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# Introductory Biology

• ### A first lesson in mathematical modeling for biologists: Rocs

Learning Objectives
• Systematically develop a functioning, discrete, single-species model of an exponentially-growing or -declining population.
• Use the model to recommend appropriate action for population management.
• Communicate model output and recommendations to non-expert audiences.
• Generate a collaborative work product that most individuals could not generate on their own, given time and resource constraints.
• ### In-class peer grading of daily quizzes increases feedback opportunities

Learning Objectives
Each of these objectives are illustrated with a succinct slide presentation or other supplemental material available ahead of class time through the course administration system. Learners found it particularly helpful to have video clips that remind them of mathematical manipulations available (in the above example objective c). Students understand that foundational objectives tend to be the focus of the quiz (objectives a-d) and that others will be given more time to work on together in class (objectives e-g), but I don't specify this exactly to reduce temptation that 'gamers' take a shortcut that would impact their group work negatively later on. However, the assignment for a focused graded group activity is posted as well, so it is clear what we are working towards; if desired individuals could prepare ahead of the class.
• ### A Close-Up Look at PCR

Learning Objectives
At the end of this lesson students will be able to...
• Describe the role of a primer in PCR
• Predict sequence and length of PCR product based on primer sequences
• Recognize that primers are incorporated into the final PCR products and explain why
• Identify covalent and hydrogen bonds formed and broken during PCR
• Predict the structure of PCR products after each cycle of the reaction
• Explain why amplification proceeds exponentially
• ### Meiosis: A Play in Three Acts, Starring DNA Sequence

Learning Objectives
• Students will be able to identify sister chromatids and homologous chromosomes at different stages of meiosis.
• Students will be able to identify haploid and diploid cells, whether or not the chromosomes are replicated.
• Students will be able to explain why homologous chromosomes must pair during meiosis.
• Students will be able to relate DNA sequence similarity to chromosomal structures.
• Students will be able to identify crossing over as the key to proper pairing of homologous chromosomes during meiosis.
• Students will be able to predict the outcomes of meiosis for a particular individual or cell.
• ### Air Quality Data Mining: Mining the US EPA AirData website for student-led evaluation of air quality issues

Learning Objectives
Students will be able to:
• Describe various parameters of air quality that can negatively impact human health, list priority air pollutants, and interpret the EPA Air Quality Index as it relates to human health.
• Identify an air quality problem that varies on spatial and/or temporal scales that can be addressed using publicly available U.S. EPA air data.
• Collect appropriate U.S. EPA Airdata information needed to answer that/those questions, using the U.S. EPA Airdata website data mining tools.
• Analyze the data as needed to address or answer their question(s).
• Interpret data and draw conclusions regarding air quality levels and/or impacts on human and public health.
• Communicate results in the form of a scientific paper.
• ### Discovering Cellular Respiration with Computational Modeling and Simulations

Learning Objectives
Students will be able to:
• Describe how changes in cellular homeostasis affect metabolic intermediates.
• Perturb and interpret a simulation of cellular respiration.
• Describe cellular mechanisms regulating cellular respiration.
• Describe how glucose, oxygen, and coenzymes affect cellular respiration.
• Describe the interconnectedness of cellular respiration.
• Identify and describe the inputs and outputs of cellular respiration, glycolysis, pyruvate processing, citric acid cycle, and the electron transport chain.
• Describe how different energy sources are used in cellular respiration.
• Trace carbon through cellular respiration from glucose to carbon dioxide.
• ### Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon

Learning Objectives
Students will be able to:
• Perturb and interpret simulations of the trp operon.
• Define how simulation results relate to cellular events.
• Describe the biological role of the trp operon.
• Describe cellular mechanisms regulating the trp operon.
• Explain mechanistically how changes in the extracellular environment affect the trp operon.
• Define the impact of mutations on trp operon expression and regulation.
• ### Coevolution or not? Crossbills, squirrels and pinecones

Learning Objectives
1. Define coevolution.
2. Identify types of evidence that would help determine whether two species are currently in a coevolutionary relationship.
3. Interpret graphs.
4. Evaluate evidence about whether two species are coevolving and use evidence to make a scientific argument.
5. Describe what evidence of a coevolutionary relationship might look like.
6. Distinguish between coadaptation and coevolution.
• ### Discovering Prokaryotic Gene Regulation by Building and Investigating a Computational Model of the lac Operon

Learning Objectives
Students will be able to:
• model how the components of the lac operon contribute to gene regulation and expression.
• generate and test predictions using computational modeling and simulations.
• interpret and record graphs displaying simulation results.
• relate simulation results to cellular events.
• describe how changes in environmental glucose and lactose levels impact regulation of the lac operon.
• predict, test, and explain how mutations in specific elements in the lac operon affect their protein product and other elements within the operon.
• ### Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

Learning Objectives
• From raw RNAseq data, run a basic analysis culminating in a list of differentially expressed genes.
• Explain and evaluate statistical tests in RNAseq data. Specifically, given the output of a particular test, students should be able to interpret and explain the result.
• Use the Linux command line to complete specified objectives in an RNAseq workflow.
• Generate meaningful visualizations of results from new data in R.
• (In addition, each chapter of this lesson plan contains more specific learning objectives, such as “Students will demonstrate their ability to map reads to a reference.”)