Microbio_Finals__1_

Chapter 1: Humans and the Microbial World

• Spontaneous Generation vs. Biogenesis
  • Spontaneous Generation: Living organisms arise from non-living matter; widely accepted until the 19th century.
  • Biogenesis: Living organisms arise from other living organisms, replacing spontaneous generation.
• Experiments Disproving Spontaneous Generation
  • Francesco Redi's Meat Experiment: Maggots on meat originate from flies, demonstrated with jars with and without lids.
  • Louis Pasteur's Swan Flask Experiment: Microbes in the air contaminate; swan-neck flask trapped microbes, broth remained sterile.
  • John Tyndall's Experiments: Confirmed Pasteur’s results. Different broths require different degrees of heat for sterilization, supporting biogenesis.
• Contributions to the Cell Theory
  • Robert Hooke's Microscopic Observations: Observed cork, coined term "cells."
  • Anton van Leeuwenhoek's Observations: Discovered "animalcules" (microorganisms) in pond water, showing microscopic life exists.
• Germ Theory of Disease
  • Concept: Microorganisms cause diseases, not spontaneous factors or miasma.
  • Joseph Lister's Antiseptic Surgery: Used carbolic acid to disinfect, reducing infections.
  • Robert Koch's Experiments: Identified Bacillus anthracis as cause of anthrax, established Koch's postulates.
• Differentiating Bacteria, Yeast, and Viruses
  • Unicellularity: Bacteria - unicellular, Yeast - unicellular/multicellular, Viruses - non-cellular.
  • Cell Type: Bacteria - prokaryotic, Yeast - eukaryotic, Viruses - not cells.
  • Living Status: Bacteria & Yeast - living, Viruses - non-living.
  • Organelles: Bacteria - absent, Yeast - present, Viruses - N/A (non-cellular).
• Role of Microbes in Human Activities
  • Health and Disease: Some microbes cause diseases, others are normal microbiota.
  • Environment: Nutrient cycling, decomposition, nitrogen fixation.
  • Food Production: Fermentation in bread, cheese, yogurt, etc.
  • Biodegradation/Bioremediation: Break down pollutants.
  • Biotechnology/Genetic Engineering: Used in research, industrial applications.
  • Research Tools: Model organisms for studying biological processes.

Chapter 10: Identification and Classification of Prokaryotic Organisms

• Three Domains of Life
  • Bacteria: Prokaryotic, no introns, peptidoglycan cell wall.
  • Archaea: Prokaryotic, some introns, cell wall lacks peptidoglycan.
  • Eukarya: Eukaryotic, contains introns, membrane-bound nucleus.
• Writing Bacterial Names
  • Genus & Species: Italicized, Genus capitalized, species lowercase (e.g., Escherichia coli).
• Molecule Used by Carl Woese to Classify Organisms
  • 16S rRNA: Conserved gene sequence for classifying organisms into domains.
• Characteristics of Eukaryotes, Prokaryotes, Acellular Infectious Agents
  • Eukaryotes: Organelles, nucleus, complex structure.
  • Prokaryotes: Lack organelles, simpler, no nucleus.
  • Acellular Infectious Agents: Viruses, viroids, prions; non-cellular.
• Taxonomy Concepts
  • Taxonomy: Science of classification (naming, describing, organizing).
  • Species Definition (Bacteria): Genetic similarity, phenotype, reproductive isolation.
  • Phylogeny and Phylogenetic Tree: Evolutionary history/relationships depicted in a tree.
• Informal Phenotypic Groupings
  • Phenotypic Groupings: Based on observable traits (morphology, behavior, metabolism).
  • Genotypic Groupings: Based on genetic sequences.
• Grouping Based on Microscopic Morphology
  • Microscopic Characteristics: Shape, arrangement, Gram stain, etc.
• Metabolic Characteristics
  • Culture Characteristics/Metabolic Capabilities: Unique growth patterns, Dichotomous keys for identification.
• Serology and Its Role in Categorization
  • Serology: Study of antigen-antibody interactions for organism identification.
• MALDI-TOF in Classifying Organisms
  • MALDI-TOF: Mass spectrometry for identifying organisms by protein fingerprints.
• Genetic Methods in Identification, Classification, and Categorization
  • Nucleic Acid Probes: Detect specific DNA/RNA sequences.
  • FISH (Fluorescence In Situ Hybridization): Visualize nucleic acids in cells.
  • NAATS/PCR: Amplify/detect specific DNA.
• Importance of Ribosomal RNA Gene Sequences
  • Stability of rRNA: 16S rRNA sequences are stable for reliable classification.
• DNA-DNA Hybridization (DDH)
  • DNA-DNA Hybridization: Measures relatedness by how much DNA strands bind.
• Species and Strains
  • Species vs. Strains: Species have high genetic similarity; strains are subgroups with unique traits for epidemiology and treatment.

Chapter 3: Cell Structure

• Components of Prokaryotic Cells
  • Capsule/Slime Layer: Protection from phagocytosis/desiccation.
  • Flagella: Motility.
  • Cell Wall: Structure/protection, peptidoglycan.
  • Plasma Membrane: Regulates transport/structural integrity.
  • Ribosomes: Protein synthesis.
  • Pili: Attachment (e.g., F-pili for conjugation).
  • Endospores: Survival in harsh conditions.
  • Genome Organization: Single circular chromosome.
  • Plasmids: Extra genes on small circular DNA.
• Comparing Prokaryotic and Eukaryotic Cells
  • Plasma Membrane: Both have phospholipid bilayers; eukaryotes more complex proteins.
  • Cell Wall: Prokaryotes typically have them, eukaryotes may not.
  • Flagella: Prokaryotic flagella rotate; eukaryotic flagella whip.
  • Ribosome Structure: Prokaryotes: 70S, eukaryotes: 80S.
  • Organelles: Absent in prokaryotes, present in eukaryotes.
  • DNA Location: Prokaryotes in nucleoid, eukaryotes in nucleus.
  • Transport: Both have passive/active; eukaryotes may have endocytosis.
• Gram-Positive and Gram-Negative Cells
  • Cell Wall Thickness: Gram-positive thicker, Gram-negative thin with outer membrane.
  • Outer Membrane: Only in Gram-negative.
  • Susceptibility to Detergents/Antibiotics: Gram-positive more susceptible to some antibiotics; Gram-negative has an outer membrane barrier.
• Compound Light Microscope and Its Main Parts
  • Main Parts: Ocular lens, objective lenses, stage, diaphragm, light source.
  • Types of Microscopes: Vary based on magnification.
  • Concepts of Microscopy: Magnification, resolution, contrast.
• Different Types of Microscopes and Electron Microscopes
  • Types of Microscopes: Phase-contrast, fluorescence, confocal, etc.
  • Electron Microscopes: TEM/SEM have higher resolution.
• Chemical Stains/Dyes and Their Use
  • Chemical Description: Acidic and basic dyes.
  • Classes of Staining: Simple, differential, special/structural.
  • Gram Stain Method: Crystal violet, iodine, alcohol, safranin to differentiate Gram-positive/-negative.
  • Heat Fixation: Adhere sample/kill cells.

Chapter 4: Dynamics of Prokaryotic Growth

• Binary Fission and Exponential Growth
  • Binary Fission: Cell divides into two.
  • Exponential Growth: Population doubles at regular intervals.
• Calculating Cell Numbers in a Culture
  • Exponential Growth Formula: Nt = N0 \times 2^n, where N0 is initial cells, n is generations, Nt is the final cell number.
• Biofilms
  • Complex communities of microorganisms adhering to surfaces, can be beneficial (water treatment) or harmful (dental plaque, medical device infections).
• Stages of a Bacterial Growth Curve
  • Lag Phase: Cells adapt.
  • Log/Exponential Phase: Rapid division, sensitive to antibiotics.
  • Stationary Phase: Division rate equals death rate.
  • Death Phase: Death rate exceeds division, logarithmic decrease.
  • Phase of Prolonged Decline: A few survivors continue to divide.
• Effect of Different Conditions on Bacterial Growth
  • Temperature: Optimal ranges differ.
  • Nutrient Availability: Affects rate and phase transitions.
  • Oxygen: Aerobes, anaerobes, microaerophiles, etc.
• Temperature Preferences and Locations in Nature
  • Psychrophiles: Low temperatures (arctic environments).
  • Mesophiles: Moderate temperatures (human body).
  • Thermophiles: Higher temperatures (hot springs).
  • Psychotrophs: Low/moderate temperatures.
  • Hyperthermophiles: Extreme temperatures (hydrothermal vents).
• Oxygen Preferences and Aerobic/Anaerobic Respiration
  • Obligate Aerobes: Require oxygen.
  • Microaerophiles: Low oxygen.
  • Obligate Anaerobes: Cannot tolerate oxygen.
  • Aerotolerant Anaerobes: Tolerate but don't use oxygen.
  • Facultative Anaerobes: Grow with/without oxygen.
• Carbon and Energy Sources
  • Photoautotrophs: Light energy, carbon dioxide.
  • Photoheterotrophs: Light energy, organic carbon.
  • Chemolithoautotrophs: Inorganic chemicals, carbon dioxide.
  • Chemoorganoheterotrophs: Organic chemicals for both.

Chapter 5: Control of Microbial Growth

• Objective 1: Differentiate between Various Processes and Outcomes
  • Sterilization: Destruction of all microbial life.
  • Pasteurization: Mild heat to destroy pathogens and reduce spoilage.
  • Sanitization: Reduction to a safe level.
  • Antisepsis: Chemicals on living tissue to destroy/inhibit microbes.
  • Disinfection: Chemicals on inanimate objects.
  • Preservation: Slow or prevent growth in foods/samples.
• Objective 2: Methods of Microbial Control (Physical and Chemical)
  • Physical Methods
    • Heat: Moist (boiling, autoclaving), dry (ovens, incineration).
    • Filtration: Membrane (liquids), HEPA (air).
    • Radiation: Ionizing (X-rays, gamma rays), non-ionizing (UV light).
  • Chemical Methods
    • Alcohols: Ethanol, isopropyl (antiseptics).
    • Halogens: Chlorine, iodine (disinfectants).
    • Oxidizing Agents: Hydrogen peroxide, peracetic acid (high-level disinfectants).
    • Phenolics: Lysol, triclosan (disinfectants).
    • Aldehydes: Formaldehyde, glutaraldehyde (sterilants).
    • Surface-Active Agents: Soaps, detergents (sanitizers).
• Objective 3: Decimal Reduction Time and Calculations
  • Decimal Reduction Time (D-value): Time to reduce population by 90%.
  • Example Calculation: D-value is 3 minutes; start with 1,000,000 bacteria -> 100,000 after 3 mins and 10,000 after 6 mins.
• Objective 4: Critical, Semicritical, and Non-Critical Items
  • Critical Items: Enter sterile tissues, require sterilization.
  • Semicritical Items: Contact mucous membranes, require high-level disinfection.
  • Non-Critical Items: Contact intact skin, require sanitization/low-level disinfection.
• Objective 5: Heat as a Microbial Killing Method
  • Moist Heat
    • Boiling: Kills vegetative cells, some spores.
    • Pasteurization: Kills pathogens, reduces spoilage.
    • Autoclave: 121°C with high-pressure steam for sterilization.
  • Dry Heat
    • Hot Air Ovens: Sterilize glassware/metal.
    • Incineration: Burning for waste disposal.
• Objective 6: Filtration Methods for Microbial Growth Control
  • Membrane Filtration: Small-pore filters to remove microbes from liquids.
  • HEPA Filters: Remove airborne microbes.
• Objective 7: Radiation for Microbial Control
  • Ionizing Radiation
    • X-rays, Gamma Rays: DNA damage, sterilize medical equipment/food.
  • Non-Ionizing Radiation
    • UV Light: DNA mutations, disinfect surfaces/air/water.
  • Microwaves: Kill microbes through heat generation (not sterilization).
• Objective 8: Chemical Germicides and Applications
  • Low-Level Germicides: Kill vegetative bacteria, fungi, enveloped viruses (non-critical items).
  • Intermediate-Level Germicides: Kill vegetative bacteria, fungi, mycobacteria, most viruses (semicritical items).
  • High-Level Germicides: Kill all vegetative organisms, most spores (semicritical/critical items).
• Objective 9: Understanding Microbial Forms and Difficulty in Control
  • Bacterial Endospores: Highly resistant.
  • Protozoan Cysts: Resistant to disinfection.
  • Naked Viruses: More resistant.
  • Enveloped Viruses: Less resistant.
  • Vegetative Bacterial Cells: Easier to kill.
  • Mycobacteria: More resistant due to waxy cell wall.
• Objective 10: Factors to Consider When Choosing a Microbial Control Method
  • Type of Microorganisms: Consider resilience/structure.
  • Environment/Surface: Living tissue, equipment, food?
  • Safety/Efficacy: Ensure method’s effectiveness/safety.

Chapter 6: Antimicrobial Medications

• Objective 1: Basic Terminology for Antibiotics
  • Selective Toxicity: Targets microbes without harming host cells.
  • Therapeutic: Effective concentration/dosage.
  • Bacteriostatic: Inhibits growth, doesn't kill.
  • Bactericidal: Kills bacteria.
  • Broad-Spectrum: Wide range of microbes.
  • Narrow-Spectrum: Specific group.
  • Antagonistic: One interferes with another.
  • Synergistic: Combined effect is greater.
  • Additive: Combined effect is the sum of separate effects.
• Objective 2: Half-Life of an Antibiotic
  • Half-Life: Time to reduce concentration by half.
  • Relevance: Affects dosing frequency/duration.
• Objective 3: Negative Consequences of Antibiotic Usage
  • Antibiotic Resistance: Bacteria develop resistance.
  • Disruption of Microbiota: Leads to secondary infections.
  • Allergic Reactions.
  • Toxicity.
• Objective 4: Different Cellular Targets of Antibiotics
  • Cell Wall Synthesis: Beta-lactams, glycopeptides.
  • Protein Synthesis: Aminoglycosides, tetracyclines, macrolides, chloramphenicol.
  • Nucleic Acid Synthesis: Fluoroquinolones, rifamycins, metronidazole.
  • Metabolic Pathways: Sulfonamides/trimethoprim.
  • Cell Membrane Integrity: Daptomycin, polymyxin B.
• Objective 5: Categorize Antibiotics by Cellular Target and Mechanism of Action
  • Beta-Lactam Drugs, Glycopeptides, Bacitracin
    • Target: Cell wall synthesis.
    • Mechanism: Interfere with peptidoglycan formation.
  • Aminoglycosides, Tetracyclines/Glycylcyclines, Macrolides, Chloramphenicol
    • Target: Protein synthesis.
    • Mechanism: Bind to ribosomal subunit, block tRNA, inhibit peptidyl transferase.
  • Fluoroquinolones/Rifamycins/Metronidazole
    • Target: Nucleic acid synthesis.
    • Mechanism: Inhibit DNA gyrase/RNA polymerase, disrupt DNA.
  • Sulfonamides/Trimethoprim
    • Target: Metabolic pathways.
    • Mechanism: Inhibit folic acid synthesis.
  • Daptomycin, Polymyxin B
    • Target: Cell membrane integrity.
    • Mechanism: Cause membrane depolarization, disrupt membrane.
• Objective 6: Purpose of the Kirby-Bauer Test, MIC, and MBC
  • Kirby-Bauer Test: Antibiotic sensitivity; measure zones of inhibition.
  • Minimum Inhibitory Concentration (MIC): Lowest concentration inhibiting growth.
  • Minimum Bactericidal Concentration (MBC): Lowest concentration that kills bacteria.
• Objective 7: Newer Tests Combining Concepts of Kirby-Bauer and MIC/MBC
  • E-test: Combines Kirby-Bauer and MIC using antibiotic concentration strips.
  • Automated Systems: Determine sensitivity/resistance quickly.
• Objective 8: Mechanisms of Antibiotic Resistance and Acquisition Methods
  • Mechanisms of Antibiotic Resistance
    • Enzymatic Degradation: Enzymes break down antibiotics.
    • Target Alteration: Alter target sites.
    • Efflux Pumps: Pump antibiotics out.
    • Reduced Permeability: Reduce antibiotic entry.
  • Acquisition Methods
    • Spontaneous Mutation: Random mutations.
    • Horizontal Gene Transfer: Transformation, transduction, conjugation.

Chapter 7/8: Bacterial Genetics

• Objective 1: Prokaryotic vs. Eukaryotic Organisms and the Central Dogma
  • Prokaryotes vs. Eukaryotes
    • Prokaryotes: No nucleus, smaller ribosomes, circular DNA.
    • Eukaryotes: Nucleus, larger ribosomes.
  • Central Dogma: DNA -> RNA -> Protein.
• Objective 2: Major Differences in Prokaryotic vs. Eukaryotic DNA Replication
  • Prokaryotic DNA Replication
    • Circular chromosome, single origin, faster replication, transcription/translation can occur concurrently.
  • Eukaryotic DNA Replication
    • Linear chromosomes, multiple origins, slower replication, distinct processes.
• Objective 3: Prokaryotic vs. Eukaryotic Transcription and Translation
  • Prokaryotic Transcription and Translation
    • Monocistronic vs. Polycistronic: mRNA can be polycistronic
    • Coupled Transcription and Translation: Occur simultaneously.
  • Eukaryotic Transcription and Translation
    • Monocistronic: Eukaryotic mRNA is typically monocistronic.
    • Separation of Processes: Nucleus for transcription; cytoplasm for translation.
• Objective 4: Operons and Regulation in Prokaryotes
  • Operon: Genes regulated together, transcribed as a single mRNA.
  • Inducers and Repressors: Regulate gene expression.
    • Inducer: Promotes transcription.
    • Repressor: Inhibits transcription.
• Objective 5: The lac Operon as a Model for Regulation
  • lac Operon: Genes for lactose metabolism.
    • Induction by Lactose: Lactose acts as an inducer.
    • Glucose Regulation: High glucose inhibits transcription.
• Objective 6: Genetic Changes in Natural Selection and Genetic Variability in Bacteria
  • Genetic Changes in Natural Selection
    • Mutations lead to variability.
    • Gene transfer promotes diversity.
  • Mechanisms for Genetic Variability
    • Spontaneous Mutations
    • Horizontal Gene Transfer: Transformation, transduction, conjugation.
• Objective 7: Studying Gene Function with Mutations
  • Prototrophs vs. Auxotrophs
    • Prototrophs: Wild-type organisms.
    • Auxotrophs: Mutants with disrupted pathways.
  • Metabolic Mutants: Useful for studying pathways/functions.
  • Antibiotic-Resistant Mutants: Used to study resistance.
• Objective 8: Mutations and Their Effects on Proteins
  • Base Substitutions
    • Silent: No change in amino acid sequence.
    • Missense: Change in amino acid sequence.
    • Nonsense: Stop codon, truncated protein.
  • Frameshift Mutations
    • Insertion/Deletion: Shift reading frame, drastic changes.
• Objective 9: DNA Error Repair During Replication
  • Proofreading: DNA polymerases correct errors.
  • Mismatch Repair: Proteins correct mismatched base pairs.
• Objective 10: Mutant Selection Methods
  • Direct Selection: Grow mutants in specific conditions.
  • Indirect Selection: Identify mutants with specific traits (replica plating).
• Objective 11: Horizontal Gene Transfer and Its Types
  • Horizontal Gene Transfer: Movement of genetic material between bacteria.
    • Transformation: Uptake of free DNA.
    • Transduction: DNA transfer via bacteriophages.
    • Conjugation: Direct cell-to-cell transfer
    • Homologous Recombination: Integration of foreign DNA.
• Objective 12: Genomes in Bacteria
  • Pan-genome: Complete gene set; Core: genes found in all strains; Accessory: genes found in some, Unique: genes unique to one strain
• Objective 13: Mobile Genetic Elements
  • Plasmids: Extrachromosomal DNA, antibiotic resistance genes.
  • Transposons: DNA sequences that can move.
  • Genomic Islands: Large acquired DNA segments.
  • Phage DNA: Bacteriophage genomes can influence bacterial traits and gene transfer.

CHAPTER 14: The Innate Immune Response

• 1. Innate vs. Adaptive Immunity
  • Level of Specificity:
    • Innate immunity is non-specific.
    • Adaptive immunity is highly specific.
  • Timing:
    • Innate immunity responds quickly.
    • Adaptive immunity has a delayed response.
  • Development of Memory Responses:
    • Innate immunity has no memory.
    • Adaptive immunity has memory.
• 2. Physical Barriers in Innate Immunity
  • Skin: Acts as a physical barrier.
  • Mucous Membranes: Line respiratory, digestive, and urogenital tracts.
  • Cells: Epithelial cells secrete antimicrobial substances.
• 3. Chemical Components of Innate Immunity
  • Lysozyme: Enzyme that breaks down bacterial cell walls.
  • Lactoferrin: Binds iron, inhibiting bacterial growth.
  • Defensins: Antimicrobial peptides that disrupt microbial membranes.
• 4. Benefits of Normal Microflora
  • Compete with pathogens for nutrients and space.
  • Produce antimicrobial substances.
  • Stimulate the immune system.
• 5. Hematopoiesis
  • Definition: Process of blood cell formation.
  • Responsible For: Producing red blood cells, white blood cells, and platelets.
• 6. Primary Types of Progenitor Cells
  • Myeloid Progenitors: Give rise to granulocytes, monocytes, erythrocytes, and megakaryocytes.
  • Lymphoid Progenitors: Give rise to B cells, T cells, and natural killer cells.
• 7. Granulocytes and Their Roles
  • Neutrophils: Phagocytic; primary responders to infection.
  • Eosinophils: Combat parasitic infections; involved in allergic reactions.
  • Basophils: Release histamine; involved in allergic reactions.
  • Why PMNs?: Called polymorphonuclear cells because they have multi-lobed nuclei.
• 8. Monocytes and Their Derived Cells
  • Monocytes: Circulate in the blood; differentiate into macrophages and dendritic cells.
  • Macrophages: Phagocytic; play a role in tissue repair and antigen presentation.
  • Dendritic Cells: Antigen-presenting cells; initiate adaptive immune responses.
• 9. Cytokines and Their Classes
  • Definition: Signaling proteins in the immune system.
  • Major Classes:
    • Interleukins (ILs): Regulate immune responses and inflammation.
    • Interferons (IFNS): Primarily involved in antiviral responses.
    • Tumor Necrosis Factor (TNF): Promotes inflammation and cell death.
    • Chemokines: Attract leukocytes to sites of infection or inflammation.
• 10. PAMPs vs. PRRs
  • PAMPS: Pathogen-associated molecular patterns.
  • PRRs: Pattern recognition receptors.
    • Types of PRRs:
      • TLRs (Toll-like receptors): Located on the cell surface or endosomes.
      • NLRS (NOD-like receptors): Located in the cytoplasm.
      • RLRS (RIG-I-like receptors): Located in the cytoplasm; recognize viral RNA.
• 11. ¡AVPs in Viral Response
  • ¡AVPS: Inactive antiviral proteins.
  • Role: Activated by interferons; inhibit viral replication.
• 12. Complement Cascade Outcomes
  • Opsonization: Coating of pathogens to facilitate phagocytosis.
  • Inflammation: Release of complement components that attract and activate immune cells.
  • Membrane Attack Complex (MAC): Formation of pores in microbial membranes, leading to cell lysis.
• 13. Steps in Phagocytosis; Macrophages vs. Neutrophils
  • Steps:
    • Recognition and attachment.
    • Engulfment and formation of phagosome.
    • Formation of phagolysosome.
    • Digestion and degradation.
    • Exocytosis of debris.
  • Macrophages: Long-lived; reside in tissues; involved in antigen presentation.
  • Neutrophils: Short-lived; recruited to sites of infection; highly phagocytic.
• 14. Features of Inflammation
  • Signs: Redness, heat, swelling, pain.
  • Relation to Immune Response: Inflammation brings immune cells to sites of injury or infection; increases permeability and promotes healing.

CHAPTER 15: The Adaptive Immune Response

• 1. Main Characteristics of the Adaptive Immune Response
  • Timing: Delayed compared to innate immunity.
  • Benefits:
    • Specificity for individual antigens.
    • Memory response for stronger future responses.
    • Ability to distinguish between self and non-self.
• 2. Primary vs. Secondary Adaptive Immune Responses
  • Primary Response: First exposure to an antigen; typically slower and less robust.
  • Secondary Response: Subsequent exposure to the same antigen; faster and stronger due to memory cells.
• 3. Humoral vs. Cell-Mediated Responses
  • Humoral:
    • Cells: B cells.
    • Characteristics: Production of antibodies that target extracellular pathogens and toxins.
  • Cell-Mediated:
    • Cells: T cells.
    • Characteristics: Direct killing of infected cells; activation of macrophages and other immune cells.
• 4. Naïve, Activated, Effector, and Memory Lymphocytes
  • Naïve: Lymphocytes that have not yet encountered their specific antigen.
  • Activated: Lymphocytes that have encountered their antigen and are undergoing proliferation.
  • Effector: Lymphocytes that are actively involved in clearing pathogens.
  • Memory: Lymphocytes that retain information about specific antigens for faster future responses.
• 5. Lymphatic System and Its Components
  • Lymphatic Vessels: Transport lymph; contain valves to prevent backflow.
  • Primary Lymphoid Organs: Where lymphocytes develop; includes bone marrow (B cells) and thymus (T cells).
  • Secondary Lymphoid Organs: Where lymphocytes interact with antigens; includes lymph nodes, spleen, and mucosa-associated lymphoid tissue (MALT).
• 6. Antigen vs. Epitope
  • Antigen: Any substance that can elicit an immune response.
  • Epitope: Specific part of an antigen recognized by immune receptors.
  • Cells/ Receptors: B cells recognize antigens via B cell receptors (BCRs), while T cells recognize antigen fragments presented by MHC molecules via T cell receptors (TCRs).
• 7. B Cell vs. T Cell Receptors
  • BCRs:
    • Bind free antigens.
    • Can recognize proteins, carbohydrates, and lipids.
  • TCRs:
    • Bind antigen fragments presented by MHC molecules.
    • Recognize only proteins.
• 8. Steps in the Humoral Immune Response
  • Naïve B Cells: Recognize and bind antigens via BCR.
  • Activation: B cells require help from T cells (specifically, CD4+ helper T cells).
  • Differentiation: B cells differentiate into plasma cells (which produce antibodies) and memory B cells.
  • Antibodies: Target extracellular pathogens for clearance.
• 9. Regions of Antibodies; Mechanisms of Antibody Activity
  • Regions:
    • Fab: Antigen-binding region; provides specificity.
    • Fc: Constant region; determines antibody effector functions.
  • Mechanisms of Antibody Activity:
    • Neutralization: Blocking pathogens or toxins from binding to cells.
    • Opsonization: Coating pathogens for easier phagocytosis.
    • Agglutination: Clumping of pathogens for easier removal.
    • Complement Activation: Triggers complement cascade.
    • Antibody-Dependent Cellular Cytotoxicity (ADCC): Directs immune cells to kill antibody-bound pathogens.
• 10. B Cell Activation Steps
  • BCR Binding Antigen: Initiates activation.
  • T Cell Help: Requires interaction with CD4+ helper T cells for full activation.
  • Cytokine Signals: Further stimulate B cell proliferation and differentiation.
• 11. Helper Cells and Cytotoxic Cells
  • Helper T Cells:
    • Recognize antigens presented by MHC class II.
    • Typically recognize extracellular pathogens.
    • Effector functions: Help activate B cells, macrophages, and cytotoxic T cells.
  • Cytotoxic T Cells:
    • Recognize antigens presented by MHC class I.
    • Typically recognize intracellular pathogens.
    • Effector functions: Directly kill infected cells.
• 12. MHC and Its Role in Cell-Mediated Immunity
  • Definition: Major histocompatibility complex.
  • Role: Presents antigen fragments to T cells.
  • Types:
    • MHC Class I: Expressed on all nucleated cells; presents to cytotoxic T cells.
    • MHC Class II: Expressed on antigen-presenting cells (APCS); presents to helper T cells.
• 13. Antigen Presentation to T Cells by APCs
  • APCs: Includes dendritic cells, macrophages, and B cells.
  • Location: Occurs in secondary lymphoid organs (e.g., lymph nodes, spleen).
  • Molecules Involved:
    • MHC Class II: Presents to helper T cells.
    • MHC Class I: Presents to cytotoxic T cells.
• 14. Selection in Primary Lymphoid Organs
  • Positive Selection: Ensures T cells recognize self-MHC.
  • Negative Selection: Eliminates T cells that react strongly with self-antigens.
  • Purpose: To create a self-tolerant and functional T cell population.
• 15. Natural Killer Cells
  • Definition: A type of lymphocyte involved in innate immunity.
  • Mechanisms of Action:
    • Direct Killing: Induces apoptosis in virus-infected or cancerous cells.
    • Antibody-Dependent Cellular Cytotoxicity (ADCC): Targets antibody-bound cells for destruction.

CHAPTER 17: The Applications of the Immune Response

• 1. Immunization vs. Immunotherapy
  • Immunization: Process of inducing immunity against a specific disease.
  • Immunotherapy: Therapeutic use of immune system components to treat or prevent diseases.
• 2. Natural vs. Artificial Immunity; Active vs. Passive Immunity
  • Natural Immunity: Acquired through natural exposure to pathogens.
  • Artificial Immunity: Acquired through deliberate means (e.g., vaccination).
  • Active Immunity: Results from the activation of the immune system, leading to memory formation.
  • Passive Immunity: Provides temporary protection through transferred antibodies.
    • Examples:
      • Illness: Natural, active immunity.
      • Antiserum: Artificial, passive immunity.
      • Breastfeeding: Natural, passive immunity.
      • Vaccine: Artificial, active immunity.
• 3. Immunoglobulins and Their Types
  • Definition: Antibodies produced by B cells.
  • Types:
    • IgG: Most common; found in blood and extracellular fluid; crosses placenta.
    • IgM: First antibody produced; involved in primary immune response.
    • IgA: Found in mucosal sites (e.g., respiratory and gastrointestinal tracts).
    • IgE: Involved in allergic reactions and defense against parasites.
    • IgD: Present on naïve B cells; role in immune response not fully understood.
• 4. Definition and Benefits of Vaccines; Herd Immunity
  • Definition: Biological preparations that provide active acquired immunity to specific diseases.
  • Benefits: Protects the immunized individual and contributes to community-wide protection.
  • Herd Immunity: Occurs when a high percentage of a population is vaccinated, reducing the spread of disease and providing indirect protection to those who cannot be vaccinated.
• 5. Attenuated (Live) vs. Inactivated (Dead) Vaccines
  • Attenuated (Live):
    • Pros: Stronger and longer-lasting immune response; often requires fewer doses.
    • Cons: Risk of reversion to virulence; not suitable for immunocompromised individuals.
  • Inactivated (Dead):
    • Pros: Safer; no risk of reversion.
    • Cons: Weaker response; often requires multiple doses.
    • Types:
      • Killed Whole Cell: Whole pathogen killed.
      • Subunit: Contains parts of the pathogen.
      • Toxoid: Inactivated toxins.
      • Conjugate: Contains antigens linked to a carrier protein to enhance immunogenicity.
• 6. Importance of Vaccines in Society and Reasons for Vaccine Hesitancy
  • Importance: Vaccines are crucial for preventing diseases and maintaining public health.
  • Reasons for Vaccine Hesitancy:
    • Concerns about vaccine safety and side effects.
    • Misinformation and distrust in medical authorities.
    • Religious or philosophical