A graduate program in Biochemistry and Biophysics

Last updated: July 1, 2014 at 12:29 p.m.

Objectives

Graduate Program in Biochemistry and Biophysics
The graduate program in Biochemistry/Biophysics leading to the degree of Doctor of Philosophy is designed to provide students with a deep understanding of the mechanisms governing the workings of biological macromolecules. The emphasis in the graduate program is placed upon experimental research work to train students to carry out independent original research. Students are required, however, to complete formal course work in advanced biochemistry and physical biochemistry and biophysics. Additional courses and seminars are available in a wide range of subjects, including enzyme regulation and mechanism, neurobiology, immunology, structural biology including protein crystallography, magnetic resonance spectroscopy and electron microscopy, membrane biology, molecular microscopy, biophysical chemistry, neuroscience, sensory transduction, chemo-mechanical energy transduction and computation.

Applicants are expected to have strong backgrounds in the physical sciences with undergraduate majors in any related field, such as biology, biochemistry, chemistry, engineering, mathematics, or physics. The course requirements for the PhD are formulated individually for each student to complement the student's previous academic work with the goal of providing a broad background in the physics and chemistry of biological processes.

Research for the PhD dissertation is carried out under the personal supervision of a faculty adviser; advisers can be from any department within the School of Science. Prospective applicants should obtain the complete list of faculty research interests and recent publications from the program or view this information at: www.bio.brandeis.edu.

The graduate program in biochemistry leading to the degree of Master of Science is designed to give students a substantial understanding of the chemical and molecular events in biological processes and experience in research. The program is divided among formal course work, biochemical and biophysical techniques, and a research project. Additional courses and seminars are available in a wide range of subjects.

How to Be Admitted to the Graduate Program

The general requirements for admission to the Graduate School are given in an earlier section of this Bulletin. Applications should include, in addition to letters of reference, a personal statement describing the reasons for the applicant's interest in the field and previous research experience, if any. Applicants are required to take the Graduate Record Examination and are encouraged to visit Brandeis for interviews, if possible.

Faculty Advisory Committee

Christopher Miller, Program Chair
(Biochemistry)

Michael Hagan
(Physics)

Dorothee Kern
(Biochemistry)

Requirements for the Degree of Master of Science

Program of Study
The MS program in Biochemistry and Biophysics is a two-year program, designed to accommodate students with previous academic majors in a wide range of fields, including biology, biochemistry, physical chemistry, engineering, and physics. The required program of study consists of four one-semester courses (BCHM 101a, BCHM 103b, BCHM 104b and one other advanced level course from the School of Science, approved in advance by the graduate program chair) with a grade of B- or higher. All students are required to take BCHM 101a in the first semester, and BCHM 103b and BCHM 104b in the second semester In addition, students are required to take two laboratory rotations (and enroll in BCBP 296) in the first semester. Starting in their second semester, students will join a research lab where they will work full-time for the three remaining semesters and enroll in BCBP 297, Master's Lab Research. To earn the M.S. degree students must satisfy the graduate school and department requirements, which includes the submission of a master's thesis (BCBP 299a) deemed satisfactory by a committee of faculty appointed by the Program Chair.

Residence Requirement
The residence requirement is two years. The program may take an additional one or two semesters to complete as an Extended Master's student.

Language Requirement
There is no language requirement.

Thesis
To qualify for the MS, a student must submit a thesis reporting a substantial piece of original research carried out under the supervision of a research adviser or advisers. The master’s thesis must be deposited electronically to the Robert D. Farber University Archives at Brandeis.

Requirements for the Degree of Doctor of Philosophy in Biochemistry and Biophysics

Program of Study
The PhD program in Biochemistry and Biophysics is designed to accommodate students with previous academic majors in a wide range of fields, including biology, biochemistry, physical chemistry, engineering, and physics. Consequently, the course requirements for the PhD are tailored to the needs of the particular student. In consultation with each entering student, the program chair formulates a program of study for the student based on the student's previous academic accomplishments and scientific interests. Successful completion of all the courses listed in the program of study with a grade of B- or higher fulfills the course requirements for the PhD. The required program of study consists of seven one-semester courses, of which four are usually completed in the student’s first year. The program chair will meet with the student to discuss the selection of courses before the student registers for courses and complete a written "Program of Study for the Biochemistry and Biophysics PhD Program". Ordinarily, all students are required to take BCBP 200b (Reading in Macromolecular Structure-Function Analysis) and the two laboratory rotation courses (BCBP 300a and 300b). All students must also complete the non-credit course CONT 300b (Responsible Conduct of Science). All students beyond the first year must register for BCHM 401d. Neither BCBP 300a nor BCBP 300b nor CONT 300b nor BCHM 401d count toward the seven course requirement. Students in their third and higher years of study will have yearly progress meetings with a faculty committee of three for the purpose of maintaining a satisfactory trajectory toward completion and defense of the thesis.

Teaching Requirement
As part of their PhD training, students are required to assist with the teaching of two one-semester courses.

Residence Requirement
The minimum residence requirement is three years.

Language Requirement
There is no language requirement.

Financial Support
Students may receive financial support (tuition and stipend) throughout their participation in the PhD program. This support is provided by a combination of university funds, training grants, and faculty research grants.

Qualifying Examinations
To qualify for the PhD degree, each student must write and defend in oral examinations two propositions related to research in biochemistry and/or biophysics. The subject of the second proposition must be outside the immediate area of the student's dissertation research.

Dissertation and Defense
The dissertation must report the results of an original scientific investigation into an approved subject and must demonstrate the competence of the PhD candidate in independent research. The dissertation research must be presented and defended in a final oral examination.

Requirements for the Degree of Doctor of Philosophy in Biochemistry and Biophysics with Specialization in Quantitative Biology

Program of Study
Students wishing to obtain this specialization must first gain approval of the graduate program chair or quantitative biology liaison. This should be done as early as possible; ideally, during the first year of graduate studies. In order to receive the PhD in Biochemistry and Biophysics with additional specialization in quantitative biology, candidates must complete the requirements for the PhD described above and the course requirements for the quantitative biology specialization that are described in the Quantitative Biology section of this Bulletin.

Any alteration to the Quantitative Biology course requirements must be approved by the graduate program chair and by the Quantitative Biology program faculty advisory committee.

Special Note Relating to Graduate Students

In addition to the formal courses listed in the following sections, all graduate students are encouraged to participate in the department's research clubs and colloquia. Colloquia are general meetings of the department in which department and guest speakers present their current investigations. Research clubs are organized by various research groups of the department.

Courses of Instruction

(100-199) For Both Undergraduate and Graduate Students

BCHM 100a Introductory Biochemistry
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Prerequisite: One year of organic chemistry with laboratory.
Topics include chemistry, reaction, and metabolism of biologically important compounds; formation and utilization of "energy-rich" compounds; introduction to enzyme mechanisms; interrelation and comparison of basic biochemical and chemical processes; and metabolic regulation. Usually offered every year in multiple sections.
Ms. 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.
Mr. Oprian

BCHM 102a Quantitative Approaches to Biochemical Systems
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Prerequisite: BCHM 100a 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.
Staff

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.
Addresses fundamental issues of information transfer in biological systems at a molecular level. Topics may include: DNA recombination and replication; transcription (DNA to RNA); processing/maturation of precursor RNA transcripts; and translation (RNA to protein). An emphasis will be placed on through review of the scientific literature, our understanding of the basics of these events in different biological systems, as well as how they are regulated. Usually offered every year.
Staff

BCHM 104a Classical and Statistical Thermodynamics
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Prerequisites: MATH 10a,b or equivalent, PHYS 11 or 15.
Covers basics of physical chemistry underpinning applications in BCHM 104b. Focus is placed on quantitative treatments of the probabilistic nature of molecular reality: molecular kinetic theory, basic statistical mechanics, and chemical thermodynamics in aqueous solution. Not offered in 2013-2014.
Staff

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.
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.
Mr. Theobald

BCHM 145a How to Decide: Bayesian Inference and Computational Statistics
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Prerequisites: Math 10a and b.
A calculus-based courses that teaches the theory and practice of modern statistical methods used by experimental scientists. Topics include Bayesian inference, maximum likelihood estimation, and computational resampling methods. The course consists of a mixture of small lectures and in-class computational exercises. Usually offered ever year.
Mr. Gelles and Mr. Theobald

BCHM 150a Research for the BS/MS Candidates
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Prerequisites: BIOL 22a and BCHM 100a, one year of organic chemistry and laboratory, and BCHM 99.
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. 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

BCHM 155b Biochemistry Laboratory
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Prerequisite: BCHM 100a must be taken before or concurrently with this course. Required course for the MS in Biotechnology. Course fee: $150.
Time-intensive laboratory class provides hands-on experience in biochemical techniques, with a focus on proteins. Students engage in skill-building and inquiry-based experiments. Students present research findings in written and oral formats. Usually offered every year.
Ms. Westover

BCHM 171b Protein X-ray Crystallography
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A practical guide to the determination of three-dimensional structures of proteins and nucleic acids by X-ray diffraction. Students learn the theory behind diffraction from macromolecular crystals and carry out all the calculations necessary to solve a protein structure at high resolution. Usually offered every second year.
Ms. Ringe

BCHM 172a Cholesterol in Health and Disease
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Prerequisite: BCHM 100a.
Considers cholesterol from the perspectives of biophysics, biochemistry, cell biology and physiology by analyzing primary research literature, historical reviews, and popular literature. Throughout this course, we will learn about the much-maligned molecule cholesterol. Students will give oral presentations. Usually offered every third year.
Ms. Westover

BIBC 126b Molecular Mechanisms of Disease
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Prerequisite: 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.
Ms. Westover

(200 and above) Primarily for Graduate Students

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. Usually offered every year.
Staff

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.
Staff

BCBP 296b Master's Lab Rotation I
See description under BCBP 296a. Usually offered every year.
Staff

BCBP 297a Master's Lab Research I
Laboratory research for Master's students in Biochemistry and Biophysics. Enrollment by others requires permission of the Program Chair. Usually offered every year.
Staff

BCBP 297b Master's Lab Research II
See description under BCBP 297a. Usually offered every year.
Staff

BCBP 299a Master's Thesis
Usually offered every year.
Staff

BCBP 300a Introduction to Research in Biochemistry and Biophysics I
BCBP 300a and 300b are laboratory rotation courses in which students gain direct experience conducting research in biochemistry and biophysics. Both courses are intended for Biochemistry and Biophysics graduate students; enrollment by others requires permission of the Program Chair. Usually offered every year.
Staff

BCBP 300b Introduction to Research in Biochemistry and Biophysics II
See description under BCBP 300a. Usually offered every year.
Staff

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.
Staff

BCHM 224b The RNA World: Chemistry, Structure, and Mechanism
Prerequisite: BCHM 100a, BIOL 105b, or permission of the instructor.
Employs seminars, lectures, and student led presentations to approach a wide range of topics in RNA research. Topics may include theories concerning the prebiotic world, RNA structure, protein-RNA interactions, RNA enzymes, RNA processing mechanisms, and RNA localization. Usually offered every third year.
Mr. Krummel

BCHM 251b Structure and Function of Membrane Proteins
Considers the molecular properties of membrane transport proteins, including ion channels, aquaporins, solute pumps, and secondary active transporters. Readings focus on primary literature aimed at interpreting the mechanisms of transmembrane solute movements in terms of the structures of these integral membrane proteins. Specific subjects chosen vary depending upon the trajectory of recent advances in this fast-moving research area. Usually offered every third year.
Mr. Miller

Required First-Year Graduate Health-Related Science Programs Course

CONT 300b Responsible Conduct of Science
Required of all graduate students supported on a sponsored project. Not for credit.
Ethics is an essential aspect of scientific research. This course, taught by university faculty from several graduate disciplines, covers major ethical issues germane to the broader scientific enterprise, including areas or applications from a number of fields of study. Usually offered every year.
Mr. Karel

Courses of Related Interest

This is a non-exclusive list of courses that may be of interest to Biochemistry and Biophysics graduate students.

CBIO 101a Chemical Biology
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Prerequisites: A satisfactory grade (C- or better) in BIOL 14a or BIOL 22a, BIOL 15b or BIOL 22b, 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 year.
Mr. Pochapsky

CBIO 106b Chemical Biology: Medicinal Enzymology
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Prerequisites: Satisfactory grade in BIOL 14a or BIOL 22a, BIOL 15b or BIOL 22b, 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.
Ms. Hedstrom

CHEM 129b Special Topics in Inorganic Chemistry: Introduction to X-ray Structure Determination
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Prerequisite: A satisfactory grade in CHEM 121a or 122b, or permission of instructor. Knowledge of point groups is essential, but such knowledge may be gained through reading and exercises provided by the instructor.
Topics include basic diffraction and space group theory, practical manipulations of crystals and X-ray diffraction equipment, solving crystal structures, and interpretation of structural chemistry. Course features self-paced exercises on PCs. Usually offered every second year.
Mr. Foxman

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.
Mr. Deng

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.
Mr. Snider

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.
Mr. Deng

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. Formerly offered as CHEM 246b.
A detailed discussion of modern NMR methods will be presented. The course is designed so as to be accessible to nonspecialists, 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 third year.
Mr. Pochapsky

COSI 178a Computational Molecular Biology
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Open to advanced undergraduate students and graduate students.
Information and computing technologies are becoming indispensable to modern biological research due to significant advances of high-throughput experimental technologies in recent years. This course presents an overview of the systemic development and application of computing systems and computational algorithms/techniques to the analysis of biological data, such as sequences, gene expression, protein expression, and biological networks. Hands-on training will be provided. Usually offered every other year.
Mr. Hong

NBIO 136b Computational Neuroscience
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Prerequisite: NBIO 140b or PHYS 10a or approved equivalents.
An introduction to concepts and methods in computer modeling 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 neuroeconomics. Usually offered every second year.
Mr. Miller

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 discuss recent experiments in single-molecule biology. Usually offered every second year.
Mr. Kondev

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.
Mr. Hagan

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.
Mr. Dogic