Chem 432/532A: Advanced Bio-organic Chemistry (Spring 2019)

MWF 10:30-11:20 am, NanoES 181

Instructor: Dr. Champak Chatterjee email: champak1@uw.edu

Office location: 204C CHB Office hours: By appointment
TA: Marissa Parker email: marissakparker@gmail.com

Course content: Chemical approaches toward understanding protein structure and function. We
will initially focus on protein modifications that occur in nature. Chemical, enzymatic and molecular
biological techniques that provide access to modified proteins will then be introduced. Finally we
will end by discussing techniques that allow exquisite control of protein function inside cells.

Tentative syllabus
1. April 1st Lecture: Post-translational modifications of proteins part 1
rd
2. April 3 Lecture: Post-translational modifications of proteins part 2
3. April 5th Lecture: Post-translational modifications of proteins part 3
In vitro approaches to study protein function
4. April 8th In-class discussion (Glycation) Nat. Chem. 2015, 7, 913-920.
5. April 10th In-class discussion (Serotonylation) Nature 2019 Muir, Maze et al.
6. April 12th Lecture: Modifying proteins with organic chemistry part 1
7. April 15th Lecture: Modifying proteins with organic chemistry part 2
8. April 17th In-class discussion (Histidine modification) Chem. Sci. 2019, 10, 427.
9. April 19th Lecture: Peptide synthesis, part 1 general principles
10. April 22nd Lecture: Peptide synthesis, part 2 coupling and protecting groups
11. April 24th Lecture: Peptide synthesis, part 3 overcoming challenges
12. April 26th In-class discussion (A mirror image enzyme) Michael Kay et al.
PNAS 2014, 111, 11679.
13. April 29th Midterm Exam, 10:30 am-11:20 am, NAN 181 (Open Book)
14. May 1st Lecture: Chemical ligation, part 1 chemical analogs
(email proposal idea by 6 pm)
15. May 3rd Lecture: Chemical ligation, part 2 native amide bonds
16. May 6th Lecture: Expressed protein ligation, part 1 inteins
17. May 8th Lecture: Expressed protein ligation, part 2 applications
18. May 10th Lecture: Ligation auxiliaries and their applications
19. May 13th In-class discussion: JACS 2016, 138, 16004 and Nat. Comm. 2018, 2847.
20. May 15th Lecture: Modifying proteins with enzymes: FGE, Biotin Ligase and Sortase
21. May 17th Lecture: Ribosomally synthesized non-natural proteins, part 1
22. May 20th Lecture: Ribosomally synthesized non-natural proteins, part 2
23. May 22nd Lecture: Ribosomally synthesized non-natural proteins, part 3
24. May 24th In-class discussion (Trapping intermediates) Nature 2019, 565, 112.

In vivo approaches to study protein function

25. May 29th Lecture: Controlling protein function with small-molecules (rapamycin)
26. May 31st Lecture: Activity-based protein profiling, part 1 serine hydrolases
27. June 3rd Lecture: Activity-based protein profiling, part 2 cysteine proteases
(CHEM 532 Proposal due by 6 pm. Please email PDF to C.C.)
28. June 5th Lecture: Protein complementation assays, Yeast two-hybrid
29. June 7th In class discussion: (Split TEV) Nature Methods 2006, 3, 985.
30. June 10th Final Exam, 8:30-10:20 am, NAN 181 (Open Book).
Grading: Research Proposal 30 pts (CHEM 532 only)
Midterm Exam 50 pts
Final Exam 100 pts
In-class Discussion 70 pts (CHEM 432 and CHEM 532)

CHEM 432 max. 220 pts, CHEM 532 max. 250 pts.

Texts: Given the diverse nature of chemical biology, there are no prescribed textbooks
for this course. References from the primary literature will be provided as needed. A
basic biochemistry textbook by Lehninger, Voert, or Stryer is a good general reference,
but not essential. Posttranslational modification of proteins: expanding nature’s
inventory by Christopher Walsh is also recommended but not essential reading.

Midterm and Final Exam: The midterm and final exams will draw upon your
knowledge from both lectures and in-class discussions.

Open Book Policy: All typed notes and any written documents are permitted in the
midterm and final exams. Electronic devices (anything with a printed circuit board) are
not permitted.

Research Proposal:
Proposal topic due: May 1st 2019
Final proposal due: June 3rd 2019
Penalty for late submissions= 5 pts per day late.

Note: Please convert to pdf and send it to me by email. Please do not send me Word
documents because their formatting may change with software and images move.

The final CHEM 532 proposal will describe an original research project in chemical
biology. The subject of the proposal is at your discretion but must be approved by me.
This is a two-phase process.

First, outline the basis of your idea on 1 page or less. Submit this page to me by May
1st. I will get back to you within 72 hours. Second, after your idea is approved, write the
full proposal (5 pages maximum, excluding references) and submit a PDF copy to me
before June 3rd at 6 pm. Minimum is 4 pages with references and figures.

You may choose to use the following format to compose your full proposal:

Cover page: List your name and the title of your proposal. Provide a single figure to
convey the gist of the proposed research to others who have not read the full proposal.
The figure could, for example, depict a key structure(s), reaction(s), or concept. You
could adopt a figure from the body of the proposal (though that is not essential).

Proposal structure (5 page maximum, 4 page minimum):

1. Overall objective: In a few sentences, state the broad goal that the proposed
research is intended to achieve.

2. Background and Significance: Briefly describe the scientific context for the
proposed research. Critically evaluate relevant existing knowledge. Specifically identify
gaps in knowledge that the proposed research will fill. Demonstrate understanding of
the subject by justifying the need for the proposed research. State concisely the
importance of the research by relating the specific aims to the overall objective- Why
would the information be useful and what could be done with it?

3. Specific Aims: First, state the hypothesis to be tested and describe its significance.
Keep in mind that a hypothesis is not a question for which there is already an answer.
A scientific hypothesis should be a testable postulate and the testing of this postulate
should result in new scientific insight. Maximum credit will be given for a clearly-
formulated hypothesis along with the proposed experiments that provide an
unambiguous test of that hypothesis. Define how the hypothesis is to be tested,
dividing the overall objectives into 2 or 3 Specific Aims.

Specific Aims are a list of items needed to achieve the long-term objectives.
Understand the difference between broad long-term Objectives (e.g. “understand
chemical aspects of a particular biological phenomenon”) and Specific Aims (e.g.
“study the influence of ligand L on the function of protein P in a human cell”).

4. Research Design and Methods: Outline the experimental design and procedures
you will use to accomplish the Specific Aims of the project. The experimental approach
should be outlined clearly and in sufficient detail that the plan can be evaluated. Do not,
however, provide experimental protocols (e.g. do not include detailed information such
as “to W mg of X will be added Y mg of Z”, or, “3 mice will be treated with 5 mg of
ritalin each.”)

5. Conclusion and Future Directions: Write a brief overview of what you hope to
accomplish and how this will impact the field.

6. References: Be thorough, relevant, and current. If you use a figure or table from
another source, be sure to cite that source. Use a consistent format (e.g. JACS) for
your reference, and include the full titles of journal articles. Note that references are not
part of the 5-page limit.

In-class Discussion (10 pts per session for CHEM 432 and CHEM 532)
One or two papers will be assigned as reading material with specific questions posted
for each paper. Please read the paper(s) and discuss them in class in small groups of
3-4 people. Answer the specific questions I will post on Canvas pertaining to these
papers. Feel free to express your opinion of the paper and validity of the results.

Brief Writing component Please write out your answers in brief (1-2 pages) and turn
them in at the end of the Discussion for each class. These will not be graded, but only
checked to make sure the paper was well understood by you and if anything is missed.
Not turning this in will imply you were absent for the discussion and lead to no points
being awarded. Points for In-class Discussion are based on your consistent
participation in the class. The format is:
1. 20 min. for small-group discussion.
2. 25 min. for paper summary and question-answer and discussion.
3. 5 min. extra time for clarifications, comments, concerns regarding the topic.
Goals: Overcome fear of public speaking, practice effective and brief communication,
think on your feet, challenge unsubstantiated conclusions, critique statistical handling.