Implementing Vision and Change Using Concept-Driven Teaching Strategies

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1 Implementing Vision and Change Using Concept-Driven Teaching Strategies NSF RCN-UBE Grant # Designing Scientific Teaching Tools for BMB Education Regional Workshop Series Viterbo University November 9, 2014 BMB Alignment Table Template Please save this template as a separate working document for your group, with the filename as: Alignment LocationAbbr LastNameA LastNameB LastNameC.docx (e.g., Alignment USD Garcia Nguyen Smith.docx) Designed by: Preston Aldrich Scott Cooper Ward Jones Selected Aspect of BMB: Foundational Concepts or Foundational Skills or Allied Fields (delete two) Keywords: Search terms relevant to your alignment Initial Overall Learning Goal: Students should understand the core concept of biological information, including the genome, the information it contains, its transmission across generations, and maintenance. Initial Learning Objective: Students should be able to describe what a mutation is at the molecular level, and how it comes about, be able to predict how changes in a nucleotide sequence can influence the expression of a gene or the amino acid sequence of the gene product (protein) and be able to translate these findings into a conclusion about how said mutation would impact the general fitness of an organism or population..

2 Overall Learning Goal: Insert refined goal Learning Objective Learning Assessment Learning Strategy The Central Dogma links genotype and phenotype. Present students with wild type and mutant dsdnas containing a protein coding sequence. Determine the amino acid sequence of each and determine the impact of the mutation on the protein and broader phenotype POGIL, PBL when taken collectively; Individual components (below) could be treated as quizzes Students should be able to describe what a mutation is at the molecular level, and how it comes about. Transcription: Students should be able to transcribe DNA into RNA Give students wt sequence and tell them that C s get oxidized to U s by exposure to cosmic rays, then what would the DNA sequence be following several rounds of replication. Given a DNA sequence with a transcription start site, transcribe it into mrna Translation: Students should be able to translate RNA into protein Protein structure: Students should be able to interpret amino acid sequence effect on protein structure Effect of protein phenotype on organismal phenotype: Link between genotype and phenotype Epigenetics Given a mrna sequence, find a protein sequence Given a wild type and mutant amino acid sequence, what is the effect on the protein activity or function Given a change in the activity of a protein in the cell, predict the effect on the phenotype of the organism Given the genotype of an individual, be able to predict their phenotype for a dominant or recessive trait Given two cells with the same genotype, explain how they could have the different phenotypes POGIL or PBL 2

3 Assessment: Score Centra l Dogm a Sum Full (3 Partia l (2 Tried (1 pt) None (0 Mutatio n Transcriptio n C T Correctly identify TSS, sense strand, T U 7-12 C U 1-6 Tried but neither of 0 No Translatio n Correctly identify AUG, stop codon, and use genetic code to identify amino acids Protein structure Id properties of amino acids, id conservativ e vs. nonconservativ e changes, and predict the effect of a change phenotyp e Proteins perform activities in cells, 50% of a protein s activity is normal; predict what happens if an activity is absent Two of the One of the No No No No Genotype to phenotype Recognize that genes have different alleles, that some alleles are dominant, based on combinatio n of alleles predict the phenotype No Strategy: This is a POGIL for the Central Dogma. Students presented with image of two dsdna molecules, one labeled wild type and other mutant. Both would identify the coding strand, phenotypic trait, and transcription start site. 1. Identify the coding strand in the wild type and mutant DNAs. 2. Which strand is the RNA polymerase going to use as the template. 3. Transcribe into mrna. 4. Identify the start codon. 5. Translate using the genetic code. 6. Identify difference in amino acid sequence between wild type and mutant. 7. Describe the chemical properties of the wild type and mutant proteins. 8. Predict the effect of that change on the function of the protein. 9. Predict the effect of that change on the organismal phenotype. 3

4 Variations on overall strategy 1. Use different kinds of mutations: frameshifts, dominant or recessive, synonymous or non-synonymous, conservative or non-conservative substitutions, missense, etc. 2. Introduce various aspects of epigenetics such as chromatin structure, methylation, micrornas, introns and alternative splicing outcomes. Overall Learning Goal: Insert refined goal Learning Objective Epigenetics Histone acetylation CpG methylation Transcription factor expression Transcription factor activation micrornas RNA degradation Learning Assessment Given two cells with the same genotype, explain how they could have the different phenotypes describe how histone acetylation affects mrna expression describe how CpG methylation with decreased mrna describe how tissue-specific co-expression of transcription factors and target DNAs describe how phosphorylation of TF is necessary for mrna production describe how in presence of an mirna, an mrna is not translated describe how mrna half-life correlates with translation Learning Strategy POGIL or PBL 4

5 Scor e Full (3 Parti al (2 Tried (1 pt) Non e (0 Epigeneti cs histones CpG TF present Explain CpG Expressi DNA islands in on of TF binds to promoter is often positively are tissuespecific; charged methylat histones, es, which these acetylatio recruits TFs bind n blocks HDACs, to this and promoter positive these deacetylate s of charge, specific and more histones genes; loosely that bound the turns on DNA is, genes the more just in transcripti those on and tissues translatio n 7-12 Two of Two of Two of the the the 1-6 Tried but neither of 0 No One of the No One of the No TF activated Cell is activated by extracellu lar signal; signal transducti on activates a TF; that TF turns on a set of genes Two of the One of the No mirna mirnas are non-coding; complement ary to mrna; and block translation of that mrna No RNA degradation mrnas can be degraded by exonuclease s; by endonucleas es; and ultimately this reduces overall expression No 5

6 Implementing Vision and Change Using Concept-Driven Teaching Strategies NSF RCN-UBE Grant # Designing Scientific Teaching Tools for BMB Education Regional Workshop Series Viterbo University November 9, 2014 BMB Alignment Table Template Please save this template as a separate working document for your group, with the filename as: Alignment LocationAbbr LastNameA LastNameB LastNameC.docx (e.g., Alignment USD Garcia Nguyen Smith.docx) Designed by: Jon Stoltzfus Pam Trotter Shawn Ellerbroek Selected Aspect of BMB: Foundational Concepts Keywords: Transformation of Energy Initial Overall Learning Goal: Students should understand the core concept of matter and energy transformation, including thermodynamics, catalysis, the coupling of exergonic and endergonic processes, and the nature of biological energy. Initial Learning Objective: Students should be able to discuss the concept of Gibbs free energy and how to apply it to chemical transformations, be able to identify which steps of metabolic pathways are exergonic and which are endergonic and relate the energetics of the reactions. Overall Learning Goal: Understand energy transformations in biological processes. Note, this is aimed at upper-level biochemistry courses. Learning Objective Given a cellular process with information relevant to energy transformation, identify instances where energy transformation (work) has taken place. Learning Assessment Learning Strategy

7 Explain how energy transformation contributes to a system. Explain the chemical/physical basis of energy transformation. Predict how changes in conditions will impact reaction direction/flux/transport direction/outcome of the process. Start with a specific biological process (for example, glycolysis, oxidative phosphorylation, or muscle contraction). Alter a condition in the system (for example, change in NAD + /NADH ratio, add an uncoupler, add an inhibitor) and ask students to predict how the process will change, explain why this change will take place, and support the prediction with evidence (for example, thermodynamic equations). Use POGIL problems where students practice analyzing systems, predicting what will happen when the system is changed, and how to support the prediction numerically. Assessment: Objective Low Low - Intermediate High - Intermediate Mastery How well does the student explain what would happen? Does not make a prediction. How well does the student explain why it happen? (mechanism) Numerical evidence to support the prediction. No coherent explanation of mechanism. No evidence. Does not accurately predict what would happen based on student's proposed mechanism and evidence. Chooses incorrect model 1,2 for mechanism of energy transfer. Inappropriate choice of equation. Chooses correct model 1,2 for mechanism of energy transfer but didn't appropriately apply. Appropriate equation but incorrect calculations. Accurately describes what would happen based on student's proposed mechanism and evidence. Chooses correct model 1,2 of mechanism of energy transfer and applied appropriately. Appropriate equation with correct calculations. 1. Wink, D.J., 1992, "Conversion of Chemical Energy: Part 1 Technological Examples", Journal of Chemical Education, 69(2): Wink, D.J., 1992, "Conversion of Chemical Energy: Part 1 Biochemical Examples", Journal of Chemical Education, 69(4):264 2

8 Strategy: POGIL Overview Part 1 Identify steps in a pathway/process that involve energy transfer. Part 2 Explain the importance of each energy transfer step in the overall transfer and conservation of energy in the process. Part 3 Explain the mechanism involved in energy transfer and calculate free energy changes. Part 4 Predict how changes in the system will impact the system and support this with calculations. POGIL Example glycolysis Part 1 of POGIL Students are given the pathway of glycolysis and asked to identify key steps where energy transfer takes place. Students would need to know that steps in pathways that use/generate ATP and redox steps involve energy transfer. In glycolysis, this is steps 1, 3, 6,7,10. Part 2 of POGIL Students are then asked to explain how each reaction identified in Part 1 contributes to the extraction and conservation of energy from sugar. For example in step 6 the relatively endergonic phosphorylation of 3PG is coupled to a relatively exergonic oxidation/reduction reaction resulting in a molecule with high enough group transfer potential to "make" ATP by substrate-level phosphorylation this extracts and conserves energy. Part 3 of POGIL Students are then asked to explain the mechanism and calculate free energy changes. For example in step 6 the transfer of e - s from 3PG to NAD + is favorable which is coupled to thioester formation. Favorable thioester hydrolysis is coupled to unfavorable phosphorylation the thioester intermediate avoids an energy trough that would prevent acylphosphate formation. Have students calculate actual free energy change using both mass action and redox based on concentrations and standard free energy changes and reduction potentials. Part 4 of POGIL Predict what would happen to both this reaction and the overall process if NAD + concentrations are reduced (for example, by inhibiting lactate dehydrogenase under anaerobic conditions)? Have students calculate free energy change using the new concentrations. Use this to support their prediction. 3