Comprehensive Study Guide for General Microbiology (BIO 240)

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Introduction to Microbiology

Living and Non-Living Microbial Forms

Microbiology studies both living and non-living entities, including bacteria, viruses, protozoa, and others. These forms differ in structure, size, and biological characteristics.

Bacteria: Unicellular, prokaryotic, typically 0.5–5 μm in size. Possess cell walls, reproduce by binary fission.
Viruses: Non-living, acellular, much smaller (20–300 nm). Require host cells for replication.
Protozoa: Unicellular, eukaryotic, larger than bacteria (10–50 μm). Exhibit complex life cycles.
Fungi: Eukaryotic, can be unicellular (yeasts) or multicellular (molds).
Helminths: Multicellular parasitic worms.

Distinguishing Features: Cell structure, reproduction, metabolism, and pathogenicity.

Example: Escherichia coli (bacterium) vs. Influenza virus.

Binomial Nomenclature

Binomial nomenclature is the formal system for naming organisms using two names: genus and species.

Genus: Capitalized, italicized (e.g., Staphylococcus).
Species: Lowercase, italicized (e.g., Staphylococcus aureus).

Example: Escherichia coli

History of Microbiology

Key figures contributed to the development of microbiology:

Antonie van Leeuwenhoek: First to observe microbes using a microscope.
Louis Pasteur: Disproved spontaneous generation, developed pasteurization.
Robert Koch: Established Koch's postulates for linking microbes to disease.
Joseph Lister: Introduced antiseptic techniques in surgery.
Florence Nightingale: Pioneered infection control in hospitals.

Cell Structure and Function

Universal Characteristics of Cells

All cells share four universal characteristics:

Cell membrane
Cytoplasm
Genetic material (DNA or RNA)
Ribosomes

Gram-Positive vs. Gram-Negative Bacteria

Bacteria are classified based on their cell wall structure:

Gram-Positive: Thick peptidoglycan layer, teichoic acids, stains purple.
Gram-Negative: Thin peptidoglycan, outer membrane with lipopolysaccharide, stains pink.

Peptidoglycan: Composed of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) with peptide cross-links.

Side Chains and Cross Links: Provide structural integrity.

Cellular Structures and Their Functions

Endospores: Allow survival in harsh conditions.
Capsules, Glycocalyx, Slime Layers: Protect against desiccation and phagocytosis.
Flagella: Motility.
Fimbriae: Attachment.
Pili: Conjugation and attachment.

Acid-Fast Staining: Used for Mycobacterium tuberculosis due to waxy cell wall (mycolic acids).

Bacterial vs. Eukaryotic Cells: Bacteria lack membrane-bound organelles; eukaryotes have nucleus and organelles.

Microscopy and Staining

Microscope Properties

Objective Lens: Magnifies specimen.
Ocular Lens: Further magnifies image.
Condenser: Focuses light.
Parfocal: Remains in focus when switching objectives.

Total Magnification: Multiply objective lens by ocular lens.

$\text{Total Magnification} = \text{Objective Magnification} \times \text{Ocular Magnification}$

Immersion Oil: Increases resolution by reducing light refraction.

Heat-Fixing: Adheres cells to slide, kills cells, preserves morphology.

Staining Techniques

Simple Stain: Uses one dye; highlights cell shape.
Differential Stain: Uses multiple dyes; distinguishes cell types (e.g., Gram, acid-fast).
Gram Stain: Crystal violet, iodine, alcohol, safranin.
Acid-Fast Stain: Detects mycolic acids.
Spore and Flagella Stains: Visualize endospores and flagella.

Cell Shapes: Cocci, bacilli, spirilla; arrangements include chains, clusters.

Infection, Infectious Disease, and Epidemiology

Definitions

Acute: Rapid onset, short duration.
Chronic: Slow onset, long duration.
Host: Organism harboring pathogen.
Iatrogenic: Caused by medical intervention.
Idiopathic: Unknown cause.
Mutualism: Both benefit.
Parasitism: One benefits, one harmed.
Pathogenicity: Ability to cause disease.
Sequelae: Aftereffects of disease.
Sign: Objective evidence.
Symptom: Subjective experience.
Syndrome: Group of signs/symptoms.
Virulence: Degree of pathogenicity.
Virulence Factor: Molecule aiding pathogenicity.

Virulence Factors and Enzymes

Hyaluronidase: Breaks down connective tissue.
Collagenase: Breaks down collagen.
Coagulase: Clots blood.
Streptokinase: Dissolves clots.

Endotoxin vs. Exotoxin: Endotoxins are lipopolysaccharides from Gram-negative bacteria; exotoxins are proteins secreted by bacteria.

Antiphagocytic Factors: Capsules, M protein, prevent phagocytosis.

Stages of Infectious Disease

Incubation
Prodromal
Illness
Decline
Convalescence

Each stage has distinct clinical features.

Transmission Modes

Contact: Direct, indirect, droplet.
Vehicle: Airborne, waterborne, foodborne, bodily fluids.
Vector: Biological, mechanical.

Incidence vs. Prevalence

Incidence: New cases in a period.
Prevalence: Total cases at a time.

Types of Disease Occurrence

Endemic: Constant presence.
Epidemic: Sudden increase.
Pandemic: Worldwide epidemic.
Sporadic: Occasional cases.

Innate Immunity

Immune Cells and Granulocytes/Agranulocytes

Cell Type	Main Function	Granulocyte/Agranulocyte
Basophil	Release histamine	Granulocyte
Mast cell	Allergic response	Granulocyte
Eosinophil	Combat parasites	Granulocyte
Lymphocyte	Adaptive immunity	Agranulocyte
Monocyte	Differentiate into macrophages	Agranulocyte
Macrophage	Phagocytosis	Agranulocyte
Neutrophil	Phagocytosis	Granulocyte

Lymphoid Tissue

Central: Bone marrow, thymus.
Peripheral: Lymph nodes, spleen.

Thymus: Maturation site for T lymphocytes.

Physical Barriers

Skin
Muco-ciliary escalator
Lacrimal apparatus

Phagocytosis

Chemotaxis
Adherence
Ingestion
Digestion
Exocytosis

Carried out by neutrophils, macrophages, dendritic cells.

Inflammation

Cardinal Signs: Redness, heat, swelling, pain.
Major Steps: Vasodilation, increased permeability, migration of phagocytes.

Lysozyme and Interferons

Lysozyme: Enzyme that breaks down bacterial cell walls; found in tears, saliva.
Interferons: Antiviral proteins; alpha and beta made by infected cells, gamma by T cells and NK cells.

Complement System

Activated by classical, alternative, lectin pathways.
Leads to opsonization, inflammation, membrane attack complex.

Adaptive Immunity

B vs. T Lymphocytes

B Lymphocytes: Mediate humoral immunity; produce antibodies.
T Lymphocytes: Mediate cell-mediated immunity; cytotoxic T cells and cytokines.

Key Terms

Antigen: Substance recognized by immune system.
Epitope: Specific region of antigen.
Antigen Receptor: B cell: membrane-bound antibody; T cell: T cell receptor.

Properties of Adaptive Immunity

Specificity
Diversity (achieved by gene recombination)
Memory
Self-tolerance

Effector vs. Memory Cells: Effector cells act immediately; memory cells persist for future responses.

Primary vs. Secondary Response: Primary is first exposure; secondary is faster, stronger.

Plasma Cell: Effector B cell producing antibodies.

Types of T Lymphocytes

Type	Main Function	CD Marker	MHC Binding
Helper T (Th)	Activate other cells	CD4	MHC II
Cytotoxic T (Tc)	Kill infected/tumor cells	CD8	MHC I
Regulatory T (Treg)	Suppress immune response	CD4	MHC II

Cytokines: Signaling proteins, associated with helper T cells.

Perforins: Proteins used by cytotoxic T cells to lyse target cells.

Bacterial Diseases

Exotoxins and Endotoxins

Endotoxin: Lipid A of LPS in Gram-negative bacteria.
Exotoxin: Secreted proteins; classified as Type I (superantigens), Type II (membrane-disrupting), Type III (A-B toxins).

Bacterial Skin Infections

Necrotizing Fasciitis: Caused by Streptococcus pyogenes; enzymes include hyaluronidase, streptokinase.
Clostridium tetani and Clostridium botulinum: Form endospores; toxins cause tetanus and botulism.
Botulinum Toxin: Used for disease treatment and cosmetics.
Trismus: Lockjaw; Opisthotonos: Muscle spasms.

Bacterial Respiratory Infections

Pharyngitis: Sore throat.
Erythema: Redness.
Exudate: Fluid accumulation.
Lymphadenopathy: Swollen lymph nodes.
Streptococcus pyogenes: Causes strep throat; virulence factors include M protein, streptolysin.
Hemolysis: S. pyogenes causes beta hemolysis on sheep blood agar.

Bacterial Gastrointestinal Infections

Helicobacter pylori: Causes ulcers; virulence factors include urease, flagella; associated with gastric cancer.
Gastroenteritis: Inflammation of GI tract.
Intoxication: Disease caused by toxins, not infection.
Staphylococcus aureus: Exotoxin causes vomiting; transmitted via contaminated food.
E. coli O157:H7: Causes hemorrhagic colitis; AE lesions, intimin, shiga toxin; can cause hemolytic uremic syndrome.
Clostridium difficile: Causes antibiotic-associated diarrhea; toxins A and B damage intestine; endospores aid transmission; fecal transplant restores microbiome.

Bacterial Urinary and Reproductive Infections

UTIs: Most commonly caused by E. coli; virulence factors include fimbriae; cranberry juice may prevent adherence.
Syphilis: Caused by Treponema pallidum; four stages.
Chlamydia trachomatis: Atypical, obligate intracellular; elementary and reticulate bodies; often asymptomatic; can cause PID, trachoma.

Eukaryotic Pathogens

Protozoa

Mastigophorans: Move by flagella.
Amebozoa: Move by pseudopodia.
Ciliates: Move by cilia.
Amebo-flagellates: Both pseudopodia and flagella.
Apicomplexans: Non-motile; Plasmodium causes malaria.
Trophozoite: Active form; Cyst: Dormant form.

Fungi

Cell Wall: Chitin.
Body Structure: Thallus, hyphae, mycelium.
Reproduction: Budding, asexual/sexual spores.
Nutrition: Heterotrophs.
Significance: Lichens, mycorrhizae, antibiotics, food.

Algae

Mostly autotrophs; some heterotrophs.
Commonly found in water.

Helminths

Tapeworms: Scolex, proglottids.
Roundworms: Cylindrical body.
Transmission: Ingestion, skin penetration.

Viruses and Viral Diseases

Virus Structure and Infection

Capsid: Protein shell.
Capsomere: Subunit of capsid.
Envelope: Lipid membrane from host.
Glycoprotein (spike): Attachment proteins.
Naked Virus: Lacks envelope.

Infection Steps: Attachment, entry, replication, assembly, release.

Release: Naked viruses lyse cells; enveloped viruses bud from membrane.

Latency: Dormant state; seen in herpesviruses.

Specific Viral Diseases

Measles: Koplik's spots, maculopapular rash, airborne transmission.
Herpes Simplex Virus 1 & 2: HSV-1: cold sores; HSV-2: genital herpes; latency in neurons; acyclovir inhibits replication.
Influenza: H (hemagglutinin), N (neuraminidase); antigenic shift/drift; new vaccines yearly; influenza A linked to pandemics.
Monkeypox: Related to smallpox virus; spreads via contact; prodromal symptoms, rash progression; vaccines developed for smallpox.
Coronavirus: Origin: zoonotic; entry via ACE2 receptor; causes COVID-19; prevention: masks, vaccines.
West Nile Virus: Flavivirus; transmitted by Culex mosquitoes; birds are reservoir; humans are dead-end hosts; febrile vs. neuroinvasive forms; avoid blood donation post-infection.
Dengue Virus: Flavivirus; transmitted by Aedes mosquitoes; typical vs. hemorrhagic fever; pathogenesis involves immune response; prevention: mosquito control.

Controlling Microbial Growth in the Environment

Effectiveness of Antiseptics/Disinfectants

Tested by microbial reduction assays.
Moist heat methods: boiling, autoclaving.

Terminology

Aseptic: Free from contamination.
Decontamination: Removal of microbes.
Disinfection: Destruction of pathogens.
Sterilization: Complete elimination of all microbes.

Mechanisms of Control

Alcohols: Denature proteins, disrupt membranes.
Radiation: Ionizing (DNA damage), non-ionizing (thymine dimers).
Boiling: Not effective against endospores.
Membrane Filtration: Sterilizes heat-sensitive liquids.
Pasteurization vs. UHT: Pasteurization reduces pathogens; UHT sterilizes.

Controlling Microbial Growth in the Body: Antimicrobial Drugs

Spectrum and Mechanisms of Action

Broad Spectrum: Effective against many microbes.
Narrow Spectrum: Target specific microbes.
Penicillin: Inhibits cell wall synthesis.
Tetracycline: Inhibits protein synthesis.
Cephalosporin: Inhibits cell wall synthesis.
Amphotericin B: Disrupts fungal membranes.
Erythromycin: Inhibits protein synthesis.

Testing Antimicrobial Effectiveness

Disk diffusion, MIC, MBC tests.
Zone of inhibition: large zone = sensitive; regrowth (satellite colonies) = resistance.

Antibiotic Resistance

Acquired by mutation, transduction, conjugation, transformation.
Resistance mechanisms: beta-lactamase, altered targets.

Immunization and Immune Testing

Vaccines

Attenuated: Live, weakened; replicate in body; not for immunocompromised/pregnant.
Inactivated: Killed; whole or subunit; inactivation by heat/chemicals.
Toxoid: Inactivated toxin; e.g., tetanus, diphtheria.
Adjuvant: Enhances immune response; e.g., aluminum salts.
mRNA Vaccines: Encode antigen; e.g., COVID-19 vaccines.
Viral Vector Vaccines: Use harmless virus to deliver antigen.

Herd Immunity: Protection of population when enough are immune.

Resurgence: Due to reduced vaccination rates; examples include measles outbreaks.