High Point University

Fall 2011

SYLLABUS Cell Biology (BIO 3000)

Instructor Dr. V. McNeil Coffield 210 Congdon Hall E-mail: vcoffiel@highpoint.edu Office Hours: MTWRF 10:30-11:30; other times available by appointment. Meeting Time and Place Lecture: MWF 9:15-10:05, Congdon Hall, Room 139 Lab Sec 01: Mon 1:25-4:25, Congdon Hall, Room 139 Lab Sec 02: Thurs 1:25-4:25, Congdon Hall, Room 139 Course Description: A study of the cell: its origins, submicroscopic structure, and functions within the context of evolution and the physical laws of nature. Four credit hours. Prerequisites: Bio 1399 or permission of the instructor. Textbook: Beckers World of the Cell, 8th Edition J. Hardin, G.P. Bertoni, and L.J. Kleinsmith. 2011. Beckers World of the Cell, 8th Edition. Benjamin Cummings, San Francisco, CA. Honor Statement I expect you to adhere to the high standards of ethical behavior as stated in the High Point University Honor Code. Specifically, I expect: 1. that you neither give nor receive assistance on tests or quizzes; 2. that all work you present for evaluation is your own work; 3. that you give proper credit to all references used in written assignments (avoid plagiarism); 4. that you deal forthrightly and honestly with me in consultations to determine the legitimacy of an absence; and 5. that you conduct yourself in the classroom and laboratory in a manner that is conducive to a learning environment. Attendance Policy Attendance in lecture and lab is required. If you incur more than three unexcused absences, I will consider you on class probation; and if absences continue, I will have you dropped from the course with a grade of WA or FA (See HPU Undergraduate Bulletin). You must consult with me to determine if your absence is legitimate, and it is your responsibility to initiate this consultation by talking to me in person or by telephone prior to your absence . Unless there are extenuating circumstances, I will not consider your absence legitimate if you do not contact me beforehand. In addition, I may require verifiable documentation concerning the reason for the absence. Before you are dropped, I will give you and your advisor notification at least one absence before the limit

BIO 3000 Sec 01, 02

High Point University

Fall 2011

is reached. If you disrupt the class, I may ask you leave the room and record you as being absence. Disruptive behavior includes entering class late; talking that is not part of class discussion; and leaving class before the end of the period. You are responsible for all course assignments and graded work regardless of your attendance. I will assign a grade of zero for any laboratory or lecture assignment, quiz or test missed unless there is a legitimate reason for the absence. Work missed because of a legitimate absence must be made up at the time I specify, or a grade of zero will be recorded for the exercise, quiz or test in question. The attendance policy in this course is in accordance with the University Attendance Policy. Academic Counseling If you feel that you need individual help or would like to come by to talk (about our course or anything else), please come by my office (Condgon 210) during office hours, or schedule a time that is more convenient. If my door is open, you are welcome to come in! You should also make use of the Academic Services Center located in the Smith Library for general academic counseling, or if you feel that a tutor would be helpful. Students with Disabilities Students who require classroom accommodations due to a diagnosed disability must submit the appropriate documentation to Disability Support in the Office of Academic Development, 4 th Floor Smith Library. Students need for accommodations must be made at the beginning of a course. Accommodations are not retroactive. Additional Resources Supplementary materials (books and periodicals) are in the Smith Library. In addition, the World Wide Web (www) has numerous sites devoted to Cell Biology. One particular site to note is the one associated with your textbook. Your text also comes with a CD-ROM, located in the front of your text. Use it to accompany the lectures. Course Objectives Cell biology is the study of cells, the fundamental integrated units of life. Cells come in a variety of shapes, sizes and functions. The goal of this course is to build upon the foundation that has been laid in courses which have presented biology at an organismal level, while concentrating on presenting life processes at the cellular level. Toward this aim, the course is divided into the following objectives: 1. To provide a strong background in Cell Biology and understand what distinguishes it from other fields. 2. To understand cellular macromolecules, energetics, metabolism and the structure and function of organelles, as well as the regulation of cellular communication. 3. To understand how these processes were elucidated by experimental methods. 4. To learn and practice laboratory techniques applied to cellular biological research, as well as learn the theoretical aspect of more complex techniques. 5. To become familiar with various applications of techniques to solve problems. 6. To gain experience in reading primary and secondary scientific literature. 7. To explore ways in which technical and theoretical advances in cell biology apply to economic, political, agricultural, medical and sociological issues.

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BIO 3000 Sec 01, 02

High Point University

Fall 2011

Methodology Course instruction is in the lecture and discussion format. I will present lectures on the subject matter listed in the schedule of topics and will lead the class in as much class discussion as possible. Your participation in class lectures is encouraged, and it is important that you read the assigned materials in the textbook prior to coming to class. Several research papers will supplement the material provided in your text book. It is absolutely pertinent that you read the literature articles! The laboratory studies consist of observations, experimentation, written reports, poster presentations, discussion and other methods pertinent to inquiry and scientific design. The exercises are designed to complement the lecture portion of the course, but will not always coordinate exactly with it. I expect you to take care of equipment in the laboratory and carefully follow the instructions given by the laboratory instructor. IMPORTANT: You may not eat food or drink beverages in the laboratories, and you must keep your work area clean and organized at all times!!!!! Student Evaluation 1. Lecture examinations: There will be 4 major lecture examinations. The first three are scheduled during regular class periods and the last is scheduled during exam week. The fourth exam will not be cumulative!! The instructor reserves the right to administer quizzes or in-class writing assignments to evaluate student progress throughout the semester. The lecture grade is 40% of your final grade for the course. 2. Laboratory evaluation: A laboratory notebook, lab reports, and 2 oral presentations will form the basis for your laboratory grade. Notebooks include drawings and summaries of observations, as well as answers to questions. I will also consider your laboratory technique and overall effort in determining your laboratory grade. Laboratory practicals will be replaced with lab reports and oral presentations. Your laboratory grade is 30% of your final grade for the course. 3. Data analysis reports: Each student must submit four (4) research data analysis reports based on their consideration of a primary research publication in the field of Cell Biology. The objective of this exercise is to develop each students analytical thinking and scientific writing skills. The research report will be based on a primary scientific research paper published in any primary journal (see me if you have a question about this) since January, 2001. Students are free to choose any topic, but it must use at least one lecture topic that was discussed in class. The major emphasis of the paper is for students to identify and discuss the one most important figure or table of the paper as it relates to the major scientific contribution of the research. The paper should include a discussion of the significance of the data in the context of the papers hypothesis. Additionally, the student should include a discussion of the material and methods used in gathering the data of the central figure or table. A copy of the article should be included with the Data Analysis Report, due the day of each exam. Further information regarding the format of the Report will be distributed soon. These reports will be 15% of your final grade for the course. 4. In-class presentations and writing assignments: During regular lecture periods, students will present figures from assigned papers on the current topics. Each student will sign up for 2 presentations throughout the semester. This presentation will be 15% of your final grade for the course.

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BIO 3000 Sec 01, 02

High Point University

Fall 2011

Course Grade and Grading Scale Your course grade will be determined as follows: Lecture Examinations (average of 4): 40% Data Analysis Reports (average of 4): 15% In Class Presentations and writing assignments: 15% Laboratory Work: 30% Scale: A+ (4.0) = 97-100 A (4.0) = 93-96A- (3.7) = 90-92 B+ (3.3) = 87-89B (3.0) = 83-86B- (2.7) = 80-82 C+ (2.3) = 77-79C (2.0) = 73-76C- (1.7) = 70-72 D+ (1.3) = 67-69D (1.0) = 60-66F (0.0) = 0-59 In the case of a borderline grade (e.g., 79.4), factors such as attendance, punctuality, attitude, progress and class participation are of utmost importance.

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BIO 3000 Sec 01, 02

High Point University

Fall 2011

Tentative Lecture Schedule Aug. 24 Ch. 1: Preview of the cell 26 Ch. 2: The chemistry of the cell 29 Ch. 3: Macromolecules (proteins and nucleic acids) 31 Ch. 3 (cont.): Polysaccharides and lipids Sept. 2 Ch. 4: Cells and eukaryotic organelles 5 Ch. 5: Bioenergetics 7 Ch. 7: Membranes (functions and early models) 9 Ch. 7 (cont.): Membranes (Fluid Mosaic Model) 12 Ch. 8: Transport across membranes (diffusion) 14 Ch. 8 (cont.): Active transport 16 Review; Data Analysis #1 due 19 EXAM #1 (Ch. 1, 2, 3, 4, 5, 7, 8; in class presentation); 21 Ch. 17: Beyond the cell 23 Ch. 12: Intracellular compartments (ER and Golgi) 26 Ch. 12 (cont.): Glycoslyation, exocytosis, endocytosis 28 Ch. 12 (cont): Lysosomes, vacuoles, peroxisomes 30 Ch. 9: Redox reactions and glycolysis Oct. 3 Ch. 10: Mitochondria and aerobic respiration 5 Ch. 11: Chloroplasts and photosynthesis 7 Ch. 15: Cytoskeletal systems (microtubules) 10 Ch. 15 (cont.): Microfilaments and intermediate filaments 12 Review; Data Analysis #2 due 14 EXAM #2 (Ch. 9, 10, 11, 12, 15, 17) 17-21 Fall Break 24 Ch. 16: Cellular movement 26 Ch. 18: DNA as the genetic material, structure of DNA 28 Ch. 18 (cont.): Genome organization, DNA packing 31 Ch. 18 (cont.): The nucleus Nov. 2 Ch. 21: Genetic code and transcription 4 Ch. 21 (cont.): RNA processing and Ch. 22: Intro to translation 7 Ch. 22 (cont.): Translation and posttranslational processing 9 Ch. 23: Overview of gene expression regulation 11 Data Analysis #3 due 14 Exam #3 (Ch. 16, 18, 21, 22, 23) 16 Ch. 13: Signal transduction-Nerve cells (selected sections) 18 Ch. 13 (cont.): in-class activity 21 Ch. 14: Signal transduction (signals and receptors) 23-25 Thanksgiving Break 28 Ch. 14 (cont.): Receptors, messengers and systems 30 Ch. 19: Cell cycle (cell division review) 2 Ch. 19 (cont.): Regulation of cell cycle, cell death Dec. 5 Ch. 24: Cancer 7 Ch. 24: (cont.); Final Exam Review; Data Analysis #4 due 9 Final Exam (1:30-4:30) (Ch. 13, 14, 19, 24; in class presentation) Page 5 of 7

BIO 3000 Sec 01, 02

High Point University

Fall 2011

Tentative Laboratory Schedule Lab 1 Lab 2 Lab 3 Lab 4 Lab 5 Lab 6 Aug. 29 Sept. 1 5 8 12 15 19 22 26 29 Oct. 3 6 10 13 17 20 24 27 31 Nov. 3 7 10 Mammalian cell microscopy; Cell morphology; Comparison of 4 distinct mammalian cell types Protein electrophoresis; evolutionary relationship between fish proteins Chromatography (ion exchange) Chromatography (glucose binding chromatography) Receptor expression analysis by microscopy (cheek epithelial cells and erythrocytes) Calf thymus nuclei and genomic DNA purification; microscopic analysis Oral Presentations NO LAB - FALL BREAK Promoter activation assay: Arabinose Operon, Plasmid DNA structure and bacterial transformation using the pGlo plasmid Complete analysis of Lab 7 experiment; Start PCR Based Alu-Element (retrotransposon) Mapping (using students DNA) Complete Lab 8 PCR experiment by comparing student profiles using gel electrophoresis; Cancer gene detection (PCR set up) DNA damage; UV exposure titrations and analysis by gel electrophoresis NO LAB Thanksgiving Holiday

Lab 7 Lab 7 (cont.) Lab 8 Lab 8 (cont.) Lab 9 Lab 10

14 17 21 24 28 Oral Presentations; Turn in Lab Notebooks during Dec. 1 lecture.

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BIO 3000 Sec 01, 02

High Point University STUDENT INFORMATION FORM

Fall 2011

Full Name: ___________________________________________________________________ Name which you prefer to be called (nick name): _____________________________________ Hometown and State: __________________________________________________________ Local Address: ________________________________________________________________ _________________________________________________________________ Local Telephone Number: _______________________________________________________ E-mail Address (required): _______________________________________________________ Class: (circle) Freshman Sophomore Junior Senior

Major: _______________________________________________________________________ Advisor: _____________________________________________________________________ Professional Goal: _____________________________________________________________ Other Bio or Chem Courses you are taking this semester: ______________________________ ____________________________________________________________________________

Please sign the following acknowledgement: I have received a copy of the syllabus and the expectations of the course have been explained to me. ________________________ (Student Signature) _____________________ (Date)

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