Chapter 8: Microbial Genetics

Genetic Terminology and Concepts

• Genetics: The study of heredity and variation in organisms.

• Gene: A segment of DNA that encodes a functional product, usually a protein.

• Chromosome: A structure containing DNA that physically carries hereditary information.

• Genome: The complete genetic content of an organism.

• Genomics: The study of genomes, including their sequencing and analysis.

• Genotype: The genetic makeup of an organism.

• Phenotype: The observable characteristics resulting from the genotype.

Bacterial DNA Structure

• Bacterial DNA is typically a single, circular, double-stranded molecule located in the nucleoid region.

• Plasmids are small, circular DNA molecules independent of the chromosome.

Gene Transfer Mechanisms

• Vertical gene transfer: Transmission of genetic material from parent to offspring during reproduction.

• Horizontal gene transfer: Transfer of genes between cells of the same generation.

• Three main horizontal gene transfer methods:

  • Transformation: Uptake of naked DNA from the environment.

  • Transduction: Transfer of DNA via bacteriophages.

  • Conjugation: Direct transfer of DNA between bacteria through cell-to-cell contact.

Mutations and Mutagenesis

• Mutation: A permanent change in the DNA sequence.

• Mutagen: An agent that causes mutations (e.g., nitrous acid, ionizing radiation, UV radiation).

• Spontaneous mutation: Occurs naturally without external influence.

• Mutation rate: The probability that a gene will mutate during a single cell division.

• Spontaneous mutation rates are typically low, but mutagens can increase these rates.

Plasmids and Transposons

• Plasmid: Small, circular DNA molecules that replicate independently; types include F (fertility), R (resistance), and Col (colicinogenic) plasmids.

• Transposons: DNA sequences that can move from one location to another within a genome; unlike plasmids, they integrate into chromosomes.

• Plasmids play a key role in recombinant DNA technology as vectors for gene cloning.

Chapter 10: Classification of Microorganisms

Taxonomy and Phylogeny

• Taxonomy: The science of classifying organisms.

• Phylogeny: The evolutionary history of organisms.

• G+C ratios (guanine + cytosine content) are used to infer phylogenetic relationships among bacteria.

• The three-domain system is based on differences in rRNA sequences: Bacteria, Archaea, and Eukarya.

Nomenclature and Classification

• Scientific nomenclature provides a universal naming system for organisms.

• A subspecies is a taxonomic category below species, often based on phenotypic or genetic differences.

• The four eukaryotic kingdoms: Protista, Fungi, Plantae, Animalia.

• Protista and Fungi can be unicellular or multicellular; Plantae and Animalia are multicellular.

• Viruses are not classified in any domain because they lack cellular structure and metabolism.

• Viral species: A group of viruses sharing the same genetic information and ecological niche.

Microbial Identification Methods

• Classification: Arranging organisms into groups based on similarities.

• Identification: Determining the identity of an organism.

• Correct identification is crucial for diagnosis and treatment.

• Identification algorithms streamline the process of microbial identification.

• Common methods:

  • Morphological characteristics (shape, arrangement)

  • Differential staining (e.g., Gram stain)

  • Biochemical testing (enzyme activity, metabolic capabilities)

• Less common techniques: Serology, phage typing, fatty acid profiles, nucleic acid hybridization.

Chapter 11: The Prokaryotes: Domains Bacteria and Archaea

Prokaryotic Domains and Extremophiles

• The two prokaryotic domains: Bacteria and Archaea.

• Types of Archaea extremophiles:

  • Halophiles (salt-loving)

  • Thermophiles (heat-loving)

  • Acidophiles (acid-loving)

  • Methanogens (produce methane)

  • Psychrophiles (cold-loving)

Proteobacteria and Other Bacterial Groups

• Proteobacteria: Large group of Gram-negative bacteria, subdivided into:

  • Alphaproteobacteria

  • Betaproteobacteria

  • Gammaproteobacteria (e.g., Yersinia pestis, cause of plague)

  • Deltaproteobacteria

  • Epsilonproteobacteria

• Each subgroup is associated with specific human diseases.

• Chlamydiae: Obligate intracellular bacteria; differ from Rickettsia in transmission requirements.

• Bacteroidaceae, Prevotellaceae, Fusobacteriaceae: Share anaerobic metabolism.

• Spirochaetes: Spiral-shaped bacteria; examples include Treponema (syphilis), Borrelia (Lyme disease), Leptospira (leptospirosis).

• Firmicutes (low G+C) vs. Actinobacteria (high G+C) distinguished by DNA base composition.

• Mycoplasmatales: Lack cell walls, pleomorphic, small genome, require sterols for growth.

Chapter 12: The Eukaryotes: Fungi, Algae, Protozoa, and Helminths

Fungi

• Fungi acquire nutrients by absorption of organic matter.

• Mycology: Study of fungi; mycosis: Fungal infection.

• Molds: Multicellular, filamentous, optimal growth at 25°C.

• Yeasts: Unicellular, non-filamentous, optimal growth at 37°C.

• Dimorphism: Ability to exist as mold at 25°C and yeast at 37°C.

• Mycelium: Mass of hyphae; hyphae: Filamentous structures.

• Yeast pseudohyphae: Chains of elongated budding cells.

• Mold reproduction: Asexual (spores like conidia) and sexual (zygospores, ascospores).

• Yeasts divide by budding or fission.

• Fungal infections are rising due to immunosuppression and increased use of antibiotics.

• Types of mycoses: Systemic, subcutaneous, cutaneous, superficial.

Protozoa

• Trophozoite: Active, feeding stage; cyst: Dormant, resistant stage.

• Malaria cycles: Exoerythrocytic (liver), erythrocytic (red blood cells).

• Transmission routes for Toxoplasma: Ingestion of oocysts, undercooked meat, transplacental, organ transplantation.

Helminths

• Major characteristics: Multicellular, eukaryotic, specialized tissues.

• Platyhelminthes (flatworms) vs. Nematoda (roundworms).

• Monoecious: Both sexes in one individual; dioecious: Separate sexes.

• Hosts:

  • Reservoir host: Maintains parasite in nature.

  • Intermediate host: Harbors larval stage.

  • Definitive host: Harbors adult stage.

  • Accidental host: Not usual host for parasite.

• Categorization: Cestodes (tapeworms), trematodes (flukes), nematodes (roundworms).

• Digenetic: Requires two hosts (e.g., Schistosoma).

• Body sites for S. haematobium (urinary bladder), S. japonicum (small intestine), S. mansoni (large intestine).

• Cestode structure: Scolex (head), proglottids (segments).

• Oncosphere: Larval form; cysticercus: Encysted larval stage.

• Taeniasis: Infection with Taenia tapeworms.

• Insect vectors transmit diseases (e.g., sand fly for leishmaniasis).

Chapter 13: Viruses, Viroids, and Prions

General Properties of Viruses

• Viruses and rickettsia/chlamydia are obligate intracellular parasites.

• Differences between viruses and bacteria:

  • Viruses lack ribosomes, do not divide by binary fission, are not sensitive to antibiotics.

  • Viruses are much smaller (20–300 nm) than bacteria.

• Host range: Spectrum of host cells a virus can infect (e.g., influenza infects humans, pigs).

• Virion: Complete viral particle; consists of nucleic acid and protein coat (capsid).

• Capsid composed of capsomeres; envelope may have spikes (e.g., hemagglutinin, neuraminidase).

• Hemagglutinin binds to host cell sialic acid; neuraminidase aids in viral release.

• Viral morphologies: Helical, polyhedral (e.g., icosahedron), enveloped, complex.

• Classification based on nucleic acid type and replication strategy.

Viral Multiplication and Identification

• Viruses require living cells for growth.

• Bacteriophage: Virus that infects bacteria; forms plaques on bacterial lawns.

• Animal viruses grown in cell cultures (in vitro), embryonated eggs, or live animals (in vivo).

• Cytopathic effect (CPE): Visible changes in host cells due to viral infection (e.g., cell lysis, syncytia formation).

• Serological tests: ELISA, neutralization, hemagglutination, Western blot.

• One-step growth curve: Demonstrates eclipse period (no infectious particles detected).

Bacteriophage and Animal Virus Life Cycles

• Bacteriophage multiplication: Attachment, penetration, biosynthesis, maturation, release.

• Lytic cycle: Host cell is lysed; lysogenic cycle: Phage DNA integrates as prophage.

• Lambda (λ) phage can undergo lysogeny.

• Animal virus multiplication: Attachment, penetration, uncoating, biosynthesis, maturation, release.

• Early gene products: Enzymes for replication; late gene products: Structural proteins.

• Viral transcriptase: Enzyme for RNA synthesis in some viruses.

• Retroviruses (e.g., HIV) use reverse transcriptase to synthesize DNA from RNA; DNA integrates as provirus.

• Oncogenic viruses: Can induce transformation of host cells (e.g., Herpesviridae/EBV is a DNA oncogenic virus).

• Viral infections: Acute (influenza), latent (herpes), chronic (HIV).

• Prions: Infectious proteins (e.g., cause spongiform encephalopathies like Creutzfeldt-Jakob disease).

• Viroids: Infectious RNA molecules, primarily in plants.

Chapter 14: Principles of Disease and Epidemiology

Basic Terminology

• Pathology: Study of disease.

• Etiology: Cause of disease.

• Pathogenesis: Mechanism of disease development.

• Pathogen: Disease-causing organism.

• Infection: Invasion and multiplication of pathogens.

• Opportunistic infection: Caused by organisms that do not usually cause disease.

• Disease: Abnormal state in which body function is impaired.

Microbiota and Symbiosis

• Symbiosis: Relationship between two organisms.

• Microbiota: Microorganisms that inhabit the body.

• Microbial antagonism: Competition between microbes.

• Bacteriocins: Proteins produced by bacteria to inhibit others.

• Probiotics: Live microbes that confer health benefits.

• Resident vs. transient microbiota: Permanent vs. temporary colonizers.

Disease Development and Epidemiology

• Koch’s postulates: Steps to prove causative relationship between microbe and disease.

• Symptoms: Subjective changes; signs: Objective changes; syndrome: Group of symptoms/signs.

• Communicable, contagious, and non-communicable diseases defined by transmission potential.

• Epidemiology: Study of disease occurrence.

• Incidence: New cases; prevalence: Total cases.

• Sporadic, endemic, epidemic, pandemic: Patterns of disease occurrence.

• Acute, chronic, sub-acute, latent: Duration of disease.

• Local, focal, systemic: Extent of infection.

• Sepsis, bacteremia, septicemia, toxemia, viremia: Presence of microbes or toxins in blood.

• Primary, secondary, subclinical infections: Sequence and severity.

• Predisposing factors: Age, genetics, lifestyle, etc.

• Phases of disease: Incubation, prodrome (mild early symptoms), illness, decline, convalescence.

• Reservoirs: Human, animal, nonliving; carriers and zoonoses defined.

• Transmission: Direct, indirect, droplet; mechanical and biological vectors.

• Nosocomial (hospital-acquired), community-acquired, iatrogenic (treatment-induced) infections.

• Morbidity, mortality, rates defined.

• CDC’s NNDSS: Tracks notifiable diseases in the U.S.

Sample Table: Comparison of Viruses, Bacteria, and Eukaryotic Cells

Sample Equations

• Mutation rate formula:

• Incidence rate:

• Prevalence rate:

Sample Multiple Choice Questions (with Answers)

• Which mutagen changes the spontaneous mutation rate of bacteria? Answer: d. none of the above

• The “strep” in Streptococcus pyogenes refers to: Answer: c. develop chains of cells

• Which Proteobacteria subgroup contains Yersinia pestis? Answer: c. gammaproteobacteria

• Dimorphic fungi are yeasts at ______ °C and molds at ______ °C? Answer: a. 37°C / 25°C

• Arthropod vector for leishmaniasis? Answer: c. sand fly

• Characteristic of viruses? Answer: d. intracellular parasite

• Function of influenza virus hemagglutinin? Answer: a. binds to host cell plasma membrane sialic acid

• Which is an oncogenic DNA virus? Answer: a. Herpesviridae (EBV)

• Phase of disease development with mild early symptoms? Answer: d. prodrome

Additional info: Where content was brief, academic context and definitions were added for completeness. Table and equations were inferred for study purposes.