Courses 2025-26

Source: https://catalog.caltech.edu/current/2025-26/department/BMB/ Parent: https://catalog.caltech.edu/

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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; offered 2025-26.

Instructors: Bjorkman, Gradinaru, Van Valen

Ch/BMB 129

Introduction to Biophotonics

9 units (3-0-6)   |  first term

Prerequisites: Ch 21 abc and 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)

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 2025-26.

BMB/Bi/Ch 173

Biophysical/Structural Methods

9 units (3-0-6)   |  third term

Basic principles of modern structural and biophysical methods used to interrogate macromolecules from the atomic to cellular levels, including light and electron microscopy, X-ray crystallography, single molecule spectroscopy and microscopy techniques, and molecular dynamics and systems biology simulations.

Instructor: Chong

BMB/Bi/Ch 174

Macromolecular Machines of the Central Dogma

6 units (3-0-3)   |  first term

Prerequisites: Ch/Bi 110 ab or equivalent.

The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein. Each step in this process depends on different macromolecular machines that copy, transcribe, and decode the information stored in DNA. This course will focus on the function of such assemblies, including the replisome, RNA Pol II, the spliceosome, the ribosome, and translocons. The course will be taught through a combination of lectures and student-led discussions of the primary literature that has shaped our understanding of how macromolecular machines operate. Students will also prepare a short research proposal that will be peer reviewed and discussed at the end of the term at a mock NIH-style study section.

Instructor: Semlow

BMB/Ch 178

Macromolecular Function: kinetics, energetics, and mechanisms

9 units (3-0-6)   |  second term

Prerequisites: Ch/Bi 110a or equivalent.

Discussion of the energetic principles and molecular mechanisms that underlie enzyme's catalytic proficiency and exquisite specificity. Principles of selectivity, allostery, and force generation in biology. Practical kinetics and their application to more complex biological systems, including steady-state and pre-steady-state kinetics, and kinetic simulations.

Instructor: Shan

Bi/BMB 189

The Cell Cycle and Genomic Stability

6 units (2-0-4)   |  third term

Prerequisites: Bi 8 and Bi 9.

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.

Instructor: Dunphy

BMB/Ch 202 abc

Biochemistry Seminar Course

1 unit   |  first, second, third terms

Prerequisites: Graduate students only. Undergrads require special instructor permission to enroll.

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).

Instructor: Shan

Bi/BE/BMB 222

The Structure of the Cytosol

6 units (2-0-4)   |  third term

Prerequisites: Bi 9, Ch/Bi 110-111 or graduate standing in a biological discipline.

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".

Instructor: Kennedy

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.

Instructor: Hoelz

Bi/BMB 251 abc

Current Research in Biology and Biological Engineering

1 unit   |  first, second

Prerequisites: graduate standing.

Presentations and discussion of research in biology and biological engineering. Presented by second and fourth year graduate students, postdocs, and faculty.

Instructors: Hay, Sternberg

BMB 299

Graduate Research

Units to be arranged   |  first, second, third terms

Students may register for research units after consultation with their adviser.

Published Date: Aug. 26, 2025