Biochemistry and Molecular Biophysics (BMB)

BMB/Bi/Ch 170 abc. Biochemistry and Biophysics of Macromolecules and Molecular Assemblies. 9 units (3-1-5); first, second, third terms. Prerequisite: Bi/Ch 110. First term: 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. Second term: basic principles of modern biophysical and structural methods to interrogate macromolecules from the atomic to cellular levels, including X-ray crystallography, NMR spectroscopy, molecular dynamics, electron and light microscopy, AFM, single molecule techniques, and systems biological simulations. Third term: detailed analysis of specific macromolecular machines and systems that illustrate the principles and biophysical methods taught in the first two terms. Instructors: Clemons, Jensen, Shan, Hoelz, staff.

Bioengineering (BE)

BE/APh 161. Physical Biology of the Cell. 12 units (3-0-9); second term. Prerequisites: Ph 2ab and ACM 95abc, or background in differential equations and statistical and quantum mechanics, or instructor’s written permission. Physical models applied to the analysis of biological structures ranging from individual proteins and DNA to entire cells. Topics include the force response of proteins and DNA, models of molecular motors, DNA packing in viruses and eukaryotes, mechanics of membranes, and membrane proteins and cell motility. Instructor: Phillips.

BE 262. Physical and Synthetic Biology Boot Camp. 9 units (1-8-0); third term. This course provides an intensive research introduction to current projects in physical and synthetic biology. Projects are based on current research directions in participating labs, including those of visiting biologists invited for the course. Representative classes of experiments include quantitative fluorescent microscopy of cell and organelle dynamics, single-cell measurement of genetic expression levels during development, and design and construction of biological circuits in microbes. Graded pass/fail. Instructor: Phillips. Not offered 2012–13.

Biology (Bi)

Bi 1 x. The Great Ideas of Biology: An Introduction through Experimentation. 9 units (0-6-3); third term. Introduction to concepts and laboratory methods in biology. Molecular biology techniques and advanced microscopy will be combined to explore the great ideas of biology. This course is intended for nonbiology majors and will satisfy the freshman biology course requirement. Limited enrollment. Instructor: Phillips.

Bi 114. Immunology. 9 units (3-0-6); second term. Prerequisites: Bi 8, Bi 9, Bi 122 or equivalent, and Bi/Ch 110 recommended. The course will cover the molecular and cellular mechanisms that mediate recognition and response in the mammalian immune system. Topics include cellular and humoral immunity, the structural basis of immune recognition, antigen presentation and processing, developmental regulation of gene rearrangement, biochemistry of lymphocyte activation, lymphokines and the regulation of cellular responses, T and B cell development, and mechanisms of tolerance. Instructor: Mazmanian.

Bi 190. Advanced Genetics. 6 units (2-0-4); third term. Prerequisites: Bi 122. Lectures and discussions covering how genetic analysis is used to solve biological problems. Emphasis is on genetic and genome-scale approaches used in model organisms such as yeast, flies, worms, and mice to elucidate the function of genes, genetic pathways and genetic networks. Instructor: Sternberg. Given in alternate years; offered 2012-13.

Bi/CNS 250 c. Topics in Systems Neuroscience. 9 units (3-0-6); third term. Prerequisite: graduate standing. The class focuses on quantitative studies of problems in systems neuroscience. Students will study classical work such as Hodgkin and Huxley’s landmark papers on the ionic basis of the action potential, and will move from the study of interacting currents within neurons to the study of systems of interacting neurons. Topics will include lateral inhibition, mechanisms of motion tuning, local learning rules and their consequences for network structure and dynamics, oscillatory dynamics and synchronization across brain circuits, and formation and computational properties of topographic neural maps. The course will combine lectures and discussions, in which students and faculty will examine papers on systems neuroscience, usually combining experimental and theoretical/modeling components. Instructor: Siapas.

Bi/BMB 251 abc. Current Research in Cellular and Molecular Biology. 1 unit. Prerequisite: graduate standing. Presentations and discussion of research at Caltech in biology and chemistry. Discussions of responsible conduct of research are included. Instructors: Sternberg, Hay.

Chemical Engineering (ChE)

ChE 101. Chemical Reaction Engineering. 9 units (3-0-6); second term. Prerequisites: ChE 62 and ChE 63 ab, or instructor’s permission. Elements of chemical kinetics and chemically reacting systems. Homogeneous and heterogeneous catalysis. Chemical reactor analysis. Instructor: Arnold.

ChE/BE 163. Introduction to Biomolecular Engineering. 9 units (3-0-6); first term. Prerequisites: Bi/Ch 110 or instructor’s permission.The course introduces rational design and evolutionary methods for engineering functional protein and nucleic acid systems. Rational design topics include molecular modeling, positive and negative design paradigms, simulation and optimization of equilibrium and kinetic properties, design of catalysts, sensors, motors, and circuits. Evolutionary design topics include evolutionary mechanisms and tradeoffs, fitness landscapes, directed evolution of proteins, and metabolic pathways. Some assignments require programming (MATLAB or Python). Instructors: Arnold, Pierce.

Geological and Planetary Sciences (Ge)

Ge/ESE 143. Organic Geochemistry. 9 units (3-2-4); first term. Prerequisite: Ch 41 a or equivalent. Main topics include the analysis, properties, sources, and cycling of natural organic materials in the environment, from their production in living organisms to burial and decomposition in sediments and preservation in the rock record. Specific topics include analytical methods for organic geochemistry, lipid structure and biochemistry, composition of organic matter, factors controlling organic preservation, organic climate and CO2 proxies, diagenesis and catagenesis, and biomarkers for ancient life. A laboratory component (three evening labs) teaches the extraction and analysis of modern and ancient organic biomarkers by GC/MS. Class includes a mandatory one-day (weekend) field trip to observe the Monterey Formation. Instructor: Sessions. Given in alternate years; offered 2012–13.

Ge 145. Isotope-Ratio Mass Spectrometry. 9 units (1-4-4); first term. This class provides a hands-on introduction to the construction and operating principles of instrumentation used for isotope-ratio mass spectrometry. The class is structured as a 1-hour lecture plus 4-hour lab each week examining the major subsystems of an IRMS, including vacuum systems, ionization source, mass analyzer, and detector. Laboratories involve hands-on deconstruction and re-assembly of a retired IRMS instrument to examine its components. Course is limited to 6 students at the discretion of the instructor, with preference given to graduate students using this instrumentation in their research. Instructor: Sessions.

Ge/Bi 246. Molecular Geobiology Seminar. 6 units (2-0-4); second term. Recommended preparation: ESE/Bi 166. Critical reviews and discussion of classic papers and current research in microbiology and geomicrobiology. As the topics will vary from year to year, it may be taken multiple times. Instructor: Orphan. Given in alternate years; not offered 2012–13.

Microbiology Core Courses

Bi 165. Microbiology Research: Practice and Proposal. 6 units (2-3-1); first term, starting in 2014. The course will serve to introduce graduate students to 1) ongoing research projects on campus involving the isolation, culture, and characterization of microbes and microbial communities; and 2) the process of writing fellowships having a microbiology focus to train students in preparing effective funding applications. The first phase will involve a series of research presentations by different laboratory groups over the course of three evenings in the first week of the Fall term. The second phase, over the Fall term, will involve training in grant writing by drafting an NSF-type proposal, and a final oral presentation of the students’ proposals. Instructors: Hoy and CEMI faculty. Enrollment limited to instructor approval.

ESE/Bi 166. Microbial Physiology. 9 units (3-1-5); first term. Recommended prerequisite: one year of general biology. A course on growth and functions in the prokaryotic cell. Topics covered: growth, transport of small molecules, protein excretion, membrane bioenergetics, energy metabolism, motility, chemotaxis, global regulators, and metabolic integration. Instructor: Leadbetter.

ESE/Bi 168. Microbial Metabolic Diversity. 9 units (3-0-6); second term. Prerequisites: ESE 142, ESE/Bi 166. A course on the metabolic diversity of microorganisms. Basic thermodynamic principles governing energy conservation will be discussed, with emphasis placed on photosynthesis and respiration. Students will be exposed to genetic, genomic, and biochemical techniques that can be used to elucidate the mechanisms of cellular electron transfer underlying these metabolisms. Instructor: Newman. Not offered 2015-16.

Ge/ESE 170. Microbial Ecology. 9 units (3-2-4); third term. Prerequisite: ESE/Bi 166. Structural, phylogenetic, and metabolic diversity of microorganisms in nature. The course explores microbial interactions, relationships between diversity and physiology in modern and ancient environments, and influence of microbial community structure on biogeochemical cycles. Introduction to ecological principles and molecular approaches used in microbial ecology and geobiological investigations. Instructor: Orphan. Not offered 2014-15.

Microbiology Courses

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