CH337 Biochemistry

for FA 2007

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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.


CH 337   Biochemistry


FA 2007 HO


Burns, Douglas M.


Associate Professor of Biology


--  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


Other Phone



Web Page

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

Semester Dates

20 August  -- 14 December, 2007

Class Days

MWF - with Labs (BI337L or CH337L on Wednesday & Thursday)

Class Time

10 -- 10:50 AM


CH318 and CH318L and/or the equivalent

Credit Hours


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 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 ( 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.
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Course Description:

       This is a junior level biochemistry course designed for biology and chemistry majors. (There is an accompanying laboratory course [BI337/CH337], but it is described on a seperate syllabus.) We will study the properties, structures, functions, and specific roles of proteins, enzymes, nucleic acids, carbohydrates, and lipids in biological organisms. We will examine the biosynthesis and utilization of these chemicals by living systems and develop an overall appreciation for the molecular processes that link energy production to biological application. 

Prerequisite:  CH 318 or permission of the instructor

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. Within the requirements of this course, the instructor will emphasize an organized interactive consideration of lecture material, readings, quizzes, projects, research papers, problem sets, examinations, internet websites, and similar exercises. Each student should strive to participate in class. In addition, course material will be applied and reinforced during laboratory exercises, and it is crucial that students attend and participate in each laboratory session 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 approximately 3 hours of study outside of class for each credit hour of class. Doing less will get you less. 
       In a science class, it is important that students transform main elements, themes, and concepts into their own words and thoughts. True knowledge apparently results from active construction/reformulation and repeated cross-referencing of new material to old (stored) material. This can only be done by the learner, and it is my job to entice you into doing this. Do not expect to succeed by simple memorization; building conceptual frameworks and internalizing new detail are essential skills in all college-level science course.

Learning Outcomes:
  Core Learning Outcomes

  1. Describe how structure and function relate in biological molecules
  2. Describe the flow of mass, energy and information in a cell in terms of biochemical pathways.
  3. Analyze the behavior of biological molecules using mathematical models.
  4. Compare biochemical pathways in prokaryotic and eukaryotic systems.

  Instructor Learning Outcomes
  1. Describe how catabolism is linked to anabolism.
  2. Compare the analysis of the different classes of macromolecule.
  3. Relate cellular function to chemistry and enzymatic function.
  4. Describe biological processes in molecular terms.
Core Assessment:

Create a review paper in the style of Annual Reviews in Biochemistry covering one biochemical or intercellular signaling pathway in a cell or cells. This paper should be at least 10 pages in length (using the attached Instructions to Authors) excluding figures and references. Information covered should include:

1. Step-by-step illustration of the biochemical or intercellular signaling pathway (CLO 1, 2).

2. Discussion of the general flows of the pathway (flow of information, flow of mass, flow of energy) and the logic underlying the pathway (why does this arrangement work well?) (CLO 1,2, 3).

3. Indication of key regulatory steps in the pathway and explanation of why this is a logical regulatory step (CLO 1, 2, 4).

4. Indication of how this pathway relates to the central metabolic pathway (glycolysis, TCA cycle, electron transport chain, oxidative phosphorylation) (CLO 2).

5. Discuss the commonalities and differences exhibited in this pathway in prokaryotes and eukaryotes (CLO 4).

6. What diseases or disease states are associated with defects in this pathway? If there is no literature, predict what would happen (indicate your rationale) (CLO 1, 2, 4).

7. Discuss how the disease states in 6 are differentially expressed in human populations (is there a difference in disease effect or prevalence based on age, sex, geographic location, environmental factors, ancestral origin, race…etc). What are the bases of these differences? If there appears to be no difference in disease effect or prevalence, discuss why.

8. Discuss methods used to combat the disease or approaches that are planned. How do/will these work?

Link to Class Rubric

Class Assessment:

        There will be 5 major lecture examinations, covering the 5 main units of this class (see class schedule). These exams are designed to total approximately 550 points. Exams will contain short answer, matching, and "long answer" questions, with some multiple-choice questions. An additional 50 points will come from home-work assignments, quizzes, or in-class exercises. These components provide a total of 600 points.
        In addition, a Final Core Assessment (see the preceeding discussion) will be in the form of a professional-quality review paper worth  150 points (and 20% of the overall grade in this course). therefore, approximately 750 total points are possible in this course.  
        There will be no extra-credit assignments in this class.


         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%.

Late Submission of Course Materials:

          Homework is due at the start of an assigned class period. 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:

        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 Schedule is Tentative and still subject to change at the Instructor's discretion.






                Topic(s) for the week




1.Wk of 8/20

Intro/Overview -Amino acids – Proteins & Protein Structure




2.Week of 8/27

Protein Function – Enzymes –Enzymatic Catalysis


7 -8 -9

3.Week of 9/04

Enzymatic Catalysis -Enzyme Regulation –  


9 -10

4.Week of 9/10

Exam I-9/10 - Lipids &Membranes – Carbohydrates


exam 12 -11

5.Week of 9/17

Carbohydrates -Basic Concepts and Design of Metabolism


11 -15

6.Week of 9/24

-Glycolysis & Gluconeogenesis -The Citric Acid Cycle


16 -17

7.Week of 10/01

Exam-II -10/01 – Membrane Proteins – Oxidative Phosphorylation


Exam -13 -18

8.Week of 10/08

Oxidative Phosphorylation – Calvin Cycle/Pentose Shunt - Glycogen


18 -20/21

Week of 10/15

Fall Break – 10/15 through 10/19



9.Week of 10/22

Glycogen Metabolism – Fatty Acid Metabolism


21 -22

10.Week of 10/29

Exam III -10/29 - Protein & Amino Acid catabolism/Amino acid biosynthesis


Exam -23/24

11.Week of 11/05

Nucleotides  -- DNA and RNA Synthesis and Function


25/4 – 28 - 29

12.Week of 11/13

Details of DNAàRNAàProtein Biosynthesis


29/30 - 30

13.Week of 11/19

Exam IV -11/19 –  Amino Acid Metabolism & Protein Turnover


Exam -23/24

14.Week of 11/26

Lipids & Steroids – Integration of Metabolism


26 - 27

15.Week of 12/03

Signal Transduction -Control of Gene Expression




   All TERM PAPERS due by 12/03/07



Week of 12/10

Finals WeekExam V at time scheduled for Final Exam








A projected schedule of Laboratory Exercises will be passed out during the first Laboratory meeting.






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 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 (lecture and/or lab)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: .
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.


CompetencyExceeds Expectation (3)Meets Expectation (2)Does Not Meet Expectation (1)No Evidence (0)
Uses 7 or more sources Uses 4 to 6 sources Uses 3 to 5 sources Uses fewer than 3 sources 
Identifies and analyzes 7 or more of the items in the assignment Identifies and analyzes 4 to 6 of the items in the assignment Identifies and analyzes 3 to 5 of the items in the assignment Identifies and analyzes fewer than 3 of the items in the assignment 
Assesses the outcomes of 7 or more of the assignment items Assesses the outcomes of 4 to 6 of the assignment items Assesses the outcomes of 3 to 5 of the assignment items Assesses the outcomes of  fewer than 3 of the assignment items 
No factual errors 1 to 2 factual errors 3 to 4 factual errors 5 or more factual errors 
Demonstrates mastery of 7 or more of the assignment items Demonstrates mastery of 4 to 6 of the assignment items Demonstrates mastery of 3 to 5 of the assignment items Demonstrates mastery of fewer than 3 of the assignment items 
Effectively incorporates 7 or more sources to support thesis Effectively incorporates 4 to 6 sources to support thesis Effectively incorporates 3 to 5 sources to support thesis Effectively incorporates fewer than 3 sources to support thesis 
Whole Artifact                                                                                                                                                                                                                                             
No errors in writing conventions 1 to 3 errors in writing conventions 4 to 6 errors in writing conventions 7 or more errors in writing conventions 
Contains no errors in the following paper format items: -Annual Review of Biochemistry format –Length -Page numbers -Works cited-Internal documentation Contains only 1 error in the following paper format items: -Annual Review of Biochemistry format –Length -Page numbers -Works cited -Internal documentation Contains 2 to 3 errors in the following paper format items: -Annual Review of Biochemistry format –Length -Page numbers -Works cited -Internal documentation Contains 4 or more errors in the following paper format items: -Annual Review of Biochemistry format –Length -Page numbers -Works cited -Internal documentation 
Exhibits an awareness and concern for contemporary items Exhibits an awareness or concern for contemporary items Exhibits some awareness and concern for contemporary items Exhibits no awareness or concern for contemporary items 


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Last Updated:8/17/2007 12:21:30 PM