Chapt 1 – A Brief History of Microbiology

Key Vocabulary and Concepts

• Prokaryote vs Eukaryote: Prokaryotes are organisms without a true nucleus or membrane-bound organelles ("before nucleus"). Eukaryotes possess a true nucleus and membrane-bound organelles ("true nucleus").

• Pathogen: An organism that causes disease.

• Bioterrorism: The use of microorganisms or toxins to intentionally cause disease in humans, animals, or plants for malicious purposes.

• Microbiome: The collection of all microorganisms living in association with the human body or a particular environment.

• Taxonomy: The science of classifying organisms.

• Protozoa vs Protist: Protozoa are a group of single-celled eukaryotes, often motile and heterotrophic. Protists is a broader category including protozoa, algae, and slime molds.

• Viruses: Acellular infectious agents composed of nucleic acid (DNA or RNA) and a protein coat; may have an envelope.

• Koch's Postulates: Four criteria to establish a causative relationship between a microbe and a disease.

• Fungi (Yeast vs Molds): Yeasts are unicellular fungi; molds are multicellular, filamentous fungi.

• Germ Theory of Disease: States that specific diseases are caused by specific microorganisms (pathogens).

• Archaea: Prokaryotes with unique cell wall polymers, often found in extreme environments; many are chemotrophs.

• Vaccinations: The process of conferring immunity by inoculation with avirulent or killed pathogens.

• Biogenesis: The principle that living cells arise only from preexisting cells.

• Spontaneous Generation: The disproven idea that living organisms can arise from nonliving matter.

Historical Figures and Discoveries

• Antonie van Leeuwenhoek: First to observe microorganisms using a simple microscope; classified microbes into six categories: bacteria, archaea, fungi, protozoa, algae, and small multicellular animals (later, viruses and prions were added).

• Robert Hooke: Coined the term "cell" after observing cork; contributed to cell theory.

• Golden Age of Microbiology: Bassi and Pasteur demonstrated the link between microbes and disease; development of disinfectants and aseptic techniques.

• Louis Pasteur: Demonstrated the role of bacteria in fermentation and spoilage; developed pasteurization to reduce contamination.

Classification of Microorganisms

• Fungi: Eukaryotic, may have cell walls; includes molds (multicellular) and yeasts (unicellular).

• Protozoa: Single-celled eukaryotes; obtain nutrients by absorption or ingestion.

• Algae: Photosynthetic eukaryotes.

• Bacteria and Archaea: Prokaryotic, unicellular, reproduce asexually (binary fission), found everywhere (ubiquitous), high water content, can survive extreme environments.

• Viruses: Acellular, require host cells for replication.

• Animalia: Includes multicellular parasites.

Key Theories

• Biogenesis vs Spontaneous Generation: Biogenesis is supported by experiments (e.g., Pasteur's swan-neck flask), disproving spontaneous generation.

Chapt 3 – Cell Structure and Function

Prokaryote vs Eukaryote

• Prokaryotes: No nucleus, no membrane-bound organelles, usually have a cell wall (peptidoglycan in bacteria), divide by binary fission.

• Eukaryotes: True nucleus, membrane-bound organelles (mitochondria, ER, etc.), cell walls (if present) are chemically distinct (e.g., cellulose in plants, chitin in fungi), divide by mitosis/meiosis.

Cell Morphology

• Size: Prokaryotes are generally smaller than eukaryotes.

• Shape: Common shapes include cocci (spherical), bacilli (rod-shaped), spirilla (spiral), vibrios (comma-shaped), coccobacilli (short rods).

• Arrangement: Single, diplo (pairs), staphylo (clusters), strepto (chains), tetrad (groups of four), sarcina (cubical packets), palisade (side-by-side arrangement).

Prokaryotic Cell Structures

• External Structures:

  • Glycocalyx: Gelatinous outer layer; capsule (organized) or slime layer (unorganized); protects against desiccation and phagocytosis.

  • Flagella: Long, whip-like structures for motility.

  • Axial Filaments: Found in spirochetes; enable corkscrew movement.

  • Fimbriae: Short, hair-like projections for attachment.

  • Pili: Longer than fimbriae; involved in conjugation (DNA transfer).

• Cell Wall:

  • Gram-Positive: Thick peptidoglycan layer, teichoic acids.

  • Gram-Negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS).

• Gram Stain: Differential stain distinguishing Gram-positive (purple) from Gram-negative (pink) bacteria.

• Plasma Membrane: Phospholipid bilayer; described by the fluid mosaic model.

• Transport Mechanisms:

  • Passive Transport: No energy required; includes simple diffusion, facilitated diffusion, and osmosis.

  • Active Transport: Requires energy (ATP); moves substances against concentration gradient.

  • Group Translocation: Substance is chemically modified during transport.

• Internal Structures:

  • Nucleoid: Region containing the bacterial chromosome (DNA).

  • Ribosomes: Sites of protein synthesis (70S in prokaryotes).

  • Inclusions: Storage granules for nutrients.

  • Endospores: Highly resistant, dormant structures formed by some bacteria (e.g., Bacillus, Clostridium).

Eukaryotic Cell Structures

• Flagella and Cilia: Used for movement; cilia are shorter and more numerous.

• Cell Wall: Present in plants, fungi, and some protists; composition varies.

• Glycocalyx: Outer coating for protection and cell recognition.

• Plasma Membrane: Similar to prokaryotes but may contain sterols; involved in endocytosis and exocytosis.

• Cytoplasm and Cytoskeleton: Provides structure and facilitates movement of organelles.

• Ribosomes: 80S in eukaryotes (except 70S in mitochondria and chloroplasts).

• Membranous Organelles: Nucleus, endoplasmic reticulum (ER), Golgi complex, mitochondria, chloroplasts, vacuoles, lysosomes, centrosomes.

Endosymbiotic Theory

• Proposes that mitochondria and chloroplasts originated from free-living prokaryotes engulfed by ancestral eukaryotic cells.

Processes of Life

• Growth, reproduction, responsiveness, and metabolism are fundamental characteristics of living organisms.

Chapt 6 – Microbial Nutrition and Growth

Key Terms and Growth Requirements

• Chemoheterotroph: Organisms that obtain energy and carbon from organic compounds.

• Photoautotroph: Organisms that use light as an energy source and CO2 as a carbon source.

• Temperature Preferences:

  • Mesophile: Optimal growth at moderate temperatures (20–45°C).

  • Psychrophile: Thrive at low temperatures (0–20°C).

  • Thermophile: Prefer high temperatures (45–80°C).

  • Hyperthermophile: Grow at extremely high temperatures (>80°C).

• Growth Curve Phases:

  • Lag Phase: Adaptation to environment; little to no cell division.

  • Log (Exponential) Phase: Rapid cell division; population doubles at a constant rate.

  • Stationary Phase: Rate of cell growth equals rate of cell death.

  • Death Phase: Cells die at a faster rate than new cells are produced.

• Aerobe: Requires oxygen for growth.

• Anaerobe: Cannot tolerate oxygen.

• Catalase: Enzyme that breaks down hydrogen peroxide; used to distinguish between bacterial species.

• Roles of Elements: Carbon, hydrogen, oxygen, nitrogen, and trace elements are essential for microbial growth.

• Endospores: Dormant, resistant structures formed by some bacteria for survival in harsh conditions.

• Biofilm: Community of microorganisms attached to a surface, embedded in a self-produced matrix.

• Nitrogen Fixation: Conversion of atmospheric nitrogen (N2) into ammonia (NH3), a form usable by living organisms.

Chapt 11 – Characterizing and Classifying Prokaryotes

Key Terms and Concepts

• Binary Fission/Budding: Methods of asexual reproduction in prokaryotes.

• Morphologies: Shapes and arrangements of prokaryotic cells (see Chapt 3).

• Extremophiles: Organisms that thrive in extreme environments (e.g., high temperature, salinity, acidity).

• Motility: Movement mechanisms such as flagella, axial filaments, or gliding.

• Ubiquitous: Found everywhere.

• Fomite: Inanimate object that can transmit infectious agents.

• Hemolysis: The breakdown of red blood cells, often used to differentiate bacterial species on blood agar.

• Chemotroph: Organisms that obtain energy from chemical compounds.

• Phototroph: Organisms that obtain energy from light.

• Endotoxin vs Exotoxin:

  • Endotoxin: Lipopolysaccharide (LPS) from Gram-negative bacteria; released upon cell death.

  • Exotoxin: Proteins secreted by bacteria; can be highly toxic.

• Prokaryotic Cell Arrangements: Cocci, coccobacilli, bacilli, vibrio, spiral; arrangements include single, diplo, staphylo, tetrad, sarcina, palisade.

• Endospore Function: Survival under adverse conditions.

• Three Domains of Life: Bacteria, Archaea, Eukarya.

• Gram-Positive vs Gram-Negative: Based on cell wall structure and Gram stain reaction.

• Main Human Diseases: Clostridium (e.g., tetanus, botulism) and Bacillus (e.g., anthrax) species cause significant diseases.

• Modern Prokaryote Classification: Based on genetic, biochemical, and phenotypic characteristics.

Chapt 13 – Characterizing and Classifying Viruses, Viroids, and Prions

General Characteristics of Viruses

• Acellular: Not composed of cells; lack independent metabolism and reproduction.

• Obligate Intracellular Parasites: Require host cells for replication.

• Genetic Material: DNA or RNA (never both), single- or double-stranded.

• Protein Coat (Capsid): Protects genetic material; composed of protein subunits (capsomeres).

• Envelope: Some viruses have a lipid membrane derived from the host cell.

• Spikes: Glycoprotein projections for attachment to host cells.

• Host Range: Determined by specific attachment sites and cellular factors.

• Size: Much smaller than bacteria (measured in nanometers).

Viral Structure and Taxonomy

• Viron: Complete, infectious viral particle (extracellular state).

• Capsid: Protein coat; may be polyhedral (spherical), helical (rod-shaped), or complex.

• Envelope: Surrounds the capsid in some viruses; contains viral proteins and host-derived lipids.

• Taxonomy: Family names end in -viridae, genus names end in -virus (e.g., Herpesviridae, Herpesvirus).

• Viral Species: Group of viruses sharing genetic information and ecological niche; subspecies designated by numbers.

Isolation, Cultivation, and Identification

• Viruses must be grown in living cells (bacteria, animal, or plant cells).

• Bacteriophages form plaques on bacterial lawns.

• Animal and plant viruses may be grown in cell cultures; continuous cell lines can be maintained indefinitely.

• Serological tests are used for identification.

Viral Multiplication Cycles

• Lytic Cycle (Bacteriophages):

  1. Attachment: Phage attaches to host cell.

  2. Penetration: Phage injects DNA into host.

  3. Biosynthesis: Phage DNA and proteins are synthesized.

  4. Maturation: Assembly of new phage particles.

  5. Release: Host cell lyses, releasing new phages.

• Lysogenic Cycle (Temperate Phages):

  1. Viral DNA integrates into host genome (prophage).

  2. Prophage is replicated with host DNA.

  3. May confer new properties (lysogenic conversion).

  4. Induction can trigger entry into lytic cycle.

• Multiplication of Animal Viruses:

  1. Attachment: Virus binds to cell membrane.

  2. Penetration: Entry by endocytosis or fusion.

  3. Uncoating: Viral genome released by host or viral enzymes.

  4. Biosynthesis: Synthesis of viral nucleic acids and proteins.

  5. Maturation: Assembly of viral components.

  6. Release: By budding (enveloped viruses) or cell rupture.

Types of Viral Genomes and Replication

• DNA Viruses: May be single- or double-stranded; replicate in the nucleus.

• RNA Viruses: May be sense (+), antisense (–), or double-stranded; replicate in the cytoplasm.

• Retroviruses: Single-stranded RNA viruses that use reverse transcriptase to synthesize DNA from RNA (e.g., HIV).

Latent and Persistent Infections

• Latent Infections: Virus remains dormant in host cells (e.g., herpesviruses); can reactivate later.

• Persistent Infections: Virus is continuously present, often causing progressive disease (e.g., measles).

Prions, Plant Viruses, and Viroids

• Prions: Infectious proteins; cause diseases such as Creutzfeldt-Jakob disease; transmissible by ingestion, transplant, or surgical instruments.

• Plant Viruses: Enter through wounds or via insect vectors.

• Viroids: Infectious RNA molecules affecting plants.

Viruses and Cancer

• Some viruses can activate oncogenes, transforming normal cells into cancerous cells.

• Transformed cells may show increased growth, loss of contact inhibition, and express tumor-specific antigens.

• Oncogenic DNA Viruses: Adenoviridae, Herpesviridae, Poxviridae, Papovaviridae, Hepadnaviridae.

Examples of DNA Viruses

Examples of RNA Viruses

• Sense (+) Strand RNA Virus: Genome can serve directly as mRNA.

• Antisense (–) Strand RNA Virus: Genome is complementary to mRNA; must be transcribed to (+) sense before translation.

• Double-Stranded RNA Virus: Contains both (+) and (–) RNA strands.

• Retroviridae: Single-stranded RNA, two RNA strands, uses reverse transcriptase (e.g., HIV).