Microbiology Exam 2 Study Guide: Genetics, Classification, Prokaryotes, Eukaryotes, Viruses, and Disease Principles

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Microbial Genetics

Key Terms in Genetics

Genetics is the study of heredity and variation in organisms. Understanding genetic concepts is fundamental to microbiology.

Gene: A segment of DNA that codes for a functional product, usually a protein.
Chromosome: A structure containing DNA that physically carries hereditary information.
Genome: The complete set of genes or genetic material present in a cell or organism.
Genomics: The study of genomes, including their structure, function, evolution, and mapping.
Genotype: The genetic makeup of an organism.
Phenotype: The observable characteristics of an organism resulting from the genotype.

Bacterial DNA Structure

Bacterial DNA is typically a single, circular chromosome located in the nucleoid region. Some bacteria also possess plasmids, which are small, circular DNA molecules.

Plasmids: Extrachromosomal DNA elements that replicate independently and often carry genes for antibiotic resistance or virulence.

Gene Transfer Mechanisms

Bacteria can exchange genetic material through vertical and horizontal gene transfer.

Vertical gene transfer: Transmission of genetic material from parent to offspring.
Horizontal gene transfer: Transfer of genes between organisms, not through inheritance. Includes:
- 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 Mutagenic Agents

Mutations are changes in the DNA sequence. They can occur spontaneously or be induced by mutagens.

Mutation: Any change in the nucleotide sequence of DNA.
Mutagen: An agent that causes mutations (e.g., chemicals, radiation).
Spontaneous mutation: Occurs naturally without external influence.
Mutation rate: The frequency at which mutations occur.
Mutagenic agents: Examples include nitrous acid, ionizing radiation, and UV radiation.

Genetic Recombination

Recombination in bacteria increases genetic diversity and can affect traits such as antibiotic resistance.

Transposons: DNA sequences that can move from one location to another within the genome, unlike plasmids which replicate independently.

Role of Plasmids in Biotechnology

Plasmids are essential tools in recombinant DNA technology, allowing for gene cloning and expression in bacteria.

Types of plasmids: Conjugative plasmids, resistance plasmids, and virulence plasmids.

Classification of Microorganisms

Taxonomy and Phylogeny

Taxonomy is the science of classifying organisms, while phylogeny refers to their evolutionary relationships.

G+C ratio: The proportion of guanine and cytosine bases in DNA, used in phylogenetic classification.
Three-domain system: Classification into Bacteria, Archaea, and Eukarya based on molecular evidence.
Scientific nomenclature: Provides a standardized naming system for organisms.
Subspecies: A taxonomic rank below species, based on genetic or phenotypic differences.

Eukaryotic Kingdoms and Virus Classification

Four eukaryotic kingdoms: Animalia, Plantae, Fungi, Protista.
Unicellular vs. multicellular: Protista and some Fungi are unicellular; Animalia and Plantae are multicellular.
Viruses: Not classified in any domain due to lack of cellular structure and metabolism.
Viral species: A group of viruses sharing genetic and ecological characteristics.

Microbial Identification Methods

Correct identification of microbes is crucial for diagnosis and treatment.

Morphological characteristics: Shape, arrangement, and staining properties.
Differential staining: Techniques like Gram staining and acid-fast staining.
Biochemical testing: Tests for metabolic activities (e.g., fermentation, enzyme production).
Less common techniques: Include molecular methods, serological tests, and phage typing.

The Prokaryotes: Domains Bacteria and Archaea

Prokaryotic Domains

Bacteria and Archaea are the two prokaryotic domains, distinguished by cell wall composition and genetic differences.

Archaea extremophiles: Thermophiles, halophiles, acidophiles, methanogens, psychrophiles.

Proteobacteria and Human Disease

Proteobacteria is a major phylum of Gram-negative bacteria, subdivided into classes with clinical relevance.

Subgroups: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria.
Example: Yersinia pestis (plague) is a Gammaproteobacteria.

Other Bacterial Groups

Chlamydiae: Obligate intracellular pathogens; transmitted differently from Rickettsia.
Bacteroidaceae, Prevotellaceae, Fusobacteriaceae: Anaerobic bacteria common in human gut.
Spirochaetes: Spiral-shaped bacteria; includes Treponema (syphilis), Borrelia (Lyme disease), Leptospira (leptospirosis).
Firmicutes vs. Actinobacteria: Differentiated by G+C content; Firmicutes have low G+C, Actinobacteria have high G+C.
Mycoplasmatales: Lack cell walls, small genome, pleomorphic, require sterols, cause diseases like pneumonia.

The Eukaryotes: Fungi, Algae, Protozoa, and Helminths

Fungi

Fungi are heterotrophic eukaryotes that absorb nutrients from their environment.

Mycology: Study of fungi.
Mycosis: Fungal infection.
Molds vs. Yeasts: Molds are multicellular, grow at 25°C; yeasts are unicellular, grow at 37°C.
Dimorphism: Ability to exist as both mold and yeast forms depending on temperature.
Mycelium and hyphae: Mycelium is a mass of hyphae (filamentous structures).
Pseudohyphae: Chains of yeast cells formed by incomplete budding.
Reproduction: Molds reproduce sexually and asexually via spores; yeasts divide by budding.
Types of mycoses: Systemic, subcutaneous, cutaneous, superficial.

Protozoa

Trophozoite: Active, feeding stage.
Cyst: Dormant, resistant stage.
Malaria cycles: Exoerythrocytic (liver), erythrocytic (blood).
Transmission routes for Toxoplasma: Ingestion of oocysts, undercooked meat, congenital, blood transfusion.

Helminths

Platyhelminthes: Flatworms (cestodes, trematodes).
Nematoda: Roundworms.
Monoecious: Both sexes in one organism.
Dioecious: Separate male and female organisms.
Hosts: Reservoir, intermediate, accidental, definitive.
Digenetic: Life cycle involving two hosts (e.g., Schistosoma).
Oncosphere: Larval form in cestodes.
Cysticercus: Encysted larval stage.
Taeniasis: Infection with Taenia species.
Insect vectors: Sand fly (leishmaniasis), mosquito (malaria), etc.

Viruses, Viroids, and Prions

Virus Structure and Classification

Viruses are acellular, obligate intracellular parasites with diverse structures and replication strategies.

Host range: The spectrum of hosts a virus can infect (e.g., influenza infects humans and birds).
Virion: Complete virus particle; consists of nucleic acid and protein coat (capsid).
Capsid and capsomeres: Capsid is made of protein subunits called capsomeres.
Envelope and spikes: Some viruses have a lipid envelope with glycoprotein spikes.
Hemagglutinin (HA): Binds to host cell sialic acid; important for viral entry and identification.
Neuraminidase (NA): Facilitates viral release from host cells.
Viral morphologies: Helical, polyhedral, enveloped, complex.
Icosahedron: 20-sided polyhedral structure.
Classification: Based on nucleic acid type (DNA, RNA, retrovirus) and structure.

Viral Replication and Identification

Bacteriophage: Virus that infects bacteria; forms plaques on bacterial lawns.
Animal virus growth: In vitro (cell cultures), in vivo (embryonated eggs, live animals).
Cytopathic effect (CPE): Visible changes in host cells due to viral infection (e.g., cell lysis, inclusion bodies).
Serological tests: ELISA, neutralization, hemagglutination, Western blot.
One-step growth curve: Describes viral replication; eclipse period is the time when no infectious virus is detected.

Bacteriophage Multiplication

Lytic cycle: Virus replicates and lyses host cell.
Lysogenic cycle: Viral DNA integrates into host genome as a prophage.
Phage conversion: Host cell acquires new traits from prophage.
Transduction: Transfer of bacterial genes via phage.

Animal Virus Multiplication

Six phases: Attachment, penetration, uncoating, biosynthesis, maturation, release.
Early vs. late gene products: Early genes regulate replication; late genes form structural proteins.
Viral transcriptase: Enzyme for viral RNA synthesis.

Oncogenic Viruses and Prions

Oncogenic viruses: Cause cancer; classified as DNA or RNA oncogenic (e.g., Herpesviridae, Retroviridae).
Retrovirus: RNA virus with reverse transcriptase; forms provirus in host genome.
Transformation: Conversion of normal cell to cancerous cell.
Proto-oncogene: Normal gene that can become oncogenic.
Tumor-specific transplant antigens: Unique antigens on transformed cells.
Prion: Infectious protein causing spongiform encephalopathies (e.g., Creutzfeldt-Jakob disease).
Viroid: Infectious RNA molecule affecting plants.

Principles of Disease and Epidemiology

Pathology and Disease Terms

Understanding disease mechanisms and epidemiology is essential for infection control.

Pathology: Study of disease.
Etiology: Cause of disease.
Pathogenesis: Development of disease.
Pathogen: Disease-causing organism.
Infection: Invasion and multiplication of pathogens.
Opportunistic infection: Infection by organisms that cause disease when host defenses are compromised.
Disease: Any deviation from normal health.

Microbiota and Symbiosis

Symbiosis: Relationship between two organisms.
Microbiota: Microbial community in 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: Resident are permanent; transient are temporary.

Koch's Postulates and Disease Classification

Koch's postulates: Sequence to prove a microbe causes a disease.
Symptom: Subjective evidence of disease.
Sign: Objective evidence of disease.
Syndrome: Group of symptoms/signs.
Communicable disease: Spread from person to person.
Contagious disease: Easily spread.
Non-communicable disease: Not spread between people.

Epidemiology and Disease Patterns

Epidemiology: Study of disease distribution.
Incidence: New cases in a time period.
Prevalence: Total cases at a given time.
Sporadic disease: Occurs occasionally.
Outbreak: Sudden increase in cases.
Herd immunity: Resistance in a population due to immunity.
Endemic: Constant presence.
Epidemic: Sudden increase.
Pandemic: Worldwide epidemic.

Types and Progression of Disease

Acute: Rapid onset, short duration.
Chronic: Slow onset, long duration.
Sub-acute: Intermediate.
Latent: Inactive for a period.
Local, focal, systemic: Localized, limited, or widespread infection.
Sepsis: Systemic inflammatory response.
Bacteremia: Bacteria in blood.
Septicemia: Active infection in blood.
Toxemia: Toxins in blood.
Viremia: Viruses in blood.
Primary, secondary, subclinical infection: Initial, subsequent, or asymptomatic infection.

Predisposing Factors and Disease Development

Predisposing factors: Age, gender, genetics, lifestyle, environment, immunosuppression, etc.
Phases of disease: Incubation, prodrome (mild early symptoms), illness, decline, convalescence.

Reservoirs and Transmission

Reservoirs: Human, animal, nonliving.
Carriers: Asymptomatic hosts.
Zoonoses: Diseases from animals.
Mechanical vs. biological transmission: Passive vs. active transfer by vectors.
Transmission routes: Contact, vehicle, vector.
Direct, indirect, droplet: Modes of contact transmission.
Community-acquired, nosocomial, iatrogenic: Types of infections based on origin.

Morbidity and Mortality

Morbidity: Illness rate.
Mortality: Death rate.
Morbidity rate: Number of cases per population.
Mortality rate: Number of deaths per population.
CDC NNDSS: National Notifiable Diseases Surveillance System for tracking diseases.

Sample Table: Proteobacteria Subgroups and Associated Diseases

Subgroup	Example Genus/Species	Associated Disease
Alphaproteobacteria	Rickettsia	Typhus
Betaproteobacteria	Neisseria	Meningitis, Gonorrhea
Gammaproteobacteria	Yersinia pestis	Plague
Deltaproteobacteria	Desulfovibrio	Not typically pathogenic
Epsilonproteobacteria	Campylobacter	Gastroenteritis

Sample Table: Types of Mycoses

Type	Site of Infection	Example
Systemic	Internal organs	Histoplasmosis
Subcutaneous	Under skin	Sporotrichosis
Cutaneous	Skin, hair, nails	Ringworm
Superficial	Surface of skin	Pityriasis versicolor

Sample Table: Viral Morphologies

Type	Structure	Example
Helical	Rod-shaped	Tobacco mosaic virus
Polyhedral	Icosahedral	Adenovirus
Enveloped	Lipid envelope	Influenza virus
Complex	Multiple structures	Bacteriophage

Sample Table: Disease Transmission Modes

Mode	Description	Example
Direct contact	Person-to-person	Common cold
Indirect contact	Via fomites	Influenza
Droplet	Short-range aerosols	COVID-19
Vehicle	Food, water, air	Salmonellosis
Vector	Arthropod transmission	Malaria (mosquito)

Sample Equations

Mutation Rate Equation:

Incidence Rate Equation:

Prevalence Rate Equation:

One-Step Growth Curve (Eclipse Period):

G+C Ratio Calculation:

Example: The sand fly is the arthropod vector for leishmaniasis. Dimorphic fungi are yeasts at 37°C and molds at 25°C. Herpesviridae (EBV) is an oncogenic DNA virus. The prodrome phase of disease development demonstrates mild early symptoms.

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