TENTATIVE SYLLABUS
142:215 Molecular Biology of Gene Expression
Spring 2008
M W F 10:30 – 11:20 AM
1117 MERF
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Course Description: This course covers principles and techniques used to study mechanisms of gene expression in prokaryotes, eukaryotes and viruses. Topics covered include transcriptional regulation, chromatin packaging, RNA processing, RNAi mechanisms, transposons, viral vectors and DNA repair. In addition, instruction on the use of internet resources for DNA sequence and protein structure analyses will be provided. Principles and techniques will be illustrated with examples taken from primary scientific literature. Critical thinking skills will be developed through data analysis. Proposal writing skills will be developed through figure construction and proposal writing exercises. Grading will be based on performances on quizzes, homework assignments, closed and open book exams, and a written proposal.
Recommended prerequisite: 156:201 Principles of Molecular Biology
Course Director:
Lori Wallrath, Department of Biochemistry
Instructors:
Teaching Assistant:
Office Hours: TA office hours will be Monday's from 4:00 - 5:00 PM in room 3112 MERF. Instructor office hours are available by individual appointment.
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PDF files of the assigned papers will be posted in ICON. To login, open your browser and go to http://icon.uiowa.edu. Enter your HawkID and password. If you have trouble logging in, call the Help Desk at 384-HELP. Under My Courses, click on the Course Title. Click on Content to download the pdf files.
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Tentative Syllabus:
Note that lectures will be held in 1117 MERF unless stated otherwise.
| Date |
|
Topic |
Instructor |
1/23 |
W |
Prokaryotic transcriptional control |
SMR |
1/25 |
F |
RNA polymerase I and cell cycle control |
SMR |
1/28 |
M |
RNA polymerase III |
SMR |
1/30 |
W |
RNA polymerase II and basal factors |
SMR |
2/1 |
F |
Enhancers and the proteins that bind them |
SMR |
2/4 |
M |
Constitutive, ubiquitous transcription factors |
SMR |
2/6 |
W |
Inducible transcription factors and nuclear receptors |
SMR |
2/8 |
F |
Cross talk along the promoter |
SMR |
2/11 |
M |
Transcription elongation |
SMR |
2/13 |
W |
Capping and polyadenylation |
SMR |
2/15 |
F |
Review |
SMR |
2/18 |
M |
Introduction to bioinformatics |
BB |
2/19 |
Tu |
Exam I, open note/book, 6:00 - 8:00 p.m., Aud 1 BSB |
SMR |
2/20 |
W |
Clustal W and Blast basics, Computer lab, Hardin Commons |
BB |
2/22 |
F |
Advanced Blast features, Computer lab, Hardin Commons |
BB |
2/25 |
M |
Advanced Viewer and SNP databases, Computer lab, Hardin Commons |
BB |
2/27 |
W |
Protein structure modeling, Computer lab, Hardin Commons |
BB |
2/29 |
F |
Transcription in a native chromatin context |
LW |
3/3 |
M |
Insulators: Preventing regulatory crosstalk |
LW |
3/5 |
W |
Histone variants/Discuss proposal |
LW |
3/7 |
F |
Histone modifications and gene therapy 2-102 MEB |
LW |
3/10 |
M |
Transcription through a nucleosome |
LW |
3/12 |
W |
DNA methylation and Rett syndrome |
LW |
3/14 |
F |
Chromosomal translocations and disease |
LW |
3/17 |
M |
SPRING BREAK |
|
3/19 |
W |
SPRING BREAK |
|
3/21 |
F |
SPRING BREAK |
|
3/24 |
M |
Epigenetics of stem cells |
LW |
3/26 |
W |
Genome-wide analysis of transcription factor function |
LW |
3/28 |
F |
Dosage compensation, 2-102 MEB |
LW |
3/28 |
F |
Proposal Due by 4:30, turn in to Mol. Cell. Biol. Office 1190 ML |
LW |
3/31 |
M |
Nutrition and epigenetics |
LW |
4/2 |
W |
Quiz, closed book, in class |
LW |
4/4 |
F |
RNA splicing |
AM |
4/7 |
M |
RNA transport/quality control |
AM |
4/9 |
W |
microRNAs |
AM |
4/11 |
F |
RNAi mechanisms, 2-102 MEB |
AM |
4/14 |
M |
Viral vectors |
AM |
4/15 |
Tu |
Exam III, closed book, 6:00 - 7:30 pm, room TBA |
AM |
4/16 |
W |
Transposon diversity across species |
AD |
4/18 |
F |
Transposon mutagenesis in prokaryotes |
AD |
4/21 |
M |
Transposon mutagenesis in mammals |
AD |
4/23 |
W |
Transposon mutagensis in mammals cont. |
AD |
4/25 |
F |
Cancer epigenetics - hypermethylation in tumors |
AD |
4/28 |
M |
Cancer epigenetics - hypomethylation in tumors |
AD |
4/29 |
Tu |
Exam IV, closed book, 6:00 - 7:30 PM, Aud 1, BSB |
AD |
4/30 |
W |
DNA replication and DNA repair: B class DNA polymerase |
TI |
5/2 |
F |
DNA replication and disease: DNA polymerase h |
TI |
5/5 |
M |
DNA helicase and disease: Bloom syndrome |
TI |
5/7 |
W |
Transcription and Disease: Cockayne syndrome |
TI |
5/9 |
F |
Chromatin and Disease: Nucleotide excision repair |
TI |
5/12 |
M |
Exam IV, 2:15 - 3:45 PM, location TBA |
TI |
Textbook: No textbook is required for this course.
Grading: Grades will be based on quizzes, homework assignments and exams. LATE HOMEWORK ASSIGNMENTS WILL NOT BE ACCEPTED. Dr. Scott Moye-Rowley’s and Dr. Wallrath’s section will be worth 100 pts each. Dr. Banfi’s, McCaffrey’s, Dupuy’s and Itoh’s will be worth 50 pts each. Therefore, there is 400 pts total.
Distribution of handouts and graded material: Handouts will be provided in class. Graded assignments will be picked up in class or obtained in 1190 Med Labs between the hours of 8:00 AM – 4:30 PM, Monday through Friday.
University Policies: Please inform us if you have a disability and may require modification of seating, testing, or other class requirements so that appropriate arrangements may be made. Please contact the course director as soon as possible.
Please see http://www.uiowa.edu/~vpss/policies/ii/c.shtml regarding “Academic Misconduct” and “Student Complaints Concerning Faculty Actions”. In the case of a complaint concerning the faculty or teaching assistant, please consult with the instructor for that section. If the matter is not resolved to your satisfaction, then contact Dr. Lori Wallrath (Course Director) or Dr. Minnetta Gardinier (Molecular and Cellular Biology Program Director).
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