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Introduction

Course Goals

Your responsibilities and mine

Hints for Success

About your Textbook

Starting at 8 am

Evening exams

Late assignments

Student Assessment

Grading Scale

Course Schedule

Instructor: Dr. Bonnie K. Baxter, bkbaxter@lclark.edu, x7653

Class Time & Place: MWF 8:00 am to 9:00 am, Thaxter 2

Office Hours: T.B.A.

Textbook: Molecular Cell Biology, by Lodish et al. 4^th edition. W.H. Freeman & Company (this is also the textbook for Biology 361: Cell Biology).

Molecular Biology is about investigating how genotype becomes phenotype. Given a certain set of genetic instructions in its DNA, how does a cell read and interpret those instructions to go about its day-to-day activities? How does it adapt these readings and interpretations to different circumstances? How does it "know," for example, when it is time to move, when to eat, when to "sleep," and when to divide? In a multicellular organism, how do cells with the same set of instructions end up with such different fates and roles? How does a cone cell in your retina come to be so different from a muscle cell or a white blood cell?

The student of molecular biology will notice several underlying themes that are characteristic of this field:

1) Reductionism. Molecular Biology is a field of study that seeks to understand the nature of life at the level of molecules. The discipline is built upon the premise that we can understand complex biological phenomena by taking them apart and reconstructing the process in a test tube from its essential components. This reductionist approach to science has been enormously successful and the rate of growth of new information in this field of study has been explosive. The reductionist approach has led molecular biologists to appreciate…

2) The unity of life. When approached at the level of molecules, all of life appears remarkably similar. All cells use DNA as their genetic material. With a few minor exceptions, all use exactly the same system for encoding protein sequences within that DNA, and the same general mechanisms for copying, transcribing, and translating that code. And as we will see in this course, there are relatively few types of control mechanisms for gene expression&emdash;the manifestation of genotype as phenotype. It is very often the case, for instance, that a mechanism discovered in a bacterial cell will turn out to be common in many other cell types, including human cells. The fact that particular discoveries are very often generalizable to other systems is one of the things that has led to…

3) Extremely rapid change. James Watson and Francis Crick published the molecular structure of DNA in 1953. Today, less than 50 years later, the human genome project is on the verge of completing the sequence of the entire human genome (about 3 billion base pairs in all). It is now possible (and even straightforward) to look up the sequence of one of the 100,000 or so human genes on the internet and to design and carry out a strategy to "clone" that gene and introduce it into another organism. (We will be doing something very similar to this in the Bio312 lab, in fact.) Changes and rearrangements of DNA can be introduced almost at will, and their effects determined in cultured cells. The use of these technologies and others like them have led to a field in which our understanding of basic molecular processes is revised and updated on an annual, monthly, or even weekly basis. It has also led to a society in which our ability to do things in biotechnology has far outpaced our thinking about the implications of what we do.

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As I see it, a science course has three quite different aspects: content, process, and context. The most straightforward thing to teach and learn is generally the content. What is our current understanding of how things work? In this case, what is DNA, how is it structured, and how its instructions interpreted? What have scientists learned about how genotype becomes phenotype? This is the sort of information that is conveyed effectively by textbooks and lectures. It is essential to build a solid foundation of understanding of this sort of material, because progress in science rests upon these foundations.

But of course science is not a static collection of "facts," but a process. Science as process relies on a solid understanding of what has gone before, but also on a willingness to expand and challenge current thinking. Learning to understand the process of science requires experience with experimental design, data analysis, and creative model building. Doing science requires thinking both inside and outside of the "box." Doing science requires skills like critical analysis, creativity, curiosity, and collaboration. These skills are learned most effectively in discussions, collaborations, and laboratory work.

Finally, science is a human activity that occurs in a social context. In molecular biology, this interface is apparent on a weekly or daily basis in the news media and in political events. Technologies such as genetic testing, genetic engineering, cloning, and molecular drug design all potentially have huge impacts on society at large. As members of society, you will be faced with those impacts and with decisions about them regardless of your choice of career.

I have designed Biology 311 to integrate these three aspects of molecular biology. We will spend a lot of our time on content&emdash;building a basic understanding of the state of this field as it is today. This will serve as your foundation. Whenever possible, this content will be provided in its experimental context, to give you an idea of the process that built it. In other words, we'll discuss not only what we know, but how we know it. In each of the four final units in the course, we will also read and discuss an article from the primary research literature in molecular biology. We'll pick these papers apart to determine what the underlying questions were, how these questions were addressed, what the data showed, and whether the conclusions are supported. These papers and discussions will give you a chance to develop and refine your science "process" skills. Finally, we'll step back now and then to discuss social context&emdash;the interplay between the field of molecular biology and society as a whole, and the impact each has on the other. My overall goals for you are as follows:

1. To gain a solid understanding of existing concepts in molecular biology, including an idea of how these concepts were developed by scientists over time.

2. To gain proficiency, confidence, and experience in reading and analyzing primary research literature in molecular biology.

3. To increase your sophistication on issues of societal importance which involve molecular biology and related technologies, as well as your confidence and experience in thinking and talking about these issues.

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1. To share with you my delight and amazement at the way that life works at the molecular level
2. To design course materials which effectively serve the course goals
3. To facilitate your learning as effectively as I know how
4. To design assessments (exams, grading criteria, etc) which are a reasonably accurate measure of your mastery of course content, and to use these materials to provide you with frequent feedback on your progress
5. To be available to you, and to listen to you with respect and attention

Your responsibilities (as I see them):

1. To commit the time and energy necessary to allow you to progress (see hints for success below)
2. To manage your time effectively so that you can complete assignments on time and be prepared for class and for exams
3. To work collaboratively, cooperatively, and respectfully with your fellow students and with me
4. To seek help promptly with all issues on which you are confused

I cannot emphasize this last point enough! Please, you must not be shy. I expect you to make clear to me when you do not understand something, preferably by asking questions in class where others may benefit. Alternatively, come see me in my office or send me a note by e-mail. You should never feel a question is too trivial to ask. Most likely, I have explained it in a way that leaves out just one crucial link for you, and it can often be something missing for others as well. Asking questions not only helps you learn, it also helps me teach.

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Research has shown that one of the least effective ways to further understanding is to sit passively and listen to a lecture, no matter how well-organized and clear the lecture may be. Your own experience may bear this out. If you wanted to learn to make quiche, for example, which do you think would be more effective&emdash;watching a beautifully presented program on public television or going into the kitchen and attempting to follow a quiche recipe?

It’s not that you wouldn’t be interested in the TV program, or motivated to learn from it. Rather, it is simply that the more different ways you can engage your brain in processing a concept the more effectively you learn. Doing something is more effective than reading about it, and explaining something is more effective yet.

If you are to gain an understanding of molecular biology, you must actively engage the material. What does this mean?

1. First, read the textbook. But don’t just run your eyes over the page. Make notes to yourself. Underline important areas. Ask yourself to restate the main point of each section. Examine the figures. Work through the equations. Answer the textbook’s study questions and complete your weekly homework assignment. Check out the CD resources available for each chapter we cover&emdash;they will often include very helpful Quicktime movies and animations, as well as additional review questions.
2. Next, come to lecture. But don’t just sit there! If you do (especially at 8 am!) you are likely to gain little. Take careful notes. Process the information as you go. Does this make sense? Do you understand what the point is? Do you see how this fits with the material in your text and in previous lectures?
3. Ask questions!! Of me, of each other, of yourself. In class, in the hallway, in my office, over e-mail. Asking questions means that you are attempting to process and make sense of the material, and is therefore enthusiastically welcomed. I will have regular office hours for this purpose, and they are much more interesting when students show up. If these hours are not convenient, feel free to come by, call, or e-mail at another time. If I am not available right then, we can make an appointment.
4. Form or join a study group with 2 or 3 of your fellow students. Meet regularly to discuss the course material and review for exams. You will often find that you can synthesize a much clearer and more complete understanding as a group than as individuals. Also, the practice you get in explaining concepts within your study group will prove invaluable on exams.
5. Manage your time well. Bio 311 is a demanding course. Your other courses this semester are likely to be demanding as well, and you are presumably balancing this course load with other commitments and a personal life. Be aware that it is my expectation that you will spend 1 &endash; 2 hours outside of class on coursework for every credit hour, which means 6 - 12 hours weekly on Bio 311 and 312. If you are spending 12 outside hours every week on Bio 311/312 and are still struggling to keep up with the course, come and see me so we can problem solve together. I may be able to suggest ways to arrange your study time more efficiently. If you cannot make this kind of time commitment for each of your classes and still meet your other responsibilities, rethink your courseload.

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Starting class at 8am. Class starts at 8 am. This may not be your favorite time of day&emdash;it's not mine. This is the time that we have together, though, and we need to make the most of it. So do what you need to do to get yourself in the classroom, notebook open, brain engaged, ready to go at 8 sharp. The extra effort will be worth your while.

Evening exams. In order for me to be able to assess whether you have been able not only to memorize, but also to synthesize and make use of new information, I need to be able to ask complex questions on our exams. Feedback that I have received from students in the past has been that it can be difficult to complete such an exam within a one-hour time frame, that it is challenging to process complex tasks at 8 am, and that more questions with fewer points attached to each would be appreciated. To accommodate this, I have scheduled our midterms as two-hour evening exams, from 7 &endash; 9 pm. Please check your schedules now to ensure that you will be able to attend these exams. If these times pose a problem for you, simply contact me to make other arrangements. For you to receive credit for the exam, we must have agreed upon an alternate arrangement by 5 pm on the Friday preceding the exam. Except in cases of medical emergency or death in your immediate family, failure to make advance arrangments with me will result in a grade of zero for any exam missed. The final exam cannot be rescheduled or taken at an alternate time. Please take this into account when making your end-of-semester travel arrangements. (And please note that Bio312 will have a separate final exam.)

At this point, take a break from reading the syllabus and send me an e-mail telling me whether the Monday evening exams are going to work for you. If I receive your e-mail by 5 pm on Monday, Sept 11^th, you will receive 5 pts extra credit. It's my way of saying thank you for your diligence in attending to these matters.

Late assignments. Assignments are due at the beginning of class on the day stated on the assignment. They will not be accepted late. To accomodate the fact that emergencies will arise, I will drop your lowest score on each set of assignments before calculating your final grade.

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Student evaluation

Midterm I (Thurs, Oct 5)	100 Pts
Midterm II (Mon, Nov 13)	100 Pts
Final Exam	180 Pts
Question sets on outside readings (6 @ 10 pts, lowest dropped)	50 Pts
Text-based homework assignments (8 @ 10 pts, lowest dropped)	70 Pts
Total:	500 pts

Grading Scale

Exams in this course will not be graded on a curve. You are not in competition with your fellow students, only with the material. The grade cut-offs will be as follows:

450-500pts	A
441-449pts	A-
435-440pts	B+
400-434pts	B
391-399pts	B-
385-390pts	C+
350-384pts	C
333-349pts	C-
250-332pts	D

A problem that be encountered with "non-curved" grades is that the instructor can misjudge and write an exam that is too difficult for most students. To compensate for this problem, if I write an exam on which the mean score is less than 75%, I will adjust the scores for that exam upward so that the mean score is 75%.

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revised Friday, October 13th

Wed, Sept 6	Welcome, introductions, expectations	Review: CH 4
Fri, Sept 8 to Mon, Sept 18	Molecular biology techniques	CH 7
Wed, Sept 20	Discussion of outside reading: "The Function of Dogma in Scientific Research" by Thomas Kuhn	On reserve at Watzek
Fri, Sept 22 to Mon, Oct 2	Chapter 7 wrap-up (9/22) and Molecular genetics (9/25 - 10/2)	CH 8
Wed, Oct 4	Review for Exam I
Thursday, Oct 5, 7 to 9 pm	EXAM I (BoDine 300)
Mon, Oct 9 to Wed Oct 11	Gene structure	CH 9
Mon, Oct 16	Gene structure continued (CH 9 wrap-up)
Wed, Oct 18	Discussion of Outside Reading: "A new S cerevisiae ankyrin repeat-encoding gene" by Lycan et al	On reserve at Watzek
Fri, Oct 20 to Fri, Oct 27	Regulation of transcription initiation	CH 10
Mon, Oct 30	Discussion of outside reading: Jacob et al, 1960	On reserve at Watzek
Wed, Nov 1 to Wed, Nov 8	Post-transcriptional regulation	CH 11
Fri, Nov 10	Discussion of outside reading: post-transcriptional control	To be assigned
Mon, Nov 13	Review for Exam II
Monday, Nov 13, 7 to 9 pm	EXAM II (BoDine 300)
Wed, Nov 15 to Wed, Nov 22	DNA replication, repair, and recombination (guest lecturer: Dr. Suzanne Deschenes)	CH 12
Fri, Nov 24	THANKSGIVING BREAK
Mon, Nov 27	Discussion of outside reading: DNA repair research	To be assigned
Wed, Nov 29 to Fri, Dec 8	Regulation of development	CH 14
Mon, Dec 11	Discussion of outside reading: research in developmental biology	To be assigned
Wed, Dec 13	Review for final exam
SAT, Dec 16, 6 to 8 pm	FINAL EXAM

Except for exam dates, schedule is subject to adjustment and revision to suit the needs of the class

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