A scientist has three ways of gaining new knowledge. These are 1) personal interaction/discussion with peers or colleagues; 2) the scientific literature; 3) experiment and observation. In most courses, you rely mainly on the first of these (by way of the instructor). In this course, you will rely on all three (more or less equally). For the first, we will use lecture and reading from Principles of Biochemistry, 5th edition, by Lehninger, Nelson and Cox. Much of the material in the text you are already familiar with from other courses, although not at this depth of detail. You might find it helpful to read some of the chapters and/or sections that are not assigned to help you recall concepts. In the first week, we will cover some or all of chapters 13, 5, and 6. We will go on to 14-19 (in chapter 18, we will not cover section 3). Finally, we will cover chapters 21 and 23. If we have more time, we can cover material of interest to the class. Chapters 1-4, 7, 8, 10 and 11 are essentially review, and I will not attempt to cover them in class. You may want to read them, anyway.   Besides the material in the text, there may be a few papers to read, which we will discuss in class. Much of the material in the text will not be discussed in class because of lack of time. You will still be responsible for it. If you read ahead, you can help direct the class discussion to those items that are less clear to you. This schedule is approximate. We will meet every day from 9 to 11, except the first Wednesday (work day for grant proposal), and test day. There will be a midterm on the second Thursday of the block.

There will be three major components to your evaluation. Exams, including a final exam, will account for 40% of your grade. All exams are open-note, open-book. Lab will be 25%. The third component is a research paper, written in the form of a grant application. You may choose any topic in the field of biochemistry. There will be examples for you to look over. You may have the opportunity to present your proposal orally, to the class, in the final week. If so, the evaluation of the presentation will be included in the grade for the grant proposal..

LAB

Lab grade will be based on effort, organization, skill and your lab report. This will be in standard format (introduction, methods, results/discussion, conclusion). You will work in the lab in pairs; each of you will hand in a separate lab report. It is not always necessary for both lab partners to be present simultaneously: Some division of labor is OK, especially in any given day. Make sure that each lab partner gets to do every procedure at some point during the block. It is fine to help others besides your lab partners and to share information, but do not share data except with your lab partners. Please consult with me or the laboratory instructor before doing any procedure you are unsure of or unfamiliar with. The lab projects are taken from published procedures. Part of the laboratory exercise in this class is to translate a published procedure into a workable lab protocol. Thinking before doing is critical to efficient and productive time in the lab, so I will want to be sure that you have thought through all you will need to do, and how you are going to analyze your data. Please arrange with me to work with you the first time you do the lab. It is a good idea to analyze your data as you go, rather than collecting a large quantity of data and saving the analysis for the end of the block.

Obviously one of the goals of this course is to help you come to rely more on yourself for learning. Lab will also be like this. There is no set lab time. Occasionally someone takes this freedom as license to do nothing in lab (or very little). Remember that you are responsible for how much you accomplish in lab. Lab counts for 25% of this course. This translates into an average of 10-12 hours a week in lab. Some days you may have to spend longer, because certain procedures may require more time. Other days, you may not need to spend as much. I will not be clocking you in and out each day. You may come in at untraditional hours to do certain things, but please do not use any of the large pieces of equipment unless I am around or you have been checked out on it. Do not 'wing it' on a spectrophotometer that you are unfamiliar with. Ask for help. How much time you spend in lab is partly related to how well you plan. Most of you have learned that already. You must organize your time and efforts to accomplish as much as possible in the block. If you run into obstacles, please consult me sooner, rather than later. The goal of this lab is for you to collect some quantitative data that you have confidence in (i.e., that is repeatable). You will be judged on results to this extent, only - that you have produced reproducible data that answer a simple question relevant to your project.

Do you need to keep a lab notebook? Of course. This is not a question that needs asking at this point. It is impossible to accurately record what you do and what you observe without one. It is even more impossible to try to find errors without one. Don't use paper towels or scrap paper. Splurge and buy a spiral notebook. Make daily entries. Include anything that might be useful: concentrations, incubation times, spills, whatever. Your lab notebook does not need to be turned in, but I will want to see it.

GRANT

A grant application has several parts. As always, an introduction -- this introduction usually emphasizes the significance, or importance of the problem you wish to study. For example, you may wish to study how bacteria move in response to chemical gradients. Successful grant applications in this area have emphasized the potential application of information from this research to the problem of sensory detection in vertebrates. Many grant applications seek to relate the area of interest to some area important to human health. After the introduction comes a review of the recent literature -- a kind of answer to the question, where are we? This is a focused and critical review. Only studies relevant to the direction you wish to pursue are included, and flaws or potential areas of question or improvement are carefully noted. Organize your review around a few major points; do not present a laundry list of results. A properly written review should point pretty clearly to the proposal; a reader should be able to predict the proposal from the review. Finally comes your proposal. What hypotheses do you want to test? What experiments do you propose to do? What controls will be necessary? What methods will you use? How will the results of these experiments help answer the questions that you noted in your review? How is your approach unique? (Why would anyone want to give you $100,000 to do this work?) You should include anticipated results and how they might be interpreted. This paper will be 12-15 double-spaced, typed pages, with at least 10 references to research articles (excluding reviews). Roughly speaking, the introduction is worth 10%, the review, 70%, and the proposal, 20%. Mary Iber is the librarian for the sciences and will be happy to help you in your search for information. The topic of the proposal must be something related to a molecular explanation or mechanism of a biological phenomenon. Many people choose to focus on a human disease. This is fine, as long as the proposal is not for clinical research. If you have an idea for a new therapy, that is great and could make a worthwhile grant proposal in another context. But here, in a biochemistry course, I expect your grant proposal to focus on mechanism, not on clinical studies. I am happy to discuss your proposal with you at any time. We will not have lecture on the first Wednesday of the block to allow time to visit the Health Sciences Library at the University of Iowa, where you can have access to a wider array of journals and reviews. I will need to meet with you by the end of the second week to discuss your proposal.

Collaboration is an important part of scientific work, and you may choose to collaborate with one other class member for your grant proposal (no groups of three or more, please). You should each contribute equally to the work of preparing the proposal. Because this may not work out to either partner's satisfaction, we will have a policy of 'no fault divorce' - either partner may decide to opt out of the collaboration, as long as this is done by the second Tuesday of the block. You may both still choose to submit a grant proposal on the same topic, but it will then be your own work.

It is usually the best strategy to choose an area of focus and begin writing the critical review before worrying very much about the proposal. Every area has unanswered questions that become more and more apparent the more you learn about the current research. Writing the review will help you to identify and clarify any areas of misunderstanding you have after reading the papers. Having a clear and thorough picture is a prerequisite to a successful proposal for further research. A stylistic note: when reporting the results and observations of others, it is generally better to avoid phrases like, "Jones studied system X and found...", or "from their results, Smith et al concluded that...". Rather, state the observation or conclusion in a straightforward manner and give a reference. Please use a standard citation style.

I strongly advise you to submit rough drafts of both the lab report and the grant proposal. It is very difficult to prepare an excellent written document without some critical input. I will accept rough drafts as late as the last Saturday of the term, perhaps later, depending on the demand.

HOMEWORK

Homework is not to be handed in; we will sometimes discuss the problems in class, and it will be good preparation for the exams. Some answers are here.

Chapter	Problems
13	4, 5, 6, 8, 9, 13, 19, 21, 23, 26, 27
5	2, 3, 6, 7, 10, 14, 15
6	2, 4, 8, 11, 12, 14, 16, 19, 22
14	6, 9, 13, 15, 18, 20, 25, 29
15	1, 4, 5, 7, 8, 10, 11
16	3, 5, 9, 10, 15, 18, 22, 24, 28, 32, 33
17	2, 5, 8, 10, 15, 16, 17
18	2, 6, 10, 11
19	1, 2, 4, 6, 7, 8, 10, 14, 18, 28, 29, 32, 37, 40
21	3, 5, 7, 10, 14, 16
23	3, 7, 9, 12, 13, 16, 19, 22