Biochemistry and Molecular Biophysics Graduate Group

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Lecture Courses

Non Lecture Courses:

Laboratory Rotation BMB 699
Independent Study

LECTURE COURSES

BMB 508 MACROMOLECULAR BIOPHYSICS; PRINCIPLES AND METHODS
Sharp
Fall, every year
Prerequisites: 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 physics, chemistry, or biology, and no necessary background in biochemistry.

BMB 509 STRUCTURAL AND MECHANISTIC BIOCHEMISTRY
Ferguson & Van Duyne
Spring, every year
Prerequisites: BMB 508 or permission of instructor

After some introductory material on the components of macromolecules and macromolecular assemblies, lectures will focus on the key biochemical 'task areas' of living cells. The course progresses from primarily molecular level events such as storage and translation of genetic information, creation, control & removal of proteins etc. to higher organization levels such as metabolic pathways, signaling pathways, regulation and homeostasis. The presentation for each topic will be 'vertically integrated'. So each section will cover structure details of the relevant molecules, appropriate binding/catalysis events, regulatory aspects, and how they fit into the relevant pathway(s) and cell function.

BMB 518 (CAMB615) (NGG 615) PROTEIN CONFORMATION DISEASES
Argon & Ischiropoulos
Fall, every year
Prerequistes: BIOM 600 or equivalent

Protein misfolding and aggregation has been associated with over 40 human diseases, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, prion diseases, alpha(1)-antitrypsin deficiency, inclusion body myopathy, and systemic amyloidoses. 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 protein folding and misfolding, protein degradation pathways, effects of protein aggregation on cell function, model systems to study protein aggregation and novel approaches to prevent protein aggregation.

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 (CHEM567) BIOINORGANIC CHEMISTRY
Dmochowski
Fall, every year

This course covers selected topics in bioinorganic chemistry. Special emphasis is placed on metal coordination in biomolecules, metal ion cell-uptake and transport processes, redox proteins, long-range biological electron transfer, electron-transfer theory, respiration and photosynthesis, oxygen-utilizing metalloenzymes, metallobiochemistry of DNA, and metallodrugs.

BMB 581 (BE 581) TECHNIQUES OF MAGNETIC RESONANCE IMAGING
Song & 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 (GCB 585) WISTAR INSTITUTE CANCER BIOLOGY COURSE: SIGNALING PATHWAYS IN CANCER
Skordalakes & Weeraratna
Fall, every year
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 themes center 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 590 (PHYS 580) BIOLOGICAL PHYSICS
Goulian
Fall, even-numbered years
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

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.

BIOM 600 CELL BIOLOGY AND BIOCHEMISTRY
Assoian
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
Spring, odd--numbered years (1/2 semester; 1/2 credit)

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 611 ADVANCED X-RAY DIFFRACTION METHODS
Van Duyne
Fall, odd-numbered years (1/2 semester; 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 618 APPLICATIONS OF HIGH RESOLUTION NMR SPECTROSCOPY TO PROBLEMS IN STRUCTURAL BIOLOGY
Wand
Fall, even-numbered years (1/2 semester; 1/2 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
Spring, even-numbered years (1/2 semester; 1/2 credit)

Introduction to the folding of mainly soluble proteins but also membrane proteins. Critical readings in the current literature and important earlier literature. Class discussion of papers from the literature 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 scientific literature.

BMB 622 PHYSICAL PRINCIPLES OF MECHANO-ENZYMES
Dominguez, Goldman, Grishchuk & Ostap
Spring, odd-numbered years (1/2 semester; 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
Spring, odd-numbered years (1/2 semester; 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 pathophysiology of human diseases (channelopathies). Intended for 2nd year graduate students or 1st years students with a strong background in biophysics or physiology.

BMB 626 MASS SPECTROMETRY AND PROTEOMICS
Speicher & Garcia
Spring, even-numbered years (1/2 semester; 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
Spring, even-numbered years (1/2 semester; 1/2 credit)
Prerequisites: Familiarity with Unix recommended; permission of instructors for non-BGS students

An introductory course on programming and algorithms for scientists with an emphasis on applications to biophysics. Students will learn to write, debug, and execute basic programs through lectures, in-class workshops, and programming projects outside of class.

BMB 628 PRINCIPLES OF SCIENTIFIC INSTRUMENTS
Liebman
Spring, even numbered years (1/2 semester; 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 629 QUANTITATIVE PROBLEMS IN BIOCHEMISTRY AND BIOPHYSICS
Kallen
Fall, even numbered years (1/2 semester; 1/2 credit)

Students will be assigned problems in a range of topics, including thermodynamics, enzyme kinetics, redox potentials, and will present their answers in class. This course is intended to complement material covered in BMB 508 and BMB 509, providing a rigorous review of quantitative methods.

BMB 632 PROBING STRUCTURE AND FUNCTION OF COMPLEX RNA-PROTEIN MACHINES
Lynch
Fall, odd-numbered years

Pre-mRNA splicing is catalyzed by the macromolecular Spliceosome complex, the activity of which is tightly regulated by numerous pre-mRNA binding proteins so as to control gene expression. In this course we will take an in-depth look at the methods used to study protein-RNA and RNA-RNA interactions, what the field understands as general concepts common to many RNA binding proteins, and how RNA binding proteins regulate pre-mRNA splicing by controlling the assembly and activity of the spliceosome. The course will be a combination of both lectures and student-lead discussion of recent literature.

BMB 700 (CHEM700) (PHRM630) FRONTIERS IN BIOORGANIC AND MEDICINAL CHEMISTRY
Petersson
Spring, every year
Prerequisites: A strong background in undergraduate chemistry is required and at least one semester of biological chemistry is very desireable.

The course will focus on current topics in chemical biology, particularly experiments in which 1) chemcial synthesis enables one to probe or control biological systems in novel ways; or 2) manipulation of biological systems facilitates novel chemical syntheses. As the goal of the course is to familiarize students with innovative recent experimental approaches and to stimulate them to conceive of their own new methodology, students will be responsible for delivering presentations on topics seleted form the literature and generating several novel reserach proposal ideas, one of which will be elaborated into a full proposal. The prepared seminar will allow students to explore topics not covered in Professor Petersson's lectures or to research one of those topics in more depth. The proposal will be evauated for creativity, feasibility and impact.

NON LECTURE COURSES

BMB 650 (CAMB 702) CURRENT BIOCHEMICAL TOPICS
Black & Shorter
Spring, every year

Participation in the "Dr. George W. Raiziss Biochemical Rounds", a weekly seminar program sponsored by the Department of Biochemistry and Biophysics. Program deals with a wide range of modern biochemical and biophysical topics presented by established investigators selected from our faculty and by leading scientists from other institutions. BMB students can take the course two times; only one time will count for elective credit.

BMB 699 LABORATORY ROTATION
Kohli
Fall, Summer and Spring, every year

Supervised mini-projects for graduate students in BMB.

BMB 705 CANDIDACY EXAM PREP CLASS
Lynch, Marmorstein and Nelson
Spring, every year (1/2 semester; 1/2 credit)

This course is designed to prepare second year BMB students for the Candidacy Exam, which must be completed before May 31 of the second year. The course is usually given for 6 weeks in the spring semester.

BMB 799 INDEPENDENT STUDY

Independent study can be taken for one-half to four credits per semester. In general, the time commitment for 1 course unit is considered to be approximately 12 weeks at 10 hours per week; 2 course units can be earned for full time indendent study in the summer