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Course Descriptions

BCH 503 Biochemical Principles, 4 credits

Dual listed with BCH 403. One-semester general biochemistry course for science majors and pharmacy students. Covers protein and membrane structure and function, metabolism and nucleic acid structure, and molecular biology. (LEC)

BCH 504 Doctoral Student Seminar, 1 credit/2 semesters

The Doctoral Student Seminar is designed to provide a mechanism for Ph.D. students to gain experience and expertise in preparing and orally presenting a Research/Teaching Seminar. Master's candidates are required to attend this student seminar but are not required to present. This participation will introduce them to current research topics being addressed in Biochemistry.

BCH 507 Protein Structure and Function, 2-3 credits

Prerequisites: BMS 503 or BCH 403/BCH 503
The primary objective of this course is for students to become familiar with the principal, broad questions in protein structural biology and the experimental strategies used to answer them. These strategies include kinetics, specific mutagenesis, and model design and analysis. Specific topics include steady-state and transient kinetics, protein origins of enzyme catalysis, folding pathways and protein design, and protein allostery in the gating function of ion channels.

BCH 508 Gene Expression, 2 credits

Familiarizes students with up-to-date concepts and experimental approaches used in the study of eukaryotic gene expression. Focuses on the molecular mechanisms involved in RNA polymerase II (RNAPII) transcription. Specific topics include the structure and function of RNAPII and required auxiliary factors, the molecular mechanisms of transcriptional activation and repression, the coupling of transcriptional elongation with mRNA processing, and specific examples of the role of regulated RNA polymerase II transcription in development and cellular differentiation. Each week, one to two selected papers from the scientific literature are discussed in class, with students taking turns presenting one or two figures and the instructor providing clarification and/or additional questions as appropriate.

BCH/GGB 512 Developmental Genomics and Stem Cell Biology, 2 credits

This course focuses on how the spatial and temporal readout of the genome is achieved during development, and conversely on how forced changes in gene expression patterns can affect developmental processes. The philosophy of the course is that “development never ends” and thus examples of processes from normal or pathological embryonic, adult and aging systems may be discussed. Each session focuses on one or more fundamental principles of developmental biology/genomics using papers from the literature to illustrate the principle(s). Every effort is made to demystify developmental biology and discuss state-of-the-art experimental approaches to address questions about the genes required for normal development. While much teaching is in the form of student presentations from the primary literature, one-hour introductions are given by the course guides on each topic in the Tuesday lecture. The goal of the course is to enable students to read papers in the areas of developmental biology and genomics, to critically evaluate them, and to propose experiments that will answer questions raised in the paper.

BCH/BIO/GGB 519 Bioinformatics and Computational Biology, 3 credits

This course introduces graduate students to the concepts and practices of bioinformatics, including computational analysis of DNA and protein sequences, analysis of large-scale DNA and protein datasets, statistical analysis of sequence alignments and gene array datasets, proteomics, and RNA and protein structure prediction. This course is taught on Tuesdays and Thursdays from 10:30 am to noon. The Tuesday session is didactic lectures introducing the topic of the week and giving out assignments for completion at or prior to the Thursday lab session. The Thursday lab focuses on practical use of the concepts taught in the Tuesday lecture and is conducted by either the Tuesday lecturer, another faculty member who is expert in the particular analysis being performed or both. Assignments completed by the students for the lab sessions are graded by the appropriate instructor and used to determine the student’s grade in the course.

BCH 522 Protein-Nucleic Acid Interaction, 3 credits

This course is cross-listed in the departments of Microbiology, Biochemistry and Biology. Recognizing that a detailed, quantitative understanding of the interactions between proteins and nucleic acids is key to studying and understanding all aspects of nucleic acid metabolism, this course familiarizes students with all relevant aspects of proteins and how they interact with nucleic acids, as well as with state-of-the art approaches to performing quantitative studies. It is taught by a team of faculty with expertise in these areas.

BCH 607 DNA Replication and Repair, 2 credits

This course is cross-listed in the departments of Microbiology and Biochemistry. This course, for advanced PhD students, consists of a single, two-hour meeting per week. It utilizes a seminar/journal club format and all class readings consist of primary research articles in the general areas of DNA replication, DNA repair, and how these processes are regulated. Students taking this course should have satisfactorily completed BMS 503 or an equivalent advanced graduate-level biochemistry course covering biosynthesis of DNA in both prokaryotes and eukaryotes. In addition, students should have experience in the reading and analysis of primary research articles. Students are graded on their presentations of the primary research articles and on their participation in class discussions.

BMS 501 Cell Biology I, 4 credits

This course concerns basic concepts and contemporary issues of cell structure and function. Topics covered include cell structure and function, protein sorting and trafficking, membrane transport and excitability, signal transduction and cell cycle. A combined lecture and conference format is used with lectures emphasizing basic principles derived from original journal articles. Conferences are used to review lecture concepts, present laboratory demonstrations, analyze original literature and solve problems.

BMS 503 Principles of Biochemistry, 4 credits

Topics covered include chemical principles of biologic systems; chemical and physical properties of nucleotides, amino acids, proteins and water; protein structure and stability; introduction to steady-state kinetics; enzyme mechanism; controlling enzyme activity; metabolic circuitry; glucose transport and metabolism; pyruvate metabolism; the TCA cycle; electron flow and Ox-Phos; glycogen metabolism; gluconeogenesis and the pentose shunt; fatty acid catabolism and synthesis; disposal of nitrogen: the urea cycle; amino acid catabolism and synthesis; integrating metabolism: fed and fasted states and exercise; structure of nucleic acids; physical properties of nucleic acids, DNA replication and repair; transcription and its control; and RNA processing and translation.