BCHM 100a Advanced Introductory Biochemistry
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Prerequisite: One year of organic chemistry with laboratory.

Topics include protein and nucleic acid structure; chemical basis of enzyme-catalyzed reaction mechanisms and enzyme kinetics; the chemical logic of metabolic pathways, including glycolysis and oxidative phosphorylation; and regulation of enzymatic pathways through allosteric control. Usually offered every year in multiple sections.

BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
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Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or equivalents.

Describes the principles of biological catalysts and the chemical logic of metabolic pathways. Discusses representative enzymes from each reaction class, with an emphasis on understanding how mechanisms are derived from experimental evidence. Topics include serine proteases, phosphatases, isomerases, carboxylases, and dehydrogenases. Usually offered every year.

BCHM 102a Quantitative Approaches to Biochemical Systems
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Prerequisite: BCHM 100a or equivalent and Math 10a and b or equivalent.

Introduces quantitative approaches to analyzing macromolecular structure and function. Emphasizes the use of basic thermodynamics and single-molecule and ensemble kinetics to elucidate biochemical reaction mechanisms. Also discusses the physical bases of spectroscopic and diffraction methods commonly used in the study of proteins and nucleic acids. Usually offered every year.

BCHM 103b Advanced Biochemistry: Cellular Information Transfer Mechanisms
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Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or equivalents. BIOL 14a or the equivalent is recommended.

Molecular mechanisms of information transfer in biological systems. Topics include nucleic acid biochemistry, processing of genetic information, and signal transduction. Each section will focus on the chemistry and regulation of a selected example from these fundamental processes. Lectures will be complemented by reading assignments and student presentations on articles from the original research literature. Usually offered every year.

BCHM 104b Physical Chemistry of Macromolecules II
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Prerequisites: BCHM 100a, and one of the following: BCHM 104a, CHEM 141a, or Phys 40a, and Math 10a and b or equivalent.

Illustrates the basic principles on which biological macromolecules are constructed and by which they function. Describes overall structures of proteins, nucleic acids, and membranes in terms of the underlying molecular forces: electrostatics, hydrophobic interactions, and H-bonding. The energetics of macromolecular folding and of the linkage between ligand binding and conformational changes will also be discussed. Recitation optional. Usually offered every year.

BCBP 200b Reading in Macromolecular Structure-Function Analysis

Introduces students to chemical and physical approaches to biological problems through critical evaluation of the original literature. Students analyze scientific papers on a wide range of topics in the fields of biochemistry and biophysics. Discussion focuses on understanding of the scientific motivation for and experimental design of the studies. Particular emphasis is placed on making an independent determination of whether the author's conclusions are well justified by the experimental results. Students are also introduced to grant-proposal writing by preparing NIH-format mock proposals for critical discussion and evaluation. Usually offered every year.

BCBP 230b Advanced Topics in Molecular Virology

Viruses infect all living things and have a role in how life works. They play a direct role in health and disease and even constitute portions of our own genetic material. The course will cover a range of topics focusing on viral mechanisms such as cell entry (membrane fusion and penetration), RNA replication and processing, and virus-particle assembly and budding, and the roles of these basic viral functions in permitting virus evolution. Through in-depth analyses of primary literature, a special emphasis will be placed on understanding experimental approaches and critically evaluating conclusions drawn from experiments. We will build upon various concepts covered in the course to discuss potential strategies for preventing undesired viral adaptations at the root of pandemics or antiviral drug resistance. The course will focus on recent discoveries and the use of modern techniques in virology research. Usually offered every year.

BCBP 240a Advanced Topics in Single-molecule Biophysics

Prerequisite: BCHM 102a or the equivalent.

Explores the use of single-molecule biophysics techniques to reveal the kinetics and mechanisms of biochemical reactions. This graduate-level advanced-topics course will cover statistical theory underlying single-molecule fluorescence experiments, computational methods used to analyze data, and practical aspects of experiment design. Usually offered every third year.

BCBP 296a Master's Lab Rotation I

Laboratory rotation courses for Master's students in Biochemistry and Biophysics. Enrollment by others requires permission of the Program Chair. Usually offered every year.

BCBP 297a Master's Lab Research I

Yields twelve semester-hour credits.

Laboratory research for Master's students in Biochemistry and Biophysics. Enrollment by others requires permission of the Program Chair. Usually offered every year.

BCBP 297b Master's Lab Research II

See description under BCBP 297a. Usually offered every year.

BCBP 299a Master's Thesis

Usually offered every year.

BCBP 300a Introduction to Research in Biochemistry and Biophysics I

BCBP 300a is a laboratory rotation course in which students gain direct experience conducting research in biochemistry and biophysics. Intended for Biochemistry and Biophysics graduate students; enrollment by others requires permission of the Program Chair. Usually offered every year.

BCBP 300b Introduction to Research in Biochemistry and Biophysics II

See description under BCBP 300a. Usually offered every year.

BCBP 401d Biochemical Research Problems

All graduate students beyond the first year must register for this course each semester.

Independent research for the MS and PhD degrees. Specific sections for individual faculty members as requested.

CBIO 101a Chemical Biology
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Prerequisites: A satisfactory grade (C- or better) in BIOL 14a, BIOL 15b, and CHEM 25a and b, or the equivalent.

Explores how scientific work in chemistry led to fundamental understanding of and ability to manipulate biological processes. Emphasis is placed on chemical design and synthesis as well as biological evaluation and utility. Content based on scientific literature readings. Usually offered every second year.

CBIO 106b Chemical Biology: Medicinal Enzymology
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Prerequisites: Satisfactory grade in BIOL 14a, BIOL 15b, CHEM 25a and 25b, and BCHM 100a or the equivalent.

Introduces students to the conceptual framework and experimental methods in medicinal chemistry. Topics include mechanisms of drug-target interactions, strategies for lead optimization and issues in metabolism, pharmacokinetics and pharmacodynamics. Readings drawn from textbooks and the original scientific literature. Usually offered every second year.

CHEM 130a Advanced Organic Chemistry: Structure
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.

Chemical bonding and structure, stereochemical principles and conformational analysis, organic reaction mechanisms, structures and activities of reactive intermediates, and pericyclic reactions. Usually offered every year.

CHEM 132b Advanced Organic Chemistry: Spectroscopy
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.

Application of spectroscopy to the elucidation of structure and stereochemistry of organic compounds, with emphasis on modern NMR and MS methods. Usually offered every year.

CHEM 134b Advanced Organic Chemistry: Synthesis
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.

Modern synthetic methods are covered, with an emphasis on mechanism and stereochemical control. Discusses the formation of carbon-carbon single and double bonds and carbocycles and procedures for oxidation, reduction, and functional group interchange. Examines selected total syntheses. Usually offered every year.

CHEM 137b The Chemistry of Organic Natural Products
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.

Natural products chemistry is surveyed within a biosynthetic framework. Occurrence, isolation, structure elucidation, biosynthesis, and biomimetic synthesis are covered with an emphasis on modern methods of establishing biosynthesis and biomimetic syntheses. Usually offered every second year.

CHEM 146b Advanced Spectroscopy
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Prerequisites: A satisfactory grade in PHYS 10a,b, 11a,b, or 15a,b or the equivalent; MATH 10a,10b.

A detailed discussion of modern NMR methods will be presented. The course is designed so as to be accessible to non-specialists, but still provide a strong background in the theory and practice of modern NMR techniques. Topics include the theory of pulse and multidimensional NMR experiments, chemical shift, scalar and dipolar coupling, NOE, spin-operator formalism, heteronuclear and inverse-detection methods, Hartmann-Hahn and spin-locking experiments. Experimental considerations such as pulse sequence design, phase cycling, and gradient methods will be discussed. Guest lecturers will provide insight into particular topics such as solid-state NMR and NMR instrumental design. Usually offered every second year.

NBIO 136b Computational Neuroscience
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Prerequisites: MATH 10a or higher and one of the following: NBIO 140b/240b, PHYS 10b/11b/15b, BIOL 107a, or any COSI course.

An introduction to concepts and methods in computer modeling and analysis of neural systems. Topics include single and multicompartmental models of neurons, information representation and processing by populations of neurons, synaptic plasticity and models of learning, working memory, decision making and neural oscillations. The course will be based on in-class computer tutorials, assuming limited prior coding experience, with reading assignments and preparation as homework. Usually offered every second year.

PHYS 105a Biological Physics
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Physical forces in living matter are studied from the perspective offered by statistical mechanics, elasticity theory, and fluid dynamics. Quantitative models for biological structure and function are developed and used to analyze systems such as single molecule experiments, transcriptional regulation networks, the forces arising during DNA packaging in a virus, and mechanisms underlying mammalian pattern formation. Usually offered every second year.

QBIO 110a Numerical Modeling of Biological Systems
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Prerequisite: MATH 10a and b or equivalent.

Modern scientific computation applied to problems in molecular and cell biology. Covers techniques such as numerical integration of differential equations, molecular dynamics and Monte Carlo simulations. Applications range from enzymes and molecular motors to cells. Usually offered every second year.

QBIO 120b Quantitative Biology Instrumentation Laboratory
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Focuses on optical and other instruments commonly used in biomedical laboratories to make quantitative measurements in vivo and in vitro. Students disassemble and reconfigure modular instruments in laboratory exercises that critically evaluate instrument reliability and usability and investigate the origins of noise and systematic error in measurements. Usually offered every year.