PAGE-BY-PAGE NOTES: Microbiology — The Microbial World and You; Structure of Atoms; Observing Microorganisms

Page 1

• Source: Microbiology an Introduction, Thirteenth Edition, Chapter 1: The Microbial World and You.
• Chapter and edition identifiers: Chapter 1, The Microbial World and You; 13th Edition; Tortora, Funke, Case.
• Purpose of Chapter 1: Introduce microorganisms, their roles in life and industry, and foundational concepts in microbiology.

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• Topic indicated: Normal Intestinal Bacteria (likely an image/label). Note presence of intestinal microbiota as part of normal flora.

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• Title slide: Microbes in Our Lives.
• Sets the stage for the pervasiveness and importance of microbes in everyday life.

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• Definition: Microbes = microorganisms too small to be seen with the unaided eye.
• Included groups: bacteria, fungi, protozoa, microscopic algae, and viruses.
• Key idea: Microbes are diverse and occupy many niches in nature and in/around the human body.

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• Some microbes are pathogenic (disease-producing).
• Beneficial/functional roles:
  • Decompose organic waste.
  • Generate oxygen via photosynthesis.
  • Produce chemical products: ethanol, acetone, vitamins.
  • Fermented foods: vinegar, cheese, bread.
  • Useful products for manufacturing and medicine: cellulose products; insulin.
• Takeaway: Microbes contribute to industry, health, and ecosystems, both positively and negatively.

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• Knowledge of microorganisms enables humans to:
  • Prevent food spoilage.
  • Prevent disease.
  • Understand causes and transmission of disease to prevent epidemics.

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• The Microbiome concept:
  • An adult human body contains around $30\times 10^{12}$ body cells and harbors $40\times 10^{12}$ bacterial cells.
  • The microbiome is a stable group of microbes living on/in the human body.
• Roles of the microbiome:
  • Help maintain good health.
  • Compete with pathogens (prevent growth of pathogenic microbes).
  • May train the immune system to distinguish threats.

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• Normal microbiota: the acquired microorganisms on or in a healthy human.
• Acquisition: Begin at birth; may colonize indefinitely or transiently (transient microbiota).
• Colonization factors: Requires suitable nutrients and environment at body sites suitable for microbial flourish.

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• Human Microbiome Project (begun 2007):
  • Primary goal: determine typical microbiota makeup of various body areas.
  • Secondary goal: understand relationships between microbiome changes and human disease.
• National Microbiome Initiative (NMI) (begun 2016): explores microbes’ roles in various ecosystems.

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• Nomenclature history: Carolus Linnaeus established the system of scientific nomenclature in 1735.
• Each organism has two names: genus and specific epithet (binomial nomenclature).

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• Scientific names:
  • Italicized or underlined; genus capitalized; species epithet lowercase.
  • Latinized and used worldwide.
  • Names may be descriptive or honor a scientist.

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• Example: Escherichia coli
  • Honors Theodor Escherich (discoverer) and describes habitat—the large intestine (colon).

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• Example: Staphylococcus aureus
  • Describes clustered (staphylo-) spherical (coccus) cells.
  • Describes gold-colored (aureus) colonies.

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• Abbreviation rules after first use:
  • Escherichia coli → E. coli; Staphylococcus aureus → S. aureus.
  • In context, E. coli is found in the large intestine; S. aureus on skin.

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• Visual/diagram page showing broad categories: prokaryote, eukaryote, acellular. The key takeaway: Living organisms are organized into prokaryotic and eukaryotic categories, plus acellular agents (viruses, viroids, prions, etc.).

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• Types of Microorganisms: Bacteria.
• Several micrographs (SEM/TEM) show cellular diversity including sporangia, pseudopods, and other structures.
• This page emphasizes the diversity of bacterial cell forms and imaging techniques.

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• Bacteria: characteristics
  • Prokaryotes; primitive nucleus (prenucleus).
  • Single-celled organisms.
  • Peptidoglycan cell walls.
  • Reproduce by binary fission.
  • Nutritional sources: organic/inorganic chemicals or photosynthesis.
  • Motility: may swim via flagella.

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• Bacteria (image-related): typical size around a few micrometers; SEM magnifications shown.

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• Archaea:
  • Prokaryotes without peptidoglycan in cell walls (may lack cell wall entirely).
  • Often live in extreme environments.
  • Include methanogens, extreme halophiles, extreme thermophiles.
  • Generally not known to cause disease in humans.

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• Fungi:
  • Eukaryotes with distinct nucleus.
  • Cell walls contain chitin.
  • Absorb organic chemicals for energy.
  • Yeasts are unicellular; molds and mushrooms are multicellular.
  • Molds form mycelia made of hyphae.

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• Visuals: types of microorganisms (sporangia). SEM imaging shows structural features.

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• Protozoa:
  • Eukaryotes; absorb or ingest organic chemicals.
  • Motility via pseudopods, cilia, or flagella.
  • Free-living or parasitic; some are photosynthetic.
  • Reproduce sexually or asexually.

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• Protozoa (image cue): Pseudopod-based movement illustrated.

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• Algae:
  • Eukaryotes; cellulose cell walls.
  • Found in freshwater, saltwater, soil.
  • Use photosynthesis for energy; produce oxygen and carbohydrates.
  • Sexual and asexual reproduction possible.

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• Visual cue: algae morphology; size indicators in LM (light microscopy).

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• Viruses:
  • Acellular; consist of DNA or RNA core.
  • Core is surrounded by a protein coat; may have a lipid envelope.
  • Replicate only inside living host cells; inert outside hosts.

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• Viruses (image): ZikV as example; TEM imaging shows virion size ~70 nm.

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• Multicellular Animal Parasites:
  • Eukaryotes; multicellular animals.
  • Not strictly microorganisms; include parasitic flatworms and roundworms (helminths).
  • Some microscopic life stages occur in life cycles.

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• Classification (Carl Woese, 1978): three domains based on cellular organization:
  • Bacteria
  • Archaea
  • Eukarya (which includes protists, fungi, plants, animals)

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• A Brief History of Microbiology: sets the stage for major discoveries and shifts in understanding.

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• The First Observations:
  • 1665: Robert Hooke observed that living things are composed of little boxes, or cells, marking the beginning of cell theory.
  • The first microbes observed 1623–1673 by Anton van Leeuwenhoek, called “animalcules.”

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• Anton van Leeuwenhoek's Microscopic Observations:
  • Microscope replica; components: lens, specimen-positioning screw, focusing control, stage, etc.
  • Emphasis on early microscopy tools enabling discovery of microbes.

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• The Debate over Spontaneous Generation:
  • Spontaneous generation: life arising from nonliving matter via a vital force.
  • Biogenesis: life arises from preexisting life.

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• Redi’s experiments (1668) with decaying meat:
  • Covered jars prevented maggots; opened jars produced maggots; sealed jars produced no maggots.
  • Conclusion: challenged spontaneous generation; supported biogenesis.

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• Needham (1745): Boiled nutrient broth in covered flasks; observed microbial growth.
  • Argued for spontaneous generation; later critiques questioned sealed-ness and boiling completeness.

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• Spallanzani (1765): Boiled broth in sealed flasks; no microbial growth.
  • Supported biogenesis; challenged Needham’s interpretation.

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• The Theory of Biogenesis: Rudolf Virchow (1858) proposed that cells arise from preexisting cells.

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• The Theory of Biogenesis (cont.): Louis Pasteur (1861) showed microorganisms are present in air.
  • Experiments: nutrient broth in an open flask shows growth; broth in a sealed flask shows no growth.
  • S-shaped (S-neck) flasks allowed air in but prevented particle entry; broth remained sterile.
  • Conclusion: microorganisms originate in air or fluids, not from mystical forces.

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• Pasteur’s S-shaped neck flask experiments reinforced germ theory and the idea that microbes are responsible for spoilage and disease.

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• Disproving Spontaneous Generation—Key Concept Summary:
  • Pasteur demonstrated microbes are present in nonliving matter (air, liquids, solids).
  • Spontaneous generation was discredited; aseptic techniques emerged to prevent contamination.
  • Some original Pasteur flasks remain on display at the Pasteur Institute.

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• The Golden Age of Microbiology (1857–1914):
  • Beginning with Pasteur’s work, discoveries linked microbes to disease, immunity, and antimicrobial drugs.

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• Golden Age Highlights:
  • Pasteur showed microbes are responsible for fermentation; fermentation converts sugars to alcohol in absence of air.
  • Microbial growth also causes spoilage of foods and beverages.
  • Aerobic bacteria can spoil wine by converting alcohol to acetic acid (vinegar).

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• Pasteurization: High heat for a short time to kill harmful bacteria in beverages while preserving alcohol content (
  • Concept: heat-treatment to reduce microbial load without destroying product quality).

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• Milestones in the Golden Age (selected):
  • Pasteur: Fermentation, Disproved spontaneous generation, Pasteurization.
  • Lister: Aseptic surgery.
  • Koch: Germ theory of disease, pure cultures.
  • Finlay: Yellow fever; Escherich: E. coli; Petri: Petri dish; etc.
  • An asterisk (*) marks Nobel Laureates.

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• The Germ Theory of Disease (history):
  • 1835: Agostino Bassi linked silkworm disease to a fungus.
  • 1865: Pasteur linked another silkworm disease to a protozoan.
  • 1840s: Ignaz Semmelweis advocated handwashing to prevent puerperal fever.

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• Germ theory and medical advances:
  • 1860s: Lister applied Pasteur’s ideas to surgical antisepsis using phenol.
  • Prevention of infection through antisepsis and aseptic technique.

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• Milestones (late 1880s–1890s):
  • Koch: Mycobacterium tuberculosis; Koch’s postulates (link a specific microbe to a specific disease).
  • Hess: Agar (solid) media.
  • Gram: Gram staining procedure.
  • Petri: Petri dish; Kitasato: Clostridium tetani; von Bering: Diphtheria antitoxin; Ehrlich: Immunity theory.
  • Winogradsky: Sulfur cycle.

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• Koch’s Postulates (1876):
  • Isolate a suspected microbe from a diseased host.
  • Grow in pure culture.
  • Reproduce disease when introduced into a healthy host.
  • Re-isolate and re-identify the microbe.

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• Milestones continued (1892–1911):
  • Shiga: Shigella dysenteriae; Ehrlich: Syphilis treatment; Chagas: Trypanosoma cruzi; Rous: Tumor-causing virus (later Nobel Prize).

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• Vaccination:
  • 1796: Edward Jenner inoculated a person with cowpox virus, conferring immunity to smallpox.
  • Etymology: vaccination from Latin vacca (cow).

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• Birth of Modern Chemotherapy:
  • Chemotherapy: treatment of disease with chemicals.
  • Antibiotics: chemicals produced by bacteria/fungi that inhibit or kill other microbes.
  • Distinction: synthetic drugs vs antibiotics.

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• First Synthetic Drugs:
  • Quinine historically used for malaria.
  • Paul Ehrlich proposed a “magic bullet” that targets pathogens with minimal host harm.
  • 1910: Salvarsan (arsenic-based) for syphilis.
  • 1930s: Sulfonamides synthesized.

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• A Fortunate Accident – Penicillin:
  • 1928: Alexander Fleming discovered penicillin from Penicillium mold inhibiting S. aureus by accident.
  • 1940s: Penicillin mass-produced and used clinically.

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• The Discovery of Penicillin (visual):
  • Demonstrates inhibition zone around Penicillium colonies in bacterial lawns.

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• Problems with antimicrobial chemicals:
  • Overuse leads to resistance.
  • Some drugs can be toxic to humans (especially antivirals).
  • Efforts to overcome these problems spurred a Third Golden Age of Microbiology (late 1980s–present).

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• Modern Developments in Microbiology: heading for ongoing advances across subfields.

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• Bacteriology, Mycology, and Parasitology:
  • Bacteriology: study of bacteria.
  • Mycology: study of fungi.
  • Parasitology: study of protozoa and parasitic worms.

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• Parasitology: The Study of Protozoa and Parasitic Worms:
  • Dracunculus medinensis (guinea worm) image illustrates human parasitism.
  • Rod of Asclepius symbol of medicine reflects medical context.

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• Immunology:
  • Immunology studies immunity; vaccines and interferons prevent/cure viral diseases.
  • 1933: Rebecca Lancefield classifies streptococci based on cell wall components, a major immunological taxonomy advance.

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• Rebecca Lancefield: work on chemical composition of polysaccharides in pathogenic streptococcal cell walls; contributed to serotyping and infection understanding.

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• Virology:
  • Study of viruses.
  • Iwanowski (1892) and Stanley (1935) identified viruses as infectious agents causing mosaic disease of tobacco; electron microscopy later clarified structure.

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• Molecular Genetics:
  • Microbial genetics: inheritance in microbes.
  • Molecular biology: DNA directs protein synthesis.
  • Genomics: gene-level organism classification advances.
  • Recombinant DNA: combining DNA from different sources.
  • 1960s: Paul Berg: inserting animal DNA into bacterial DNA yielded expression of animal protein in bacteria.

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• Milestones in Molecular Genetics:
  • 1941 Beadle & Tatum: genes encode enzymes (one gene–one enzyme concept).
  • 1944 Avery, MacLeod, McCarty: DNA is hereditary material.
  • 1953 Watson & Crick: proposed DNA double-helix structure.
  • 1961 Jacob & Monod: role of mRNA in protein synthesis.

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• Milestones in the Golden Age continued (displayed timeline and Nobel laureates):
  • Lister, Koch, Pasteur, Elhrich, Winogradsky, etc. highlighted with Nobel recognitions.
  • Visual emphasis on a network of foundational microbiology breakthroughs.

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• Milestones in Second and Third Golden Ages (1940s–present):
  • Second Golden Age: antibiotics like penicillin discovered (Fleming, Chain, Florey), streptomycin (Waksman).
  • 1950s–1960s: Krebs cycle enzymology; viral culture in cell culture systems; Beadle & Tatum genetic control; tumor immunology work; monoclonal antibodies era.
  • 1960s–1980s: DNA sequencing, recombinant DNA technologies become central.
  • 1990s–2000s: transplants, cancer genetics, monoclonal antibody therapies, HIV discovery and deepening immunology, etc.
  • 2010s: rapid advances in genomics, proteomics, and systems biology; renewed emphasis on HIV, malaria, and emerging pathogens.

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• Microbes and Human Welfare: linkage to daily life and industry via microbial processes.

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• Recycling Vital Elements:
  • Microbial ecology studies relationships between microbes and environments.
  • Bacteria transform carbon, oxygen, nitrogen, sulfur, and phosphorus into forms usable by plants and animals.

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• Sewage Treatment: Using Microbes to Recycle Water:
  • Sewage is ~99.9% water; treatment removes solids and uses microbes to convert organic material to by-products like CO₂.
  • Physical removal of large solids; biological treatment to mineralize organics.

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• Bioremediation: Using Microbes to Clean Up Pollutants:
  • Bacteria degrade organic matter in sewage and detoxify pollutants like oil and mercury.

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• Composting Municipal Wastes: microbes decompose organic waste into useful compost.

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• Insect Pest Control by Microorganisms:
  • Microbes harmful to insects serve as natural pesticides; Bt (Bacillus thuringiensis) produces crystals toxic to insects but safe for animals/plants.
  • Some Bt toxin genes introduced into crops to confer resistance.

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• Bacillus thuringiensis toxin (Bt) image: endospore and parasporal body structure visualized; toxin selectively targets insects.

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• Biotechnology and Recombinant DNA Technology:
  • Biotechnology: use of microbes for practical applications (foods, chemicals).
  • Recombinant DNA: microbes engineered to produce proteins, vaccines, enzymes.
  • Gene therapy concept: replace defective genes in human cells.
  • GM bacteria used to protect crops from insects and freezing.

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• Microbes and Human Disease: overview of interactions between microbes and disease processes.

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• Normal Microbiota:
  • Microbes normally present in/on the human body = normal microbiota.
  • Roles: Prevent growth of pathogens; produce growth factors like vitamins B and K.
  • Resistance: body’s ability to ward off disease; factors include skin, stomach acid, antimicrobial chemicals.

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• Biofilms:
  • Microbes attach to surfaces and form masses (biofilms) on rocks, pipes, teeth, implants.
  • Biofilms are often resistant to antibiotics and can cause persistent infections.

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• Biofilm image on plastic (Serratia liquefaciens): capsule material shown; SEM image illustrates structure.

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• Emerging Infectious Diseases (EIDs): new or rapidly increasing diseases; pathogens emerging or increasing in incidence.

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• Zika virus disease:
  • Virus discovered 1947; human epidemics in Micronesia (2007), French Polynesia and Brazil (2013–2015).
  • Transmission: Aedes mosquito bite; can be sexually transmitted.
  • In pregnancy, can cause severe birth defects.

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• MERS (Middle East Respiratory Syndrome):
  • Caused by MERS-CoV; similar to SARS in some aspects.
  • Human cases since 2014; ~1,800 cases and ~630 deaths (as of the data).

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• H1N1 influenza (swine flu):
  • First detected in the US in 2009; declared a pandemic by WHO in 2009.
• Avian influenza A (H5N1):
  • Primarily in waterfowl/poultry; sustained human-to-human transmission has not occurred.

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• Morphology of an Enveloped Helical Virus: TEM image showing spikes; approximate size ~20–100 nm range (example label 20 nm).

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• MRSA and antibiotic resistance trends:
  • MRSA emerged with penicillin resistance in the 1950s, methicillin resistance in the 1980s, and vancomycin resistance (VRSA) reported in the 1990s.
  • Designations: VISA (vancomycin-intermediate S. aureus) and VRSA (vancomycin-resistant S. aureus).

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• Ebola hemorrhagic fever (EHF):
  • Virus causes fever, hemorrhaging, and coagulopathy.
  • Transmission via contact with infected blood or body fluids.
  • Outbreak history includes 2014 outbreak in Guinea with over 28,000 infections.

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• Ebola Hemorrhagic Virus image (SEM): ~400 nm scale bar.

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• Marburg virus:
  • Causes hemorrhagic fever similar to Ebola.
  • Historical cases in Europe among lab workers exposed to African green monkeys; 13 outbreaks in Africa (1975–2016).
  • Fruit bats are natural reservoir suspected for both Marburg and Ebola.

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• Chapter 2 transition: From Chapter 1 to Chemical Principles; overview of moving from microbiology’s broad life-science context to foundational chemistry.

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• The Structure of Atoms:
  • Chemistry studies interactions between atoms and molecules.
  • The atom is the smallest unit of matter; atoms form molecules.

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• Subatomic components:
  • Electrons (e−): negatively charged.
  • Protons (p+): positively charged.
  • Neutrons (n0): neutral.
  • Nucleus contains protons and neutrons; electrons orbit the nucleus.

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• The Structure of an Atom:
  • Diagrammatic representation: nucleus with protons and neutrons; electron shells around.

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• Chemical Elements:
  • Atoms with the same number of protons belong to the same element (unique atomic number Z).
  • Atomic number = number of protons.

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• Atomic Mass and Isotopes:
  • Atomic mass equals total number of protons and neutrons.
  • Isotopes: atoms with different neutron counts.
  • Example: isotopes of oxygen vary in neutron number.

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• The Elements of Life (Table 2.1):
  • Hydrogen (H), Carbon (C), Nitrogen (N), Oxygen (O) are most abundant in living organisms.
  • Total list includes Sodium (Na), Magnesium (Mg), Phosphorus (P), Sulfur (S), Chlorine (Cl), Potassium (K), Calcium (Ca), Iron (Fe), Iodine (I).
  • Atomic numbers and approximate atomic masses provided in the table for each element.

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• The Elements of Life (continued):
  • Continuation of Table 2.1 with remaining elements and their approximate atomic masses.

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• Electronic Configurations:
  • Electrons are arranged in electron shells that correspond to energy levels.

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• How Atoms Form Molecules: Chemical Bonds
  • Atoms form molecules to fill outer electron shells; valence = number of electrons missing or extra in the outer shell.
  • Bonds arise from attractive forces between atomic nuclei due to valence electrons.

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• Compounds:
  • A compound is a molecule containing two or more kinds of atoms.
  • Example: Water, $\mathrm{H_2O}$, consists of two hydrogen atoms and one oxygen atom.

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• Ionic Bonds:
  • Ions are charged atoms formed by loss or gain of electrons.
  • Cations: positively charged (lost electrons); Anions: negatively charged (gained electrons).

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• Ionic Bond Formation (example):
  • Sodium (Na) donates an electron to chlorine (Cl), forming Na⁺ and Cl⁻; the two ions attract to form NaCl.

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• Ionic Bonds (continued):
  • Cations: lose electrons; Anions: gain electrons.

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• Ionic Bonds (continued):
  • Ionic bonds are attractions between oppositely charged ions.

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• Ionic Bond Formation (illustration):
  • Na⁺ and Cl⁻ attract to form NaCl (sodium chloride) via ionic bond.

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• Covalent Bonds:
  • Form when two atoms share one or more pairs of electrons.
  • Covalent bonds are stronger and more common in organisms than ionic bonds.

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• Covalent Bond Formation (example: H2):
  • Hydrogen atoms share electrons to form a hydrogen molecule (H–H).

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• Covalent Bond Formation (example: CH4 - methane):
  • A carbon atom forms four single covalent bonds with four hydrogen atoms.

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• Hydrogen Bonds:
  • Form when a hydrogen atom covalently bonded to O or N is attracted to another N or O atom in a different molecule.

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• Hydrogen Bond Formation in Water (illustration):
  • Water molecules form hydrogen bonds through the O–H bonds, contributing to water’s unique properties.

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• Molecular Mass and Moles:
  • Molecular mass = sum of atomic masses in a molecule.
  • One mole of a substance = its molecular mass expressed in grams.
  • Unit of molecular mass is the dalton (Da).
  • Example: Water: $\mathrm{H_2O}$ has 2×1 (H) + 16 (O) = 18 Da; 1 mole weighs 18 g.

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• Chemical Reactions:
  • Reactions involve making or breaking chemical bonds; energy changes occur.
  • Endergonic reactions absorb energy; exergonic reactions release energy.

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• Synthesis Reactions:
  • Atoms/ions/molecules combine to form larger molecules.
  • Anabolism: synthesis of molecules in a cell.

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• Decomposition Reactions:
  • Molecules split into smaller units.
  • Catabolism: decomposition reactions in a cell.

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• Exchange Reactions:
  • Involves both synthesis and decomposition processes.

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• Reversibility of Chemical Reactions:
  • Reactions can proceed in either direction depending on conditions.

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• Important Biological Molecules: Organic vs Inorganic
  • Organic compounds: contain carbon and hydrogen; typically structurally complex.
  • Inorganic compounds: lack carbon; usually small and simple.

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• Inorganic Compounds: (overview; examples to be discussed elsewhere)

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• Water:
  • Inorganic, polar molecule; solvent for many substances.
  • Polar dissolution leads to dissociation of many solutes.
  • Hydrogen bonding absorbs heat; acts as a temperature buffer.

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• Hydrogen Bond Formation in Water (illustration):
  • Depicts hydrogen bonds between water molecules.

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• Hydrogen Bond Formation in Water (continuation):
  • Visuals showing hydrogen bonding network and properties.

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• How Water Acts as a Solvent for NaCl:
  • Na⁺ and Cl⁻ ions are solvated by water molecules; hydration spheres form around ions.

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• Acids, Bases, and Salts – Overview:
  • Acids dissociate to release H⁺ and anions.
  • Bases dissociate to release OH⁻ and cations.
  • Salts dissociate into cations and anions; neither is H⁺ nor OH⁻ in general.

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• Acids (example): HCl dissociates to H⁺ and Cl⁻.

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• Bases (example): NaOH dissociates to Na⁺ and OH⁻.

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• Acids and Bases – continued with visual examples.

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• Salts – continued: general dissociation into cations and anions.

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• Acid-Base Balance: The Concept of pH
  • pH expresses H⁺ concentration: $pH = -\log_{10}[H^+]$
  • Increasing acidity lowers pH; increasing alkalinity raises pH.
  • Most organisms grow best between pH $6.5$ and $8.5$.

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• Additional notes on pH range for biological systems (as above; practical tolerance ranges).

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• Organic Compounds (lead-in): overview of organic chemistry principles; emphasis on carbon-based molecules.

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• Organic Compounds (lead-in image): focus on carbon-containing molecules.

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• Structure and Chemistry:
  • Organic compounds typically contain hydrogen, oxygen, and/or nitrogen in addition to carbon.
  • The carbon skeleton forms the backbone of organic molecules.

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• Functional Groups:
  • Functional groups attached to the carbon skeleton determine chemical properties and biological functions.

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• The Hydroxyl Group of Alcohols:
  • Structure: R–OH (example methanol, ethanol, isopropanol).

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• Representative Functional Groups and the Compounds in Which They Are Found (Part 1):
  • Alcohol (R–OH): biological importance in lipids and carbohydrates.
  • Aldehyde (R–CHO): reducing sugars (e.g., glucose).
  • Ketone (R–CO–R): metabolic intermediates.
  • Methyl (R–CH3): DNA and energy metabolism.
  • Amino (R–NH₂): proteins.

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• Representative Functional Groups and the Compounds in Which They Are Found (Part 2):
  • Ester (R–COO–R’): bacterial and eukaryotic plasma membranes (lipids).
  • Ether (R–O–R’): archaeal plasma membranes.
  • Sulfhydryl (R–SH): energy metabolism; protein structure.
  • Carboxyl (R–COOH): organic acids; lipids; proteins.
  • Phosphate (R–O–P=O(OH)₂): ATP and DNA.
  • Note: In an aldehyde, the C=O is at the end (terminal); in a ketone, the C=O is internal.

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• Functional groups in amino acids:
  • Amino group (–NH2) and carboxyl group (–COOH) attached to an α-carbon; side chain (R) distinguishes each amino acid.

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• Macromolecules:
  • Small organic molecules (monomers) join to form large polymers (polymers/macromolecules).
  • Macromolecules: polymers composed of many repeating monomers.

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• Linkage of Monomers:
  • Monomers join by dehydration synthesis (condensation) reactions to form polymers; water is released.

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• Dehydration Synthesis (illustration):
  • Demonstrates formation of a glycosidic bond as two monosaccharides join with release of water (H₂O).

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• Carbohydrates:
  • Serve as cell structures and energy sources.
  • Composed of C, H, O with general formula (CH₂O)n; many are isomers (same formula, different structures).

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• Monosaccharides:
  • Simple sugars with 3–7 carbon atoms (e.g., glucose, deoxyribose).

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• Disaccharides:
  • Formed when two monosaccharides join via dehydration synthesis.
  • Can be broken down by hydrolysis.

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• Dehydration Synthesis and Hydrolysis (illustrations):
  • Dehydration: two monosaccharides join, releasing water.
  • Hydrolysis: bonds broken with water intake; example: glucose, fructose, sucrose.

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• Polysaccharides:
  • Long chains of monosaccharides joined by dehydration synthesis.
  • Examples: starch, glycogen, dextran, cellulose; differ by the bonding and function of glucose units.

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• Lipids:
  • Contain C, H, O; nonpolar and insoluble in water; primary components of cell membranes.

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• Simple Lipids (Fats):
  • Triglycerides consisting of glycerol and fatty acids; formed by dehydration synthesis.

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• Structural Formulas of Simple Lipids (illustrations):
  • Glycerol backbone with fatty acid chains; saturated fatty acids (no double bonds).
  • Palmitic acid example; hydrocarbon chains.

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• Simple Lipids (continued):
  • Saturated fats have no double bonds; unsaturated fats have one or more double bonds.
  • Cis configuration: hydrogen atoms on same side of the double bond; Trans configuration: on opposite sides.

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• [Content not legible in transcript; likely continuation of lipid discussion or a schematic image.]

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• Complex Lipids:
  • Contain C, H, O plus P, N, and/or S.
  • Cell membranes consist of complex lipids called phospholipids.
  • Structure: glycerol, two fatty acids, and a phosphate group; amphipathic properties with polar and nonpolar regions.

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• [Image/diagram-heavy page; content likely emphasizes more details on phospholipids and membrane composition.]

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• Steroids:
  • Four carbon rings with attached group(s).
  • Important in membranes to maintain fluidity; cholesterol is a key steroid.

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• Cholesterol, a Steroid (structure):
  • Cholesterol depicted with ring structures and methyl/alkyl substituents to illustrate membrane-associated steroid function.

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• Proteins:
  • Made of C, H, O, N, and sometimes S.
  • Roles: essential in cell structure and function; enzymes catalyze reactions; transporters across membranes; flagella; bacterial toxins and cellular components.

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• Amino Acids:
  • Proteins are composed of 20 amino acids (monomers).
  • Each amino acid has: an amino group, a carboxyl group, an α-carbon, and a distinctive side chain (R).

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• Amino Acid Structure (illustrations):
  • General amino acid: H₂N–CH(R)–COOH; α-carbon (Cα) central.
  • Tyrosine example shows aromatic R group.

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• The 20 Amino Acids Found in Proteins (Table 2.5; three-letter and one-letter codes):
  • Glycine (Gly, G)
  • Alanine (Ala, A)
  • Valine (Val, V)
  • Leucine (Leu, L)
  • Isoleucine (Ile, I)
  • Serine (Ser, S)
  • Threonine (Thr, T)
  • Cysteine (Cys, C)
  • Methionine (Met, M)
  • Glutamic acid (Glu, E)
  • Aspartic acid (Asp, D)
  • Lysine (Lys, K)
  • Arginine (Arg, R)
  • Asparagine (Asn, N)
  • Glutamine (Gln, Q)
  • Phenylalanine (Phe, F)
  • Tyrosine (Tyr, Y)
  • Histidine (His, H)
  • Tryptophan (Trp, W)
  • Proline (Pro, P)
  • Note: cysteine and methionine contain sulfur.

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• The 20 Amino Acids Found in Proteins (continued):
  • Structural representations for each amino acid; emphasis on diversity of R groups (branched/unbranched, polar/nonpolar, acidic/basic).

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• Amino Acids as Stereoisomers:
  • D and L isomers exist; L-forms are most common in nature.

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• L- and D-Isomers of an Amino Acid (models):
  • Handedness (left vs right): L-amino acids predominate in proteins.

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• Peptide Bonds:
  • Peptide bonds link amino acids via dehydration synthesis.

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• Peptide Bond Formation by Dehydration Synthesis (dipeptide example Gly–Gly):
  • N–C–C linkage formed with release of water (H₂O).

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• Levels of Protein Structure: Primary structure = amino acid sequence (polypeptide chain).

Page 162

• Protein Primary Structure (image/line diagram):
  • Shows amino acid sequence along a polypeptide chain; peptide bonds hold sequence.

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• Levels of Protein Structure: Secondary structure arises from folding into helices or pleated sheets.

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• Protein Secondary Structure:
  • Helix and pleated sheet stabilized by hydrogen bonds (C=O…N–H bonds).

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• Levels of Protein Structure: Tertiary Structure
  • Irregular folding forms 3D shape.
  • Stabilized by disulfide bridges, hydrogen bonds, ionic bonds between amino acid side chains.

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• Protein Structure: Tertiary structure in 3D space; examples of stabilizing interactions.

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• Levels of Protein Structure: Quaternary Structure
  • Two or more polypeptides assemble to form a functional protein.

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• Protein Structure: Quaternary arrangement and interactions among multiple polypeptides.

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• Recap of Structural Levels:
  • 1° Primary: amino acid sequence.
  • 2° Secondary: helices/pleated sheets.
  • 3° Tertiary: 3D folding, bonds like disulfide, H-bonds, ionic.
  • 4° Quaternary: multiple polypeptides interacting.

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• Denaturation:
  • Proteins can lose their shape and function under hostile conditions (temperature, pH).

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• Conjugated Proteins:
  • Proteins combined with other organic molecules (e.g., glycoproteins, nucleoproteins, lipoproteins).

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• Nucleic Acids:
  • Consist of nucleotides (pentose sugar, phosphate group, nitrogenous base).
  • Nucleosides: pentose sugar + nitrogenous base (without phosphate).

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• DNA (Deoxyribonucleic Acid):
  • Contains deoxyribose; exists as a double helix.
  • Base pairs: Adenine (A) pairs with Thymine (T); Cytosine (C) pairs with Guanine (G).
  • Order of bases encodes genetic information.

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• Structure of DNA (diagrammatic description):
  • Nucleotide: nitrogenous base + deoxyribose sugar + phosphate.
  • Backbone: alternating sugar and phosphate groups.
  • Rungs: base pairs via hydrogen bonds (A–T: 2 H-bonds; G–C: 3 H-bonds).
  • Antiparallel strands: one strand runs 5'→3', the other 3'→5'.
  • Key concepts: DNA stores genetic information; nucleotides form the backbone; complementary base pairing.

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• RNA (Ribonucleic Acid):
  • Contains ribose; typically single-stranded.
  • Bases: Adenine (A) pairs with Uracil (U) in RNA (instead of Thymine); Cytosine (C) pairs with Guanine (G).
  • Several kinds of RNA participate in protein synthesis.

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• Uracil Nucleotide of RNA:
  • Chemical structure representation for uracil nucleotide; U pairs with A in RNA.

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• Adenosine Triphosphate (ATP):
  • Chemistry: Adenosine + three phosphate groups.
  • Structure includes adenine, ribose, and phosphate chain.

Page 178

• The Structure of ATP (illustration):
  • Shows adenine, ribose (adenosine), and three phosphates (α, β, γ).

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• ATP Function:
  • Stores chemical energy from cellular reactions.
  • Hydrolysis releases energy: ATP + H₂O → ADP + Pᵢ + Energy.

Page 180

• ATP Hydrolysis Energy Release (schematic):
  • Illustrates conversion of ATP to ADP and inorganic phosphate with energy release.

Page 181

• Transition to Chapter 3: Observing Microorganisms through a Microscope.

Page 182

• Helicobacter pylori image: example of a clinically relevant microbe.

Page 183

• Microscopes and Magnification:
  • Various microscopy techniques have different magnifications and resolutions (LM, SEM, TEM, AFM).
  • Example organism sizes used for teaching: E. coli, viruses, red blood cells, etc.
  • Dimensions given in μm, nm, etc.
  • Resolution improves with shorter wavelengths; size bars help interpret images.
  • A red icon indicates artificially colorized micrographs.
  • Practical exercise: estimating how many bacteria fit end-to-end on a finger using size relationships (example answer: ~65,000 bacteria per finger length).

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• Units of Measurement:
  • Microorganisms measured in micrometers (μm) and nanometers (nm).

Page 185

• Microscopy Instru​​ments – Simple Microscope:
  • One-lens instrument analogous to a magnifying glass but with higher magnification.

Page 186

• Anton van Leeuwenhoek’s Microscopic Observations (image/description):
  • Details of a simple single-lens microscope similar to a modern hand lens.
  • Key components listed (lens, specimen positioning, focusing, stage, etc.).

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• Light Microscopy:
  • Any microscope using visible light to observe specimens.
  • Types include: compound light microscopy, darkfield, phase-contrast, differential interference contrast (DIC), fluorescence, confocal.

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• [Content likely image-focused; in transcript this page is largely decorative/instructional about microscope usage.]

Page 189

• Compound Light Microscopy:
  • In a compound microscope, the image is magnified again by the ocular lens.
  • Total magnification = objective lens × ocular lens.

Page 190

• The Compound Light Microscope (diagrammatic components):
  • Ocular lens, objective lenses, body tube, condenser, illuminator, stage, etc.
  • Path of light from illumination to the eye described.

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• Resolution in Compound Light Microscopy:
  • Resolution is the ability to distinguish two points.
  • Example: resolving power of 0.4 nm can distinguish points 0.4 nm apart (note: typical practical resolutions are larger; the text uses nm for illustrative purposes).
  • Shorter wavelengths yield greater resolution.

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• Refractive Index and Immersion Oil:
  • Refractive index measures light-bending ability of a medium.
  • Light can refract away from the objective lens; immersion oil reduces refraction, improving resolution.

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• Refraction with Oil Immersion Objective:
  • Using oil creates continuous medium between slide and lens; reduces light loss.
  • Illustration contrasts unrefracted vs refracted light with and without oil.

Page 194

• Brightfield Illumination:
  • Bright background; specimen appears dark against bright field.
  • Direct light does not reflect off specimen into the objective.

Page 195

• Brightfield Microscopy (illustration):
  • Path of light through the objective and ocular lenses; a basic setup.

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• Darkfield Microscopy:
  • Light objects on a dark background.
  • Condenser with opaque disk blocks central light; only oblique light enters the specimen and is collected by the objective.

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• Darkfield Microscopy (continued):
  • Edges of cells appear bright; internal structures may sparkle; pellicle outline visible.

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• Phase-Contrast Microscopy:
  • Enables viewing living organisms and internal cell structures.
  • Combines direct and diffracted light to enhance contrast.

Page 199

• Phase-Contrast (illustration):
  • Annular diaphragm creates two light paths; phase differences yield contrast.
  • Pellicle and internal structures become clearer.

Page 200

• Differential Interference Contrast (DIC) Microscopy:
  • Uses two light beams and prisms to increase contrast and add color-like shading for 3D appearance.

Page 201

• DIC (image):
  • Demonstrates higher-contrast, 3D-like rendering of specimens.

Page 202

• Fluorescence Microscopy:
  • Uses UV light to excite fluorescent substances (fluorochromes) that emit visible light.
  • Specimens may be stained with fluorescent dyes if they do not naturally fluoresce.

Page 203

• Principle of Immunofluorescence (illustration):
  • Antibody-based labeling enables specific visualization of target antigens.

Page 204

• Confocal Microscopy:
  • Cells stained with fluorochromes; short-wavelength light excites a single plane.
  • Computer reconstructs 3D image from sequential optical sections; depth up to ~$100\,\mu\text{m}$.

Page 205

• Confocal Microscopy (illustration):
  • Nucleus example; multi-plane imaging.

Page 206

• Two-Photon Microscopy (TPM):
  • Uses two photons of longer wavelength to excite fluorophores; penetrates up to ~1 mm in living tissue.

Page 207

• TPM (illustration):
  • Nucleus image; depth penetration emphasized.

Page 208

• Super-Resolution Light Microscopy:
  • Uses two laser beams; one stimulates fluorescence, the other cancels out most fluorescence except in a 1-nm volume.
  • Computer assembles nm-scale images to surpass conventional resolution.

Page 209

• Super-Resolution (illustration):
  • SRM achieves near-atomic scale resolution for light microscopy.

Page 210

• Scanning Acoustic Microscopy (SAM):
  • Measures sound waves reflected from a specimen; useful for studying cells attached to surfaces.
  • Resolution around ~$1\,\mu\text{m}$.

Page 211

• SAM image: bacterial biofilm on glass; scale ~$170\,\mu\text{m}$.

Page 212

• Electron Microscopy: overview
  • Uses electrons; shorter wavelengths yield higher resolution.
  • Essential for visualizing viruses and other ultrastructural details beyond light microscopy.

Page 213

• Transmission Electron Microscopy (TEM):
  • Electron beam passes through ultrathin sections; heavy-metal stains provide contrast.
  • Typical magnification: 10{,}000\x2013 10{,}000{,}000\times; resolution ~$10\,\text{pm}$.

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• (Image-heavy content; likely continuation of TEM/SEM discussion with captions.)

Page 215

• Transmission Electron Microscopy (continued):
  • Magnification and resolution ranges reiterated.

Page 216

• Scanning Electron Microscopy (SEM):
  • Electron beam scans the surface; secondary electrons create a 3D-like surface image.
  • Typical magnification $1{,}000 \text{ to } 500{,}000\times$; resolution ~$10\,\text{nm}$.

Page 217

• (Image-heavy content; likely continuation of SEM/TEM discussion.)

Page 218

• Scanning Electron Microscopy (continued):
  • Emphasizes 3D surface topology.

Page 219

• Scanning Tunneling Microscopy (STM):
  • Uses a tungsten probe to scan a specimen; reveals surface details.
  • Resolution ~1/100$^{\text{th}}$ of an atom (approximate).

Page 220

• Scanned-Probe Microscopy (STM) – Illustration: STM setup and image details.

Page 221

• Atomic Force Microscopy (AFM):
  • Uses a probe to feel surface contours; produces 3D images at near-atomic detail.

Page 222

• Scanned-Probe Microscopy (AFM) – Illustration: AFM setup and image details.

Page 223

• Preparation of Specimens for Light Microscopy:
  • Overview of steps preceding staining (smearing, fixing).

Page 224

• Preparing Smears for Staining:
  • Staining colors microorganisms; smears are fixed to kill organisms and affix them to slides.
  • Live/unfixed specimens have low contrast.

Page 225

• Staining Rationale:
  • Stains are salts with a positive or negative chromophore.
  • Basic dyes: chromophore is a cation; acidic dyes: chromophore is an anion.
  • Negative staining stains the background, not the cell, to visualize capsules or morphology.

Page 226

• Simple Stains:
  • Use of a single basic dye to color the entire microorganism.
  • Mordant used to intensify stain or coat specimen.

Page 227

• Differential Stains:
  • Distinguish between bacteria (different cell wall properties) using special staining methods like Gram stain and acid-fast stain.

Page 228

• Gram Staining:
  • Wet lab procedure divides bacteria into Gram-positive or Gram-negative.
  • Principle: crystal violet (primary stain) + iodine (mordant) + alcohol decolorization + safranin (counterstain).
  • Gram-positive: thick peptidoglycan retains crystal violet; appear purple.
  • Gram-negative: thin peptidoglycan and outer membrane lose crystal violet but take up safranin; appear pink/red.

Page 229

• Gram Staining – Stepwise Visualization: 1) Application of crystal violet (purple dye). 2) Application of iodine (mordant). 3) Alcohol wash (decolorization). 4) Application of safranin (counterstain).
  • Representative outcomes: Gram-positive (purple) vs Gram-negative (pink).

Page 230

• Gram Staining – Visuals:
  • Coccus (Gram-positive) vs Rod (Gram-negative) differentiation demonstrated in LM.

Page 231

• Acet Staining – Acid-Fast Stain:
  • Binds to bacteria with waxy cell walls that resist decolorization by acid-alcohol.
  • Used to identify Mycobacterium and Nocardia.

Page 232

• Acid-Fast Bacteria:
  • M. tuberculosis example; Gram stain may fail for mycobacteria due to mycolic acids; acid-fast staining is used.

Page 233

• Special Stains (overview):
  • Used to distinguish specific parts of microorganisms (capsules, endospores, flagella).

Page 234

• Capsule/Negative Staining (capsules):
  • Capsules are gelatinous coverings that do not accept most dyes.
  • Negative staining uses India ink or nigrosin to stain the background, leaving capsules as clear halos.

Page 235

• Endospore Staining:
  • Endospores are dormant, resistant structures; use malachite green as primary stain with heat.
  • Decolorize with water; counterstain with safranin.
  • Endospores appear green within red/pink cells.

Page 236

• Endospore Staining (image):
  • Visualization of endospores within cells via differential staining.

Page 237

• Flagella Staining:
  • Flagella require thickening with mordant and carbolfuchsin to be visible under light microscopy.

Page 238

• Special Staining (summary):
  • Capsule staining (negative), Endospore staining, Flagella staining described with LM visuals.

Page 239

• Special Staining (conclusion):
  • Practical lab applications for identifying microbial structures via differential staining.

Page 240

• [Content likely continues with additional staining techniques or summary of staining methods.]

Page 241

• [Content ends; transition likely to additional microscopy topics or end of chapter materials.]

// Key formulas and constants used throughout the notes

• Number of human body cells: N_{body} \approx 30 \times 10^{12}$</li> <li>Number of bacterial cells in microbiome:$N_{microbes} \approx 40 \times 10^{12}$</li> <li>Total magnification:$\text{Total magnification} = (\text{objective}) \times (\text{ocular})$</li> <li>pH:$pH = -\log_{10}[H^+]$</li> <li>DNA base pairs (complementarity):$A \leftrightarrow T\quad (2\text{ H-bonds})\quad;\quad G \leftrightarrow C\quad (3\text{ H-bonds})$</li> <li>Water:$\mathrm{H_2O}$; molecular mass of water =$18\ \text{Da per molecule}$; 1 mole of water weighs$18\ \text{g}$</li> <li>ATP hydrolysis (energy release):$\mathrm{ATP} + \mathrm{H2O} \rightarrow \mathrm{ADP} + \mathrm{Pi} + \text{Energy}$$
• Glass/water interactions in immersion oil: refractive-index matching concept (no explicit formula).