Biochemistry and Biophysics


This track represents a traditional strength in the department involving protein and RNA biochemistry, experimental and computational biophysics, and systems biology. The collaborative web extends well into Chemical Biology and towards the departments of Biology, Pharmacology, and the Pharmacy School. The NIH-funded Molecular Biophysics Training Grant (MBTG) and the NCI Training Grant in Cellular Growth and Oncogenesis have been important anchors of this track for many of the high achieving students. The recent founding of the BioCircuits Institute (BCI) and the NIH-funded San Diego Center for Systems Biology (SDCSB) have affirmed the department’s leadership in quantitative biology.

Course Offerings:

  • CHEM 204 X-ray Crystallography (W)
  • CHEM 207 Protein NMR (S)
  • CHEM 209 Macromolecular Recognition (F)
  • CHEM 210 Lipid Cell Signaling Genomics, Proteomics, and Metabolomics (W)
  • CHEM 213 Physical Chemistry of Biological Macromolecules (S)
  • CHEM 214 Molecular and Cellular Biochemistry (F)
  • CHEM 217 RNA Structure, Function, and Biology (S)
  • CHEM 219A Special Topics in Biochemistry (F)
  • CHEM 221 Signal Transduction (W)
  • CHEM 264 Structural Biology of Viruses (S)
  • CHEM 265 3D Electron Microscopy of Macromolecules (W)
  • CHEM 280 Applied Bioinformatics(W)

Course Descriptions

CHEM 204 X-ray Crystallography (W)

(Conjoined with Chem 104.) Analysis of macromecular structures by X-ray diffraction. Topics include symmetry, geometry of diffraction, detection of diffraction, intensity of diffracted waves, phase problem and its solution, heavy atom method, isomorphous replacement, anomalous dispersion phasing methods (MAD), direct methods, molecular replacement. Chem 204 students will be required to complete additional paper and/or exam beyond that expected of students in Chem 104.

CHEM 207 Protein NMR (S)

A broad introduction to the uses of nuclear magnetic resonance to characterize and understand proteins. Not highly mathematical, this course should be accessible to chemistry graduate students working with proteins.

CHEM 209 Macromolecular Recognition (F)

Structures and functions of nucleic acids, folding and catalysis of nucleic acids, motifs and domains of proteins, principles of protein-protein interactions, chemistry of protein/DNA and protein/RNA interfaces, conformational changes in macromolecular recognition. Prerequisites: biochemistry background and graduate standing, or approval of instructor.

CHEM 210 Lipid Cell Signaling Genomics, Proteomics, and Metabolomics (W)

Overview of new systems biology “-omics” approached to lipid metabolism and cell signaling, including interrogating gene and lipid databases, techniques for lipidomics, and implications for profiling and biomarker discovery in blood and tissues relevant to inflammatory and other human diseases. Cross-listed with BIOM 209 and PHAR 208. Recommended preparation: one quarter of undergraduate biochemistry.

CHEM 213 Physical Chemistry of Biological Macromolecules (S)

(Conjoined with Chem 113.) A discussion of the physical principles governing biological macromolecular structure and function, and the physicochemical experiments used to probe their structure and function. Chem 213 students will be required to complete an additional paper and/or exam beyond that expected of students in Chem 113. Prerequisites: Chem 140C or 140CH; and Chem 127 or 131 (113); or graduate standing (213).

CHEM 214 Molecular and Cellular Biochemistry

(Conjoined with Chem 114D.) This course represents a continuation of 114C, or an introductory course for first- and second-year graduate students, and covers topics in molecular and cellular biochemistry. Emphasis will be placed on contemporary approaches to the isolation and characterization of mammalian genes and proteins, and molecular genetic approaches to understanding eukaryotic development and human disease. Chem 214 students will be required to complete additional course work beyond that expected of students in Chem 114D. Prerequisites: Chem 114A–C or consent of instructor. (May not be offered every year.)

CHEM 217 RNA Structure, Function, and Biology (S)

Selected topics in RNA structure and function, such as the ribosome, ribozyme, antibiotics, splicing and RNA interference, as they relate to the RNA role in gene expression and regulation. Emphasis on techniques to study the dynamics of macromolecular complexes and the mechanism of RNA catalysis.

CHEM 219 Special Topics in Biochemistry (F)

This special topics course is designed for first-year graduate students in biochemistry. Topics presented in recent years have included protein processing, the chemical modification of proteins, the biosynthesis and function of glycoproteins, lipid biochemistry and membrane structure, and bioenergetics. Prerequisites: undergraduate courses in biochemistry, Chem 114A or equivalent. (May not be offered every year.)

CHEM 221 Signal Transduction (W)

The aim of this course is to develop an appreciation for a variety of topics in signal transduction. We will discuss several historical developments while the focus will be on current issues. Both experimental approaches and results will be included in our discussions. Topics may vary from year to year. Prerequisites: biochemistry and molecular biology. (May not be offered every year.)

CHEM 264/SPPS 268 Proteomics for Biologists (S)

(Cross-listed with BGGN 264.) An introduction of virus structures, how they are determined, and how they facilitate the various stages of the viral life cycle from host recognition and entry to replication, assembly, release, and transmission to uninfected host cells. Students will be required to complete a term paper. (May not be offered every year.) Recommended: elementary biochemistry as treated in Chem 114A or BIBC 100 and a basic course in cell biology or consent of the instructor.

CHEM 264 Structural Biology of Viruses (S)

(Cross-listed with BGGN 264.) An introduction of virus structures, how they are determined, and how they facilitate the various stages of the viral life cycle from host recognition and entry to replication, assembly, release, and transmission to uninfected host cells. Students will be required to complete a term paper. (May not be offered every year.) Recommended: elementary biochemistry as treated in Chem 114A or BIBC 100 and a basic course in cell biology or consent of the instructor.

CHEM 265 3D Electron Microscopy of Macromolecules (W)

(Cross-listed with BGGN 262.) Biological macromolecules and supramolecular complexes as well as organelles, and small cells are being examined in three-dimensions by modern electron cryomicroscopy and image reconstruction techniques. The basic principles of transmission electron microscopy and 3D image reconstruction are discussed. Chem 265/BGGN 262 students will be required to complete an additional oral presentation or paper or exam beyond that expected of students in Chem 165/BGGN 162. (May not be offered every year.) Recommended: elementary biochemistry as treated in Chem 114A or BIBC 100 and a basic course in cell biology, or consent of instructor.

CHEM 280 Applied Bioinformatics (W)

Publicly available databases and bioinformatics tools are now an indispensable component of biomedical research. This course offers an introductory survey of selected tools and databases; the underlying concepts, the software, and advice on using them. Practical exercises will be included.