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Courses of Study:
Major (BA/BS)
Combined BS/MS
Master of Science
Doctor of Philosophy
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 a variety of introductory and advanced courses in more specialized subjects such as neurobiology, X-ray crystallography, and physical biochemistry. These courses sample the range of subjects that can be studied by biochemical methods and from a biochemical point of view.
Graduate Program in Biochemistry
The graduate program in biochemistry leading to the degree of Doctor of Philosophy is designed to provide students with a deep understanding of the chemical principles governing the workings of biological macromolecules. The bioorganic chemistry specialization of this program gives students the option of training in organic chemistry in addition to biochemistry. 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. Students in the bioorganic chemistry specialization supplement this core curriculum with courses in organic synthesis and other topics in organic chemistry. Additional courses and seminars are available in a wide range of subjects, including enzyme regulation and mechanism, neurobiology, immunology, structural biochemistry, membrane biology, and molecular genetics. Students are encouraged to choose advanced courses and seminars according to their particular interests. Doctoral research topics are chosen in areas under investigation by the faculty; these include problems in macromolecular structure and function, enzyme function and regulation, RNA processing, gene regulation, membrane transport and receptor function, molecular pharmacology, mechanisms of cell motility, microbial metabolism, and the biochemistry of cellular electrical excitability. A theme running through this research is the relationship of biochemical functions to underlying molecular structures and mechanisms.
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 techniques, and a research project. Additional courses and seminars are available in a wide range of subjects.
How to Become a Major
How to Be Admitted to the Graduate Program
Faculty
Gregory Petsko, Chair
X-ray crystallographic analysis of protein structure and enzyme mechanisms.
Jeff Gelles
Mechanisms of mechanoenzymes. Stochastic processes in single-enzyme molecules. Light microscopy as a tool to study enzyme mechanisms.
Nikolaus Grigorieff
High-resolution electron cryo-microscopy of membrane proteins and channels.
Dorothee Kern
Dynamics of enzymes. Magnetic resonance methods.
Christopher Miller, Graduate Program Chair
Structure and function of ion channel proteins. Membrane transport and mechanisms of electrical excitation.
Daniel Oprian, Undergraduate Advising Head
Structure-function studies of visual pigments and other cell surface receptors.
Dagmar Ringe
Structures of enzymes and enzyme-substrate complexes. X-ray crystallography.
Douglas Theobald
Structural bioinformatics analysis of telomeric complexes, integrating X-ray crystallographic structure determination, molecular evolution, and structure-function studies.
Requirements for the Major
Degree of Bachelor of Science
In addition to the degree requirements listed previously for the Bachelor of Arts degree, the Bachelor of Science degree requires one semester each of BCHM 101a and 103b (Advanced Biochemistry).
Required of all students: No course offered for major requirements may be taken pass/fail. Grades below C- in upper-level courses (any course numbered 100 or higher) cannot be used to fulfill the requirements for the major. Furthermore, no more than one D will be allowed in any other course required for the major.
Senior Honors Program
In addition to the degree requirements listed previously, departmental honors require completion of two semesters 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 three semester credits. Petition to the department for participation in this program is made at the beginning of the senior year.
Combined BS/MS Program
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.
Requirements for the Degree of Master of Science
A. BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
BCHM 102a Quantitative Approaches to Biochemical Systems
BIOP 200b Reading in Macromolecular Structure-Function Analysis
One advanced (100-200 level) course from the School of Science, approved in advance by the graduate program chair.
BCHM 300a,b Biochemical Techniques (laboratory rotations)
Residence Requirement
The minimum residence requirement is one year.
Language Requirement
There is no language requirement.
Thesis
The student must complete an acceptable MS thesis describing original research.
Requirements for the Degree of Doctor of Philosophy in Biochemistry
Students must successfully complete:
A. The core curriculum consisting of:
BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
BCHM 102a Quantitative Approaches to Biochemical Systems
BCHM 300a,b Biochemical Techniques (laboratory rotations course)
BIOP 200b Readings in Macromolecular Structure-Function Analysis
CONT 300b Ethical Practices in Health-Related Sciences
B. Elective courses: four advanced (100- and 200-level) courses from the
C. Students in their second and higher years of study must register for BCHM 401d (Biochemical Research Problems)--a dissertation research course--during every semester in which they are enrolled.
D. 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 of the thesis defense.
Students ordinarily complete the core curriculum plus one elective in the first year and complete the remaining requirements in their subsequent years in the program.
Requirements for the Degree of Doctor of Philosophy in Biochemistry with Specialization in Bioorganic Chemistry
In order to receive a PhD in biochemistry with a specialization in bioorganic chemistry, students must complete the requirements defined for the biochemistry PhD degree, with the following restrictions:
A. As one of their four elective courses, students must complete one course in synthetic organic chemistry, chosen from the following:
CHEM 134b Advanced Organic Chemistry: Synthesis
CHEM 135a Advanced Organic Chemistry: Synthesis II
B. As one of their four elective courses, students must complete one other advanced chemistry course approved in advance by the graduate program chair.
Requirements for the Degree of Doctor of Philosophy in Biochemistry with Specialization in Quantitative Biology
In order to receive a PhD in biochemistry with a specialization in quantitative biology, students must complete the requirements defined for the biochemistry PhD degree, and in addition must satisfy 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 quantitative biology program faculty advisory committee. With the approval of the biochemistry graduate program chair, courses taken to satisfy the quantitative biology specialization requirements can be used to satisfy course requirements of the biochemistry PhD degree.
Students wishing to obtain the 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.
Teaching Requirement
As a 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 Requirements
There is no foreign 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 individual research grants.
Qualifying Examinations
A qualifying examination must be taken following the first year of course work. In this examination, the student will be asked to present and defend an original proposition put forth by the student. In addition, the student must successfully pass a comprehensive examination administered following the second year of course work.
Dissertation and Defense
The required dissertation must summarize the results of an original investigation of an approved subject and demonstrates the competence of the candidate in independent research. This dissertation will be presented in a departmental lecture and defended in a final oral examination.
Special Note Relating to Graduate Students
BCSC 1a Designer Genes
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Does NOT satisfy the requirement for the major in biochemistry.
We are living during a far-reaching biological revolution. Information is stored in genes as DNA, the hereditary material of life, and the conversion of this information into proteins. This course investigates: identifying undesirable mutations; creating desirable mutations; cloning of cells, organs, and animals in agriculture and medicine. Usually offered every second year.
Staff
BCHM 98a Readings in Biochemistry
Prerequisites: BIOL 22a (formerly BIBC 22a), 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 faculty mentor and student. Usually offered every year.
Staff
BCHM 99a Research for Undergraduates
Prerequisites: BIOL 22a (formerly BIBC 22a), BCHM 100a, and one year of organic chemistry with laboratory. Requirement of BCHM 100a may be waived.
Undergraduate research. A maximum of three course credits may be taken as BCHM 99a and/or 99b. At the discretion of the department, one semester may be taken for double credit (99e). Offered every year.
Staff
BCHM 99b Research for Undergraduates
See BCHM 99a for special notes and course description.
Staff
BCHM 99e Research for Undergraduates
See BCHM 99a for special notes and course description.
Staff
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.
Mr. Oprian
BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
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Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or their equivalent.
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. Hedstrom
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.
Ms. Kern
BCHM 103b Advanced Biochemistry: Information Transfer Mechanisms
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Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or their equivalent.
Addresses fundamental issues of gene expression and signal transduction at a molecular level. Discusses parallels between nucleic acid and protein biosynthesis, modification, transport, and degradation with an emphasis on understanding the mechanisms of specificity and regulation of these complex macromolecular processes. Usually offered every year.
Mr. Oprian
BCHM 104b Physical Chemistry of Macromolecules
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Prerequisites: CHEM 141a 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 150a Research for the B.S./M.S. Candidates
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Prerequisites: BIOL 22a and BCHM 100a, one year of organic chemistry and laboratory, and BCHM 99.
The final semester(s) of laboratory research under the B.S./M.S. program, to be pursued under the supervision of a faculty advisor. Usually offered every year.
Staff
BCHM 150b Research for the B.S./M.S. Candidates
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See BCHM 150a for special notes and course description. Usually offered every year.
Staff
BCHM 150e Research for the B.S./M.S. Candidates
See BCHM 150a for special notes and course description.
Staff
BCHM 153b Methods in High-Resolution Electron Cyro-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 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. Miller and Mr. Oprian
BIOP 200b Reading in Macromolecular Structure-Function Analysis
Required for first-year biochemistry and biophysics and structural biology graduate students.
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
BCHM 219b Enzyme Mechanisms
Ms. Hedstrom
BCHM 220a Proteases
Ms. Hedstrom
BCHM 223a Enzymology of Biofuels, Bioplastics, and Bioremediation
Mr. Oprian
BCHM 224a Single-Molecule Biochemistry and Biophysics
Mr. Gelles
BCHM 225b Protein Dynamics
Prerequisite: BCHM 101a.
Introduces the fundamental concept of atomic fluctuations in proteins and their relation to protein function. Protein dynamics on different timescales is discussed with emphasis on different experimental and computational approaches to this problem. Usually offered every third year.
Ms. Kern
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
BCHM 300a Biochemistry Techniques
Prerequisite: BCHM 101. May be taken concurrently.
Usually offered every year.
Staff
BCHM 300b Biochemistry Techniques
Prerequisite: BCHM 101. May be taken concurrently.
Usually offered every year.
Staff
BCHM 401d Biochemical Research Problems
All graduate students beyond the first year must register for this course.
Independent research for the M.S. and Ph.D. degrees. Specific sections for individual faculty members as requested.
Staff
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. Lectures and relevant case studies are complemented by public lectures during the course. Usually offered every year.
Staff
PHYS 105a
Biological Physics
QBIO 110a
Numerical Modeling of Biological Systems
QBIO 120b
Quantitative Biology Instrumentation Laboratory
CHEM 123b
Bioinorganic Chemistry
CHEM 129b
Special Topics in Inorganic Chemistry: Introduction to X-ray Structure Determination
CHEM 130a
Advanced Organic Chemistry: Structure
CHEM 131a
Advanced Organic Chemistry: Topics in Structure and Reactivity
CHEM 132b
Advanced Organic Chemistry: Spectroscopy
CHEM 134b
Advanced Organic Chemistry: Synthesis
CHEM 137b
The Chemistry of Organic Natural Products
CHEM 143b
Kinetics, Dynamics, and Transport
CHEM 144a
Computational Chemistry
CHEM 146a
Single Molecule Spectroscopy
CHEM 147b
Mass Spectrometry
COSI 230a
Topics in Computational Biology
CHEM 246b
Advanced NMR Spectroscopy