Fall 2007 Course Syllabus

Instructional Staff

Lectures and Lab Sessions

Expected Student Background

• BIOC 463A is an introductory biochemistry laboratory techniques and methodology course. Students are required to have taken CHEM 243A (Organic chemistry lab) or an equivalent course (Chem 244A or 247A). Students are also expected to be currently registered in or have completed BIOC 462A.

Course Objectives 

• One goal of the course is to introduce biochemistry students to the techniques and methods used to study biochemical systems. Initially, students will be introduced to a series of individual techniques that are commonly employed to study bio-molecules. In the second half of the course, these individual techniques will be used to isolate, purify, characterize, and determine the steady-state kinetics of alkaline phosphatase from E. coli. The techniques learned in this course will certainly serve a student well when they enter a research laboratory to begin their own research project.
• An equally important goal is to help students develop the ability to critically analyze and interpret data obtained from an experiment. It is hoped that as the data is being collected, and then analyzed, the concepts and theories learned in BIOC 462A and B will be brought more sharply into focus. The course material will attempt to closely parallel material presented in BIOC 462A or B lecture whenever possible, however some deviation will occur. In other words, there is to be no mental disconnect between 462 and 463!
• The final goal is to have some fun doing biochemistry!

Information on the Web

• The course web site will be used as a mechanism by which the instructors can post announcements, list the schedule of experiments, protocols for experiments, instructions for use of specific instruments, and other miscellaneous information. For ease of printing, every attempt will be made to post this material in PDF format.
• Students are still expected to read (and are responsible for) the assigned material in the Ninfa and Ballou textbook.

Protocols for Experiments

• Many of the experimental protocols will come directly your textbook. However, the BIOC 463A instructional staff have developed a number of experiments, the protocols for which are posted on the website, and can be downloaded in PDF format. Access to these protocols can be made via the Laboratory Schedule page or by clicking Experimental Protocols button on the left side of each page. In addition to providing details about conducting the experiment, you will often find introductory information concerning the theory behind the technique that is not covered adequately in your text. You are expected to become familiar with (and will be held responsible for) this information PRIOR to coming to class (see FLOW CHART below). Again, you are still expected to be familiar with and will be held responsible for the introductory material in each assigned chapter in the Ninfa and Ballou textbook.
• Revisions to protocols given in the course textbook (see next section) can be obtained at the following URL: www-personal.umich.edu/~aninfa/book/index.html

Texts

• Fundamental Laboratory Approaches for Biochemistry and Biotechnology (1998) Alexander J. Ninfa and David P. Ballou, Fitzgerald Science Press, Inc., Bethesda, Md. (required).
• Textbook web site: www-personal.umich.edu/~aninfa/book/index.html
• Biochemical Calculations, 2nd Edition (1976) Irwin H. Segel, John Wiley and Sons, New York. (Optional, but highly recommended)

Required and Optional Materials

• Safety Glasses: Required. We will provide these in class.
• Closed-toed shoes: Required. NO SANDALS, FLIP FLOPS, ETC.
• Hand held calculator: Required.
• Laboratory notebook: Required. The best ones are the heavy-duty brown notebooks sold at the ASUA bookstore.
• Several waterproof fine point marking pens such as Sharpies: Required.
• Ruler(s): Optional. It is best to have a clear, see-through ruler for drawing lines through data (yes, at times we will plot data by hand!).
• Fine-lined graph paper: Optional. Since this type of medium is rapidly becoming obsolete, I'll probably make photocopies and pass them out in class.
• Lab coat: Optional. We use some materials that can permanently stain clothes.

Course Format 

• Laboratory lecture: The purpose of the lecture is to familiarize the students with the technique that will be investigated as well as providing any special precautionary information about the protocol for the experiment.
• Laboratory exercise: On special occaisions, we shall use the entire time period for the class for the experiment. Students will work with a lab partner (sometimes in larger groups) depending upon availability of equipment. Throughout the semester we will rotate lab partners. In some lab exercises, groups will work on different experiments, then share the data with the whole class, in order to more fully understand the system under investigation.
• Lab make-up days: specific days of the semester will be set aside for lab makeup work. On these days, students are expected to come to the lab either to finish or repeat experiments, work on data analysis and lab report preparation, or consult with the course instructors about problems they are having. These days are NOT considered holidays.
• Overall: In the first half of the semester, students will be introduced to individual techniques that will lay a foundation for the latter experiments in which most of these techniques or methods will be used to comprehensively study a protein or enzyme. In biochemistry , like any other science, knowledge that is gained in one experiment is necessary to design, and/or interpret data from, future experiments.

Course Expectations  

• Attendance:Faithful attendance of every class is very critical to success in this course. On each day of the semester, a lot of information is disseminated in both the lecture and lab sessions. Missing a single lab will put you seriously behind the other students with respect to learning how to perform a given laboratory technique. For this reason and with NO EXCEPTIONS, no one will be allowed to register for the class once the semester has begun. Furthermore, while you may obtain data from your lab partner for writing up your lab report, you absence is both unfair and discourteous toward that partner. Habitual absence from class will prove to be EXTREMELY deleterious to your final grade! The following criteria will be rigorously adhered to:

  · > 2 unexcused absences will result in an automatic 1 letter grade drop.

  · > 3 unexcused absences will result in an automatic 2 letter grade drop.

  · > 4 absences, you should seriously consider dropping the course.

• Attitude: As stated above, a major goal of the course is to teach students how to perform biochemical experiments efficiently, not to see how fast one can complete a given day's assignment. The reality of conductiong an experiment is that despite our best efforts, sometimes they do not work out the way we expected (or hoped). Therefore, patience, perseverance, and, most importantly, careful preparation are all required to obtain high quality data that can be interpreted in a meaningful manner. Because of these requirements, and the fact that experiments will be performed in groups, (see Format of Course, above), two stringent requirements of the students will be made:

  1. Students are expected to arrive promptly at the beginning of the class. Habitual late arrivals, without a valid excuse, will have a very negative impact on one's grade.

  2. Students are expected to come to each class prepared to perform the experiment. In order to achieve this goal, students are expected to read the introductory part of the assigned chapter as well as the Experimental Protocol(s) for that day's experiment. Some Protocols can be downloaded from the course website. Please consult the LABORATORY SCHEDULE for downloadable Protocols. Finally, students must turn in a Flow Chart (see below) for that day's experiment prior to commencing their laboratory work.

  These requirements will hopefully ensure that:

  1. Work is equitably shared between partners.

  2. Students have a good idea what they are expected to learn from the experiment, both in terms of the techniques used and data interpretation, as well as the procedure they will follow during the experiment.

  3. Experiments can be completed in the allocated time. This latter point is important because in biochemical research, as well as in this class, the results from one experiment (either an isolated protein, data, or knowledge of how to perform a specific task) are often important for the design and implementation of the next experiment. In this manner, research becomes a continuum of gaining knowledge about the biochemical system you are studying.

• On days when the experiments are finished before the end of the class period, we encourage the students to remain in the lab in order to begin their data analysis and to talk with the instructors about the data as well as the technical aspects of the experiment itself. Often, such informal discussions can be often be very helpful in furthering ones understanding of biochemistry.
• Again, although you will do a tremendous amount of work, both in the lab and at home, we believe you will have fun in the course, will learn a tremendous amount about how biochemical systems are studied, and will be very well prepared to work in a biochemistry reserach laboratory!

Scientific Literature

• Throughout the semester you will be given manuscripts from the scientific literature related to that week's experiment. As is the case for your textbook, you are expected to read the material in the papers PRIOR to coming to class because there may some information in the paper that you must be aware of in order to conduct the experiment.

Flow Chart

• In order to help you prepare for each lab, beginning with Experiment 1 a Flow Chart will be turned in to a TA PRIOR to beginning the experiment. There will be two parts to the Flow Chart: (1) You will give a short two or three sentence statement about what is the Scientific Goal of the experiment. This is perhaps the most important thing you can do the prepare, to understand the principle behind the experiment AND (2) You will have a detailed schematic or explanation, IN YOUR OWN WORDS, about what you will be doing that day. For an example of what we expect, click on FLOW CHART to see a printable example. Keep a copy for your own reference. The flow chart will comprise 10% of the grade for that experiment's lab report.

Lab Notebooks

• Keeping a well-organized and useful lab notebook is a learned art. While the researcher may employ some personal preferences, the format of the notebook usually follows some well-established guidelines, which we shall discuss in class. We suggest that students obtain sturdy lab notebooks from the bookstore (the big ones with the brown covers) with removable pages. During the course of semester, you will also be making plots of your data while you are collecting more data. While importation of data into various computer graphics programs and hard-copy output is common place today, we shall endeavor to be "old school" about such matters, i.e. you'll actually use graph paper and a ruler to make "hand" plots as you collect your data. For estimating the value for an intercept point, it is often easier to determine the value from "crude" hand plots than it is from computer printouts.
• Information that should be kept in lab notebook :

  1. Date of the experiment and lab partner.

  2. Purpose of the experiment.

  3. Your copy of the Flow Chart to follow during the experiment

  4. Concentrations of stock solutions of reagents. Often the actual supplier (e.g. Sigma or Aldrich), the catalog number, and Lot number are recorded.

  5. Any notes on what you did during the experiment itself (i.e. how much material weighed out, volumes added, etc.).

  5. Data collected during the experiment.

  6. Any cautionary notes (i.e. "I forgot to ....... ).

  7. Plots of data either from the spectrophotometers or hand plots made at the lab bench.

  8. Numerical data tables.

  9. Literature references.

• The quality of your lab reports will be very closely related to the thoroughness of the information you record in your notebook.
• Finally, it is worth noting that in academic research, a lab notebook is the "property" of the government agency funding the research (i.e. NIH, NSF, etc.), while in industry it is the property of the company, NOT the individual researcher! In this class, the instructors may ask to see your lab notebook at any time to determine if you are following the above guidelines.
• Last, but not least, the Instructional Staff will randomly conduct "Shake Tests" of your notebook. That is, we will pick up your notebook, give it a good shake and see what falls out. We will then kindly suggest that you begin to use a stapler or tape to PERMANENTLY affix material into the notebook.

Lab Reports

• A general guide book for scientific writing can be accessed at : BMB_Sci_Writing.pdf
• Laboratory reports will be written as if they are papers being submitted for publication to the journal Biochemistry. Specific instructions, for this journal, will be handed out in class. The format will be discussed in greater detail during the first laboratory meeting, however should be the following:
  • Title Page
  • Abstract
  • Materials and Methods
  • Results
  • Discussion
  • Figures
  • References
  • Supplementary Material (ie., Calculations)

A more detailed description of the format can be downloaded from: Lab_Report.pdf

• Because this will be a novel adventure for some, we will ease into the process of writing a complete lab report.
• In some cases, we will ask you to submit your data and answer questions posed in N&B (or in the downloaded protocol) instead of the formal report described above. Whether we ask you to turn in the questions or not, you are urged to answer all the questions found at the end of each chapter in N&B in order to test your understanding of the experiment. These questions might also assist you in writing your formal lab reports.
• Grading of Lab Reports: Lab reports will be critically graded as if they were manuscripts being submitted to a journal for publication. The intended goal early in the semester is to develop good scientific writing skills, thus students are expected to carefully look at comments made by the graders and incorporate suggested changes into subsequent lab reports. As the course goes on, the graders will become increasingly more critical of you lab reports. Reports may be turned in as hardcopy or via email as an Adobe Acrobat .pdf file.
• Grading of Late Lab Reports: The maximum grade for each lab report will be 10 points (with the exception of the alkaline phosphatase report, which is worth 50 points). Ample time will be given to write each report, therefore there is no excuse for late reports. Each day (including weekends) that a lab report is late will result in a 1 point (5 points for the AP manuscript) automatic decrease in the maximum possible grade. If you want to guarantee that you will not get an A in the class, then consistently turn in you Reports late!!!
• Cheating on Lab Reports: Working with you lab partner, or other students, in analyzing your data, trying to draw some conclusions about the data as well as interpretation of the data is NOT considered cheating. Copying someone else's Lab Report is considered cheating and is surprisingly easy to detect. A student caught cheating on Lab Reports (i.e. copying) will be dealt with as described below under CHEATING.

Class Presentations

There will be three types of presentations you will be called upon to give during the semester: Review of the previous laboratory class material, a review of a reference paper assigned to you during the alkaline phosphatase set of experiments, and a discussion of your current research or the research of a Biochemistry faculty member under whom you might want to do your Senior Research Thesis project. A more detailed explanation of the formats and goals of these presentations can be obtained by clicking on the links below:

• Review of previous laboratory class material.
• Review of alkaline phosphatase literature.
• Current reseach presentation.

Lab Equipment

• We have endeavored to obtain equipment that is commonly found in most modern biochemistry research laboratories, and in most cases, this equipment is expensive. In order to ensure that the equipment is kept in a functioning state, we shall place a strong emphasis on proper usage of all of the laboratory equipment. Accidents will happen, and it is important that the instructor staff be immediately notified if something does get broken. Careless handling of the devices used in the lab will not be tolerated.
• In order to minimize hoarding tendencies, the equipment necessary for the days experiment will be handed out for that lab and will be returned at the end of the lab. While some equipment will be issued to individual groups, many devices will be shared. In a working laboratory, specialized equipment is shared by everyone, which means that sometimes you will have to wait for your turn. While you are waiting, however, you can usually find something useful to do(a calculation, re-reading the protocal, etc.). You also need to be considerate of the next user. Always leave the equipment in a condition by which it can be immediately used by the next group. If you find the instrument in an unusable condition, contact one of the instructors immediately.
• Special note on the Cary 50 spectrophotometers: We have purchased very high precision UV-visible spectrophotometers that are interfaced with a PC. COLLECTION OF SPECTRAL DATA ALWAYS TAKES PRIORITY OVER DATA FITTING!! If you want to use the software for data fitting outside the normal course hours, please contact Dr. Hazzard.
• GAME PLAYING ON THE COMPUTERS WILL NOT BE PERMITTED!!

Lab Safety

• Every effort has been made to make sure that the experiments are conducted in a manner which poses the least threat to the safety of the students and staff. We shall cover lab safety procedures and what to do in case of an accident on the first day of class. Several rules will be rigorously followed:
  • If you are hurt or injured, immediately inform one of the teaching staff, no matter how insignificant you think the injury may be.
  • For life-threatening emergencies, dial 911 on the phone inside the prep room door.
  • Many of the experiments encountered in this course will require making dilutions of stock solutions. NEVER pipette any solution by mouth, no matter how harmless you might think it is!
  • Dispose of material (glass, pipette tips, PAGE, chemical waste, Ethidium Bromide containing gels and solutions) in their proper trash receptacles.
  • No drinking or eating in the lab.
  • If you have to leave the lab for any reason, WASH your hands.
• All students are expected to have a lab coat and safety glasses with side protectors (or goggles) for each class. When necessary, latex gloves will be issued free of charge.
• You will be informed of any potentially hazardous reagents or procedures that may be encountered in an experiment.

email  

• We encourage the use of email to ask questions. Questions and answers may be posted on the web anonymously. Your question may help other students, so please use this forum to ask questions.

Grading Policies

• Laboratory Experiment Reports and Homework (10 points per Report): There will be approximately 6 lab reports and 2 Homework assingments handed in during the semester in addition to the Alkaline Phosphatase manuscript (see below). One point will be deducted for each day the lab report is late (see Lab Reports above). The Due Date for Lab Reports will be given in class.
• Alkaline Phosphatase Manuscript (50 points): This report will cover approximately three weeks work and will represent a scientific journal caliber manuscript.
• Examination (50 points): There will be one 50 point examination covering material that is presented in the lecture and utilized in either performing an experiment or analyzing data. Any student who has carefully prepared themselves for the lab experiment (reading the chapter and preparing the flow chart), done a good job collecting and analyzing the data (lab notebook), and been thorough in their lab report should have no problem with these exams. Students are expected to take the exam at their scheduled times. Students will only be excused from an exam for illness or a death in the family. Written proof of the problem, such as a note from a physician, is required.There will be no make-up exams.
• Current Research Presentation (20 points): see information above under Class Presentations.
• Laboratory Notebook (5points): see above for details.
• Laboratory Performance Evaluation (5 points): Consider this a classroom "savings account". Each student will start with 100 points, which can be taken away for such things as habitually arriving late to class (without a valid excuse), excessive breakage of equipment, not taking an active part in performing an experiment with your partner, and an uncooperative attitude. Students will be warned about a specific problem before we begin to deduct points from this category. We fully anticipate that all students will have no problem receiving full credit at the end of the course.
• Final Course Grading.   We will not assign letter grades until the end of the course. The final grade will be determined based on the total points in the class, and will roughly correspond to a point total that relative to all the other scores is:

• Re-grading of Exams.   Requests for re-grading exam questions must be made in writing within two class periods after the return of exams. In your request, you should explain why your answer is correct. If you feel the resulting response from the grader is not satisfactory, a further appeal may be made to one of the instructors. Be aware that the entire test may be re-graded when a re-grade request is made.
• Cheating.  Cheating is disgusting, disrespectful, unnecessary, and will not be tolerated. Anyone caught cheating will fail this course and be subject to disciplinary proceedings as described in the Student Code of Conduct (outlined on page 15 of the 2003-2004 General Academic Manual). Potential outcomes from this include expulsion from the University. Changing your answer on a test after it has been returned, and requesting a re-grading of the exam, is cheating. We will copy exams to discourage this form of cheating, so don't do it! Save yourself the embarrassment, time, and hassle - Don't do it! Note: Working together with your lab partner or other students in the class or when preparing you Lab Report IS NOT considered cheating, in fact it is encouraged. However, copying verbatim anyones Lab Report is considered cheating and is VERY easy to detect. Have no doubt, we will "get in the face" of anyone suspected of cheating, before we hand the matter over to Administration.
• Students with Special Needs. Students requiring accommodation in testing or notetaking must notify Dr. Hazzard and must deliver to Dr. Hazzard the Disability Resource Center letter within the first two weeks of the course.