University Bulletin (2023-2024)

• Major (BS)
• Combined BS/MS

Undergraduate Major

The Biochemistry major is designed to equip students with a broad understanding of the chemical and molecular events involved in biological processes. The Biochemistry major provides a foundation for careers in medicine, biotechnology, or research in all branches of the biological sciences.

The general aim of the major is to ensure that the students first learn the necessary chemical and physical chemical background and then the basic principles and observations of biochemistry and molecular biology. The department also offers advanced courses in more specialized subjects such as enzyme mechanisms and X-ray crystallography. These advanced courses sample the range of subjects that can be studied by biochemical methods and from a biochemical point of view.

The modern discipline of biochemistry lies at the nexus of what classically have been considered the three “hard” sciences: physics, chemistry, and biology. This subject draws from physics and chemistry fundamental principles governing the behavior of molecules, and seeks to understand how these principles underlie the workings of living cells. The focus of the Brandeis biochemistry curriculum - the fulcrum around which the fundamental molecular principles are brought to bear upon life-processes - is the study of macromolecules. These huge molecular complexes - proteins, nucleic acids, and membrane assemblies - are the molecular machines that directly carry out virtually all operations of living cells: transmission of genetic information through the generations, catalysis of the chemical reactions that allow energy to flow through biological systems, generation of electricity in the nervous system, communication amongst tissues of multicellular organisms, disruption of healthy life-processes by pathogenic micro-organisms, to name a tiny fraction of the myriad examples of macromolecular function.

Two features of biochemistry as a discipline strongly influence our undergraduate curriculum. First, biochemistry is intrinsically reductionist in attitude. It finds value in studying the isolated parts of biological machines as a means of understanding those more complicated machines themselves, as well as their interactions with the cellular milieu. It asserts that macromolecules, despite their own complexity, can be understood by judicious application of physical-chemical law. Second, as a young field still exploding with new techniques and insights (rather analogous to physics in the first half of the 20th century), biochemistry is very much a moving target. While the fundamental physical-chemical principles underlying macromolecular behavior are timeless, the biochemical manifestations of these principles continue to change on the rapidly expanding edge of discovery. Our curriculum must be designed to track this change - to train students to engage with future issues in life-science that do not currently exist.

Knowledge

All students graduating with a Biochemistry major should have knowledge of the following general areas:

1. Basic principles of cell biology.
2. Firm understanding of general chemistry and organic chemical reaction mechanisms, particularly in the area of carbonyl chemistry.
3. Molecular forces determining protein and nucleic acid folding and membrane assembly.
4. Mechanisms by which enzymes catalyze cellular chemical reactions.
5. Strategies by which cells store and transmit information in DNA and RNA.
6. Mechanisms for communicating changes in the extracellular environment to the cell’s interior.
7. Techniques for determining molecular structures of macromolecules.
8. Relation of impairment in macromolecular function to disease.
9. All Honors majors will be additionally required to carry out an original research project in the laboratory of a Brandies life-science faculty member.

Core Skills

Our curriculum requires majors to use a set of basic skills to attack problems particular to biochemistry, some of which should be mastered through prerequisites taken even before encountering our introductory course. The core skills needed for the major are:

1. Facility with familiar mathematical functions, proficiency in univariate calculus, and understanding of basic elements of probability and statistics.
2. Familiarity with the application of calculus to problems in classical physics.
3. Mastery of basic principles of equilibrium thermodynamics and chemical kinetics.
4. Ability to read and analyze primary research literature.

Goals of Preparation in Biochemistry

Upon graduation, biochemistry majors will be well-placed for:

1. Graduate and postdoctoral study in preparation for careers in biomedical research.
2. Employment in pharmaceutical and biotech companies.
3. Careers in other biologically related areas, such as patent law, public health policy, etc.

Goals for Non-majors

The Biochemistry curriculum also serves many students with majors in other departments, particularly Biology, Neuroscience, and Chemistry. Our goals for these students are aimed less at the quantitative mastery of the subjects listed above for majors, and more towards attaining a basic literacy regarding behavior of proteins and nucleic acids in cellular function.

Students who are interested in majoring in biochemistry should speak with the Undergraduate Advising Head.

Niels Bradshaw
Regulation of Protein Phosphatases and the Evolution of Cellular Signaling.

Jeff Gelles
Mechanisms of mechanoenzymes and macromolecular machines. Single-molecule light microscopy as a tool to study enzyme mechanisms.

Julia Kardon
Mechanisms for control of mitochondrial protein activity, quality, and lifespan.

Dorothee Kern
Dynamics of enzymes. Magnetic resonance methods.

Daniel Oprian (on leave fall 2023)
Structure-function studies of visual pigments and other cell surface receptors.

Maria-Eirini Pandelia
Mapping the functional repertoire of bioinorganic systems and protein metallocofactors; paradigms of biocatalysts relevant to human health and environment.

Timothy Street, Undergraduate Advising Head
Mechanisms of protein folding in the cell.

Douglas Theobald, Chair
Empirical studies of the evolution of macromolecular structure and function, integrating structure determination methods, molecular evolutionary theory, Bayesian analysis, and biochemical structure-function studies.

Emily Westover (on leave spring 2024)
Instructional methods for undergraduate science education.

Degree of Bachelor of Science

A minimum of 22 total courses are required for the major:

• One year of general chemistry with laboratory (CHEM 11a, 11ab, 18a, 18b or honors equivalent)*
• One year of organic chemistry with laboratory (CHEM 25a, 25b, 29a, 29b)*
• One year of physics taught using calculus (PHYS 11a, 11b or PHYS 15a, 15b) with laboratory (PHYS 19a, 19b)*
• BIOL 14a (Genetics and Genomics)*
• BIOL 15b (Cells and Organisms) with laboratory (BIOL 18b)*
• BIOL 18a* (Students doing an honors thesis will not be required to take BIOL 18a)
• BCHM 100a (Advanced Introductory Biochemistry)
• BCHM 101a (Advanced Biochemistry: Enzyme Mechanisms)
• BCHM 103b (Advanced Biochemistry: Cellular Information Transfer Mechanisms)
• BCHM 104a (Physical Chemistry of Macromolecules I)
• BCHM 104b (Physical Chemistry of Macromolecules II)
• One elective consisting of a biochemistry-related 100-level course (excluding research courses) from any department in the Division of Science. The course used to fulfill the elective requirement must be approved in advance by the Undergraduate Advising Head. In some cases, courses below 100-level in mathematics or statistics can be used to fulfill the elective requirement if approved by the Undergraduate Advising Head.

*These courses must be taken prior to a student's senior year.

Foundational Literacies: As part of completing the Biochemistry major, students must:

• Fulfill the writing intensive requirement by successfully completing: BIOL 18a or a yearlong honors thesis, culminating in BCHM 99b.
• Fulfill the oral communication requirement by successfully completing: BCHM 103b.
• Fulfill the digital literacy requirement by successfully completing: BCHM 104b.

No course used to fulfill major requirements may be taken pass/fail. Grades below C- cannot be used to fulfill the requirements for the major. The advanced courses required for the Biochemistry major are demanding and require a strong background in Chemistry, Physics, and Mathematics. Biochemistry majors are typically students with excellent performance in the introductory courses in these subjects.

Senior Honors Program

In addition to the degree requirements listed previously, departmental honors require completion of eight credits of BCHM 99 (Research for Undergraduates), submission of an acceptable research thesis, and a final GPA 3.00 or better in the sciences and mathematics. Honors candidates are also expected to give a short oral presentation of their thesis research to members of the department at the end of their senior year. BCHM 99 may not exceed 12 credits. Petition to the department for participation in the honors program is made at or before the beginning of the senior year.

The Biochemistry BS/MS program is a research-intensive program. The program is intended for students who have independently arranged for a Brandeis professor to supervise a research project and have begun research no later than the beginning of their third undergraduate year.  Students must apply to the department for admission to the BS/MS program no later than the last day of course registration for first semester of the third year. Admission to the program is contingent on departmental approval of the research topic.

In addition to all courses required for the BS degree, the BS/MS degree requires completion of BCHM 102a (Quantitative Approaches to Biochemical Systems) one additional 100-level elective (excluding research courses) approved in advance by the Undergraduate Advising Head, four semesters of research courses (consisting of one or two semesters of BCHM 99 plus two or three semesters of BCHM 150), a full-time (i.e., no concurrent course work) summer research residency lasting at least ten weeks, submission of an acceptable thesis, a GPA of 3.00 or better in the sciences and mathematics, and grades of B- or better in all courses used for the major. No course used to fulfill BS/MS requirements may be taken pass/fail.

The BS/MS program requires completion of thirty-eight courses and the total credits required for the BS/MS degree is 152; no more than 24 credits of research (BCHM 99 or BCHM 150) can count toward this total (note that no more than one research course BCHM 99a, 99b, 150a, or 150b may be taken in a given semester). In addition, students must complete at least four graduate-level courses beyond the courses used by that student to fulfill the requirements for any undergraduate major (including the Biochemistry BS). BCHM 102a and BCHM 150 courses can be used to fulfill this four-course requirement. Application to the BS/MS program is made to the department no later than the last day of course registration in the first semester of the Junior year, and all work, including the thesis, must be completed by the time the BS is awarded.

To qualify for the BS/MS degree, the thesis must constitute a significant research contribution; if a thesis is found to be unacceptable under the BS/MS program, it will automatically be considered under the honors program. Students must electronically deposit their thesis to ProQuest ETD. For instructions on how to do this, visit the GSAS Thesis and Dissertation Guide.

In order to complete the honors program or the combined BS/MS program, it is advisable to gain exemption where possible from introductory courses in science and mathematics. This is especially important for the premedical students who must also fulfill the requirements imposed by medical schools.

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.
Emily Westover

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.
Staff

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.
Staff

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.
Staff

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

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.
Staff

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.
Emily Westover

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.
Dorothee Kern

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.
Maria-Eirini Pandelia

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.
Niels Bradshaw

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.

Timothy Street

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. Usually offered every year.
Julia Kardon

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.
Staff

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.
Staff

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.
Emily Westover

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.
Staff

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.
Maria-Eirini Pandelia

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. Usually offered every year.
Julia Kardon

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.
Niels Bradshaw

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

BIOL 18a General Biology Laboratory
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Prerequisite: BIOL 14a, BIOL 18b and sophomore standing. 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.
Melissa Kosinski-Collins

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.

Sebastian Kadener

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.
Staff

BIOL 159a Project Laboratory in Microbiology
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Prerequisites: BIOL 18a and BIOL 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.
Deani Cooper

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.
Thomas Pochapsky

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.
Lizbeth Hedstrom

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.
Hao Xu

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.
Chi Ting

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.

Chi Ting

CHEM 146b Advanced NMR 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.
Thomas Pochapsky

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.

Nathalie Vladis

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.
Staff