Microbiology - Ch. 10 Classification of Microorganisms - flashcards

Why do we need to classify microorganisms?

Helps with quick identification — being able to name the living thing

What is identification of microbes useful for?

1. Diagnosis = Name of DZ.

2. Treatment — has to be specific.

3. Prevention — in the form of education, vaccines.

How is classification of microorganisms accomplished?

Through taxonomy

What is taxonomy?

The science of classification

What is a taxonomist?

A scientist who studies classification

What is a taxon/taxa?

• Taxon = singular, taxa = plural

• A class, group, or category of something being classified — an individual unit of something

  • They get organized/ranked by some order (ex: ranked from large groups to small groups)

What is phylogeny?

Evolutionary relationship/history between organisms in a group — shown via evolutionary trees, compares similarities/differences (e.g., humans vs. apes).

What is the taxonomic hierarchy used for?

Naming, classifying, and identifying living things (taxonomy)

How many taxa are in the taxonomic hierarchy and how are they arranged?

8 taxa, ranked in some order for the purpose of classifying/identifying living things (broadest to most specific).

What are the 8 levels of the taxonomic hierarchy in order (largest to smallest)?

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species

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What are the 2 highest taxa and what makes them unique? = (most inclusive or least specific).

• Domain & Kingdom

• Very broad, large groups/categories

What are the 2 lowest taxa and what makes them unique?

= (least inclusive or most specific)

• Genus & Species

• Very specific, small groups

What is the scientific name of a leopard and what does each part represent?

• Panthera pardus

• Panthera = Genus (first letter capitalized)

• pardus = Species (no capitalization)

What is binomial nomenclature?

• A two-part naming system used to identify living things

• Consists of Genus name + species name (spell out both in full)

What are examples of binomial nomenclature?

• Escherichia coli, Helicobacter pylori = bacteria (E. Coli)

• Penicillium chrysogenum = fungus (mold)

• Homo sapiens = humans

What is the Three Domain System?

A type of biological classification system developed in 1990; Domain is the highest taxon

What are the three Domains of living organisms?

1. Domain Archaea

2. Domain Bacteria

3. Domain Eukarya

What are domains based on?

Cell type — prokaryote vs eukaryote

• All cellular life exists as either prokaryotic or eukaryotic cells

• Prokaryotes → placed into 2 different Domains

• Eukaryotes → placed into 1 Domain

Cell types (visual tree map)

What is the origin of all prokaryotic and eukaryotic cells?

• All cells came from a common ancestor called the Last Universal Common Ancestor (LUCA)

• LUCAs eventually evolved into 3 different cell groups = the 3 Domains (Bacteria, Archaea, Eukarya)

What kingdoms do the 3 Domains contain?

• Domain Archaea & Domain Bacteria → contain all members of Kingdom Monera

—

• Domain Eukarya → contains the other 4 Kingdoms:
  1. Kingdom Protista
  2. Kingdom Fungi
  3. Kingdom Plantae
  4. Kingdom Animalia

—

• Monera — no nucleus (bacteria)

• Protista — single-celled, has nucleus, "leftover" category

• Fungi — decomposers (mushrooms)

• Plantae — makes own food (sunlight)

• Animalia — eats others, moves

How do you distinguish between Domain Archaea and Domain Bacteria?

1. Cell wall differences

2. Habitat differences

What do Domain Archaea and Domain Bacteria have in common?

1. All members are prokaryotic cells

2. All members belong to Kingdom Monera

Compare Domain Archaea vs Domain Bacteria — cell walls & habitat

	Archaea	Bacteria
Cell wall	No peptidoglycan	Yes, peptidoglycan (gives structure & rigidity)
Habitat	"Extreme" habitats	"Normal" habitats
Type	Thermophile, halophile, methanogens.

What are examples of Domain Archaea organisms?

• Thermophiles

  • (hot loving microbes) hot springs & volcanoes.

• Halophiles

  • (Salt loving microbes) in ocean, on skin.

• Methanogens

  • (Produce & tolerate methane gas)

What is another name for Kingdom Monera?

Kingdom Prokaryotae or Kingdom Bacteria

What are the characteristics of Kingdom Monera?

• Prokaryotes

• Unicellular

  • Example: Bacterium (E. coli)

What are the characteristics of Kingdom Protista?

• Simplest eukaryotes.

• Mostly unicellular, some multicellular.

  • Example: Amoeba (Amoeba proteus).

  • Algae.

What are the characteristics of Kingdom Fungi?

• Eukaryotes

• Some unicellular, others multicellular

  • Examples: Yeast & Mold

Compare Yeast vs Mold

	Yeast	Mold (M for multicellular)
# of cells	Unicellular	Multicellular
Temp requirement	Warm/hot	Cold
Example	Saccharomyces cerevisiae	Penicillium chrysogenum

What are the characteristics of Kingdom Plantae?

• Eukaryotes

• Multicellular, has cell wall, autotroph “self feeders”

  • Example: Plant (Sequoiadendron giganteum - Giant Redwood)

What are the characteristics of Kingdom Animalia?

• Eukaryote

• Multicellular, complex, heterotroph (rely on other organisms as food source)

  • Examples:

    • Large round worm (Ascaris lumbricoides)

    • Common house fly (Musca domestica)

Compare Autotrophs vs Heterotrophs

	Autotrophs	Heterotrophs
Produce own food?	Yes	No
Definition	Produce their own food (self feeders)	Rely on consuming other organisms
Types	Photoautotrophs, Chemoautotrophs	Photoheterotrophs, Chemoheterotrophs
Examples	Plants, Algae (Plantae, Protista)	Herbivores, Carnivores, Omnivores (Animalia)

What is the difference between "photo—" and "chemo—" energy sources?

• Photo = energy from sunlight used to make food

• Chemo = energy from chemicals used to digest food

What 3 kingdoms can photosynthesize?

1. Kingdom Plantae = plants.

2. Kingdom Protista = algae.

3. Kingdom Monera = cyanboacteria.

What is a species and what are the two types?

• Lowest taxon; species name always spelled with lowercase letter

• Divided into:

  1. Prokaryotic species (bacterial species)

  2. Eukaryotic species (non-bacterial species)

What is a eukaryotic species?

• A group of organisms that differ from each other but are closely related genetically

• Several related species form a Genus (Genus → Species #1, #2, #3, etc.)

• Ex: Homo neanderthalensis, Homo erectus, Homo sapiens

Is subspecies a taxon Y/N?

No — subspecies is NOT a taxon

What is a prokaryotic species?

• Prokaryotic species = Bacterial species

• A population of bacterial cells with similar characteristics

• Ex: Streptococcus pneumoniae & Streptococcus pyogenes (both in genus Streptococcus)

What are clones in microbiology?

• Prokaryotic/Bacteria:

  • A population of bacterial cells derived from a single parent cell

  • All are genetically identical

What is a subspecies/strain/serovar?

• Members of a clone that are NO longer genetically identical

  • Clones that genetically diverged over time through genetic mutations (DNA CHANGE)

    • Gene = DNA.

    • Mutation = Change.

==

• Identified by numbers/letters that follow the species name

  • Ex: E. coli O157:H7, Influenza A virus H1N5

Why are viruses not classified under any Domain or Kingdom?

Are viruses living things? Yes or no?

• Viruses are acellular (not cellular) — NOT prokaryotic or eukaryotic

  • Do NOT have cell membrane or cytoplasm

  • Therefore → no Domain, no Kingdom

• No, viruses are not living things.

What does it mean that viruses are obligate intracellular parasites?

They MUST invade a host cell in order to multiply

• Viruses do not reproduce.

How are viruses classified?

• By Family, Genus, and Species

  • Family = highest taxon for viruses; family name ends in "-viridae"

    • Ex: Retroviridae ("Retrovirus family"), Herpesviridae

• Can also have viral subspecies/strains identified by letters & numbers

  • Example: Influenza A virus → H1N1 (Swine Flu), H1N5 (Avian Flu)

What are the 6 methods of classifying & identifying microbes?

1. Morphological Characteristics

2. Differential Staining

3. Biochemical Tests

4. Serology

5. PCR

6. Textbooks/Manuals (Bergey's Manual)

What is the morphological characteristics method of identifying microbes?

• Look at shape, arrangement & size of bacteria (structural)

• Bacteria can exist as single, pairs, or groups

What is differential staining and what is an example?

• Using dyes to identify microbes

• Ex: Gram staining of bacterial cell wall

  • Differentiates Gram-positive vs Gram-negative bacteria

  • Based on cell wall differences — specifically the amount of peptidoglycan present (varies between bacteria)

What are biochemical/physiological tests for identifying microbes?

• Using yes/no questions to determine metabolic characteristics of bacteria

• Ex: "Can this bacterium break down glucose?"

  • Yes → E. coli

  • No → H. pylori & S. pneumoniae

What is serology and how is it used to classify microbes?

• Serology = study of blood serum (clear part of blood)

• Serological testing differentiates among strains within a species by analyzing the DNA sequence of the microorganism

• Ex: pathogenic E. coli (O157:H7) vs non-pathogenic E. coli (normal microbiota type)

What is PCR (Polymerase Chain Reaction)?

• PCR (Polymerase Chain Reaction) = DNA amplification

• Method used to make many copies of (amplify) a specific DNA segment from a single copy of a DNA sequence

• 1 DNA → 2 DNAs → 4 DNAs (exponential copying)

What are the 3 steps of PCR?

(prof said not to worry about the 3 steps but know what PCR is)

1. Denaturation — at 94-96°C

2. Annealing — at ~68°C

3. Elongation — at ~72°C

What is Bergey's Manual of Determinative Bacteriology?

• A textbook ("Bible of Bacteria")

• Provides systematic schemes for identifying unknown bacteria