Chemistry 135 - Chemical Biology

Fall 2014

Course Objectives
Chem 135 is a one-semester course designed to provide undergraduate students with an introduction to the
subjects of biochemistry and chemical biology. During the semester, you will have the opportunity to actively
apply and practice your knowledge of course materials in the form of problem-solving sessions during office
hours, problem sets, and exams. By the end of the semester, you will have a working knowledge of the
structures and functions of the major classes of biomolecules, the key concepts in enzymatic catalysis, the
mechanisms behind the central dogma of biology, and the chemical reactions underlying central metabolism.

Faculty Instructor Ming Chen Hammond (mingch@berkeley.edu)

Graduate Student Omer Ad (omerad@berkeley.edu)
Instructors (GSIs) David Litt (dlitt@berkeley.edu)
Cheng-Ting (Jason) Tsai (cttsai@berkeley.edu)

Lecture Time: MWF 9:10 am sharp-10:00 am 120 Latimer Hall
Office hour sections, times, and locations will be announced after a class poll

Website The main website for this course will be on Piazza (piazza.com/berkeley/fall2014/
chem135/home). Sign up here: piazza.com/berkeley/fall2014/chem135. All class
information (syllabus, announcements, slides, problem sets) except for grades will be
posted and updated here. Grades will be posted on bCourses (bcourses.berkeley.edu).
Prerequisites: Chem 3B or 112B (or taken concurrently). Students that have not taken these courses are
advised that in lecture, the instructor will only quickly review concepts covered in
prerequisite courses.

Required Materials: "Lehninger Principles of Biochemistry," David Nelson and Michael Cox. Figures from
lecture slides will be taken from the sixth edition, which is available in Cal Bookstore.

Exams: There will be two closed-book midterm exams in class scheduled for Sept 29 and Nov 5.
The final exam is scheduled for Thurs, Dec 18, 7-10 pm.

Assignments: Problem sets will be posted on Piazza and due in class. Solutions will be posted on Piazza
immediately after problem sets are turned in, so late problem sets will not be accepted.

Grading: Grades will be based on problem sets (20%), Piazza participation (5%), two in-class exams
(40%), and final exam (35%).

Piazza: We will be using Piazza for class discussions. The system is highly catered to getting you help
fast and efficiently from classmates, GSIs, and the instructor. Rather than email, I highly
encourage you to post your questions about lecture or problem sets on Piazza posts can be
completely anonymous. Your participation in our online learning community will contribute to
your course grade.

How Piazza participation bonus works: If you are a top contributor to our online learning
community and your final grade is very close to a grade division (e.g. B+/A- or B-/B), you will
receive a bump up to the higher grade. There is no penalty for not participating, but there is a
potential bonus for doing so!


Chem 135 Course Policies (the fine print)

1. To avoid distracting other students, please sit in the back of the class if you are using a laptop or other
electronic device. The instructor also reserves the right to ask you to stop use of the electronic device.

2. Problem sets are due at the end of class on the specified due date. Solutions will be posted immediately after
problem sets are turned in, so late problem sets will not be accepted.

3. Letter grades are assigned based on highest scores earned (from current and previous years) and percentages
thereof. This means that students who learn 100-90% of the material compared to historical high scores will
earn an A+ to A-, 89-80% will earn a B+ to B-, etc. Historically, over 50% of students receive a B+ or better
and the number of students who can earn As or Bs is not limited.

4. All exams are "closed book". Notes, books, backpacks, cell phones, etc. must be placed out of sight. Unless
otherwise announced in advance, calculators are not allowed for exams.

5. Missed midterm exams will receive zero points unless the student has an approved excuse (see policy below).
In the case of approved excuses, the other exam scores will be prorated. No make-up exams will be given.

6. Medical excuses are approved for serious illness or injury, and in these cases must be confirmed by a note
from the student health service or a physician. Excuses for other reasons must be submitted prior to the exam
and must be approved by the faculty instructor; follow-up documentation will be required as a condition for
approval.

7. It should not be necessary for students to leave the examination room during the relatively short period of the
midterm exam.

8. Changes in the recorded score for midterm exams ("re-grades") will be made only to correct clerical or
procedural errors; this is the same policy as is required for all final exams at Berkeley. Applying this same
policy to midterm exams gives maximal assurance that exams for all students are graded uniformly and
consistently. Midterm exams will be returned during office hours, during which exam solutions will be covered
and students will have the opportunity to submit re-grade requests. Otherwise, an exam written in pencil or
erasable ink is not eligible for re-grading once it is taken out of the possession of the GSI. The instructor and
GSIs will not discuss your request until you have explained it in writing.

9. Cheating of any sort is an extremely serious offense. In addition to resulting in an F for the course, cheating
may result in further punishment at the recommendation of the Student Conduct Officer.


TIPS FOR SUCCESS: The field of biochemistry / chemical biology is vast. While we will focus on
representative examples in lectures and problem sets, you will be challenged on exams to apply what you've
learned from these examples to new scenarios. The best way to prepare yourself for this is to be an active
learner - ask questions in class and on Piazza, take part in problem-solving sessions during office hours, read
through your notes after lecture, and challenge yourselves and each other. I highly encourage students to attend
office hours and to form study groups. You may work on problem sets with whomever you wish, but you must
turn in original work for your grade. Previous exam problems will be presented during office hours, so make
sure that you can work through these types of problems on your own as well as when you are in a group.




Chem 135 Course Schedule, Fall 2014 (All dates are approximate)

Lecture Date Topic Problem Sets
1 Aug 29 Course Introduction / The Solvent of Life
- Sept 1 NO CLASS LABOR DAY
2 Sept 3 pH and pKa
3 Sept 5 Protein Structure I
4 Sept 8 Protein Structure II PS1 due
5 Sept 10 Protein Structure III
6 Sept 12 Ligand Binding
7 Sept 15 Enzyme Catalysis PS2 due
8 Sept 17 Enzyme Mechanisms
9 Sept 19 Enzyme Kinetics I
10 Sept 22 Enzyme Kinetics II
11 Sept 24 Enzyme Inhibition
12 Sept 26
Review / Chembio Topic I (Post-Translational
Modifications, Jason Tsai)
PS3 due
13 Sept 29 IN-CLASS EXAM I
14 Oct 1 Central Dogma / Nucleic Acids
15 Oct 3 Replication
16 Oct 6 PCR and DNA Sequencing
17 Oct 8 DNA Methylation and Restriction
18 Oct 10 Transcription PS4 due
19 Oct 13 RNA Processing
20 Oct 15 The Genetic Code (Guest lecture)
21 Oct 17 Translation (Guest lecture)
22 Oct 20
Catch-Up / Chembio Topic II (Beyond the Central
Dogma, David Litt)

23 Oct 22 Gene Regulation PS5 due
24 Oct 24 Bioenergetics and Metabolism
25 Oct 27 Glycolysis I
26 Oct 29 Glycolysis II
27 Oct 31 Glycolysis III
28 Nov 3 Gluconeogenesis PS6 due
29 Nov 5 IN-CLASS EXAM II
30 Nov 7 Fermentation
31 Nov 10 Citric Acid Cycle I
32 Nov 12 Citric Acid Cycle II
33 Nov 14 Lipids / Fatty Acid Catabolism
34 Nov 17 Oxidative Phosphorylation I
35 Nov 19 Oxidative Phosphorylation II PS7 due
36 Nov 21 ATP Synthesis
37 Nov 24 Photosynthesis
38 Nov 26 Calvin Cycle
- Nov 28 NO CLASS (Thanksgiving)
39 Dec 1 Fatty Acid Synthesis
40 Dec 3
Review / Chembio Topic III (Metabolic Engineering,
Omer Ad)

41 Dec 5 Review / Chembio Topic IV (Imaging Biomolecules) PS8 due
- Dec 8-12 RRR WEEK (Final Review Session)
- Dec 18 FINAL EXAM (7-10 pm)