BIOCHEMISTRY AND MOLECULAR BIOPHYSICS (MD) {BMB}
508. Macromolecular Biophysics I. (A) Van Duyne/Wand. This course introduces students to the physical and chemical
properties of proteins, nucleic acids and membranes.
The emphasis of the course 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.
509. Macromolecular Biophysics II. (B) Van Duyne and Wand. Prerequisite(s): BMB 508 or permission of instructors.
This course introduces fundamental concepts
in chemical kinetics and their application to
problems in biochemistry such as protein folding
and enzymoloyg. There is an emphasis on dynamic
processes in proteins and the techniques used
to characeterize 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 proteomics with an emphasis on mass spectrometry
518. (CAMB615) Topics in Conformation Disease. (A) Yair Argon, Harry Ischiropoulos. Prerequisite(s): BIOM 600. 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, alppha(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.
550. Molecular Mechanisms of Signal Transduction and Control. (B) Lemmon. Prerequisite(s): General biochemistry or cell biology, and BIOM 600 or permission of instructor. Molecular
structure and function of receptors, GTP binding
proteins, second messengers, kinases, lipases, phosphatases
etc. given at the current research level. Specific
signaling cycles and their coupling mechanisms are
examined with the aim of understanding what and how
molecular communication chains mediate sensory, hormone
and neurotransmitter action that control cellular
physiologic functions like growth, secretion, electrical
activity, cell cycle, gene expression, etc. and how
so many interacting cycles are kept coordinated in
health. Biochemical, molecular biological and structural
chemical approaches are developed and used to achieve
both a broad and deep understanding of cellular events
that constitute the life force that we know and love
so well and knowledge of which will be used to explain
associated disease states.
554. (CHEM555) Macromolecular Crystallography: Methods and Applications. (A) Emmanuel Skordalakes and Ronen Marmorstein. Prerequisite(s): 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.
560. Methods of Scientific Inquiry in Biological Systems. (B) Wilson and Domotor. Prerequisite(s): 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.
567. (CHEM567) Bio-Inorganic Chemistry. (A) Dmochowski. 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.
SM 571. Seminar. (B) Staff. Student seminars on selected topics from current scientific literature
580. (BE 567) Mathematical Computational Methods for Modeling Biological Systems.
(B) Schotland. Prerequisite(s): Graduate Standing or instructor's permission. 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.
581. (BE 581) Techniques of Magnetic Resonance Imaging. (K) Wehrli and Song. Detailed introduction to the physics and engineering of magnetic resonance imaging
as applied to medical diagnosis. Covered are magnetism, spatial encoding principles, Fourier analysis, spin relaxation,
imaging pulse sequences and pulse design, contrast mechanisms, chemical shift, flow encoding, diffusion
and perfusion and a discussion of the most relevant clinical applications.
585. Wistar Institute Cancer Biology Course: Cell Cycle Checkpoints and Cancer Course.
(A) Kissil & Dahmane. Prerequisite(s): Undergraduate students require permission from the
course director. 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 key signaling pathways that drive tumorigenesis with emphasis on biochemistry and
genetic model systems and their relevance to human cancer. The course is taught by the organizer and guest lecturers
from universities and research institutes in the Northeast. Following every lecture, the 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 invited to attend.
598. Tutorial. (C) Black. Literature studies in a specific research area under supervision of Biochemistry
and Molecular Biophysics Graduate Group faculty, concluded by a written summary and a seminar presentation. May
be taken in fall, spring and summer semesters.
601. Fundamentals of Magnetic Resonance. (A) Reddy. 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, and classical and quantum strategies to compute nuclear spin resonses in liquids,solids
and biological tissues, polarization transfer and mujltiple 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 this course,visit www.mmrrcc.upenn.edu
603. Advanced Topics in Magnetic Resonance. (K) Reddy. Advanced topics in theory and applications of magnetic resonance spectroscopy
and imaging (Nuclear Magnetic Resonance - NMR; and Electron Spin Resonance - EPR) of biological tissues and
solid-state materials to problems in biochemistry, biology, bioengineering and medicine.
604.(BE 619) Statistical Mechanics. (H) Schotland. Prerequisite(s): CBE 618 or equivalent. A modern introduction to statistical mechanics with biophysical applications.
Theory of ensembles. Noninteractingsystems. Liquid theory. Phase transitions and critical phenomena. Nonequilibrium
systems. Applications to reaction kinetics, polymers and membranes.
610. Life and the Electronmagnetic Spectrum. (H) Vanderkooi. Course meets for 8 weeks and is offered for 1/2 credit. Spectroscopy applied to biological molecules. Emphasis is placed on the common
principles of absorption and relaxation techniques for infrared and visible light and includes discussion
of light absorption and emission processes used by living organisms.
611. Advanced X-ray Diffraction Methods. (J) Van Duyne. Prerequisite(s): BMB 554/CHEM 555 or equivalent,or permission of instructor. Course meets for 8 weeks and is offered
for 1/2 credit. 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.
614. Membrane Structural Biology. (A) Lemmon. Course meets for 8 weeks and is offered for 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 cellullar perspectives.
616. Medical Problems in Modern Biochemistry. (K) Nelson. Prerequisite(s): Undergraduate biochemistry; undergraduates need 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 biochemical 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).
618. Applications of High Resolution NMR Spectroscopy to Problems in Structural
Biology. (I) Wand. Prerequisite(s): Undergraduate biochemistry and physical chemistry and BMB 601,
or permission of instructor. Course meets for 8 weeks and is offered for 1/2 credit. 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.
619. Protein Folding. (I) Axelsen and Englander. Course meets for 8 weeks and is offered for 1/2 credit. Introduction to the folding of especially soluble proteins but also membrane
proteins; critical readings in current literature and important earlier literature; class discussion of papers interspersed
with didactic lectures as required. Exposure to equilibium, kinetics, thermodynamics principles and use as they
occur in the real literature. Exposure to the range of biophysical technologies as used in the literature.
622. Physical Principles of Mechano-Enzymes. (J) Goldman and Ostap. Prerequisite(s): Biochemistry. Course meets for 8 weeks and is offered for 1/2 credit. This course will provide an introduction to the biochemical, structural, and
mehanical properties of energy-transducing enzymes. We will emphasize the relationships of mechanical, thermal, and chemical
forces in mechano-enzyme function.
624. Ion Channels and Pumps. (H) Kallen and Lu. Prerequisite(s): permission of course directors. Course meets for 8 weeks and is offered for 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 year students with a strong background
in biophysics or physiology.
625. Optical Methods in Cell Physiology. (J) Salzberg. Prerequisite(s): Undergraduate physics; calculus. Course offered for 8 weeks for 1/2 credit. 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 moleccule
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 MD/PhDs and postdocs are welcome.
626.Mass Spectrometry and Proteomics. (J) Speicher. Course meets for 8 weeks and is offered for 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 first and second year graduate students
and others with an interest in proteomics and mass
spectrometry.
627.Computer Programming for Biochemists and Biophysicists. (I) Sharp and Van Duyne. Prerequisite(s): Familiarity with Unix recommended. Permission
of instructor for nonBGS students. Course meets for
eight weeks and is offered for 1/2 credit. 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.
628. Principles of Scientific Instruments. (J) Liebman. Course meets for eight weeks and is offered for 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 instrument 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.
SM 650. Current Biochemical Topics. (C) Black and Shorter. 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.
699. Laboratory Rotation. (C) Shorter. Supervised "mini-projects" for graduate students in Biochemistry and
Molecular Biophysics. May be taken in fall, spring
and summer semesters.
700. (CHEM700, PHRM630) Selected Topics in Chemistry (Bioinorganic and Bioorganic
Chemistry). (C) Cooperman/DeGrado. Course topics include: 1) oxygen uptake and utilization, O2 transport, O2 and
0 atom incorporation into substrates; 2) the bioinorganic chemistryof C-C bond formation; 3) metallobiochemistry and
DNA; 4) metal-sulfide proteins: 5) manganese containing metalloproteins, photosystem II, the biological water splitting
reaction; 6) biological electron transfer, electron transfer theory; mechanisms of energy storage and release,
long-distance electron transfer reactions.
SM 705. Prelim Exam Preparation Course. (B) DeGrado. This course is designed for second year BMB students to prepare them for the
Preliminary Exam, which must be completed before May 31st of their second year. The course is usually given
for 6 weeks in the spring semester.
990. Master's Thesis Research. (C) Staff. See Department for section numbers.
995. Dissertation Research. Staff. See Department for section numbers.
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