Biochemistry/Genetics 431, Sections 201 and 202 (Honors) Spring Semester 2010


Supplemental Syllabus for Honors Section



Dorothy Shippen, Professor of Biochemistry

            office: 413A Biochemistry Building

            phone: 862-2342



Gary R. Kunkel, Associate Professor of Biochemistry

            office: 406A Biochemistry Building

            phone: 845-6257


webpage URL:



Format of extra sessions for Honors students:

Students in the Honors section (BICH/GENE431(201 and 202)) will attend the same lectures and complete exams and homework assignments as for BICHGNE431(501 and 502).  In addition, Sections 201 and 202 will meet 4 times during the semester to discuss published papers that pertain to material covered in the course.  These meetings will be approximately 1-1.5 hours in length (allow 1.5 hours on your schedule).  We will meet on Tuesdays from 5:30-7PM in Room 203 Biochemistry (1/26, 2/2, 2/23, 3/30, 4/13). The first meeting will be organizational, and student discussion leaders will be selected for the subsequent sessions.


Prior to each meeting, students will read a research paper selected by the instructors. You must have read the paper BEFORE the session.  A group of two students will lead a discussion of the paper.  Issues to consider while reading and discussing the paper are:

á      What previous information led to the question(s) being asked in the paper?

á      How does the paper relate to material covered in lecture and the textbook?

á      What is the hypothesis being tested in the paper?

á      Understand the experimental methods used by the investigators.

á      How do the results relate to the hypothesis?

á      Did the authors prove their point?  Why or why not?  What else could be done?


The two primary discussants for each session should make an appointment to discuss the paper with the presiding instructor during the week prior to their presentation.


After completing the discussion of the paper, students will take a short quiz.  The quiz questions may be selected from a list written by the discussion leader(s) for that week.  Five potential questions must be submitted to the presiding instructor via email no later than 24 hours before our meeting time.





Excused Absence:

See the regular course syllabus handed out on the first day of the semester for general policies regarding excused absences. We expect that you will make every honors session, unless you are sick.  By the nature of the work we will do, it is difficult to make up an absence. If you must miss a session, make arrangements with the presiding instructor as soon as possible.




The total number of points will be the same as for Sections 501 and 502 (500 pts).  Points from exams and quizzes will be multiplied by a factor of 0.9.  Honors points will comprise 10% of the total (max. possible = 50 pts).  Honors points will be accumulated by the following formula:


            Participation in discussion when not a primary discussant:  10 pts

            Performance as a primary discussant team:                            20 pts

            Quizzes (total of 4):                                                                          20 pts (5 each time)




Schedule of Papers and Presiding Instructor for each Session:

pdf files for each paper can be accessed on Dr. ShippenŐs or KunkelŐs eLearning pages, or Dr. KunkelŐs webpage.


Feb. 2 (instructor: Kunkel)

ChIP-seq accurately predicts tissue-specific activity of enhancers (2009) Visel et al. Nature 457:854-858.


Feb. 23 (instructor: Kunkel)

ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex (1992) Bell, SP and Stillman, B. Nature 357:128-134.


March 30 (instructor: Shippen)

Rates of in situ transcription and splicing in large human genes (2009) Singh, J and Padgett, RA.  Nat. Struct. Mol. Biol. 16:1128-1133.


April 13 (instructor: Shippen)

Extension of Life-Span by Introduction of Telomerase into Normal Human Cells (1998) Bodnar, AG et al. Science 279:349-352.