SYLLABUS AND COURSE POLICIES

Transcription

1 SYLLABUS AND COURSE POLICIES BIOLOGY 334-MOLECULAR BIOLOGY- FALL 2015 Time and Room: 9:45-11:35 T-Th CLSB 1A001 We will run with one break: 9:45-10:35, break (10 min.), 10:45-11:35. These are approximate times. Instructor/Office Hours: Jeffrey Singer, Ph.D., Associate Professor, Biology Department, PSU Office CLSB 3N032 Office Hours M, W, F 11:30-12:30 and by appointment (NOTE: for this you must go to this room: CLSB 5S021, they do not let me use my office for student office hours) jsinger@pdx.edu Tel: Textbook (required): Alberts et al., Molecular Biology of the Cell, 6th Edition, 2014 Garland Science. HARDBACK LOOSELEAF This will be used for both 334 and 336. i>clicker, sold at bookstore (or online), we will use these for quizzes and in class questions. Note: THESE ARE REQUIRED! You need to have them on the first day! Also, please make sure you register these online! Go to the iclicker website and select registration. Can use iclicker, iclicker + or iclicker 2. We will not use the iclicker go app. Prerequisites: Principles of Biology and General Chemistry (one year of each). Taking these courses at the same time as this one is not acceptable. Organic Chemistry recommended but not required. Biochemistry is helpful but not required. Subject Matter: We will cover the basics of DNA structure and replication, transcription and translation, and an introduction to the regulation of gene expression. We will also cover various methodologies used in modern molecular biology labs to examine these processes. Learning Objectives: DNA structure Identify a Watson-Crick base pair Recognize polarity and explain its significance in intramolecular and intermolecular interactions. Identify 2' and 3' positions on ribose Identify Major and minor grooves and explain the significance for DNA binding

2 Describe the cause and significance of hydrogen bonding Describe the basics of chromosome structure and the role of histone modification Recognize gene and repeat content of human genome Compare and contrast Twist and Writhe and positive and negative supercoils Replication List the steps in the mechanism of elongation and proofreading by DNA polymerases Describe reasons and mechanisms for high fidelity replication List the proteins present at replication forks in both bacteria and eukarya Describe the functions of origins of replication in bacteria and eukarya and the proteins that bind them Diagram the mechanism of licensing of replication origins Transcription Diagram and describe the significant steps and components of the transcription cycle Identify the components and describe the function of a promoter Explain the meaning of Consensus sequence and give an example of one Describe the role and function of sigma factors Describe the role and function of General Transcription Factors TF2D, B, and H Protein structure Recognize and describe the basic structure of Alpha helix hydrogen bonds and side chain orientation Recognize and describe the basic structure of Beta strand/sheet hydrogen bonds and side chain orientation List all the basic, acidic and OH-containing amino acids Regulation Contrast positive and negative regulation and provide examples of each Describe the role and function of enhancers and enhancer binding proteins and provide examples of each. Diagram and explain the operon model Describe the structure and role of eukaryotic enhancer binding proteins and their modularity Describe HTH, Homeodomain, and Zn finger DNA binding domains and know that others exist Identify the targets, both direct and indirect of eukaryotic enhancer binding proteins Identify the targets, both direct and indirect of eukaryotic repressors Compare and contrast combinatorial control, master regulators, and cell-type specific transcriptional regulators Identify the molecules involved and explain the processes of post-transcriptional control, translational initiation regulation, alternative splicing, and mrna editing. Compare and contrast small regulatory RNAs of the sirna and mirnas classes and basic aspects of their mechanisms of silencing/repression. D2L: Lecture presentations Supplemental reading materials Lecture Presentations: Lectures will be available online using D2L. These are an outline of what was covered in lecture and are provided to assist you. These files should not be considered a complete coverage of the lecture materials and are certainly not an acceptable replacement for attending lectures.

3 In addition, these are not notes, they are merely an outline of what I discussed in class. You should take your own notes. Remember-note taking is part of the learning process! Evaluation: Daily quizzes during class, (1/4 of grade), using clickers. Two Midterms (1/4 of Grade each)-oct. 20 th and Nov. 10 th in class. One Final (1/4 of Grade). Dec. 10 th, Thursday 8:00 AM-9:50 AM. This exam is not comprehensive. Note: If you cannot make these dates then do not take the course! Exam policies: Exams will likely involve multiple-choice, written short-answer, and drawing/labeling diagrams. For multiple-choice exams, students will need to provide a scantron sheet. Be sure to bring a form SC982-E* scantron sheet to every exam. *This is a large form, not the small one and has new features; I have uploaded a PDF of this form for you to see. You must bring this form; we will have 75-point exams. There are NO make-up exams (see below). It is your obligation to be present to take the scheduled exams. Please, do not take this course if you cannot be present for the exams at the scheduled times. This is not negotiable. The only acceptable reasons for missing an exam are a death in the family, serious illness verified by a doctor s note, or a required University sanctioned event. If you take the test in the testing center you must get an appointment for the correct day, take the test when the class takes it, and inform me at least one week ahead of time for each test!!!!! Also, you are responsible for keeping track of time during the exams!! Statement regarding recording and distribution of course sessions: Students who wish to make an auditory or visual recording of any portion of the class must speak with the instructor ahead of time. Any such recording is for personal use only. It may not be shared, copied, uploaded to the Internet, and/or distributed without written permission from the instructor as well as any student who appears or is heard in the recording. Statement regarding students with disabilities: Accommodations are collaborative efforts between students, faculty and the Disability Resource Center (DRC). Students with accommodations approved through the DRC are responsible for contacting the faculty member in charge of the course prior to or during the first week of the term to discuss accommodations. Students who believe they are eligible for accommodations but who have not yet obtained approval through the DRC should contact the DRC immediately at Safe Campus Module: If you have not done so already, please complete the Safe Campus Module in d2l. The module should take approximately 30 to 40 minutes to complete and contains important information and resources. If you or someone you know has been harassed or assaulted, you can find the appropriate resources on PSU s Enrollment Management & Student Affairs: Sexual Prevention &

4 Response website at: PSU's Student Code of Conduct makes it clear that violence and harassment based on sex and gender are strictly prohibited and offenses are subject to the full realm of sanctions, up to and including suspension and expulsion. Notes on clickers and quizzes: I will ask a few questions sometime during the lecture about the material covered in the previous lecture topic. Please do not communicate with others during the quiz. You are welcome to look at notes to answer these; you will have 90 seconds to answer each one using your clicker. These will comprise 25% of your grade, thus obtaining and registering your clicker is very important. Note, these are worth 75 points total. There will be more than 75 questions. The extras are there for those who must miss a few (sick, snow, etc.). Thus, there are no makeups. I will also ask questions that are not graded using the clickers. This will serve as a method to determine how well I am getting the material across to the class. Problem Sets: I will upload problem sets every week. At the end of the week I will upload solutions. These are optional and not graded. Doing them will help you with the concepts, please come to office hours to talk about these. Makeup/Cheating: Makeup exams are only given under extreme circumstances, e.g birth/death in family or illness, which requires medical attention (note from medical professional required). The instructor will determine the format and date of the makeup examination. Cheating on any examination or quiz will result in a zero. Grade determination: Grades will be determined as follows (percentage of total possible points*; your points divided by the total possible points* multiplied by 100): 90% -100% A 80% - 89% B 70% - 79% C 60% - 69% D 59% F *This number might be adjusted if necessary. Regrade Policy: Must be requested in writing within a week of return of examination. Note: Entire exam will be regraded and the grade may go down. Incompletes: I will follow the university policies. Those policies are shown here: Please review these.

5 Syllabus (note: topics, reading and subject matter may change): Date Day. Lecture Topic(s) Reading in Alberts et al. CELL CHEMISTRY AND PROTEINS Tues Sept Topic 1: Cells and Genomes, and Topic 2: Chemistry in Biology Chapters 1 and 2 Thurs Oct 1 2. Topic 3: Chemical Equilibria and Topic 4: Proteins 1: Structure and folding Chapter 3 Tues Oct 6 3. Topic 5: Proteins 2: Binding, Regulation and Catalysis Chapter 3 THE CENTRAL DOGMA-DNA TO RNA TO PROTEIN DNA Metabolism and Chromosomes Thurs Oct 8 4. Topic 6: DNA Chemistry and Structure, and Topic 7: Chapter 4 Chromosomes and Genomes Watson and Crick paper Tues Oct Topic 8: Chromatin compaction and nucleosomes and Topic 9: Epigenetics and higher order structures Chapter 4 Thurs Oct Topic 10: Genome Evolution Chapter 4 Tues Oct 20 EXAM 1 Thurs Oct Topic 11: DNA Replication 1: Mechanisms and machinery and Topic 12: DNA Replication 2: Origins, regulation and telomerase Chapter 5 Tues Oct Topic 13: DNA damage and repair, Topic 14: Recombination and Topic 15: Transposition Chapter 5 RNA Metabolism Thurs Oct Topic 16: Transcription I-Prokaryotic machinery and Topic 17: Transcription II: Eukaryotic machinery Tues Nov 3 Post-transcriptional Events 10. Topic 18: mrna processing and splicing and Topic 19: Translation I: The Genetic Code, trna structure and function, trna synthetases, Prokaryotic initiation Crick-Wobble hypothesis paper Thurs Nov Topic 20: Translation 2: Eukaryotic Initiation and Topic 21: RNA world Tues Nov 10 EXAM 2 TRANSCRIPTIONAL REGULATORY MECHANISMS Thurs Nov Topic 22: Transcriptional Regulation 1: DNA Binding and Topic 23: Transcription Regulation 2: Bacteria Chapter 7 Tues Nov Topic 24: Transcription Regulation 3: Eukarya Chapter 7 Thurs Nov Topic 25: Regulatory Circuits, Topic 26: Epigenetics and Topic 27: Post Transcriptional Regulation Chapter 7 METHODS IN MOLECULAR BIOLOGY Tues Nov Topic 28: Protein Methods Chapter 8 Thurs Nov 26 Thanksgiving Tues Dec Topic 29: DNA methods Chapter 8 Thurs Dec Topic 30: Genetic Methods and Topic 31: Viruses Chapter 8 Thurs Dec 10 Final Examination Thursday Dec 10 8:00 AM-9:50 AM Last Updated: September 28, 2015