Department of Biochemistry

Last updated: April 15, 2014 at 5:03 p.m.

Objectives

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.

Learning Goals

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:

  • Basic principles of cell biology.
  • Firm understanding of general chemistry and organic chemical reaction mechanisms, particularly in the area of carbonyl chemistry.
  • Molecular forces determining protein and nucleic acid folding and membrane assembly.
  • Mechanisms by which enzymes catalyze cellular chemical reactions.
  • Strategies by which cells store and transmit information in DNA and RNA.
  • Mechanisms for communicating changes in the extracellular environment to the cell’s interior.
  • Techniques for determining molecular structures of macromolecules.
  • Relation of impairment in macromolecular function to disease.
  • 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:

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

Goals of preparation in biochemistry
Upon graduation, biochemistry majors will be well-placed for:

  • Graduate and postdoctoral study in preparation for careers in biomedical research.
  • Employment in pharmaceutical and biotech companies.
  • 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.

How to Become a Major

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

Faculty

Dorothee Kern, Chair
Dynamics of enzymes. Magnetic resonance methods.

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

Steve Goldstein, Provost
Ion channels in health and disease - heart, nervous system and muscle. Single molecule and ensemble electrophysiology, spectroscopy, and microscopy augmented by protein, phage and molecular techniques.

Daniel Pomeranz Krummel
Structure-function studies of RNA-protein complexes critical to eukaryotic RNA maturation.

Christopher Miller (on leave academic year 2013-2014)
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 (on leave fall 2013)
Structures of enzymes and enzyme-substrate complexes. X-ray crystallography.

Timothy Street
Mechanisms of protein folding in the cell.

Douglas Theobald
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
Instructional methods for undergraduate science education.

Requirements for the Major

Degree of Bachelor of Science
One year of general chemistry with laboratory; one year of organic chemistry with laboratory; one year of physics taught using calculus (PHYS 11a,b or PHYS 15a,b) with laboratory; BIOL 14a or 22a with laboratory (Genetics and Genomics); BIOL 15b or 22b with laboratory (Cells and Organisms)--the above courses must be taken prior to the senior year; BCHM 100a (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); and one elective consisting of a biochemistry-related 100-level course (excluding research courses) from any science department. The course used to fulfill the elective requirement must be approved in advance by the Undergraduate Advising Head. CHEM 141a (Classical and Statistical Thermodynamics) may be substituted for BCHM 104a with approval of the Undergraduate Advising Head.

No course offered for major requirements may be taken pass/fail. Grades below C- cannot be used to fulfill the requirements 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 the honors program is made at the beginning of the senior year.

Combined BS/MS Program

In addition to all courses required for the BS degree, the BS/MS degree requires completion of BCHM 102a (Quantitative Approaches to Biochemical Systems) and one additional elective (excluding research courses) approved in advance by the Undergraduate Advising Head, three semesters of research (one or two semesters of BCHM 99 plus one or two 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.

This program requires completion of thirty-eight courses; no more than four semesters of research (BCHM 99 or BCHM 150) can count toward this total. Application to this program is made to the department and Graduate School no later than May 1 preceding the senior 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. The BS/MS thesis must be deposited electronically to the Robert D. Farber University Archives at Brandeis.

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.

Courses of Instruction

(1-99) Primarily for Undergraduate Students

BCHM 93a Research Internship and Analysis
Supervised research experience in a Brandeis University laboratory. In consultation with a Brandeis Biochemistry department faculty member, the student will design and execute an individual research project, culminating in an oral and written presentation. Usually offered every year.
Staff

BCHM 98a Readings in Biochemistry
Prerequisites: BIOL 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 Biochemistry department faculty mentor and student. Usually offered every year.
Staff

BCHM 99a Research for Undergraduates
Prerequisites: BIOL 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 Undergraduate Advising Head, one semester may be taken for double credit (99e). Usually 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

(100-199) For Both Undergraduate and Graduate Students

BCHM 100a Introductory Biochemistry
[ qr sn ]
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
[ sn ]
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
[ sn ]
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
[ sn ]
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
[ sn ]
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
[ sn ]
Prerequisites: BCHM 104a or CHEM 141a; and 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 145a How to Decide: Bayesian Inference and Computational Statistics
[ sn ]
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
[ sn ]
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
[ sn ]
See BCHM 150a for special notes and course description. Usually offered every year.
Staff

BCHM 153b Methods in High-Resolution Electron Cryo-Microscopy
[ sn ]
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.
Staff

BCHM 155b Biochemistry Laboratory
[ oc sn ]
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
[ sn ]
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
[ sn ]
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
[ sn ]
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

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

Cross-Listed in Biochemistry

BIOL 70a Immunology
[ sn ]
Prerequisites: BIOL14a or BIOL 22a, BIOL 15b or BIOL 22b. CHEM 25a is recommended. May not be taken for credit by students who took BIOL 125a in prior years.
Topics include properties and functions of cells involved in innate and adaptive immunity; genes, structure and function of immunoglobins, 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.
Ms. Press

BIOL 105b Molecular Biology
[ sn ]
Prerequisites: BIOL 14a or BIOL 22a and BIOL 15b or BIOL 22b.
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.
Mr. Marr and Mr. Lau

BIOL 111a Developmental Biology
[ sn ]
Prerequisites: BIOL 14a or BIOL 22a and BIOL 15b or BIOL 22b.
How do complex organisms build themselves starting from single cells? Examines how processes such as fertilization, embryogenesis, cell differentiation, and tissue-specific gene expression occur; what is known about the key molecules and genes that orchestrate these processes; and how genetic changes affecting these processes underlie the evolution of body form. Usually offered every second year.
Ms. Paradis

BIOL 159a Project Laboratory in Microbiology
[ sn ]
Prerequisites: BIOL 18a and b. Laboratory fee: $150 per semester.
A discovery-based laboratory to study the diversity of microorganisms in particular environments. We will isolate microbes with ability to metabolize complex compounds from special environments, characterize their properties and identify them by DNA sequence analysis. This course will teach the fundamentals of microbiology through hands-on activities. Usually offered every year.
Staff

CBIO 101a Chemical Biology
[ oc sn ]
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
[ sn ]
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
[ sn ]
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
[ sn ]
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 134b Advanced Organic Chemistry: Synthesis
[ sn ]
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 137b The Chemistry of Organic Natural Products
[ sn ]
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 146b Advanced NMR Spectroscopy
[ sn ]
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

NBIO 140b Principles of Neuroscience
[ sn ]
Prerequisite: Sophomore standing, BIOL 15b or BIOL 22b, 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.
Examines the basic 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.
Ms. Turrigiano

PHYS 105a Biological Physics
[ sn ]
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