rRNA visualization for 2 nd year Cell Biology Course

1. rRNA visualization for 2nd year Cell Biology Course

2. Goals • Familiarize students with gel electrophoresis principles • Connect lecture material (ribosomal function) with observable phenomena (bands of RNA on a gel) • Evolution connection (compare different organisms – bacteria, yeast, animal, plant)

3. Lesson Plan (Lecture) • In lecture • Protein synthesis, ribosomal structure and function • Comparison between bacterial rRNA structure and eukaryotic rRNA structure • How rRNA was one of the keys to initially reconstructing big picture phylogeny (** Archaea)

4. Using rRNA

5. Lab • Instructor / lab staff • Grow bacterial cultures, prep samples for eukaryotic organisms • Students • Isolate rRNA from bacteria • Load bacterial rRNA, eukaryotic rRNA samples • Run gel • Visualize bands • Discuss

6. Beautiful stolen gel image big small

7. Learning outcomes • Students will • State that ribosomes have 2 subunits • State that bacteria and eukaryotic ribosomes are different sizes • Predict how the large and small subunits will move on a gel • Use molecular size markers to determine the size of the bands on the gel • Demonstrate how to pour, load, and run an agarose gel • Interpret a mock gel of an unknown organism’s rRNA • Explain why results might differ from expectations

8. Possible problems • RNAses everywhere • Equipment issues (gel imaging equipment)

9. Sample post-lab questions / ideas • Bioinformatics link • Students (in groups of 4) choose a sample set of organisms (bacteria, archaea, fungus, animal, plant) and construct a rRNA phylogeny using NCBI • Ask students why they see so much rRNA and not as much tRNA or mRNA. • If RNA degrades, ask students why it degrades more easily than DNA.

10. Possible extensions of lab • Acquire samples of archaea RNA and run in tandem with bacteria and yeast • Subject different organisms’ RNA to degrading conditions and see if there is any difference in RNA stability between eukaryotic and prokaryotic organisms (??)