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 About the B.S. Degree ProgramDeclaring Biochemistry HOT CoursesTeaching FacultyUndergraduate ResearchSeminars, Events & PresentationsAwards & FellowshipsFacilities & ResourcesCareer OptionsBiochemistry HonorsImportant Dates & DeadlinesFAQ |
HOT Courses BCM 430: Journal Club in Molecular Pharmacology and Structural Biology (1 credit, Fall)Students read and present critical summaries of recent journal articles describing work in areas such as the structure and interaction of proteins, nucleic acids, and other biomolecules, and the interaction of drugs with these molecules. Students typically present two papers per semester.
 Students learn the principles by which models of proteins, nucleic acids and other biomolecules are created. Topics include the hands-on manipulation of biomolecular structures using computer programs widely used in the pharmaceutical and biochemical communities, a synopsis of algorithms for energy minimization and molecular dynamics, and an overview of the methods by which biomolecular structures are determined (including uv-vis and fluorescence spectroscopy, nuclear magnetic resonance, and x-ray diffraction). Students complete assignments in the computer laboratory and present two modeling projects in addition to homework and exams.
 This course, with lecture and laboratory components, is designed for students with interests in biochemistry, bioinorganic chemistry, medicinal chemistry, biology, pharmacology, and bioengineering. The lecture part of the course is divided into three parts. Part I presents bonding concepts in inorganic chemistry and physical/chemical properties of transition metal complexes which are important for understanding the structure and function of metallo-drugs. Part II of the course addresses the pharmaceutical properties and mechanism of action of metal complexes for treating cancer, including compounds of platinum, ruthenium, gallium, and titanium, agents used in photodynamic therapy and natural products which may require metal ion cofactors for activity such as bleomycin. Part III of the course focuses on the role of gold in treating arthritis, technetium and gadolinium for biomedical imaging, vanadium for treating diabetes, zinc compounds for attacking AIDS and copper in Wilson's, Menkes, and Alzheimer's diseases.The laboratory part of CHE 412 consists of three experiments covering the binding of platinum drugs to DNA, cleavage of DNA by metallo-porphyrins, and the active site of carbonic anhydrase as a target for drug action. The written reports for the laboratory experiments, which follow a specified journal format, include plots, graphs, and charts of data and images derived from crystal structures in the Protein Data Bank (PDB). The computer program HyperChem is used to create figures from PDB files to be used in the written report.
 This course has lecture and laboratory components and is designed to give students hands-on experience of working in a molecular biology laboratory. While learning basic techniques in recombinant DNA technology, students apply scientific method to address questions in molecular biology. Experimental methods covered in this course including DNA isolation, restriction endonuclease cleavage of DNA, gene cloning, PCR, protein purification, tissue culture techniques, construction of transgenic plants, gene expression analysis, bioinformatics and other methods central to Molecular Biology. By the end of this course, students gain insight into these techniques and the reasons why they are used by molecular biologists.
 CHE 474 covers basic physical chemistry for the undergraduate biochemistry major. Part I of the course discusses the interactions between biological molecules in solution, acid/base equilibria, chemical equilibrium and the application of the 1st and 2nd laws of thermodynamics to biochemical systems. Part II of the course addresses important physical and structural properties of DNA and RNA. In this part of the course, chemical kinetics and its application to biological systems is also presented and discussed. The last part of the course covers bonding theory using quantum mechanics and analyzes the absorption spectra of biological macromolecules.In addition to discussing the physical and chemical properties of biological systems, students also learn how to search the biochemical literature, download structures from the Protein Data Bank, and use a molecular modeling program to build and analyze proteins, DNA and drugs. These computer exercises comprise the "homework" portion of CHE 474.
 This course introduces the student to experimental methods for biologically synthesizing, chemically purifying, introducing site-directed directed mutations into, and crystallizing macromolecules in order to analyze their structure and function. While students have the opportunity to carry out in vitro transcription of an RNA molecule, emphasis is placed on examining membrane proteins and the genes that code for them. Two particular proteins that are examined in numerous experiments are the G-protein coupled receptor CCR5, for which a natural polymorphism in human populations has been found to modulate susceptibility to HIV infection; and the oceanic light-harvesting, retinal protein, proteorhodpsin.
 The constellation of two hundred or more neoplastic diseases called "cancer" are defined, classified, and described in their clinical, epidemiological, cellular, tissue, and in vivo manifestations in the first third of the course. This descriptive phenomenology is presented with two goals in mind for the remaining two-thirds of the course. (1) What does the phenomenology of cancer tell us about biochemistry, molecular biology, cell biology, and genetics that generate and maintain these malignancies? (2) How can we use our knowledge about the biology of cancer for improved diagnosis, management, and prevention of neoplastic diseases? The course incorporates the new textbook by Dr. Robert A. Weinberg, the Biology of Cancer and the accompanying CD to illustrate and illuminate these goals. The accompanying photomicrograph is from the Weinberg book, attributed to A.T. Sarkin, Atlas of Oncology, 3rd edition, Elsevier Science Ltd., 2003) and shows chronic myelogenous leukemia (CML) accelerating toward blast crisis with large poorly differentiated myeloblastic cells beginning to dominate the more differentiated monocytic and granulocytic cells and the combined white blood cells beginning to overwhelm the small discoidal red blood cells. The molecular basis for CML is traced to an aberrant protein produced by the translocated fusion of chromosomes 9 and 22. Based on this detailed molecular knowledge, CML is now treatable and curable by use of the drug Gleevec (imatinib mesylate). |
Department of Chemistry • 1-014 Center for Science & Technology • Syracuse, New York 13244-4100 • ph: 315.443.2925 / fax: 315.443.4070