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1 BIO-366 MICROBIAL GENETICS Instructor BIO-366 MICROBIAL GENETICS Instructor: Makkuni Jayaram Office: NMS-2.116 Phone number: 512-471-0966 e. mail: [email protected] Office hours: Wednesdays, 1.00 pm to 3.00 pm Course webpage: http://www.sbs.utexas.edu/jayaram/Bio-366/ Overview of the course The purpose of the course is to familiarize you with the fundamental features of gene organization, function and regulation. We will discuss the coding, duplication, retrieval, rearrangement and processing of genetic information using microbial examples. Topics will be treated with emphasis on molecular aspects, and biochemical mechanisms will be alluded to when relevant. It is hoped that the concepts you learn here will make it easier for you to follow more specialized molecular biology courses on the genetic regulatory mechanisms in higher systems. We will also critically analyze three original articles published in first tier journals that apply the concepts we cover for answering important biological questions. Topics Covered 1. Nucleic Acids. The chemical stuff of nucleic acids. Structure of DNA. Physical properties of DNA and RNA. Genetic information as the chemical sequence of nucleic acids. 2. Higher-order Structure of DNA. DNA topology. Negative and positive supercoiling. Plectonemic and solenoidal supercoiling. Regulation of negative supercoiling in vivo. Topoisomerase and their in vivo functions. Epigenetics: silencing of chromatin regions. 3. DNA Replication. 1 Initiation, elongation and termination of replication. Uni-directional and bi-directional replication. Fidelity of replication. The concept of the cell cycle and checkpoints; how it operates in bacteria. 4. Genetic Recombination. Recombination in bacteria and fungi. Homologous and site-specific recombination. Models of recombination. The Holliday intermediate in recombination. Double strand break repair in fungi and higher systems. Applications of gap-repair in gene targeting. DNA transposition. Use of transposons as mutagens. 5. Regulation of Gene Expression Positive and negative control of gene expression. Control by repression, anti-repression and attenuation. 6. Alternative Modes of Gene Regulation in Bacterial Viruses Lysogenic and lytic life cycles of phage lambda. Termination and anti-termination in control of gene expression. The developmental program in phage T4. Switching of gene expression patterns by protein factors. Modification of DNA bases for self-protection. 7. Application of Bacterial Genetics to Genetic Engineering and Technology. 6. Discussion of three original papers. Course Goals The purpose of the course is to familiarize you with the fundamental features of gene organization, function and regulation in the microbial world. It is hoped that the concepts you learn here will make it easier for you to follow more specialized molecular biology courses on the genetic regulatory mechanisms in higher systems. Course policies: suggestions for maximizing the benefits from the course It is important to attend classes. Many of the concepts will be presented in a manner that will be somewhat different in style from their description in standard text books. Students are encouraged to ask questions during lectures, so that difficulties may be clarified for the whole class. Please read the notes posted on the course web page, go over the power point presentations, and pay special attention to the ‘Discussion Points’. You could bring your questions to me during office hours, and I will try to answer them. I will also send out the answers to the whole class in e. mail format using ‘Black Board’. I will do my best to avoid other engagements during the office hours. However, it is always a good idea to e. mail me ahead of time to make sure that I have not run into unanticipated conflicts 2 Tests/Grading There will be multiple tests. They will examine your comprehension of concepts rather than your memory of facts. There will be no essays to write. Brief answers with illustrative diagrams, where appropriate, will serve you well. The dates of exams will be posted well in advance on the course web page, and also announced in class. There may be unannounced short quizzes. Your final grade will depend on the total scores from all tests and quizzes. I may discard the worst test score for each student while assigning the final grade. Grades will be A, B, C etc. with no ‘+’ or ‘-‘ superscripts. Text Books There are no prescribed text books for this course. ‘Microbial Genetics’ by Maloy, Cronan and Freifelder has a couple of chapters that will help you with some of the topics we discuss. I will direct you to them during the lectures. This book will be on reserve in the Life Sciences Library. It will also be available on-line. You may supplement class lectures and notes posted on the course web page by reading appropriate chapters from other good molecular biology text books. Examples are: Lehninger, Principles of Biochemistry by Nelson and Cox; Molecular Biology of the Gene by J. D. Watson. Accessing the course web page After you type in the URL address for the course (www.sbs.utexas.edu/jayaram/Bio-366/) in the window of your browser and press ‘enter’, you will be asked for a username and password in order to access the web page. I will provide these on the first day of class. You can e. mail me if you run into problems when attempting to open the page. 3 .
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