BIO 175 Microbiology Midterm Study Guide: Chapters 1, 2, 3, 5, 7, 8, 9, 10, 14

Chapter 1 – Introduction to Microbiology

Importance of Microbiology in Clinical Practice

• Microbiology is essential for understanding infectious diseases, antibiotic stewardship, and infection control in healthcare settings.

• Healthcare-associated infections (HAIs) are a major concern; proper hand hygiene and aseptic technique are critical for prevention.

Key Historical Figures

• Antonie van Leeuwenhoek: First to observe microbes using a microscope.

• Louis Pasteur: Disproved spontaneous generation; developed pasteurization and vaccines.

• Joseph Lister: Introduced antiseptic surgery.

• Robert Koch: Established Koch's postulates for linking microbes to disease.

• Florence Nightingale: Pioneered infection control in nursing.

• Ignaz Semmelweis: Advocated hand hygiene to prevent puerperal fever.

Koch's Postulates

• Set of criteria to establish a causative relationship between a microbe and a disease.

• Limitations: Asymptomatic carriers, unculturable pathogens, and viruses that require host cells.

Classification of Life

• Three domains: Bacteria, Archaea, Eukarya (includes fungi, protists, helminths).

Symbiotic Relationships

• Commensalism: One benefits, other unaffected (e.g., skin microbiota).

• Mutualism: Both benefit (e.g., gut flora synthesizing vitamins).

• Parasitism: One benefits, one harmed (e.g., Plasmodium in malaria).

• Opportunism: Normally harmless but can cause disease if host is compromised (e.g., E. coli in UTIs).

• Zoonosis: Disease transmitted from animals to humans (e.g., rabies).

Staining and Microscopy

• Simple stain: Highlights entire organism.

• Differential stain: Distinguishes groups (e.g., Gram stain, acid-fast stain).

• Structural stain: Highlights specific structures (e.g., endospore stain).

• Gram stain: Differentiates Gram-positive (purple) and Gram-negative (pink) bacteria; guides antibiotic therapy.

• Acid-fast stain: Identifies mycolic acid-rich bacteria (e.g., Mycobacterium tuberculosis).

• Microscopy:

  • Light microscopy: General morphology.

  • Fluorescence microscopy: Specific labeling with fluorescent dyes.

  • SEM (Scanning Electron Microscopy): Surface details, high resolution.

  • TEM (Transmission Electron Microscopy): Internal structures, highest resolution.

Key Terms

• Aseptic technique, biogenesis, germ theory, microbiota/microbiome, pathogen, nosocomial infection, zoonosis, taxonomy, binomial nomenclature, resolution, magnification.

Chapter 2 – Biochemistry Basics

Atoms, Ions, Molecules, and Macromolecules

• Atoms: Basic units of matter (CHON: Carbon, Hydrogen, Oxygen, Nitrogen are most abundant in biology).

• Ions: Charged atoms or molecules.

• Molecules: Two or more atoms bonded together.

• Macromolecules: Large biological molecules (carbohydrates, lipids, proteins, nucleic acids).

Chemical Bonds

• Covalent bonds: Atoms share electrons (polar or nonpolar).

• Ionic bonds: Transfer of electrons between atoms.

• Hydrogen bonds: Weak attractions between polar molecules (important in DNA and protein structure).

• Hydrophobic interactions: Nonpolar molecules aggregate to avoid water.

Water and pH

• Water: Polar molecule, forms hydrogen bonds, excellent solvent.

• pH: Measures hydrogen ion concentration; human blood pH is tightly regulated (7.35–7.45).

• Buffer: Substance that resists pH changes.

Biomolecules

• Carbohydrates: Energy source and structural component (e.g., peptidoglycan in bacteria).

• Lipids: Membrane structure (phospholipid bilayer), energy storage, signaling (steroids).

• Proteins: Enzymes, structure, transport; made of amino acids linked by peptide bonds.

• Nucleic acids: DNA and RNA; genetic information storage and transfer.

Enzymes and Protein Structure

• Enzymes: Biological catalysts; lower activation energy for reactions.

• Protein structure: Primary (sequence), secondary (alpha-helix, beta-sheet), tertiary (3D folding), quaternary (multiple subunits).

• Denaturation: Loss of structure and function due to heat, pH, or chemicals.

Chapter 3 – Introduction to Prokaryotic Cells

Bacteria vs. Archaea vs. Eukaryotes

• Bacteria: Prokaryotic, peptidoglycan cell wall, diverse shapes.

• Archaea: Prokaryotic, unique membrane lipids, often extremophiles.

• Eukaryotes: Membrane-bound organelles, include fungi, protists, helminths.

Prokaryotic Shapes and Arrangements

• Coccus: Spherical.

• Bacillus: Rod-shaped.

• Spirillum/Spirochete: Spiral-shaped.

• Arrangements: Diplo- (pairs), strepto- (chains), staphylo- (clusters).

Cell Wall Structure

• Gram-positive: Thick peptidoglycan, teichoic acids, no outer membrane.

• Gram-negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS/endotoxin), periplasmic space.

• Clinical relevance: Gram-negative bacteria can cause septic shock via LPS release.

Extracellular Structures

• Capsule/Glycocalyx: Protection from phagocytosis, aids in biofilm formation.

• Fimbriae/Pili: Attachment to surfaces, conjugation (gene transfer).

• Flagella: Motility, chemotaxis.

• Biofilms: Communities of microbes attached to surfaces, resistant to antibiotics.

Transport Across Membranes

• Passive diffusion: Movement down concentration gradient.

• Facilitated diffusion: Uses transport proteins.

• Osmosis: Water movement across membrane.

• Active transport: Requires energy (ATP).

Endospores

• Formed by: Bacillus and Clostridium species.

• Highly resistant to heat, chemicals, and desiccation; survive autoclaving but not ethanol sterilization.

Chapter 5 – Microbial Genetics

Genotype vs. Phenotype

• Genotype: Genetic makeup.

• Phenotype: Observable traits.

DNA Structure and Central Dogma

• DNA: Double helix, antiparallel strands, base pairing (A-T, G-C).

• Central dogma: DNA → RNA → Protein.

Protein Synthesis

• Replication: DNA copied (cytoplasm in bacteria, nucleus in eukaryotes).

• Transcription: DNA to RNA (cytoplasm in bacteria, nucleus in eukaryotes).

• Translation: RNA to protein (ribosomes in cytoplasm).

Mutations

• Point mutations: Silent (no change), missense (amino acid change), nonsense (stop codon).

• Frameshift mutations: Insertion or deletion shifts reading frame.

• Mutagens: UV light, chemicals, reactive oxygen species.

Horizontal Gene Transfer

• Transformation: Uptake of naked DNA.

• Transduction: Transfer by bacteriophages.

• Conjugation: Direct cell-to-cell transfer via pilus.

Gene Regulation

• Operon: Cluster of genes under one promoter (e.g., lac and trp operons).

• Quorum sensing: Cell-density-dependent gene regulation (important in biofilms).

Chapter 7 – Fundamentals of Microbial Growth & Control

Microbial Growth

• Binary fission: Main method of bacterial reproduction.

• Growth curve phases: Lag, log (exponential), stationary, death.

Microbial Classification by Growth Conditions

• Temperature: Psychrophile (cold), mesophile (moderate), thermophile (hot), hyperthermophile (very hot).

• Oxygen: Obligate aerobe, obligate anaerobe, facultative anaerobe, microaerophile, aerotolerant.

• pH and salt tolerance: Acidophiles, alkaliphiles, halophiles.

Culture Media

• Defined vs. complex: Known vs. unknown composition.

• Selective media: Inhibits some, allows others.

• Differential media: Distinguishes based on metabolic traits.

• Enriched media: Extra nutrients for fastidious organisms.

Measuring Microbial Growth

• Direct counts: Microscopy, viable plate count (CFU/mL).

• Indirect counts: Turbidity (optical density).

Control of Microbial Growth

• Sterilization: Destroys all microbes (autoclave).

• Disinfection: Reduces pathogens on surfaces.

• Antisepsis: Reduces microbes on living tissue.

• Sanitization: Lowers microbial counts to safe levels.

• Physical methods: Autoclave, dry heat, pasteurization, filtration, UV/ionizing radiation, refrigeration.

• Chemical methods: Alcohols, halogens, phenolics, biguanides, aldehydes, ethylene oxide.

Chapter 8 – Microbial Metabolism

Metabolism Overview

• Metabolism: All chemical reactions in a cell.

• Catabolism: Breakdown of molecules, releases energy.

• Anabolism: Synthesis of molecules, requires energy.

• ATP: Universal energy currency.

Enzymes

• Lower activation energy; affected by temperature, pH, inhibitors.

Aerobic Cellular Respiration

• Glycolysis: Glucose → pyruvate; net 2 ATP, 2 NADH.

• Krebs (TCA) cycle: Pyruvate → CO2; produces NADH, FADH2, 2 ATP.

• Electron transport chain: Uses NADH/FADH2 to generate proton gradient; ATP synthase produces ATP.

• Net ATP yield: ~38 per glucose in prokaryotes.

Anaerobic Respiration and Fermentation

• Anaerobic respiration: Uses non-oxygen electron acceptors (e.g., nitrate).

• Fermentation: Organic molecule as final electron acceptor; yields 2 ATP per glucose.

• Fermentation end-products: Lactic acid, ethanol, acid + gas; used in clinical identification.

Classification by Energy and Carbon Source

• Autotroph: Uses CO2 as carbon source.

• Heterotroph: Uses organic carbon.

• Phototroph: Uses light for energy.

• Chemotroph: Uses chemicals for energy.

• Lithotroph: Uses inorganic molecules for electrons.

• Organotroph: Uses organic molecules for electrons.

Chapter 9 – Principles of Infectious Disease & Epidemiology

Disease Vocabulary

• Infection: Microbe enters and multiplies in host.

• Disease: Host function is impaired.

• Symptom: Subjective (e.g., pain).

• Sign: Objective (e.g., fever).

• Acute, chronic, latent: Duration and pattern of disease.

• Local, focal, systemic: Extent of spread.

• Primary, secondary infection: Initial vs. subsequent infection.

• Sequela: Long-term consequence.

• Communicable, contagious: Ability to spread.

• Nosocomial (HAI), iatrogenic, opportunistic: Healthcare-related and host-dependent infections.

Reservoirs and Transmission

• Reservoirs: Human, animal, environmental, asymptomatic carriers.

• Modes of transmission: Contact, droplet, airborne, vehicle, vector (mechanical, biological).

Stages of Disease

• Incubation → Prodromal → Illness → Decline → Convalescence.

Epidemiological Studies

• Cross-sectional: Snapshot in time.

• Longitudinal: Follows subjects over time.

Healthcare-Associated Infections (HAIs)

• Big Four: CAUTI (catheter-associated UTI), CLABSI (central line-associated bloodstream infection), SSI (surgical site infection), VAP (ventilator-associated pneumonia).

Key Epidemiological Terms

• Incidence rate, prevalence, attack rate, case-fatality rate, mortality rate, morbidity, endemic, epidemic, pandemic, index case, outbreak, surveillance, herd immunity, eradication, elimination.

Chapter 10 – Host–Microbe Interactions & Pathogenesis

Normal Microbiota vs. Pathogens

• Normal microbiota: Non-pathogenic organisms living on/in the body.

• Dysbiosis: Disruption of normal microbiota, leading to opportunistic infections (e.g., C. difficile after antibiotics).

Exotoxins vs. Endotoxins

• Exotoxins: Secreted proteins (e.g., tetanus, diphtheria, cholera, botulism toxins); highly potent, heat-labile, vaccines available.

• Endotoxins: Lipid A component of Gram-negative LPS; released on cell death, heat-stable, no vaccine, causes endotoxic shock.

Steps to Infection

• Portal of entry → Adherence → Invasion/nutrient acquisition → Immune evasion → Exit/transmission.

Virulence Factors

• Adhesion: Fimbriae, biofilms.

• Invasion: Hyaluronidase, collagenase, coagulase.

• Iron acquisition: Siderophores.

• Immune evasion: Capsule, IgA protease, antigenic variation, intracellular survival.

Biosafety Levels (BSL)

• BSL-1 (minimal risk) to BSL-4 (high risk, deadly pathogens).

Infection Control Precautions

• Standard precautions: For all patients.

• Transmission-based precautions: Contact, droplet, airborne; PPE selection based on route.

Chapter 14 – Vaccines & Biotechnology-Based Diagnostics

Types of Immunity

	Natural	Artificial
Active	Infection	Vaccination
Passive	Maternal antibodies	IVIG (immunoglobulin therapy)

Vaccine Types

• Live attenuated: Weakened pathogen (e.g., MMR, varicella); strong immunity, not for immunocompromised/pregnant.

• Inactivated: Killed pathogen (e.g., polio, hepatitis A).

• Subunit/recombinant: Purified antigens (e.g., HPV, hepatitis B).

• Toxoid: Inactivated toxin (e.g., tetanus, diphtheria).

• Conjugate: Linked polysaccharide to protein (e.g., Hib, pneumococcal).

• mRNA/viral vector: COVID-19 vaccines.

Herd Immunity

• High vaccination rates protect unvaccinated individuals; measles requires ~95% coverage.

Vaccine Components and Adverse Events

• Adjuvants: Enhance immune response.

• Boosters: Maintain immunity.

• Adverse events: Local reactions, fever, rare anaphylaxis or Guillain-Barré syndrome.

Diagnostic Techniques

• ELISA: Detects antigens or antibodies (direct, indirect, sandwich formats).

• Western blot: Confirms protein presence (e.g., HIV).

• Immunofluorescence: Uses fluorescent antibodies for detection.

• Agglutination: Clumping reaction for antigen/antibody detection.

• IGRA: Interferon-gamma release assay for TB.

• PCR: Amplifies DNA; detects pathogens early.

Test Interpretation

• Sensitivity: Ability to detect true positives.

• Specificity: Ability to detect true negatives.

• True positive/false positive: Correct vs. incorrect positive results.

Key Terms

• Antigen, epitope, antibody (IgG, IgM, IgA, IgE, IgD), seroconversion, titer, recombinant DNA, CRISPR, gene therapy.

Example Table: Vaccine Types and Examples

Vaccine Type	Example	Notes
Live attenuated	MMR, varicella	Strong, long-lasting; avoid in immunocompromised
Inactivated	Polio (IPV), hepatitis A	Safe for most; may need boosters
Subunit/recombinant	HPV, hepatitis B	Few side effects
Toxoid	Tetanus, diphtheria	Targets toxin, not organism
Conjugate	Hib, pneumococcal	Effective in young children
mRNA/viral vector	COVID-19 vaccines	Rapid development, no live virus

Sample Equation: pH Calculation

• pH is calculated as: $\mathrm{pH} = -\log_{10}[\mathrm{H}^+]$

Sample Equation: ATP Yield in Aerobic Respiration

• Net ATP per glucose (prokaryotes): $\mathrm{Glycolysis} + \mathrm{Krebs\ Cycle} + \mathrm{ETC} = 2 + 2 + 34 = 38~\mathrm{ATP}$

Sample Table: Comparison of Exotoxins and Endotoxins

Feature	Exotoxin	Endotoxin
Source	Gram-positive & Gram-negative bacteria	Gram-negative bacteria (LPS)
Chemical nature	Protein	Lipid A (part of LPS)
Heat stability	Heat-labile	Heat-stable
Vaccine available	Yes (toxoids)	No
Clinical effect	Specific (e.g., neurotoxic, enterotoxic)	General (fever, shock)

Additional info: These notes expand on the study guide by providing definitions, examples, and clinical context for each topic. Tables and equations are included for clarity and exam preparation.