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BI 337L Biochemistry Laboratory
Burns, Douglas M.


Mission Statement: The mission of Park University, an entrepreneurial institution of learning, is to provide access to academic excellence, which will prepare learners to think critically, communicate effectively and engage in lifelong learning while serving a global community.

Vision Statement: Park University will be a renowned international leader in providing innovative educational opportunities for learners within the global society.

Course

BI 337L (and CH 337L)   Biochemistry Laboratory

Semester

FA 2007 HO

Faculty

Burns, Douglas M.

Title

Associate Professor of Biology

Degrees/Certificates

--  Ph.D. in Molecular Biology, Vanderbilt University
--  B.A. (Honors) in Biological Sciences, University of Missouri -Columbia
--  Postdoctoral Training in Biochemistry & Endocrinology, Case Western Reserve University School of Medicine

Office Location

101A  Science Hall

Office Hours

2-4pm, M; 12-1 pm, T. 12-1pm R;  and 1-3:00, F

Daytime Phone

816-584-6592

Other Phone

none

E-Mail

dburns@park.edu

Web Page

None at this time. Look to E-companion (at parkonline.org) for postings.

Semester Dates

20 August  -- 14 December, 2007

Class Days

Labs on Wednesday -- with supplemental time on Thursday (when necessary)

Class Time

1:50 -- 4:40 pm

Prerequisites

CH318 and CH318L and/or the equivalent

Credit Hours

3:0:3


Textbook:
Biochemistry by Berg, Tymoczko, & Stryer, 6th edition, 2006, WH Freeman & Co. New York, NY (ISBN: 0-7167-8724-5). This textbook will provide the basis for all the material covered in lecture class or laboratory class.

Textbooks can be purchased through the MBS bookstore

Textbooks can be purchased through the Parkville Bookstore

Additional Resources:
         Additional information, informational links, suggested readings, and supplemental lab exercises will be presented in class or online as they become available. All official class announcements and outlines will be posted on the E-Companion site (www.parkonline.org). It is therefore crucial that each student find and learn how to use this important site. The instructor is more than willing to help, but it is the responsibility of each student to make certain that they get the posted information.

McAfee Memorial Library - Online information, links, electronic databases and the Online catalog. Contact the library for further assistance via email or at 800-270-4347.
Career Counseling - The Career Development Center (CDC) provides services for all stages of career development.  The mission of the CDC is to provide the career planning tools to ensure a lifetime of career success.
Park Helpdesk - If you have forgotten your OPEN ID or Password, or need assistance with your PirateMail account, please email helpdesk@park.edu or call 800-927-3024
Resources for Current Students - A great place to look for all kinds of information http://www.park.edu/Current/.


Course Description:
            This is a junior level biochemistry laboratory designed for biology and chemistry majors. Laboratory applications will be focused on developing biochemical techniques, but will also expand on study of the properties, structures, functions, and specific roles of proteins, enzymes, nucleic acids, carbohydrates, and lipids in biological organisms. (A very simple example of this idea would be to study the abilities of certain amino acids to function as biological buffers at the same time that students learn how to correctly use a pH meter.)
        Emphasis in most lab exercises will be on hands-on experience with the common modern techniques of wet-bench biochemistry. These techniques will include: dilution/pipetting, making buffered solutions suitable for biochemical applications, native and denaturing systems of electrophoresis, staining and analysis of protein and nucleic acid, enzymatic analysis, enzyme purification, western-blots, PCR methodology, and similar.

Educational Philosophy:

       Learning is an active and interactive process. Ideally, it would best be promoted by a combination of questioning and feedback involving each student -- followed by direct hands-on application of the principles and processes. Within the requirements of this course, the instructor will emphasize an organized interactive consideration of course material, wh;ich may include readings, quizzes, projects, problem sets, examinations, internet websites, and routine wet-bench exercises. 
        Due to expenses and availability of equipment, students will need to work in groups of 2 or 3. Each student should strive to participate within their laboratory group, because you will learn very little if you are not actually involved. Put another way -- it is crucial that students attend and participate in each laboratory session.  
         This lab will feature both theory and practical hands-on techniques. One supplements the other, and both most go together to train you to be technically competent and capable of getting a job in someone's laboratory. Learning requires actual work; it is a real job. Rigor leads to achievement, and practice familiarizes you with course materials. Thus, each student should expect to spend the entire time in each lab session. Doing less will get you less.
 

  Instructor Learning Outcomes

  1. Supplement bichemistry topics with hands-on application.
  2. Develop the basic set of wet-lbench lab techniques for biochemistry.
  3. Understand the theory behind practical application of native and denaturing methods of electrophoresis for proteins and nucleic acid.
  4. Purify and characterize 1 or more enzymes.
  5. Learn basic characterization of cell expression patterns via two-dimensional electrophoresis (the "poor man's proteomics").
Class Assessment:

         This is a laboratory and hands-on work will be a priority. The total number of points possible for this semester in lab is approximately  450 points.   
         LABORATORY NOTEBOOK:  You are required to keep a laboratory notebook for Biochemistry Lab in a standard composition book (100 pages or so, bound with cover). You should take rough notes, schema, and observations while in laboratory and then use these data to complile an organized professional-quality Laboratory Report entered into the pages of your bound Lab Notebook. Each Laboratory Report (or Project Report) should be organized so as to have an Introduction (explaining the purpose or the hypothesis being examined), a Summary/Abstract (that contains a Rationale statement explaining the theory or technique or scheme that enables the particular exercise/measurement/project), a detailed Methods & Materials (explaining what you did),  a Narrative/Results section (wherein results and measurements are described and tabulated), and a Conclusion  section  wherein results are interpreted and discussed, conclusions are made, and new ideas are put forward.  You will always be graded on the completeness, legibility, organization, and content of ;your Labratory Notebook. These will be collected and examined at least twice during the semester and on December 10th at the beginning of Finals Week. Each laboratory examination will be worth 100 points -- making a perfect Lab Book worth 300 points during the semester. 
           Exercises and Projects in the Lab Book: Our exercises will start at a simple level and progressively become more complicated as the semester develops. There are a number of laboratory exercises that will be graded simply on the degree of completeness,"utility," and overall quality of the notes found within the notebook.
         In addition, each group will also have 1 or 2 extended projects that must be completed before the end of the semester; these will be explained within the first few weeks of the semester. Due to various limitations, not every group will be pursuing the same project during the later stages of the course. However, all possible consideration has been given to making each project similar in difficulty to the others. Each project is assigned a worth of 50-points.
          EXAMINATIONS over course content:  There will be a mid-term (at the beginning of class on October 10th) and a final exam (during Finals Week) in this course over the lab exercises and discussions. Each exam will be worth approximately 50-points, for a total of 100 points. 
      

Grading:

         It is not anticipated that this class will be graded on a curve. Instead, a traditional grading scale will be followed with: greater than 89.9% being an A, greater than 79.9% being a B, greater than 69.9% for a C, greater than 59.9% for a D, and less than 59.9% being an F. Your cumulative percentage in the class is simply your accumulated points divided by the points possible and then multiplied by 100%.
       Laboratory assignments and exams are set out as described in the preceeding section.

Late Submission of Course Materials:

          Homework and laboratory assignments are due at the start of class on the assigned date. Work will not be accepted after the stated deadline without penalty -- except under only the most severe of extenuating circumstances or prior arrangements recorded in writing. Any such emergency must be documented by specific written evidence -- which will then be judged by the instructor as to its acceptability. Nothing else will work as an excuse.
        Late homework and assignments (including lab notebooks when called in for review or lab projects with a dated deadline) will be reduced in credit by 25% for each day that the work is late. Students missing class due to participation in athletic or other university-sponsored events must turn in all due assignments PRIOR to their expected absence (see below).

Classroom Rules of Conduct:

         This is a Laboratory course. Therefore, great care must be exercised by all students to follow the detailed Rules of the Laboratory that will be distributed to you on the first day of lab. In general, sandals should not be worn. If shorts are worn, then a lab coat must be worn over them (each student is responsible for buying their own). In most circumstances gloves and lab glasses must be worn while working with chemicals. Each group will be assigned an area on a laboratory bench, and they will be expected to keep this area clean and free of chemical spills and debris. Students must respect the fragility of delicate instruments and apparatuses,  and everyone is expected to calmly learn how to use all equipment before they rush ahead with an exercise. Inappropriate laboratory behavior will be immedidately addressed by the instructor.
              All students must follow the common rules of acceptable and courteous behavior while within class. There can be no disruptive or crude behavior during class, and students should be careful not to attend under the influence of an intoxicant of any sort. Students should prepare in advance for each class and expect to be called on from time to time to make the class more interactive.
        Disruptive or intoxicated behavior will result in removal of the student from the class and a recorded absence. Notable problems will be reported to the Dean of the College and the University Provost so that suitable discipline can be officially determined.
       All cell phones, CD players, iPODs, beepers, bells, whistles, gongs, and video devices should be turned off during class time. Do not use laptop computers, cell phones, PDAs, or othere commication devices in class during an examination or quizz. 

       ENROLLMENT STATUS OF THE STUDENT:  This is solely the responsibility of the student. Be certain to file the appropriate paperwork with the Registrar if you seek to change your status in this course. If you decide to drop, be careful to file the appropriate forms before the deadline; otherwise, not finishing the course, or inadequate attendance will result in an F. 

Course Topic/Dates/Assignments:

          This laboratory course accompanies Biochemistry BI337/CH337 but is organized as a separate course. Unfortunately, it will not always be possible to parallel the lab schedule with the lecture schedule.

               This Schedule is Tentative and still subject to change at the Instructor's discretion:
Week One:   Organization, forming Groups, Pipetting/Dilution exercises. Discussion of the amino acids
Week Two:  The pH meter and the amino acids, buffers & solutions used in bichemistry, making solutions
Week Three:  Determination of protein content, properties of proteins
Week Four:   Enzymes and Enzyme Assays; Exercises on Enzyme Kinetics
Week Five: Determining Carbohydrates. Properties of carbohydrates.
Week Six:  Chromatography of a protein. Principles and simple ion-exchange procedure.
Week Seven:  Principles of Electrophoresis and making Agarose or Polyacrylamide separation gels.
Week Eight:   Electrophoresis of proteins and DNA-- by native agarose gel  -- by native polyacrylamide gel
Week Nine:  50-point Mid-Term Exam.
           (then)  denaturing SDS polyacrylamide gel electrophoresis for analysis
Week Ten:   Purifying an Enzyme: Project One
Week Eleven:  Project One (cont'd) -- and monitoring progress through electrophoresis
Week Twelve: Purifying an Enzyme: Project Two
Week Thirteen: Project Two (cont'd) -- and monitoring progress by electrophoresis
Week Fourteen:  The Polymerase Chain Reaction and Principles of PCR Assay
Week Fifteen: Two-dimensional gel electrophoresis -- the "Poor Man's Proteomics"
Finals Week:   Finished Lab Notebooks are due;  50-point end-of-semester exam

Academic Honesty:
Academic integrity is the foundation of the academic community. Because each student has the primary responsibility for being academically honest, students are advised to read and understand all sections of this policy relating to standards of conduct and academic life.   Park University 2007-2008 Undergraduate Catalog Page 85-86
       Please do not share or copy answers for any assignment, including lab write-ups, exam answers, and lab projects. Students should never copy verbatim from books, manuals, or internet sources (see below). Do not  copy from someone else's exam paper or whisper answers to each other during exams. (Both students will receive a 0 for that exam.)

Plagiarism:
Plagiarism involves the use of quotations without quotation marks, the use of quotations without indication of the source, the use of another's idea without acknowledging the source, the submission of a paper, laboratory report, project, or class assignment (any portion of such) prepared by another person, or incorrect paraphrasing. Park University 2007-2008 Undergraduate Catalog Page 85
Please be careful not to plagiarize; we have several programs that will detect such behavior within the patterns of your written work.

Attendance Policy:
Instructors are required to maintain attendance records and to report absences via the online attendance reporting system.

  1. The instructor may excuse absences for valid reasons, but missed work must be made up within the semester/term of enrollment.
  2. Work missed through unexcused absences must also be made up within the semester/term of enrollment.
  3. Work missed through unexcused absences must also be made up within the semester/term of enrollment, but unexcused absences may carry further penalties.
  4. In the event of two consecutive weeks of unexcused absences in a semester/term of enrollment, the student will be administratively withdrawn, resulting in a grade of "F".
  5. A "Contract for Incomplete" will not be issued to a student who has unexcused or excessive absences recorded for a course.
  6. Students receiving Military Tuition Assistance or Veterans Administration educational benefits must not exceed three unexcused absences in the semester/term of enrollment. Excessive absences will be reported to the appropriate agency and may result in a monetary penalty to the student.
  7. Report of a "F" grade (attendance or academic) resulting from excessive absence for those students who are receiving financial assistance from agencies not mentioned in item 5 above will be reported to the appropriate agency.

Park University 2007-2008 Undergraduate Catalog Page 87-88
      It is MANDATORY that you attend all class meetings and all scheduled laboratories. Part of a university education is preparation for professional conduct in your future life. Attendance at work or graduate/professional school is mandatory -- if you wish to remain employed or enrolled.
    In addition, education is a cooperative effort, and you are as responsible for furthering the education of your fellow classmates and the instructor as the instructor is for educating you. Get in the habit of being here on time, for this is a behavior you will need to cultivate if you wish to succeed.

    Be advised that a student is always responsible for any class material, whether they are present in a particular class session -- or not. It is the responsibility of the student to obtain notes and any notice of assignments due or announcements made on their own.

     There are NO EXCUSED ABSENCES in this course for any reason (medical, personal, job-related, mechanical failure, death in the family, death of a beloved pet, death of ambition, and so forth). However, since personal emergencies may nonetheless occur during the semester, your first four (4) absences are free and will draw you no penalty.
    HOWEVER, with each additional absence past the first four, 5% will be deducted from the student's final overall grade for the course. Furthermore, eight (8) absences in a twice-a-week semester class is an excessive number, and you will automatically be given an F after you miss eight (8) lecture or lab sessions (for ANY reason).

    TARDINESS or LEAVING:  If you are more than 10 minutes late by my watch or just happen not to be present when the attendance sheet is passed around, you will be counted tardy even if you do attend the remainder of class. If you decide to leave class before we are finished, this will also count the same as a tardy. Two tardies constitute one absence, and this will count towards your limit of four.

      EXCEPTION FOR SCHOOL ACTIVITIES:  Athletes who miss class for an athletic event or contest or students who miss class due to  other school sponsored events will not be penalized IF AND ONLY IF THE INSTRUCTOR IS GIVEN WRITTEN NOTICE ONE WEEK IN ADVANCE -- AND -- BOTH WORK ASSIGNMENTS AND EXAMS ARE TAKEN BEFORE ACTUAL ABSENCE! This is the rule; please follow it.

Disability Guidelines:
Park University is committed to meeting the needs of all students that meet the criteria for special assistance. These guidelines are designed to supply directions to students concerning the information necessary to accomplish this goal. It is Park University's policy to comply fully with federal and state law, including Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act of 1990, regarding students with disabilities. In the case of any inconsistency between these guidelines and federal and/or state law, the provisions of the law will apply. Additional information concerning Park University's policies and procedures related to disability can be found on the Park University web page: http://www.park.edu/disability .
       Although you have the right to keep all conditions private, my desire is to help anyone who has any sort of trouble taking the class. If you come and talk with me about known problems, we can make certain that you are getting the help you deserve.

Copyright:

This material is protected by copyright and can not be reused without author permission.

Last Updated:8/17/2007 4:32:47 PM