BCHM 88b Introductory Biochemistry
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Prerequisite: One year organic chemistry with laboratory, BIOL 14a, and BIOL 15b. Does not meet the requirements for the majors in Biochemistry or Chemistry, and does not serve as a prerequisite for most upper level BCHM, CHEM and CBIO classes.

Topics include protein and nucleic acid structure; metabolism of biologically important compounds; formation and utilization of "energy-rich" compounds; introduction to enzyme mechanism; comparison of basic biochemical and chemical processes; and biochemical basis of disease. Offered primarily for majors outside of Biochemistry and Chemistry. Usually offered every year.

BCHM 91g Introduction to Research Practice

Prerequisite: Student must complete online safety training relevant to the research group. Offered exclusively on a credit/no-credit basis. Yields quarter-course credit. May be repeated once for credit. Does not meet the requirements for the major in Biochemistry. May not be taken concurrently with another research course (e.g., BCHM 99a, 99b, 150a, and 150b). Enrollment limited to students who are declared Biochemistry majors or are supervised by Biochemistry department faculty members.

Students engage in Biochemistry research by working in the laboratory of a faculty member for a minimum of 3 hours per week for one semester. Students who have declared a Biochemistry major must receive permission from the Biochemistry Undergraduate Advising Head as well as the faculty sponsor to enroll in BCHM 91g. Usually offered every year.

BCHM 98a Readings in Biochemistry

Prerequisites: BIOL 14a, BCHM 100a, and one year of organic chemistry with laboratory. Does NOT satisfy the requirement for the major in biochemistry.

Directed scholarship on selected topics in biochemistry for outstanding juniors or seniors. Regularly scheduled discussion and written assignments leading to a substantive term paper. The tutorial is arranged only by mutual agreement between a Biochemistry department faculty mentor and student. Usually offered every year.

BCHM 99a Research for Undergraduates

Prerequisite: One year of organic chemistry with laboratory. Corequisite: BCHM 100a. The BCHM 100a corequisite may be waived at the discretion of the Undergraduate Advising Head.

Undergraduate research. A maximum of three course credits may be taken as BCHM 99a and/or 99b. No more than one research course (BCHM 99a, 99b, 150a, or 150b) may be taken in a given semester. Usually offered every year.

BCHM 99b Research for Undergraduates
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See BCHM 99a for special notes and course description.

BCHM 99e Research for Undergraduates

At the discretion of the Undergraduate Advising Head, one semester of BCHM 99 may be taken for double credit as 99e. Registration in this course requires written approval of the Biochemistry Undergraduate Advising Head.

See BCHM 99a for special notes and course description.

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 104a Physical Chemistry of Macromolecules I
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Prerequisites: MATH 10a,b or equivalent, PHYS 11 or 15.

Covers fundamentals of physical chemistry underpinning macromolecular applications in BCHM 104b. Focus is placed on quantitative treatments of the probabilistic nature of molecular reality: molecular kinetic theory, basic statistical mechanics, introductory quantum mechanics, free energy, entropy, and chemical thermodynamics in aqueous solution. 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.

BCHM 150a Research for the BS/MS Candidates
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Prerequisites: BCHM 100a, one year of organic chemistry and laboratory, and BCHM 99. A maximum of three course credits may be taken as BCHM 150a and/or 150b.

BCHM 150a and 150b are the final semester(s) of laboratory research under the BS/MS program, to be pursued under the supervision of the faculty adviser. No more than one research course (BCHM 99a, 99b, 150a, or 150b) may be taken in a given semester. Usually offered every year.

BCHM 150b Research for the BS/MS Candidates
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See BCHM 150a for special notes and course description. Usually offered every year.

BIBC 126b Molecular Mechanisms of Disease
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Prerequisite: BCHM 88b or BCHM 100a. May not be taken for credit by students who took BIOL 126b in prior years.

Explores biochemical changes in proteins, enzymes and metabolic pathways that underlie human diseases. Examines molecular mechanisms for a variety of diseases, with a particular focus on molecular mechanisms for therapies. Draws heavily on current literature. Usually offered every second 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.

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 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.

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 99b Research for Undergraduates
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See BCHM 99a for special notes and course description.

BIOL 18a General Biology Laboratory for Biology Majors
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Prerequisites: BIOL 14a, BIOL 18b, sophomore standing, and a declared biology major. Yields full-course credit. This lab is time-intensive and students will be expected to come in to lab between regular scheduled lab sessions. In order to accommodate students with time conflicts it may be necessary to re-assign students without conflicts to another section of the course. Students' section choice will be honored if possible.

Provides firsthand experience with a wide array of organisms and illustrates basic approaches to experimental design and problem solving in genetics and genomics. Usually offered every year.

BIOL 105b Molecular Biology
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Prerequisites: BIOL 14a and BIOL 15b.

Examination of molecular processes in replication and expression of genetic information and techniques by which this understanding has been achieved. Topics include recombinant DNA and other molecular biological techniques, structure and organization of DNA in chromosomes, DNA replication, transcription and regulation of gene expression, RNA structure and processing, mRNA stability, and other mechanisms of post-translational control. Usually offered every year.

BIOL 125a Immunology
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Prerequisites: BIOL14a and BIOL 15b. CHEM 25a is recommended. May not be taken for credit by students who took BIOL 70a in prior years.

Topics include properties and functions of cells involved in innate and adaptive immunity; genes, structure and function of immunoglobulins, B cell receptors and T cell receptors; lymphocyte differentiation; genetic regulation; MHC restriction; cell interactions and signaling; pathogen immunity (bacteria, viruses) and vaccines; tolerance and autoimmunity. Usually offered year.

BIOL 159a Project Laboratory in Microbiology
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Prerequisites: BIOL 12a and 12b or BIOL 18a and 18b.

A discovery-based laboratory to study the diversity of microorganisms in particular environments. Students will isolate microbes with ability to metabolize complex compounds from special environments, characterize their properties and identify them by DNA sequence analysis. After students learn foundational microbiology concepts and techniques, they will choose, design, and carry out a short research project. This project lab is primarily for seniors and master's students. Usually offered every year.

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 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 140b Principles of Neuroscience
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Prerequisites: Sophomore standing, BIOL 15b, one additional BIOL, BCHM, NBIO or NPSY course and one of the following: One year of college-level chemistry with lab, one year of college-level physics with lab, or any math course above 10a,b. AP scores are not accepted to meet the prerequisite. Junior standing recommended.

Examines the fundamental principles of neuroscience. Topics include resting potentials, action potentials, synaptic transmission, sensory systems, motor systems, learning, neural circuits underlying behavior, neurological diseases, and mental illness. Usually offered every 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.