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:

 

Preparation and Participation
20 pts
Quizzes (10 x 5 pts)
50 pts
Midterm Exams (3 x 100 pts)
300 pts
Final Exam
150 pts
Projects (2 x 50 pts)
100 pts
Total Points Possible
620 pts

 

The grading scheme for the course is based on the standard grade cut-offs:

Grade
Percent of Total Points Earned
A
100-90%
B
89-80%
C
79-70%
D
69-60%
F
<60%

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:

124 Experiment 5

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

BRENDA Enzyme Database

Chemistry Skills Tests:

Intermolecular Forces

Tentative Schedule:

Back to courses page

Session Date Topic Reading Sections (Suggested Problems) Lecture Supplements Work Due
1 1/15 Introduction to Biophysical & Medicinal Chemistry  

Science Web

Ants and Butterflies

 
2 1/17 Introduction to Medicinal Chemistry

Handout, Questions

Pfizer: Torcetrapib

Notes

NSAID Case Study

Metabolism Overview

 
3 1/19 Introduction to Medicinal Chemistry (Review Equilibrium) 14.1-14.5

Notes

Biophysics of AA binding

Key Equilibrium Concepts

 
4 1/22 Organic Chemistry Basics 24.1 - 24.2 (24.13, 24.24, 24.25, 24.26, 24.66)

Representations and FG's

Lab Handout

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)

Organic Practice

FG Identification Practice

 
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)

Notes Part I

Notes Part II

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

Hybridization Practice

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

Notes - Degree of Unsaturation

 
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

Intermolecular Forces Practice

   
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)

Perspective Article and Case Study

Project Groups

 
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

Woodward Rules

UV-vis practice

Extra IM Forces Practice

 

Notes-Interaction of Light and Matter

Light and Matter Reading

 

 
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)

Nucleic Acid Basics

DNA Chime Model

Notes-Biomacromolecules

 
27 3/30 Biophysical Analysis of DNA

Reading: B-DNA recognition

B-DNA recognition Reading Questions

Case Study B-DNA  
28 4/2 Biophysical Analysis of DNA    

Quiz 7

(Avg 5/5)

29 4/4 Protein Structure, Temporins

Helical Wheel Practice

Protein Basics

Magainin 2

Neomycin Resistance Protein

Exam Results
30 4/6 Temporins, Biophysical Analysis of Proteins

 

Temporins Paper

Temporins Questions

 

CD Background

Temporin Notes

 
31 4/9 Kinetics

13.1-13.2 (13.7-8, 13.15, 13.16-20)

Method of Initial Rate Practice

Notes: Kinetics

Quiz 8

(Avg 3.8/5)

32 4/11 Kinetics

13.3-13.4 (13.28, 13.29, 13.30)

Integrated Rate Law Practice

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