CHEMISTRY 2320-1 Organic and Bioorganic Chemistry

Fall 2004

InstructorDr. Steven Bachrach
Office215D MEB
emailsbachrach@trinity.edu
phone999-7379
Office HoursMWF 1:30-2:30pm
Peer tutors

Sarah Wingfield
swingfie@trinity.edu
North-South Foyer: Su 10pm-12am, W 10-11:30pm

Christina Crump
christina.crump@trinity.edu
phone 3243
North-South Foyer: M 9-11pm, Th 7-9pm
Help SessionsTo Be Determined
Text

John McMurry, “Organic Chemistry” Sixth Edition (required)
Susan McMurry, “Study Guide and Solution Manual” (recommended)
DescriptionThis is the second semester of a two-semester sequence of organic chemistry. In this course, we will build upon your foundation in organic chemistry by introducing many more functional groups and learning how to interconvert them. The last portion of the course will focus on bioorganic molecules, discussing their properties, nomenclature, preparation and their biosynthesis and action.
Grading

Your grade for the course will be based on your highest three exam scores (out of four), your six highest quiz scores (there will be at least 7 quizzes) and the final exam. Each exam is worth 100 points for a total of 300 points possible, each quiz is worth 10 points for 60 possible points and the final exam is worth 140 points. I have scheduled three exams; the fourth exam will be the standardized American Chemical Society Organic Chemistry Exam. This test is multiple choice and covers materials from both semesters of organic chemistry. It will be scheduled for an evening to be determined, likely sometime in mid-November. The grade scale for will be discussed in class after each exam; the scale will be no more severe than >90% A, >80% B, >70% C, >60% D, <60% F. Exam dates (other than the standardized test) are listed in the course outline; quiz dates will be announced in class and we may have some pop quizzes.

Quiz Scores:60 points
Top 3 Exams:300 points
Final Exam:140 points
Total:500 points
Make-upsNo late or make-up exams will be given. If you know in advance that you will be absent for one of the exam dates you must inform me at least one week in advance and that will be the exam you drop. If you miss an exam for an emergency (sickness, death in the family, etc.), that exam can be dropped. If you miss an exam for an unexcused reason, you will get a zero. Note that if there is any subsequent missed exam, you will receive a score of zero for that exam.
Homework

Homework problems for the class are listed below. Additional relevant homework problems from the textbook will be announced periodically throughout the class. No homework will be collected or graded, however, I am willing to check/discuss your answers in office hours and study sessions.

Chapter 17

26, 31, 33, 35, 37, 40, 41, 44, 47, 52, 55, 64

Chapter 18

25, 27, 30, 37, 40, 44, 49, 51, 54

Chapter 19

28, 30, 32, 34, 39, 41, 45, 48, 52, 61, 67

Chapter 20

20, 23, 25, 29, 32, 33, 35, 37, 42, 45, 49, 53, 55

Chapter 21

32, 35, 37, 41, 42, 49, 53, 60, 65

Chapter 27

17, 20, 22

Chapter 22

21, 23, 26, 28, 34, 36, 40, 44, 48

Chapter 23

27, 29, 34, 35, 39, 42, 43, 46, 51, 56

Chapter 24

27, 29, 31, 34, 37, 39, 42, 45, 56, 58, 67

Chapter 25

34, 38, 39, 41, 43, 44, 49, 55, 65, 67

Chapter 26

27, 30, 33, 34, 36, 45, 46, 51, 53, 55, 62

Chapter 27

24, 32, 34, 38, 39, 44

Chapter 28

25, 30, 33, 35, 36, 37, 39, 40, 41, 46, 48

Chapter 29

34, 42

Additional problems can be found on the textbook’s web site: http://chemistry.brookscole.com/mcmurry6e

Web Site http://www.trinity.edu/sbachrac/chem2320

Tips for Success in Organic and Bioorganic Chemistry

  1. The material from the first semester is still applicable and necessary for this class. Organic chemistry continually builds upon itself. If you don’t remember topics from last semester, you absolutely must spend some time early in the semester to get up to speed.
  2. The pace of this class will be even more relentless than last semester. You cannot fall behind at all. Come to class having already read the material from the text before I discuss it. Do the homework problems as we go along; don’t wait until right before the exams.
  3. Do at least all of the problems I assign as homework. Do more if you are having difficulty. Don’t keep repeating the same problems. There are lots of other organic chemistry textbooks and web sites that offer many alternative (and useful) problems.
  4. Be real careful in using the answer book. Do not come to rely on it!
  5. If you are having difficulties, don’t wait to get some help. You are welcome to see me as often as you need, whether it is during my office hours, at the help sessions or at some other time that we arrange. Come to the help sessions with questions to ask. I am available for assistance at pretty much any other time during the day. I am happy to help via email but this is somewhat limited by not being able to easily include chemical structures. Make use of the peer tutor.

Tentative Course Outline

Week

 Topics

 Text

 

 

 

8-22

Review of organic I

 

 

 

 

8-29

Alcohols, synthesis and reaction

Ch. 17.1-17.8

 

Phenols, synthesis and reactions, ethers

Ch. 17.9-17.12, 18.1-18.5

 

 

 

9-5

Reactions of Ethers, Thiols

Ch. 18.6-18.11

 

Prep of aldehydes, ketones

Ch. 19.1-19.5

 

 

 

9-12

Nucleophilic attack

Ch. 19.6-19.12

 

conjugate addition, Problem solving

Ch. 19.13-19.16

 

 

 

9-19

Exam 1 (Tuesday Sept. 20)

 

 

Carboxylic acids

Ch. 20.1-20.10

 

 

 

9-26

Carboxylic acid derivatives

Ch. 21.1-21.3

 

Reactions of acid derivatives, esters, amides

Ch. 21.4-21.10

 

 

 

10-3

Fats, phosopholipids, Enols and enolates

Ch. 27.1-3, Ch. 22.1-22.6

 

Condensation reactions-Aldol

Ch. 22.7-22.8, Ch. 23.1-23.7

 

 

 

10-10

Condensation reactions-Claisen, intro to metabolism

Ch. 23.8-23.14

 

Approaching chemical synthesis, Problem solving

 

 

 

 

10-17

Exam 2 (Tuesday Oct. 18)

 

 

Amines, basicity

Ch. 24.1-24.7

 

 

 

10-24

Synthesis and reactions of amines, carbohydrates

Ch. 24.6-24.10, Ch. 25.1-25.2

 

Carbohydrates, reactions

Ch. 25.3-25.7

 

 

 

10-31

Polysaccharides, amino acids

Ch. 25.8 -25.12, Ch. 26.1-26.2

 

Synthesis of amino acids and peptides

Ch. 26.3-26.11

 

 

 

11-7

Protein structure and enzymes

Ch. 26.12-26.16

 

prostaglandins, terpenes, steroids

Ch. 27.4-27.9

 

 

 

11-14

Heterocycles, nucleic acid

Ch. 28.1-28.10

 

Exam 3 (Thursday, Nov. 17)

 

 

 

 

11-21

Transcription, translation, DNA sequencing

Ch. 28.11-28.15

 

 

 

11-28

PCR

Ch. 28.16-28.17

 

Catabolism of fats and sugars

Ch. 29.1-29.4

 

 

 

12-6

Citric acid cycle, anabolism of fats and sugars

Ch. 29.5-29.9

 

 

 

12-15

 FINAL EXAM – Dec. 10, 2:00pm – 5:00pm

 

Please note that I will try very hard to follow this schedule. However, the only rigorously maintained items on the schedule are the dates of the exams (listed in bold).

Test Answers

Quiz answers