- MB&B 600a, Principles of Biochemistry I
Michael Koelle, Thomas Biederer
Discussion of the physical, structural, and functional properties of proteins, lipids, and carbohydrates, three major classes of molecules in living organisms. Energy metabolism, hormone signaling, and muscle contraction as examples of complex biological processes whose underlying mechanisms can be understood by identifying and analyzing the molecules responsible for these phenomena.
- MB&B 601b, Principles of Biochemistry II
Joan Steitz, Scott Strobel
A continuation of MB&B 600a that considers the chemistry and metabolism of nucleic acids, the mechanism and regulation of protein and nucleic acid synthesis, and selected topics in macromolecular biochemistry.
- MB&B 630b/MCDB 630b, Biochemical and Biophysical Approaches in Molecular and Cellular Biology
- MB&B 635a1, Mathematical Methods in Biophysics
Thomas Pollard, Andrew Miranker, and staff
This graduate course introduces the theory and application of biochemical and biophysical methods to study the structure and function of biological macromolecules. The course considers the basic physical chemistry required in cellular and molecular biology but does not require a previous course in physical chemistry. One class per week is a lecture introducing a topic. The second class is a discussion of one or two research papers utilizing those methods.
- MB&B 710b4/C&MP 710b, Electron Cryo-Microscopy for Protein Structure Determination
Charles Sindelar, Fred Sigworth, Hongwei Wang
Understanding cellular function requires structural and biochemical studies at an ever-increasing level of complexity. The course is an introduction to the concepts and applications of high-resolution electron cryo-microscopy. This rapidly emerging new technique is the only method that allows biological macromolecules to be studied at all levels of resolution from cellular organization to near atomic detail
- MB&B 720a, Macromolecular Structure and Biophysical Analysis
Andrew Miranker, Anna Marie Pyle, Yong Xiong
An in-depth analysis of macromolecular structure and its elucidation using modern methods of structural biology and biochemistry. Topics include architectural arrangements of proteins, RNA, and DNA; practical methods in structural analysis; and an introduction to diffraction and NMR.
- MB&B 721b, Macromolecular Interactions and Dynamic Properties
Anna Pyle, Donald Engelman, Elizabeth Rhoades, Hongwei Wang
This course examines dynamic properties of macromolecules, their interactions, catalytic activities, and methods for analyzing their behavior. Topics include macromolecular folding, binding interfaces, ligand interactions, and the properties of membrane proteins, enzymes, ribozymes, and molecular motors. These areas are presented together with modern methods for analysis of macromolecular associations and dynamic properties.
- MB&B 750a2, Biological Membranes
Thomas Biederer, Donald Engelman
Biological membranes and their resident proteins are essential for cellular function; yet comparatively little is known about their structure and dynamics. This class provides an introduction to the biochemistry and biophysics of lipids, lipid bilayers, and lipid-derived second messengers. In addition, structural as well as functional aspects of the different classes of membrane proteins are discussed along with an outline of experimental approaches used to achieve an understanding of membrane protein structure and function at a molecular level.
- MB&B 752b/CB&B 752b/CPSC 752b/MCDB 752b, Genomics and Bioinformatics
Mark Gerstein, Michael Snyder, Dieter Söll
Genomics describes the determination of the nucleotide sequence and many further analyses to discover functional and structural information on all the genes of an organism. Topics include the methods and results of functional and structural gene analysis on a genome-wide scale as well as a discussion of the implications of this research. Bioinformatics describes the computational analysis of genomes and macromolecular structures on a large scale. Topics include sequence alignment, biological database design, comparative genomics, geometric analysis of protein structure, and macromolecular simulation.
- MB&B 760b3: Principles of Macromolecular Crystallography
Rigorous introduction to the principles of macromolecular crystallography, aimed at students who are planning to carry out structural studies involving X-ray crystallography or who want to obtain in-depth knowledge for critical analysis of published crystal structures.
- MB&B 761b4: X-ray Crystallography Workshop
Yong Xiong, Yorgo Modis, and staff
This laboratory course provides hands-on training in the practical aspects of macromolecular structure determination by X-ray crystallography. Topics include data collection, data reduction, phasing by multiwavelength anomalous diffraction and molecular replacement, solvent flattening, non-crystallographic symmetry averaging, electron density interpretation, model building, structure refinement, and structure validation. The course includes training in the use of computer programs used to perform these calculations.
- Pharmacology 529b: Structural Pharmacology
Ya Ha, Titus Boggon
The goal of this course is to show students how concepts of structural biology are applied to areas of great importance in pharmacology such as protein kinases, proteases, cell surface receptors, integrins and other membrane-bound enzymes, transporters and channels, and how these concepts facilitate drug development.
- Chemistry 440/540: Molecules and Radiation I
An integrated treatment of quantum mechanics and modern spectroscopy. Basic wave and matrix mechanics, perturbation theory, angular momentum, group theory, time-dependent quantum mechanics, selection rules, coherent evolution in two-level systems, lineshapes, and NMR spectroscopy.
- Chemistry 548b: Nuclear Magnetic Resonance in Liquids
J. Patrick Loria
A theoretical treatment of solution NMR spectroscopy with emphasis on applications to proteins and biological macromolecules. This includes classical and quantum mechanical descriptions of NMR, product operator formalism, multidimensional NMR, phase cycling, gradient selection, relaxation phenomena, and protein resonance assignments.
- Chemistry 556: Biochemical Rates and Mechanisms
J. Patrick Loria
An advanced treatment of enzymology. Topics include transition state theory and derivation of steady-state and pre-steady-state rate equations. The role of entropy and enthalpy in accelerating chemical reactions is considered, along with modern methods for the study of enzyme chemistry. These topics are supplemented with in-depth analysis of the primary literature.