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Biochemistry & Molecular Biophysics (BMB) Courses (2020-21)

Bi/BE/BMB 115. Viruses and Applications to Biological Systems. 9 units (3-2-4): third term. Learn about viruses as fascinating biological machines, focusing on naturally-occurring and evolved variants, in silico viral vector engineering, and computational methods that include structure visualization and machine learning. This course will introduce the fundamentals in the chemistry and biology of viruses, emphasizing their engineerable properties for use in basic research and translational applications. Topics include: viruses by the numbers, mammalian and non-mammalian (plant, bacteria) viruses, enveloped vs. non-enveloped viruses, host-virus interactions, viral life cycles (replication vs. dormancy), immune responses to viruses, zoonosis, diverse mechanisms of entry and replication, the application of viruses as gene-delivery vehicles (with a focus on adeno-associated viruses or AAVs, lentiviruses, and rabies), and how to engineer viral properties for applications in basic research and gene therapy. The lectures will be complemented by short lab exercises in AAV preparation, bioinformatics and machine learning, and structure visualization. Given in alternate years; not offered 2020-21. Instructors: Bjorkman, Gradinaru, Van Valen.
Ch/BMB 129. Introduction to Biophotonics. 9 units (3-0-6): first term. Prerequisites: Ch 21 abc required. Ch 125 recommended. This course will cover basic optics and introduce modern optical spectroscopy principles and microscopy techniques. Topics include molecular spectroscopy; linear and nonlinear florescence microscopy; Raman spectroscopy; coherent microscopy; single-molecule spectroscopy; and super-resolution imaging. Instructor: Wei.
BMB/Bi/Ch 170. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3- 0-6): first term. Prerequisites: Ch/Bi 110. Detailed analysis of the structures of the four classes of biological molecules and the forces that shape them. Introduction to molecular biological and visualization techniques. Not offered in 2020-21.
BMB/Bi/Ch 173. Biophysical/Structural Methods. 9 units (3-0-6): second term. Basic principles of modern biophysical and structural methods used to interrogate macromolecules from the atomic to cellular levels, including light and electron microscopy, X-ray crystallography, NMR spectroscopy, single molecule techniques, circular dichroism, surface plasmon resonance, mass spectrometry, and molecular dynamics and systems biological simulations. Not offered 2020-21. Instructors: Jensen, and other guest lecturers.
BMB/Bi/Ch 174. Advanced Topics in Biochemistry and Molecular Biophysics. 6 units (3-0-3): first term. Prerequisites: Ch/Bi 110 or equivalent. Discussion of research fields in biochemistry and molecular biophysics at Caltech. Development of skills in literature analysis and information synthesis. Instructors: Shan, Semlow, and guest lecturers.
BMB/Ch 178. Macromolecular Function: kinetics, energetics, and mechanisms. 9 units (3-0-6): first term. Prerequisites: Ch/Bi 110 or equivalent. Discussion of the energetic principles and molecular mechanisms that underlie enzyme's catalytic proficiency and exquisite specificity. Principles of allostery, selectivity, and enzyme evolution. Practical kinetics sections discuss how to infer molecular mechanisms from rate/equilibrium measurements and their application to more complex biological systems, including steady-state and pre-steadystate kinetics, kinetic simulations, and kinetics at single molecule resolution. Instructor: Shan.
BMB/Ch 202 abc. Biochemistry Seminar Course. 1 unit: first, second, third terms. The course focuses on a seminar on selected topics from outside faculty on recent advances in biochemistry. Components for each faculty visit include participation in a recitation, a formal discussion section with visiting faculty, and attendance of the Biochemistry seminar. Biochemistry Seminars take place 1-2 times per month (usually 4pm on Thursdays).
BMB/Ch 230. Macromolecular Structure Determination with Modern X-ray Crystallography Methods. 12 units (2-4-6): third term. Prerequisites: Consent of instructor. Advanced course in macromolecular crystallography integrating lecture and laboratory treatment of diffraction theory, crystallization (proteins, nucleic acids and macromolecular complexes), crystal characterization, X-ray sources and optics, crystal freezing, X-ray diffraction data collection (in-house and synchrotron), data reduction, multiple isomorphous replacement, single- and multi-wavelength anomalous diffraction phasing techniques, molecular replacement, electron density interpretation, structure refinement, structure validation, coordinate deposition and structure presentation. In the laboratory component, one or more proteins will be crystallized and the structure(s) determined by several methods, in parallel with lectures on the theory and discussions of the techniques Not offered in 2020-21. Instructor: Hoelz.
Bi/BMB 251 abc. Current Research in Cellular and Molecular Biology. 1 unit: . Prerequisites: graduate standing. Presentations and discussion of research at Caltech in biology and chemistry. Discussions of responsible conduct of research are included. Instructors: Sternberg, Hay.
BMB 278. Fundamentals of Molecular Genetics. 9 units (3-0-6): third term. Principles and mechanisms of DNA repair and replication, transcription and splicing, and protein synthesis. Not offered 2020-21.
BMB 299. Graduate Research. Units to be arranged: first, second, third terms. Students may register for research units after consultation with their adviser.

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