Skip to main content
Biology LibreTexts

Lecture 1

  • Page ID
  • \( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)

    \( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)

    \( \newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\)

    ( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\)

    \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\)

    \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\)

    \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\)

    \( \newcommand{\Span}{\mathrm{span}}\)

    \( \newcommand{\id}{\mathrm{id}}\)

    \( \newcommand{\Span}{\mathrm{span}}\)

    \( \newcommand{\kernel}{\mathrm{null}\,}\)

    \( \newcommand{\range}{\mathrm{range}\,}\)

    \( \newcommand{\RealPart}{\mathrm{Re}}\)

    \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\)

    \( \newcommand{\Argument}{\mathrm{Arg}}\)

    \( \newcommand{\norm}[1]{\| #1 \|}\)

    \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\)

    \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\AA}{\unicode[.8,0]{x212B}}\)

    \( \newcommand{\vectorA}[1]{\vec{#1}}      % arrow\)

    \( \newcommand{\vectorAt}[1]{\vec{\text{#1}}}      % arrow\)

    \( \newcommand{\vectorB}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)

    \( \newcommand{\vectorC}[1]{\textbf{#1}} \)

    \( \newcommand{\vectorD}[1]{\overrightarrow{#1}} \)

    \( \newcommand{\vectorDt}[1]{\overrightarrow{\text{#1}}} \)

    \( \newcommand{\vectE}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash{\mathbf {#1}}}} \)

    \( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)

    \( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)

    -Microbes in the news: Yersinia pestis and Bubonic Plague, Legionella pneumophila and Legionnaire’s Disease. Pseudogymnoascus destructans and White-nose Syndrome/ WNS, Ebola virus and Ebola vaccine

    -what are “pathogens”? pathos=suffering

    -why are some of the pathogens’ names italicized and others are not?

    -Why do we care about microbiology?

    Why is teamwork important in microbiology?

    -Ebola outbreak, work to control, work to develop Ebola vaccine

    -Why is micro history of importance? (Bubonic Plague and Ebola)

    -other Micro topics “ in the news”:

    -microbes and climate change (see paper/Ppt on D2L site)

    -Human microbiome and influence on human health,

    - Harmful Algal Blooms/ HAB’s along Pacific coast, Alexandrium/Pseudonitzschia species, neurotoxin domoic acid and Amnesic Shellfish Poisoning/ASP (update: cyanobacteria and toxins in freshwater Russian River, Sonoma County, CA 8.2015)

    -What is microbiology? The study of microbes/microorganisms

    I. Microorganisms: (Gr. mikros, small) organisms too small to be seen with the naked eye

    Microbes = <~100-200 µm

    -resolving power of human eye without magnifying device ( the “naked eye”) ~200 µm

    - what is “µm” ? micrometer= µm = 10-6 m

    2. Evolution of microbes

    Bya= billion years ago What is a billion? billion= 109

    ~4.6-4.8 bya Earth forms

    ~3.6-3.8 bya first cells evolve LUCA= Last Universal Common Ancestor

    -LUCA= single cell, no nucleus = prokaryote

    -Earth’s atmosphere= no free molecular oxygen, O2 = anoxic/anaerobic

    -Biological evolution: the change in the genetic make-up of a population of organisms over time

    -One mechanism by which biological evolution may occur is “natural selection” roughly described = those variants in a population of organisms best adapted to a specific environment will survive and reproduce and pass on their genetic information at higher rates than those variants less adapted to a specific environment (drives biological evolution)

    ~2.5 bya cyanobacteria and oxygenic photosynthesis evolve, Earth atmosphere slowly

    accumulates O2 (O2 is toxic to most cells at this time unless living in anaerobic environments for e.g. sea bottoms). Through endosymbiosis, a primitive nucleated phagocytic cell may have phagocytized a primitive bacterium which evolved into a “peroxisome”, detoxifying toxic hydrogen peroxide made in an aerobic environment... Subsequent endocytosis of aerobic respiring bacteria may have led to evolution of eukaryotic mitochondria.

    ~ 2 bya evolution of eukaroytes as described above

    ~2 bya eukarotes evolve ( have a membrane bound nucleus and other membrane organelles such as mitochondria, chloroplasts)

    ~ 1.3 bya algal diversity

    ~ 1.2 bya sexual reporduciton evolves

    ~1 bya multicellular animals evolve

    ~600 mya early animals sponges evolve

    ~2.8 Homo appears in East Afric

    ~ 2.3 mya early human ancestor Homo habilis evolves

    ~200-250 kya earliest Homo sapiens?

    A. Distinguish cellular microbes (example bacteria) vs acellular “agents” (examples viruses, prions)


    Acellular microbial agents Cellular microorganisms

    prions viruses prokaryotes eukaryotes

    spongiform encephalopathies HIV Bacteria: Protozoa:

    “Mad Cow Disease” Ebola Mycobacterium tuberculosis/TB Plasmodium/malaria

    Kuru Hanta Staphylococcus Cryptosporidium

    Creutzfeldt-Jakobs Disease Polio Bacillus anthracis/anthrax Giardia

    Chronic Wasting Disease Rabies E. coli Trypanosoma/sleeping sickness

    Hepatitis Salmonella

    Smallpox Chlamydia/STD Fungi:

    Treponema pallidum/syphilis Candida/yeast



    Family Trees of Cellular Life based on rRNA sequences by Carl Woese

    Acellular microbes:

    Do not synthesize cell membranes

    Prions: misfolded cellular proteins, no nucleic acid/gentic info. “BSE, Mad Cow

    Disease, Kuru

    Viruses: nucleic acid wrapped in protein, obligate intracellular parasites

    Cellular Microbes: 3 Domains

    Prokaryotes lack a nucleus= Domain Bacteria and Domain Archaea

    Eukaryotes have a nucleus and other membrane bound organelles such as

    mitochondria, chloroplasts= Domain Eukarya


    1. Domain Bacteria: unicellular, most have cell walls containing peptidoglycan

    2. Domain Archae: lack peptidoglhycan, methanogens, extremophiles such as

    thermophiles and halophiles

    Eukaryotes Domain Eukarya

    - divided into “Kingldoms:

    -(outdated Kingdom Protista: e.g. protozoa, algae)

    Kingdom Fungi: yeast, mold, fleshy fungi

    -Kingdom Plantae: e.g. Elodea in lab

    -Kingdom Animalia: parasitic worms/helminths, arthropod vectors, human hosts

    - Processes associated with microorganisms-all associated with microbes search for and acquisition of energy and building blocks for growth and reproduction
    A. Decomposition (recyclers), fermentation (preservation), pathogenesis (cause diseases by toxin production/interrupting normal host homeostasis), production of beneficial compounds (ex. antibiotics, vitamins), geochemical agents (nitrogen, carbon, sulfur cycles), bioremediation (breakdown, detoxify compounds in environement).


    -. Microbes receive a lot of “bad press” as causes of infectious diseases but there are many more “good” microbes than “bad” microbes.

    Microbes could easily survive without humans, other animals and plants; humans, other animals and plants could NOT survive without microorganisms.


    “Cast of Characters” details


    I. Acellular Agents

    A. Viruses: NOT cells; subcellular metabolic parasites; single- or double stranded DNA or RNA; protein coats/capsids; +/- envelope derived from host cell membrane; ex influenza, vaccinia, small pox, polio, Ebola, hanta virus, Human Immunodeficiency Virus HIV

    B. Prions: proteinaceous infectious particles. Infectious agents made only of protein (hypothesis).

    Cause spongiform encephalapathies such as Kuru, Mad Cow Disease, Creutzfeldt-Jakobs Disease

    II. Cellular Microorganisms

    A. Prokaryotic microorganisms (L, Gr pro, before; Gr karyo, nut or nucleus) organisms lacking a membrane-bound nucleus and other membrane bound organelles. Unicellular.

    1. Domain Archaea: (archaea pl. /archaeon sing.) primitive anaerobes, found in extreme environments ex. methanogens, halophiles, thermophiles (no known pathogens)

    2. Domain Bacteria (bacteria pl./ bacterium sing.)

    a. Cyanobacteria : photosynthetic with generation of oxygen; autotrophs therefore do not need to invade other organisms; variable habitats; some fix nitrogen; some toxin producers

    b. Gram-positive bacteria: saprophytes, pathogens: ex Streptococcus, Staphylococcus, Clostridium, Bacillus, Corynebacterium

    c. Gram-negative bacteria: ex “enterics”= Escherichia coli E. coli, Salmonella, Shigella, Yersinia; others= Neisseria gonorrhoeae/gonorrhea, Legionella, Brucella, Bordetella pertussis/whooping cough

    d. Mycoplasma: very small, lack cell wall, sterol in cell membrane, saprophytes, human and animal pathogens ex Mycoplasma pneumoniae

    e. Spirochetes/Spirillla: helical, motile, outer sheaths, axial filaments: sewage, mud, mouth, genitals. pathogens= Treponema pallidum=syphilis

    Borrelia burgdorferi=Lyme Disease

    f. obligate intracellular parasites

    i. Rickettsia: enzyme deficiencies; many transmitted by arthropod vectors. Rickettsia typhi= endemic typhus; R. rickettsia=Rocky Mountain Spotted Fever

    ii. Chlamydia: Chlamydia psittaci=ornithosis; C. trachomatis= STD, sterility, conjunctivitis, infant pneumoniae

    B. Eukaryotic Microorganisms (Gr eu, well, good, true) organisms containing membrane-bound nucleus. Unicellular, colonial, or multicellular.

    1. Domain Eukarya

    a.Protista:i. protozoa:unicellular ex Plasmodium=malaria, Giardia, Entamoeba

    ii. plantlike: algae, euglenoids, diatoms, dinoflagellates:oxygenic photosynthetic; major CO2 fixers; chlorophyll a; some toxin producers. Phytoplankton, diatoms, dinoflagellates Gymnodinium, Gonyaulax produce red pigment and neuortoxin= ”red tides”

    b. Fungi: unicellular yeast=Candida, Saccharomyces; multicellular Penicillium, Trichophyton, Coccidioides, Aspergillus

    Brief History of Microbiology I. Era of Speculation: 5000 BCE-1675 CE

    -. Era of Observation: approx 1675-1850’s

    A. Development of Microscopy

    1. Robert Hooke;coins term “cell”

    2. Anton van Leeuwenhoek 1632-1723; first to observe and report existence of microbes/ “animalcules”

    B. Disproof of Spontaneous Generation Theory

    1. Francesco Redi-1660

    (2. Lazzaro Spallanzani-1760)

    3. Louis Pasteur-1861

    4. John Tyndal

    C. Early medical advances

    1. Edward Jenner: 1798 smallpox vaccine

    2. Ignaz Semmelweiss-1840 need to wash hands after performing autopsies and before performing exam on patients

    III. Era of cultivation (Golden Age of Microbiology) 1850-1890

    A. Louis Pasteur

    1. spontaneous generation (swan-neck flasks) 1859

    2. distribution of microbes in air

    3. fermentation

    4. pasteurization

    5. vaccines (chicken cholera/rabies)

    6. laid foundation for germ theory of disease

    B. Joseph Lister (1860’s-70’s): antisepsis , carbolic acid during surgery, wounds, bandages

    C. Germ Theory of Disease

    D. Robert Koch (1870’s)-”one disease-one organism”

    1. pure culture technique

    2. agar (red algae Gelidium/Gracilaria, w. Pacific Ocean); petri dish/agar plate 3. Koch’s postulates

    4. anthrax (Bacillus anthracis), tuberculosis (Mycobacterium tuberculosis), cholera (Vibrio cholera)

    IV. Immunology

    A. Elie Metchnikoff- 1880’s phagocytes

    V. Virology

    A. Dimitri Iwanowski-1892: provides evidence for virus causation of Tobacco Mosaic Dz.

    B. Electron Microscope: Germany; US. approx 1939

    VI. Chemotherapy

    A. Paul Ehrlich-1910: chemotherapeutic agent for syphilis; “salvarsan”

    B. Alexander Fleming-1928; discovers penicillin

    C. Gerhard Domagk-1935: discovers prontosil (sulfa drugs) inhibits bacteria

    VII. Microbes as geochemical agents

    A. Sergius Winogradsky and Martinus Beijerinck-1887-1890

    1. Carbon, nitrogen and sulfur cycles

    2. enrichment culture

    Lecture 1 is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

    • Was this article helpful?