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 the study of microscopic organisms, including bacteria, viruses, fungi, and protozoa.

• Understanding microbiology is essential for preventing healthcare-associated infections (HAIs) and practicing antibiotic stewardship.

• Clinical practice relies on microbiological techniques for diagnosis, infection control, and treatment selection.

Historical Contributions

• 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: Demonstrated the importance of hand hygiene.

Koch's Postulates and Limitations

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

• Limitations include asymptomatic carriers, unculturable pathogens, and viruses that require host cells for growth.

Classification of Life

• Three domains: Bacteria, Archaea, Eukarya.

• Bacteria and Archaea are prokaryotes; Eukarya includes fungi, protists, and 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 defenses are compromised (e.g., E. coli in UTIs).

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

Staining and Microscopy

• Simple stains: Highlight entire organism.

• Differential stains: Distinguish cell types (e.g., Gram stain for Gram-positive vs. Gram-negative; acid-fast stain for Mycobacterium).

• Structural stains: Visualize specific structures (e.g., endospores).

• Microscopy types:

  • Light microscopy: General morphology.

  • Fluorescence microscopy: Specific labeling.

  • Scanning Electron Microscopy (SEM): Surface details.

  • Transmission Electron Microscopy (TEM): Internal structures.

Key Terms

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

Example:

A Gram stain of cerebrospinal fluid can rapidly guide empiric therapy for suspected bacterial meningitis.

Chapter 2 – Biochemistry Basics

Atoms, Bonds, and Water

• Atoms are the basic units of matter; ions are charged atoms; molecules are combinations of atoms.

• Major biological elements: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N).

• Bond types:

  • Covalent bonds: Shared electrons (strong; hold protein backbone).

  • Ionic bonds: Electron transfer (form salts).

  • Hydrogen bonds: Weak attractions (hold DNA double helix).

  • Hydrophobic interactions: Nonpolar molecules cluster in water.

• Water is polar, forms hydrogen bonds, and is an excellent solvent.

pH and Buffers

• pH measures hydrogen ion concentration: $\mathrm{pH} = -\log_{10}[\mathrm{H}^+]$

• Human blood pH is tightly regulated (~7.35–7.45); pathogens can disrupt this balance.

• Buffers help maintain pH stability.

Biomolecules

• Carbohydrates: Energy and structure (e.g., peptidoglycan in bacteria).

• Lipids: Membranes (phospholipid bilayer), energy storage.

• Nucleic acids: Genetic information (DNA, RNA).

• Proteins: Enzymes, structure, signaling; built from amino acids.

Enzymes and Protein Structure

• Enzymes are biological catalysts; lower activation energy.

• Protein structure: primary, secondary, tertiary, quaternary.

• Denaturation (by heat, acid, etc.) disrupts protein function.

Example:

Penicillin targets peptidoglycan synthesis, which is unique to bacteria.

Chapter 3 – Introduction to Prokaryotic Cells

Prokaryotes vs. Eukaryotes

• Bacteria and archaea are prokaryotes (no nucleus); eukaryotes have a nucleus and organelles.

Shapes and Arrangements

• Common shapes: coccus (spherical), bacillus (rod), spirillum/spirochete (spiral).

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

Cell Wall Structure

• Gram-positive: Thick peptidoglycan, teichoic acids.

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

• Cell wall structure affects antibiotic susceptibility and immune response.

Extracellular Structures

• Capsule/glycocalyx: Protection, immune evasion.

• Fimbriae/pili: Attachment.

• Flagella: Motility (chemotaxis).

• Biofilms: Communities of microbes attached to surfaces.

Transport and Survival Mechanisms

• Transport: Passive diffusion, facilitated diffusion, osmosis, active transport.

• Endospores: Dormant, resistant forms (e.g., Bacillus, Clostridium); survive harsh conditions.

Example:

Clostridioides difficile spores resist alcohol-based sanitizers; require soap and water for removal.

Chapter 5 – Microbial Genetics

Genotype, Phenotype, and DNA Structure

• Genotype: Genetic makeup; phenotype: Observable traits.

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

• Central dogma: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

Protein Synthesis

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

• Transcription: DNA to RNA.

• Translation: RNA to protein (ribosomes).

Mutations and Gene Transfer

• Point mutations: Silent, missense, nonsense.

• Frameshift mutations: Insertions/deletions shift reading frame.

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

• Horizontal gene transfer:

  • Transformation: Uptake of naked DNA.

  • Transduction: Bacteriophage-mediated.

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

• Operons: Gene clusters regulated together (e.g., lac, trp operons).

Example:

Conjugation spreads antibiotic resistance genes (e.g., MRSA, ESBL E. coli) in hospitals.

Chapter 7 – Fundamentals of Microbial Growth & Control

Microbial Growth

• Binary fission: Main method of bacterial reproduction.

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

• Classification by environment:

  • Temperature: Psychrophile, mesophile, thermophile, hyperthermophile.

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

  • pH and salt tolerance also important.

Culture Media and Cell Counts

• Defined vs. complex media; selective vs. differential vs. enriched media.

• Cell counts: Direct (microscopy, plate count), indirect (turbidity).

Control Methods

• Sterilization: Destroys all microbes (autoclave).

• Disinfection: Reduces pathogens on surfaces.

• Antisepsis: Reduces microbes on skin.

• Sanitization: Lowers microbial load to safe levels.

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

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

Example:

Endospores require autoclaving (121°C, 15 psi) for sterilization; alcohol is insufficient.

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 is the universal energy currency.

Enzymes and Energy Production

• Enzymes lower activation energy; affected by temperature, pH, inhibitors.

• Stages of aerobic respiration:

  • Glycolysis: Glucose to pyruvate; net 2 ATP.

  • Krebs (TCA) cycle: Pyruvate oxidation; produces NADH, FADH2, CO2.

  • Electron transport chain: Generates proton motive force; ATP synthase produces ATP.

• Net ATP yield (aerobic): ~38 per glucose.

Respiration Types and Fermentation

• Aerobic respiration: O2 as final electron acceptor.

• Anaerobic respiration: Other inorganic acceptors (e.g., nitrate).

• Fermentation: Organic molecules as acceptors; yields 2 ATP.

• Fermentation end-products (lactic acid, ethanol) aid in microbe identification.

Microbial Nutrition

• Classified by carbon and energy source:

  • Autotroph: CO2 as carbon source.

  • Heterotroph: Organic carbon.

  • Phototroph: Light energy.

  • Chemotroph: Chemical energy.

  • Lithotroph: Inorganic electron donors.

  • Organotroph: Organic electron donors.

Example:

Clostridium species are obligate anaerobes; thrive in oxygen-poor wounds.

Chapter 9 – Principles of Infectious Disease & Epidemiology

Disease Terminology

• Infection: Microbe enters host; disease: Host damage occurs.

• Symptom: Subjective (e.g., pain); sign: Objective (e.g., fever).

• Course: Acute, chronic, latent.

• Spread: Local, focal, systemic.

• Primary vs. secondary infection; sequela: Long-term consequence.

Reservoirs and Transmission

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

• Transmission: Contact, droplet, airborne, vehicle, vector (mechanical/biological).

Stages of Disease

• Incubation → prodromal → illness → decline → convalescence.

Epidemiology Concepts

• Incidence, prevalence, attack rate, case-fatality rate, morbidity, mortality.

• Outbreak, endemic, epidemic, pandemic, index case.

• Study types: Cross-sectional vs. longitudinal.

• HAIs: CAUTI, CLABSI, SSI, VAP.

Example:

Hand hygiene is the most effective way to break the chain of infection.

Chapter 10 – Host–Microbe Interactions & Pathogenesis

Normal Microbiota and Pathogenesis

• Normal microbiota: Non-pathogenic residents; dysbiosis can lead to opportunistic infections.

• Pathogen: Causes disease; virulence: Degree of pathogenicity.

Exotoxins vs. Endotoxins

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

• Endotoxins: Lipid A of LPS (Gram-negatives); less potent, heat-stable, no vaccine.

Steps to Infection

• Portal of entry → adherence → invasion/nutrient acquisition → immune evasion → exit/transmission.

• Virulence factors: Fimbriae, biofilms (adhesion); enzymes (invasion); siderophores (iron acquisition); capsule, antigenic variation (immune evasion).

Biosafety and Precautions

• Biosafety levels (BSL-1 to BSL-4) correspond to pathogen risk.

• Standard and transmission-based precautions (contact, droplet, airborne) guide PPE selection.

Example:

Endotoxic shock from Gram-negative bacteria requires rapid identification and management in the ICU.

Chapter 14 – Vaccines & Biotechnology-Based Diagnostics

Immunity Types

• Active immunity: Host produces antibodies (natural: infection; artificial: vaccination).

• Passive immunity: Antibodies received (natural: maternal; artificial: IVIG).

	Natural	Artificial
Active	Infection	Vaccination
Passive	Maternal antibodies	IVIG, antitoxin

Vaccine Types

• Live attenuated: Weakened pathogen (e.g., MMR); strong, long-lasting immunity; avoid in immunocompromised/pregnant.

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

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

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

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

• mRNA/viral vector: Genetic material encoding antigen (e.g., COVID-19 vaccines).

Herd Immunity and Adjuvants

• Herd immunity: High coverage protects vulnerable individuals; measles requires ~95% coverage.

• Adjuvants: Enhance immune response; some vaccines need boosters.

Diagnostics and Interpretation

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

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

• Immunofluorescence: Visualizes antigens with fluorescent antibodies.

• Agglutination: Detects antigen-antibody reactions.

• IGRA: Measures T-cell response to TB antigens.

• PCR: Amplifies DNA; detects pathogens early.

• Sensitivity: True positive rate; specificity: True negative rate.

Example:

Live attenuated vaccines (e.g., MMR) are contraindicated in pregnancy and severe immunodeficiency.