BMB 508 MACROMOLECULAR BIOPHYSICS I
Van Duyne & Wand
Fall, every year
This course introduces students to the physical and chemical properties of proteins, nucleic acids, and membranes. The emphasis in BMB508 is on thermodynamics and structure, with several lectures devoted to the biophysical methods used to study biological macromolecules. This is intended to be a first course for graduate students with an undergraduate background in physics, chemistry, or biology. The companion course BMB 509, which is taught in the spring, builds on this course and covers kinetics, dynamics, and catalysis.
BMB 509 MACROMOLECULAR BIOPHYSICS II
VanDuyne & Wand
Spring, every year
Prerequisites: BMB 508 or permission of instructor
This course introduces fundamental concepts in chemical kinetics and their application to problems in biochemistry such as protein folding and enzymology. There is an emphasis on dynamic processes in proteins and the techniques used to characterize them over a wide range of timescales. The latter half of the course focuses on emerging areas in biochemistry and biophysics including membrane biochemistry, single molecule methods and proteomifcs with an emphasis on mass spectrometry.
BMB 518 Protein Conformation Diseases
(CAMB 615)
Argon & Ischiropoulos
Fall, every year
Prerequistes: BIOM 600 or equivalent; graduate students only and with permission of course director
Protein misfolding and aggregation has been associated with a number of human diseases, ranging from Alzhemier's and Parkinson's Disease to Respiratory Distress Syndrome, alpha-1-antitrypsin deficiency and Mad Cow Disease. This seminar course will include lectures, directed readings and student presentations to cover seminal and current concepts in the biochemistry and cell biology of conformational diseases. Examples of topics: effects of mutations on folding in the cell, inclusion bodies formation, protein degradation pathways, and effects of protein aggregation on cell function.
BMB 554 MACROMOLECULAR CRYSTALLOGRAPHY: METHODS AND APPLICATIONS
(CHEM 555)
Skordalakes & Marmorstein
Fall, every year
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 560 METHODS OF SCIENTIFIC INQUIRY IN BIOLOGICAL SCIENCES
Wilson & Domotor
Spring, every year
Prerequisites: graduate students in biological sciences or permission of instructors.
The foundational, social and methodological aspects of scientific reasoning in biomedical disciplines are discussed, including: 1) theories, laws, causal/functional explanation and experimental methodology in biology and medicine, 2) case studies in selected fields of biomedical sciences with special regards to strategies in concept and hypothesis formation, discovery, gathering evidence and testing and 3) social and moral factors pertinent to the research enterprise.
BMB 567 BIOINORGANIC CHEMISTRY
(CHEM567)
Therien
Fall, every year
This course covers selected topics in bioinorganic chemistry. Special emphasis is placed on dioxygen chemistry and electron transfer processes. Course topics include: 1) oxygen uptake and utilization; 2) oxygen transport; 3) oxygen and O atom incorporation into substrates; 4) metalloenzyme-catalyzed C-C bond formation; 5) the metallobiochemistry of DNA; 6) metal-sulfide proteins; 7) manganese containing metalloproteins: 8) photosystem II, light-driven electron transfer and the biological water-splitting reaction; 9) biological electron transfer; 10) electron transfer theory; 11) mechanisms of energy storage and release; and 12) long-distance electron transfer reactions.
BMB 580 Mathematical Computational Methods for Modeling Biological Systems
(BE 567)
Schotland
Spring
This course will present a comprehensive account of the application of modeling methodology to the investigation of biological systems. The emphasis will be on an organized overview of the tools and techniques rather than the detailed mathematical structures upon which they may rely. The course will draw examples widely from the current literature in an attempt to not only show the topical relevance of the subject matter but also to equip participants with an understanding of the diversity of domains to which the techniques and methodologies apply.
BMB 581 TECHNIQUES OF MAGNETIC RESONANCE IMAGING
(BE 581)
Wehrli
Spring, odd numbered years
Detailed introduction to the physics and engineering of magnetic resonance imaging as applied to diagnostic medicine. Covered are magnetism, spin relaxation, spatial encoding principles, Fourier analysis, imaging pulse sequence and pulse design, contrast mechanisms, chemical shift, flow encoding, diffusion and perfusion and a discussion of the most relevant clinical applications.
BMB 585 WISTAR INSTITUTE CANCER BIOLOGY COURSE: SIGNALING PATHWAYS IN CANCER
Kissil & Dahmane
Fall, every year
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 themes center around signal transduction pathways and mechanisms governing cell behavior in cancer. These topics will be discussed at the molecular, cellular and whole organism levels. 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 590 / PHYS 580 Biological Physics
Goulian
Fall, even-numbered years
A survey of basic biological processes at all levels of organization (molecule, cell, organism, population) in the light of simple ideas from physics. Both the most ancient and the most modern physics ideas can help explain emergent aspects of life, i.e., those which are largely independent of specific details and cut across many different classes of organisms. Topics may include thermal physics, entropic forces, free energy transduction, structure of biopolymers, molecular motors, cell signaling and biochemical circuits, nerve impulses and neural computing, populations and evolution, and the origins of life on Earth and elsewhere.
Prerequisites: PHYS 401 or CHEM 221-222 (may be taken concurrently) or familiarity with basic statistical mechanics and thermodynamics. Recommended: Basic background in chemistry and biology.
BIOM 600 CELL BIOLOGY AND BIOCHEMISTRY
Weisel
Fall, every year
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 601 FUNDAMENTALS OF MAGNETIC RESONANCE
Reddy
Fall, every year
This course introduces basic theoretical and experimental concepts of magnetic resonance and its applications in biochemistry, biology and medicine. Topics covered include description of the phenomenon of magnetic resonance, classical and quantum strategies to compute nuclear spin responses in liquids, solids and biological tissues, polarization transfer and multiple quantum effects and their applications in biomedicine. Nuclear spin relaxation in solid-state materials and in biological systems will be discussed. Concepts of magnetic resonance imaging, imaging strategies, image contrast, and diagnostic applications are discussed. The course includes several practicals dealing with the demonstration of NMR hardware and experiments to compute basic NMR parameters on high resolution and clinical MRI scanners. For further details of the course visit: www.mmrrcc.upenn.edu
BMB 604 (BE 619) STATISTICAL MECHANICS
Schotland
Fall, even numbered years
Prerequisites: permission of the instructor
A modern introduction to statistical mechanics with biophysical applications. Theory of ensembles. Noninteracting systems. Liquid theory. Phase transitions and critical phenomena Nonequilibrium systems. Applications to reaction kinetics, polymers and membranes.
BMB 610 LIFE AND THE ELECTRONMAGNETIC SPECTRUM
Vanderkooi
Fall, even-numbered years (1/2 semester course; 1/2 credit)
Spectroscopy applied to biological molecules. Emphasis is placed on the common principles of absorption and relaxation techniques and includes discussion of light absorption and emission processes used by living organisms.
BMB 611 ADVANCED X-RAY DIFFRACTION METHODS
Van Duyne
Spring, even-numbered years (1/2 semester course; 1/2 credit)
Prerequisites: BMB 554/CHEM555 or equivalent, or permission of course director
Advanced topics in macromolecular x-ray diffraction. Crystallization, synchrotron data collection, data processing, anomalous diffraction, phasing methods, density modification methods, refinement. Emphasis is on applications and currently available methodology.
BMB 614 MEMBRANE STRUCTURAL BIOLOGY
Lemmon
Fall, every year (1/2 semester course; 1/2 credit)
The composition, structure, and physical properties of cell membranes will be considered, as will recent advances in structural studies of membrane proteins. Topics will range from membrane structure to membrane protein folding, combining biophysical and cellular perspectives.
BMB 616 MEDICAL PROBLEMS IN MODERN BIOCHEMISTRY
Nelson
Spring, odd-numbered years
Prerequisites: undergraduate biochemistry; undergraduates require permission of course director.
This course on metabolic pathways will focus on diseases and other clinical conditions that have biochemical basis. We will try to understand the mechanisms and manifestations of the biochemical defects, ranging from dysregulation of the pathways to the implications of organ specificity of the defects. Clinical case topics will include familiar diseases such as diabetes, gout, and hypercholesterolemia, as well as rarer diseases such as: MCAD and CPT deficiencies (i.e. fatty acid oxidation defects); von Gierke’s and McArdles disease (i.e. glycogen storage diseases); and propionic acidemias (i.e. amino acid degradation diseases).
BMB 618 APPLICATIONS OF HIGH RESOLUTION NMR SPECTROSCOPY TO PROBLEMS IN STRUCTURAL BIOLOGY
Wand
Fall, odd-numbered years (1 credit)
Prerequisites: Undergraduate biochemistry and physical chemistry and BMB 601, or permission of instructor.
A lecture-based course designed to introduce graduate students to applications of modern high-resolution multinuclear and multidimensional NMR spectroscopy to problems in structural biology. The course will first introduce classical definitions and descriptions of nuclear magnetic resonance and a convenient formalism for the analysis of advanced NMR experiments. Concepts and applications of multidimensional homonuclear 1H NMR and multidimensional heteronuclear spectroscopy of proteins and nucleic acids will be described. Resonance assignment strategies including analysis of triple resonance spectroscopy will be covered. The origin, measurement and extraction of structural restraints and their use in structure determination will be surveyed and illustrated with recent examples.
BMB 619 PROTEIN FOLDING
Axelsen & Englander
Fall, odd-numbered years (1/2 semester course; 1/2 credit)
Introduction to the folding of especially soluble proteins but also membrane proteins; critical readings in the current literature and important earlier literature; class discussion of papers interspersed with didactic lectures as required. Exposure to equilibrium, kinetics, thermodynamics principles and use as they occur in the real literature. Exposure to the range of biophysical technologies as used in the literature.
BMB 622 PHYSICAL PRINCIPLES OF MECHANO-ENZYMES
Goldman & Ostap
Spring, even-numbered years (1/2 semester course; 1/2 credit)
Prerequisite: Biochemistry
This course will provide an introduction to the biochemical, structural, and mechanical properties of energy-transducing enzymes. We will emphasize the relationships of mechanical, thermal, and chemical forces in mechano-enzyme function.
BMB 624 ION CHANNELS AND PUMPS
Kallen & Lu
Fall, even-numbered years (1/2 semester course; 1/2 credit)
This course will introduce students to the fundamentals of ion channel function, with the course loosely organized around major classes of ion channels (voltage, mechanical and ligand gated). Discussion will focus on methods of study, mechanisms of ion selectivity and gating, and pathophysiologyof human diseases (channelopathies). Intended for 2nd year graduate students or 1st years students with a strong background in biophysics or physiology.
BMB 625 OPTICAL METHODS IN CELL PHYSIOLOGY
Baylor & Salzberg
Spring, even-numbered years (1/2 semester course; 1/2 credit)
Prerequisites: Undergraduate physics; calculus
This course will provide an introduction to the principles and application of modern optical methods to the investigation of physiological processes. These include optical measurement of membrane potential, fluorescent indicator measurement of intracellular ion concentrations, single molecule fluorescence measurements, TIRF, FRET, LRET, confocal and multi-photon microscopy, and dynamic light scattering. The course will consist of lectures and discussions of original literature. Intended for 2nd year graduate students, but M.D./Ph.D.’s and postdocs are welcome.
BMB 626 MASS SPECTROMETRY AND PROTEOMICS
Speicher
Spring, even-numbered years (1/2 semester course; 1/2 credit)
This course will provide a detailed introduction to proteomics and mass spectrometry. The role of mass spectrometry in both characterizing proteins for traditional protein structure – function studies and identification of proteins in proteome studies will be emphasized. Targeted and global proteomes, quantitative protein profiling and compositional proteomics, and applications of proteome studies will be discussed. Intended for second year graduate students and others with an interest in proteomics or mass spectrometry.
BMB 627 COMPUTER PROGRAMMING FOR BIOPHYSICISTS AND BIOCHEMISTS
Sharp & Van Duyne
Fall, odd numbered years (1/2 semester course; 1/2 credit)
Prerequisites: Familiarity with Unix recommended
An introductory course on programming and algorithms with an emphasis on applications to biophysics. Brief lectures followed by extensive hands on programming on Linux workstations
BMB 628 PRINCIPLES OF SCIENTIFIC INSTRUMENTS
Liebman
Spring, even numbered years (1/2 semester course; 1/2 credit)
Proper use of the tools of one’s trade is essential to quality assurance. General confidence in the infallibility of scientific instruments can be the cause of serious misapplication of research effort. This course systematically reviews first principles of instrumental detection, operation, calibration, truth-testing, trouble shooting and data analysis. Approaches to error appraisal and avoidance are developed using common laboratory examples. Anyone who cares is welcome. And we should all care.
BMB 700 Frontiers in Bioorganic and Medicinal Chemistry
Petersson, Cooperman and DeGrado
Fall, every year
The course explores how recent developments in our abilities to make and analyze biologically important macromolecules provide new approaches to drug development and discovery.
