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CELL AND MOLECULAR BIOLOGY The purpose of this course is to deepen your understanding of the chemical processes and structures that occur in the cell and how they are related to the observable characteristics of cells. We will begin with an overview of the "typical" cell and the structures that are found in it. We will examine the molecules from which cell structures are assembled. We will discuss the ways in which cells capture and use energy to produce order. And we will spend a lot of our time talking about the supermolecular structures in the cell -- what their functions are, and how function is related to structure. One of the important goals of this course is to enable you to understand the evidence and reasoning that have led to the current view of the cell, and provide you with a basis on which to judge evidence and reasoning that will, in the future, change our view of the cell. In order to accomplish this, you will also be introduced to some of the techniques that are used in this area. Other information is found in supporting files. GRADING Your grade will be determined as follows: Three exams 300 points Lab report first half 20 points Critiques (2) 25 points each Lab report second half 40 points Lab attendance/participation 20 points Quizzes Up to 50 points Grading scale A 425 points A- 400 points B+ 375 points B 350 points B- 325 points C+ 300 points C 275 points and so on SCHEDULE We will usually begin at 9:00 daily, although lab work may require you to come in as early as 8:30. We will be done by 11:15 each morning. We will begin most afternoons at 12:30 and be done by 3:00. Tests will be in the morning. You are expected to have read the text material before the lecture. The overall lab schedule is attached to the lab handout. We will be moving back and forth between lecture and lab often; please do not dawdle. The text for this course is Cell and Molecular Biology, 6th Ed., by G. Karp. We will cover chapters 1-6, 8, 11, 13, and perhaps some of 18 of the text. There will also be a small number of supplementary reading assignments that I will provide. All necessary materials will be found at the course Moodle site. THE LAB REPORTS These reports should be patterned after research articles that appear in scientific journals. Be sure to read the document on lab reports; it will give you some hints about writing your report (it will be obvious to me if you haven’t read it). As you will discover, research articles consist of: 1) an introduction, which lays out the questions to be answered and considers their significance - use this section to tell why anyone would be interested in these questions; 2) a section on material and methods which describes how the work was done - don't include all the detail found in the manual, but be sure to include the detail not found in the manual (such as gel loads and restriction enzymes used); 3) a description of how the methods are supposed to work (i.e., why you did what you did) and the presentation of the results, including (but don't limit yourself to) figures and tables - be careful in your use of significant figures; and 4) discussion of the results and conclusions to be drawn. This last section is a chance to critique your own work. Put the results together into a coherent whole; comment on the expected as against the actual results. Don't use platitudes (like, "we learned a lot", or "our poor results were due to human error"). Be specific, not general. Each lab report is to be no more than 6 pages of normal (10-12 point) typewritten double-spaced text (excluding figures and tables). The introduction will be worth 20%, the methods section, 20%, the results, 30% and the discussion, 30%. Remember, plagiarism may result in a zero for this assignment (see the Compass). The first report (for the first week) is due on day 10 of the block. For this report, you should prepare only a methods section and a results section. Save the introduction and the discussion for the second report. This report should include in the results section a clear explanation of the method of isolation that we used. The second report is due the last day of the term. This report should include a clear explanation of how we isolated organellar DNA, and how we visualized the DNA of interest in the Southern blot. In both this and the first report, these are not simply descriptions of what we did, as much as they are descriptions of why we did it, and what roles the reagents played in the processes. THE PAPER SUMMARIES You are required to choose two research articles from scientific journals (no earlier than 2011) and critique/summarize them. The articles can be in any area of cellular and/or molecular biology. I suggest that you look through the following journals in order to find research on a relevant topic: Cell, Developmental Biology, Development, Journal of Cell Biology, Journal of Biological Chemistry, Journal of Heredity, Nature, Plant Physiology, Proceedings of the National Academy of Sciences, Science, or Genetics. You are welcome to consult any other scientific journal to which you have access. I recommend that you clear the article with me, first, and read the article at least twice before you decide to use it for your critique. Don’t be intimidated by the word ‘critique’. Most of what you write will be in the nature of a summary. The idea of this assignment is to read a research article critically (or deeply); to discover what question(s) the researchers were attempting to answer, what techniques they used to obtain the answer(s), and to evaluate how successful they were in answering the question(s). Choose three or four of the central experiments reported in the paper and discuss their design and how they do or do not contribute to the conclusion(s) the authors are attempting to draw Your first task will be to understand the purpose of the paper. Are the authors testing a hypothesis or model? If so, what is it? There will be competing or alternative hypotheses or models that they will try to eliminate. Frequently, these are not clearly identified. Rather, it is left to the reader to understand them from the experiments and controls that are done. You should also take this general approach when examining individual experiments. Why was it done? What alternatives were they trying to eliminate? Once you have understood these bases for their work, you need to try to understand and explain their experimental design and methodology. Do they adequately test the hypothesis and possible alternative explanations (pay special attention to controls)? Should they have considered other alternative hypotheses? Some papers are not easily interpreted as hypothesis testing. Frequently, the researchers are gathering data on which to base a hypothesis. In this case, rather than beginning with a hypothesis, the authors begin with a set of questions about the system of interest, questions that have definite, usually quantitative answers. Here, your job is to critique the significance of their questions, the experimental design and methodology used to answer them, and whether the results of these experiments gave or can give useful answers. Do not comment on whether or not you enjoyed the paper, or found it well written; stick to an analysis of the science. It may be necessary for you to read related papers (for instance, references) in order to understand the article. It is not necessary for you to describe in detail every experiment in the article. However, you must describe some (3 to 4). Some of them may not be directly related to the main focus of the work. Some may be more important or central to their point. Concentrate on these. It is usually best to center your critique on the figures/tables that are most important. It is not necessary to launch an attack on the authors' work. Sometimes no weakness will be apparent to you; other times, your criticisms might be very mild. Please avoid direct quotations from the article. Use your own words and express your own ideas. Remember that good writing includes a clear and informative introduction and a coherent conclusion. When you hand in the critique, attach a copy of the paper being critiqued. The first critique is due on day 9 of the term. The second is due on day 17. The critiques should not be more than 3 pages long. Course Schedule - Lectures Week Day Chapter 1 Monday 1&2 Tuesday 2 Wednesday 2, 18 Thursday 3 Friday 3, 4 Membrane composition and function Monday Tuesday Exam I 4, 5 Mitochondrial structure and function Wednesday 5&6 Electron transport, ATP synthesis, chloroplasts Thursday 6 & 11 Light and dark reactions of chloroplasts, genes and proteins Friday 11 Transcription in prokaryotes and eukaryotes Monday 11 Translation Tuesday Wednesday Exam II 13 Thursday 13 DNA repair Friday 8 Cytoplasmic membranes, endoplasmic reticulum, Golgi Monday 8 Lysosomes, proteasomes, endocytosis 2 3 4 Tuesday Wednesday Topic Properties of cells, cell types, small molecules of cells Biological macromolecules Sections 6,7,9,11,12,13 (to page 766) of ch. 18 for lab Glycolysis and regulation DNA replication Supplementary Science and society; ethics readings Final Exam Problem assignments: These problems are assigned for your benefit and are not to be handed in. They are the most useful of the end-of-chapter problems. Chapter Problems 2 1,4,7,8,13,14,15,16,18 3 1,2,3,4,7,8,10,12,17,20 4 2,6,9,11,12,13,15,17,19,21 5 2,3,4,5,6,8,10,12,13,14,16 6 3,4,6,7,8,9,10,13,15,17,19 11 1,2,3,4,6,10,12,14,15,18 13 1,3,4,5,6,7,11,12,13 8 1,4,6,7,9,11,14,15,17 Academic honesty: ‘Cornell College expects all members of the Cornell community to act with academic integrity. An important aspect of academic integrity is respecting the work of others. A student is expected to explicitly acknowledge ideas, claims, observations, or data of others, unless generally known. When a piece of work is submitted for credit, a student is asserting that the submission is her or his work unless there is a citation of a specific source. If there is no appropriate acknowledgement of sources, whether intended or not, this may constitute a violation of the College’s requirement for honesty in academic work and may be treated as a case of academic dishonesty. The procedures regarding how the College deals with cases of academic dishonesty appear in The Compass, our student handbook, under the heading “Academic Policies – Honesty in Academic Work.”’ Accommodation for learning disabilities: ‘Students who need accommodations for learning disabilities must provide documentation from a professional qualified to diagnose learning disabilities. For more information see cornellcollege.edu/disabilities/documentation/index.shtml Students requesting services may schedule a meeting with the disabilities services coordinator as early as possible to discuss their needs and develop an individualized accommodation plan. Ideally, this meeting would take place well before the start of classes. At the beginning of each course, the student must notify the instructor within the first three days of the term of any accommodations needed for the duration of the course.’ These are official college policies.