Biochemistry I
CHE 4310
Summer 2012
Mon & Wed 9am-12:30pm
Room: SI 3079
Course Website: http://bonhamchemistry.com
Instructor: Dr. Andrew J. Bonham
Office Hours: TBA
Contact: abonham@mscd.edu
Office: SI 3048, 303-556-3929
Why Study Biochemistry?
Biochemistry is the study of the chemical processes of living organisms—both those in the world around us and ourselves. A solid
understanding of biochemistry will provide a better understanding of how your body works (whether that be in exercise, nutrition,
or disease response) 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?
Biochemistry 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, biochemistry 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!
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:
 Lehninger Principles of Biochemistry, 5th ed. Nelson, D.M. and Cox, M.M. W.H. Freeman and Company, New York, NY, 2008.
This book is available at the Auraria Bookstore, but may be available elsewhere (such as online) more affordably.
 Scientific Calculator for Quizzes & Exam (no cell phones, laptops, tablet computers, or other web devices).
 i>clicker, available at the Auraria Bookstore.
Reading:
The course’s textbook is Lehninger Principles of Biochemistry, a good, informative, and even fun read. Reading the assigned
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 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:
There will be no graded homework due for this class. However! Every set of lectures is accompanied by suggested practice
problems from the textbook, and you will need to do these problems to master the material and perform well on the quizzes and
exam. There is no way around the need to actually solve biochemistry problems; doing the suggested problems is your best way to
ensure a good grade in this class and a good understanding of the material.
Quizzes:
Quizzes will be given approximately bi-weekly (see schedule for dates). The seven quizzes will consist of approximately 30 short
answer / calculation / structure and/or multiple choice questions. Quizzes are worth 70% of the course grade and will cover the
material stated on the lecture schedule (2-3 chapters per quiz). Study questions will be provided. The quizzes will be given during the
first 1 hour of the class. Lecture will follow.
Final Exam:
The ACS standardized Biochemistry Exam will be used as the final exam. The final is required for all students. It is worth 25% of
your course grade and will be given during finals week in December (TBA).
Grade Calculation & Policies:
Class Participation / iClicker points
4 Quizzes
Final Exam (ACS)
5%
70 %
25 %
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 (August 3rd). Grades will be available by web and kiosk on August 9th at noon at metroconnect.mscd.edu.
FERPA policies prohibit me from releasing your grades via phone or email unless you register with the Registrar’s office and obtain a nonidentifying security code.
Drop Dates:
Students will be expected to know and observe the MSCD regulations regarding class drop dates and No-Credit Withdrawal (NC).
It is the student’s responsibility to withdraw from a course. See www.mscd.edu/MetroCal/tools/acal.jsp
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 College 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.mscd.edu/~access/
-----------------------------------------------------------------------------The Metropolitan State College 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 College 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 college is prohibited by the Americans with Disabilities Act.
------------------------------------------------------------------------
Students at Metropolitan State College of Denver (MSCD) 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 MSCD 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, MSCD 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 MSCD student who believes that an MSCD faculty member has violated this policy is entitled to seek relief under Section
V of the MSCD 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 4310 Lecture Schedule (subject to change)
Week
Dates
Lecture Topics
Spring 2012
Reading
Practice Problems
(before class)
Chapter 1,2
(not exclusive!)
Chap 1: 4, 6, 7, 8, 11, 14
Chap 2: 1, 2, 3, 4, 7, 8, 11, 13,
14, 17, 21, 28, 29
Chap 13: 1, 2, 3, 4, 6, 9, 19,
28
Chap 3: 1, 2, 8, 12, 20, 21
Chap 4: 1, 3
Chap 3: 5, 15, 16
Chap 4: 2, 6, 7, 8, 11, 14
Chap 5: 1, 4, 5, 6, 10
Chap 8: 2, 3, 5, 6, 8, 12, 15
Chap 9: 1, 3, 5, 6, 11, 13
Chap 7: 1, 2, 4, 7, 8, 10, 16
Chap 7: 18, 21, 25, 29, 31
Chap 10: 2, 3, 7, 9, 10, 14,
17, 22
Chap 6: 1, 2, 4, 7, 8, 9, 11, 19
Chap 14: 2, 4, 5, 7, 8, 14, 16,
25
Chap 14: 6, 10, 12, 26
Chap 16: 1, 2, 6, 8, 16, 29
Chap 16: 4, 10, 20, 26, 30,
31, 32
Chap 14: 20, 21, 23
Chap 15: 4, 5, 6, 12
1
May 30th
 Introduction
 Water & Foundations of
2
June 4th and
June 6th
 Bioenergetics
 Amino Acids & Proteins
Chapter 13
Chapter 3,4
Biochemistry
(last full refund drop day June 4th)
3
June 11th and
June 13th
 Quiz June 11th Chap 1,2,13
 Protein Structure & Function
 Nucleic Acids
Chapter 3,4,5
Chapter 8,9
4
June 18th and
June 20th
 Carbohydrates
 Carbohydrates & Lipids
Chapter 7
Chapter 7,10
5
June 25th and
June 27th
 Quiz June 25th Chap
Chapter 6,14
Chapter 14,16




3,4,5,7,8,9
Enzyme Kinetics
Glycolysis
Glycolysis & TCA Cycle
TCA Cycle
6
July 2th
7
July 9th and
July 11th
 Quiz July 9th Chap 6,10,14,16
 Gluconeogenesis
 Regulation of Metabolism

(Last day to receive “NC”)
Chapter 14,15
8
July 16th and
July 18th
 Electron Transport & Oxidative
Chapter 19
Chapter 17
Chap 19: 1, 2, 5, 6, 7, 10, 11,
15, 17, 23
Chap 17: 1, 2, 3, 4, 6, 13, 16,
17, 23, 29
9
July 23rd and
July 25th






Quiz July 23rd Chap 14,17,19
Amino Acid Metabolism
Photosynthesis
Special Topics
Review
ACS Final Examination
Chapter 18
Chapter 19
Chap 18: 4, 7, 9, 10, 13, 19
Chap 19: 26, 28, 31, 39, 40
FINAL
July 30th
Phosphorylation
 Lipid Metabolism
Chapter 16
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