G.E. Whiz (Gene Expression)

1. The Life and Death of Eukaryotic mRNA G.E. Whiz (Gene Expression)

2. Learning goals • Students will: • Explain the role of post-transcriptional regulatory processes in establishing cell diversity. • Describe the steps that regulate the production of a functional mRNA. • Use information on splicing to explain the paradox that there are fewer genes than proteins. • Use a (mathematical) simulation of synthesis and degradation of mRNA to predict the quantitative regulation of mRNA levels.

3. Teaching Challenges Students often confuse transcription and translation. Discussion of the regulatory events that occur between these two steps may help differentiate transcription and translation in the students’ minds. Control of gene expression at the post-transcriptional level is often overlooked in introductory biology. Biology students do not often apply quantitative approaches (math) to biological questions.

4. Assessment • Content mastery • clicker questions • problem solving - RNA splicing • Peer instruction (group work) – lots of proteins, few genes • Data analysis – northern blot • Quantitative application/synthesis – mRNA decay

5. Context Introductory (general biology, genetics, cell biology) Large class size (>250). DNA to RNA to protein General features of transcription and translation Biological macromolecules Cellular structure Differential gene expression determines cell type

6. Which genes are expressed determines the phenotype of the organism Green Blue Genotype A B Genes Transcription mRNA Translation protein Phenotype

7. Gene expression is regulated at multiple levels 1. Transcriptional DNA structure Repressors Enhancers Green Blue A B Genes 2. Post-transcriptional Transcription RNA splicing RNA trafficking RNA degradation mRNA Translation 3. Translational Ribosome binding Termination protein 4. Post-Translational P P Folding Modification Trafficking

8. Schedule of Activities for the Entire Teachable Unit Step 1: Background: Importance of mRNA splicing in gene expression – hook, group work. Step 2: Mini lecture on pre-mRNA processing: Mini-lecture and animation – clicker question. Step 3: Alternative splicing: Question-driven discussion and a small group activity. Step 4: Export from the nucleus: A mini-lecture with animation. Step 5: Simulation of mRNA levels in the cytoplasm Clicker questions employing graphs and mathematical simulation.

9. Post-transcriptional processing Transcription DNA exon Intron exon Intron exon Intron exon Pre-mRNA RNA splicing, capping, polyadenylation AAAAA mRNA cap Export from nucleus AAAAA cap degradation AA AAAAA cap storage

10. Exon Intron Intron Intron Exon Exon Exon Splicing IAMAPREMRNQRSTVAWHICHHQPBASTRVASBEEQABDFCTVNSPLICED IAMAPREMRNAWHICHHASBEENSPLICED I AM A PRE MRNA WHICH HAS BEEN SPLICED

11. Exon Intron Intron Exon Intron Exon Exon In the heart In the brain IAMTHEHEARTTROPOMYOSIN (I am the heart tropomyosin) IAMTHEBRAINTROPOMYOSIN (I am the brain tropomyosin) Alternative Splicing of Tropomyosin IAMTHEQSRTVHEARTQPBASRTVBRAINQABDEVTROPOMYOSIN

12. Schedule of Activities for the Entire Teachable Unit Step 1: Background: Importance of mRNA splicing in gene expression – hook, group work. Step 2: Mini lecture on pre-mRNA processing: Mini-lecture and animation – clicker question. Step 3: Alternative splicing: Question-driven discussion and a small group activity. Step 4: Export from the nucleus: A mini-lecture with animation. Step 5: Simulation of mRNA levels in the cytoplasm Clicker questions employing graphs and mathematical simulation.

13. Northern Blot of mRNA

14. Northern Blot of mRNA • What do you notice about the patterns of the different RNAs over time? • Describe one mechanism that could account for these patterns

15. Q: Which of the following curves represents the proportion of remaining ND-5 in the blot? B A C D

16. Half-life of mRNA • What does “half-life” mean? • What is the half-life of the mRNA shown for curve C? A. About 1 hour B. About 2 hours C. About 15 minutes C

17. Half-life of mRNA B A D C

18. Half-life of mRNA • If the half-life increases, will the curve become more steep, less steep, or remain the same? • Illustrative simulation B A D C

19. Synthesis and degradation of mRNA • The amount of any specific mRNA in a cell doesn’t only depend on its half-life • Often, new mRNA molecules are also being synthesized, processed, and exported from the nucleus

20. Homework • Download the simulation from the course website. • BEFORE moving any of the controls, describe the shape of the curve. Does it always increase, always decrease, or does it reach a limit at some point? • Increase the half-life of the mRNA and describe how changing this parameter changes the shape of the curve. Save this curve by pressing the “Save Data” button.

21. Decrease the production rate of the mRNA and describe how changing this parameter changes the shape of the curve. • Click on the “Mystery curve” button, and adjust the parameters so that the blue curve matches the green curve. Record the corresponding parameter values. • Explore the simulation to your heart’s content and WRITE A QUESTION that you can ask your groupmates tomorrow. • Be prepared to share your answers with the rest of the class.

22. Decrease the production rate of the mRNA and describe how changing this parameter changes the shape of the curve. • Click on the “Mystery curve” button, and adjust the parameters so that the blue curve matches the green curve. Record the corresponding parameter values. • Explore the simulation to your heart’s content and WRITE A QUESTION that you can ask your groupmates tomorrow. • Be prepared to share your answers with the rest of the class.