Biochemistry and Molecular Biophysics Graduate Group

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Fall 2011 Courses

BMB 508 Macromolecular Biophysics I  (required for BMB students)
Van Duyne & Wand
M/W, 1:30 – 3:00 p.m.
255 Anatomy-Chemistry Building
Course starts Wednesday, September 7

Prequisites:  Senior undergraduate or graduate level biochemistry or biophysics

This course introduces students to the physical and chemical properties of biological macromolecules, including proteins and nucleic acids. It surveys the biophysical techniques used to study the structure and thermodynamics of macromolecules. It is intended to be a first course for graduate students with an undergraduate background in either physics, chemistry, or biology, and no necessary background in biochemistry.

BMB 518 (CAMB/NGG 615) Protein Conformation Diseases
Argon & Ischiropoulos
M, 3 – 5 p.m.
Course starts Monday, September 12

Prerequisites: BIOM 600 or equivalent

Protein misfolding and aggregation has been associated with a number of human diseases, ranging from Alzheimer’s and Parkinson's disease to Respiratory Distress Syndrome, alpha(1)-antitrypsin deficiency and "mad cow" disease. This course will include lectures, directed readings and student presentations to cover seminal and current papers on the cell biology of conformational diseases including topics such as aggresome formation, protein degradation pathways (proteosome vs ER-associated degradation), effects of protein aggregation on cell function and mutations which lead to autosomal dominant diseases.  

BMB 554 (CHEM 555) Macromolecular Crystallography: Methods and Applications
Marmorstein & Skordalakes
Tu/Th, 10:30 – 12:00 noon (1/2 credit; first half of semester)
319 Towne Building
Course starts Thursday, September 8

Prerequisites: Undergraduate calculus and trigonometry

The first half of the course covers the principles and techniques of macromolecular structure determination using x-ray crystallography. The second half of the course covers extracting biological information from x-ray crystal structures with special emphasis on using structures reported in the literature and presented by faculty and students.

BMB 559 Biomedical Imaging
Tu/Th, 10:30 a.m. to 12:00 noon. (1/2 credit; second half of semester)
315 Towne Building

Course starts Tuesday, November 1

This course considers the noninvasive, quantitative, and repetitive imaging of targeted macromolecules and biological processes in living cells and organisms. Imaging advances have arisen from new technologies, probe chemistry, molecular biology, and genomic information. This course covers the physical principles underlying many of the latest techniques, and defines experimental parameters such as spatial and temporal resolution, gain, noise, and contrast. Applications to cellular and in vivo imaging are highlighted for confocal, two-photon, and force microscopies; single-molecule, CARS, and fluorescencecorrelation spectroscopy; FRET and fluorescence bleaching; mass spectroscopy; MRI, PET and SPECT. The role of molecular imaging agents comprised of proteins, organic or inorganic materials is widely discussed.

BMB 585 (GCB 585) Wistar Institute Cancer Biology Course: Signaling Pathways in Cancer
Huang & Skordalakes
Th, 2 – 4:30 p.m.
Wistar Auditorium
Course starts Thursday, September 8

Prerequisites: Undergraduates require permission from the course directors.

This course is intended to provide foundational information about the molecular basis of cancer. When necessary the significance of this information for clinical aspects of cancer is also discussed. The main theme centers around cell cycle checkpoints with specific emphasis on the biochemistry and genetics of DNA damage signaling pathways, DNA damage checkpoints, mitotic checkpoints and their relevance to human cancer. The course is taught by the organizers and guest lecturers from universities and research institutions in the Northeast. Following every lecture, students present a research paper related to the topic of that lecture. The course is intended for first and second year graduate students, but all graduate students are welcome to attend

BMB 598 Tutorial (does not count towards required elective credits for BMB students)

The tutorial course is designed to provide students with an in-depth appreciation of a specific subject, and present their knowledge orally. A tutorial can be used to enable students to become more deeply acquainted with the literature of a specific field or experimental approach related to their thesis project. The tutorial can also be used to better prepare students for their Candidacy Exam. Students are encouraged to select a tutorial with faculty members other than their thesis advisor.

BIOM 600 Cell Biology and Biochemistry (required for BMB students)
M/W/F, 10:30 – 12 noon
Austrian Auditorium, CRB
Course starts Monday, September 12

BIOM 600 is an intermediate level graduate course designed to introduce students to the molecular components and physiological mechanisms that underlie the structure and function of cells. The course is designed as an in-depth survey to cover general concepts central to the field of biochemistry and cell biology and to emphasize these concepts within the context of current scientific research questions and technical approaches. Lectures will focus on recent discoveries in contemporary cell biology involving: (i) basic cellular biochemistry; (ii) mechanisms of membrane transport and excitability; (iii) intracellular compartmentalization and protein/vesicle targeting, organelle biogenesis; (iv) cytoskeletal architecture, cell motility and adhesion; and (v) molecular mechanisms of signal transduction. Efforts will be made to familiarize students with recent technical advances in molecular, biochemical, microscopic, spectroscopic, and electrophysiologic techniques.

BMB 619 Protein Folding
Axelsen & Englander
Tu/F, 2 - 3:30 p.m. (1/2 credit; second half of semester)
1001 Stellar-Chance Labs
Course starts Tuesday, October 25

Introduction to the folding of soluble proteins mainly but also membrane proteins; critical readings in the current literature and important earlier literature; class discussion of papers with didactic lectures as required. Exposure to principles and use of equilibrium, kinetics, thermodynamics and the range of biophysical technologies as they occur in the real literature.

BMB 633 Cellular Biochemistry and Biophysics (new course, Fall 2011)
Ferguson & Kallen
Tu/Th, 9 - 10:30 a.m.
255 Anatomy-Chemistry Bldg.
Course starts Thursday, September 15

The syllabus of this course is linked to BIOM600, Cell Biology and Biochemistry. It is intended to reinforce and extend select aspects of the material covered in BIOM600 that are relevant to students in the Biochemistry and Molecular Biophysics graduate group. For each class one or two papers will be assigned that relate to the topics covered in the BIOM 600 lectures. In-class discussion of other areas of material covered in BIOM600 is encouraged. Priority will be given to 1st year BMB students. The course will also be open to 2nd year BMB students and to students from other programs who are either currently taking or have completed BIOM600 (with permission of course directors). Grading will be based on student presentations and participation in discussion.

BMB 699 Laboratory Rotation (BMB students are required to carry out rotations in 3 different labs)

Supervised mini-projects for graduate students in BMB, seminar presentation required. Course offered fall, spring and summer semesters.