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Open Access Publications from the University of California

Studying the Effects of Familial Alzheimer’s Disease Mutations on the Assembly of a Constrained β-Hairpin Peptide Derived from Aβ And Developing and Implementing Specifications Grading Systems in an Organic Chemistry Laboratory Course and a Chemistry Writing Course

  • Author(s): McKnelly, Kate Joy
  • Advisor(s): Nowick, James S
  • Link, Renee D
  • et al.

The dissertation is composed of two main parts. The first half describes efforts to study amyloid peptides using macrocyclic peptide model systems, and the potential deleterious effects of uronium peptide coupling agents on human health. The second half focuses on my experience in chemistry teaching and the chemical education research I conducted.

Chapter 1 describes the design and synthesis of seven peptides and acetylated variants containing familial Alzheimer’s disease mutations (FADs). All peptides are based on a macrocyclic β-hairpin peptide derived from amyloid beta (Aβ), residues 16-36. The supramolecular structure of Aβ aggregates remains unknown due to the heterogeneous and unstable nature of Aβ oligomer formation. Elucidating the structure of Aβ aggregates will lead to insights into the function of Aβ in the progression of AD and FAD. Peptides derived from Aβ assemble in a crystalline state as dimers, trimers, hexamers, and even dodecamers, which recapitulates oligomeric species observed of full-length Aβ. In particular, the Aβ16-36 region is important for Aβ oligomer formation. Lactate dehydrogenase release assays and dye-release assays with lipid-bilayers indicate that the mutant peptides exhibit more toxicity towards neuronally derived SH-SY5Y cells and cause more membrane destabilization than the parent peptide. Sodium dodecyl sulfate - polyacrylamide gel electrophoresis reveals that mutant peptides assemble as higher-order oligomers, and the E22 mutant peptides all assemble to form hexamers, similar to the parent peptide. Size exclusion chromatography and circular dichroism indicate that similarly charged mutant peptides exhibit similar solution-phase behavior. X-ray crystallography reveals that the E22 mutant peptides assemble to form hexamers in the crystal state. These studies will aid in our understanding of how mutations of full-length Aβ perturb the biophysical characteristics and assembly of Aβ oligomers, which may give insight into Aβ’s mode of causing toxicity in AD and FAD.

Chapter 2 presents a case study of chemical sensitization. Anaphylactic reactions can occur from repeated exposure to peptide coupling agents. Many researchers in the peptide and protein chemistry fields recognize the peptide coupling agent DCC as an infamous immune sensitizer. Fewer researchers know that the uronium coupling agents HATU and HBTU are also sensitizers. Reports of sensitization caused by these peptide coupling agents have been published in allergy and immunology journals, but these sources are not generally read by researchers who use uronium coupling agents. In this chapter, I present my case study of anaphylaxis induced by three uronium agents: HATU, HBTU, and HCTU, as a cautionary note for researchers who handle peptide coupling agents frequently. I also include recommendations for handling coupling agents more safely in the research laboratory.

Chapter 3 overviews my journey towards becoming an effective instructor. I chronicle my experience as a TA, Head TA, and Instructor of Record. I also discuss my time as a Pedagogical Fellow, TAP-STEM trainee, TA Mentor, and the Safety Fellow for the Department of Chemistry. Each experience taught me something different that helped prepare me to pursue and obtain a teaching focused faculty position at Emory University starting in summer 2020.

Chapter 4 describes the design and implementation of specifications grading systems in organic chemistry laboratory courses and a “Writing for Chemists” course. I worked with Dr. Renée Link to convert her entire three-course organic chemistry laboratory series from a traditional, points-based grading system to a specifications grading system, first as a pilot study during a summer term course and then scaled up for the large (1,000+ students) course in winter 2020. I worked with Dr. Stephen Mang concurrently to redesign the “Writing for Chemists” course he started in 2017 using a specifications grading system and adapting assignments from a textbook on the practice of nonfiction writing. I taught the course in fall 2019 and used the redesigned course materials. In both courses, we collected surveys of students perceptions of the grading system, and in the organic chemistry laboratory courses we also collected feedback from the course TAs. Responses from students about the nature of the grading system in the laboratory course were mixed. Their perceptions indicate that initial buy-in and multiple reminders about the bigger picture of the grading system will be essential to the success of this grading system on a larger scale. After the writing course, students self-reported increased propensities to pre-write and edit, and several mentioned that they appreciated the transparency of rubrics and the control the specifications system gave them over their grades.

Chapter 5 describes the development of an educational activity I designed and implemented with Dr. Renée Link — the Extraction on Paper Activity. Undergraduate students often find it difficult to understand the chemical principles underlying liquid-liquid extractions. Explanations

on how extractions work at the molecular level in textbook and internet resources are plentiful, but students still do not seem able to grasp how extractions work before having to perform the technique in a laboratory course. To address student discomfort with conducting extractions, I developed an Extraction on Paper Activity. I envision this activity as a tool to help students understand and apply the chemical principles underlying liquid-liquid extractions outside of and before entering into a laboratory setting.

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