Arsenic life – a case study for introductory biology

This fall, I am determined to switch my teaching method to a structured, active-inquiry format with students working in groups for most of the class period. Instead of lecturing during class, I post pre-recorded talks from my slides on T-square (Georgia Tech’s implementation of Sakai).

For my first class, on the topic of biological macromolecules, I built a case study from the controversial report published in Science, that claims that a bacterial strain adapted for growth in a high arsenic environment actually incorporates arsenate into DNA and other macromolecules in lieu of phosphate (Wolfe-Simon et al., 2011). This question could address elements and atomic structures, the Periodic Table and valence electrons, the elemental composition of organic molecules, the structure and composition of macromolecules, evolution and natural selection, the origin of life, and the ongoing process of science.

I asked my freshman biology classes to at least read the abstract and the first two paragraphs (introduction) before class, and answer these three questions (on a worksheet uploaded to T-square, our implementation of Sakai):

1. What are the six major elements that comprise living organisms?

2. What cellular macromolecules contain P?

3. Why is arsenate (AsO43-) toxic to living organisms?

Then, in class, I had them working in groups of 3, 4, or 5 students. Each group had to assign 3 roles: a note-taker who completes the worksheet with the group consensus answer, a questioner who communicates questions the group cannot resolve to the instructor and the rest of the class via Piazza.com (or Twitter), and 1-3 researchers who hunt for information and answers using all the resources available on the internet.

The groups’ first task was to determine from reading the paper what they do not understand, and to list their questions on Piazza.com or Twitter, in order to answer the following questions on the worksheet:

4. Describe to your group mates the procedure Wolfe-Simon et al. used to isolate GFAJ-1. Do you think GFAJ-1 existed in the original inoculum from Mono Lake sediment, or did it come into being during culture?

5. What do you conclude from Figures 1A and 1B? Do these look like logistic growth curves?

6. Compare the measured intracellular content of As and P (Table 1) in cells grown in +As/-P medium and -As/+P medium. What are the As and P concentrations in these media? Do GFAJ-1 cells accumulate (and use) As as well (or as much) as they do P?

7. Wolfe-Simon et al. used a radioactive isotope of As to determine whether As became incorporated into macromolecules (Table 2). Discuss how strongly the data support their claim that they observed arsenic “in protein, metabolite, lipid, and nucleic acid cellular fractions.” Do you have any questions about their fractionation method, before you can make a judgment?

8.Wolfe-Simon et al. explicitly assume that the distribution of As in GFAJ-1 cells would be similar to the distribution of P. Do you think this assumption is valid?

9. Summarize the evidence that As is in the DNA of GFAJ-1 cells. Identify the controls in the experiments.

We then went over the answers to these questions in the last 10 minutes of class, followed by two clicker questions. Many students answered that the Wolfe-Simon demonstrated As was in proteins (based on table 2), and that GFAJ-1 was able to “breathe” arsenic. They just weren’t ready to handle this paper. I’ll have to think about writing a digest that simplifies the experimental approach and focuses on just a couple of the easier to understand data.

Wolfe-Simon, F. et al. 2010, A bacterium that can grow by using arsenic instead of phosphorus. Science doi:10.1126/science.1197258

Biol1510A module 3 1 arsenic life pdf file of questions formulated for Learning Catalytics, from Fall 2013.

B1510_module3_1_arseniclife powerpoint slides with clicker questions and figures from Wolfe-Simon et al. paper

ArsenicLife Class Worksheet doc file of in-class group worksheet

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About jchoigt

I'm an Associate Professor in the School of Biology at Georgia Tech, and Faculty Coordinator of the Professional MS Bioinformatics degree program.
This entry was posted in Teaching and learning biology. Bookmark the permalink.

One Response to Arsenic life – a case study for introductory biology

  1. jchoigt says:

    The amount of P per bacterioplanckton cell in P-limited cultures is 2.3 +/- 0.6 fg (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC123973/); an opportunity for students to calculate how much bacterial growth would result from the 3 micromolar background levels of P present in the “no-P” medium http://www.sciencemag.org/content/332/6034/1149.10.full.

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