IV. Bacteriology
Key focus of this chapter: Bacteria vs. Viruses.
This chapter compares bacteria and viruses and summarizes prions, viroids, viral types, animal viruses, bacteriophages, and key concepts in bacterial biology.
A. Prions
- Composed of infectious proteins.
- Misfolded prion protein (PrPSc) can induce misfolding of normal PrP and cause neurodegeneration in mammals.
- Scrapie disease in sheep, Mad cow disease (BSE), and Creutzfeldt-Jakob disease (CJD) in humans.
B. Viroids
- Composed of circular and single stranded RNA molecules without protein capsid.
- Plant pathogens.
C. Virus
: an infectious agent that requires a host cell to replicate.
- Composed of DNA or RNA molecules and protected by protein coat.
- Lacks organelles and cell wall.
- Host range depends in part on specific interactions between viral attachment proteins and host-cell receptors.
- Cannot reproduce without a host cell.
- Viruses are not classified as living organisms.
1. Viral types
Classification | Shapes | Features |
Adenoviruses |  | • Naked virus • Double stranded DNA • Icosahedral capsid with fiber proteins projecting from its vertices. • Infects respiratory tracts |
Tobacco mosaic virus |  | • Naked helical virus • Single stranded RNA Virus • Capsomere of helical capsid with rod shape • Infects tobacco plant |
Influenza viruses |  | • Enveloped virus • Single stranded RNA Virus • Membranous envelope with glycoprotein • RNA molecules wrapped in helical capsid |
Bacteriophage T4 |  | • DNA virus • Polyhedral head, tail sheath, and tail fiber • Infects E. coli. • Only lytic phase |
2. Reproductive cycle of virus
a. Animal virus
- RNA virus
– Most non-retroviral RNA viruses replicate their RNA genomes using an RNA-dependent RNA polymerase. Positive-sense RNA can act as mRNA; negative-sense RNA must first be transcribed into mRNA.
– e.g., Influenza virus (negative-sense RNA), hepatitis C virus, and SARS-CoV (positive-sense RNA).
- Retrovirus
– reverse transcriptase (synthesizing DNA from RNA).
– Host RNA polymerase II transcribes the integrated proviral DNA to produce viral genomic RNA and mRNA.
– Retroviral replication involves reverse transcription, integration into host DNA, transcription, translation, assembly, and budding.
– e.g., HIV (which can cause AIDS) and oncogenic retroviruses.
- DNA virus
– synthesizes new genomes from viral DNA.
– replication and assembly sites vary by virus; many DNA viruses replicate in the nucleus, while poxviruses replicate in the cytoplasm.
– e.g., Adenovirus, herpesvirus, papillomaviruses (Papillomaviridae), and polyomaviruses (Polyomaviridae).
b. Bacteriophage
- Infects bacteria
- Some bacteriophages have complex head-tail structures.
- Transduction
- Bacteriophage T4
– composed of polyhedral head, tail sheath, and tail fiber
– virulent phage
– only lytic cycle
- Bacteriophage lambda (λ)
– temperate phage (both lytic cycle and lysogenic cycle)
– infection Escherichia coli bacteria
- Lytic cycle
: phage replication that ends with host-cell lysis; virulent phages use only this cycle.
– ① approaching and attachment.
– ② entry of phage DNA.
– ③ phage DNA replication and viral protein synthesis.
– ④ phage assembly.
– ⑤ host-cell lysis and release of new phages.
- Lysogenic cycle
: in temperate phages such as λ, phage DNA integrates into the host chromosome as a prophage and replicates with the host without immediate lysis. Induction can switch it to the lytic cycle.
– ① approaching and attachment
– ② entry of phage DNA
– ③ integration into the host chromosome (prophage formation)
– ④ replication of the prophage with host DNA
– ⑤ bacterial division passes the prophage to daughter cells
** Comparison of animal virus and bacteriophage multiplication
Stage of reproduction | Animal Virus | Bacteriophage |
Attachment | • Envelope or capsid to host cell surface | • Phage attachment proteins bind specific bacterial surface receptors; tail fibers mediate attachment in phages such as T4. |
Penetration | • Enveloped viruses may enter by membrane fusion or endocytosis. • Non-enveloped viruses commonly use receptor-mediated entry to deliver their genomes; entry mechanisms vary among viruses. | • Nucleic acid into host cell |
Synthesis and Assembly | • In the cytoplasm and/or nucleus, depending on the virus | • At cytoplasm only |
D. Bacteria
1. Shapes
- Bacilli – rod shaped
- Cocci – spherical
- Spiral – helical
** Arrangement of prefixes
- Diplo (pair), staphylo (clusters), strepto (chains)
- E.g., Staphylococci (spherical clusters)
2. Cell-surface Structures
- Gram-positive
– cell wall with thick sheet of peptidoglycan (network composed of modified sugar and amino acids).
- Gram-negative
– cell wall with outer membrane and thin sheet of peptidoglycan.
– outer membrane containing lipopolysaccharide.
3. Motility
- Bacterial flagellar rotation is powered by a proton-motive force (H⁺ gradient), or in some species a sodium-motive force (Na⁺ gradient).
- Flagellum made of basal apparatus, hook, and filament.
- Prokaryotic flagella are not extensions of the plasma membrane.
- Taxis – directed movement of a motile cell toward or away from an environmental stimulus.
4. Genetic recombination
: horizontal gene transfer can increase bacterial genetic diversity; it is distinct from asexual reproduction by binary fission.
- Transduction
– transfer of bacterial DNA from one bacterium to another by bacteriophages.
- Transformation
– uptake of extracellular naked DNA by a competent bacterium; the DNA may recombine with the genome or be maintained as a plasmid.
- Conjugation
– direct DNA transfer from a donor to a recipient through cell-to-cell contact; in many Gram-negative bacteria a sex pilus helps establish contact.
– genetic exchange without production of new cells.
– Plasmids are usually extrachromosomal, independently replicating DNA molecules, commonly circular. They may carry antibiotic-resistance genes, and some can be transferred between bacteria.
5. Binary fission
: a form of asexual reproduction by cell division in bacteria.
- Chromosome replication
– starting point of replication in both directions.
– bi-directional progress
6. Gene expression
- Lac operon (inducible system)
– controlling enzyme synthesis for metabolizing lactose to glucose and galactose in E. coli.
– operon off: Active repressor is bound to the operator and inhibits transcription of the lac genes.
– operon on: Allolactose (inducer) binds and inactivates the repressor. RNA polymerase transcribes lacZ, lacY, and lacA into mRNA; ribosomes translate β-galactosidase, permease, and transacetylase.
– strongest expression occurs when lactose is present and glucose is low: increased cAMP binds CAP, and the cAMP–CAP complex promotes transcription.
Enzymes | Functions |
β-Galactosidase | • Made from lac Z • Hydrolyzing lactose to glucose and galactose |
Permease | • Made from lac Y • Moving lactose into cell |
Transacetylase | • Made from lac A • Transfers an acetyl group from acetyl-CoA to certain β-galactosides; not required for lactose hydrolysis. |
- Trp operon (repressible system)
– controlling repressible enzyme synthesis for making tryptophan in E. coli.
– operon on: When tryptophan is scarce, the repressor is inactive. RNA polymerase transcribes the trp genes into mRNA; ribosomes translate enzymes for tryptophan synthesis.
– operon off: Tryptophan acts as a corepressor: binding activates the repressor, which binds the operator and inhibits transcription.
7. Metabolic adaptation
- Oxygen relationship
Classification | Features |
Obligate aerobes | • Aerobic organisms that need O2 for cellular respiration • Without O2 aerobic organisms cannot grow |
Obligate anaerobes | • Anaerobic organisms that cannot grow with O2 |
Facultative anaerobes | • Use aerobic respiration when O₂ is available; without O₂, use fermentation or, when the organism and electron acceptor permit, anaerobic respiration. • E.g., E. coli |
- Biofilms
– communities of microorganisms attached to surfaces and embedded in a self-produced extracellular polymeric substance (EPS) matrix, which promotes adhesion, protection, and retention of water and nutrients.
8. Bacterial pathogens and diseases
Bacterial pathogens | Diseases |
Borrelia burgdorferi | • Lyme disease |
Salmonella enterica serovar Typhi | • Typhoid fever |
Escherichia coli (pathogenic strains) | • Diarrhea, sepsis, urinary tract infection |
Neisseria gonorrhoeae / N. meningitidis | • Gonorrhea (N. gonorrhoeae); meningitis (N. meningitidis) |
Corynebacterium diphtheriae (toxigenic strains) | • Diphtheria |
Clostridium tetani / C. perfringens | • Tetanus (C. tetani); gas gangrene (commonly C. perfringens) |
Streptococcus pneumoniae | • Pneumonia |
E. Benefits of Microbes
- Gut bacteria can synthesize vitamin K₂ (menaquinones), although the amount absorbed and its contribution to human vitamin K requirements remain uncertain.
- Breakdown of organic materials and recycling of nutrients.