1BIOL 434, Molecular Biology Gene Expression Control Mechanisms Spring 2011, TTh 11:00‐12:15, 212 Wilson Hall Professor: Dr. Lillie L. Searles, 508 Fordham Hall, 966‐4989, [email protected] Office hours: by appointment Course Description: This course is designed for upper level undergraduate students who have completed BIOL 202 (or its equivalent) and want to explore specific topics in gene expression from an experimental approach. Substantial student participation is expected throughout the semester. Most class discussions will be based on assigned readings from the textbook Molecular Biology, fourth edition, by Robert Weaver. Review articles or research papers will also be assigned for some lectures, and occasionally experiments from primary research articles will be discussed in class. Students are not expected to have prior experience with conducting research or reading scientific papers. In this class, we will examine a relatively small number of molecular processes in considerable depth. From taking the molecular biology portion of BIOL 202, you will be familiar with many of the topics that we discuss. However, in BIOL 434, we will approach these subjects in a very different way. Our focus will be on the experiments that provide the basis for concepts in molecular biology. Other topics are likely to be ones that you have not learned about previously. During each class, our discussion will be focused on the experiments from the reading that are presented in the assigned figures. When reading, pay close attention to the pages of the textbook that are relevant to those figures. Read the other pages within the assignment less thoroughly to gain a general understanding of the concepts and ideas contained therein. UNC Blackboard: PowerPoint presentations, review articles, papers, and other lecture materials will be posted on Blackboard in the Course Documents section. Exams: The two mid‐terms and the final exam each count 25% of the final grade. The mid‐term and final exams will be open‐note format. The final exam will not be cumulative. Students who cannot be present for an exam are expected to inform Dr. Searles in advance and make arrangements to take the exam at an alternate time. Class Participation counts 15% of the final grade. Student Presentations count 10% of grade. Teams of students will make oral presentations, based on a research article, during the final class periods. Date Topic Reading Assignment Figures & Tables 2 Mechanism of transcription in bacteria 1/11 Introduction and overview; RNA polymerase‐promoter interactions; initiation 6:126‐134 5:115 (filter binding assay) 5:110 (run‐off transcription) Table 6.1; Figs. 6.3, 4, 8, 10, 11 1/13 Initiation (continued) and elongation 6:135‐143; 146‐151 6.14, 15,17, 30 1/18 Elongation (continued) and termination 6:159‐168 6.47‐6.50 Fine control of bacterial transcription 1/20 The lac operon 7:172‐174; 178‐188 Figs. 7.6‐7.9; Table 7.2 1/25 The ara operon 7:188‐192 7.22‐7.25 1/27 The trp operon; riboswitches 7:192‐199; research article on riboswitches 7.33 and figs. from the research article Major shifts in bacterial transcription 2/01 Sigma factor switching 8:201‐209 8.2,5,6,7 2/03 Bacteriophage  infection 8:209‐224 8.16, 21 2/08 DNA‐protein interactions in bacteria 9:228‐229; 232‐235; 241‐247 9.4, 17, 18, 19, 20 2/10 Exam 1 (covers 1/11‐2/08) Mechanism of transcription in eukaryotes 2/15 Eukaryotic RNA polymerases, promoters and other cis‐regulatory elements 10:250‐258; 266‐270; 274‐276 10.7,21,23,29, 30 2/17 General class II transcription factors (with emphasis on TFIID, H, and S) 11:280‐294;297‐306 11.1, (2, 3),5,10, (20‐22), (27, 30) 2/22 Transcription activators 12:321‐354 12.15, 18, 19, 22, 32 Chromatin structure and its effect on transcription 2/24 Chromatin structure; nucleosome positioning 13:359‐368 (background); 370‐377; review article on nucleosome positioning 13.14,15,22; figs in article 3/01 Post‐translational modification of histones 13:377‐381; review article on genomic approaches to studying chromatin modifications; review article on chromatin modifications and their function 13.25; figs in articles 3/03 Chromatin remodeling; heterochromatin and gene silencing 13:382‐395; review article on the logic of chromatin modification and remodeling 13.30, 31, 37, 30, 40 3/08 Spring Break – no class 3/10 Spring Break – no class 3/15 In‐class review session 3/17 Exam 2 (covers 2/15‐3/03) Eukaryotic pre‐mRNA processing 3/22 Splicing mechanism 14:399‐405;418‐424; review article on the spliceosome 14.5, 25, 26, 29, (30,31) 3/24 Role of RNA Pol II CTD in splicing 14:427‐434; review article on coupled transcription 14.35, 36, 40 3and alternative splicing 3/29 Capping and polyadenylation 15:444‐464 Table 15.1 Figs. 15.(17, 18),20, 21, 22, 24, 27 3/31 Coordination of transcription and RNA processing 15:467‐476 15.32, 33, 34,35,37,38 Post‐transcriptional control of gene expression 4/05 Control of mRNA stability; nonsense mediated decay 16:494‐500; review article on nonsense mediated decay Table 16.1 Figs. 16:23, 24, 25,26 4/07 Nuclear RNAP quality control Review article 4/12 RNA interference 16:501‐516 16.30,31,32,36,43,44 4/14 Using RNAi as a tool to study nonsense mediated decay Research article on the role of SMG6 in nonsense mediated decay 4/19 Student Presentations 4/21 Student Presentations 4/26 Student Presentations 5/05 12:00 Final Exam (covers 3/22‐4/21)