Courses of Study
Sections
A graduate program in Biochemistry and Biophysics
Last updated: August 23, 2011 at 3:25 p.m.
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.
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 for Biochemistry and Biophysics
Christopher Miller, Program Chair
(Biochemistry)
Michael Hagan (on leave spring 2012)
(Physics)
Dorothee Kern
(Biochemistry)
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 100-200 level course from the School of Science, approved in advance by the graduate program chair) with a grade of B- or higher and two laboratory rotations (BCBP 300a). All students are required to take BCHM 101a and BCBP 300a in the first semester, and BCHM 103b and BCHM 104b in the second semester. The student will join a lab at the end of the first semester and then work full-time in this lab the three remaining semesters for the MS thesis. To earn the M.S. degree the student must satisfy the graduate school and department requirements, which include submission of an M.S. thesis that is judged satisfactory by a committee of faculty appointed by the Program Chair.
Residence Requirement
The minimum residence requirement is one year.
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.
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 (Ethical Practice in Health-Related Sciences). All students beyond the first year must register for BCHM 401d. Neither 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.
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.
Ms. Kern
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.
Mr. Gelles
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.
Mr. Pomeranz Krummel
BCHM
104a
Physical Chemistry of Macromolecules I
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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. Usually offered every second year.
Mr. Miller and Mr. Oprian
BCHM
104b
Physical Chemistry of Macromolecules II
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Prerequisites: BCHM 104a, CHEM 141a, PHYS 40a or equivalent; and BCHM 100a 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.
Mr. Theobald
BCHM
107b
Advanced Topics in Biochemistry: Research Hoedown
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Prerequisite: BCHM 100a. May not be taken for credit by students who took BCHM 103b in spring 2009.
An eclectic series of lectures taught by members of the faculty in their own area of research, with the intent that the student gain an in-depth appreciation for current research in the field, as well as a first hand exposure to biochemical research at Brandeis. Usually offered every year.
Staff
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
153b
Methods in High-Resolution Electron Cryo-Microscopy
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Transmission electron microscopy is introduced as a method in structural biology. Instrumentation, data collection, image processing, and interpretation of biological structures visualized by this method are discussed. Usually offered every second year.
Mr. Grigorieff
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. This is an experiential learning course.
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
170b
Bioinformatics
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Prerequisites: Familiarity with computing is necessary and a basic biochemistry course is recommended. A joint offering between Brandeis University and Wellesley College.
Familiarizes students with the basic tools of bioinformatics and provides a practical guide to biological sequence analysis. Topics covered include an introduction to probability and statistics; sequence alignments; database searches; alignments and phylogenetic trees; sequence pattern discovery; structure determination by secondary structure prediction; and three-dimensional structure prediction by homology modeling. In all cases, the strengths and limitations of the methods will be discussed. Usually offered every third year.
Ms. Ringe
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.
Mr. Petsko and Ms. Ringe
BCHM
172a
Cholesterol in Health and Disease
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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
(200 and above) Primarily for Graduate Students
BCBP
200b
Reading in Macromolecular Structure-Function Analysis
Formerly offered as BIOP 200b.
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.
Mr. Petsko
BCBP
300a
Biochemistry Techniques
Formerly offered as BCHM 300a.
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
Biochemistry Techniques
Formerly offered as BCHM 300b.
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. Formerly offered as BCHM 401d.
Independent research for the MS and PhD degrees. Specific sections for individual faculty members as requested.
Staff
Required First-Year Graduate Health-Related Science Programs Course
CONT
300b
Ethical Practice in Health-Related Sciences
Required of all first-year graduate students in health-related science programs. 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.
Ms. Ringe
Courses of Related Interest
This is a non-exclusive list of courses that may be of interest to Biochemistry and Biophysics graduate students.
CHEM
123b
Bioinorganic Chemistry
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Prerequisite: A satisfactory grade in CHEM 25a and b.
Bioinorganic chemistry involves the study of metal species in biological systems. Nearly one-third of proteins contain a metal cofactor. These cofactors catalyze an enormous breadth of chemical reactions, including many not yet accessible through conventional syntheses. Usually offered every second year.
Mr. Agar
CHEM
129b
Special Topics in Inorganic Chemistry: Introduction to X-ray Structure Determination
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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. 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.
Mr. Snider
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.
Mr. Snider
CHEM
143b
Kinetics, Dynamics, and Transport
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Prerequisites: A satisfactory grade in CHEM 11a, 15a and CHEM 11b, 15b or equivalent; MATH 10a,b or equivalent; PHYS 11a,b or 15a,b or equivalent. Organic chemistry is also recommended.
Macroscopic kinetics: elementary reactions and rate laws. Kinetic study of reaction mechanisms: techniques for kinetic measurements, fast reactions, treatment of kinetic data. Microscopic kinetics: molecular dynamics, transition state theory, reactions in the gas phase and in solution. Catalytic and chain reactions, enzyme kinetics. Nonlinear dynamics: chemical oscillations and waves. Usually offered every other year.
Staff
CHEM
144a
Computational Chemistry
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Prerequisites: A satisfactory grade in CHEM 11a,b 15a,b or equivalent; MATH 10a,b or equivalent; PHYS 11a,b or 15a,b or equivalent. Organic chemistry is also recommended.
Topics in computational chemistry: applications of quantum mechanics to structural and spectroscopic analysis of small molecules; molecular dynamics and Monte Carlo simulations of biomacromolecules. Standard computational programs are used by students to perform homework exercises. Usually offered every other year.
Staff
CHEM
147b
Advanced Mass Spectrometry Laboratory
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This is an experiential learning course. Prerequisites: A satisfactory grade (C- or better) in CHEM 18b or equivalent and CHEM 25a or equivalent, or permission of the instructor. Organic chemistry is also recommended.
Explores the fundamentals and historical significance of mass spectrometry. Students are trained to perform multidimensional liquid chromatography, and operate four different types of mass spectrometers, including MALDI-TOF MS, ESI-IonTrap MS, GC-MS, and ESI/MALDI-Fourier transform MS and gain practical experience in the following mass spectrometry applications: 1) organic and inorganic structure and reaction mechanism elucidation, 2) biological applications, including proteomics, imaging mass spectrometry, and forensics, and 3) environmental/green chemistry. Students will be briefly exposed to the next generation of mass spectrometry applications, including quantum computation and fusion research. In the last third of the course, students are given free reign to design an independent project based upon personal or thesis research interests. One hour lecture and one afternoon of laboratory per week. Usually offered every second year.
Mr. Pochapsky
CHEM
246b
Advanced NMR Spectroscopy
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
COSI
230a
Topics in Computational Biology
Prerequisite: COSI 178a.
This course aims to transcend traditional departmental boundaries and facilitate communications between experimental biologists and computational scientists. Through reading literature and small research projects, students will be introduced to problems in computational biology and learn the methods for studying them.
Mr. Hong
NBIO
136b
Computational Neuroscience
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Prerequisite: MATH 10a 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. Hagan
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.
Staff
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. Gelles