Introduction to Organic & Biological Chemistry CHE 2100
Fall 2013
Lecture: Mon & Weds 10am-11:50am
Science Building (SI) 3079
Laboratory: Mon OR Weds 1pm-3:50pm
Science Building (SI) 3093
Course website: http://bonhamchemistry.com
Instructor: Dr. Andrew J. Bonham Office Hours: Wed 12:00-3:00, Thu 10:00-12:00
Contact: abonham@msudenver.edu
Office: Science Building 3048
Why Study Organic Chemistry & Biological Chemistry?
Organic & biological chemistry encompass the chemical foundations of almost every process that we encounter in our daily lives. A
solid understanding of these essential topics will provide a better understanding of how modern industry works, how life functions,
and give insight into the endless, fascinating examples of the beauty and complexity of the living world.
What do I expect from you? How can you succeed at this course?
Chemistry is a complex topic, and while I believe that every student can succeed at this course, like any challenge, certain
expectations must be met for you to succeed.
 Regular Attendance and Daily Practice: Science and math are their own language, with specialized vocabulary and ways of
approaching problems. Just like the study of a foreign language, I expect regular attendance and daily practice. If you cannot
commit to thinking about, and solving problems in, chemistry every day, you will not acquire enough skill to confidently pass the
exams and master this topic to the level that you will need for future careers.
 Plan for the Future: I expect you to be aware of the lecture schedule and exam dates, and plan accordingly. I expect at least
two weeks notification for any quiz you may miss (see Homework & Quizzes, below), and there will not be any flexibility on the
date and time of the Final Exam. Review the schedule now, and plan for the future.
 Pay Attention and Work Through Problems: It is exceedingly easy to fall into the trap of half-listening to lectures, nodding along
with the material, only to find that you cannot answer the test questions. You cannot succeed by listening alone. I expect you
to take notes, engage with the class and your classmates, do the homework exercises, and commit to the often difficult process
of learning unfamiliar topics. Note well that simply looking at a problem set, then at the answer key, and saying to yourself,
“That makes sense,” is not the same as actually solving the problem!
 Take the lab work seriously. Labs are designed to reflect, as much as possible, real-world laboratory experiences. This is a
great opportunity to learn useful skills, but requires careful attention to safety hazards, details of experiments, and awareness of
the lab environment.
What can you expect from the instructor?
I will give clear, relevant, on-time lectures that encourage class participation. I will provide clear assignments, clear and fair grading
policies as outlined in this syllabus, and relevant practice problems. I will offer reasonable availability outside of class (e.g., office
hours). Through my actions, I will encourage your understanding and enjoyment of the science of biochemistry.
Required Materials:
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Bettelheim, et al., Introduction to Organic and Biochemistry, 7e.
Laboratory Manual: Available in the Auraria Bookstore.
i>clicker. Available in the Auraria Bookstore.
Molecular models are highly recommended but not required. Four model sets are on reserve in the library.
Safety glasses in the laboratory will be required at all times. A lab coat or an apron is highly recommended.
Scientific Calculator for Quizzes (no cell phones, graphing calculators, laptops, tablet computers, or other web devices).
Reading:
The course will be primarily based on lecture notes, which will be available online. However, the Bettelheim textbook is a good,
informative read, and reading the suggested chapters will improve your understanding of the material immensely—there is only so
much lecture time, and a world of interesting things to learn. Additionally, the practice problems are from the book, and quizzes will
partly be based on that content. If you attend lecture, read the textbook, and do the homework problems, you will be well
prepared to succeed.
Class Participation / iClickers:
Regular attendance and involvement in the classroom learning process is important. This class will use the iClicker evaluation
system for in-class responses. These responses, regardless of whether they are “correct” answers, will constitute a 5% (“half a
letter grade”) participation portion of your grade.
Homework:
We will be using the Sapling Learning online homework system ( http://www.saplinglearning.com ). Additionally, you may want to do
practice problems from the textbook, and review sheets that I will provide before tests. There is no way around the need to
actually solve chemistry problems; doing homework is your best way to ensure a good grade in this class and a good understanding
of the material. The Sapling homework will constitute a 10% portion of your grade.
Laboratory Reports:
Lab reports are due for completed labs on the day of the associated quiz (see schedule). All lab reports should be typed and data
should be analyzed using an appropriate spreadsheet/graphing program when necessary. There will be 14 lab reports; 13 will used to
compute your report portion of the grade. Laboratory reports must be concise, well-organized and be presented well. Do not
round your data; record the exact precision in your lab report that you were able to record in the laboratory depending on the
measuring instrument used. Calculated values should follow rules of significant figures. Please note that for questions and data
manipulations involving calculations, you MUST show your work (one example per calculation type) to obtain full credit. If only the
final answer is shown without the work, only partial credit for the computed values will be given. To receive full credit for your
work, you MUST show ALL of the work required to solve the problem and you MUST include units in your calculations/answers.
Check your work carefully and be sure to include all units and the appropriate number of significant figures; consult a general
chemistry text to review rules for addition/subtraction, multiplication/division, and logarithms. Please see the instructor for
assistance if you have difficulty with this task.
Typical point values (to total 100 pts. per lab): name (2 pts.), date (2 pts.), partner (2 pts.), objective (5 pts.), data (25 pts.), values (2
pts.), calculations (sample of each type, 5 pts. each), questions (2-5 pts. per part/question), graphs (10-15 points), conclusion (5 pts.).
Points will be deducted if these parts are missing or incorrect as well as incorrect number of significant figures (0.5 pts. per number)
or missing units (0.5 pts. per number).
Your lab reports should be typed and should be entirely your own work. Graphs and tables may be done in Excel. Use the best fit
line for points to calculate the slope. For all graphs, if you work with a partner, do not hand in photocopy or word-processing
replicas of their report materials and call them your own. This is plagiarism. When in doubt, cite your source. Late laboratory
reports will be penalized 5 points per day and will not be accepted after 7 days (1 week).
Quizzes:
Quizzes will be given approximately bi-weekly (see schedule for dates). The six quizzes will consist of 30 short answer / calculation /
structure and/or multiple choice questions. Quizzes are worth 50% of the course grade and will cover the material stated on the
lecture schedule (2-3 chapters per quiz). Study questions and old quiz questions will be provided on MetroConnect. The quizzes will
be given during the first 45 minutes of the class. Lecture will follow. At the end of the course, your lowest quiz grade will be
dropped (we all have bad days).
Final Exam:
The final exam will be the American Chemical Society General-Organic-Biochemistry exam. The final is required for all students. It
is worth 20% of your course grade and will be given during finals week in December (TBA).
Grade Calculation & Policies:
Class Participation / iClicker points
Sapling Homework
4 Quizzes (lowest dropped, remaining three are 15% each, 25 questions)
Lab Experiments & Writeups
Final Exam
5%
45 %
10%
25 %
15 %
100 %
Total
Points are tentative and subject to change by the instructor.
The grading scale is as follows: A (90 -100%), B (80 - 89%), C (70 - 79%), D (60 - 69%), F (< 60%)
Grades will be available at the next regularly-scheduled course meeting. For Finals, final grades will be available from me in person on
Friday of finals week (Dec 14th). Grades will be available by web and kiosk on Dec 21st at noon at connectu.msudenver.edu.
FERPA policies prohibit me from releasing your grades via phone or email unless you register with the Registrar’s office and obtain a
non-identifying security code.
Drop Dates:
Students will be expected to know and observe the MSU Denver regulations regarding class drop dates. It is the student’s
responsibility to withdraw from a course. See www.msudenver.edu/MetroCal/tools/acal.jsp Effective fall 2013 the NC grade
notation will no longer be applied to academic records. For information on this and other academic policy changes, please see
http://www.msudenver.edu/advising/student/academicpolicies/.
Academic Dishonesty:
Academic dishonesty is a serious offense. Any occurrence diminishes the quality of scholarship and the learning experience for
everyone on campus. An act of Academic Dishonesty will lead to sanctions including a reduction in grade (up to and including a
permanent F for the course), probation, suspension, or expulsion. Academic dishonesty includes cheating, fabrication, plagiarism,
submitting the same paper or work for more than one class, and facilitating academic dishonesty. For definitions and more
information, see the Student Handbook which is available online through Metro-Connect.
Disability Accommodation, Discrimination Policy, and Class Attendance on Religious Holidays:
The Metropolitan State University of Denver is committed to making reasonable accommodations to assist individuals with
disabilities in reaching their academic potential. If you have a disability, which may impact your performance, attendance, or grades
in this class and are requesting accommodations, then you must first register with the Access Center, located in the Auraria Library,
Suite 116, 303-556-8387. I cannot provide accommodations prior to my receipt of a faculty notification letter from the Access
Center. Please note that accommodations are never provided retroactively (i.e., prior to the receipt of your faculty notification
letter.) Once I receive your official Access Center faculty notification letter, I would be happy to meet with you to discuss your
accommodations. All discussions will remain confidential. More information is available by visiting the Access center website
www.MSU Denver.edu/~access/
-----------------------------------------------------------------------------The Metropolitan State University of Denver does not discriminate on the basis of race, color, creed, national origin, sex, age, sexual
orientation or disability in admission or access to, or treatment in, its educational programs or activities. Inquiries concerning Title
VI, Title IX and Section 504 may be referred to Dr. Percy Morehouse, Director, Equal Opportunity, Metropolitan State University of
Denver, 303.556.2939; or to the Office for Civil Rights, U.S. Department of Education, 1244 Speer Boulevard, Suite 300, Denver,
CO 80204. Discrimination based on disability in admission to, access to or operation of programs, services or activities of the
University is prohibited by the Americans with Disabilities Act.
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Students at Metropolitan State University of Denver (MSU Denver) who, because of their sincerely held religious beliefs, are unable
to attend classes, take examinations, participate in graded activities or submit graded assignments on particular days shall without
penalty be excused from such classes and be given a meaningful opportunity to make up such examinations and graded activities or
assignments provided that advance written notice that the student will be absent for religious reasons is given to the faculty
members during the first two weeks of the semester.
Nothing in paragraph one of this policy shall require MSU Denver faculty members to reschedule classes, repeat lectures or other
ungraded activities or provide ungraded individualized instruction solely for the benefit of students who, for religious reasons, are
unable to attend regularly scheduled classes or activities. However, presentations, critiques, conferences and similar activities
involving individual students shall be scheduled to avoid conflicts with such students’ religious observances or holidays provided that
reasonable advance notice of scheduling conflicts is given to faculty members. Because classroom attendance and participation is an
important aspect of learning, MSU Denver students should not register for courses if regularly scheduled classes or activities
routinely conflict with their religious observances or holidays (e.g., conflicts resulting in weekly absences for an entire semester).
Any MSU Denver student who believes that an MSU Denver faculty member has violated this policy is entitled to seek relief under
Section V of the MSU Denver Equal Opportunity Grievance Procedure.
Syllabus Changes and Policy:
Any changes in this syllabus I may deem necessary during the semester will be announced in class and made available in
writing. I reserve the right to revise the syllabus and grading policies at any time.
CHE 2100 Lecture Schedule (subject to change)
Week Dates
Topics
Aug 19th and
1
 Introduction
Aug 21st
 Alkanes
Aug 26th and
2
 Alkanes
Aug 28th
Last “drop day” Aug 26th)
Sept 2nd
Labor Day break
th
Sept 4
3
 Alkenes and Alkynes
Reading
Chap 1,2
Chap 2
-Chap 3
4
Sept 9th and
Sept 11th
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Aromatics
Quiz Sept 11th Ch 1,2,3
Chap 4
5
Sept 16th and
Sept 18th
Sept 23rd
and Sept 25th
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Alcohols, Ethers and Thiols
Chap 5
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Aldehydes, Ketones
Carboxylic Acids
Chap 9,10
7
Sept 30th
and Oct 2nd
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8
Oct 7th and
Oct 9th
Oct 14th and
Oct 16th
6
9
Carboxylic Anhydrides,
Esters, and Amides
nd
 Quiz Oct 2 Ch
4,5,9,10
 Amines
Chap 11
Chap 8
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Chirality
Chap 6
Carbohydrates
Lipids
Quiz Oct 23rd Ch 6,8,11
Chap 12,13
10
Oct 21st and
Oct 23rd
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11
Oct 28th and
Oct 30st
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12
Nov 4th and
Nov 6th
Proteins
(Last day to withdraw
Oct 28th)
 Enzymes
 Nucleotides
13
Nov 11th and
Nov 13th
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Gene Expression
Bioenergetics
Chap 18,19
14
Nov 18th and
Nov 20th
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Chap 20
Fall
Break
15
Nov 25th to
Nov 29th
Metabolic Pathways
Quiz Nov 20th Ch
12,13,14,15,17
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Dec 2nd and
Dec 4th

FINAL
TBA
Final Exam TBA
Review
Chap 14
Chap 15,17
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Fall 2013
Suggested Problems
1, 2, 4, 7, 9, 11, 13, 15, 17, 19,
21, 23, 27, 29, 33, 41
1, 2, 4-9, 11-15, 17 ,19, 21, 24,
25, 27, 30, 31, 33, 35, 37, 41, 43
1-6, 8, 10, 11, 13, 17, 19, 21, 23,
25, 29, 31, 33, 37, 39, 41, 43, 45,
53, 55, 57
1, 3, 7, 9, 11, 13, 15, 17, 21, 23,
29, 31, 41, 43, 47
1-7, 9, 11, 13, 15, 19, 21, 23, 25,
27, 31, 33, 35, 41, 43, 53, 57, 59
Chap 9: 1, 3-9, 15, 17, 19, 21,
23, 25, 27, 29, 31, 33, 35, 37, 39,
41, 43, 45, 47, 49, 51, 53, 57, 59
Chap 10: 1-3, 5, 7, 9, 11, 13, 15,
17, 19, 21, 23, 27, 29, 33, 35, 37
1-3, 5, 7, 9, 11, 13, 15, 17, 21,
25, 27, 35, 37, 41, 43
2, 7, 9, 11, 15, 17, 19, 25, 29, 31,
37, 39, 41, 43, 45
4-6, 9, 11, 13, 15, 17, 21, 23, 29,
31, 33, 37
Chap 12: 1-5, 7, 9, 11, 13, 15,
17, 19, 21, 23, 25, 27, 29, 31, 33,
37, 39, 41, 43, 45, 47, 49, 51, 53
Chap 13: 1, 3, 5, 7, 9, 11, 13, 15,
17, 19, 21, 25, 27, 29, 33, 39,
43,45, 47, 49, 51, 55, 59, 65, 71
1, 2, 5, 7, 11, 13, 15, 17, 19, 21,
25, 27, 29, 31, 33, 35, 37, 39,
41, 45, 47, 51, 55, 57, 69, 73, 75
Chap 15: 1, 5, 7, 9, 11, 13, 15,
17, 19, 21, 23, 25, 27, 29, 31, 33
Chap 17: 5, 7, 9, 13, 15, 17, 19,
21, 23, 25, 27, 31, 33, 35, 37, 39,
45, 49, 53, 55, 59, 63,65, 95
Chap 18: 2, 3, 5, 7, 9, 11, 15, 17,
19, 21, 23, 25, 27, 29, 41, 43, 61
Chap 19: 1, 3, 7, 9, 11, 13, 15,
17, 19, 21, 23, 25, 27, 29, 31, 33
3, 5, 7, 9, 13, 15, 17, 21, 23, 25,
27, 29, 33, 35, 37, 39, 41, 43,
45, 51, 53, 55, 57, 59, 61, 63, 65