BIOL 261 Introduction to Cell and Molecular Biology 4 Credits Instructor: Dr. Kristin O Brien Prerequisites: BIOL and CHEM 105/106 474-5311 ffko@uaf.edu T/TH 11:30-1:00, Irving I 207 office: 216 WRBB Lab: TH 2:00 5:00, Irving I 208 office hrs: Tues. 9-10 am Fri. 11-12 T.A.: Matt Urschel, fsmru@uaf.edu, office hours: Wed. 1-3 pm in WRBB lobby Required textbook: Essential Cell Biology (2nd edition) by Alberts et al. Garland Publishing. Course description: This course will provide an introduction to cell biology and will cover the following topics: cell chemistry, transcription, translation, cell architecture, metabolism, signal transduction pathways, cell division, and the cell cycle. Students will also learn current molecular biological techniques used in the study of cell biology. Course goals: Students will gain knowledge of cell structure and function, learn techniques commonly used in cell biology, sharpen their critical thinking skills, and gain insight to the cellular and molecular basis of disease. Instructional methods: This course will be taught through a combination of lectures, laboratories, group problem solving, and student-led presentations. Policies: Students are expected to attend lectures and laboratories. Exams will be based on material covered in both the lecture and lab and account for a significant portion of your grade. As a result, missing classes will undoubtedly have a negative impact on your performance in this course. If you anticipate missing an exam for family or work commitments, please let me know in advance so that we can make other arrangements. If you miss an exam because of unexpected, extenuating circumstances (ie; family death, medical excuse), please contact me as soon as possible. Grading: Your final grades will be based on the following: 1
1. Exams (550 points): There will be four exams during the semester and one final exam (5 total). Each exam during the semester will count for 100 points (400 points total). The final exam will be cumulative and will be worth 150 points (100 points of cumulative material and 50 points on the last two subjects covered in class). 20 points of each exam will be in the form of short essay questions to be answered outside of class. I will post these questions on Blackboard each Friday prior to the exam by 5 pm. They are due in class on the morning of the written exam, prior to taking the exam. You must work alone to answer these questions. 2. Class participation (20 points): Towards the end of each lecture period, we will spend ~15 minutes working in groups of three to answer questions related to the lecture. Each group will then present their answers to the class. This will allow us to review important concepts covered in the lecture. It also provides me with immediate feedback to determine what concepts you are having difficulty with and what topics we need to review. You will be expected to present answers and contribute to class discussions. There are 22 days of lecture this semester; each day is worth one point and you may miss up to two days without losing credit. 3. Laboratory assignments (100 points): There will be ~5 questions to answer following most labs. Each assignment will be worth 10 points each. One lab (lab 8), requires a short lab report worth 20 points. Some of the questions will cover material in the lab for the following week. Therefore, it is important for you to read the lab handouts before you come to lab. Many of the labs we will do are complex. You are much more likely to enjoy the lab, understand it and obtain good results, if you come prepared. 4. Lab report and presentation (125 points): We will be spending four weeks in lab using microarrays to study gene expression. Once we ve carried out the experiments and collected the data, you will spend one day in lab discussing your results. Each lab group will be asked to present a 15-20 min report on their project. You may use overheads or Powerpoint in your presentation. This assignment is worth 25 points. You will also write a formal lab report on your project. You will be given the opportunity to write a first draft that will be edited by your TA prior to the second draft that will be graded (100 points). 2
5. Optional research paper. You are given the option of writing a 10 page paper addressing a current topic in cell biology. If you choose to do this assignment, it will replace your lowest exam grade (but not the final). In this paper, you will select a current issue in cell biology that has been reported in the news media. You will compare the news report to the evidence in the scientific literature and assess whether the news media accurately portrayed this scientific study/ phenomenon. For example, a recent story in the news reported that scientists at the University of Wisconsin had successfully, grown a beating heart in a dish. You would describe how this story was covered in the news and compare it to the published scientific study. Questions you might address include, was the heart really, grown? Will this technology replace heart transplants? What might be the advantages of this system over heart transplants? Once you have selected a topic, please discuss it with me to be sure that it is appropriate before you begin writing. Assignments are due on the last day of class. They must be 10 pages long, double spaced, written in 12 point font. Include one story from a news article and at least two references from the scientific literature. In summary your grade will be based on the following: Exams: 4 X 100 = 400 Final exam: 150 Class participation 20 Lab questions: 100 Lab report and presentation: 125 795 points total Tips for succeeding in cell biology: We will cover a large amount of material during this semester. Some of it may be familiar to you, but many topics will be new. Here are some suggestions for doing well in this course (and others as well!). (1). Read the book before coming to lecture. This will allow you to familiarize yourself with the material before we cover it in lecture. Also, if you have questions about what you have read, you can ask during the lecture. Please, never be reluctant to ask a question! Undoubtedly there is someone else in the 3
room wondering the same thing, and it will help everyone if I have an opportunity to explain something in a slightly different way, or clarify a concept. (2). Take notes during class. This is an excellent way to reinforce your learning of the material. Although I will post slides on Blackboard before the lecture, I will discuss the material in much more detail then is on each slide and you will be responsible for this material on the exam. (3). Review your notes shortly after lecture, and ask me again if something is unclear, and/or fill in gaps with information from the text. (4). Quiz yourself. Use the questions at the end of each chapter to test your understanding of the material. (5). Ask questions. Please feel free to visit me or your TA during office hours. Ask questions before, during or after lecture. My job is to ensure that you all succeed in this class. (6). Keep up with the material. You will not do well on exams if you postpone all studying until the night before the exam; there is simply too much material to review in one night. I encourage you to form study groups that meet each week to review the material. The material you will learn in this course will form a foundation for most all of your advanced course work in biology. If you put in the effort now, you will do better in your future courses and they will be more enjoyable. Email etiquette: I will do my best to respond to your email inquiries within 24 hr. Please be considerate in your letters, use proper English and complete sentences, and sign your letter. Disabilities: I will work with the Office of Disabilities Service (203 WHIT, 474-7043) to provide accommodations in both the classroom and laboratory to provide equal access to all materials in this course to all students. 4
Laboratory Schedule: 1/24: Lab 1: Introduction to laboratory techniques 1/31: Lab 2: Microscopy 2/7: Lab 3: Spectrophotometry for quantifying nucleic acids and PCR 2/14: Lab 4: Agarose gel electrophoresis 2/21: Lab 5: Microarray Part I: Synthesis of cdna 2/28: Lab 5: Microarray Part II: Hybridization of microarrays*** 3/6: Lab 5: Microarray Part III: Analysis of microarray data 3/13: Spring Break 3/20: Presentation of microarray results 3/27: Lab 6: Protein assay 4/3: Lab 7: SDS polyacrylamide gel electrophoresis 4/10: Lab 8: Western blotting 4/17: Lab 9: Enzyme analysis 4/24: Lab 10: Cellular respiration 5/1: Catch-up ***Hybridization of microarrays will begin in this lab, but will continue on Friday. Please attend, if possible. We will let you know in advance of the meeting time on Friday. 5
Lecture Schedule Reading in Alberts et al. 1/24 Overview of the Cell I Chapter 1 pgs.1-33 1/29 Overview of the Cell II and Cell Chemistry I Chapter 2 pgs. 39-81 1/31 Cell Chemistry II 2/5 Structure of DNA Chapter 5 pgs. 170-214 Chapter 9 pgs. 311-317 2/7 DNA Replication Chapter 6 pgs. 195-214 2/12 Cell Cycle Chapter 18 pgs. 610-633 2/14 Cell division (Mitosis) Chapter 19 pgs. 638-656 Meiosis Chapter 20 pgs. 658-672 2/19 Exam 1 2/21 Transcription Chapter 7 pgs. 229-243 2/26 Gene Expression Chapter 8 pgs. 267-286 2/28 Translation Chapter 7 pgs. 243-263 3/4 Proteins Chapter 4 pgs. 119-155 3/6 Exam 2 3/10-3/14 SPRING BREAK 3/18 Membrane Structure Chapter 11 pgs. 365-388 3/20 Membrane Transport Chapter 12 pgs. 389-422 3/25 Membrane Transport II 6
3/27 Cytoskeleton Chapter 17 pgs. 573-607 4/1 Cell Junctions Chapter 21 pgs. 698-716 4/3 Exam 3 4/8 Protein sorting Chapter 15 pgs. 497-530 4/10 Protein sorting II 4/15 Metabolism Chapter 13 pgs. 427-449 4/17 Mitochondria and Chloroplasts I Chapter 14 pgs. 453-488 4/22 Mitochondria and Chloroplasts II 4/24 Exam 4 4/29 Cell communication Chapter 16 pgs. 533-569 5/1 Cell communication II Please note: This schedule is subject to change. 7
DATE LECTURE MATERIAL LAB MATERIAL ASSIGNMENTS DUE Thursday Jan. 24 Intro. Ch. 1 Lab 1: Introduction to lab techniques Tuesday Jan 29 Intro. Ch. 1/ Cell Chemistry Ch. 2 Thursday Jan 31 Cell chemistry, Ch. 2 Lab 2: Microscopy Lab 1 questions Tuesday Feb 5 Structure of DNA, Ch. 5 and 9 Thursday Feb 7 DNA replication, Ch. 6 Lab 3: DNA Lab 2 questions Tuesday Feb 12 Cell cycle, Ch. 18 Thursday Feb 14 Mitosis and Meiosis, Ch. 19 and 20 Lab 4: Agarose electrophoresis Lab 3 questions Tuesday Feb 19 EXAM 1 Take-home exam questions Thursday Feb 21 Transcription, Ch. 7 Lab 5: cdna Lab 4 questions synthesis for microarrays Tuesday Feb 26 Gene expression, Ch. 8 Thursday Feb 28 Translation, Ch. 7 Lab 5: Microarrays Tuesday March 4 Proteins, Ch. 4 Thursday March 6 EXAM 2 Lab 5: Analysis of microarrays Tuesday March 11 SPRING BREAK Take-home exam questions Thursday March 13 SPRING BREAK Tuesday, March 18 Membranes, Ch. 11 Thursday March, 20 Tuesday March 25 Thursday March 27 Membrane transport, Ch. 12 Membrane transport, Ch. 12 Cytoskeleton, Ch. 17 Tuesday April 1 Cell junctions, Ch. 21 Presentations of microarray results Lab 6: Protein assay Rough draft of lab report 8
Thursday April 3 EXAM 3 Lab 7: Protein polyacrylamide gels Tuesday April 8 Protein sorting, Ch. 15 Thursday April 10 Protein sorting, Ch. 15 Lab 8: Western blotting Tuesday April 15 Metabolism, Ch. 13 Take-home exam questions Lab 6 questions Lab 7 questions Final draft of lab report due Thursday April 17 Cellular respiration, Ch. 14 Tuesday April 22 Photosynthesis, Ch. 14 Lab 9: Enzyme analysis Lab 8 questions Thursday April 24 EXAM 4 Lab 10: Cellular respiration Take-home exam questions Lab 9 questions Tuesday April 29 Cell communication, Ch. 16 Thursday May 1 Cell communication, Ch. 16 Catch up Optional research paper due Lab 10 questions 9