Chemistry and Chemical Biology
Graduate Program
CCB Courses
Curriculum
The CCB curriculum includes a series of core required courses including Mechanistic Organic Chemistry, and Molecular Thermodynamics (Fall), Physical Organic Chemistry (Winter) and Chemical Biology (Spring). Courses in all four areas are offered through the CCB program and are taught by CCB faculty. Students are also required to do three lab rotations in their first year. CCB students are required to take the core courses and the lab rotations for a letter grade.
In addition to these required courses, students must also take two electives, chosen from graduate courses available at UCSF. One elective in the winter quarter and one in the spring are required for the main CCB path. These will be selected in consulation with a faculty advisor taking into consideration the student's background in both chemistry and biology and their research interests. With two required courses and a laboratory rotation in the Fall quarter of the first year, students would typically be advised to take other fall quarter elective courses in the second year, if desired. Common electives taken by students in the program are listed below.
Course Descriptions
Required Core Courses
Chem. 241 - Molecular Thermodynamics, Fall (5 U)
K. Dill
This is a course on molecular thermodynamics and statistical mechanics. It covers the concepts of entropy, enthalpy, heat capacity, free energy, ligand binding, solvation, the properties of water, the hydrophobic effect, solution electrostatics, adsorption, and physical and chemical kinetics.
BP204a – Macromolecular Interactions, Fall (4 U)
R. Stroud
This team-taught course focuses on a discussion of the molecular basis of biological interactions, protein structure and function, and the current methods in use at the forefront of this field. The required fall quarter for CCB students introduces key principles of protein structure, folding, interactions with ligands and enzymatic catalysis. Class times are split about half and half between lecture and discussion of key landmark papers in each field. (The second winter quarter, which expands to more specialized discussion of protein-protein and nucleic acid interactions, trans membrane proteins and protein assemblies, is not required for CCB students but may be taken as an elective.)
Chem. 244 - Reaction Mechanisms, Winter (3 U)
K. Shokat
This course is designed to develop the student's knowledge of organic reaction mechanisms. This interactive course involves some lectures, but enforces student learning through intensive arrow pushing sessions with students at the board. Current topics include: electrocyclic reactions, Woodward-Hoffman rules, sigmatropic reactions, migration reactions, neighboring group effects, carbanions and free radicals, carbenes, carbenoids, nitrenes, six-membered heterocyclic rings, five-membered heterocyclic rings.
Chem. 243 - Chemical Biology, Spring (5 U)
C. Craik
This survey course is team taught and designed to illustrate the use of chemical approaches to investigate biological processes at the biochemical, the cellular and the organismal level.
Other Required Courses
Pharm Chem 206 Laboratory Rotation. (3) Project. (3 quarters, 1st year only)
Staff
Chem 219 CCB Mini Course: Special Topics in Chemical Biology
Block 1: Synthetic Chemistry. (3)
J. Taunton
Block 2: NMR Practical (3)
M. Kelly
Block 3: Mass Spec (3)
A. Burlingame
Pharm Chem 221 Seminar Program. (1) Lecture 1 hours. (every quarter, every year)
T. James
A series of weekly research conferences in chemistry, chemical biology, and biophysics given by visiting lecturers, faculty, and advanced graduate students.
Pharm Chem 223 CCB Student Seminar Program. (1) Lecture 1 hours. (every quarter, every year)
C. Craik
This seminar will provide graduate students with a forum in which to develop seminar and poster presentation skills; critically organize and critically review scientific data; and analyze and question oral scientific presentations.
Pharm Chem 225 Graduate Research Opportunities. (1/1) Seminar 1 hours. (F, W, 1st year only)
J. Craig
A series of weekly presentations of the research interests of the CCB faculty members.
Chem 297 BBC Journal Club. (1) Presentation 1 hours. (every quarter, 1st and 2nd year)
C. Craik
Students are required to present in Journal Club, once in the first year and once in the second year. This experience will assist students in perfecting communication skills of the scientific literature.
Pharm Chem 250 Research. (1-8) Project 3-24 hours. (2nd yr and above)
Staff
Pharm Chem 266 Research Planning Conference. (1) Lecture 1 hours. (2nd yr and above)
Staff
Discussion and practice in research problem formulation and design selection. Core classes and small group sessions are organized around students' interests by faculty within the area of specialization.
Neuroscience 214 Ethics and the Responsible Conduct of Research. (1) Spring Quarter, 2nd year, Eight sessions
Data management; Animals in research; Human subjects in research; Publications: rules and etiquette; Grants: procedures and rules; Corporate-academic interactions
Elective Courses
Biochem 200A Structure of Macromolecules. (3) Lecture 3 hours.
J. Weissman
Fundamental principles governing the behavior of, and modern techniques for, study of biological macromolecules. Topics covered are: thermodynamics (entropy, equilibrium, cooperative interactions); kinetics and catalysis; structure and function of macromolecules (DNA, membranes, proteins) by X-ray and electron optics; kinetics and structure of cooperative enzymes and systems of biological control.
Biochem 200C Chromosome Structure and Function. (1.5) Lecture 3 hours.
J. Sedat
Structure and function of chromosomes in eukaryotes will be discussed in depth, beginning with basic underlying experiments and leading to the most recent proposals for structure. Emphasizes both theoretical and experimental approaches to this area of cell and molecular biology.
Biochem 201A Biological Regulatory Mechanisms. (4) Lecture 3 hours. Seminar 1 hours.
J. Li
The discovery of principles forming the foundation of molecular biology and recent advances in rapidly developing areas of the field. Topics covered are: RNA transcription, protein translation, DNA replication, control mechanisms, and genome structure and organization.
Biochem 242 Protein Crystallography. (3) Laboratory 3 hours.
R. Stroud
Principles of X-ray crystallography applicable to protein structure analysis will be presented in a course oriented toward research level understanding of the field. Course will involve group participation and some experimental work.
Biophysics 202 Biophysical Methods. (3) Lecture 3 hours.
D. Agard
This course is a comprehensive survey of the experimental methods of biophysics and the principles on which they are based, including spectroscopy, UV/visible absorption/emission spectroscopy, NMR, IR/Raman, hydrodynamics and ultracentrifugation, scattering, separation technology, fast reactions, imaging and mass spectrometry.
Biophysics 204 Macromolecular Structure and Interactions. (3) Lecture 3 hours. Discussion 1 hours.
R. Stroud
This course covers modern methods that have defined the molecular basis for macromolecular interactions and their function in biology. Emphasis will focus on the physical principles of macromolecular structure and interactions, and will describe modern methods.
Biophysics 206 Computation of Biological Molecules. (3) Lecture 3 hours.
To be announced
This course is a survey of computational methods used in the study of biomolecules. Covered are: modeling of molecular interactions and dynamics; approaches for protein folding and drug design, and computational methods for NMR, X-ray and microscopy.
Cell Biology 245 Cell and Developmental Biology. (4) Lecture 3 hours. Conference 1 hours.
Robert Edwards
Modern aspects of the molecular basis of cell function are examined with emphasis on how cells move, secrete, divide, and communicate with each other.
Chemistry 204 Introduction to Proteomics
R. Chalkley
Starting with a review of protein chemistry, emphasizing chemical modification and separation technologies, the course will review current approaches to the study of proteomics and predict what is likely to be realized in the next several years.
In addition to the lectures, each student will present a review of a published paper selected by the instructors and write a paper on a topic of current interest to the field (from a list provided, or select their own topic after instructor approval).
Chemistry 262 Advanced Physical Chemistry. (4) Lecture 4 hours.
M. Jacobson
Quantum mechanics and applications to molecular problems.
Chemistry 264 Advanced Statistical Mechanics and Molecular Mechanics. (2) Lecture 2 hours.
K. Dill
Advanced aspects of statistical mechanics and molecular mechanics; topics covered vary from year to year.
Genetics 200A Principles of Genetics. (3) Lecture 3 hours.
C. Bargmann
In-depth analysis of genetic mechanisms in selected procaryotes, eucaryotes. Topics include genetic exchange (conjugation, generalized and specialized transduction, transformation), recombination (general, site-specific, illegitimate), mapping, mutagenesis (induction and consequences), mobile genetic elements, gene expression, meiotic and mitotic segregation, allelism, position effects.
MIS-203 Introduction to Biocomputing Algorithms. (3) Lecture
P. Babbitt
Introduction to basic computational issues and methods used in the field of bioinformatics and computational biology.
MIS-206 Introduction to Bioinformatics. (3) Lecture
P. Babbitt
This course introduces the primary fields of Bioinformatics and related areas of Biocomputing; provides an overview of how these fields are changing and enhancing biological and biochemical research; and teaches basic skills in Bioinformatics and Biocomputing prerequisite for advanced research in these areas.
Neuroscience 201 Basic Concepts in Neuroscience. (4) Conference 2 hours.
L. Reichardt
An interdisciplinary introduction to fundamental aspects of nervous system function. Course emphasizes the ionic basis of neuronal signaling, neurochemistry, the cell biology of the neuron, and mechanisms of neuronal integration.
Pharm Chem 230 Spectroscopy. (2) Laboratory 3 hours.
M. Kelly
Practical applications of NMR spectroscopy to chemical and biological studies of small molecules and macromolecules. Introduction to the basic hardware and software components of modern state-of-the-art NMR spectrometers. Small group sessions will be conducted at a spectrometer console. The processing, analysis, and interpretation of NMR data will be taught for basic 1D and 2D spectral sequences. Elucidation of NMR applications to ligand binding studies and modern drug discovery.
Pharm Chem 231 Nuclear Magnetic Resonance. (3-4) Lecture 3-4 hours.
Staff
Theory and application of nuclear magnetic resonance for biomolecular structure determination.
Pharm Chem 235 Mass Spectrometry of Proteins. (2)
A. Burlingame
Mass spectrometry of proteins is revamped graduate elective that will combine lectures and laboratory for the first time focused on the principles of mass spectrometry and state of the art methodology used in solving current problems in protein biology. This suite of technologies including capillary HPLC and2-d SDS PAGE are important in addressing post-genome challenges defining protein expression, the composition of large subcellular scale protein machines and posttranslational or chemical modifications.