Graduate Courses
Molecular Biology CoursesBCH 5413 Eukaryotic Molecular Biology and Genetics This course is designed for graduate or advanced undergraduate students desiring a course in molecular biology beyond an introductory course. Lectures and discussions will emphasize modern molecular and biochemical approaches to solving problems of current interest. NOTE: BCH 5413 replaces BCH 6415, and is a prerequisite for BCH 6415. Students should have a working knowledge of molecular biology such as that covered in “Lehninger’s Principles of Biochemistry”, third edition; or Mathews and van Holde’s “Biochemistry”, second edition. We DO NOT recommend this course for students who have not had an introductory course in molecular biology, e.g., BCH 4024 or its equivalents. Coordinator: Thomas P. Yang, Ph.D. tpyang@ufl.edu 294-8401 GMS 5905 Fundamentals of Biochemistry and Molecular Biology This course is designed to provide early-stage graduate students in the life sciences with a firm foundation in the structure, function, and metabolism of amino acids, proteins, carbohydrates, lipids, and nucleic acids. It also introduces concepts in cell structure, replication, cell signaling, growth control, and metabolic regulation. The course also introduces students to critical evaluation of primary research literature and small group presentations. Coordinator: Kevin D. Brown, Ph.D. kdbrown1@ufl.edu 273-5458 BCH 6415 Advanced Molecular and Cell Biology An advanced course in the molecular biology of pro- and eukaryotic organisms, with an emphasis on understanding the experimental approaches which have led to recent developments in the field. Topics include chromosome structure and organization, RNA transcription, selected aspects of the molecular regulation of gene expression, protein synthesis and post-translational regulation, DNA synthesis, repair, and recombination. The prerequisites for this course are BCH 5413 or GMS 6001. Students lacking these prerequisites may be admitted with consent of instructor. Coordinator: Thomas P. Yang, Ph.D. tpyang@ufl.edu 294-8401 BCH 7410 Advanced Gene Regulation This course will serve as a literature-based assessment of the most recent advances in factors governing eukaryotic gene regulation. This course will consist of a series of faculty lectures, group discussions and student presentations at the level of original research papers. Coordinator: Suming Huang, Ph.D. sumingh@ufl.edu 273-8098 BCH 7412 Epigenetics of Human Disease and Development In-depth assessment of epigenetic mechanisms of mammalian gene regulation: DNA methylation, histone modifications, genomic imprinting, inherited genetic diseases, viral gene regulation, and epigenetic reprogramming in embryonic stem cells and cloning. Prerequisite: GMS 6001. BCH 6415 is recommended. Coordinator: Jianrong Lu, Ph.D. jrlu@ufl.edu 273-8200 BCH 7414 Advanced Chromatin Structure In-depth, lecture and literature-based assessment of chromatin structure: the nucleosome, nucleosome dynamics, higher-order chromatin folding, chromatin remodeling, histone variants, chromatin domains and creating, interpreting and modifying the histone code. Prerequisite: BCH 5413, GMS 6001, or consent of instructor. Coordinator: Thomas Yang, Ph.D. tpyang@ufl.edu 294-8401 Metabolism and Cell Biology CoursesBCH 6206 Metabolic Control Analysis The reactions of intermediary metabolism with emphasis upon their integration, mechanism. and control. One of the three core departmental courses. Coordinator: Susan C. Frost, Ph.D. sfrost@ufl.edu 294-8386 BCH 6207 Advanced Metabolism: Role of Membranes in Signal Transduction and Metabolic Control Fundamentals of membrane biochemistry. The course will include discussions of membrane structure, nutrient and ion transport, protein targeting, signal transduction. Students will learn experimental methods and techniques used to gather and analyze data related to membrane biochemistry and its regulation. Coordinator: Susan C. Frost, Ph.D. sfrost@ufl.edu 294-8386 BCH 6208 Advanced Metabolism: Regulation of Key Reactions in Carbohydrate and Lipid Metabolism Lectures will emphasize key reactions in the metabolic pathways of carbohydrate and lipid metabolism with special attention to the exploration of the experimental basis for our current understanding of these processes. Understanding of the interactions between major metabolic pathways and control of these pathways under different physiological conditions are central themes of the course. Coordinator: Susan C. Frost, Ph.D. sfrost@ufl.edu 294-8386 BCH 6209 Advanced Metabolism: Regulation of Key Reactions in Amino Acid and Nucleotide Metabolism Lectures will emphasize key reactions in the metabolic pathways of amino acid and nucleotide metabolism with special attention to understanding interactions between major metabolic pathways and control of these pathways under different physiological conditions. Special emphasis will be placed on the structural basis of enzyme function and regulation. Coordinator: Susan C. Frost, Ph.D. sfrost@ufl.edu 294-8386 Structural Biology/Advanced Physical Biochemistry CoursesBCH 6107 Biophysical Techniques in Proteomics and Protein Science Theory and application of modern biophysical techniques relevant to proteomics and protein science. Coordinator: Robert McKenna, Ph.D. rmckenna@ufl.edu 294-8395 BCH 6740 Structural Biochemistry Physical chemistry of biological molecules and the techniques for their study. Constitutes one of the three core departmental courses. This three-part course introduces theoretical and practical aspects of structural biology and biophysical chemistry. The course will be of interest to graduate students and well-prepared undergraduates with interests in biochemistry, molecular and cellular biology, pharmacology, microbiology and cell science, chemistry, physics, plant sciences, and chemical engineering. Coordinator: Thomas H. Mareci, Ph.D. thmareci@ufl.edu 273-5348 BCH 6741C Magnetic Resonance Imaging and Spectroscopy in Living Systems The course provides students with knowledge necessary to apply modern methods of MR imaging and spectroscopy in vivo to solve research problems. Lectures will provide a detailed treatment of theory of MR imaging and current methods for visualizing the structure of cells, tissues, whole animals, and humans with a focus on living systems. Also current methods will be discussed which allow the monitoring of biochemical processes in cells suspensions, whole animals, and humans using in vivo MR spectroscopy. In addition, a lab will be taught so that the students will have practical experience in sample preparation, operation of the instrumentation, preliminary data analysis and construction of simple MR radio frequency coils. A student can register for the lecture portion of the course of two-credit hours, or both the lecture and lab for three-credit hours or just the lab portion for 1 hour credit. The best option is registration for both the lecture and lab portions, which reinforce each other. Coordinator: Thomas H. Mareci, Ph.D. thmareci@ufl.edu 273-5348 BCH 6744 Molecular Structure Determination by X-Ray Crystallography The objective of the course is to provide detailed theoretical instructions on the methodology of X-ray crystallography, a biophysical technique at the forefront of research efforts aimed at structure-function elucidation of macromolecules. Students will learn the theory behind the technique of X-ray crystallography and will apply the knowledge obtained to the three-dimensional structure determination of a macromolecule lysozyme. 15 hours of lectures on X-ray crystallography. The anticipation is that students will take both BCH 6744 and BCH 6744L, which will run concurrently. However, students may enroll in either BCH 6744 or BCH 6744L. Coordinator: Robert McKenna, Ph.D. rmckenna@ufl.edu 294-8395 BCH 6744L Molecular Structure Determination by X-Ray Crystallography, Laboratory This laboratory class will complement the lectures in BCH 6744. It will provide practical experience in sample preparation, operation of the instrumentation, data acquisition, data analysis, phasing, and refinement. This hands-on approach will reinforce the applicability of this methodology in the analysis of the functional properties of a biological macromolecule. 15 hour of lab/applications. The anticipation is that students will take both BCH 6744 and BCH 6744L, which will run concurrently. However, students may enroll in either BCH 6744 or BCH 6744L. Coordinator: Mavis Agbandje-McKenna, Ph.D mckenna@ufl.edu 294-8393 BCH 6745 and 6745L Molecular Structure and Dynamics by NMR Spectroscopy This course is an introduction to modern NMR experiments and their application to biological problems. The class will provide an understanding of multidimensional (2D, 3D, 4D) and multinuclear (1H, 15N, 13C, .. ) NMR experiments. Emphasis will be placed on practical applications of molecular structure and dynamics determination, and extensive use will be made of computer software packages. In the lecture part of the course, students will learn the principles underlying NMR experiments as well as the basic tools to mathematically describe complex NMR experiments. In the laboratory part of the class, students will be trained to use modern NMR instrumentation, data processing, and data analysis. At the end of the laboratory students will have enough training to be users of the NMR instrumentation in the UF Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) facility. 15 hours of lectures on NMR spectroscopy, 15 hour of lab/applications. Coordinator: Joanna Long, Ph.D. jrlong@ufl.edu 294-8399 BCH 6746 Structural Biology: Macromolecular Structure, Determination This module will provide instruction in experimental approaches to biological macromolecular structure determination, with emphasis on current understanding of protein-protein, protein-nucleic acid structure motifs, dynamics and aspects of protein folding. Coordinator: Robert McKenna, Ph.D. rmckenna@ufl.edu 294-8395 BCH 6747 Structural Biology/Advanced Physical Biochemistry: Spectroscopy and Hydrodynamics The first half of the class will focus on the application of spectroscopic techniques (circular dichroism, fluorescence, nuclear magnetic resonance) to determine the structure of biological macromolecules. The second half will cover hydrodynamic approaches including light scattering, molecular diffusion, viscosity and ultracentrifugation. Coordinator: Thomas H. Mareci, Ph.D. thmareci@ufl.edu 273-5348 BCH 6749C Numerical Methods in Structural Biology Provides an overview of mathematical and computational methods needed to understand current structural models, biophysical processes, data acquisition methods, and analysis of data acquired with current methods in structural biology. For students without advanced course work in physical and mathematical methods this course will be taught as a complement to the Techniques courses (BCH 6741C, BCH 6744 and 6745). The course objective is to provide the students with an overview of mathematical and computational methods necessary to perform complex analysis of biophysical and structural data. Prerequisite: BCH 6740 or equivalent and an undergraduate course in calculus or equivalent. 15 hr of lecture/lab. Coordinator: Robert McKenna, Ph.D. rmckenna@ufl.edu 294-8395 BCH 7515 Structural Biology/Advanced Physical Biochemistry: Kinetics and Thermodynamics This module will provide the student with the fundamentals of chemical kinetics and thermodynamic analysis of equilibria. The emphasis will be the application of this knowledge to our understanding of basic enzyme kinetics, pulse-chase kinetics, protein polymerization, DNA dynamics, protein-nucleic acid interactions and cooperative ligand binding. Coordinator: Daniel L. Purich, Ph.D. dlpurich@ufl.edu 294-8400 Journal Clubs and SeminarsBCH 6875 Methodologies and discoveries in crystallography and cryo-electron microscopy Current literature on topics on the methodologies (both theoretical and practical) and the applications and discoveries in the biophysical techniques of crystallography and cryo-electron microscopy are dicussed. Each week a paper is presented by a student or faculty member of the journal club and discussed in depth. Emphasis is on current developments, data interpretation and critical analysis. Classes are held informally in small groups. Coordinator: BCH 6876 Recent Advances in Membrane Biology Journal Club Literature of membrane biology, presented by students and faculty, discussed in depth. Emphasis is on current developments, data interpretation and critical analysis. Classes are held informally in small groups. Coordinator: Matthew Merritt, Ph.D. matthewmerritt@ufl.edu 294-8397 BCH 6877 Recent Advances in Structural Biology Journal Club Literature on structural biology, presented by students and faculty, discussed in depth. Emphasis is on current developments, data interpretation and critical analysis. Classes are held informally in small groups. Coordinator: Robert McKenna, Ph.D. rmckenna@ufl.edu 294-8395 BCH 6878 Recent Advances in Cytoskeletal Processes Journal Club Literature on cytoskeletal processes, presented by students and faculty, discussed in depth. Emphasis is on current developments, data interpretation and critical analysis. Classes are held informally in small groups. Coordinator: Daniel L. Purich, Ph.D. dlpurich@.ufl.edu 294-8400 BCH 6936 Biochemistry and Molecular Biology Journal Club Reports and discussions of current research literature given by students and faculty. Coordinator: Kevin Brown, Ph.D. kdbrown1@ufl.edu 273-5458 BCH 6040 Research Discussion in Biochemistry and Molecular Biology Current research in Biochemistry and Molecular Biology is presented by departmental faculty and invited speakers. The goal is to stimulate discussion in diverse areas of research and help students develop skills in critically evaluationg scientific data. Coordinator: Linda Bloom, Ph.D. lbloom@ufl.edu 294-8379 Laboratory and other CoursesBCH 6905 Independent Studies in Biochemistry and Molecular Biology Individual literature-based or experimental research problem. Prerequisite: permission of faculty member supervising work. BCH 6910 Supervised Research Experimental research in the field of biochemistry or molecular biology performed under the supervision of a Biochemistry and Molecular Biology faculty member. Prerequisite: Permission of faculty member supervising work. BCH 6971 Research for Master’s Thesis Experimental research done as part of a Master’s thesis project that is performed with guidance from the Master’s Thesis Advisor. Prerequisite: Permission of faculty member supervising work. GMS 5905 Grant Writing for Graduate Students This course will guide students through the process of preparing a NIH F30/F31 fellowship application. During this course students will 1) discuss strategies for preparing a section of the application that will be assigned as homework, and 2) discuss critiques of proposal sections from the previous assignment. Coordinator: Linda Bloom, Ph.D. lbloom@ufl.edu 294-8379
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