University of Pennsylvania

Chemistry Department
Chemistry 452 Biological Chemistry II
Spring 2017 Syllabus
Texts: Alberts et al.: Molecular Biology of the Cell, Sixth Edition 2015.
Watson et al.: Molecular Biology of the Gene, Seventh Edition 2014.
Milo and Philips: Cell Biology by the Numbers, 2016
Current General Biochemistry Text
Turning Technologies clicker or ResponseWare device required
Additional assigned and recommended reading will be posted to the course CANVAS site.
Assigned Seminars, usually Thursdays at Noon and 3:00PMattendance monitored by clicker.
There will be occasional, once or twice a week, questions posed in class where you will be asked
to give answers using TurningTechnologies clicker or ResponseWare. Total score on these
questions for the whole semester is equal to one of the examinations.
There will be three written examinations, two hours each, where you will submit written
essaystwo will be during the semester (about February 20 and March 25) and one will be
during the Registrars assigned final examination slot (Wednesday May 3).
There will be a required peer reviewed term paper with research proposal below.
Course grade will be determined by the weighting the sum of your examination and in class
answers results equally with your term paper grade. A passing grade is expected on both parts.
(F in either part is an F in the course).
Course content: You should make a plan to read all of the two texts in parallel between now and
the end of the term. You will be able to skip some of the background chemistry and genetics in
these texts. All of the examinations are open book and anything, on paper-no electronics, you
can bring in a standard airline carry-on bag (56 x 36 x 23 cm) is permitted.
Approximate Course Outline:
I. Structure of nucleic acids and base pair interactions
II. Transcription
III. Translation
IV. Information content of genomes
V. Gene expression, regulation in space and time
VI. Cell complexes and more
TERM PAPER and Research Proposal: Must pass, about half of the term grade.
A research proposal is to be submitted by 9:00AM on Monday April 17 on a biological
chemistry or molecular biology topic selected from the review of the year 2016 in last issues of
Nature (December 24) or Science (December 23) for 2016 or the predictions in the first issue of
each for 2017 (Nature 5 January, Science 6 January). Novel interrogation or use of Central
Dogma molecular systems is required.
Wednesday 18 January in class: Introduction to the assignment, genre analysis and introduction
to peer review.
Wednesday January 25, in class, how to submit drafts and do peer reviews in MyReviewers will
be discussed.
DUE Wednesday January 25, 5:00PM submit topic choice with specific references to the
article(s) from the four issues of Science and/or Nature as noted above and why to MyReviewers.
DUE Friday February 10, 1:00AM: DRAFT ONE due: Literature review, background and what
needs to be done next on the topic chosen-about 5 pages 11 point single spaced (per NIH
instructions: not more than 15 characters and spaces per inch and 6 lines per vertical inch).
Figures, tables and references not counted towards the 5 pages. We expect strict adherence to the
Cell reference format guidelines (http://www.cell.com/cell/authors). This will be the
background and justification for your proposed experiments or research program.
Monday, February 13, in class: review of peer review techniques and assessment criteria. Assign
reviewers.
DUE Monday February 27, 1:00AM: Peer reviews of DRAFT ONE from classmates (5 each).
DUE Saturday March 18, 12Midnight: Response to peer reviews. DRAFT TWO: Introduction,
Revised Literature review and background with Research proposal-an additional 5 pagesnot
counting figures nor references.
DUE Saturday April 1, 12Midnight: Peer review (5 each) of first draft of the complete paper
Introduction and background (revised)+ proposal (first draft).
DUE Monday April 17: Response to Peer Reviews. Final Draft of complete paper submit
electronically by 9AM.
DUE Wednesday April 26: Peer grades of final draft and comments (5 each).
Use of clickers or ResponseWare identification other than your own, and electronic submission
of content other than your own are academic integrity violations. The consequences will be
determined by the Office of Student Conduct.