Microbiology Study Guide: Genetics, Viruses & Prions, Microbial Growth, and Metabolism

Ch. 5: Genetics

5.1: Hereditary Basics

Genetics is the study of heredity and variation in organisms. The genotype, or genetic makeup, determines the phenotype, which is the observable traits. Genes are small segments of DNA that encode specific traits, while the genome is the entire collection of genetic material in a cell or virus.

• Genotype: The genetic composition of an organism; determines phenotype.

• Genes: Segments of DNA that code for traits.

• Genome: All genetic material in a cell or virus; can be DNA (prokaryotes, eukaryotes, viruses) or RNA (some viruses).

• Chromosomes: Packaged strands of DNA and proteins; number does not correlate with organism complexity.

• Prokaryotic Genomes: Usually 1–3 chromosomes in the nucleoid; most bacteria have a single circular chromosome.

• Eukaryotic Genomes: Larger and more complex; 6,000–24,000+ genes.

• Histone-like Proteins: Organize prokaryotic DNA.

• Plasmids: Extra-chromosomal DNA; often carry beneficial genes (e.g., antibiotic resistance).

Example: E. coli strains have 4,400–5,500 genes; eukaryotic cells may have well over 24,000 genes.

5.4: Regulating Protein Synthesis

Protein synthesis is energy-intensive, so cells regulate gene expression. Only about 20% of genes are expressed at any time. Genes are classified as house-keeping (constitutive) or facultative, depending on their expression patterns.

• House-keeping Genes: Continuously expressed; encode essential proteins.

• Facultative Genes: Expressed in response to environmental changes.

• Pre-transcriptional Regulation: Controls RNA production; includes operons.

• Operons: Groups of genes regulated together; contain promoter, operator, structural genes, and repressor protein.

• Inducible Operons: Activated by specific conditions; e.g., lac operon in E. coli is induced when lactose is present and glucose is absent.

Example: The lac operon produces lactase only when lactose is available, preventing unnecessary energy expenditure.

5.6: Genetic Variation Without Sexual Reproduction

Bacteria can exchange genetic material without cell division through horizontal gene transfer, increasing genetic diversity and adaptability.

• Vertical Gene Transfer: Genetic information passed to offspring via cell division.

• Horizontal Gene Transfer: Genetic information exchanged between cells independent of division.

• Conjugation: Transfer of plasmids via pilus; requires fertility plasmid (F factor).

• Transformation: Uptake of environmental DNA by competent cells.

• Transduction: Transfer of DNA via bacteriophage; includes generalized and specialized transduction.

Example: R plasmids confer antibiotic resistance and can be transferred between bacteria via conjugation.

Ch. 6: Viruses & Prions

6.1: General Virus Characteristics

Viruses are acellular, nonliving pathogens that require host cells for replication. They exhibit diverse structural and genomic features.

• Virion: Single infectious virus particle; consists of a protein capsid and genetic material (DNA or RNA).

• Capsid: Protein shell made of capsomeres; protects genome.

• Capsid Types: Helical, icosahedral, or complex (e.g., bacteriophages).

• Envelope: Lipid-based membrane surrounding capsid; acquired from host cell membrane.

• Naked Viruses: Lack envelope; released by cell lysis.

• Spikes (Peplomers): Glycoprotein extensions for host cell attachment; determine host range and tissue tropism.

• Viral Genome: DNA or RNA; single or double-stranded; linear or circular; usually <300 genes.

Example: Influenza A virus has hemagglutinin (HA) and neuraminidase (NA) spikes, which mutate frequently.

6.2: Classifying and Naming Viruses

Viruses are classified based on nucleic acid type, capsid symmetry, envelope presence, genome architecture, host range, and tropism.

• Host Range: Species a virus can infect; e.g., measles virus infects only humans.

• Tropism: Specificity for certain tissues or cells.

• Virus Sizes: Range from 30 nm (Rhinovirus) to 1,500 nm (Pithovirus).

6.3: Viral Replication Pathways

Viruses hijack host cell machinery to replicate. Bacteriophages and animal viruses have distinct replication pathways.

• Lytic Replication (Bacteriophages): Attachment, penetration, replication, assembly, release; host cell lyses.

• Lysogenic Replication (Temperate Phages): Phage genome integrates into host genome (prophage); can later enter lytic cycle.

• Animal Virus Replication: Attachment, penetration, uncoating, replication, assembly, release; enveloped viruses bud, naked viruses lyse host cell.

• Persistent Infections: Chronic (continuous virion release) or latent (flare-ups with dormancy).

• Oncogenic Viruses: Can cause cancer by stimulating uncontrolled cell division; e.g., human papilloma viruses (HPVs).

Example: Herpesviridae family causes latent infections such as cold sores and shingles.

6.5: Prions

Prions are infectious proteins lacking genetic material. They cause transmissible spongiform encephalopathies (TSEs), which can be inherited or acquired.

• Prions: Infectious proteins; do not replicate like viruses.

• Spongiform Encephalopathies: Neurodegenerative diseases; e.g., Creutzfeldt-Jakob disease (CJD), fatal familial insomnia.

Ch. 7: Fundamentals of Microbial Growth & Decontamination

7.1: Microbial Growth Basics

Bacterial species vary in generation time, which is the time required for a cell to divide. Growth in closed batch systems follows four distinct phases.

• Generation Time: Time for one cell division; varies by species and conditions.

• Growth Phases:

  • Lag Phase: Adjustment to environment.

  • Log Phase: Rapid exponential growth.

  • Stationary Phase: Growth rate equals death rate; nutrients decrease, waste accumulates.

  • Death Phase: Exponential cell death; some cells survive by adaptation.

• Chemostat: Device to maintain cells at a specific growth phase by adding fresh medium and removing waste.

7.2: Prokaryotic Growth Requirements

Prokaryotes adapt to various environmental conditions, including temperature, pH, oxygen, nutrients, and growth factors.

• Temperature Classifications:

  • Psychrophiles: -20°C to 10°C

  • Psychrotrophs: 0°C to 30°C; associated with foodborne illness

  • Mesophiles: 10°C to 50°C; most pathogens

  • Thermophiles: 40°C to 75°C

  • Extreme Thermophiles: 65°C to 120°C; often barophiles

• pH Classifications:

  • Acidophiles: pH 1–5

  • Neutralophiles: pH 5–8

  • Alkaliphiles: pH 9–11

• Oxygen Requirements: See Table 7.1 (not provided).

• Capnophiles: Require high CO2 levels.

• Fastidious Organisms: Require multiple specific growth factors.

Example: Listeria monocytogenes is a psychrotroph associated with foodborne illness.

7.3: Growing, Isolating, & Counting Microbes

Microbes are grown in various media, which differ in physical state, chemical composition, and function. Proper techniques are essential for collecting, isolating, and identifying microbes.

• Media Types:

  • Liquid Media: Broth; for large batch growth.

  • Solid/Semisolid Media: Agar; for isolating colonies.

  • Complex Media: Contains undefined nutrients; used for fastidious organisms.

  • Defined Media: Precisely known ingredients.

  • Differential Media: Visually distinguishes microbes; e.g., blood agar.

  • Selective Media: Promotes growth of specific microbes; e.g., Mannitol salt agar.

• Aseptic Techniques: Prevent contamination during sample collection and handling.

• Streak Plate Technique: Isolates individual colonies by decreasing cell concentration across agar.

• Identification Methods: Physical (staining, microscopy), biochemical (metabolic tests), genetic (PCR, DNA fingerprinting).

7.4: Basics of Microbial Growth Reduction & Decontamination

Microbial control strategies aim to reduce or eliminate contamination. Physical and chemical methods are used for disinfection and sterilization.

• Decontamination: Removes/reduces microbial populations.

• Disinfection: Reduces microbial numbers; used for surfaces and equipment.

• Sterilization: Eliminates all microbes, including endospores.

• Physical Methods:

  • Temperature: Refrigeration, freezing, autoclave, pasteurization, dry heat.

  • Radiation: Ionizing (gamma, X-rays) and nonionizing (UV).

  • Filtration: HEPA filters for air; membrane filters for liquids.

• Chemical Methods:

  • Germicides: Microbiocidal (kill) or microbistatic (inhibit).

  • Disinfectants: For inanimate objects.

  • Antiseptics: For living tissue.

  • Alcohols: Denature proteins; e.g., ethanol, isopropanol.

  • Aldehydes: Sterilize equipment; e.g., formaldehyde.

  • Phenols: Destroy cell walls; e.g., Lysol.

  • Halogens: Oxidize cell components; e.g., chlorine bleach.

  • Peroxygens: Strong oxidizers; e.g., hydrogen peroxide.

  • Ethylene Oxide: Sterilant for sensitive materials.

  • Detergents: Amphipathic molecules; remove substances and damage lipids.

• Selection Factors: Item use, germicide reactivity, concentration, treatment time, agent type, presence of matter, toxicity.

Ch. 8: Microbial Metabolism

8.1: Defining Metabolism

Metabolism encompasses all chemical reactions in a cell, divided into catabolic (breakdown, exergonic) and anabolic (building, endergonic) pathways. These reactions are often coupled via ATP.

• Catabolic Pathways: Break down substances; release energy.

• Anabolic Pathways: Build new substances; require energy.

• ATP: Cellular energy currency; composed of adenine, ribose, and three phosphate groups.

• ATP–ADP Cycling: Dephosphorylation releases energy; phosphorylation stores energy.

Equation:

$\text{ATP} \rightarrow \text{ADP} + \text{P} + \text{energy}$

$\text{ADP} + \text{P} + \text{energy} \rightarrow \text{ATP}$

8.2: Enzymes

Enzymes are protein catalysts that accelerate metabolic reactions by lowering activation energy. Their activity is influenced by temperature and pH.

• Active Site: Region where substrate binds.

• Enzyme-Substrate Complex: Temporary association during reaction.

• Induced Fit Model: Enzyme molds to substrate for optimal reaction.

• Factors Affecting Activity: Temperature (too low slows, too high denatures), pH (extremes denature).

8.3: Obtaining & Using Energy

Cells use redox reactions to extract energy from nutrients, recharging ADP to ATP. Oxidation involves electron loss; reduction involves electron gain.

• Oxidation: Loss of electrons; molecule becomes less negative, lower energy.

• Reduction: Gain of electrons; molecule becomes more negative, higher energy.

• Common Agents: Oxygen (oxidizing), hydrogen (reducing).

Equation:

$\text{O}_2 + 4e^- + 4H^+ \rightarrow \text{H}_2\text{O}$

$\text{H} \rightarrow \text{H}^+ + e^-$

8.4: Catabolic Process of Cellular Respiration

Cellular respiration is a major pathway for energy extraction from nutrients, primarily carbohydrates. It involves glycolysis, an intermediate step, Krebs cycle, and electron transport chain.

• Glycolysis: Initial breakdown of glucose.

• Krebs Cycle: Further oxidation of metabolites.

• Electron Transport Chain: Final stage; produces most ATP.

8.5: Other Catabolic Pathways for Oxidizing Nutrients

Fermentation allows cells to catabolize nutrients without a respiratory chain, yielding less ATP. It is used by many prokaryotes and some eukaryotes under anaerobic conditions.

• Fermentation: Incomplete oxidation; uses organic compounds as terminal electron acceptors.

• ATP Yield: ~2 ATP per glucose.

• End Products: Vary by organism; e.g., lactic acid, alcohol.

Example: Yeast fermentation produces alcohol; muscle cells produce lactic acid.

8.9: Using Metabolic Properties to Identify Bacteria

Biochemical tests are used to identify bacteria based on their metabolic profiles, which act as biochemical fingerprints.

• Oxidase Test: Detects cytochrome c oxidase.

• Catalase Test: Detects catalase enzyme; positive result produces bubbles.

• Rapid Identification: API® system, Enterotube/Enteropluri test.

Additional info:

Some tables referenced (e.g., Table 5.1, Table 7.1, Table 8.1) were not provided; key content was inferred and summarized based on standard microbiology knowledge.