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Course Descriptions

BCH 503 Biochemical Principles (4 cr)

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)

BMS 503 Principles of Biochemistry (4 cr)

Covers 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; RNA processing and translation. (LEC)

BCH 504 Doctoral Student Seminar (1 cr)

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. This includes three components :1) the Research Proposal (BCH 565), 2) a Journal Club, 3) Thesis Research Progress Presentation (BCH 703). (SEM)

BCH 507 Protein Structure and Function (variable, 2-3 cr)

Familiarizes students with the principal, broad questions in protein structural biology and the biophysical strategies used to answer them, including protein engineering, kinetics, calorimetry, fluorescence, atomic force microscopy, surface plasmon resonance, electron paramagnetic resonance and mass spectrometry. Specific topics include folding pathways and protein design, steady-state and transient kinetics, protein origins of enzyme catalysis and protein allostery. Students have optional opportunity to earn 3 credits by preparing a graduate-level quality research project description based on material covered in the course. (LEC).

BCH 508 Gene Expression (2 cr)

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. (SEM)

BCH 512 Developmental Genomics & Stem Cell Biology (2 cr)

Designed for second-year graduate students, Developmental Genomics 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. (SEM)

BCH 519/BIO 519 Introduction to Bioinformatics and Computational Biology (3 cr)

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: 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 for the lab sessions are graded by the appropriate instructor and are used to determine the student’s grade in the course.

BCH 522/MIC 522/BIO 522 Principles of Protein Nucleic Acid Interactions (3 cr)

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 covers relevant aspects of proteins and how they interact with nucleic acids, as well as state-of-the-art approaches to performing quantitative studies. Taught by a team of faculty with expertise in these areas. (LEC)

BCH 607/MIC 607 DNA Replication and Repair (2 cr)

This course is cross-listed in the departments of Microbiology and Biochemistry. This is for advanced PhD students. Consists of a single, two-hour meeting per week. Utilizes a seminar/journal club format; class readings consist of primary research articles in the general areas of DNA replication, DNA repair and how these processes are regulated. Students 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 participation in class discussions. (SEM)