Illinois Institute of Technology
Biological, Chemical, and Physical Sciences Department
Biology Division
Biology 403 / 504: Biochemistry, spring 2009

Instructors and TA:

Name Andrew J Howard Nicholas Menhart Feng Guo
Title Associate Professor of Biology and Physics Associate Professor of Biology Graduate Teaching Assistant
Office Life Sciences 174 Life Sciences 352  
Phone 312-567-5881 312-567-3123 312-567-3414
email howard@iit.edu menhart@iit.edu guofeng@iit.edu
Fax 312-567-3576 312-567-3494 312-567-3494
Office Hours M 3:15-6, W 4:15-6 TBA TBA
Other Cell: 773-368-5067    
Prof. Howard will teach the first half of the course, covering chapters 1-10, 19, and perhaps 20-22;
Prof. Menhart will teach the second half, covering chapters 10-18. Mr. Guo will be involved in grading homework, midterms, and the final exam under their guidance.

Class sessions:
held in Life Sciences Room 111, Mondays 1:50-3:05pm and Wednesdays 1:50-4:05pm.<.br> In most weeks we will give the class a ten-minute break midway through the long (Wednesday) session. All class sessions will be available online about 36 hours after the lecture is delivered.

  • Textbook: H.Robert Horton, Laurence A. Moran, K.Gray Scrimgeour, Marc D. Perry, and J.David Rawn, Principles of Biochemistry, 4th Edition, (Pearson / Prentice-Hall, 2005), 852 pp., cloth, ISBN 0131453068. You may use other printings of this edition, but not other editions of Horton. So don't ask. You're welcome to consult other introductory textbooks on biochemistry; The book we use in biology 401/402 is particularly good: it's Reginald H. Garrett & Charles M. Grisham, Biochemistry, 3rd Edition. Many of Prof. Howard's lecture notes will be referenced to both Horton's book and Garrett & Grisham's, so you might want to see if you could get access to a copy.
  • iClickers: All students in biology 403-1 and biology 504-1 (the two live sections) will need to purchase an iClicker, which is a wireless transmitter roughly the size of a TV remote. These are available at the IIT bookstore for about $37, and you may sell yours back to the bookstore at the end of the semester for half-price if it's still functional. You will need to bring your iClicker to class every Monday and Wednesday. We will use these in two ways during the semester: see below. Students in the television and Internet sections (biology 504-2 and 504-3) do not need to purchase an iClicker.

    • Grading plans:

    The percentage of your grade contributed by various sources will be as follows.

    Item Date Weight
    Midterm 16 February 16%
    Midterm 23 March 16%
    Midterm 20 April 16%
    Final 12 May (approx.) 26%
    Homework roughly weekly 10%
    Quizzes roughly weekly 4%
    Peer-reviewed
    Literature Assignments    		 Weekly 6%
    Class Participation passim. 6%

    We may fine-tune the details of the grading system as the semester develops: watch this space for details. Note that the TV and Internet students (those enrolled in biology 504-2 and -3) will not be taking the iClicker-based quizzes, because iClickers don't readily transfer to the Internet environment. The TV and Internet students will instead do some additional assignments that will take the place of the quizzes. See below for further discussion of iClickers.

    Electronic communication:

    We expect to be able to reach you by electronic mail and through Blackboard throughout the semester. You should use your official IIT e-mail address. If you choose to use another address for most of your e-mail, you have two choices: either check your IIT address in addition to your non-IIT address, or arrange to forward your IIT mail to your non-IIT mail system. Instructions for doing so are available on the IIT website.

    Class participation:

    The class participation grade will be determined based on your participation in several activities:

    1. Comments contributed in class;
    2. E-mail exchanges with us;
    3. Telephone conversations with us;
    4. Contributions to the "Content" forum of the class discussion board. This is the best of all.
    Recognize that this last kind of participation will be positively scored even if it involves disagreements with our assertions; but the participation needs to be related to the content of the course, not the structure of the course offering. Thus your contributions won't be positively scored if they are limited to questions like "which chapters are going to be covered on the exam?" That's a legitimate question, and we'll endeavor to answer it, but it won't help your class-participation grade. With that in mind, we are creating two separate Discussion-Board forums: one called "Content" and the other called "Logistics". Questions about exam structures and arrangements should be posted to the "Logistics" board; questions about the actual subject matter of biochemistry should be posted to the "Content" board. The Content board is the one that will be graded. Regular participation, rather than a flurry of last-minute contributions, will help you and your fellow students more, and will therefore earn you more points.

    Midterms:

    The dates for the midterms are listed above. Each will include definitions, short-answer questions, and more substantial questions that require one to three paragraphs each to answer. The full 75 minutes will be available for for the exam. You will not be permitted to use your textbook or class notes. For Prof. Howard's midterms you will receive a help-sheet to help you remember factual information like the gas constant and the relationship among free energy, entropy, and enthalpy. He will also provide some relevant mathematical constants, like e, ln(2), log102, and ln(10). Prof. Menhart will provide instructions as to the structure of his midterm later.

    Final Examination:

    The final will be given at the University's mandated date and time, which has not been set: watch this space for this result. There will probably be a help-sheet for the final as for the midterms. The final will be closed-book and closed-notes. The final will be comprehensive, i.e. it will cover all the material in the course; but it will be especially geared toward the material from the final five lectures, since we will not have had a midterm on that material.

    Homework:

    Submit your homework assignments through the "assignments" section of the Blackboard system itself. Do not use the Digital Dropbox, email, or paper submissions. These assignments will be due at 1700 CDT on the date stated on Blackboard. We will accept late homework assignments, but your grade will be lowered relative to the score you'd get if you turn it in on time. Once we have posted the answer key for a homework assignment, you will not be able to submit your contribution. We encourage you to do the homework assignments for three reasons:

    Your answers to most non-calculational homework questions should require about a paragraph. For study purposes, we encourage you to try the problems in the textbook for which the answers are found in the back, and the problems given in the textbook website. If you've gotten them right, you probably understand the material.

    Literature Assignments:

    Students in biology 403 will need to turn in a brief report roughly once per week summarizing a paper from the peer-reviewed literature. Students in biology 504 will generally do two of these reports per week. The specifics of these assignments are outlined on the Assignments page on Blackboard. It is your responsibility to find the assigned journal articles, but many of them will be posted in PDF form on the Blackboard site under "Course Documents" → "Journal Articles". Those of you with access to libraries that are well-stocked in biological journals may be able to find the papers that are not available on the Blackboard site in your own libraries; those of you without that kind of access are welcome to look for the papers at the IIT library or request them by interlibrary loan. The latter can take a day or two in some cases, so plan ahead.

    Schedule:

    This is the plan for what topics we'll cover. This information is provided in greater detail in the course schedule. Note that some of the chapters, or sections of chapters, in Horton et al are not on the list at all; that's deliberate. This is a 900-page book, and there's no way to move through the entire book in one semester without oversimplifying things to the point of incoherence. So we'll pick and choose.
    Topics Lectures Dates Chapters in Text Exam
    Methods,
    building blocks,
    enzymes    		 Lectures 1-7 21 Jan-11 Feb 1-5, 10.5-10.7 16 Feb
    Enzymes,
    Cofactors,
    Metabolites    		 Lectures 8-14 18 Feb-11 Mar 6-9, 19 23 Mar
    Metabolism I Lectures 15-21 25 Mar-15 Apr 10-16 20 Apr
    Metabolism II,
    Molecular Biology    		 Lectures 22-26 22 Apr- 6 May 17-18, 20-22 12 May (approx.)

    Taking the Exams:

    Those of you taking the exams at IIT should be aware that we will go to substantial lengths to minimize the likelihood of cheating. Any undergraduate student who is found to be cheating will be given a summary zero on the exam on which he or she is found to be cheating; a second infraction will result in an automatic E for the course. Graduate students will be held to an even higher standard: you will earn an automatic E for the course with the first infraction. The teaching assistant will be present to proctor the exams, and will keep an eye out for low-tech and high-tech forms of cheating. No hats or other headgear, apart from those required by your religious practices, will be allowed at exams. You will not be allowed to bring any electronic devices, notes, or books to the exams; the calculational problems will be numerically straightforward, so that you can do them with a pencil and paper. We reserve the right to impound calculators, cell phones, MP3 players, PDAs, laptops, and other electronic devices brought into exams. Any numbers that you might ordinarily have to obtain from a calculator will be provided on the help-sheet. We reserve the right to provide some mathematical and physical constants that you will not need; don't assume that if a constant is on the help-sheet, you're going to have a use for it. If you haven't done long division in six years, you might want to practice a bit before the first midterm. Prof. Howard's exams tend to be reasonably easy, but long, so planning and prioritization are important.

    How we'll use the iClickers:

    We'll use the iClickers in two ways. A few times per lecture, we plan to ask multiple-choice questions for which you should punch in your answers on your iClicker. These questions will not be graded; instead, they'll be used as votes, and we'll look at the vote totals before we provide an actual answer. Sometimes I'll ask you to produce the answer on your own; other times, I'll ask you to work in small teams. Roughly once per week, we'll have an actual in-class quiz, consisting of a few multiple-choice questions that you will answer by iClicker. These quizzes will count in your final grade. If you miss one of these quizzes, you'll get a zero on it, unless you have notified me in advance that you have a legitimate excuse for missing the class. We're the ones who decide whether your excuse is legitimate. We are also conscious of the fact that there are ways to cheat in using iClickers; we'll watch for these phenomena and will apply the same rules as described in the "Exams" section regarding iClicker cheating.

    Special note for Internet students (biology 504-3):

    Many of you have never taken an Internet-based course at IIT before. Recognize that if you are a far-distant student, i.e. if you're viewing these lectures from more than 50 km from IIT, then you will need to find a local proctor who can administer these exams according to the conditions that we set out. Mr. Charles Scott (scott@iit.edu, 312-567-5217) is the Client Service Administrator for IIT Online Support Services. He can help you find find a proctor. If you're local, then we are planning to have you take the exam onsite, and a teaching assistant or one of us will proctor the exam on campus. If any of you lives close to IIT but cannot take the exams on campus, please let me know early in the semester so we can make alternative arrangements. It's your responsibility to set these arrangements up in advance, not ours. Discovering on the day of the exam that your proctor is on vacation is not a legitimate excuse for delaying taking an exam.