer | Thick (multi-layered) | Thin (single layer) |
| Outer membrane | Absent | Present (LPS) |
| Stain color | Purple (retains crystal violet) | Pink/red (counterstained with safranin) |
| Example | Staphylococcus aureus, Bacillus subtilis | Escherichia coli, Salmonella, Neisseria |
| Antibiotic sensitivity | Penicillin-sensitive (targets peptidoglycan) | LPS outer membrane gives some resistance |
The outer membrane of Gram-negative bacteria contains lipopolysaccharide (LPS), which is the endotoxin responsible for septic shock during severe infection.
Bacterial Shapes
- Cocci (spherical): Streptococcus, Staphylococcus
- Bacilli (rod-shaped): E. coli, Bacillus anthracis
- Spirilla/Spirochetes (spiral): Treponema pallidum
- Vibrios (comma-shaped): Vibrio cholerae
Horizontal Gene Transfer
Bacteria reproduce asexually by binary fission, but they swap genes laterally through three mechanisms:
- Conjugation - Direct cell-to-cell transfer via a sex pilus; an F+ (donor) cell passes a plasmid to an F- (recipient) cell. This is the classic route for antibiotic-resistance spread.
- Transformation - Uptake of free DNA from the environment, often released by dead cells. Frederick Griffith's 1928 Streptococcus pneumoniae experiment first demonstrated transformation.
- Transduction - DNA transfer by a bacteriophage that mistakenly packages host DNA into new phage particles and delivers it to the next cell it infects.
These processes explain why antibiotic resistance spreads rapidly across bacterial populations (and even between species) and why hospital-acquired infections become multi-drug-resistant.
Archaea: Life at the Extremes
Archaea look like bacteria under a microscope but are biochemically a separate domain. Three classic extremophile groups appear on the Praxis:
| Type | Habitat | Example |
|---|---|---|
| Thermophiles / Hyperthermophiles | Hot springs, hydrothermal vents (60-122 °C) | Thermus aquaticus (source of Taq polymerase used in PCR) |
| Halophiles | High-salt environments (Great Salt Lake, Dead Sea) | Halobacterium |
| Methanogens | Anaerobic environments - swamps, guts, sewage; produce methane (CH₄) | Methanococcus |
Archaeal vs. Bacterial Biochemistry
| Feature | Bacteria | Archaea |
|---|---|---|
| Cell wall | Peptidoglycan | Pseudopeptidoglycan or protein S-layers (no peptidoglycan) |
| Membrane lipids | Ester-linked straight-chain fatty acids | Ether-linked branched isoprenoid chains |
| RNA polymerase | Single, simple enzyme | Multi-subunit, eukaryote-like |
| Histones | Absent | Present (in many archaea) |
| Sensitivity to penicillin | Yes | No (no peptidoglycan) |
Ether-linked branched lipids are more heat-stable - one reason hyperthermophilic archaea survive boiling temperatures.
Viruses: Acellular Pathogens
A virus is a non-living, obligate intracellular parasite consisting of:
- A nucleic-acid genome - either DNA or RNA, single- or double-stranded
- A protein capsid (built from repeating subunits called capsomeres)
- Sometimes an envelope - a lipid bilayer stolen from a host membrane, studded with viral glycoproteins
Viruses are not in any domain because they lack ribosomes, cannot make ATP, and cannot reproduce without a host cell.
Lytic vs. Lysogenic Cycles
Bacteriophages (viruses that infect bacteria) follow one of two life cycles - a favorite Praxis topic.
Lytic cycle (virulent phage):
- Attachment to host receptor
- Penetration / injection of viral genome
- Biosynthesis - host machinery makes viral proteins and nucleic acids
- Assembly of new virions
- Lysis of the host cell, releasing progeny phages (host dies)
Lysogenic cycle (temperate phage):
- Viral DNA integrates into the host chromosome as a prophage
- The prophage is replicated along with host DNA during binary fission (host survives, often for many generations)
- Environmental stress (UV light, nutrient limits) can trigger induction, switching the prophage back to the lytic cycle
DNA vs. RNA Viruses
| Type | Genome | Examples |
|---|---|---|
| dsDNA | Double-stranded DNA | Herpesviruses, adenovirus, smallpox |
| ssDNA | Single-stranded DNA | Parvovirus |
| dsRNA | Double-stranded RNA | Rotavirus |
| (+)ssRNA | Positive-sense single-stranded RNA (acts as mRNA directly) | Poliovirus, SARS-CoV-2 |
| (-)ssRNA | Negative-sense single-stranded RNA | Influenza, rabies, Ebola |
| Retrovirus | (+)ssRNA → uses reverse transcriptase to make DNA → integrates into host genome | HIV |
HIV is a classic retrovirus: it carries reverse transcriptase, copies its RNA into DNA, and the DNA inserts into a host T helper cell's genome as a provirus. This integration is why HIV infection is permanent.
Prions and Viroids
- Prions ("proteinaceous infectious particles") are misfolded versions of normal cellular proteins. They convert normal proteins into the misfolded form, accumulating as plaques. Diseases: Creutzfeldt-Jakob disease, mad cow disease (BSE), scrapie. Prions are protein only - no nucleic acid.
- Viroids are small (~250-400 nucleotide) circular RNA molecules without a capsid that infect plants and cause diseases such as potato spindle tuber disease.
A clinical microbiologist performs a Gram stain on a bacterial sample and observes that the cells appear pink under the microscope. Which of the following is the BEST conclusion about this bacterium?
HIV is classified as a retrovirus. Which feature of HIV's replication cycle uniquely justifies the "retro" designation?