BI202: Cellular and Molecular Biology Fundamentals Spring 2013 It's one thing to know how something works, but it's another thing to know why it behaves the way it does. by Carl Niklas. Instructor: Class Schedule: Jennifer R. Kowalski, Ph.D. Lecture: Gallahue Hall 158, MWF, 9:00-9:50AM Office: Gallahue Hall 271 Lab: Gallahue Hall 160, R, 2:25-5:15PM Phone: 940-8879 Office Hours: 10:00-11:30 a.m. Mondays & Wednesdays E-mail: jrkowals@butler.edu Course Description: Cell biology is the discipline of science that is concerned with the processes occurring in the typical life of a cell. These processes are so basic to life that they affect all aspects of a whole organism. Hence, it can be said that all areas of biology are linked in some way to the events that occur in the cell. For example, evolution is better understood with a broad knowledge of DNA and its structure, and the physiology of nerve cells is better understood with a broad knowledge of the structure and properties of cellular membranes. That is not to say that you couldn't learn about how evolution works unless you have had a cell biology course, but you wouldn't fully understand it unless you have a good grasp of cell biology. It s one thing to know how something works, but it's another thing to know why it behaves the way it does. By having taken a course in cell biology, you will find yourself well prepared to continue studying and to really understand other focused topics in biology. This goal of this course is to introduce students to the basic properties and functions of cells, as well as the methods by which scientists investigate cellular function. The major subjects of this course will include the following: properties of biological macromolecules, bioenergetics, membrane function, intracellular transport, cell communication, photosynthesis, respiration, cell reproduction, and the relationship between the structure and function of diverse cell types. The laboratory is a critical and significant component of the course. Laboratory activities will emphasize basic skills and techniques in cell biology along with experimental design and scientific communication. Course Learning Objectives: Students should be able to explain and demonstrate the fundamental organization and principles of cell biology that govern basic cellular processes important to all life and be able to relate cell biology to other areas of biology such as cancer, evolution, etc. Students should be able to demonstrate basic molecular laboratory techniques, such as microscopy, basic laboratory calculations, electrophoresis, etc. Students should be able to read scientific literature, apply the scientific method, and communicate scientifically both orally and in writing. Cellular and Molecular Biology and the Liberal Arts: It would be incorrect to suggest that biology has always been a part of the liberal arts tradition. However, in the Middle Ages, when what we would recognize as the first western universities were established, the sciences were a vital part of the program of study. The prevailing science of the day, astronomy, was a critical aspect of the quadrivium, along with mathematics, geometry, and music theory. As the liberal arts tradition evolved, other sciences came to take their place in the curriculum: physics then alchemy which gave rise to chemistry. Biology would not exist as a distinct discipline until Darwin suggested a unifying theme for zoology, botany, and other studies of living things. Despite its relative youth, since its ascension as a formal discipline, biology has become a key component of the natural sciences area of most modern liberal arts curricula. As a natural science, biology is based on the use of observations, logic and mathematics (both key components of the liberal arts tradition) to propose and rigorously test ideas about the rules that organize living systems. 1
Challenges and Student Responsibility: The nature of most biology courses is such that the student must remember facts as well as interpret and use them. This means that pure memorization of the lecture material will not be enough. The challenge to you in this course is to keep on top of the subjects and to clarify incongruities when you are studying. It is my suggestion that you organize yourself while studying by making lists of terms after each lecture and by ACTIVELY reviewing your notes daily to become familiar with terminology and concepts. I expect you to develop a good understanding and correct usage of both the terminology and the broad concepts important to understanding cellular structure and function, as well as to be able to apply those concepts to new situations. For new students of cell biology, the topics and concepts may initially seem abstract and difficult to master due to the fact that most cells, organelles, and molecules are not readily demonstrable or easily visible to the observer. For example, no one has ever seen with their own eyes the inside of a cell or DNA replicating itself, but we do know in great detail what the inside of cells look like and how DNA replication works. To help us to visualize these microscopic structures and processes, we will use animations, images, and diagrams whenever possible in class to illustrate the microscopic processes and structures we are investigating, and you are encouraged to draw, diagram, etc. as much as possible in your own studying, as well. For my part, I also will make every effort to prepare lectures that are clearly presented, well organized, and engaging, and I will be readily available to answer questions and provide additional help outside of class, as needed. However, you are ultimately responsible for your own learning and the more effort you put in and the more engaged you become with the material, the more you will learn (and hopefully, the more you will enjoy learning about the amazing wonder of the cellular world!) You will be most successful in this course if you follow these tips: (1) attend and actively participate in each class, (2) review the information often, (3) read the assigned pages in the text, (4) complete homework thoughtfully and on time, and (5) ask for help from me, your classmates, and/or peer tutors, as soon as you realize there is a concept you don t fully understand. All the things we will discuss in cell biology have direct effects on your life - after all, you are cellular. Fact: most strategies of modern medicine were developed from knowledge of cell biology. If at any time during the term you feel you need some extra help (or just want some extra information on a topic) please email and/or stop by and we can talk. I want you to succeed!! Texts: Essential Cell Biology, 3 rd edition, 2010. B. Alberts, D. Bray, K. Hopkin, A. Johnson, J. Lewis, M. Raff, Roberts, and P. Walter. Garland Science, New York. ISBN: 9780815341291. The Immortal Life of Henrietta Lacks, 2010. Rebecca Skloot. Crown Publishers, New York. ISBN: 978-1-4000-5217-2. **Moodle: Lecture notes, lab handouts, and other course announcements and materials will be posted on the course Moodle site. I recommend that you check the website frequently for information and updates. Some assignments may be due uploaded to Moodle or as a post on the Discussion board. Final Grade Determination: Your final grade will be determined by summing your total points earned in the course divided by the total points possible in the course. The following is a tentative list of the point distribution in the course: 100pts Mini-exams (2 @ 50pts each) 100pts Midterm exam (along with lecture content, will include some lab practical questions) 100pts Final exam 70pts Quizzes (6 @ 10pts each, dropping 1 lowest; 6 @ 4pts each, dropping 1 lowest) 40pts Other assignments (in-class activities/homework) 80pts Lab assignments (55pts)/quizzes (25pts, 6 quizzes @ 5pts each, dropping 1 lowest) 40pts Writing assignments (2 @ 20pts each) 40pts Poster presentation 100pts Lab practical 670 Total points 2
The grading scale for this course is: A 92-100% C 72-77% A- 90-91% C- 70-71% B+ 88-89% D+ 68-69% B 82-87% D 62-67% B- 80-81% D- 60-61% C+ 78-79% F < 60% Exams: Format: There will be two mini-exams, each worth 50 pts, as well as a 100pt midterm exam and a 100pt final exam. The format of these exams may include any of the following types of questions: compare and contrast, multiple choice, short answer, essay, fill in the blank, true or false, diagrams, or matching. There will also be a number of critical thinking questions that will require you to go above and beyond simple memorization. These questions are meant to assess whether or not you can integrate and apply your knowledge to answer broader, more challenging questions and/or analyze data that you may not have seen before. The mini-exams will each be 1 hour exams that will take place during the lecture period; the midterm and final will be 2 hour exams. The midterm exam will take place during the first portion of lab during the week of March 4 th. It will be comprehensive over the material covered in the first half of the semester and will also include a small lab practical portion. The final exam will be held at the time set by the university, Wednesday, May 1 st, 8-11AM, and will test your understanding of comprehensive information from the second half of the semester (i.e., all material that was not covered on the midterm exam). However, because of the nature of how the information builds upon itself and the value this information will have on your success in other biology courses you will take, a good grasp of the general concepts and principles are expected to be retained throughout the course. Quizzes: Throughout the semester, a variety of in-class exercises and quizzes may be given. The purpose for these is to make sure that you are keeping up with the reading, to reinforce the material, and to assess how well you understand the material. Quizzes may cover lecture material and also reading assignments for that day s lecture. Some quizzes will be unannounced. Therefore, missed quizzes cannot be made-up. There will be at least 6 graded large quizzes during the semester, each worth 10 pts, for a total of 50 points. There will also be at least 6 graded mini quizzes during the semester, each worth 4 pts, for a total of 20 points. The lowest quiz grade in each quiz category will be dropped for each student to reach the final 70 quiz points in the course. Quizzes start promptly at 9:00AM, so please arrive at class on time and ready to begin. No extra time or make-up quizzes will be given. Quizzes will be a mixture of multiple choice, short answer/fill-in questions, and problems. They will focus on the previous week s material, but may require integration of concepts learned earlier in the course. They may include 1 question based on the reading for that day s class. The purpose of these quizzes is to help you keep up in the course and to identify areas to work on prior to the exams. Homework/In-class activities: A variety of in- and out-of-class activities will be used to reinforce concepts, assess your understanding of the course material, and help you to keep up with the reading. The activities will vary in size and scope and may include short writing pieces, concept maps, problem sets, and online assignments. Sometimes these may be completed as group assignments for which all members receive the same numbers of points. All out-of-class homework assignments are due promptly at the start of class or by the online due date. No late homework (i.e., homework turned in at any time after class has begun) will be accepted. In-class activities will be unannounced and you must be in class to be eligible for the points i.e. you cannot make-up a missed in-class exercise due to an unexcused absence from class. Together, all homework and in-class exercises will constitute 40 points of your final grade. Special note about Active Class Participation: Throughout the semester, we will use variety of active learning methods in the classroom ranging from small group discussions, to class-wide polls, to short writing assignments or other activities. Their purpose is to promote your engagement and participation in the course. Active student involvement has been shown to increase student learning, so the more you participate in all of 3
these activities questions, group work, problem solving, and other exercises, the more you will learn - and the better you should do on the exams! Labs: Labs are an integral part of the course (lab-related assignments comprise close to 40% of your course grade). Because of the amount of preparation and fresh material needed for the labs, labs cannot be made up. For these reasons, laboratory attendance each week is mandatory. Students are expected to attend the entire length of lab sessions. In addition, during much of the semester, students will be culturing HeLa cells (human cervical carcinoma cells), which they will use for a multi-week project during the second half of the semester. While this is an exciting opportunity to learn and participate in a critical technique in used in modern cell biology, it does require that students come outside of the weekly lab period in order to maintain the cells. The cell biology laboratory will be left unlocked during regular business hours for your convenience. Lab Assignments and Quizzes: There will be frequent, brief reading quizzes (5 pts each) given in the lab to ensure that you have read the lab and are prepared for that day s experiments. There will also be pre-lab or follow-up activities/assignments associated with each week s lab. Some pre-lab assignments or reading questions will be graded for completion credit, while other more analysis-based questions will be graded for correctness, with 80 points total allotted for both quizzes and lab assignments. Quiz points will comprise 25 of the 80 total lab points. Poster Presentation: A group of students will design and execute an independent experiment investigating enzyme function from which they will collect and analyze data. A summary of their findings will be presented to the class in the form of a scientific poster presentation to be given during a brief evening poster session during week of February 25 th. Students will be evaluated on their use of the scientific method, poster content and design, and presentation skills. This assignment will be worth 40 points. More information will be provided on an assignment handout. Writing assignments: During the semester, students will read scientific literature and discuss the content of sections within reports. Following these discussions, students will practice writing Materials and Methods and Discussion sections for a scientific manuscript. Each of these two assignments will be worth 20 pts for a total of 40 writing assignment points. More information will be provided during the semester. Lab Practical: There will be a 2 hour, comprehensive lab exam worth 100pts that will be administered on the final day of lab, (see lab schedule below). This exam will contain both written and practical components testing your knowledge of techniques and skills used throughout the semester, as well as your ability to analyze and interpret data in various forms. Note: If you need additional help with the course material, please come to see me during my office hours or make an appointment. The Department of Biological Sciences provides student-led study sessions and peer tutoring throughout the semester. The tutors are available on Mon-Thur nights in GH 202. Tutoring session times will be announced in class. Limited one-on-one tutoring may also be possible through the Learning Resource Center. In addition, the LRC staff is available to assist all students with their study habits both individually and via seminars. These seminars include the following topics: memory, reading, note-taking, testtaking, problem-solving and time management. The LRC is located in Jordan Hall 136, ext. 9308. Academic honesty: Any form of cheating or plagiarism will not be tolerated in this course. It is assumed that the work you do is your own. Please review the sections of the Student Handbook (located through the Student Life link on the Butler website) on academic integrity that outline what cheating and plagiarism entail. Keep in mind that 4
plagiarism includes but is not limited to copying from past or present students, failure to cite the sources of ideas or information, and the use of quotes without quotation marks. If you have questions about what is or is not permitted please contact me. Upon the first offense of cheating or plagiarism, a student will receive a zero for the assignment in question and the Dean will be notified. A second offense is grounds for failure in the course and a letter will be submitted to the student s academic file. All students have the right to appeal any decision following the appeals process outlined in the Student Handbook. Requests for academic accommodations: It is the policy and practice of Butler University to make reasonable accommodations for students with properly documented disabilities. Written notification from Student Disability Services is required. If you are eligible to receive an accommodation and would like to request it for this course, please discuss it with me and allow one week advance notice. Otherwise, it is not guaranteed that the accommodation can be received on a timely basis. If you have questions about Student Disability Services, you may wish to contact Michele Atterson, JH 136, ext. 9308. Attendance: I consider it totally your responsibility to attend lecture. However, I am aware of who is in attendance each day, and I will make a point of contacting students who do not attend. Keep in mind that you must attend regularly if you wish to do well in the course. We will not be able to cover all material in the text and I may discuss material not covered in the text. Thus, you need to make it to class to see what information is covered and emphasized, as this material will be expected of you for each exam. You are responsible for contacting a fellow student and borrowing their notes if you have missed a lecture. Also, note that you will not receive credit for quizzes or exercises missed due to unexcused absences. If you have a legitimate excuse for missing an exercise or quiz, please contact me but realize that what you consider a legitimate excuse might not pass for one in my book. Consideration for make-ups will only be given if you contact me PRIOR to the next class meeting. If you are not in attendance because of health reasons, you must provide a written excuse from a health care provider. Best advice, make it easy on yourself and come to class! Missing exams is not a good thing! If you know that you must miss an exam, you MUST CONTACT ME BEFORE THE EXAM. If you fail to notify me before the exam, I reserve the right to decide whether or not you will have the option to take a make-up exam. If you miss an exam because of a legitimate excuse that can be documented (i.e. written excuse from a health care provider, etc.), you must contact me as soon as possible to schedule a make-up exam. Barring extreme circumstances, you will be expected to make up the exam within one to two days of the original exam date. A FINAL IMPORTANT NOTE ABOUT THIS CLASS This class will function as a community of learners working in an environment that fosters inquiry and free expression. Such communities work best when all members feel free to express themselves without fear of ridicule or disrespect. Respect for the community also means that individuals do not disrupt the focus of the class with behaviors/actions that may distract others. Examples of such behaviors/actions include tardiness, ringing/vibrating cell phones, texting, leaving/re-entering class once it begins, or packing up prior to the end of lecture. If you participate in disruptive behavior, you may be asked to leave class and will not get credit for any assignment that day. Communications: I suggest that if you do not do so already, begin checking both your Butler University email account and Moodle on a daily basis. E-mail is my preferred means of communication, and I will send the class communiqués, information, and reminders via e-mail. If you need to contact me, use e-mail for best results. 5
BI202 Lecture Schedule Week Topic Textbook pages January 14 th January 21 st Course Overview/Introduction to Cells, Cancer, HeLa Cells and their components MONDAY (NO CLASS MLK day) Chemistry and Intro to Biomolecules Chp.1, 1-35 Chp.2, 39-50; Chp.2, 58-63, 64-67, 76-77 January 28 th Biomolecules: nucleic acids, lipids, carbs, & proteins Chp.2, 50-58, 68-75; Chp.4, 119-142 February 4 th Bioenergetics and Enzymes *Mini-Exam I (50pt)* Chp.3, 81-113; Chp.4, 143-157 February 11 th Membranes: structure and transport Chp.11, 363-384; Chp.12, 387-420 February 18 th Photosynthesis Chp.14, 476-486; Ch.3,86-88,107-110 February 25 th Respiration Chp.13, 425-445; Chp.14, 453-476 March 4 th Central Dogma: transcription & translation MIDTERM EXAM 100pt (in lab) Chp.5, 171-188 Chp.7, 231-257 March 11 th March 18 th March 25 th SPRING BREAK NO CLASSES! Control of Gene Expression Intracellular transport: protein production and modification, secretion, & vesicle trafficking Chp.8, 269-278; Chp.5, 188-192 Chp.7, 258-293 Chp.15, 500-09, 514-18; 510-14, 518-27 April 1 st Cell communication Chp.16, 531-567 April 8 th Signal transduction *Mini-Exam II (50pt)* FRIDAY - Undergraduate Research Conference April 15 th Cell Reproduction: Binary fission, mitosis, cell cycle Chp.18, 609-638 Chp.18, 638-646 April 22 nd Cell Reproduction: Cell cycle control & apoptosis April 29 th (Mon - last class) May 1 st (Wed.) Integrated Topics: Cancer & Course Wrap-up Chp.20, 717-729 FINAL EXAM (100pt) 8-11AM, GH158 The textbook readings will complement lectures. The series of page numbers refers to the flow of a topic, so the order in which you read them is important. 6
BI202 Laboratory Information Tell me and I will forget. Show me and I will remember. Involve me and I will understand. (Chinese proverb) Laboratory Objectives: Because cell biology is a field that uses laboratories and equipment to great extents, the labs in this course are designed with four primary objectives: 1) To demonstrate some of the ideas and concepts that we will have talked about in lecture. 2) To develop your ability to use several different skills, techniques, and equipment important to cell biology and many other biological sub-disciplines. 3) To develop your ability to analyze data to interpret its meaning. 4) To develop your ability to effectively communicate scientific information both orally and in writing. The specific communication and technical skills that you should be comfortable using by the end of the course are as follows: Scientific Communication Skills: Reading and interpreting primary scientific literature Begin scientific writing: M&M section, Figures & Discussion section Oral scientific communication: Poster presentation on independent projects, informal minipresentations Laboratory Skills: Experimental design Data analysis and graphing Doing lab math molarity, dilutions Using ph meter Pipetting Generating and using a standard curve Using a spectrophotometer Protein extraction Protein gel electrophoresis Protein quantification (protein assay) Western blot Sterile technique Cell culture basics Basic microscope use Special Notes: Students will be doing mathematical calculations fairly often, so it is recommended that students bring with them a calculator. It need not be a scientific calculator. Because of our limited lab time, it is essential that you come to lab prepared. You are required to read the lab guide before coming to the lab. During the first 10 minutes of class there frequently will be a 5 question quiz testing whether or not you have prepared for the lab. During most of the semester, you and members of your lab group will be expected to come to lab outside of the weekly lab period in order to passage and maintain your HeLa cell cultures. Details will be provided in lab. 7
Week of: January 14 th January 21 st January 28 th February 4 th February 11 th February 18 th February 25 th March 4 th March 11 th BI202 Laboratory Schedule (Thursdays, 2:25-5:15pm) Topic Cells: an amazing diversity of structure and function; Microscopy Scientific Method, Graphing, Bio-Math Book Discussion; HeLa cell culture and sterile technique Scientific Literature; Biological buffers Exploring enzyme function (catalase); Plan independent enzyme experiment Independent Project (enzymes) (T/W- 30 minute evening Enzyme Poster Presentation session) Photosynthesis and herbicides Midterm Exam (2hrs); HeLa Cell Paper/Intro SPRING BREAK NO LAB March 18 th HeLa cell- W. blot: Protein isolation, analysis, & sample preparation (Chp. 4, 157-167) March 25 th April 1 st April 8 st April 15 th April 22 nd HeLa cell W. blot: Gel electrophoresis, transfer, & blocking HeLa cell W. blot: Antibody treatment & protein detection; Prep for IF lab HeLa cell - Immunofluorescence analysis of apoptosis Cytoskeleton, cell adhesions, extracellular matrix (Chp.17, 571-604; Chp.20, 690-707) Discussion paper/hela project results; Lab practical review Lab Practical (2 hrs) April 29 th (Mon) Discussion Section Paper due (12noon, GH271) Scientific writing: 1. February 11 th : Materials and Methods section for Enzyme lab (due Feb. 18 th ) 2. April 15 th : Discussion section on HeLa protein project (due April 29 th ) Reading literature: 1. January 21 st : Paper on scientific method 2. January 28 th : Paper on HeLa cell culture 3. March 4 th : Paper on HeLa cell gene expression related to Western blot & IF activities 4. March 25 th : Paper on W. blot application to other cellular questions The Immortal Life of Henrietta Lacks Discussion Question Due Dates: Part I: Life due week of January 14 th Part II: Death due week of January 21 st Part III: Immortality due week of January 28 th 8