Using Biotechnology to Classify Domains
Lesson 4 of 5
Objective: Students will use data to determine how scientists describe the lines of evolutionary descent of domains.
Because of the museum design challenges, students have a basic understanding of how evolutionary biologists think. Now it is time to deepen that understanding by using some of the tools and techniques that biologists use. Here is what students will learn today.
Present each student with several types of nails, screws, and nuts like casing nails, flathead machine screws, dry wall nails, flathead wood screws, wing nuts, hex nuts. Ask students to place their objects into three groups based on some sort of rationale. In their lab notebooks, they should place a heading above each group that indicates what those objects have in common and make a quick sketch of each object.
For the next portion of this activity, have students work with their shoulder partner (the person seated to the left or right of them). Ask shoulder partners to combine their objects and place those objects into three groups based on some sort of rationale. In their lab notebooks, they should place a heading above each group that indicates what those objects have in common and make a quick sketch of each object.
Bring students back together and ask:
- What additional items were you given to add your original set of nuts, nails, and screws?
- How did you have to modify your system so you could incorporate these additional items?
Explain that this exercise was to get them thinking about the criteria taxonomists and evolutionary biologists use to place into living things into domains.
(Note: These items can be found at a hardware or building supply store. This works best if individual students have four to five objects at the beginning of the exercise and eight to ten objects with their shoulder partner.)
Students use a virtual lab simulation that allows them to analyze results from several tests that scientists use to classify domains. For this lab, students will only look at living organisms that could be placed into the domains Bacteria or Archaea. Even if one does not have the simulation, this virtual lab can be easily done by simply having students observe several different species of bacteria by its appearance, its stainability using gram staining, the ratio of guanine and cytosine content of its DNA. and its ribosomal RNA sequence. Students then compare their unknowns to results of known species to determine into what domain the unknowns should be placed.
Students analyze three samples. First, students look at the results of gram staining to determine if the samples are gram positive or gram negative. Next, students look under the microscope to view the results of the staining. In the data table created in their lab notebook, students record the results of the gram stain. They also note the cell shape (for example: round, spiral, comma, or rod) and cell arrangement (for example: chain, pair, or single).
Next, students look at the bacteria's ribosomal RNA sequences using a virtual ribosomal RNA gene sequencing electrophoretic unit. Once they receive the results to the test, they must compare them with known rRNA gene sequences.
Finally, students look at the the ratio of guanine to cytosine content using a virtual GC content measuring apparatus. By analyzing G-C ratios and comparing them to known species, students can determine into what domain the unknowns need to be placed.
Each student or student group should have a different set of unknowns so student can compare their results. Using Claim, Evidence, Reasoning, first ask students to describe the characteristics and the process they used to determine the identity of one of the organisms in the virtual lab.
Then ask if the students if their claim would be strengthened or weakened if they found out that organism 1 might cause pneumonia (an infection of the lungs). Have them explain their answer.
Guide the discussion by asking if it is possible that two prokaryotic organisms show phenotypic similarities, but not show close evolutionary relatedness.
(Note: Organisms might show phenotypic similarities, but not show evolutionary relatedness if there was divergent evolution instead of convergent evolution. Therefore, it is necessary to look at a large number of factors to determine in which domain a living thing belong. See my reflection in the next section for a more detailed description.)
Next, talk about the evidence that many streptococci and lactobacilli were traditionally grouped together as lactic acid bacteria because of their characteristic lactic acid fermentation. However, when the ratio of guanine to cytosine content was analyzed. Streptococci bacteria was found to have a G-C content of 40% while lactobacilli was found to have a G-C content of 58%. Armed with this new information, ask students
- Should scientists change the taxonomic classification? Why or why not?
(The answer will depend on which domain the student chose. If they chose Bacteria as the domain, the answer would not change. However, if they chose Archaea, then their classification would need to change because of the lower G-C content.)
- After looking at all of the information that you collected, describe how a taxonomist or evolutionary biologist would define the domain Bacteria and Archaea.
(Bacteria are either Gram-positive or gram-negative. They vary in their ratio of G-C content. They typically live in an environment where human can live. Archaea can only be Gram-positive. They can also vary in their ratio of G-C content, but tend to have a higher G-C content because they live in extreme environments. Students should determine though that they need more information than just looking at the results these three tests.)
This lesson specifically looks at three of the evidences for a three domain system, namely, the G-C ratio in the living thing's genome, similarities in rRNA sequences, and Gram stainability. For scientists, this evidence is the start of a long list of evidence used to place living things in one of three domains.
Help the student groups compile the data from their lab results and see if definitions for the domains Bacteria and Archaea can be generated. Ask the following questions to help them:
- Do either of the domains have specifically Gram-negative or Gram-positive living things?
- Are the living things in each domain a particular cell type?
- What about their G-C content or ribosomal RNA sequence?
Next, ask student to consider the type of habitat where their specimens might be found.
Scientists determine Archaea by looking at its habitat, cell wall structure, and types of proteins that these living things contain particularly the proteins used in DNA replication, RNA translation, and protein synthesis. Because they mostly live in extreme environments, their cell membrane and cell wall make-up is quite different to those in domain Bacteria. Recently, because of PCR testing of rRNA sequences, Archaea that do not live in extreme environments have been found. Archaea also do not respond to antibiotics.
Living things placed in the domain Bacteria are either gram-negative or gram-positive. They live in non-extreme environments. Their DNA is circular and the proteins used in DNA replication, RNA translation, and protein synthesis are distinctive. Students should list this information in the lab notebook.
Explain to the students the other types of things that scientists use to help classify living things in the domains Bacteria and Archaea. A full explanation is provided in the reflection below.
Finally, ask students to classify the three specimens they analyzed in the lab as Archaea or Bacteria. Have them record their findings in their lab notebook. In the online simulation, there is a reference section which students use. If not using the online simulation, then an internet search should give the same necessary information. Have students specifically look at DNA structure (circular v. non-circular), cell wall composition (pepitidoglycan vs. S-layers or pseudopeptidoglycan), and sensitivity or resistance to antibiotics. Students should make a categorizing grid chart to show whether the organisms has the characteristics or not. Include all characteristics (Gram-stain results, G+C content, rRNA results, DNA structure, cell wall composition, and sensitivity/resistance to antibiotics.)
Have students pair up with their shoulder partner and compare lab results. Determine if where they should place his or her partner's specimen and record those findings in their lab notebook.
Finally, present the following scenario to the students.
- Gram Test: Gram positive
- Cell Arrangement: single rods
- Habitat: Mammallian intestine
- G-C content: ~56%
- rRNA gene sequence: E. coli
Using Claim, Evidence, Response, determine what domain should the following specimens be classified? Give two reasons for your classification.
Student should record their responses into their lab notebooks. Notebooks should be turned in at the end of the hour for evaluation.
(Note: Students should determine that this living thing should be placed in domain Bacteria)