BIO344 MOLECULAR BIOLOGY (Spring 2017)

BIO344 MOLECULAR BIOLOGY (Spring 2017) SYLLABUS AND COURSE SCHEDULE Unique number: 49520, 49525, 49530, 49535 Lectures: Monday and Wednesday 10:00-11:30AM BUR 224 Instructor: Jonghwan Kim, Ph.D Assistant Professor, Department of Molecular Biosciences Office: NMS 4.314 Phone: 512-232-8045 Email: Jonghwankim@mail.utexas.edu Web: http://web.biosci.utexas.edu/kimlab Office hours: Monday and Tuesday: 4:00-5:00PM, NMS 4.314 Teaching Assistant: Haridha Shivramy Office: MBB 3.212 Email: haridh@utexas.edu Office hours: by email appointment Discussion sections: Thursday Discussion sections are conducted by the TA. You are welcome to attend any of the listed discussions (highly recommended). Thursday: 10-11AM, JGB 2.202 11-12PM, WEL 3.266 3-4PM, RLM 6.112 4-5PM, ETC 2.102 DESCRPTION AND OBJECTIVES Biology 344 is a one-semester course covering the principles of modern molecular biology focusing on analyzing gene expression. The course will start with a general overview of molecular biology followed by the mechanisms of replication, transcription, epigenetic regulation, and translation, focusing on the regulation of key regulatory processes, as well as experimental plans and research tools. We will also study a variety of recently developed high-throughput and systems biology techniques that are widely used in molecular biology. The goals of this course are 1) to gain a better understanding of the concepts in modern molecular biology, 2) to think critically about the primary data underlying experiments, and 3) to analyze and interpret the results. You should be able to propose experiments based on techniques we have learned during the course that allow you to answer scientific questions. I am a faculty member in the Department of Molecular Biosciences and a member of the Institute for Cellular and Molecular Biology. I have a broad background in stem cell biology with specific training and expertise in systems biology approaches and technology development. The long-term goal of my research program is to decipher the underlying mechanisms of global transcriptional and epigenetic 1

regulations in early embryo development, especially by using embryonic stem (ES) and trophoblast stem (TS) cells as model systems. My previous studies focused on a structural and mechanistic understanding of regulatory networks modulating ES cell identity using various modern molecular biology tools. PREREQUISITE BIO 325 (Genetics) with a grade of at least a C TEXTBOOK (Optional) Fundamental Molecular Biology, 2 nd Edition; Author: Lizabeth A. Allison; Publisher: Wiley ATTENDANCE This course is designed for upper-division students, so I will not take attendance to deduct your point. You are responsible for attending the lectures, discussion sessions, and putting in the time and effort to pass the course. Although I do not plan to count your attendance for every lecture, there will be unannounced in-class quizzes that can take place at anytime during the lecture (see below), and I may count your attendance without notice using the Top Hat (see below) if necessary. If you do not miss any quizzes and my random attendance count, you will receive 1% increase on your final grade (1% of what you earn). I highly recommend that you attend the lectures. Simply looking at the lecture slides will not substitute for your attendance, and please be on time otherwise you might miss important announcements. STUDY This course consists of a series of lectures covering a broad range of topics in molecular biology. Lectures will be mainly based on materials in the textbook (optional) and research articles assigned. To be successful in this class, make sure that you understand what happened in class. It will be great for you to read materials (lecture note) for the lecture before and after each class, and identify questions to bring to discussion sessions or office hours. Lecture slides, reading materials, relevant research articles, and detailed answers to the exams and quizzes will be provided at the course Canvas website. It is important to understand the underlying concepts and how to apply them to new experimental situations. If concepts are not clear, go to the discussion sections or the office hours to ask questions. The University Course Guidelines suggests that for each hour a course meets, an average of 2 additional hours of studying is expected of the student. EXAMS AND QUIZZES There will be total four exams in the course without a comprehensive final exam. All four exams will take place during the class. Please look at the dates and times of all exams and be certain that you are able to attend. Make-up exams will be allowed only for officially sanctioned reasons, such as a documented serious illness, interview, etc., and with proper documentation from the Office of the Dean or your physician indicating that you are not in physical condition to take the exam at the scheduled time. Proper documentation should be provided in advance (at least 7 days) except medical emergency. There will be no make-up exams for any absences, such as weddings, vacations, voluntary activities, or 2

anything of that nature. There will be in-class quizzes without any specific notice. Also, there will be no make-up quizzes without an official document. If you miss the class, you miss the quiz and will receive a zero point for that quiz (see grade policy for details). Homework assignments may be given if necessary to help you understand scientific journal articles and/or lecture materials. Each quiz (or assignment) has the same weight to the total 10% of your grade. Please note that the lecture handouts on Canvas will not include additional material mentioned in class or presented on the board during lectures. Students who miss class are responsible for obtaining these notes from their classmates. GRADES AND RE-GRADE POLICY All four exams will be multiple-choice and short/long-answer/essay format tests. The best three will count towards 90% of the final grade (30% each exam), and the lowest of the four exams will be dropped. The remaining 10% will be from your quizzes and/or homework assignments. As indicated above, students will receive 1% increase on their final grade if they do not miss any quizzes/attendance count. There is no additional extra credit. All exams must be taken in pen, and it will be your responsibility to bring pens for the tests. Any tests written in pencil will not be considered for re-grading. Your final course grade will be computed as follows: 120 points Exam 1 120 points Exam 2 120 points Exam 3 120 points Exam 4 (The best three will be counted, 30% of total grade each) 40 points Quizzes (10%) 400 points Total (100%) All exams will be copied before being returned, and if a grade is contested, comparisons of the contested exam will be made to my copy to make sure no changes have been made. If you change your test and submit it for re-grading that is considered cheating (see below Scholastic dishonesty). If you feel that there is a mistake in grading of your exam, you must submit your entire exam for regrading directly to me after class with an attached explanation for why you believe an error has been made in your grading, no later than one week after they are returned. Explanations must be complete and to the point. This must be done for each question to be re-graded and the question must be clearly identified. Exams submitted after the one week deadline will not be re-graded. Once an exam is regraded, it will not be re-graded again. This is the only acceptable way to challenge your grade. Exams will be graded by my TA and myself, but your TA cannot influence your grade so please do not discuss re-grading issues with your TA. Your final grade will be determined by the scores that you achieve as follows: Scale for grading: A, 91-100; A-, 86-90; B+, 81-85; B, 76-80; B-, 71-75; C+, 66-70; C, 61-65; C-, 56-60; D+, 54-55; D, 52-53; D-, 50-51; F, <50 The final class average will be at least 72 and I will linearly raise class grades to 73 if that average final grade is not attained. 3

IMPORTANT DAYS Exam 1: February 8 (Wed) Exam 2: March 8 (Wed) Exam 3: April 12 (Wed) Exam 4: May 3 (Wed) COMMUNICATIONS WITH THE INSTRUCTOR The best way to contact me outside of class is by email (jonghwankim@mail.utexas.edu). You can email me to make a specific appointment during the Tuesday office hours. If not, you might have to wait while I speak with other people who made an appointment. I may use email to send out important announcements to the whole class. It is University policy that all students have a functioning email address and you should check email at least once a day (http://www.utexas.edu/cio/policies/). Full email inbox, failing to check email, failing to check Canvas are not excuses for missing an assignment or an important announcement. It is your responsibility to ensure that your email address on record is current. INSTRUCTOR OFFICE HOURS During instructor office hours, I will not simply repeat the lectures. Instructor office hours are for specific questions that were not covered in the discussion sessions or perhaps additional questions that you might have from the lectures or class materials. TOP HAT We will be using the Top Hat (www.tophat.com) classroom response system in class for quizzes. You will be able to submit answers to in-class questions and take attendance using Apple or Android smartphones and tablets, laptops, or via text message (SMS). You can visit http://tinyurl.com/thstudentregistration for the Student Quick Start Guide which outlines how you will register for a Top Hat account, as well as providing a brief overview to get you up and running on the system. Top Hat will require a subscription. There are multiple options and it costs $24 for 1 term subscription (4 months). CLASSROOM POLICY Be considerate of others. Any behavior that can be a distraction to other students or the instructor including unnecessary talking, cell phones, texting, web-surfing, video games, MP3 players, and sleeping in class will not be tolerated and you will be asked to leave. Students are expected to follow the Standards of Conduct outlined by the University: http://deanofstudents.utexas.edu/sjs/conduct.php. UNIVERSITY POLICY ON SCHOLASTIC DISHONESTY Incidents of scholastic dishonesty will be reported to the Dean of Students and will be strictly dealt with according to University policies. Information regarding academic dishonesty, the UT Honor Code (or statement of ethics) and an explanation or example of what constitutes plagiarism can be found through 4

this link to the University Honor Code and University policies on scholastic dishonesty: http://deanofstudents.utexas.edu/conduct/academicintegrity.php OTHER UNIVERISTY POLICIES You are responsible for keeping track of the deadlines for dropping the course. Students with disabilities: you may request appropriate academic accommodations from the Division of Diversity and Community Engagement, Services for Students with Disabilities, 471-6259 http://ddce.utexas.edu/disability/ Accommodations for religious holy days: you must notify me of your pending absence at least fourteen days prior to the date of observance of a religious holy day by UT Austin policy. If you must miss a class or an examination in order to observe a religious holy day, you will be given an opportunity to complete the missed work within a reasonable time after the absence. Additional University Policies Here are recommendations regarding emergency evacuation from the Office of Campus Safety and Security, 512-471-5767, http://www.utexas.edu/safety/: Occupants of buildings on The University of Texas at Austin campus are required to evacuate buildings when a fire alarm is activated. Alarm activation or announcement requires exiting and assembling outside. Familiarize yourself with all exit doors of each classroom and building you may occupy. Remember that the nearest exit door may not be the one you used when entering the building. Students requiring assistance in evacuation shall inform their instructor in writing during the first week of class. In the event of an evacuation, follow the instruction of faculty or class instructors. Do not re-enter a building unless given instructions by the following: Austin Fire Department, The University of Texas at Austin Police Department, or Fire Prevention Services office. Behavior Concerns Advice Line (BCAL): 232-5050 Link to information regarding emergency evacuation routes and emergency procedures can be found at: www.utexas.edu/emergency 5

COURSE SCHEDULE: Wk Month Lecture Weekly Topic Daily Topic Chapter 1 Jan. 18 1 Introduction Orientation, A brief history 1 2 Jan. 23 2 Components in gene regulation DNA 2 Jan. 25 3 RNA, Protein 3, 4 3 Jan. 30 4 Genome Genome organization 5 Feb. 1 5 DNA replication 6 4 Feb. 6 6 Methods in molecular biology Recombinant DNA technology I 8 Feb. 8 Exam 1 Lectures 1-5 5 Feb. 13 7 Gene expression Recombinant DNA technology II 8 Feb. 15 8 Analyzing gene expression 9 6 Feb. 20 9 Transcription Transcription I 10 Feb. 22 10 Transcription II 11 7 Feb. 27 11 Epigenetic mechanism Epigenetic regulation I 12 Mar. 1 12 Epigenetic regulation II 12 8 Mar. 6 13 Special topic I Cell fate conversion Mar. 8 Exam 2 Lectures 6-12 9 Spring Break No class Topics listed are tentative, but the dates of exams will not be changed. Optional textbook chapters are also shown. 6 No class 10 Mar. 20 14 Post-transcriptional events RNA splicing 13 Mar. 22 15 RNA editing 13 11 Mar. 27 16 RNA interference RNA interference (RNAi) I 13 Mar. 29 17 RNA interference (RNAi) II 13 12 Apr. 3 18 Translation Translation I 14 Apr. 5 19 Translation II 14 13 Apr. 10 20 Genetically modified organisms GMO 15 Apr. 12 Exam 3 Lectures 13-19 14 Apr. 17 21 Special topic II Genome editing Apr. 19 22 Omics study High-throughput biology 16 15 Apr. 24 23 Global Gene expression profiling 16 Apr. 26 24 Medical molecular biology Medical molecular biology 17 16 May. 1 25 Summary, Q and A May. 3 Exam 4 Lectures 20-24