Viruses and Applications to Biological Systems
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; offered 2023-24.
Introduction to Biophotonics
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. Not offered 2023-24.
Biochemistry and Biophysics of Macromolecules and Molecular Assemblies
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 2023-24.
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 2023-24.
Advanced Topics in Biochemistry and Molecular Biophysics
Discussion of research fields in biochemistry and molecular biophysics at Caltech. Development of skills in literature analysis and information synthesis.
Macromolecular Function: kinetics, energetics, and mechanisms
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 and their application to more complex biological systems, including steady-state and pre-steady-state kinetics, kinetic simulations, and kinetics at single molecule resolution.
The Cell Cycle and Genomic Stability
The course covers the mechanisms by which eukaryotic cells control their duplication in a properly regulated manner. A large emphasis will be placed on the controls that cells employ to replicate and segregate their chromosomes with the necessary precision. In addition, the course will examine the mechanisms by which cells detect and rectify damaged DNA throughout the cell cycle. These various processes, collectively known as checkpoint-regulatory mechanisms, lie at the heart of how organisms maintain genomic integrity throughout their lifetimes. These pathways are essential for the prevention of cancer, birth defects, and other maladies. As part of the course, students will give presentations on key publications in the field, including both classic papers and newer papers that employ cutting-edge technologies.
Biochemistry Seminar Course
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).
The Structure of the Cytosol
The cytosol, and fluid spaces within the nucleus, were once envisioned as a concentrated soup of proteins, RNA, and small molecules, all diffusing, mixing freely, and interacting randomly. We now know that proteins in the cytosol frequently undergo only restricted diffusion and become concentrated in specialized portions of the cytosol to carry out particular cellular functions. This course consists of lectures, reading, student presentations, and discussion about newly recognized biochemical mechanisms that confer local structure and reaction specificity within the cytosol, including protein scaffolds and "liquid-liquid phase separations" that form "membraneless compartments".
Macromolecular Structure Determination with Modern X-ray Crystallography Methods
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 2023-24.
Current Research in Biology and Biological Engineering
Students may register for research units after consultation with their adviser.