Spring 2012 Course Syllabus

“Your worth as a human being is not determined by how much, or how little, Biochemistry you know!”

The late and beloved Regent's Professor Michael A. Wells

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 

• Our purpose is to serve as your guides as you begin to open your eyes to the wonders of biology as viewed from the molecular world.  This is a very exciting time to be studying Biochemistry because so many important discoveries are being made each day. If you diligently work at the course material, you will be able to share in the excitement by learning how biochemistry is actually done!
• The first 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 or for students currently working in labs to more fully understand the theories underlying the methods they are using on a daily basis.
• The second 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. Most importanly there is to be no mental disconnect between Bioc 462 and Bioc 463A!
• The final goal is to have some fun learning, because if biochemistry is not fun, you have chosen the wrong major!

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, Ballou, & Benore (NB&B) textbook.

Protocols for Experiments

• Some 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 course homepage or the Laboratory Schedule 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

• Required: Fundamental Laboratory Approaches for Biochemistry and Biotechnology; 2nd Ed. (2010) Alexander J. Ninfa, David P. Ballou, and Marilee Benore, John Wiley&Sons, Inc., Hoboken, N.J. (required).
• Textbook web site: www-personal.umich.edu/~aninfa/book/index.html
• Optional: Biochemical Calculations, 2nd Edition (1976) Irwin H. Segel, John Wiley and Sons, New York. This book, though dated, is highly recommended for those who are contemplating going to graduate school or who desire to tutor biochemistry, because the greatest problem students run into is the math of biochemistry.

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 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.
• A warm sweater, sweat shirt, or jacket: Optional. The lab does get cold during the winter due the highly ineffective heating/cooling system.

Course Format 

• Laboratory lecture: The purpose of the lecture is to familiarize the students with the theory behind the technique that will be investigated as well as providing any special precautionary information about the protocol for the experiment.
• Laboratory exercise: On special occasions, we shall use the entire time period 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 if the need arises. In the event of personality clashes, we will redistribute people. 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: In most cases, repeating an experiment can be logistically difficult, therefore it will not happen.
• Overall: In the first two-thirds 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 future experiments, therefore attendence is absolutely mandatory (see below). Strange as it may seem, most students actually look forward to coming to class!

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 in knowing how to perform a given laboratory technique. For this reason and with NO EXCEPTIONS, no one will be allowed to register for the class after the first experiment. 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:

  We will determine the actual grade you would have obtained based on your cumulative score. Then for:

• 2 unexcused absences your grade will automatically result in a1 letter grade decrease.

• 3 unexcused absences your grade will automatically result in a 2 letter grade decrease.

• 4 absences, drop the course.

• In the advent of a prolonged medical issue forcing missing several classes, the student will be stringently urged to withdraw from 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 conducting an experiment is that despite our best efforts, sometimes they do not work out the way we expected (or hoped). Furthermore, RARELY is the equipment or instrumentation at fault! 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 lecture. Habitual late arrivals, without a very very good excuse, will have a very negative impact on one's grade. A late arrival will be considered an 1/2 day unexcused absence.

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 them. Finally, students must be able to produce at the instructors request a Flow Chart (see below) for that day's experiment prior to commencing their laboratory work. Failure to be able to do so will result in the student being told to leave the class room (i.e. = 1 unexcused absence day).

3. Students are expected to be actively engaged in the lab exercise and not sitting passively letting others do the work. The contrary is also expected - overly domineering students will be told to take a back seat and allow others to learn as well.

4. In order to facilitate writing your Lab Report AND being prepared, TA's will circulate through class on Thursday making sure that you analyzed your data from the previous Tuesday class. Failure to provide this information will prove to be very detrimental to your standing in the class.

5. Lab Reports are the primary way for us to access comprehension of the course material. Failure to turn in the first two lab reports will result in an immediate ADMINISTRATIVE DROP.

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.

• Finally, the instructional staff's primary responsibility is to help you understand the course material. We can not address your problems if you do not ask for help, so PLEASE seek help before you fall behind. Trying to catch up is almost impossible in this foundational course!

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. You will be asked questions in class about the material and a blank stare or "I didn't read it" response is not acceptable.

Lab Notebooks (see Sec. 1.5 in NB&B)

• 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 might 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.
• Failure to obtain and use a lab notebook (and we are NOT talking about lap tops!) will result in an immediate 2 point deduction from each lab report.
• 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. When available 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 (especially for those who foolishly wait until the last minute).
• 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.

Quizzes (variable points)

• In order to make sure you come to class prepared, we will have frequent unannounced quizzes throughout the semester, the value will vary from six to ten points per quiz.
• The material covered will include information from the lecture notes and the protocols. You will also be held respoonsible for showing evidence that you analyzed the data from Tuesday's lab.
• Quizzes will begin promptly at 8 am and 1 pm, if you come in after the quiz has begun, you will not be able to scramble and turn something in.

Flow Chart

• In order to help you prepare for each lab, beginning with Experiment 1 you will need to prepare a Flow Chart 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 (not the educational goal) of the experiment. This is perhaps the most important thing you can do the prepare, to understand the principle behind the experiment.
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 Instructional Staff will randomly check to your Flow Charts. Failure to produce a Flow Chart will result in being told to leave the room and not return until you can provide one.

• Failure to have a Flow Chart for each experiment will result in a mandatory 2 pt. deduction from your lab report.

Lab Reports (see Sec. 1.6 in NB&B) (20-30 pts each; Final AP report = 100 pts)

• THIS COURSE IS NOT A SPECTATOR SPORT! FAILURE TO TURN IN EVERY LAB REPORT FOR THE FIRST FOUR WEEKS OF THE COURSE WILL RESULT IN AN ADMINISTRATIVE DROP!
• General information about writing scientific papers is given under Lab Report and Scientific Writing Tips on the course homepage.
• A more descriptive explanation on the format and ways to organize ones thoughts can be downloaded from: Lab_Report.pdf.
• For "full blown" Reports, we will follow the Instructions to Authors for the journal Biochemistry, which will be handed out in class (see below).
• Lab Reports will typically be due the Tuesday after completion of the previous week's experiments.
• Because this exercise will be a novel adventure for some, we will "ease" into the process of writing a complete lab report:

1. Initially we will provide you with detailed information on presenting your data in the form of graphs or plots, and guide you in writing a bried explanation of the data. Often there will be questions posted at the end of the protocols that you will have to answer and turn in with your lab report. Sometimes we will ask you to answer questions posed in NB&B. 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 NB&B in order to test your understanding of the experiment. These questions might also assist you in writing your formal lab reports.
2. As the semester progresses, you will be expected to have the intuition and experience to determine what should be included in your report with respect to data, written results, and the discussion.
3. At this point we will distribute Instructors to Authors from the journal Biochemistry. This will become your guide for writing a peer reviewed journal-like manuscript, which will prove very useful for your Senior Research Thesis. Specific instructions for this journal will be handed out in class at which time the specifics of the format will be discussed in greater detail. The overall format will be:

• Title Page
• Materials and Methods (sometimes)
• Results
• Discussion
• Figures
• References
• Supplementary Material (ie., Calculations)

• Grading of Lab Reports: The experimental portion of the Lab Report will be worth 20 points; supplemental questions will be worth 2 points each. Typically the Reports will be turned in the Tuesday after completion of the previous week's experiment. Waiting until Monday night to begin writing your Report will prove disastorous! Therefore, the instructional staff will circulate throughout the room on Thursday in order to verify that you have plotted your data from the previous class. Failure to do so will have deleterious results! In lieu of an exam, the Reports will be very critically graded as if they were manuscripts being submitted to a journal for publication. To that end, since the intended goal early in the semester is to develop good scientific writing skills, 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. Since you are all University juniors or seniors, there is absolutely NO EXCUSE for spelling and grammatical mistakes. They are a sign of laziness, a lack of pride in the product you are turning in, and most likely, waiting until the last minute to compose the Report. TA's will be directed to severely deduct points for these types of mistakes such that despite the fact you have excellent data and a brilliant interpretation, you may get no points on your Lab Report due to these types of errors! Reports must be turned in as hardcopy. Reports may be double sided and no more than two figures per page (printing more figures per page will reduce their size to the point where they are too difficult to evaluate).
• Grading of Late Lab Reports: Each day (including weekends) that a lab report is late will result in a 2 point (10 points for the AP manuscript) automatic decrease in the maximum possible grade. No lab Reports will be accepted after Friday on the week the Report was due. If you begin analyzing your data the day of the experiment, there is ample time to write each report, therefore there is no excuse for late reports. Data kept over many semesters and many classes clearly indicates that students who chronically turn in late lab reports will not do well in this course.
• 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 (and YES, some have been stupid enough to try!) on Lab Reports (i.e. copying) will be dealt with as described below under CHEATING.

Homework (20 pts.)

Periodically, homework will be assigned in lieu of, or in addition to, your Lab Reports. These assignments will be due on Tuesday at the beginning of class.

Molecular Graphics

You will be required to become familiar with the use of the molecular graphics programs Jmol, PyMol, and Cn3D this semester, utilizing molecular graphics to describe and discuss your results in your Lab Reports. Links to a variety of different websites dedicated to molecular graphics can be accessed through the Molecular Graphics Project page. More detailed instructions about this material will be available as the semester progresses. For the spring 2012 semester, disregard any information about the Molecular Graphics Project itself.

Special Research Project

At the end of the semester each lab group will participate in a guided inquiry Special Research Project that is scientifically based upon results from an earlier experiment. Choices for experiments can be made from the list provided on the SPR page or from an acceptable proposal made by your group. There will be no lectures or posted protocols for these experiments; rather it is the responsibility of each student (and group) to be familiar with the techniques that will be employed by examining the scientific literature. This project will span three days, allowing for fine tuning of each group's experimental approach. After the experiments have been completed, each group will make a brief oral Powerpoint presentation of their results to the entire class. The data and conclusions for this Project will be included in your final AP manuscript. Data from the previous semester's class will be provided to serve as a basis for the current semester's projects and the current semester's data will be provided to the following semester's classes, therefore this project will represent a continuing research project unique to Bioc 463a.

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 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 instructional staff be immediately notified if something gets broken. Careless handling of the any device 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.
• Protective eye wear is mandatory every lab and will be handed out at the beginning of the semester.
• Lab coats are optional.
• Nitrile protective 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 (20-30 points per Report; 20 points per Homework): 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). See Lab Reports above for a detailed explanation. Experimental part of Lab Report will be worth 20 points. Each question will be worth 2 points.
• Alkaline Phosphatase Manuscript (100 points): This report will cover approximately four week's work and is expected to be of the highest caliber, similar to what one would submit for your Senior Thesis or to a scientific journal, following the same format given in the Instructions to Authors for the journal Biochemistry.
• Homework (Varies): There will be a minimum of two homework assignments during the semester.
• Quizzes (Varies).
• SPR Presentation (20 points): see SPR material.
• Current Research Presentation (50 points): see information above under Class Presentations.
• 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:

• Cheating.  Cheating is disgusting, disrespectful, unnecessary, and simply STUPID! It 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 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. We make ever effort to accomodate the needs according to the ADA criteria.