Discovering Prokaryotic Gene Regulation with Simulations of the

Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon Audrey Crowther 1†, Heather E. Bergan-Roller 2†, Nicholas J. Galt 3†, Christine Booth 1, Joseph T. Dauer 4, Tomáš Helikar 1* Affiliations: 1 Department of Biochemistry, University of Nebraska-Lincoln, NE 68588 2 Department of Biological Sciences, Northern Illinois University, De. Kalb, IL 60115 3 Department of Science, Valley City State University, Valley City, ND 58072 4 School of Natural Resources, University of Nebraska-Lincoln, NE 68583 †Authors contributed equally to this work *Corresponding Author Tomáš Helikar 1901 Vine Street Lincoln, NE 68588 -0664 Phone: 402 -472 -2932 Email: thelikar 2@unl. edu

Today’s Agenda 1. Hand in pre-class assignment 2. Overview of operons 3. Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon Lesson Due prior to class Background Reading Assessment Questions During class Discovering Prokaryotic Gene Regulation Lesson

Anthranilate synthase (trp. D and trp. E) Chorismate N-5 -phosphoribosyl-anthranilate Anthranilate N-(5'-phosphoribosyl) anthranilate isomerase Indole-3 - phosphate synthase (trp. C) Tryptophan synthase (trp. A and trp. B) 1 -o-carboxyphenylamino-1 deoxyribulose-5 -phosphate Tryptophan Indole-3 Glycerol Phosphate

Regulation of Gene Expression in Prokaryotes

Today’s Agenda 1. Hand in pre-class assignment 2. Overview of operons Due prior to class Background Reading Assessment Questions During class Discovering Prokaryotic Gene Regulation Lesson

Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon • Table 1: define the interactions in the trp operon model. • Access Cell Collective Learn and set up simulations • Investigations A. B. C. D. E. F. Predict the outcome Support your prediction with a mechanism Test your prediction with the simulation Report your simulation results Evaluate your prediction based on results (repeat A-E until you understand how your simulation results translate to events inside the cell) Accurately describe the mechanism • Insight: Attenuation

Learning Goals • Students will discover how computational modeling and simulations can be used to observe and semi-quantitatively measure the dynamics of gene expression and regulation. • Students will recognize the biological significance of the trp operon. • Students will be able to think mechanistically about a system. • Students will discover how prokaryotic cells maintain homeostasis in the context of the trp operon. • Students will evaluate how mutations influence gene expression.

Learning Objectives • Students will be able to perturb and interpret simulations of the trp operon. • Students will be able to define how simulation results relate to cellular events. • Students will be able to describe the biological role of the trp operon. • Students will be able to describe cellular mechanisms regulating the trp operon. • Students will be able to explain mechanistically how changes in the extracellular environment affect the trp operon. • Students will be able to define the impact of mutations on trp operon expression and regulation.

Mechanistic Explanation What is a mechanistic explanation? • Explains HOW something happens. • Identifies the components involved in a phenomenon and HOW those components interact.

Mechanistic Explanation What is a mechanistic explanation? • Explains HOW something happens. • Identifies the components involved in a phenomenon and HOW those components interact. Example Question: Considering the model below, provide an mechanistic explanation for how the trp repressor is involved in regulating trp m. RNA production.

Mechanistic Explanation What is a mechanistic explanation? • Explains HOW something happens. • Identifies the components involved in a phenomenon and HOW those components interact. Example Question: Considering the model below, provide an mechanistic explanation for how the trp repressor regulates trp m. RNA production. When the trp repressor is active, it binds to the operator of the trp operon. This inhibits binding of RNA polymerase to the trp operon. Without binding from RNA polymerase, there is no transcription of trp m. RNA.

What you’ll need to continue A. learn. cellcollective. org B. Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon activity packet C. About 60 minutes

Table 1: define the interactions in the trp operon model 10 minutes • Please work as individuals to fill our Table 1 (about 10 minutes) • Discuss your results with your lab group • Change your answers as needed, based on the discussion

Access software 5 minutes • Go to learn. cellcollective. org • Sign in/up • Find access the “Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon” model. Enter the simulation workspace • Set settings according to the instructions • Simulate the trp operon • Compare your results with your group

Investigation 1 -4 30 minutes A. Predict outcomes B. Defend your prediction • Compare your mechanistic prediction with your lab group C. Test your prediction D. Record your results • E. Compare your results with your lab group Evaluate your prediction (repeat A-E until you understand how your simulation results translate to events inside the cell) F. Accurately describe the mechanism

Insight: Attenuation 15 minutes • Read the overview of transcription attenuation • Analyze the data presented in Table 2 • Answer the discussion question

When you’re done • Please hand in your activity packet. Be sure your name is on the packet!