MCB 2010C Midterm Study Guide: Microbiology Core Concepts (Chapters 8, 9, 10 Focus)

Foundations of Microbiology

Louis Pasteur’s S-Necked Flask Experiment

Louis Pasteur’s experiment was pivotal in disproving spontaneous generation and establishing the principle of biogenesis.

• Design: Broth was boiled in S-necked flasks to kill existing microbes. The unique flask shape prevented airborne microbes from contaminating the broth while allowing air exchange.

• Significance: No microbial growth occurred unless the flask was tilted, allowing particles to enter. This demonstrated that life does not arise spontaneously but from existing life.

• Impact: Foundation for aseptic techniques and modern microbiology.

Koch’s Postulates of Disease

Koch’s postulates are criteria to establish a causative relationship between a microbe and a disease.

• Postulate 1: The suspected pathogen must be present in all cases of the disease and absent from healthy organisms.

• Postulate 2: The pathogen must be isolated from the diseased host and grown in pure culture.

• Postulate 3: The cultured pathogen must cause the same disease when introduced into a healthy, susceptible host.

• Postulate 4: The pathogen must be re-isolated from the newly infected host and shown to be the same as the original organism.

• Limitations: Some pathogens cannot be cultured, and some diseases are caused by multiple agents or only in humans.

Binomial Nomenclature

Scientific names use a two-part format: Genus species.

• Conventions: Genus is capitalized, species is lowercase, both italicized (e.g., Escherichia coli).

• Importance: Provides universal, standardized naming for organisms.

Microbial Staining and Culturing Techniques

Acid-Fast Stain

The acid-fast stain differentiates bacteria with waxy cell walls (e.g., Mycobacterium).

• Steps: Primary stain (carbol fuchsin), heat, acid-alcohol decolorizer, counterstain (methylene blue).

• Chemistry: Mycolic acids in cell walls retain carbol fuchsin despite acid-alcohol wash.

• Usefulness: Identifies acid-fast bacteria, important in diagnosing tuberculosis and leprosy.

Streak Plate Technique

Used to isolate pure bacterial colonies on solid media.

• Method: Sequentially spread a sample over quadrants of an agar plate to dilute cells.

• Purpose: Isolates single colonies for further study.

Bacterial Colony

• Definition: A visible mass of microbial cells arising from a single cell or group of identical cells.

Gram Staining

Differentiates bacteria based on cell wall structure.

• Steps: Crystal violet (primary stain), iodine (mordant), alcohol (decolorizer), safranin (counterstain).

• Results: Gram-positive bacteria appear purple; Gram-negative appear pink/red.

• Troubleshooting: Omitting decolorizer results in all cells appearing purple; omitting mordant may cause weak staining.

Microbial Cell Structure and Classification

Bacterial Cell Shapes and Arrangements

• Shapes: Coccus (spherical), bacillus (rod-shaped), spirillum (spiral), vibrio (comma-shaped), spirochete (flexible spiral).

• Arrangements: Chains (strepto-), clusters (staphylo-), pairs (diplo-), tetrads, sarcinae.

Extracellular Structures

• Capsules: Protective, anti-phagocytic polysaccharide layers.

• Fimbriae/Pili: Attachment and genetic exchange.

• Flagella: Motility; arrangements include monotrichous, lophotrichous, amphitrichous, peritrichous.

Bacterial Endospores

• Structure: Highly resistant, dormant forms produced by some Gram-positive bacteria (e.g., Bacillus, Clostridium).

• Function: Survival under harsh conditions (heat, desiccation, chemicals).

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes: No nucleus, circular DNA, 70S ribosomes, no membrane-bound organelles.

• Eukaryotes: Nucleus, linear DNA, 80S ribosomes, membrane-bound organelles (mitochondria, ER, Golgi, etc.).

Taxonomic Kingdoms

Kingdom	Key Features	Examples
Animalia	Multicellular, heterotrophic, no cell walls	Humans, insects
Plantae	Multicellular, autotrophic, cell walls (cellulose)	Trees, mosses
Fungi	Unicellular/multicellular, chitin cell walls, decomposers	Yeasts, molds
Protista	Mostly unicellular, diverse nutrition	Amoeba, algae
Bacteria	Prokaryotic, peptidoglycan cell walls	Escherichia coli
Archaea	Prokaryotic, unique membranes, extremophiles	Halophiles, thermophiles

Fungal Infections

• Ringworm: A superficial fungal infection (not a worm) caused by dermatophytes.

• Mycoses: Fungal diseases; often difficult to treat due to similarity to human cells and resistance to antifungals.

Microbial Genetics

DNA and RNA Structure

• DNA: Double helix, deoxyribose sugar, bases A-T, G-C.

• RNA: Single-stranded, ribose sugar, bases A-U, G-C.

Epigenome

• Definition: Chemical modifications to DNA/histones that regulate gene expression without altering the DNA sequence.

DNA Replication

• Key Enzymes: Helicase (unwinds DNA), DNA polymerase (synthesizes new strand), primase (lays RNA primer), ligase (joins fragments).

• Process: Semi-conservative; each new DNA molecule has one old and one new strand.

Building Blocks of DNA and RNA

• Nucleotides: Composed of a phosphate group, a five-carbon sugar (deoxyribose or ribose), and a nitrogenous base.

Protein Synthesis

• Transcription: DNA to mRNA in the nucleus (eukaryotes) or cytoplasm (prokaryotes).

• Translation: mRNA to protein at the ribosome.

Horizontal Gene Transfer in Bacteria

• Transformation: Uptake of naked DNA from the environment.

• Transduction: Transfer via bacteriophages (viruses).

• Conjugation: Direct transfer via pilus between bacteria.

Mutations

• Types: Point mutations (silent, missense, nonsense), insertions, deletions, frameshifts.

• Outcomes: Can be neutral, beneficial, or harmful.

Viruses and Prions

Viruses: Structure and Replication

• Structure: Nucleic acid (DNA or RNA), protein capsid, sometimes lipid envelope.

• Replication Stages: Attachment, penetration, uncoating, synthesis, assembly, release.

• Release Mechanisms: Budding (enveloped viruses), lysis (non-enveloped viruses).

Viral Evolution

• High Mutation Rates: Especially in RNA viruses due to lack of proofreading.

• Genetic Drift: Small, gradual changes in viral genome.

• Genetic Shift: Major changes due to reassortment (e.g., influenza).

Types of Viral Infections

• Acute: Rapid onset, short duration (e.g., influenza).

• Chronic: Persistent, long-term (e.g., hepatitis B).

• Latent: Dormant periods with reactivation (e.g., herpes simplex).

Oncogenic Viruses

• Definition: Viruses that can cause cancer (e.g., HPV, EBV).

Prions

• Definition: Infectious proteins causing neurodegenerative diseases (e.g., Creutzfeldt-Jakob disease).

Microbial Metabolism

Catabolic and Anabolic Reactions

• Catabolism: Breakdown of molecules to release energy.

• Anabolism: Synthesis of complex molecules from simpler ones; requires energy.

• Interconnection: Catabolic reactions provide energy and building blocks for anabolic reactions.

Enzymes and Coenzymes

• Enzymes: Biological catalysts that speed up reactions by lowering activation energy.

• Coenzymes: Organic molecules (often vitamins) that assist enzymes (e.g., NAD+, FAD).

Cellular Respiration Pathways

Pathway	Location	Key Inputs	Key Outputs
Glycolysis	Cytoplasm	Glucose	2 ATP, 2 NADH, 2 pyruvate
Intermediate Step	Cytoplasm (prokaryotes), mitochondria (eukaryotes)	Pyruvate	Acetyl-CoA, CO2, NADH
Krebs Cycle	Cytoplasm (prokaryotes), mitochondria (eukaryotes)	Acetyl-CoA	2 ATP, 6 NADH, 2 FADH2, CO2
Electron Transport Chain	Cell membrane (prokaryotes), inner mitochondrial membrane (eukaryotes)	NADH, FADH2, O2 (aerobic)	~34 ATP, H2O

• CO2 Loss: Occurs during intermediate step and Krebs cycle.

Aerobic vs. Anaerobic Respiration

• Aerobic: Uses O2 as final electron acceptor; higher ATP yield.

• Anaerobic: Uses other inorganic molecules (e.g., nitrate, sulfate); lower ATP yield.

Fermentation

• Definition: Anaerobic process; regenerates NAD+ from NADH, allowing glycolysis to continue.

• Benefits: Enables ATP production without oxygen; produces various end products (lactic acid, ethanol).

Principles of Infectious Disease and Epidemiology

Pathogen Types

• True Pathogen: Causes disease in healthy hosts.

• Opportunistic Pathogen: Causes disease in immunocompromised hosts.

Key Epidemiological Terms

Term	Definition
Endemic	Constantly present in a population
Pandemic	Worldwide epidemic
Epidemic	Sudden increase in cases in a region
Immunocompromised Host	Weakened immune system
Virulence	Degree of pathogenicity
Pathogenicity	Ability to cause disease
Attenuated Pathogen	Weakened form, less virulent

Antiseptics, Disinfectants, and Microbial Control

• Antiseptic: Used on living tissue to reduce microbes.

• Disinfectant: Used on inanimate objects to destroy microbes.

• Microbiostatic: Inhibits growth.

• Microbiocidal: Kills microbes.

Oxygen Requirements of Bacteria

Type	Oxygen Requirement
Aerotolerant Anaerobe	Does not use O2 but tolerates it
Microaerophile	Requires low O2
Facultative Anaerobe	Can use O2 or grow without it
Obligate Aerobe	Requires O2
Obligate Anaerobe	Cannot tolerate O2

Physical Requirements for Growth

Term	Definition
Decimal Reduction Time (D-value)	Time to kill 90% of microbes at a given temperature
Thermal Death Point	Lowest temperature to kill all microbes in 10 min
Thermal Death Time	Time to kill all microbes at a set temperature
Barophiles	Grow best under high pressure
Acidophiles	Grow best at low pH
Halophiles	Grow best in high salt
Neutralophiles	Grow best at neutral pH
Psychrophiles	Grow best at low temperatures

Equipment and Germicides

Category	Examples
Critical Equipment	Surgical instruments, needles
Non-critical Equipment	Stethoscopes, blood pressure cuffs
High-level Germicides	Kill all microbes, including spores
Intermediate-level Germicides	Kill mycobacteria, most viruses, and bacteria
Low-level Germicides	Kill some viruses and bacteria

Emerging and Reemerging Pathogens

• Emerging Pathogen: Newly identified or previously rare.

• Reemerging Pathogen: Previously controlled but increasing in incidence.

Pathogen Sources and Transmission

• Exogenous Pathogen: Originates outside the host.

• Endogenous Pathogen: Originates from host’s own flora.

• Normal Flora: Microbes normally present in/on the body.

• Biological Vector: Organism that transmits pathogen and is part of its life cycle (e.g., mosquito for malaria).

• Mechanical Vector: Transmits pathogen without being infected (e.g., fly landing on food).

• Source: Immediate origin of infection.

• Reservoir: Long-term host or environment for pathogen.

• Asymptomatic Carrier: Infected but shows no symptoms.

• Chronic Carrier: Harbors pathogen long-term.

Morbidity and Mortality

• Morbidity: Incidence of disease.

• Mortality: Incidence of death.

ID50 and LD50

• ID50: Infectious dose for 50% of population.

• LD50: Lethal dose for 50% of population.

Toxemia and Ribozymes

• Toxemia: Presence of toxins in the blood.

• Ribozymes: RNA molecules with enzymatic activity.

Disease Transmission Mechanisms

• Direct Transmission: Physical contact (e.g., touching, droplets).

• Indirect Transmission: Via fomites, vectors, or airborne particles.

Culture Media Types

Type	Description
Complex Media	Contains unknown components (e.g., nutrient broth)
Synthetic/Defined Media	All components and concentrations known
Differential Media	Distinguishes microbes by biochemical reactions
Selective Media	Suppresses unwanted microbes, encourages desired ones

Healthcare-Acquired Infections (HAIs)

• Definition: Infections acquired in healthcare settings.

• Examples: MRSA, C. difficile, catheter-associated UTIs.

Septic Shock

• Definition: Life-threatening low blood pressure due to infection.

• Common Causes: Gram-negative bacteria (due to endotoxin/LPS).

• Signs/Symptoms: Fever, hypotension, organ dysfunction.

Disease Eradication

• Criteria: No new cases worldwide, no natural reservoirs, effective intervention available.

Immune Evasion Mechanisms

• Antigenic Variation: Altering surface proteins to avoid immune detection.

• Latency: Remaining dormant within host cells.

• Intracellular Survival: Hiding inside host cells.

Stages of Infectious Disease

Stage	Features
Incubation	Time between infection and symptoms
Prodromal	Early, mild symptoms
Acute	Peak of illness
Decline	Symptoms subside
Convalescence	Recovery period

Endotoxins vs. Exotoxins

Type	Source	Properties
Endotoxin	Gram-negative bacteria (LPS)	Heat stable, causes fever/shock
Exotoxin	Gram-positive/negative bacteria	Proteins, heat labile, specific effects

Classes of Exotoxins

• Type I: Superantigens (stimulate immune response).

• Type II: Membrane-disrupting toxins.

• Type III: A-B toxins (active and binding components).

Biosafety Levels (BSL)

Level	Description
BSL-1	Non-pathogenic microbes
BSL-2	Moderate risk, standard precautions
BSL-3	Serious/lethal pathogens, controlled access
BSL-4	High-risk, life-threatening agents, maximum containment

Diagnostic Test Specificity vs. Sensitivity

• Specificity: Ability to correctly identify those without disease (true negatives).

• Sensitivity: Ability to correctly identify those with disease (true positives).

Reportable Infections and Public Health

• Obligations: Healthcare providers must report certain infections to public health authorities for surveillance and control.

Disease Eradication Candidates

• Factors: No animal reservoir, effective vaccine, clear symptoms, limited transmission, strong public health infrastructure.