Lecture 12 - Classification and Identification

Question 1

what is the definition of taxonomy?

Answer 1

the study of organisms to arrange them into groups for purposes of classification or identification

Question 2

what are the two components of taxonomy?

Answer 2

Classification and Identification

Question 3

what component of taxonomy is emphasized in medicine?

Answer 3

identification

Question 4

what is the classification of organisms? what is phylogeny?

Answer 4

Classification is the universal way of organizing organisms based on their evolutionary relationships, which is phylogeny

Question 5

What is the identification of organisms used for?

Answer 5

it is important in medicine

Question 6

what is the purpose of taxonomic hierarchy?

Answer 6

The purpose of the taxonomic hierarchy is to help scientists understand and organize the diversity of life on our planet.
Hierarchical classification basically means that we classify groups within larger groups

Question 7

what are the selected components in the levels of taxonomic hierarchy?

Answer 7

1. Domain
2. Genus
3. Species (some may or may not have strains)

Question 8

what is an example of the domain level of taxonomic hierarchy?

Answer 8

Bacteria

Question 9

what is an example of the genus level of the taxonomic hierarchy?

Answer 9

Escherichia

Question 10

what is an example of the species level with a strain of the taxonomic hierarchy?

Answer 10

coli with the strain 0157:H7

Question 11

what exactly are strains within species?

Answer 11

they are different subtypes or forms within a species

Question 12

in the following Bacteria, what is the domain, genus, species, and strain?
E. coli 0157:H7

Answer 12

Domain: bacteria
E - genus
coli - species
0157:H7 - strain

Question 13

what naming system do we use for taxonomic hierarchy?

Answer 13

binomial nomenclature

Question 14

what is a prokaryotic species?

Answer 14

A group of genetically related cells that are identified on the basis of their DNA sequence similarity or genotype

Question 15

how do we name a species?

Answer 15

based on the DNA sequence AKA genotype

Question 16

in a phylogeny chart, what does it mean when the bacteria are closer together?

Answer 16

the closer the bacteria, the more similar they are

Question 17

what does phylogeny mean?

Answer 17

evolution

Question 18

what is the three-domain classification system?

Answer 18

It is derived from the 16s rRNA gene sequencing - it classifies the 3 domains: Bacteria, Archaea, and Eukarya

Question 19

what are the two parts of ribosomes?

Answer 19

rRNA and proteins

Question 20

when performing 16s rRNA gene sequencing, why is rRNA preferred?

Answer 20

Because this rRNA gene is present in all organisms. It makes rRNA, which makes up the small subunit of ribosomes. Ribosomes perform an essential function for the cell (protein synthesis) and less mutations/changes are tolerated in the rRNA gene, so it is well-conserved in closely related organisms.

Question 21

organisms are divided into the 3 Domains based on the sequence of what gene?

Answer 21

of the rRNA gene

Question 22

T/F: the more similar the DNA sequences of organisms, the more closely related they are

Answer 22

True

Question 23

what are the 4 ways to identify prokaryotes?

Answer 23

1. Phenotype (how it looks)
2. Biotype (it’s metabolic properties)
3. Serotype (proteins on the surface of the cell for immunology)
4. Genotype (DNA)

Question 24

what is a phenotype and 2 ways to help identify the phenotype of an organism?

Answer 24

It is the physical features of an organism.
Two ways to identify it:
1. Microscopic morphology: The size, shape, and arrangement. Included Gram and special stains.
2. Colony morphology: The unique appearance and pigments. May require differential media (EMB). Example: Pseudomonas aeruginosa will be green on an agar plate.

Question 25

what is the biotyping of a prokaryote?

Answer 25

The metabolic testing. It tests for enzymes, groups of enzymes (a pathway), and uses dichotomous key.

Question 26

what is serotyping?

Answer 26

Performing immunological tests. It is based on different antigens/proteins located on the cell's surface. It has Antigen (Ag)-Antibody (Ab) reactions.

Question 27

what is the genotype identification for prokaryotes? what are three different ways to do so?

Answer 27

It detects the genetic composition of an organism using: - DNA fingerprinting - DNA probes - Sequencing DNA/rRNA (can be used in diagnosis and is used to classify different organisms)

Question 28

in traditional clinical microbiology, what does genotyping a sample look like?

Answer 28

-Collect the sample -Transfer -Delivery to laboratory -Wait for the cultures -Interpretation by laboratory personnel -Individual reports by culture

Question 29

in 16s rRNA sequencing, what does genotyping a sample look like?

Answer 29

-Collect the sample -Transfer -Deliver to laboratory -DNA extraction -Sequencing and bioinformatics identification -Comprehensive microbiome report

Question 30

when genotyping what are the important steps/buzzwords?

Answer 30

1. DNA isolation 2. PCR amplification (with 16s rRNA gene primers?) 3. DNA sequencing

Question 31

which steps will you use to identify unknown microbes in a soil sample?

Answer 31

1. DNA isolation 2. PCR 3. DNA sequencing

Question 32

in the 3 domains, compare the following: -Cell type -Cell wall -Membrane lipids -First amino acid in protein

Answer 32

Bacteria: -Cell type: prokaryotic -Cell wall: usually PG -Membrane lipids: straight fatty acid chains attached to glycerol by ester linkage -First amino acid in protein: Formyl methionine Archaea: -Cell type: prokaryotic -Cell wall: varies; no PG -Membrane lipids: branched fatty acid chains attached to glycerol by either linkage -First amino acid in protein: Methionine Eukarya: -Cell type: Eukaryotic -Cell wall: varies; no PG -Membrane lipids: straight fatty acid chains attached to glycerol by ester linkage -First amino acid in protein: Methionine

Question 33

In the scientific name, Enterobacter aerogenes, Enterobacter is the:

Answer 33

Genus

Question 34

Which of the following is not true in the three-domain classification system? 1. Bacteria and Archaea are prokaryotes. 2. Bacteria, Archaea and Eukarya arose from a common prokaryotic ancestor. 3. Bacteria and Archaea contain the same membrane lipids. 4. Bacteria and Archaea have a significantly different 16srRNA sequences. 5. Eukarya have a membrane-bound nucleus.

Answer 34

3. Bacteria and Archaea contain the same membrane lipids.

Question 35

You discover an organism that is single-celled but with no nucleus or peptidoglycan. What might this be?

Answer 35

An archaea

Question 36

Which of the following can be used to identify the genotype of an unknown organism? 1. Gram stain 2. Metabolic tests 3. PCR 4. Colony morphology 5. Serology

Answer 36

3. PCR

Question 37

study dichotomous key and from practice q's

Answer 37

*

Question 38

Why is a pure culture necessary for metabolic tests, but not for DNA probes?

Answer 38

Answer: A pure culture is necessary for metabolic tests because mixed bacteria can create confusing results. For example, in a specific medium, different bacteria will use the medium differently; some will have a negative reaction and others will have a positive reaction. In addition, there may be a medium, such as glucose, where two results are possible (acid and gas), and one bacterium may produce acid while another produces gas. In contrast, a pure culture is not necessary for DNA probes because the DNA probe is highly specific and will only bind to its specific counterpart in a mixed culture. This reflects the specificity of complementary base pairing.

Question 39

What is the most inclusive and most exclusive level in the taxonomic organization?

Answer 39

The most inclusive level in the taxonomic organization is: Domain The most exclusive level in the taxonomic organization is: Species

Question 40

Identify the domain, genus, species, and strain in the archaeon Methanosarcina barkeri Fusaro.

Answer 40

Domain: Archaea Genus: Methanosarcina Species: barkeri Strain: Fusaro

Question 41

Which gene sequence is used to build the phylogenetic tree of life and why?

Answer 41

The gene sequence that is used to build the phylogenetic tree of life is the 16s rRNA gene since this rRNA gene is present in all organisms. It makes rRNA, which makes up the small subunit of ribosomes. Ribosomes perform an essential function for the cell (protein synthesis) and less mutations/changes are tolerated in the rRNA gene, so it is well-conserved in closely related organisms.

Question 42

What are the four ways used to identify microbes?

Answer 42

Phenotype Biotype Serotype Genotype

Question 43

List the steps used to identify microbial species on your skin.

Answer 43

- DNA isolation from the specimin - PCR amplification of the bacterial 16s rRNA gene - DNA sequencing