Biology 367:
Advanced Molecular biology
A. Course policies
MWF
12:00 Ð 1:00, Parker 104
Office
hours
My official office hours
are Monday 10-12 and 1-2, and Thursday 10-11 and 12-2.
I will be happy to arrange
for a different time to meet with you. To do that you can stop by my office and
leave a note if IÕm not there, send me an email, or leave me a telephone
message.
Office
230 Parker Hall; email zpasman@ic.edu; phone
245-3435.
Written
resources
See
references below.
Assignments
There
will be two take-home exams (dates indicated on the syllabus). In addition, students will take turns
presenting research papers throughout the semester. Exams will account for 40% of the final grade and
presentations for 40%. Every
student is expected to be able to discuss each paper, irrespective of the
presenter. Students who are not
presenting are required to submit 3 questions about the paper (ideally, one
question each from the Introduction, Results, and Discussion sections). These questions will account for 20% of
the final grade.
Grading
90-100% A
80-89% B
70-79% C
60-69% D
I do not
anticipate using a curve, but I will do so if necessary. Ò+Ó and Ò-Ò grades can be assigned.
Attendance
You are
expected to attend lectures regularly and contribute to discussions. Remember that material on the exams
will be drawn heavily from the material covered in class. Also, remember that a large amount of
your final grade depends on class discussion, which usually cannot be
accomplished without regular attendance.
Academic
Honesty
I will
prosecute any case of academic fraud or dishonesty that I can document. Academic dishonesty, simply put, is
representing work as your own when it is not. Also, please see the Illinois College Honor Code. If, in your judgment, an issue might be
subject to academic honesty considerations, ask me for clarification as soon as
possible.
|
Week |
Material |
reading |
|
8/25 |
Regulation
of gene expression during transcription initiation |
Alberts
et al., Ch. 6,7 |
|
9/1 |
Regulation
of gene expression during transcription initiation |
Alberts
et al., Ch. 6,7 |
|
9/8 |
Regulation
of gene expression during transcription initiation |
Svejstrup
et al., 1997; Rani et al., 2004 |
|
9/15 |
Post-initiation
transcription regulation in lambda phage |
Alberts
et al., Ch. 5,6,7 |
|
|
Friday,
September 19, exam 1 |
|
|
9/22 |
Post-initiation
transcription regulation in lambda phage |
van
Gilst et al., 1997; Rees et al., 1996 |
|
9/29 |
Post-initiation
transcription regulation in retroviruses |
Alberts
et al., Ch. 5,6,7,13,25 |
|
10/6 |
Post-initiation
transcription regulation in retroviruses |
Keen
et al., 1995 |
|
10/13 |
Discovery
of RNA splicing |
Berget
et al., 1977; Chow et al., 1977 |
|
10/20 |
Regulation
of gene expression by RNA splicing, fall break |
Cech
et al., 1981 |
|
10/27 |
Ribosome
structure and catalytic mechanisms |
Nissen
et al., 2000; Muth et al., 2000 |
|
11/3 |
Ribosome
structure and catalytic mechanisms |
Bayfield
et al., 2001 |
|
11/10 |
Ribosome
structure and catalytic mechanisms |
Polacek
et al., 2001 |
|
11/17 |
Endoribonuclease-RNA
interactions, student-selected presentations |
Plantiga
et al., 2008; student-selected papers |
|
11/24 |
Student-selected
presentations, Thanksgiving break |
Student-selected
papers |
|
12/1 |
Student-selected
presentations |
Student-selected
papers |
|
|
Wednesday,
December 12, 12:30-2:30, exam 2 |
|
Molecular
Biology of the cell, 4th edition,
B. Alberts et al., 2002.
Berget,
SM, Moore, C, and Sharp, PA.
Spliced segments at the 5Õ terminus of adenovirus 2 late mRNA. Proc. Natl. Acad. Sci. U.S.A. 74,
3171-3175, 1977.
Cech,
TR, Zaug, AJ, and Grabowski, PJ.
In vitro splicing of the ribosomal RNA precursor of Tetrahymena:
involvement of a guanosine nucleotide in the excision of the intervening
sequence. Cell 27, 487-496, 1981.
Chow,
LT, Gelinas, RE, Broker, TR, and Roberts, RJ. An amazing sequence arrangement at the 5Õ ends of adenovirus
2 messenger RNA. Cell 12, 1-8,
1977.
Graveley,
BR. Sex, AGility, and the
regulation of alternative splicing.
Cell 109, 409-412, 2002.
Keen,
NJ, Gait, MJ, and Karn, J. Human
immunodeficiency virus type-1 Tat is an integral component of the activated
transcription-elongation complex.
Proc. Natl. Acad. Sci. U.S.A. 93, 2505-2510, 1996.
Muth,
GW, Ortoleva-Donnelly, L, Strobel, SA.
A single adenosine with a neutral pKa in the ribosomal
peptidyl transferase center.
Science 289, 947-950, 2000.
Nissen,
P, Hansen, J, Ban, N, Moore, PB, and Steitz, TA. The structural basis of ribosome activity in peptide bond
synthesis. Science 289, 920-930,
2000.
Plantiga,
MJ, Korennykh, AV, Piccirilli, JA, and Correll, CC. Electrostatic interactions guide the active site face of a
structure-specific ribonuclease to its RNA substrate. Biochemistry, in the
press, 2008.
Polacek,
N, Gaynor, M, Yassin, A, and Mankin, A.
Ribosomal peptidyl transferase can withstand mutations at the putative
catalytic nucleotide. Nature 411,
498-501, 2001.
Rani,
PG, Ranish, JA, and Hahn S. RNA
polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable
Pol II complexes and their activity in transcription initiation and
reinitiation. Mol. Cell Biol.,
1709-1720, 2004.
Rees, W,
Weitzel, SE, Yager, TD, Das, A, and von Hippel, PH. Bacteriophage l N protein
alone can induce transcription antitermination in vitro. Proc. Natl. Acad. Sci. U.S.A. 93,
342-346, 1996.
Svejstrup,
JQ, Li, Y, Fellows, J, Gnatt, A, Bjorklund, S, and Kornberg RD. Evidence for a mediator cycle at the
initiation of transcription. Proc.
Natl. Acad. Sci. U. S. A. 12, 6075-6078, 1997.
Van
Gilst, MR, Rees, WA, Das, A, and von Hippel, PH. Complexes of N antitermination protein of phage l with
specific and non-specific RNA target sites on the nascent transcript. Biochemistry 36, 1514-1524, 1997.
Presenter ____________________________ Reviewer _____________________________
Date
____________________
Title ______________________________________________
A. (10%) Title
1. The title was descriptive _______
B. (20%) Introduction
2. The introduction contained a sufficient
amount of relevant
background
information _______
3. The introduction identified the
question and/or hypothesis
that
is/are being addressed in this study _______
C. (20%) Methods
4. The methods were described clearly _______
5. The methods included sufficient detail _______
D. (20%) Results
6. All relevant data were included _______
7. Graphs and tables were used
appropriately _______
8. Appropriate conclusions that address
the questions/hypothesis
(see
item 3 above) were drawn _______
9. The results were explained (why did
your experiments produce
these
results?) _______
10. The presenter exhibited confidence and
clear enunciation _______
What was the best aspect of
the presentation?
What aspect of the
presentation should be improved?