Molecular Biology Courses
BCH 5413 Eukaryotic Molecular Biology and Genetics
3 credits, Fall semester
M-W-F, 7th period
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: Jianrong Lu, Ph.D. | jrlu@ufl.edu | (352) 273-8200
GMS 5905 Fundamentals of Biochemistry and Molecular Biology
4 credits, Fall semester
M-T-W-F, 4th or 6th period
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: Linda B. Bloom, Ph.D. | lbloom@ufl.edu | (352) 273-5458
BCH 6415 Advanced Molecular and Cell Biology
3 credits, Spring semester
M,W,F 5th period
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: Linda B. Bloom, Ph.D. | lbloom@ufl.edu | (352) 273-5458
BCH 7410 Advanced Gene Regulation
1 credit, Fall semester
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.
- Syllabus
Coordinator: Jörg Bungert , Ph.D. | jbungert@ufl.edu | (352) 273-8098
BCH 7412 Epigenetics of Human Disease and Development
1 credit, in Spring 2022 this course is being offered in combination with BCH 7410 Advanced Gene Regulation (see above)
1 credit, Fall semester
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 | (352) 273-8200
BCH 7414 Advanced Chromatin Structure
1 credit, Spring semester (even years only)
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: TBD
Metabolism and Cell Biology Courses
BCH 6206 Metabolic Control Analysis
3 credits, Fall semester
M,W,F 2nd Period
The reactions of intermediary metabolism with emphasis upon their integration, mechanism. and control. One of the three core departmental courses.
Coordinator: Matthew Merritt, Ph.D. | matthewmerritt@ufl.edu | (352) 294-8397
BCH 6207 Advanced Metabolism: Role of Membranes in Signal Transduction and Metabolic Control
1 credit, Fall semester, Module 1
M,W,F 2nd period
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: Matthew Merritt, Ph.D. | matthewmerritt@ufl.edu | (352) 294-8397
BCH 6208 Advanced Metabolism: Regulation of Key Reactions in Carbohydrate and Lipid Metabolism
1 credit, Fall semester, Module 2
M,W,F 2nd period
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: Matthew Merritt, Ph.D. | matthewmerritt@ufl.edu | (352) 294-8397
BCH 6209 Advanced Metabolism: Regulation of Key Reactions in Amino Acid and Nucleotide Metabolism
1 credit, Fall semester
M,W,F 2nd period
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: Matthew Merritt, Ph.D. | matthewmerritt@ufl.edu | (352) 294-8397
Structural Biology/Advanced Physical Biochemistry Courses
BCH 6740 Structural Biochemistry
3 credits, Spring semester
M,T,W,F 3rd period
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 | (352) 273-5348
BCH 6741C Magnetic Resonance Imaging and Spectroscopy in Living Systems
3 credits, Fall Semester
Lectures: Tuesday/Thursday, 4th period
Lab: Thursday (last 5 weeks of semester)
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 | (352) 273-5348
BCH 6744C Molecular Structure Determination by X-Ray Crystallography
1 credit, Fall Semester (Not offered Fall 2020)
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 | (352) 294-8395
BCH 6744L Molecular Structure Determination by X-Ray Crystallography, Laboratory
1 credit, Fall semester (Not offered Fall 2020)
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 | (352) 294-8393
BCH 6745 and 6745L Molecular Structure and Dynamics by NMR Spectroscopy
1 credit each, Fall Semester (odd years only)
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 | (352) 294-8399
BCH 6746 Structure of Biological Molecules
1 credit, Spring semester, Module 1 of BCH 6740
M,T,W,F 3rd period
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 | (352) 294-8395
BCH 6747 Biophysical Methods of Structure Determination
1 credit, Spring semester
M,T,W,F 3rd period
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 | (352) 273-5348
BCH 6749C Numerical Methods in Structural Biology
1 credit, TBD
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 | (352) 294-8395
BCH 7515 Kinetics and Thermodynamics
1 credit, Spring semester, Module 3 of BCH 6740
M,T,W,F 3rd period
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 | (352) 294-8400
Journal Clubs and Seminars
BCH 6877 Recent Advances in Structural Biology Journal Club
1 credit, Fall and Spring semesters
M 8th period
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 | (352) 294-8395
BCH 6936 Biochemistry and Molecular Biology Journal Club
1 credit, Fall and Spring semesters
Reports and discussions of current research literature given by students and faculty.
Coordinator: Antonette Bennett, Ph.D. | matthewmerritt@ufl.edu | (352) 294-8394
BCH 6040 Research Discussion in Biochemistry and Molecular Biology
1 credit, Fall and Spring semesters
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 evaluating scientific data.
Coordinator: Linda B. Bloom, Ph.D. | lbloom@ufl.edu | (352) 273-5458
Laboratory and Other Courses
BCH 6905 Independent Studies in Biochemistry and Molecular Biology
1-5 credits each semester; max. of 12
Individual literature-based or experimental research problem. Prerequisite: permission of faculty member supervising work. Letter graded.
BCH 6910 Supervised Research
1-5 credits each semester; maximum of 5
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. S/U graded.
BCH 6971 Research for Master’s Thesis
1-15 credits
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. 3 credits of this course are required in the final semester of study during Fall and Spring semesters; 2 credits in the Summer semester.
GMS 5905 Grant Writing for Graduate Students
1 credit
Offered Summer semester in even years
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.
Coordinators:
- Linda B. Bloom, Ph.D. | lbloom@ufl.edu | (352) 273-5458
- Dietmar Siemann, Ph.D. | siemadw@ufl.edu | (352) 273-8231