Spring 2003

CH 314 BIOORGANIC CHEMISTRY

REFERENCE: Organic Class Notes and Any Introductory Organic Text.
 
 

EVALUATION:

Mid-term Take-Home Exam	20%
Library Projects	20%
Internet Projects	20%
Class Participation & Group Assignments	20%
Final Exam	20 %

COURSE OUTLINE:

I.   Enzymes as Catalysts: What do they do?

     A.    Rate Acceleration

     B.    Reaction Specificity

II.  Enzymes as Proteins: What do they look like?

     A.    Amino Acids

     B.    Protein Structure:

1.   Primary Sequence
2.   Secondary Structural Features
3.   Tertiary Structure
4.   Quaternary Structure

      A.   Proximity Effects

      B.   General Acid-Base Catalysis

      C.   Covalent Catalysis

      D.   Metal Ion Effects

      E.   Coenzymes in Enzyme Catalyzed Reactions

IV.  A Mechanistic Look at Enzymes in Metabolic Pathways: What can they accomplish?

      A.   Glycolysis

      B.   Tricarboxylic Acid Cycle

V.    Approaches to Studying Enzyme Catalyzed Reactions: How do we learn about them?

       A.   Isotope Tracers

       B.   Detection or Isolation of Intermediates

       C.   Kinetic Studies

1.     Steady-State Kinetics
2.     Inhibitor Studies
3.     Site Specific Mutagenesis
4.     Kinetic Isotope Effects

       A.   Nicotinamide Coenzyme Models

       B.   Heme Enzyme Models

VII.  Chloroperoxidase: Undergraduate research on an enzyme catalyzed reaction.
 

Approximate Schedule of Events

TEXT: An Introduction to Enzyme and Coenzyme Chemistry, by Tim Bugg, Blackwell Science, London 1997

REFERENCE:  Organic Class Notes and Any Introductory Organic Text.

COURSE GOALS:

CHEM 314 is an upper-level chemistry course that focuses on the applications of chemistry to biological systems (living organisms).  Since the academic area termed bioorganic chemistry is ill defined so it involves many more topics than could be reasonably considered in one semester.  Thus this course will focus primarily on protein structure and functions of catalytic proteins, enzymology.  Enzymology is my particular area of interest.  After we have developed our understanding of the fundamentals of enzymology, we will spend a few classes considering some of the results of my undergraduate research program over the last 20 years.  Hopefully, your experience in this course will give you some appreciation of how enzymes can take advantage of fundamental physical and chemical interactions to catalyze the specific organic reactions necessary to maintain the life in organisms.

EVALUATION:
 

Mid-term Take-Home Exam  Library Projects Internet Projects Class Participation & Group Assignments Final Exam

20  % 20  % 20  % 20  % 20  %

STUDY GROUPS:

Class Organization and Daily Assignments: To promote preparation for class and discussion in class, you have each been assigned to study groups.  In general each new topic or concept that you encounter in this class will be presented to your group as a series of questions or tasks.  Usually an assignment will consist of a few leading questions.  To answer the questions you will usually need to do research.  Thus, you will be required to work as a group to find information and devise what you believe to be reasonable responses, interpretations or other analyses.  These group analyses will then be shared with the class and we will work together to settle differences and come to a consensus on how best to deal with the material.  The course structure encourages you to take responsibility for and an active part in your education.

Group Composition and Dynamics: Because the groups are small, two or three students, there seems to be no need to assign specific roles to individuals. However, you will need to develop a plan for sharing duties and responsibilities in preparing for class. The memberships of the groups may change during the semester.

Tuesday Problem Sessions:
The Tuesday class meeting will be dedicated to a series of Internet exercises and projects.  Each week for the first few weeks there will be some exercises to get you accustomed to searching for information and software on the internet.  Later in the semester you will have two more extensive projects to complete.  The projects will account for 20% of your course grade.

Collaboration and Academic Honesty:
Collaboration among students in class and in preparation for class discussion is generally encouraged and required for most classes.  Educational research indicates that students learn best when they engage in discussions and analyses of class material with their peers.  However, the final version of all written work submitted for evaluation must be prepared without consultation with other students.  To be fair to all students in the course and to assure maximum learning for each student, we follow all the guidelines for academic honesty spelled out in the Moravian College Student Handbook 2002-2003 (pages 50-56).  Particularly relevant passages are excerpted on the following page.
 

Academic Honesty at Moravian College

Academic integrity is the foundation on which learning at Moravian College is built. Moravian College expects its students to perform their academic work honestly and fairly. In addition, a Moravian student should neither hinder nor unfairly assist the efforts of other students to complete their work successfully. The College's expectations and the consequences of failure to meet those expectations are outlined below.
In an academic community, students are encouraged to help one another learn. In fact, because no two students learn in exactly the same way or take exactly the same things away from a lecture, the College encourages students to study together. The boundaries on what is or is not acceptable work may not always be clear; thus, if at any point in academic work at Moravian the student is uncertain about his or her responsibility as a scholar or about the propriety of a particular action, the instructor should be consulted. The list below is not to be considered complete but rather covers the most common areas of concern. In general, students should be guided by the following principles.

Plagiarism

A major form of academic dishonesty is plagiarism, which the College defines as the use, whether deliberate or not, of any outside source without proper acknowledgement. While the work of others often constitutes a necessary resource for academic research, such work must be properly used and credited to the original author. This principle applies to professional scholars as well as to students. An "outside source" is any work (published or unpublished) composed, written, or created by any person other than the student who submitted the work. . . .  All work that students submit or present as part of course assignments or requirements must be their original work unless otherwise expressly permitted by the instructor. . . .  When students use the specific thoughts, ideas, writings, or expressions of others, they must accompany each instance of use with some form of attribution to the source. Direct quotes from any source (including the Internet) must be placed in quotation marks (or otherwise marked appropriately) and accompanied by proper citation, following the preferred bibliographic conventions of the department or instructor. . . .  Student ignorance of bibliographic convention and citation procedures is not a valid excuse for having committed plagiarism. . . .  A student may not present oral or written reports written by others as his or her own work. . . .  You may not use writings or research obtained from any other student previously or currently enrolled at Moravian or elsewhere or from the files of any student organization (such as fraternity or sorority files) unless expressly permitted to do so by the instructor. . . .  Students must keep all notes, drafts, and materials used in preparing assignments until a final course grade is given. . . .  All such materials must be available for inspection by the instructor at any time.

Cheating

Students may not submit homework, computer solutions, lab reports or any other coursework prepared by, copied from, or dictated by others. If the student is employing the services of a tutor (whether from the College community or elsewhere), the tutor may not prepare the student's work for class.

Students may not provide or receive unauthorized help in taking examinations, tests, or quizzes or in preparing any other performance requirements for a course. Such restrictions are illustrated by but not limited to the following: Using unauthorized material in an examination, test, or quiz.

Using crib notes in any form, regardless of who prepared them.

Using calculators or any other hand-held electronic devices unless authorized by the instructor.

Using e-mail or text messaging during any exam without the permission of the instructor.

Stealing, using or transmitting in writing, electronically, or verbally, actual examinations, tests, quizzes or portions there of prior to or during an exam.

Reading or observing another's work without his or her consent, whether it be on paper, electronically, or in any other form.

Soliciting or using a proxy test-taker or acting in that capacity.

False Testimony

Students may not submit or present a falsified excuse for an absence from an examination test, quiz, or other course requirement either directly or through another source.
Students may not falsify laboratory results, research data, or results. They may not invent bibliographical entries for research papers, websites, or handouts. They may not falsify information about the date of submission for any coursework.
 

Tuesday Problem Sessions: The Tuesday class meeting will be dedicated to a series of internet exercises and projects. Each week for the first few weeks there will be several exercises to get you accustomed to searching for information and software on the internet, downloading useful software, and using the some specific packages that are use to explore biomolecular structures. Your grade on these activities will be based upon reports on specific tasks. The projects will account for 20% of your course grade.