Microbiology 509 Lectures
© Stephen T. Abedon
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this page, though not useless, nevertheless is no longer regularly maintained
for an up-to-date, day-to-day schedule see elsewhere
an index to this site is also available
last updated on Tuesday, September 14, 1999

At this site you will find . . .

1. central contents elsewhere
2. class schedule elswhere
3. overview this page
4. lecture text this page
5. lectures this page
6. bacteria binomials elsewhere
7. infectious diseases elsewhere
8. read me first (key) elsewhere
9. home elsewhere
10. send comments mail to

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Overview

lectures ---

This lecture schedule indicates order only. This reflects the temporally variable nature of lecture presentations.

Students should attempt to keep ahead of lectures in their text reading. The reading assignments are indicated above.

More lectures are shown below than will be presented in class. Students will not be tested on lectures not presented in class unless otherwise indicated.

For those individuals simply "checking out" this page, please keep in mind as you go that microbiology 509 is a one-quarter (10 week) introduction to microbiology which is presented by lecture over only three hours a week (plus we have two two-hour labs per week). Translation: This is not meant to be a comprehensive exploration of the topic.

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following the text ---

I hope to stick fairly close to the order and content of your lecture text.

I say hope because rearranging a course to fit a text is never an easy proposition. It is one which I will be very much in the process of doing throughout the quarter. Already, however, the proposed class and assignment schedules reflect this proposition.

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on-line lecture notes ---

My lecture notes will, to at least some extent be on-line throughout the quarter. However, note the following caveats:

  1. Notes are not completed and likely will not be completed until on or about when the lecture is actually given. Even then, changes made while preparing for a lecture will not necessarily make their way into the on-line notes in a timely manner.

  2. Which notes will be employed for a given lecture will not be set in stone until lectures are actually given.

  3. Sample questions present in notes will not necessarily cover material presented during lectures.

  4. Unless instructed otherwise, you are responsible on exams for what is actually presented in lectures rather than for what is presented in notes. If there are contradictions, point them out to me.

  5. Notes are not considered to be well edited, finished documents. In general they serve as a guide to me during lecture preparation and presentation. If you have any questions on the material presented in the notes, please consult your text or ask me for clarification.

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using this page ---

Consult the class schedule (elsewhere) for important dates, reading assignments, and to determine which lab you are responsible for on a given day.

Consult the lecture text section (above) for a list of chapter names as well as the name of your text.

Both of the above sections are linked chapter by chapter to a slightly more detailed overview of chapters (this section). Included particularly in these overviews are chapter names, statements of the degree you are responsible for each chapter, and links to my on-line lecture notes.

Next to these links are one word statements designating the degree to which you are responsible for these notes. Note, again, that you are primarily responsible on exams for material at least nominallly presented during lectures. Only those on-line lectures tagged "PRESENTED" will you be exposed to during actual, in class lectures.

Chapters 20, 21, 22, 23, 24, and 25 are exceptions to the "if it's not presented during lecture you are not responsible for it on exams" rule. You may be held responsible on exams for some proportion of the material presented in these chapters. Stay tuned for more details.

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everything is tentative ---

I present what I do on this page to give you an "up to the moment" idea of where we are headed during the coming quarter. Since course development and presentation always demand at least some flexibility, I cannot guarantee that we will succeed in adhering to these schedules with exceptionally high precision.

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Microbiology 509 Lecture Text

lecture text ---

Black, J. G. (1996). Microbiology. Principles and Applications. Third edition. Prentice Hall, Upper Saddle River, New Jersey.

chapters ---

  1. Scope and history of microbiology
  2. Fundamentals of chemistry
  3. Microscopy and staining
  4. Characteristics of prokaryotic and eucaryotic cells
  5. Essential concepts of metabolism
  6. Growth and culturing of bacteria
  7. Genetics I: Gene action, gene regulation, and mutation
  8. Genetics II: Transfer of genetic material and genetic engineering
  9. An Introduction to Taxonomy: The Bacteria
  10. Viruses
  11. Eukaryotic microorganisms and parasites
  12. Sterilization and disinfection
  13. Antimicrobial therapy
  14. Host-microbe relations and disease processes
  15. Epidemiology and nosocomial infections
  16. Nonspecific host defenses and host systems
  17. Immunology I: Basic principles of specific immunity and immunization
  18. Immunology II: Immunological disorders and tests
  19. Diseases of the skin and eyes; wounds and bites
  20. Diseases of the respiratory system
  21. Oral and gastrointestinal Diseases
  22. Cardiovascular, lymphatic, and systemic diseases
  23. Diseases of the nervous system
  24. Urogenital and sexually transmitted diseases
  25. Environmental microbiology
  26. Applied microbiology

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Microbiology 509 Lectures

scope and history of microbiology (ch. 1) ---

assignment:

Read chapter.

lectures:

1 scope and history of microbiology no list PRESENTED
--- introduction to microbiology microbiology, microorganism, environmental microbiology, industrial microbiology, medical microbiology, pathogen, normal flora, normal microbiota, transient microbiota, bacteria, cyanobacteria, blue-green algae, fungi, yeast, mold, protozoa, algae, virus, binomial nomenclature questions, optional
--- germ theory of disease germ theory of disease, spontaneous generation, Anton van Leeuwenhoek, Louis Pasteur, aseptic technique, pasteurization, Ignaz Semmelweis, Joseph Lister, Robert Koch, Dimitri Iwanowski, chemotherapy, chemotherapeutic agent, synthetic drug, antibiotic, Alexander Fleming questions, optional

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fundamentals of chemistry (ch. 2) ---

assignment:

Read Chapter.

lectures:

2 fundamentals of chemistry no list PRESENTED
--- water no list questions, optional
--- biochemistry no list questions, optional
--- organic chemistry review no list optional
--- carbohydrates no list questions, optional
--- glucose model no list optional
--- lipids no list questions, optional
--- proteins no list questions, optional
--- nucleic acids no list questions, optional

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microscopy and staining (ch. 3) ---

assignment:

Read chapter.

lectures:

3 microscopy and staining no list PRESENTED

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characteristics of prokaryotic and eukaryotic cells (ch. 4) ---

assignment:

Read chapter.

lectures:

4 characteristics of prokaryotic and eukaryotic cells no list PRESENTED
--- bacteria cell shapes and arrangements bacteria sizes, surface to volume ratio, cocci, coccus, diplococci, streptococci, tetrad, sarcinae, staphylococci, bacilli, bacillus, diplobacilli, streptobacilli, coccobacilli, additional bacterial shapes, monomorphic, pleomorphic, polymorphic questions, optional
--- membranes lipid bilayer, unit membrane, semipermeability, plasma membrane, cytoplasmic membrane, cell membrane, extracellular, intracellular, semipermeable cell membrane, membrane proteins, membrane asymmetry, fluid mozaic model questions, optional
--- osmosis osmosis, osmotic pressure, colligative property, osmosis and cells, tonicity, isotonic, hypertonic, hyperosmotic, hypotonic, hypoosmotic questions, optional
--- transport across membranes lipid bilayer excluded substance, concentration gradient, diffusion, selective permeability, facilitated diffusion, active transport, ATP-driven ion transport, sodium-potassium pump, cotransport, group translocation questions, optional
--- procaryote cell walls and membranes plasma membrane, cell envelope, binary fission, cell wall, peptidoglycan, murein, gram-positive cell envelope, teichoic acids, gram-negative cell envelope, inner membrane, outer membrane, lipopolysaccharide, LPS, lipid A, O polysaccharide, periplasmic space, periplasm, acid-fast cell envelope, lysozyme, lysis, osmotic lysis, plasmolysis, protoplast, spheroplast, cell theory, cell doctrine, cells questions, optional
--- procaryote cytoplasmic organelles procaryote, prokaryote, cytoplasm, protoplasm, bacterial chromosome, genophore, plasmid, ribosome, inclusions, granules questions, optional
--- procaryote extracellular appendages glycocalyx, bacterial glycocalyx, capsule, slime layer, flagella, flagellum, motility, motile, run, tumble, twiddle, taxis, chemotaxis, phototaxis, -trichous, atrichous, monotrichous, amphitrichous, lophotrichous, peritrichous, axial filaments, endoflagella, pili, pilus, fimbria, fimbriae, attachment pili, F pili, conjugation pili, sex pili questions, optional
--- eucaryotic cellular anatomy no list questions, optional
--- endomembrane system no list questions, optional

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essential concepts of metabolism (ch. 5) ---

assignment:

Read chapter.

lectures:

5 essential concepts of metabolism no list PRESENTED
--- enzymes no list questions, optional
--- energetics of life no list questions, optional
--- glycolysis and fermentation fermentation, the word, fermentation, the process, fermentation ecology, electron donor, hydrogen donor, reducing agent, electron acceptor, oxidizer, final electron acceptor, terminal electron acceptor, substrate level phosphorylation, glycolysis, NAD+, nicotinamide adenine dinucleotide, NADH, biochemistry of glycolysis (outline), structures of glycolytic intermediates (glucose-6-phosphate, fructose-1,6-diphosphate, glyceraldehyde-3-phosphate, 1,3-diphosphoglycerate, 3-phosphoglycerate, 2-phosphoglycerate, phosphoenolpyruvate, pyruvate), NAD+ regeneration, NADH recycling, lactic acid fermentation, homolactic-acid fermentation, lactic acid, alcohol fermentation, ethanol, mixed acid fermentation, gas formation questions, optional
--- glycolysis in detail no list optional
--- cellular respiration no list questions, optional
--- photosynthesis no list questions, optional

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growth and culturing of bacteria (ch. 6) ---

assignment:

Read chapter.

lectures:

5,6 growth and culturing of bacteria no list PRESENTED
--- microbial growth microbial growth, increase in cell number, increase in cell mass, binary fission, generation, generation time, doubling time, standard bacterial growth curve, exponential growth, exponential phase, logarithmic growth, log growth, log phase, vegetative cell, lag phase, stationary phase, cell death, death phase, logarithmic decline, exponential decline, endospore, spore, sporulation, sporogenesis, activation, germination questions, optional
--- counting microbes methods of cell quantification, direct count, viable count, total count, estimation of cell number, plate counts, pour plate, spread plate, filtration, most probable number method, MPN, direct microscopic count, turbidity, metabolic activity, dry mass questions, optional
--- exponents and logarithms no list optional
--- diluting and concentrating methods of concentration, concentrating, diluting, algebra of concentration, dilution factor, dilution factor calculation from concentration information, turning dilution factors into dilutions, diluting while plating, calculating absolutes from volumes, calculating concentration from plate count, serial dilution, minimizing serial dilution errors questions, optional
--- microbial nutrition nutrient, nutritional pattern, energy source, conversion of food to energy, other substrates for ATP yielding catabolism, carbon source, phototroph, chemotroph, autotroph, lithotroph, heterotroph, organotroph, photoautotroph, photoheterotroph, chemoautotroph, chemoheterotroph, nutritional patterns of pathogens, microbial nutrient requirements, nitrogen, nitrogen fixation, sulfur, phosphorus, trace elements, essential amino acids, organic growth factors, fastidious, auxotroph, autotrophic mutation questions, optional
--- non-nutrient factors affecting growth physical parameters affecting growth, optimal growth temperature, psychrophiles, thermophiles, mesophiles, thermoduric, refrigeration, psychrotroph, optimal pH, acidophile, neutrophile, alkaliphile, optimal osmotic pressure, halophile, oxygen requirements, aerobe, obligate aerobe, facultative anaerobe, anaerobe, obligate anaerobe, strict anaerobe, aerotolerant anaerobe, microaerophile questions, optional
--- culturing microbes culture, culture medium, media, solid medium, agar, broth medium, non-synthetic medium, chemically undefined medium, simple non synthetic medium, complex non synthetic medium, chemically defined medium, synthetic medium, preprepared medium, enriched medium, reducing medium, selective medium, enrichment culture, differential medium, pure culture technique, pouring a plate, spreading a plate, preserving cultures, refrigeration, stabbing, slant method, lyophilization, freezing, colony, colony morphology, colony size, type of margin, colony elevation, colony texture, colony light transmission, colony pigmentation, petri dish, loop, streaking, streaking a plate questions, optional

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genetics I: gene action, gene regulation, and mutation (ch. 7) ---

assignment:

Read chapter: pp. 165-169 (skip "DNA replication"), 184-185 ("Phenotypic variation"), 169-171 (skip "Kinds of RNA"), 192-193 ("Polymerase chain reaction").

lectures:

7 genetics I: gene action, gene regulation, and mutation no list PRESENTED
--- DNA replication no list questions, optional
--- mutation no list questions, optional
--- from gene to protein no list optional
--- transcription and translation no list questions, optional
--- control of gene expression no list questions, optional

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genetics II: transfer of genetic material and genetic engineering (ch. 8) ---

assignment:

Read chapter: pp. 196-203, 207-209 (start with "Gene transfer mechanisms compared" and stop with "Transposons"), and 211 through end of chapter.

lectures:

7 genetics II: transfer of genetic material and genetic engineering no list PRESENTED

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an introduction to taxonomy: the bacteria (ch. 9) ---

assignment:

Read chapter in two parts: pp. 222-236 and 237-252.

lectures:

8,9 an introduction to taxonomy: the bacteria no list PRESENTED
--- classification of organisms no list questions, optional
--- domains and kingdoms no list questions, optional
--- archaeabacteria no list questions, optional
--- identification of bacteria bacterial species, Bergey's Manual, strain, type strain, serovar, serotype, biovar, biotype, morphovar, morphotype, isolate, classification, identification, morphological identification, serological methods, agglutination test, ELISA, Western blot, flow cytometry, phage typing, protein analysis, gel electrophoresis, SDS-PAGE, establishment of clonality, comparison of nucleotide sequences, Southern blot, nucleic acid hybridization, RFLP, DNA fingerprinting questions, optional
--- bacteria bacterial abundance, bacterial sex, rapid evolutionary adaptation, bacterial biochemical diversity, cellular diversity, gram staining, germ theory of disease, questions, optional
--- eubacterial classification major eubacteria taxonomic categories, gram positive bacteria, proteobacteria, facultatively anaerobic gram negative rods, Enterobacteriaceae, enterics, Pasteurellaceae, Vibrionaceae, gram-staining characteristics (summary), chlamydias, spirochetes, cyanobacteria, blue-green algae, rickettsias, actinomycetes, bacteria binomials (summary) questions, optional
--- bacteria binomials no list questions, optional

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viruses (ch. 10) ---

assignment:

Read chapter.

lectures:

10 viruses no list PRESENTED
--- virus particles obligate intracellular parasite, what is a virus, size of viruses, virion, virus particle, free virus, utility of nucleic acid packaging, adsorption, attachment, penetration, virus genes, virus protein, receptor molecule, capsid, capsomer, nucleocapsid, envelope, enveloped virus, envelope protein, spike, peplomer, nonenveloped virus, naked nucleocapsid, inactivation by antibody binding, inactivating antibody, inactivation of free virus (HIV vs. HBV) questions, optional
--- virus growth progeny producing machines, virus growth, search for a host, entry, penetration, genome replication, maturation, release, lytic infection, lytic cycle, continuous infection, chronic infection, latent infection, lysogenic infection, temperate infection, general animal virus life cycle, general bacteriophage life cycle, growth of viruses, plaque assay, growth in liquid culture, growth in tissue culture, growth in host organisms, growth in embryonated eggs questions, optional
--- virus types virus species, nomenclature, viral permutations, target cell, tropism, enteric virus, host range, arbovirus, bacteriophage, phage, virus morphology, helical viruses, polyhedral viruses, icosahedral, enveloped helical virus, enveloped polyhedral virus, complex virus, virus genome, plus strand, minus strand, virus taxonomy, virus types questions, optional

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eukaryotic microorganisms and parasites (ch. 11) ---

assignment:

Read chapter.

lectures:

11 eukaryotic microorganisms and parasites no list PRESENTED
--- protozoa no list questions, optional
--- algae no list questions, optional
--- fungi no list questions, optional
--- multicellular parasites no list questions, optional
--- arthropod vectors no list questions, optional

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sterilization and disinfection (ch. 12) ---

assignment:

Read chapter.

lectures:

12 sterilization and disinfection no list PRESENTED
--- control of microbial growth microbial death, exponential death, stasis, bacteriostasis, static, bacteriostatic, -cidal, bactericidal, sterilization, disinfection, antisepsis, asepsis, surgical asepsis, medical asepsis, degerming, sanitization, antimicrobial, germicide, disinfectant, antiseptic, disinfectant efficacy, questions, optional
--- specific antimicrobials specific antimicrobials, physical agents, chemical agents, death by heat, moist heat, autoclaving, pasteurization, dry heat, filtration, filter sterilization, freezing, desiccation, ionizing radiation, ultraviolet radiation, UV radiation, phenolics, halogens, iodine, tincure, iodophore, chlorine, hypochlorite ion, halogen-based water purification, alcohols, heavy metals, heavy metal compounds, surfactants, surface-active agents, soaps, detergents, quats, quaternary ammonium compounds, organic acids, aldehydes, formaldehyde, formalin, glutaraldehyde, gaseous chemosterilizers, ethylene oxide, propylene oxide, beta propiolactone, oxidizing agents, hydrogen peroxide, ozone questions, optional

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antimicrobial therapy (ch. 13) ---

assignment:

Read chapter.

lectures:

13 antimicrobial therapy no list PRESENTED
--- antimicrobial drugs spectrum of activity, narrow spectrum of activity, broad spectrum of activity, broad spectrum vs narrow spectrum of activity, superinfection, sites of action, inhibition of cell wall synthesis, inhibition of protein synthesis, injury to plasma membrane, antifungals that bind sterols, other sites of antimicrobial activity, antibiotic resistance questions, optional

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host-microbe relations and disease processes (ch. 14) ---

assignment:

Read chapter.

lectures:

14 host-microbe relations and disease processes no list PRESENTED
--- normal flora symbiosis, symbiont, symbiotic, commensalism, mutualism, parasitism, parasite, normal flora, normal microbiota, transient microbiota, normal flora are symbionts, microbial antagonism, microbial competition, acquisition of normal flora, normal flora, large intestine, normal flora, mouth, normal flora, skin, examples of human normal flora questions, optional
--- principles of disease disease, sign, symptom, sequelae, syndrome, pathogen, parasite, pathogenesis, pathogenicity, pathology, Koch's postulates, problems with Koch's postulates, etiology of disease, etiologic agent, infection, colonization, symptomatic infection, asymptomatic infection, subclinical infection, inapparent infection, opportunistic infection, local infection, systemic infection, focal infection, primary infection, secondary infection, mixed infection, acute infection, chronic infection, subacute infection, latent infection, bacteremia, septicemia, viremia, intracellular infection, types of microbial diseases, infectious disease, communicable disease, contagious disease, noncommunicable disease, disease caused by opportunists, periods of infectious disease, period of incubation, prodromal period, prodromal phase, period of illness, illness phase, acme, period of decline, decline phase, period of convalescence questions, optional
--- bacterial mechanisms of pathogenicity pathogenicity, ID50, infectious dose 50%, LD50, lethal dose 50%, adherence, damage to the host, direct damage, hypersensitivity reaction, toxin, toxicity, toxemia, toxigenicity, toxin induced damage, exotoxin, cytotoxin, enterotoxin, neurotoxin, antitoxin, toxoid, endotoxin, digestive system intoxication, digestive system infection, botulin, tetanospasmin questions, optional

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epidemiology and nosocomial infections (ch. 15) ---

assignment:

Read chapter.

lectures:

15 epidemiology and nosocomial infections no list PRESENTED
--- epidemiology epidemiology, incidence of disease, index case, prevalence of disease, sporadic disease, endemic disease, epidemic disease, common source outbreak, propagated epidemic, emerging infectious disease questions, optional
--- acquisition of disease sources of infectious disease, reservoir, carrier, zoonosis, zoonotic portals of entry, mucous membrane portal of entry, skin portal of entry, parenteral portal of entry, portals of exit, transmission, endogenous infection, contact transmission, direct contact transmission, person-to-person transmission, indirect contact transmission, fomite, droplet transmission, vehicle transmission, airborne transmission, foodborne transmission, waterborne transmission, vector transmission questions, optional
--- nosocomial infections nosocomial infections, hospital acquired infections, presence of pathogens, compromised hosts, chain of transmission, universal precautions, preventing nosocomial infections questions, optional
--- evolution of virulence no list no link

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nonspecific host defenses and host systems (ch. 16) ---

assignment:

Read chapter.

lectures:

16 nonspecific host defenses and host systems no list PRESENTED
--- nonspecific defenses of the host susceptibility, resistance, nonspecific resistance, barriers, skin barrier, mucous membrane barrier, one-way valves, removal by washing, antimicrobials of the body, inhibition within the body, leukocytosis, phagocytosis, macrophage, neutrophil, phagocyte, pus, wandering macrophage, inflammation, fever, complement, interferon questions, optional

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immunology I: basic principles of specific immunity and immunization (ch. 17) ---

assignment:

Read chapter.

lectures:

17 immunology I: basic principles of specific immunity and immunization no list PRESENTED
--- humoral immunity acquired immunity, humoral immunity, antibody-mediated immunity, lymphocytes, B cells, antigen, immunogen, antibody, Ig, IgG, epitope, antigenic determinant, active immunity, passive immunity, antiserum, gamma globulin, artificially acquired immunity, antibody diversity, consequence of antibody binding, monoclonal antibodies, MAbs, distinguishing self from nonself questions, optional
--- viral mechanisms of pathogenicity cytopathic effects, CPE, cytocidal effects, noncytocidal effects, syncytia, giant cells, inclusion bodies, cell-mediated immunity, antibody-dependent cellular cytotoxicity, ADCC, natural killer cells, cytotoxic T cell mediated immunity, major histocompatibility complex, MHC, cytotoxic T lymphocyte, CTL, latent infection questions, optional
--- vaccination vaccine, vaccination, immunization, prophylactic vaccine, booster, booster dose, booster shot, control of viral disease, immunization against exotoxins, toxoids, herd immunity, difficulties in developing vaccines, types of vaccines, whole-agent vaccines, whole-killed vaccines, live-attenuated vaccines, subunit vaccines, recombinant vaccines, specific common vaccines, DTP vaccine, hepatitus B vaccine, influenza vaccine, flu shot, MMR vaccine, Sabin vaccine, Salk vaccine, Smallpox vaccine questions, optional

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immunology II: immunological disorders and tests (ch. 18) ---

assignment:

Read chapter.

lectures:

18 immunology II: immunological disorders and tests no list PRESENTED

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diseases of the skin and eyes; wounds and bites (ch. 20) ---

Not covered; this material is also covered to some extent in the following: "Infectious Diseases of the skin and eyes" and "Localized infections of the skin."

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diseases of the respiratory system (ch. 21) ---

Not covered; this material is also covered to some extent in the following: "Infectious Diseases of the respiratory system."

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oral and gastrointestinal diseases (ch. 21) ---

Not covered; this material is also covered to some extent in the following: "Infectious Diseases of the digestive system."

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cardiovascular, lymphatic, and systemic diseases (ch. 23) ---

Not covered; this material is also covered to some extent in the following: "Infectious Diseases of the cardiovascular and lymphatic systems."

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diseases of the nervous system (ch. 24) ---

Not covered; this material is also covered to some extent in the following: "Infectious Diseases of the nervous system."

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urogenital and sexually transmitted diseases (ch. 25) ---

Not covered; this material is also covered to some extent in the following: "Infectious Diseases of the urinary and reproductive systems."

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environmental microbiology (ch. 26) ---

Not covered.

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applied microbiology (ch. 27) ---

Not covered.

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Contact Dr. Abedon (abedon.1@osu.edu) with suggestions, criticisms,
comments, or anything else that might help make this a better site.