Teaching Portfolio

Teaching Portfolio Justin F. Shaffer, Ph.D.SPIRE Postdoctoral Fellow, University of North Carolina at Chapel Hill Visiting Lecturer, Department of Biology, University of North Carolina at Chapel Hill Former Adjunct Professor, Department of Biology, North Carolina A&T State University Last update: January 2013 Contents 1. Teaching Responsibilities 2. Teaching Philosophy 3. Teaching Methods and Strategies 4. Course Materials 5. Evidence of Student Learning 6. Teaching Evaluation 7. Efforts to Improve Teaching 8. Educational Outreach 9. Future Goals 10. Appendices Appendices A. Teaching experience B. Sample syllabus C. Sample lesson plan D. Sample exam E. Sample worksheet F. Pre- and post-test data G. Student evaluations H. Faculty evaluations

Teaching Responsibilities As a SPIRE (Seeding Postdoctoral Innovators in Research and Education) Postdoctoral Fellow at the University of North Carolina at Chapel Hill, I have been trained in pedagogy, effective teaching strategies, and course design. I have been able to use my training as an Adjunct Professor in the Department of Biology at North Carolina A&T State University. During the Spring 2012 semester, I taught Biological Sciences (Biology 100), an introductory biology course, to 71 non-major undergraduate students. During the Fall 2012 semester, I taught Designer Proteins and Society (Biology 642), a novel course of my own design. This course was a mixed lecture and lab course that explored the recombinant protein design and production processes and their link to medicine, industry, and agriculture. This course also included a 5-week laboratory module where students expressed, purified, and assessed dihydrofolate reductase (DHFR), an important enzyme involved in nucleic acid synthesis. I taught this course to 16 undergraduate and graduate biology students. During the Spring 2013 semester, I was a Visiting Lecturer in the Department of Biology at the University of North Carolina at Chapel Hill where I taught Biology 101 (Principles of Biology) to 400 undergraduate students in an active, student-centered classroom. More information about my teaching experience is listed in Appendix A. Teaching Philosophy While teaching my first college science course (an introductory biology course for nonmajors), I realized something and knew it to be completely true: I love teaching and I want to do this for the rest of my career. This was a great feeling to have, but I also needed to ask myself this important question: why do I want to teach? After racking my brain and writing down a long list of things, I came up with what is an ultimately simple answer (the essence of my teaching philosophy if you will): I want to get students excited to learn about science. This short statement sums up who I am as a teacher. Everything that I do as a teacher, from the way I teach, to my interactions with students, and to community outreach, all comes down to the fact that I want my students (and society as a whole for that matter) to appreciate, understand, and ultimately be excited about science. I believe that student excitement and engagement are the foundation for improving scientific literacy, building solid critical thinking and analysis skills, and preparing for successful scientific and technical careers. For those students that already really like science, I want to cultivate their interests and help them prosper into the scientists, researchers, doctors, and engineers of tomorrow. I like to say that I know that I wont ever find a cure for cancer, but maybe I will inspire a student who will someday do just that. Teaching Strategies and Methods My teaching style revolves around backward design (i.e. determining student learning objectives before classroom activities), student engagement, and having a studentcentered classroom. Putting my learning objectives first allows me to efficiently plan lessons and to focus on the key concepts that I want my students to learn. I believe that if my students are not engaged then I cannot properly teach them the material at hand and that they will not learn effectively. I use many active learning techniques, interactive

lecturing, real-world examples, case studies, and technology in order to engage my students. I also use formative in-class assessments to gauge what my students are learning and understanding. Class session structure I start each class session on time and end on time, and I try to use every minute in between as effectively as possible. I write on the board the list of topics that we will be covering in the lesson so that my students know what to expect, and I also write a list of any important class announcements (which I then email to the class afterwards). If I am using PowerPoint slides, I make them available (with missing information and blanks) to my students the night before so that they can print them out and take notes on them during class. I begin each class session with a list of the learning objectives for the day, and as we achieve them during the course of the class I make sure to tell my students that they just did so, which can bolster their confidence in learning the material. Throughout a typical class period, I use interactive lecturing interspersed with 5 7 active learning activities. I encourage students to ask questions, and I take the time to answer them and make sure everyone is following along before I move on. I plan my lessons so that they will fit into the allotted class time, and usually I am able to do so. If a lesson is running long, I do not rush through the material at the end in order to fit it all in; rather, I present the lesson without rushing and catch up the following class session. Please see the following section (Course Materials) for more details on my lesson plans as well as Appendix C for a sample lesson plan from my Spring 2012 Biology 100 course. Active learning methods In order to engage my students during class, I use a variety of active learning methods that requires them to interact with each other and myself. Research has demonstrated that students learn more when they are actively engaged in class, and I also think that these techniques are fun and more interesting than traditional lecturing. I use the think pair-share technique when I want my students to come up with an answer to a question (e.g. Why are cotton bath towels so water absorbent?). I also encourage my students to talk to each other when brainstorming to come up with lists of ideas about topics, such as the causes and effects of global warming. In order to do group work, I have used the jigsaw method to teach my students about cellular organelles and also about animal diversity. The use of real-world examples and case studies (see below) are also extremely useful in actively engaging my students during class. Active learning techniques can also provide feedback to me as the instructor about what my students are learning and what they are having troubles with. I used Poll Everywhere, a variant of the personal response system, and one minute papers to collect formative assessment data from my students during or at the end of class. Please see the below sections for more details on how I used these methods in class. Real-world examples and case studies Real-world examples and case studies are two of the most important tools in my teaching arsenal because they provide a direct link between the course material and my students personal lives. When I use case studies, my students interest levels pique and they become more engaged in the class session. The story-like manner in which case studies are presented leaves them hanging and wanting more, and they eagerly await the end of the case, while simultaneously learning

the lesson material. I used several cases from the National Center for Case Study Teaching in Science (http://sciencecases.lib.buffalo.edu/cs/) during my Spring 2012 Biology 100 class to teach cellular respiration in the context of energy drinks and marketing claims (I drank a Red Bull at 930am during class to see how much energy (or jitters) it would give me), to teach mitosis through the story of a 20-year old student that had ovarian cancer, and to teach meiosis through the process of sex determination and gender testing of athletes. I also incorporate real-world issues in my lessons that pose ethical dilemmas, such as genetic testing of an unborn baby, or how human activities influence climate change and the future of the earth. These real-world examples help make connections between the students lives and the course content, while simultaneously building students critical thinking, analysis, and evaluation skills. Interactive lecturing When I lecture in class, it happens for at most 10 minutes at a time, and even then it rarely involves me talking straight to the class without interruption. I routinely pose questions to my students in an interactive manner, whereby I am aiming to stimulate their interest in the topic and force them to come up with answers to questions before moving on. In this way my lecturing becomes more of a group conversation or discussion with my students. These blocks of lecturing are broken up with 5 - 7 active learning activities during a typical class session. Technology I am well skilled in using many forms of technology in the classroom to provide an effective and engaging learning experience. I use PowerPoint slides to display lecture material (text, images, and videos), and I also play videos from youtube.com (or other websites) to enhance certain topics, especially those involved biological processes. I provide links to these videos, media stories, or other helpful websites in the PowerPoint slides or as posts on Blackboard. During my Spring 2012 Biology 100 course I used Mastering Biology, an online homework and tutorial system, to assign homework, lab exercises, and some exams. Mastering Biology allowed my students to gain extra instruction on the course materials through animations, videos, and interactive exercises, all of which are incorporated into their homework assignments. I created a cumulative final exam in Mastering Biology which included pictures, videos, and links to other websites which gave my students an interactive exam experience that is not possible with a traditional paper exam. Additionally, I used Poll Everywhere to receive feedback from my students in real-time during class. Poll Everywhere allows students to answer multiple-choice or open-ended questions by texting with their cell phones, going to a website, or by tweeting. Formative in-class assessment I do my best to ensure that my students are learning during class and that they are not confused or lost at any point. To do this, I use formative in-class assessment methods to check my students understanding in realtime, which allows me to spend more time on a confusing topic before moving forward in the lesson. As described above, Poll Everywhere is a fantastic tool for these types of assessments, especially for larger classes. I use multiple Poll Everywhere questions during class sessions that serve as checkpoints in the lesson. Before moving on to the next part of the lesson, I can see what percentage of the class correctly answers a question about an important point or topic. If a substantial proportion of the class answers incorrectly, then I will go back and discuss the topic in a different way, then I will re-pose the question to the class to check for improved understanding. Additionally,

I may have my students talk to each other to try to convince each other what answer is correct, then have them answer the question again. I also use one-minute papers at the end of a class to ask my students what they are most confused about or what the most important topic from the day was, and then I use their feedback to address conceptual misunderstandings. If needed, I will then begin the next class session with a response to their comments and feedback. Finally, I also strongly encourage students to ask questions during class which provides yet another avenue for me to collect information about what my students learn during class. Course Materials Below is a description of some of the materials and student assessment methods that I use during a course in order to maximize student engagement and learning. Syllabus I intend to make my course syllabi as detailed and complete as possible so as to give my students a full sense of what they will learn in my course, what is expected of them, and how my course is structured. I include measurable course goals on the first page of my syllabi which lets my students know up front what they will be able to do at the end of my course. I revisit these course goals on the last day of class to demonstrate to my students how much they have learned during the semester. Please see Appendix B for a sample syllabus from my Fall 2012 Biology 642 course. Lesson plans I construct lesson plans using backward design which guides me in the delivery and presentation of each class lesson. The first thing I do when designing a lesson is to determine what my learning objectives are; that is, what my students will be able to do by the end of the lesson. I use learning objectives that are measureable and that address all levels of Blooms Taxonomy. Once I have my learning objectives in place, I decide how they will be assessed and how I will know whether they have been met or not. This can be accomplished through the use of a Poll Everywhere question, asking questions of individuals in the class, or having students write or draw on the board. Finally, I plan the actual layout or outline of the class, in which I determine what content to include, when I will lecture, and when I will use active learning techniques, all while ensuring that my learning objectives are met. Please see Appendix C for a sample lesson plan from my Spring 2012 Biology 100 course. Exams I use multiple exams during a course in order to assess student learning. When writing exams, I first put together a list of all of the learning objectives from the lessons that the exam is covering. Then I tailor each exam question to specifically address each of the learning objectives. Therefore, for a student to do well on an exam, they need to be able to achieve each of the learning objectives: in fact, this is exactly what I tell my students how to prepare for the exams. In order to gauge the difficulty of each exam, I assign a score of 1 6 to each question based on Blooms Taxonomy, with 1 being the lowest level (knowledge), and 6 being the highest (synthesis). I then take an average score of all of the exam questions which allows me to compare exams throughout a course. I have worked with a colleague to score exams and I am confident that I am assigning proper Blooms scores to my exam questions. Please see Appendix D for a sample exam from my Spring 2012 Biology 100 course. Worksheets In addition to providing my students with lecture slides and in-class handouts, I also prepare supplementary worksheets for them to use at their discretion.

These worksheets are not graded and do not have to be handed in, but I encourage my students to use the worksheets for extra help. I either provide the worksheets after a lesson that I know will be difficult, or I will create them in response to student demand. For instance, in my Spring 2012 Biology 100 course, my students were having difficulties determining the polarity of molecules. I therefore created a worksheet that explained in more detail how to determine a molecules polarity, as well as providing several examples for them to try out. See Appendix E for a copy of this worksheet. Projects For upper-division courses with lower enrollments, I use semester-long projects to challenge students to apply the course material in real-life situations. For example, in my Fall 2012 Designer Proteins and Society course, students were required to develop a design proposal outlining the steps required to clone, express, purify, and functionally assess a recombinant protein of their choice. Students completed assignments throughout the semester which allowed me to give them feedback on their design process. The project culminated in a written design proposal and an oral presentation to the class. Evidence of Student Learning I engage my students as much as possible during a class session by being an enthusiastic teaching and by using a variety of teaching methods and strategies, but engagement is fruitless if it does not result in learning. In order to assess student learning, I use several assessment strategies, from in-class formative assessments, homework assignments and exams, pre-tests and post-tests, and student feedback. These strategies provide evidence for what my students are learning and allows me to alter my teaching to address student weaknesses and strengths. Performance across the semester As the semester progresses, I use a variety of both formative and summative assessments to gauge what my students are learning. I routinely use in-class formative assessment tools such as Poll Everywhere questions, group brainstorm activities, and questioning to check my students understanding in real-time. These assessments let me change my teaching on the fly and linger on a topic if students are having difficulty understanding a concept. I also track my students learning through summative assessments such as homework assignments and exams. I assign daily homework assignments to force my students to stay up to date and to give them many opportunities to earn points towards their final grade. I administer multiple in-class examinations that directly assess the learning objectives in the course, and through the semester I can track class performance. In my Spring 2012 Biology 100 course, I administered five in class exams plus a cumulative online final exam, and the averages on these exams were 53%, 60%, 75%, 77%, 73%, and 61%, respectively. I believe that an improvement in my students study habits were partly due to the increase in exam scores, because many of them reported poor study habits as a primary cause of their low Exam 1 grade on a post-exam reflection worksheet. I would attribute the low average on the cumulative final exam to two causes: (1) the exam was more difficult than the in-class exams (average Blooms score of 2.5 vs. 2.1); and (2) since it was an open-notes, open-book exam, I think that my students did not take the exam seriously and did not study as well as they should have. A sample exam is provided in Appendix D.

Pre- and post-test data I use a pre-test and post-test to assess what my students know coming into my class and also to see what they learned by the end of the class. Giving my students a pre-test on the first day of class allows me to establish a baseline and lets me adjust my expectations accordingly. As the semester progresses, my teaching naturally covers the topics that are on the pre-test without explicitly addressing the pre-test questions. Finally, I use a post-test (which is identical to the pre-test) to assess what my students learned, how well I taught my students during the semester, and to help plan my future courses. During my Spring 2012 Biology 100 course, I administered a 16 question multiple choice pre-test on the first day of class, and the same test on the day of their final exam. My students performed significantly better on the post-test compared the pre-test, with 9 of the 16 questions showing significant improvement (P < 0.05). Overall, 49 students (out of 71) answered all 16 questions on both the pre-test and post-test, and the average learning gain was 0.23 0.21. Please see Appendix F for a copy of this pre-test / post-test and a data summary. Student feedback My students regularly give me feedback on how I am doing as a teacher, and how much they are learning. I encourage students to stop me during class and ask questions if they do not understand something. When students stay after class to ask questions, I usually ask them how they thought the preceding class session was and if there were any topics that did not make sense. I take this one step further when students visit my office by asking them in more depth how they are enjoying my class, if they are having any troubles with any of the concepts, and if there is anything I can do to help them learn more effectively. I also collect student feedback from a course evaluation at the five-week point in the semester that helps me to address potential problems while there is still a large portion of the semester remaining. Teaching Evaluation In order to become a better teacher, evaluations from my students and faculty colleagues are essential. Self-reflection is also critical so that I can implement these evaluations in my teaching. Student Evaluations I have my students provide feedback on the course and on myself as a teacher after 5-weeks and again at the end of the semester. I use the feedback that I collect from the 5-week evaluations to respond to student concerns and to improve the remainder of the course. While I was evaluated very positively by my Spring 2012 Biology 100 students at the 5-week mark (average 9.0/10.0 rating), I used their feedback to improve my teaching for the remainder of the course, including slowing the pace of my lectures, adding more engagement and activities, and helping them build a strong biological vocabulary. I also feel that this shows my students that I truly care about how they are doing and how the course is proceeding. I also use end-of-course evaluations to reflect on my performance during the semester as a whole and also to improve my teaching for future courses. These data provide evidence (in addition to student performance on summative assessment items) that I use to assess the success of a course. I received very high marks on my student evaluations for my Spring 2012 Biology 100 course, and a sample of these ratings are shown below in Table 1. Please see Appendix G for sample student comments as well as end-of-course evaluations from my Spring 2012 Biology 100 course and Fall 2012 Biology 642 course.

Statement This course was excellent. The organization of this course was excellent. This instructor was an effective teacher.

Mean STD (1.0 to 5.0) 4.65 0.57 4.79 0.47 4.81 0.45

Table 1: Summary of overall course ratings from Biology 100, Spring 2012. A higher mean response indicates higher level of agreement, as Strongly Disagree equaled the value of 1 and Strongly Agree equaled the value of 5. Number of students enrolled = 71; number of responses = 43. Peer Evaluations Equally important to student evaluations are faculty or colleague evaluations, and I like to have a departmental colleague observe my class at least one time per semester (I had three colleague evaluations during my Spring 2012 Biology 100 course) so as to gain important feedback that I can use to improve my teaching and my courses. See Appendix H for evaluations from two colleagues that I received during my Spring 2012 Biology 100 course and one from my Fall 2012 Biology 642 course. Self-reflection I am constantly self-evaluating and reflecting on my teaching experiences. After each class session, I write in my teaching journal about what worked, what didnt work, and any other comments about the preceding class session. This not only helps me improve the content of class sessions for the next time I teach them, but it also helps me think about how I responded to student questions, how I presented certain course material, and how I responded to classroom disruptions. Efforts to Improve Teaching I am actively involved in several ways to improve my teaching and my courses so that my students can be more engaged and effectively learn the course material. I have attended the 2011 IRACDA Annual Meeting in Houston, TX in June 2011 that focused on ways to improve student learning in biology classrooms, as well as the 2012 Association for Biology Laboratory Education Conference in Chapel Hill, NC in June 2012. I also attended the Bridging the Gap NC Conference in Raleigh, NC in October 2012 where I presented a poster on a novel case study I developed that explores the development of recombinant human insulin, the worlds first bioengineered drug. As a SPIRE Postdoctoral Fellow, I have been trained in effective pedagogy, active learning techniques, and course design through several workshops including an 8-week seminar on college teaching. I have also participated in several workshops hosted by the UNC Center for Faculty Excellence, and a semester-long course on college science teaching taught by faculty in the UNC Biology department. Responding to and evaluating student feedback is an effective way to improve my teaching. I use feedback received from students in class, from comments after class or from emails, and from mid-term and end-of-course evaluations to reflect on and improve my teaching. I also use feedback and critiques from colleague and faculty observations to improve my teaching. In order to stay up to date on effective teaching practices, innovations in pedagogy, and happenings in the higher education community, I follow and read several scholarly journals on teaching, including The Journal of College Science Teaching, CBE: Life Sciences Educations, The Journal of Chemical Education, and Biochemistry

and Molecular Biology Education. I also routinely check The Chronicle of Higher Education website for news and updates about higher education. Educational Outreach I believe I have a responsibility as a scientist to give back to my community and educate and inspire the public about scientific issues. I especially like to talk with middle school and high school students (i.e. the next generation of scientists and engineers). When I was in high school, I dont remember ever having a single visit from a scientist, engineer, or any other professional for that matter. I want students in my community to be exposed to scientists and engineers before they go to college so that they can possibly be inspired to study bioengineering, microbiology, biochemistry, or any other type of science. Ive had extensive experience leading, planning, and executing educational outreach visits to community middle and high schools since I have graduated college, and I intend to continue this extremely important and rewarding activity throughout my career. In the future, I want to impart my devotion to community outreach to my students by including a service-learning component in my classrooms wherein my students will visit community high schools and give presentations on scientific issues. Future Goals My major and most important short-term goal is to obtain a faculty position at a university where I can excel in teaching and mentoring undergraduate students. I thoroughly enjoy being a part of the academic culture, and I feel that I can significantly impact many students in the classroom. In this future role, I would like to teach introductory science courses for majors and non-majors students, coordinate and teach laboratory courses, develop and teach upper division courses in biotechnology and recombinant protein design, establish an lead a community educational outreach program, and serve as an advisor and mentor to undergraduate students. I also have several goals for improving my teaching and adding new components to my courses. First, I believe that case studies are extremely useful tools that engage students and promote student learning, and I have a goal to develop my own case studies for teaching science courses. I have developed and implemented a case study that explores the history of the development of recombinant human insulin, the worlds first bioengineered drug. I have also submitted this case study to be added to the National Center for Case Study Teaching in Science collection. Second, I have a goal of incorporating my passion for educational outreach into my courses. I would like to include a service learning component into a future upper division biotechnology course, where my students would prepare presentations on the many facets of the biotechnology industry and give these presentations to local high schools in order to promote interest in the STEM fields and also to dispel misconceptions about biotechnology. Finally, I aim to incorporate an educational research component into my career. I am interested in how to effectively teach large classes, how to properly motivate students in non-majors introductory science classes, and developing concept inventories for biotechnology courses.

Appendix A

Teaching Experience Courses Taught Biology 101 Principles of Biology Spring 2013 Department of Biology University of North Carolina at Chapel Hill Enrollment: 400 undergraduate students Introduction to biology for mixed-majors students exploring the major concepts in biology including macromolecules, cell structure and function, genetics and inheritance, evolution, diversity, and ecology Mentored and supervised four graduate teaching assistants and four undergraduate supplemental instructors Biology 642 Designer Proteins and Society Fall 2012 Department of Biology North Carolina A&T State University Enrollment: 16 undergraduate and graduate students A self-developed novel course that explores the recombinant protein design and production processes and their link to medicine, pharmaceuticals, industry, and agriculture Implemented a 5-week laboratory module based on the Bio-rad Biotechnology Explorer Protein Expression and Purification series where students expressed, purified, and assessed recombinant dihydrofolate reductase Biology 100 Biological Sciences Spring 2012 Department of Biology North Carolina A&T State University Enrollment: 71 undergraduate students Introduction to biology for non-major students Supervised three graduate student TAs for three laboratory sections MCP 290 / NPB 198 Major Discoveries in Muscle Contraction Fall 2009 Department of Neurobiology, Physiology, and Behavior University of California, Davis Enrollment: 11 graduate students, 1 undergraduate student Self-developed novel seminar exploring the major scientific advances in muscle physiology research over the past 50 years Guest Lectures Biology 472 Comparative Physiology Spring 2011 Department of Biology University of North Carolina at Chapel Hill Enrollment: ~70 undergraduate students Presented two original guest lectures on the topics of 1) invertebrate excretion; and 2) animal movement and muscle physiology

Appendix A

Biology 4610 The Physics of Life Fall 2010 Department of Biology North Carolina Central University Enrollment: 10 undergraduate students Presented original guest lecture on muscle mechanics and motor proteins Teaching Assistant Experience BIS 2C Introduction to Biology: Biodiversity and the Tree of Life Winter 2010 College of Biological Sciences University of California, Davis Enrollment: 24 undergraduate students Assisted students on weekly in-lab assignments and answered student questions Bioengineering 481 Senior Capstone Project Fundamentals Spring 2007 Department of Bioengineering University of Washington, Seattle Enrollment: ~60 undergraduate students Advised students on research and design projects Taught three original lectures on good notebook practices, how to find funding sources, and how to write a research paper

Appendix B

NORTH CAROLINA AGRICULTURAL AND TECHNICAL STATE UNIVERSITY Course SyllabusCourse Information Course Number & Section Course Title Term Location Days & Times Website Biology 642 Section 001 (CRN 17632) Designer Proteins and Society Fall 2012 224 Barnes Hall Tuesday & Thursday 12:30pm - 1:45pm http://blackboard.ncat.edu

Professor Contact Information Professor Dr. Justin Shaffer Email Address [email protected] Office Phone 724-301-2712 Office Location G10 Barnes Hall Office Hours Tuesday 10:00am 12:00pm Thursday 2:00pm 4:00pm Course Description and Goals Proteins can be so much more than what you find in a burger or a nutritional supplement! Did you know that scientists and engineers can design and produce custom proteins to meet specific functional and technical needs? Whether they are for medical, pharmaceutical, industrial, agricultural, or environmental settings, recombinant proteins are used in a variety of ways to benefit society. This course provides an introduction to the fascinating and diverse field of recombinant proteins. Once we cover the basics of how recombinant proteins are made, youll learn how to use recombinant DNA technology to design protein expression vectors. Next, youll learn how various expression systems (bacterial, insect, and animal cells) and purification schemes (chromatography, centrifugation, dialysis, etc) are used to produce and purify recombinant proteins. Youll also have the opportunity to perform a realistic laboratory research project to express, purify, and functionally assess a recombinant protein. Throughout the course well discuss the many ways that recombinant proteins are used in modern day medicine, industry, and agriculture, and will discuss their societal and ethical impacts. Specifically, at the end of this course, you will be able to Define and explain key fundamental terms and concepts of protein biochemistry Apply molecular biology methods and recombinant DNA technology to create recombinant protein expression vectors Design an expression and purification scheme for a recombinant protein based on the proteins biochemical properties Develop a design proposal to clone, express, purify, and assess a recombinant protein Explain how recombinant proteins are used in medical, pharmaceutical, industrial, environmental, and agricultural applications and why they are so important to society Explain and evaluate the ethical implications surrounding recombinant DNA technology and the use of recombinant proteins Design, execute, and troubleshoot laboratory experiments and methods relating to recombinant protein expression and purification

Appendix BPage 2 More specific learning objectives and goals are presented for each unit as described in the course schedule below, and will also be provided at the beginning of each day of class. Prerequisites Molecular biology (BIOL 401). If you do not meet the prerequisites please contact me. Required Textbooks and Materials There are no required textbooks for this course. You might want to consult your biology, molecular biology, or biochemistry textbooks from time to time to help brush up on some material. Reading materials will be posted on Blackboard for you to read and print out. Course Requirements and Evaluation Active Learning: You might be used to taking courses in which the professor simply lectures the entire class period. This course is going to be very different, as it is going to be an active classroom. By active I mean that you will be required to interact with myself and your fellow students to learn the material presented in this course. We will be using activities such as small group work, case studies, and class discussions to actively engage in the learning process. In order to have an active classroom, attendance is extremely important. By attending class and working through these active learning exercises you will develop critical thinking and problem solving skills that are essential to performing well in this course and others. Recombinant Protein of the Day: Recombinant proteins are essential to medicine, industry, agriculture, and the environment. To highlight the importance of recombinant proteins in our society, each day of class will feature a Recombinant Protein of the Day. During these short, 5 minute presentations, we will learn about the function of the recombinant protein, how it is used by society, and how it is produced. I will give the first handful of presentations, but then you as a class will be responsible for presenting the remainder. The goal is not to learn everything possible about the specific recombinant protein, but rather to be exposed to the many, many ways that recombinant proteins positively affect our society! See the handout for more details. Design Project: The overall goal of this course is that you will be able to design and map out a procedure to clone, express, purify, and functionally assess a recombinant protein. This project will be in the form of a written proposal. The proposal will include the following sections: 1) background on the biological importance of the protein you want to produce; 2) design of the cloning process (choice of vector, primer design, choice of restriction enzymes, etc); 3) choice of the expression system; 4) design of a purification scheme (type of chromatography, etc); and 5) design of experiments to assess the function of the protein. All sections will require justifications as to why you designed the process the way you did. Throughout the semester, there will be checkpoints where you will have to turn in parts of the project to keep you on track. The final project will be due at the end of the semester. Further instructions and guidelines for the project will be given out in class. Laboratory Project: During the last few weeks of this course you will have the chance to take part in a realistic research project where you will express, purify, and functionally assess a recombinant protein, dihydrofolate reductase (DHFR), an important enzyme involved in the synthesis of nucleic acid precursors. We will be using the Bio-rad Biotechnology Explorer Protein Expression and Purification series of modules that will give you the opportunity to grow E. coli bacteria to express DHFR, to purify DHFR using affinity chromatography, and to assess the enzymatic activity of DHFR using a spectrophotometric assay. Assessments of the lab portion of the class will include pre-lab assignments, in-class worksheets, and a written lab report. Further instructions and guidelines will be given out in class.

Appendix BPage 3 Guest Speakers and Field Trip: In this course you will be exposed to a variety of techniques and principles that are used in the biotechnology sector. To give you more insight into this type of industry, we will be having a guest speaker in class from a local biotechnology company to share their experiences in working with recombinant proteins in industry. We will also be taking a field trip to a local biotechnology company to see the production of recombinant proteins on a large scale. Further details will be announced in class. Evaluation: There will be multiple grading opportunities in this course, giving you many chances to do well. A summary of the various grading opportunities is given below. Pre-Test: The pre-test will cover basic DNA and protein concepts that you need to know to do well in this course. The pre-test is worth 50 points, or 5% of your course grade. Recombinant Protein of the Day: You are required to give a 5 minute presentation describing the recombinant protein of your choice. The due date is variable, as you will sign up for a specific date to present. This presentation is worth 50 points, or 5% of your course grade. Quizzes: Throughout the semester, we will have brief, unannounced in-class quizzes that will assess your knowledge of the course material. If you miss a quiz, you will not be able to make it up. Quizzes are worth 50 points, or 5% of your course grade. Homework Assignments: There will be four homework assignments that will help you stay up to date on the course material. Homework assignments will be due at the beginning of class on the day they are due. Homework due dates are listed in the detailed course schedule below. Homework assignments are worth 100 points, or 10% of your course grade. Exams: There will be two take-home exams in this course, with each worth 10% of your course grade. The first exam will be due on September 25th and will cover material from Units 1 and 2. The second exam will be due on October 23rd and will cover material from Unit 3. Laboratory Project: There will be several components of the lab project, including pre-lab assignments, in-class worksheets, and a final written report (due December 5th at 5pm). All of these activities will add up to 250 points, or 25% of your course grade. More details about the laboratory project will be handed out in class. Design Project: There will be several due dates throughout the semester where you will have to turn in updates on your design project. The project will culminate in oral presentations held during the final exam period (Friday December 7 from 1 3pm). All of the components of the design project will add up to 300 points, or 30% of your course grade. More details about the design project will be handed out in class. The breakdown for course points is as follows: Pre-Test Protein of the Day Quizzes Homework Exams Laboratory Project Design Project Total 5% 5% 5% 10% 20% 25% 30% 100% 50 points 50 points 50 points 100 points 200 points 250 points 300 points 1000 points (see handout for details) (4 at 25 points each) (2 at 100 points each) (see handout for details) (see handout for details)

Appendix BPage 4 Based on the above point structure, you can calculate your grade at any time during the semester (ask for help if you need it), and you should calculate your grade regularly to keep track of how you are doing in the course. The number of points will be converted to letter grades based on the following: 895 1000 points 795 894 points 695 794 points 595 694 points Less than 595 points A B C D F

Course Policies Courtesy to Fellow Students: We are going to have a positive learning environment in this class, so courtesy to your fellow students (and to me!) is imperative. Do you want to be distracted while trying to learn? Probably not, so please treat your classmates as you want to be treated. This includes putting your cell phones on silent before class starts, not using cell phones during class, limiting side conversations and comings and goings during class, not reading newspapers or doing the crossword puzzles, and other possible distractions. Attendance: Attendance is vital to succeeding in this course. Participation in the active learning activities during class will help you develop your critical thinking and problem solving skills which will help you on the exams in this course and in other courses. Finally, attendance is required by North Carolina A&T State University, and failure to attend class regularly will result in a reduction of your grade and possible failure of the course. Academic Integrity: Enrollment in this class means that you agree to abide by the expectations of North Carolina A&T State University regarding academic integrity. For specific information, refer to your Student Handbook. Also, refer to the most current Undergraduate Bulletin for the academic dishonesty policy. The Universitys Academic Honor Code will be strictly enforced. Your responsibilities in the area of honor include, but are not limited to, avoidance of cheating, plagiarism and improper or illegal use of technology. Your assignments are expected to be your own work. If you have questions, please ask. Integrity is an important characteristic that should be exemplified in the lives of all North Carolina A & T State University students. Dishonesty will not be tolerated in any form in this class. Any student caught cheating on an examination or any other class assignment will be given a grade of zero for that examination or class activity and reported to University officials for further disciplinary actions. Plagiarism (i.e. citing information written by another person without referencing the persons work) will also lead to a grade of zero for the assignment. Changing a few words in material taken from a book or the internet without referencing the author of the material is still plagiarism. Late Work: No late work will be accepted. All assignments are due at the beginning of class on the day that they are due. Please plan accordingly to make sure your homeworks and other assignments are turned in on time. Make-up Work: If you have an official university excuse for missing an exam (death in the family, sickness, university activity), then a make-up exam will be possible. Please see me ahead of time if you know you will miss an exam due date. Quizzes cannot be made up. Field Trips: We will be going on a field trip in this course. See the university policy on field trips and class travel. More details will be announced in class.

Appendix BPage 5 Course Schedule The following is the schedule for the course. The course is broken up into four units, with the first three units being classroom-based, and the last unit being a hands-on laboratory project. Due dates for homework (HW), exams, design project (DP), and pre-lab (Pre) assignments are listed when appropriate. See design project and laboratory project hand-outs for more details on these assignments. The schedule is subject to change. Unit 1: Introduction to Recombinant Proteins BIG QUESTION: What is a recombinant protein? At the end of this unit you will be able to Evaluate the use of recombinant DNA technology to make recombinant proteins Outline the major steps in the design and production of a recombinant protein Use online tools and databases to research and create recombinant proteins Thursday August 16 Tuesday August 21 Thursday August 23 Tuesday August 28 Course introduction and overview Insulin: the first recombinant drug How to make a recombinant protein Online tools for protein design Unit 2: Recombinant DNA Technology BIG QUESTION: How do you use recombinant DNA technology to make proteins? At the end of this unit you will be able to Outline the steps necessary to prepare a functional expression vector Identify and describe the essential features of cloning and expression vectors Design PCR primers to clone a gene of interest Explain how restriction enzymes are used to clone genes Explain how to screen for positive recombinant clones Thursday August 30 Tuesday September 4 Thursday September 6 Tuesday September 11 Thursday September 13 Tuesday September 18 Overview and RNA and cDNA preparation Polymerase chain reaction & primer design Plasmids and Expression vectors DNA manipulation (restriction enzymes & ligation) Transformation and screening of recombinants Verification of vector contents & DNA sequencing HW 1 DP 1 HW 2

Pre-test due

Unit 3: Recombinant Protein Expression and Purification BIG QUESTION: How do you produce and purify a recombinant protein? At the end of this unit you will be able to Compare and contrast recombinant protein expression systems Describe protein purification methods and technologies Evaluate purification methods for a given protein given its properties Describe methods used to assess protein purity Explain how to quantify and assess recombinant protein activity/function Thursday September 20 Tuesday September 25 Thursday September 27 Expression systems Cell culture growth, induction, and expression Crude purification methods Exam 1

Appendix BPage 6 Tuesday October 2 Thursday October 4 Tuesday October 9 Thursday October 11 Tuesday October 16 Thursday October 18 Tuesday October 23 Chromatography I Chromatography II Fall Break no class Assessment of protein purity and yield Assessment of protein function Scale-up of protein production schemes Guest lecture X-ray crystallography Unit 4: Laboratory Project BIG QUESTION: How do you express, purify, and functionally assess DHFR? At the end of this unit you will be able to Grow, induce, and handle E.coli bacteria using sterile techniques Express and purify DHFR from E.coli using affinity chromatography Assess the purity and function of DHFR using SDS-PAGE and enzymatic assays Collect and analyze data in a realistic research project Thursday October 25 Tuesday October 30 Thursday November 1 Tuesday November 6 Thursday November 8 Tuesday November 13 Thursday November 15 Tuesday November 20 Thursday November 22 Tuesday November 27 Thursday November 29 Introduction to project & basic lab techniques Lyse cells Crude purification of DHFR Affinity purification of DHFR Desalting and SDS-PAGE Concentration measurement of DHFR Enzymatic assay of DHFR activity Data analysis Thanksgiving break no class Guest speaker Course summary and evaluations Pre 1 Pre 2 Pre 3 Pre 4 DP 3, Pre 5 Pre 6 Pre 7 HW 3 DP 2 HW 4 Exam 2

DP 4 DP 5

Final lab report due December 5 at 5pm Final exam period: Friday December 7 from 1 3pm

Appendix CBiology 100, Lecture 17 DNA Profiling Learning Objectives: Explain how PCR is used to amplify DNA molecules Predict the size of a DNA molecule using gel electrophoresis Define STR analysis and explain how it is used in DNA profiling Use DNA profiling results to match a suspect to a crime scene Reading: Chapter 12 (sections 12.11 12.15) Class Outline: Discuss Exam 3 and study tips Last time we talked about cloning, today were going to talk about another example of DNA biotechnology, and next week were going to talk about GMOs Describe Earl Washingtons case 5 minutes Interweave Earls story with rest of lecture, ending with how he got pardoned Did the criminal justice system work? Is there a better way to prove someones guilt or innocence? What other forms of evidence are used in court? Think-pair-share Eye-witness testimony, biological samples, video evidence DNA profiling overview Show figure from book, explain each step Go through each step in more detail Can also be used in paternity tests OJ Simpson, Bill Clinton, Thomas Jefferson 10 minutes 3.22.12 Spring 2012

10 minutes

1. DNA is isolated 5 minutes DNA can be taken from several biological samples Where is DNA found? in the nuclei of cells Blood, semen, bone, tissue, lip print on a glass or cigarette, saliva, hair o Only white blood cells have nuclei (mature red blood cells lose their nucleus because they dont divide) Blood typing used to be used, but there are only a few blood types What if you dont have enough sample? o Make more DNA with PCR 2. DNA of selected markers is amplified 15 minutes How do you tell if your DNA is different from someone elses? You could compare your entire genomes, but that would take a while Instead, compare only select regions of DNA that are known to differ between individuals You need lots of DNA to do this

Appendix CBiology 100, Lecture 17 DNA Profiling 3.22.12 Spring 2012

You usually dont have much DNA at a crime scene to work with Using PCR you can get lots of DNA, starting with as few as 20 cells! Show figure for how PCR works Show youtube video for how PCR works What regions are getting amplified? o Talk about what regions are used as markers later STR analysis

3. DNA is compared 15 minutes Now you have all of this DNA and you need to know more about it Gel electrophoresis lets you see the size of DNA molecules Show book figures for how it works If you wanted to compare the STR regions between two (or more) people, this would be the way to go PE question about DNA size o Show gel with bands and a ladder how big is band A? o Also ask is band B larger than band A? or vice versa STR analysis 15 minutes Define STRs and give example for what they are Ask class (TPS) to come up with a method for how STRs can be used to compare peoples DNA o The answer is the method of DNA profiling Show 13 STR regions and CODIS Show how STR analysis works by comparing STR lengths from a suspect to a crime scene (book figure 12.14A) Show figure 12.11 and ask which suspect could have committed the crime? Odds of two people having the same 13 STR regions is 1 in a billion (or greater) Case wrap-up 5 minutes Earl was innocent, but was wrongfully imprisoned for 17 years DNA profiling is a powerful tool to determine innocence or guilt Since 1989, 218 convicts have been released after being proven innocent using DNA profiling

Appendix DBiology 100 Section 002 Spring 2012 Name: _________________________________ Please answer the following questions by clearly circling your answer. There are 33 questions worth 3 points each, for 100 points total (you get one free point for showing up). There is one extra credit question at the end that is worth 5 points, making it possible to score 105 out of 100 points on this exam. Please ask questions if you dont understand a question and good luck! 1. What is the central dogma of molecular biology? A. RNA makes protein makes DNA B. DNA makes RNA makes protein C. Protein makes RNA makes DNA 2. In dogs, short hair is dominant (H), whereas long hair is recessive (h). What phenotype does a hh dog have? A. Long hair B. Short hair C. Intermediate-length hair 3. What is the most important type of gene regulation in eukaryotes? A. DNA unpacking B. Transcriptional control C. RNA splicing 4. What is the DNA complement of this DNA sequence? ATCACCGGATGC A. CGTAGGCCACTA B. TAGTGGCCTACG C. UAGUGGCCUACG 5. The DNA in skin cells contains genes for which of the following? A. Skin color B. Hair color C. Both skin color and hair color 6. If two animals are heterozygous for a single gene and have 100 offspring, approximately how many of the offspring will exhibit the dominant phenotype? A. 75 B. 50 C. 25 7. TPOX is one of the STRs that are used to compare DNA between different people. Why is TPOX useful for comparing DNA between different people? A. TPOX varies in the number of repeats between people B. TPOX varies in sequence between people C. TPOX is only present in some peoples genomes 8. If you inherit two identical copies of a gene from your parents, you are said to be ____________ for that gene. A. Recombinant B. Heterozygous C. Homozygous 9. What is the main difference between DNA and RNA? A. RNA is longer than DNA B. DNA uses the base T, whereas RNA uses the base U C. DNA uses the base U, whereas RNA uses the base T Exam 3 3.29.12

Appendix DName: ___________________

Use the figure to the right for the next three questions. Each band in the ladder is in 100 base increments, starting with 100 bases at the bottom and going to 700 bases at the top. 10. Of the four DNA molecules shown (A, B, C, and D), which is the longest? A. Molecule A B. Molecule B C. Molecule C D. Molecule D 11. Approximately how many bases are in DNA molecule C? A. 480 bases B. 520 bases C. 600 bases 12. If DNA molecules A and D are STRs from two different people, what can you say about them? A. STR A is longer than STR D B. The sequence of STR A is different than the sequence of STR D C. STR A is shorter than the STR D 13. What is the name of the method that is used to make billions of copies of DNA? A. CODIS B. STR C. PCR 14. Imagine John Horner was successful in creating a male chickensaurus by turning on and off genes in somatic cells during the development of a chicken embryo. If this male chickensaurus mated with a normal female chicken, what kind of offspring would they have? A. A chickensaurus B. A normal chicken C. Part chicken, part chickensaurus 15. What is the transcription product of this sequence? GCTAGCGATGAC A. CGAUCGCUACUG B. CAGTAGCGATCG C. CGATCGCTACTG 16. A mutation in DNA changes a codon from ACU to ACG. What happens to the amino acid this codon codes for? A. The amino acid stays the same B. It changes from one amino to another C. The amino acid is deleted 17. What is the first step towards turning a gene on through transcriptional control? A. RNA polymerase binds the promoter B. Transcription factors bind the promoter C. Activators bind enhancers 18. Why do DNA molecules move from the top (negatively charged) to the bottom (positively charged) in gel electrophoresis? A. Because DNA is negatively charged B. Because DNA is neutrally charged C. Because DNA is positively charged

Appendix DName: ___________________ Use the figure to the right for the next two questions. Each band in the ladder is in 100 base increments, starting with 100 bases at the bottom and going to 700 bases at the top. CS crime scene; S1 suspect 1; S2 suspect 2; S3 suspect 3 19. Based on the results in the figure to the right, what suspect likely committed the crime? A. Suspect 1 B. Suspect 2 C. Suspect 3 D. You dont have enough information to know 20. What is this method that you used in the previous question called? A. PCR B. STR analysis C. Translation 21. What is the translation product of this sequence? AUGGCAUGCGAUUGC A. Met Ala Trp Asp Stop B. Met Ala Cys Asp Cys C. TACCGTACGCTAACG 22. What is the difference between a dominant and a recessive allele? A. Dominant alleles are more common in the human population than recessive alleles B. Dominant alleles are always found in homozygous pairs, whereas recessive alleles are always found in heterozygous pairs C. Only one copy of a dominant allele is needed to show its trait, whereas two recessive copies are needed to show its trait 23. What is the molecular basis for genotype and phenotype? A. Genotype is the DNA, and phenotype is the proteins B. Genotype is the RNA, and phenotype is the proteins C. Genotype is the proteins, and phenotype is the DNA 24. The contractile protein myosin is abundant in a muscle cell. Is the gene for myosin turned on in this muscle cell? A. Yes, because the myosin protein is present B. Yes, because the myosin gene is turned on in every cell in the body C. No, because silencers are prohibiting transcription from taking place 25. There is a mutation in a promoter that does not allow RNA polymerase to bind correctly. Will transcription take place? A. Yes, because DNA polymerase and not RNA polymerase is needed for transcription B. No, because the transcription factor / activator complex cant bind the promoter C. No, because if the RNA polymerase cant bind correctly then RNA cant be made 26. A genetic counselor tells you and your partner that you have a 50% chance of having a baby with a recessive disease. If the dominant allele for this disease is D, and the recessive allele is d, what are your and your partners genotypes? A. One is DD and one is dd B. One is Dd and one is Dd C. One is Dd and one is dd 27. What is the definition of a gene? A. A polymer of amino acids B. A trait or characteristic such as eye color C. A discrete unit of hereditary information (DNA)

Appendix DName: ___________________ 28. Being able to taste PTC is dominant (T), whereas not being able to taste PTC is recessive (t). If your dad is heterozygous and can taste PTC, and your mom cannot taste PTC, what is the chance that you can taste PTC? A. 75% B. 50% C. 25% 29. In labs, black fur is dominant (B), whereas chocolate fur is recessive (b). A black lab (BB) is bred with a chocolate lab (bb). What is the chance that they have a chocolate lab puppy? A. 100% B. 50% C. 0% 30. What method was used to make dinosaurs in Jurassic Park? A. Cloning B. Gene transfer C. Manipulation of hox genes 31. Different cells in your body make different proteins. Why dont they all make the same proteins? A. Because different cells have different genes B. Because gene expression is regulated C. Because not every cell has a supply of amino acids 32. What type of DNA mutation causes hemoglobin proteins to become mutated in people with sickle cell anemia? A. Substitution B. Insertion C. Deletion 33. A man has a DNA replication error causing a deletion of DNA in a reproductive cell about to enter meiosis. A womans skin cell acquires a substitution mutation during replication prior to mitosis due to the suns radiation. If these two individuals mate, which of the mutations might be passed onto their children? A. The mans deletion mutation B. The womans substitution mutation C. Both mutations are possibly inherited Extra credit: Using your knowledge of the central dogma, determine the end product starting from the DNA sequence below. If you use the one-letter abbreviation of each monomer in the final product, you will spell out a secret message! Make sure to write out all steps in the process and to show your work!

TTA ACG CGA TGA TAT TCG GCC CGG CTA

Appendix EPolarity worksheet Dr. Justin Shaffer Biology 100 Spring 2012

This worksheet will help you learn how to distinguish between polar and non-polar molecules, and whether a molecule is hydrophilic (water loving) or hydrophobic (water fearing). Read through the first two pages, then try out the examples on the last page. How do you tell if a bond is polar or non-polar? Covalent bonds form between atoms when atoms share electrons The bonds between carbon (C) and hydrogen (H) in methane are covalent, as are the bonds between oxygen (O) and hydrogen (H) in water

The polarity of a covalent bond depends on the electronegativity of an atom. Electronegativity refers to how strongly an atoms pulls electrons towards itself. Atoms have different electronegativities. For the major atoms that make up biomolecules, the strength of electronegativities is shown below (from most electronegative to least electronegative) Oxygen (O) > Nitrogen (N) > Carbon (C) ~ Hydrogen

Oxygen is the most electronegative, followed by nitrogen, followed by carbon and hydrogen, which have about the same electronegativity When two atoms with the same electronegativity form a covalent bond, neither atom pulls electrons closer to itself. There is an equal distribution of electrons (everything is balanced), and this kind of bond is referred to as a non-polar covalent bond. o The bonds between carbon and hydrogen in methane are non-polar covalent bonds because carbon and hydrogen have the same electronegativities.

If two atoms with different electronegativities form a covalent bond, then electrons are pulled closer to the atom that is more electronegative. This results

Appendix E

in that atom becoming more negatively charged, and the other atom becoming more positively charged. There is an unequal distribution of electrons, and this kind of bond is referred to as a polar covalent bond. o The bonds between oxygen and hydrogen in water are polar covalent bonds because oxygen is more electronegative than hydrogen, so it pulls the electrons closer to itself, making the oxygen slightly negative and the hydrogen atoms slightly positive.

How do you tell if a molecule is polar or non-polar? If a molecule (or part of a molecule, like the R group of an amino acid) contains only non-polar covalent bonds, then the molecule is non-polar. o QUICK TIP: If a molecule (or part of the molecule) only contains carbon (C) and hydrogen (H) atoms then the molecule is always non-polar. If a molecule (or part of a molecule, like the R group of an amino acid) contains one or more polar covalent bonds, then the molecule is most likely polar. o QUICK TIP: If a molecule (or part of the molecule) contains oxygen (O) or nitrogen (N) atoms bound to carbon (C) or hydrogen (H) atoms, then it is most likely polar. o EXCEPTION: Carbon dioxide (CO2) is non-polar because it is a linear molecule (a straight line). This is a special case. In the examples above, methane is a non-polar molecule because it contains only non-polar covalent bonds between carbon and hydrogen atoms. Water is a polar molecule because it contains polar covalent bonds between the oxygen and hydrogen atoms (remember the QUICK TIPS to help you figure this out!) How do you tell if a molecule is hydrophobic or hydrophilic? Hydrophobic molecules are water fearing. That is, they dont mix well with water and would rather interact with other hydrophobic molecules. Hydrophobic molecules can be identified if they contain mostly non-polar covalent bonds. Lipids and amino acids with only carbon and hydrogen R groups are hydrophobic molecules. Hydrophilic molecules are water loving. That is, they mix very well with water. Hydrophilic molecules can be identified if they contain polar covalent bonds. Carbohydrates, amino acids that contain polar R groups (hydroxyl, carboxyl, and amino groups), and positively or negatively charged molecules are hydrophilic molecules.

Appendix E

Practice set: Try applying the information you just learned to the following examples. In each molecule, identify what bonds are polar or non-polar, and then determine if the entire molecule is polar or non-polar.

For this set of macromolecules, identify which are hydrophilic and which are hydrophobic, and say why. For the amino acids, only evaluate the R groups (highlighted in the pink boxes).

Appendix F

Pre- and Post-test data from Biology 100, Spring 2012, NC A&T State University This test was given on the first day of class without prior notification. The same test was also given on the day of the final exam, also without prior notification. All of the questions (except two) are from the AAAS Project 2061 Science Assessment Website (http://assessment.aaas.org/), which provides validated questions that tests misconceptions students have about a variety of science topics. Question 8 was taken from Impey et al, J Coll Sci Teaching, 40: 31-37, 2011, and Question 14 was of my own design. The actual test can be found on the next two pages. A summary of the performance of my Spring 2012 Biology 100 class is shown below.

Figure F1: Summary data for pre-test and post-test for Spring 2012 Biology 100. The bars represent the percentage of students who responded correctly. Asterisks indicate a significant improvement on the post-test compared to the pre-test (P < 0.05). Between 61 and 66 responses were recorded for each question. Further statistical analysis was performed on the pre-test and post-test data. The learning gain was calculated for each student that answered all 16 questions on both the pre-test and the post-test (n = 49). The average learning gain for the class was 0.23 0.21, or a 23% improvement from the pre-test to the post-test. The Wilcoxon SignedRank test was performed to determine if the improvements on the post-test as a whole were significant. The P value was 5.0 x 10-7, suggesting that the improvements on the post-test as a whole were significant. The Wilcoxon Signed-Rank test was also used to determine whether there was significant improvement on individual questions. There were significantly more correct answers to 9 questions on the post-test compared to the pre-test (P < 0.05, see Figure F1). The reason for limited improvement or decline on the other 7 questions is not immediately apparent, as I felt that I covered those topics equally well during the semester. This data set will be extremely useful in planning further courses as it will allow me to improve my teaching in specific areas.

Appendix FThis is a pre-test that will help me understand what you know coming into this course. Please answer all questions. This does not count toward your grade. Please dont write on this test.1. Which of the following represents the correct order from smallest to largest? The smallest should be listed first. A. An atom, a DNA molecule, a cell B. An atom, a cell, a DNA molecule C. A cell, an atom, a DNA molecule D. A cell, a DNA molecule, an atom 2. What is TRUE about cells? A. All living things are made up of many cells, and all cells are the same size and shape. B. All living things are made up of many cells, but not all cells are the same size and shape. C. All cells are the same size and shape, but not all living things are made up of many cells. D. Not all cells are the same size and shape, and not all living things are made up of many cells. 3. Which of the following statements is TRUE? A. DNA is made up of proteins C. DNA is made up of amino acids B. Proteins are made up of DNA D. Proteins are made up of amino acids

4. What does the information in genes provide instructions for? A. Assembling protein molecules B. Assembling chromosomes into DNA C. Rearranging DNA into protein molecules D. Rearranging DNA into traits 5. The DNA molecules in skin cells contain information about which of the following? A. Eye color and skin color B. Eye color, but not skin color C. Skin color, but not eye color D. Neither eye color nor skin color 6. Which of the following is TRUE about genes? A. Genes are traits. C. Genes are sequences of nucleotides. B. Genes are proteins. D. Genes are sequences of amino acids.

7. A change commonly referred to as a mutation occurs to a DNA molecule in an organism's skin cell before the organism reproduces. When the organism reproduces, how many of its children will have the mutation? A. All of the organism's children will have the mutation. B. Some of the organism's children will have the mutation. C. None of the organism's children will have the mutation. D. It will depend on how much time passes between when the mutation occurs and when the organism has children. 8. A doctor tells a couple that they have a one in four chance of having a child with an inherited illness. Which of the following is true? A. If they have only three children, none will have the illness B. If their first child has the illness, the next three will not. C. Each of the couples children will have the same risk of suffering the illness. D. If the first three children are healthy, the fourth will have the illness. 9. Which of the following statements is TRUE about the carbon dioxide that is used by plants? A. It is combined with oxygen to make sugar molecules. B. It is absorbed through the roots of plants. C. It comes from the air. D. It is food for plants. 10. Where does the food that a plant needs come from? A. The food comes in from the soil through the plants roots. B. The food comes in from the air through the plants leaves. C. The plant makes its food from carbon dioxide and water. D. The plant makes its food from minerals and water. 11. Milk contains water, carbohydrates, proteins, minerals, and fat. Is milk food for people? A. No, because liquids cannot be food, and milk is a liquid B. No, because for something to be food it must provide both energy and building materials, and milk does not provide energy C. Yes, because for something to be food it must provide energy, and the minerals in milk provide energy D. Yes, because food is a source of energy and building materials, and milk provides energy and building materials

Appendix F

12. According to the theory of natural selection, what would happen to a species of lizards when a new predator is introduced into the environment where the lizards live? A. The lizards that already have the physical traits needed to avoid the new predator would be more likely to survive and reproduce, and the ones that do not would be less likely to survive and reproduce. B. All of the lizards would try to develop new physical traits to avoid the new predator. C. Some of the lizards would try to develop new physical traits to avoid the new predator, and the other lizards would die. D. Because all lizards of the same species have the same physical traits, one lizard would not have an advantage over another lizard. They would either all survive or all die. 13. Which of the following statements is TRUE about the evolution of plants and animals? A. All plants and all animals share a common ancestor with each other. B. All plants share a common ancestor, but all animals do not share a common ancestor. C. All animals share a common ancestor, but all plants do not share a common ancestor. D. No plants share a common ancestor with each other, no animals share a common ancestor with each other, and no plants share a common ancestor with any animals. 14. How do antibiotics work? A. They kill viruses B. They kill bacteria C. They kill viruses and bacteria D. They kill something else 15. A student is interested in the behavior of fish. He has 4 fish bowls and 20 goldfish. He puts 8 fish in the first bowl, 6 fish in the second bowl, 4 fish in the third bowl and 2 fish in the fourth bowl. He places each fish bowl under light, he keeps the temperature at 75F for all 4 bowls, and he observes the behavior of the fish.

What can the student find out from doing just this experiment? A. If the number of fish in the fish bowl affects the behavior of the fish. B. If the temperature of the fish bowl affects the behavior of the fish. C. If the temperature of the fish bowl and the amount of light affect the behavior of the fish. D. If the number of fish, the temperature, and the amount of light affect the behavior of the fish.

16. A farmer wants to find out which type of soil is best for growing his corn. He also wants to find out which type of fertilizer is best for growing his corn. He does the following experiment using two different types of soil and two different types of fertilizer:

What can the farmer conclude from this experiment? A. He can conclude that Soil B is the best soil for growing his corn. B. He can conclude that Fertilizer Y is the best fertilizer for growing his corn. C. He can conclude that Soil B is the best soil for growing his corn and that Fertilizer Y is the best fertilizer for growing his corn. D. It is NOT possible to conclude from this experiment which soil is best for growing his corn or which fertilizer is best for growing his corn.

Appendix G

Spring 2012 Course Evaluation Results Shaffer BIO 100Information about the Students 1. What is your year in school?First Year Sophomore Junior Senior Grad Student PostBacc Missing TotalCount 23 15 5 0 0 0 0 43 % 53.5% 34.9% 11.6% 0.0% 0.0% 0.0% 0.0% 100.0%

2. What is your gender?Male Female Missing TotalCount 19 24 0 43 % 44.2% 55.8% 0.0% 100.0%

3. Race Are youCount American Indian Asian Black or African-American Hispanic or Latino Native Hawaiian or Other Pacific Islander White Multiracial Missing Total0 1 36 0 0 3 0 3 43

%0.0% 2.3% 83.7% 0.0% 0.0% 7.0% 0.0% 7.0% 100.0%

4. How many semesters of biological science course work have you had prior to enrolling in this course?Count None One Two Three Four or more Missing Total21 12 5 4 1 0 43

%48.8% 27.9% 11.6% 9.3% 2.3% 0.0% 100.0%

SPIRE Descriptive Data Tables for Spring 2012 Course Evaluation Forms Prepared by Strategic Evaluations, Inc. (Submitted May 24, 2012)

1 of 6

Appendix G

5. Which best describes you?Count I am a science major. I am a non-science major. I am currently undecided on my major.6 33 4

%14.0% 76.7% 9.3%

Course Ratings 6. Instructora. The instructor was organized and presented material in a logical order. b. The instructor presented material clearly. c. The instructor clearly communicated the goals and objectives of the course. d. The instructor showed enthusiasm for the subject matter. e. The instructor developed a good rapport with the students. f. The instructor was available to students outside of class. g. The instructor provided helpful feedback. h. The instructor varied class activities over the course of the semester. i. The instructors lectures were at an appropriate level for me. j. The instructor taught in a manner that served my needs as a student. k. The instructor used technology appropriately for the course material and course objectives. l. The instructor evaluated my work and performance fairly in this class. m. The instructor made connections to current topics in science research throughout the semester. Strongly Disagree0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%

Disagree0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%

Neutral0.0% 0.0% 0.0% 0.0% 2.3% 0.0% 0.0% 4.7% 2.3% 2.3% 0.0% 0.0% 0.0%

Agree20.9% 16.3% 11.6% 11.6% 18.6% 16.3% 18.6% 27.9% 23.3% 23.3% 20.9% 18.6% 16.3%

Strongly Agree79.1% 83.7% 88.4% 88.4% 79.1% 83.7% 81.4% 67.4% 74.4% 74.4% 79.1% 81.4% 83.7%

Mean STD4.79 .41 4.84 .37 4.88 .32 4.88 .32 4.77 .48 4.84 .37 4.81 .39 4.63 .58 4.72 .50 4.72 .50 4.79 .41 4.81 .39 4.84 .37

A higher mean response indicates higher level of agreement, as Strongly Disagree equaled the value of 1 and Strongly Agree equaled the value of 5.


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Appendix G

7. Course Formata. The textbook used was current and comprehensible. b. Lectures were delivered in a clear and interesting manner. c. Lecture material was relevant to the course objectives. d. In-class activities (e.g., labs and discussions) were interesting, relevant and helped me understand the concepts better. e. Out-of-class activities (e.g., group projects and assignments) were interesting, relevant and helped me understand the concepts better. f. Writing assignments were interesting and helped me understand concepts better. g. Instructional technologies and media used in this course contributed to me learning the concepts. h. Exams were clearly written and fair.

Strongly Disagree0.0% 0.0% 0.0% 0.0%

Disagree0.0% 0.0% 0.0% 0.0%

Neutral17.9% 2.3% 0.0% 4.7%

Agree30.8% 23.3% 25.0% 30.2%

Strongly Agree51.3% 74.4% 75.0% 65.1%

Mean STD4.33 .77 4.72 .50 4.75 .44 4.60 .58

2.4%

0.0%

14.3%

45.2%

38.1%

4.17 .85

0.0% 0.0% 0.0%

2.6% 0.0% 0.0%

23.1% 9.5% 4.7%

25.6% 38.1% 37.2%

48.7% 52.4% 58.1%

4.21 .89 4.43 .67 4.53 .59


Course Ratings cont 8. Student Expectationsa. This course taught me what I wanted to know about the subject matter. b. This course challenged me to think critically and in new ways about the subject matter. c. Taking this course has motivated me to pursue a career in the sciences. d. Taking this course has motivated me to pursue additional courses in this field. e. This course helped motivate me to attend graduate/professional school after I complete my undergraduate degree. Strongly Disagree0.0% 2.3% 20.9% 25.6% 9.3%

Disagree2.3% 0.0% 23.3% 14.0% 2.3%

Neutral11.6% 0.0% 16.3% 23.3% 27.9%

Agree44.2% 44.2% 14.0% 11.6% 23.3%

Strongly Agree41.9% 53.5% 25.6% 25.6% 37.2%

Mean STD4.26 .76 4.47 .74 3.00 1.51 2.98 1.54 3.77 1.25



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Appendix G

9. Overall Overall, considering content, design, and structure, this course was excellent. Overall, considering the syllabus and objectives, the organization of this course was excellent. Overall, considering course content and objectives, this instructor was an effective teacher.

Strongly Disagree0.0% 0.0%

Disagree0.0% 0.0%

Neutral4.7% 2.3%

Agree25.6% 16.3%

Strongly Agree69.8% 81.4%

Mean STD4.65 .57 4.79 .47

0.0%

0.0%

2.3%

14.0%

83.7%

4.81 .45


Open-Ended Comments (Alphabetized and edited for student anonymity)10. Describe ways this course was different from other science courses you have taken at this university.

Because this teacher took the time with me even through science isn't my strong subject. Dr. Shaffer was very enthusiastic about the course. Everything was very organized from the lecturers to the homework assignments. From what I hear about other biology professors Dr. Shaffer actually cares about us passing his class. He actually helped the students and explained the information. He did a lot of discussion on different subjects, whereas my other classes didn't. He used a lot of real life experiments when discussing main topics and lectures. He was always available to help and was fantastic teacher. He was more engaging than my last bio/chemistry professor. He worked with the students more than my other science teacher. I thought it was good. I actually enjoyed this class I usually hate all my science classes. I actually learned something and he wanted to see me successful. I felt like was in part of the class, and that made me learn better. I have never taken a science class at the university, but taking this class was beneficial, my professor was understanding and willing to help at any time. I have never taken science courses in college. I have not took any other science courses. I was actually interacted in learning bio. The teacher was helpful. It was actually interesting. Science is normally boring but he made it fun. It was more hands on than my other classes. It also was more interesting. It was more personal he connected with us and you could tell he cared about you as a student It was very interactive and very hands on. It was well explained It was, actually to learn in a fun and enthusiastic way that kept me tagged along. Mr. Schaffer covered information that we can use in our daily lives. Teacher actually cared about everybody being successful in the class. This course actually challenged me to think and study. This course should not change at all. This course was easy and beneficial, Enjoyed it.


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Appendix G

This course was different from other science courses because we did pull everywhere and a little bit of hands on activities. This course was more in detail about the things he wanted us to learn. This is the first science course I've taken.

11. What aspects of this course were most valuable?

After the 1st test, study guides were helpful. All because all can be valuable in its own way. Dr. Shaffer always had slides that related to worldly things we could relate to. Dr. Shaffers patience. Everything Everything Everything Everything, learned a lot. I loved how the teacher was so willing to put everything aside to make sure everyone got the lesson. I think that the lectures wee. Learning about the body. Learning about things that I never knew. Lecturing was great, which in turn really help me grasp different concepts. Most valuable to me was, being able to do the honors contracts. Study guides, powerpoints The bond he had with us. The dialogue. The in class lectures because he gave great information. The instructor The involvement and interaction with students during lecture and lab. The lecture on diabetes. The lectures in the course they were outlined as well as gone over in class. The lectures of this course were most valuable. The lectures, like the powerpoints. I enjoyed them the most. The lectures. The power points lectures. The powerpoint lectures. The real life lectures where Dr. Shaffer appealed to his lectures and made sure students understood the material. The subjects that related to real life. The way he teaches and explained things. When we had a real life situation.


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Appendix G

12. What suggestions do you have for how the instructor can improve the teaching of this course?

Aside from being a great teacher already, the only thing I would add is maybe more group activities outside of class. Be a little more engaging. Continue to be happy about teaching, superb job, thank you. Dr. Shaffer is a great professor. For labs less group work. He did a good job at teaching this course. He did well for a first year teacher. He is perfectly fine right now. He listens to students suggestions and put it in good use. Honestly, nothing. Dr. Shaffer did a wonderful job. I could actually tell that he cared about us and if we were learning anything, best Bio teacher I ever had. I don't think he needs to improve on anything. He is a great teacher and enjoys teaching biology. I think he should do actual lessons and not so much lectures. I think Prof. Shaffer is an outstanding biology teacher. I really don't think he should change anything about the way he teacher because he is able to relate science to people and things in everyday life. Just keep doing what you are doing. Just to offer make up exams, some circumstances are unpredictable, especially because they count so much towards grade. Keep doing a great job, you are an awesome teacher. Keep doing what he been doing, he's a great instructor. Keep doing what he's doing. Keep doing what you're doing! Keep up the good work, you are going to be an outstanding professor. Keep up the good work. Make class a little more interactive to keep the class attention. Mr. Shaffer had done a wonderful job with the subject and relating with the students. None at all, just keep up the good work. None he's a great teacher. None that I can think of. None, he did a very good job. None. Did a great job. Nothing, he done great to me. Sometimes the wording on the test can be a little tricky and need explanation, that's the only thing some questions are wither very broad or need complete explanation. The instructor did a great job teaching this class. I would not advise him to change anything. The labs need to be every week from the first week to the last week and actually test formatted study guides would help. To keep doing what he is doing.


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Appendix G

Fall 2012 Course Evaluation Results Shaffer BIO 642 Special TopicsInformation about the Students 1. What is your year in school?Count %

First Year Sophomore Junior Senior Grad Student PostBacc Missing Total

0 0 2 9 2 0 0 13

0.0% 0.0% 15.4% 69.2% 15.4% 0.0% 0.0% 100.0%

2. What is your gender?Count %

Male Female Missing Total

3 10 0 13

23.1% 76.9% 0.0% 100.0%

3. Race Are youCount American Indian Asian Black or African-American Hispanic or Latino Native Hawaiian or Other Pacific Islander White Multiracial Missing Total 0 0 13 0 0 0 0 0 13 % 0.0% 0.0% 100.0% 0.0% 0.0% 0.0% 0.0% 0.0% 100.0%

4. How many semesters of biological science course work have you had prior to enrolling in this course?None One Two Three Four or more Missing Total Count 0 0 0 1 12 0 13 % 0.0% 0.0% 0.0% 7.7% 92.3% 0.0% 100.0%

SPIRE Descriptive Data Tables for Fall 2012 Course Evaluation Forms Prepared by Strategic Evaluations, Inc. (Submitted December 9, 2012)

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Appendix G

5. Which best describes you?I am a science major. I am a non-science major. I am currently undecided on my major. Count 13 0 0 % 100.0% 0.0% 0.0%

Course Ratings 6. Instructora. The instructor was organized and presented material in a logical order. b. The instructor presented material clearly. c. The instructor clearly communicated the goals and objectives of the course. d. The instructor showed enthusiasm for the subject matter. e. The instructor developed a good rapport with the students. f. The instructor was available to students outside of class. g. The instructor provided helpful feedback. h. The instructor varied class activities over the course of the semester. i. The instructors lectures were at an appropriate level for me. j. The instructor taught in a manner that served my needs as a student. k. The instructor used technology appropriately for the course material and course objectives. l. The instructor evaluated my work and performance fairly in this class. m. The instructor made connections to current topics in science research throughout the semester. Strongly Disagree 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% Disagree 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 7.7% 0.0% 0.0% 0.0% 0.0% 0.0% Neutral 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% Agree 15.4% 15.4% 15.4% 0.0% 0.0% 7.7% 7.7% 0.0% 7.7% 7.7% 0.0% 7.7% 0.0% Strongly Agree 84.6% 84.6% 84.6% 100.0% 100.0% 92.3% 92.3% 92.3% 92.3% 92.3% 100.0% 92.3% 100.0% Mean STD 4.85 .38 4.85 .38 4.85 .38 5.00 0.00 5.00 0.00 4.92 .277 4.92 .28 4.77 .83 4.92 .28 4.92 .28 5.00 0.00 4.92 .28 5.00 0.00


SPIRE Descriptive Data Tables for Fall 2012 Course Evaluation Forms Prepared by Strategic Evaluations, Inc. (Submitted December 9, 2012)

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Appendix G

7. Course Formata. The textbook used was current and comprehensible. b. Lectures were delivered in a clear and interesting manner. c. Lecture material was relevant to the course objectives. d. In-class activities (e.g., labs and discussions) were interesting, relevant and helped me understand the concepts better. e. Out-of-class activities (e.g., group projects and assignments) were interesting, relevant and helped me understand the concepts better. f. Writing assignments were interesting and helped me understand concepts better. g. Instructional technologies and media used in this course contributed to me learning the concepts. h. Exams were clearly written and fair.

Strongly Disagree 0.0%

Disagree 0.0%

Neutral 7.7%

Agree 0.0%

Strongly Agree 0.0%

N/A 92.3%

Mean STD 3.00 N/A

0.0

Teaching Portfolio

Documents

teaching philosophy

graduate biology students

teaching experience

teaching methods

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