Chemistry 124: Biophysical and Medicinal Chemistry
Syllabus Spring 2007
Course Description:
The chemistry by which nature interconverts the molecules of life obeys the same essential principles as reactions in the laboratory. An understanding of these common principles allows chemists to examine biological processes in molecular detail. In Biophysical and Medicinal Chemistry (CHEM 124) we will explore fundamental concepts in chemistry using case studies from biochemical research.
Through the lens of biophysical chemistry, we will discuss the assembly, structure, and interactions of biological macromolecules. And we will study how biological catalysts increase the rate of the reactions that enable life.
Drawing from concepts in biophysical chemistry and biochemistry, we will learn
how medicinal chemists discover and develop therapeutic chemicals into medicines.
And we will use examples from research in medicinal chemistry to examine the
interaction of small molecule medicines with their biological targets.
Instructor and Other Resources:
| Instructor: | Dr. John E. Hofferberth |
| Email: | hofferberthj@kenyon.edu |
| Office: | 312 Tomsich Hall |
| Office Hours: | Tuesday, Wednesday, Thursday, Friday 8-9 AM (or by appointment) |
| Class Times: | MWF, 9:10-10:00 AM |
| Text: | Chemistry, 8th ed, by Raymond Chang |
| Other Resources: | Math Skills Center; Allison Goldsmith |
Course Policies and Expectations:
| Tentative
Grade Scheme: |
The grading scheme for the course is based on the standard grade cut-offs:
The instructor reserves the right to adjust the grading scale by reducing the points required to earn a given grade at the end of the semester. Individual assignments and exams will not be 'curved'. |
||||||||||||||||||||||||
| Attendance: |
Your attendance at every lecture is expected. You will be permitted three unexcused absences. Every absence thereafter
will result in a grade reduction of 1/2 of a letter grade for the course.
You will be expelled from the course after six unexcused absences. |
||||||||||||||||||||||||
| Preparation: |
Strongly suggested study habits include: 1) Neatly recopying and annotating course notes with material from the text, course web page, and other resources. 2) Completing all assigned homework problems. 3) Keeping up with all aspects of the course and seeking help quickly if questions arise. You can get help on any assigned homework, view homework keys, and access laptops with course specific programs, 5 days a week, from the following resources: 1) The instructor (Tuesday, Wednesday, Thursday, Friday 8-9 am or by appointment) 2) The Math Science Skills Center (TBA; 207 Tomsich) 3) The student assistant for this course, Allison Goldsmith (MSSC hours TBA, 207 Tomsich) |
||||||||||||||||||||||||
| Suggested Problems: |
The best way to master any subject is to practice. A reading assignment and suggested practice problems will be indicated on the syllabus for each day of lecture. The practice problems will not be graded. However, working these problems is essential for your comprehension of the material. The suggested problems will appear on quizzes and exams.
|
||||||||||||||||||||||||
| Announced Quizzes: |
Announced quizzes will be given at the beginning of lecture on the dates indicated on the schedule (below). The announced quizzes will each be composed of a single homework question assigned since the last quiz. You will have 5 minutes to complete each quiz. There will be no make-up quizzes, however, your lowest quiz score for the semester will be replaced by your highest quiz score.
|
||||||||||||||||||||||||
| Group Projects: |
There will be two group projects assigned during the semester. You must select a group for the first project and remain with that group for the entire semester. Groups may have either 2 or 3 members. All group members will receive the same grade for the the projects. Work submitted after the due date will be penalized 3 points per day. Problem sets turned in more than 3 days after the due date will not be accepted.
|
||||||||||||||||||||||||
| Midterm Exams: |
Three midterm examinations will be given during the semester on the dates indicated on the syllabus. The examinations will be closed note and will not be cumulative. You will be given 50 minutes to complete each examination.
|
||||||||||||||||||||||||
| Final Exams: |
The final exam for the course will be cumulative and closed note. The exam will occur on on the date indicated in the schedule below in 101 Tomsich. You will be given 2 hours and 50 minutes to complete the final examination.
|
||||||||||||||||||||||||
| Academic Integrity: |
Academic integrity is expected in all aspects of this course. A detailed description of academic integrity and the College policy regarding academic dishonesty can be found in the "The Course of Study." |
Resources:
RPI Biochemistry of Metabolism
University of Alberta, Drug Database
Theoretical and Computational Biophysics Group, Univeristy of Illinois
Supramolecular Chemistry, Julius Rebek Homepage
KEGG Metabolic Pathway Database
Chemistry Skills Tests:
Tentative Schedule:
| Session | Date | Topic | Reading Sections (Suggested Problems) | Lecture Supplements | Work Due |
| 1 | 1/15 | Introduction to Biophysical & Medicinal Chemistry | |||
| 2 | 1/17 | Introduction to Medicinal Chemistry | |||
| 3 | 1/19 | Introduction to Medicinal Chemistry (Review Equilibrium) | 14.1-14.5 | ||
| 4 | 1/22 | Organic Chemistry Basics | 24.1 - 24.2 (24.13, 24.24, 24.25, 24.26, 24.66) | Quiz 1 (Avg. 4.2/5) |
|
| 5 | 1/24 | Functional Groups | 24.3 - 24.4 (24.31, 24.36, 24.39, 24.42, 24.60) | ||
| 6 | 1/26 | Thermodynamics | 18.1- 18.5 (18.9, 18.11, 18,12, 18.13, 18.14) | Notes-Vancomycin Case Study | |
| 7 | 1/29 | Thermodynamics | 18.6 - 18.7 (18.16, 18.18, 18.21, 18.24, 18.25, 18.28) | Notes-Optical Isomers of Drugs Case Study | Quiz 2 (Avg. 3.5/5) |
| 8 | 1/31 | Thermodynamics | Organic and Medicinal Practice Problems | Notes | |
| 9 | 2/2 | Thermodynamics, Coupled Reactions | (18.33, 18.34, 18.36, 18.43, 18.44, 18.79, 18.81, 18.85) | Notes | |
| 10 | 2/5 | Molecular shape, VB theory |
(Please review 10.1 - 10.2) 10.3 - 10.5 (10.27) |
Quiz 3 (Avg. 3.7/5) |
|
| 11 | 2/7 | Molecular shape, VB theory | Study! | ||
| 12 | 2/9 | Guest Lecture: Prof. Laura Furge |
P450 Enzymes | ||
| 13 | 2/12 | Exam I (Avg. 78/100) | |||
| 14 | 2/14 | Hybridization |
10.6 (10.30, 10.43, 10.88, 10.103, 10.45, 10.47, 10.51, 10.52, 10.57) |
||
| 15 | 2/16 | Molecular Orbitals |
|
Notes- Molecular Orbitals (I) | |
| 16 | 2/19 | Molecular Orbitals | (10.85, 10.87, 10.92, 10.93, 10.104) | MO Practice | Quiz 4 (3.2/5) |
| 17 | 2/21 | Molecular Orbitals |
|
||
| 18 | 2/23 | Molecular Orbitals, Intermolecular Forces | Degree of Unsaturation Practice | ||
| 19 | 2/26 | Intermolecular Forces | 11.1 - 11.3 (11.10, 11.11, 11.15, 11.18, 11.19) | Notes - Intermolecular Forces | Quiz 5 (3.7/5) |
| 20 | 2/28 | Intermolecular Forces |
|||
| 21 | 3/2 | Electrostatic Potential Maps, Phases Consequences of Intermolecular Forces | 11.8-11.9 (11.22, 11.24, 11.94, 11.103, 11.113) |
||
Spring Break |
|||||
| 22 | 3/19 | Implications of Intermolecular Forces | Lapinski's Rule Practice , 11.78, 11.80, 11.86, 11.88, 11.108 | Quiz 6 (Avg 4.5/5) |
|
| 23 | 3/18 | Interactions of Light and Matter |
Notes-Interaction of Light and Matter
|
||
| 24 | 3/20 | Interactions of Light and Matter | |||
| 25 | 3/26 | Exam II | |||
| 26 | 3/28 | Biomacromolecules, Nucleic Acids, Biophysical Analysis of DNA | 25.1, 25.3 and 25.4 (25.13-16, 25.19-24. 25.26-28, 25.30, 25.37, 25.39, 25.40, 25.42, 25.44) |
||
| 27 | 3/30 | Biophysical Analysis of DNA | Case Study B-DNA | ||
| 28 | 4/2 | Biophysical Analysis of DNA | Quiz 7 (Avg 5/5) |
||
| 29 | 4/4 | Protein Structure, Temporins | Exam Results | ||
| 30 | 4/6 | Temporins, Biophysical Analysis of Proteins |
|
||
| 31 | 4/9 | Kinetics | 13.1-13.2 (13.7-8, 13.15, 13.16-20) |
Notes: Kinetics | Quiz 8 (Avg 3.8/5) |
| 32 | 4/11 | Kinetics | 13.3-13.4 (13.28, 13.29, 13.30) |
Group Project 2 | |
| 33 | 4/13 | Kinetics | 13.4-13.5 | ||
| 34 | 4/16 | Kinetics | Pauling Paper (handout) (13.43-13.49, 13.51, 13.52, 13.54) |
Quiz 9 (Avg 3.4/5) |
|
| 35 | 4/18 | Kinetics | (13.31-13.33, 13.37, 13.39-13.41) | ||
| 36 | 4/20 | Kinetics | Enzyme Kinetics Practice (13.55, 13.61, 13.64, 13.70, 13.88) |
Brief Introduction To Enzyme Kinetics Supplemental Background on Enzyme Kinetics (optional, pgs 186-196) |
|
| 37 | 4/23 | Kinetics | Study!! | Acid-Base Notes | |
| 38 | 4/25 | Exam III | (Avg 82/100) | ||
| 39 | 4/27 | Acid-Base | 15.1-15.4 (15.3, 15.5, 15.6, 15.8, 15.15, 15.21, 15.23, 15.31, 15.33) | Perspective article and case study due. | |
| 40 | 4/30 | Acid-Base | 15.5-15.7 (15.43, 15.45, 15.47, 15.53, 15.55) | ||
| 41 | 5/2 | Acid-Base | 16.2 (16.1-16.5) | ||
| 42 | 5/4 | Case Study Presentations, Wrap-Up and Evaluations | Study! | Group Project 2 Due | |
| 5/9 | Review Session | 11:00 AM, 101 Tomsich | |||
| 5/10 | Final Examination | 8:30 AM, 101 Tomsich | |||