BIOL 461/ 661 Cell Biology 4 Credits Instructor: Dr. Kristin O Brien Prerequisites: BIOL 362 Principals of Genetics Office: 226 Arctic Health CHEM 321 Organic Chemistry Laboratory: 229 Arctic Health T/TH 11:30-1:00, Irving I 208 Office hours: M 9-10, TH 3-4 Lab: Wed. 2:00 5:00, Irving I 207 474-5311; ffko@uaf.edu T.A.: Manuela Schmoll; ftms1@uaf.edu Required textbook: Molecular Biology of the Cell (4 th edition) by Alberts et al. Garland Publishing. Other material: Bound laboratory notebook. Course description: This course will provide an in-depth look at many cellular processes including: protein and membrane structure, organelle structure and function, intracellular trafficking of proteins, metabolism, and cell-cell and intracellular signaling. Course goals: Students will gain knowledge of cell structure and function, learn laboratory 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, exams, and problem solving. Powerpoint slides for each lecture will be posted on Blackboard each evening before lecture. These are meant as a template, and not a substitution for taking notes. Policies: Students are expected to attend lectures and laboratories. Exams will be based on material covered in both the lecture and lab. These exams account for a significant portion of your grade. Thus, 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: Exams: There will be four exams during the semester, one of which is the final. All exams will count 100 points, except the final, which will be worth 200 points (total= 500 points). 25 points of each exam will be take-home questions which involve applying what you ve learned in lecture to experimental problems, similar to the homework questions (see written assignments below). Graduate students will have 2-3 additional, essay or data interpretation type questions they must answer on each exam. These will account for an extra 10 points on each exam, so that each exam for graduate students is worth a total of 110 points. Grades on these exams (and course) will be absolute and will not be based on a class curve.
Written assignments: There will be two types of written assignments during the course of the semester. There will be 10 assignments total, each worth 10 points (100 points total). Graduate students are not required to do the written assignments, and will not be graded on them. There will be 5 assignments which are short answer questions that will require you to apply the information you learn in lecture. I encourage you to work together in study groups. However, answers must be turned in written in your own words. We will discuss the answers for each problem set after they have been turned in and graded. The second type of written assignment will involve writing a short synopsis of papers read on specific topics. There are 5 of these assignments. These are papers that will be read and discussed in class, with graduate students leading the discussion. Each synopsis must be ½ - one page long, single spaced, 12-point Times New Roman font. They are due at the beginning of the class period. The synopsis should include the following: what is the purpose of the study and what question(s) are being addressed; what are the techniques used to address the question(s); what were the conclusions; and do you agree or disagree with the conclusions? Laboratory: Each student will be expected to maintain a neat and detailed laboratory notebook. Notebooks will be collected three times during the course of the semester and graded out of a total of 20 points (60 points total). In addition, there will be 5 written assignments during the semester, each worth 20 points (100 points total). The laboratory notebook should contain a detailed description of the experiments carried out during the lab. It should contain the following sections for each laboratory (except the first one): (1). Purpose: What is the purpose of the experiment and what question is being addressed? This must be written before you come to class. You will not be allowed to participate in the lab if you have not completed this before coming to class. (2). Methods: A detailed description of how you carried out the experiment. This is written in lab as you go through the experiment. It is not a copy of the protocol that is distributed; many times we alter the protocol slightly and your notebook should reflect this. There is often plenty of time during the lab (ie; as gels are running, samples are being centrifuged, samples are incubating) for you to complete this during class. (3). Results: This should include the data in the form of graphs and/or gel images, and statistical analysis if appropriate. All data should be clearly labeled (ie; graph axis, lines, gel lanes). (4). Conclusions: This should be an interpretation of your results and detail any problems and how you would alter the experiment to address these problems. Keep in mind as you work on your laboratory notebook that anyone should be able to pick up your notebook at anytime and compete the experiments that you have done without having to ask any questions. Presentations for graduate students: Each graduate student in the course will lead a 30- minute discussion of one journal article on a topic related to one we cover in class. This will be worth 50 points. Topics are listed below in the lecture schedule. Grad students, please let me know within the first week of class which topic you would like to cover. Undergraduate students will write a short synopsis of each article which will be turned in at the beginning of the class period and graded out of a total of 10 points (see written assignments ).
In summary your grades will be based on the following: Undergraduates: Graduates: Exams: 500 points Exams: 550 points Lab: 160 points Lab: 160 points Homework: 100 points Presentation 50 points Discussion participation 15 points Discussion participation 15 points TOTAL 775 points TOTAL 675 points 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.
Laboratory Schedule: 9/6: Introduction to cell biology: equipment, calculations, databases and yeast biology** 9/13: Cell fractionation 9/20: Protein Assay** 9/27: Gel electrophoresis 10/4: Western blotting (Notebook check #1) 10/11: Analyze western blots** 10/18: Principals of quantitative PCR (QT-PCR) and primer design 10/25: RNA quantification and cdna synthesis 11/1: QT-PCR (Notebook check #2) 11/8: Analyze QT-PCR** 11/15: Proteomics I- Ciphergen 11/22: Thanksgiving Break- no lab 11/29: Proteomics II: Ciphergen 12/6: Mass spectrometry lab** (Notebook check #3) **Indicates that lab will have a written assignment associated with it that will be due the following week at the start of the lab period. However, the last lab assignment will be completed during the lab period and will be due at the end of class.
Lecture Schedule and Assigned Reading* Date Topic Reading in Alberts et al. 8/31 Introduction to cell biology pgs. 3-19, 29-37, 47-68 What is a cell? Cell Structure Prokaryotes vs. eukaryotes Cell chemistry 9/5 Metabolism/ mitochondrial biology pgs. 91-108, 767-793 Glycolysis The citric acid cycle Oxidative phosphorylation 9/7 Regulation of cellular metabolism Uncoupling proteins Suspended animation: Carbon monoxide-induced suspended animation protects against hypoxic damage in Caenorhabditis elegans Nystul and Roth. (2004). PNAS 101: 9133-9136. 9/12 No class 9/14 Lipid membranes (Manuela Schmoll) pgs. 583-613 Membrane structure Membrane proteins Membrane lipids in cell signaling 9/19 Chloroplasts and photosynthesis pgs. 793-821, 808-828 Photosynthesis Mitochondrial and chloroplast genomes Mitochondrial-nuclear cross-talk 9/21 Membrane transport pgs. 615-631 ***Problem set #1 due**** 9/26 Cytoskeleton pgs. 907-948 Microtubule dynamics Actin Intermediate filaments 9/28 EXAM I
10/3 Cell Movement pgs. 949-981 Molecular motors Arginylation of -actin regulates actin cytoskeleton and cell motility. Karakozova et al., (2006). Science. 313 :192-196. 10/5 DNA Replication pgs. 235-298 DNA structure Replication DNA repair Recombination 10/10 Cell cycle pgs. 983-1010 Cyclins and cyclin-dependent kinases ***Problem set # 2 due*** 10/12 Cell division pgs. 1027-1060, 1130-1139 Mitosis Meiosis 10/17 Apoptosis pgs. 1010-1014 At the gates of death and Mitochondria primed by death signals determine cellular addiction to antiapoptotis BCL-2 family members. (2006). Certo et al., Cancer Cell. 9: 351-365. 10/19 Transcription pgs. 299-330 Transcription in prokaryotes vs. eukaryotes Post-transcriptional modification 10/24 Gene regulation pgs. 375-414, 435-452 DNA binding proteins Lac operon Activators and repressors Post-transcription regulation: transcript stability, irna, alternative splicing ***Problem set #3 due**** 10/26 Gene regulation II Active genes dynamically colocalize to shared sites of ongoing transcription. Osborne et al. (2004). Nature Genetics. 36: 1065-1071. 10/31 EXAM II
11/2 Translation and proteins pgs. 335-365 Translation Protein folding Protein degradation 11/7 Proteins II Translating tumor hypoxia: unfolded protein response (UPR)-dependent and UPR-independent pathways. Koumenis and Wouters (2006). Mol. Cancer Res. 4(7). 423-436. 11/9 Protein sorting pgs. 659-710 Transport to nucleus, mitochondria and peroxisome 11/14 Secretory pathway pgs. 711-766 **Problem set #4 due**** 11/16 Cell Signaling pgs. 831-892 G-protein coupled receptors Enzyme-linked receptors 11/21 EXAM III 11/23 No Class- Thanksgiving 11/28 Cell signaling II pgs. 893-906, 1177-1196 Signaling and regulated proteolysis Signaling and the development in Drosophila 11/30 Cell Junctions pgs. 1066-1089 ***Problem set #5 due*** 12/5 Extracellular matrix pgs. 1090-1118 12/7 Review/ catch-up 12/15 Final Exam 10:15-12:15 * Please note: This schedule and reading assignments are subject to change. I will alert you to changes at least one week in advance and I will also post changes to the schedule on Blackboard.