1997-98 University Bulletin Entry for:



Undergraduate Concentration

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

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 and to train students to carry out independent original research. Major emphasis in this program is placed upon experimental research work. However, students are required to complete formal course work in advanced biochemistry, molecular biology, and physical biochemistry. Additional courses and seminars are available in a wide range of subjects, including enzyme regulation, 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, as described above.

How to Become an Undergraduate Concentrator

The general aim of the concentration 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, toxicology, and physical biochemistry. These courses sample the range of subjects that can be studied by biochemical methods and from a biochemical point of view.

How to Be Admitted to the Graduate Program

The general requirements for admission to the Graduate School, given in an earlier section of the Bulletin, apply here. Applicants for admission to the biochemistry Ph.D. program are also required to take the Graduate Record Examination. It is strongly suggested that the applicant take one of the advanced sections of this examination. The applicant's undergraduate curriculum should include fundamental courses in biology and chemistry.


Daniel Oprian, Chair

Structure-function studies of visual pigments and other cell surface receptors.

Robert Abeles

Mechanism of enzyme action. Design of highly specific enzyme inactivators. Design of inhibitors with potential pharmacological significance. Mechanism of drug action.

Jeff Gelles

Mechanisms of mechanoenzymes. Stochastic processes in single enzyme molecules. Light microscopy as a tool to study enzyme mechanisms.

Lizbeth Hedstrom

Enzyme structure-function studies. Protein engineering. Design of enzyme inhibitors.

Thomas Hollocher, Undergraduate Advising Head

Role and mechanism of action of oxidation-reduction enzymes. Mechanism, enzymology, and pathway of nitrogen in denitrification and nitrification.

Irwin Levitan (Director, Center for Complex Systems)

Neurobiology. Regulation of neuronal membrane properties. Modulation of ion channels.

John Lowenstein

Role of phospholipids in hormone action. Regulation of lipogenesis. Regulation and function of the purine nucleotide cycle. Regulation and function of adenosine production in heart. Techniques include cloning and high level expression of proteins concerned.

Susan Lowey (Rosenstiel Center)

Structure and function of myofibrillar proteins and their relation to the muscle cell. Techniques include physical chemistry, protein chemistry, molecular biological techniques, fluorescence, and electron microscopy.

Christopher Miller

Structure and function of ion channel proteins. Membrane transport and mechanisms of electrical excitation.

Melissa Moore

Molecular biology of self-splicing introns and the splicesome. Mechanisms of RNA catalysis.

Gregory Petsko (Director, Rosenstiel Center)

X-ray crystallographic analysis of protein structure and enzyme mechanisms.

Alfred Redfield (Rosenstiel Center)

Magnetic resonance in biopolymers. Physical biochemistry. Macromolecular structure.

Dagmar Ringe (Rosenstiel Center)

Structures of enzymes and enzyme-substrate complexes. X-ray crystallography.

Helen Van Vunakis

Interaction of biologically active compounds with specific antibodies and natural receptors. Nicotine metabolism and physiological effects.

Pieter Wensink (Rosenstiel Center)

Molecular biology. Regulation of gene expression during the development of higher organisms. Protein-nucleic acid interactions.

Requirements for the Undergraduate Concentration

Required of all candidates: One year each of general chemistry with laboratory, organic chemistry with laboratory, and physics taught using calculus (PHYS 11) with laboratory (this must be taken before the senior year); a year of physical biochemistry (CHEM 41a and BCHM 104b or CHEM 41b); introductory biochemistry (BCHM 100a); genetics and molecular biology (BIBC 22a) with laboratory; molecular biology (BIBC 105b). The laboratory associated with CHEM 41 is optional. AP credit or advanced standing awarded by the chemistry department can stand in lieu of general chemistry.

No course offered for concentration requirements may be taken pass/fail. Grades below C- in biochemistry courses offered for the concentration (and in CHEM 41a and b) cannot be used to fulfill the requirements of the concentration.

A student may graduate with a double concentration in biochemistry and biology, or in biochemistry and chemistry, if the concentration requirements in each department are fully met.

Honors Program

Courses required of all candidates listed above plus one year each of BCHM 101 and 99, submission of an acceptable research dissertation, and a grade point average of 3.00 in the sciences and mathematics. BCHM 99 may not exceed three semester course credits. Petition for this program is made at the beginning of the senior year.

Combined B.A./M.S. Program

This program requires completion of 38 courses, including the courses required of all candidates listed above, plus a summer research residency and four one-semester 100-level courses beyond any such courses used to fulfill minimal requirements for the concentration in biochemistry. These additional 100-level courses are approved by the department and would normally include a year of BCHM 101 and one or two semesters of research under BCHM 150. Not less than three nor more than four semesters of research credit total (BCHM 99 plus 150) are required for the research component of the B.A./M.S. Program. A candidate must have a grade point average of 3.00 in the sciences and mathematics, and grades of B- or better are required in the above four 100-level semester courses counted under the graduate part of the B.A./M.S. Program. Application to this program is made to the department and Graduate School no later than May 1 preceding the senior year, and all work must be completed by the time the B.A. is awarded, including the thesis. A substantial research contribution is required and, if a thesis is found unacceptable under this program, it will automatically be considered under the Honors Program. It is advisable, in order to complete the Honors Program or the combined B.A./M.S. Program, to gain exemption where possible from introductory courses in science and mathematics. This is especially important for the premedical student who must also fulfill requirements imposed by medical schools.

Requirements for the Degree of Master of Science

Program of Study

Students must successfully complete an approved program of at least eight courses. These courses would normally include five graduate-level courses in biochemistry and related areas with the remaining courses being thesis research. The five graduate-level courses would normally include advanced biochemistry (BCHM 101a and b) and three of the following four courses: physical biochemistry (BCHM 104b); molecular biology (BIBC 105b); biochemical techniques (BCHM 200a and b). Students who complete the program and thesis with distinction may be invited by the department to continue under the Ph.D. program. Note that the above named courses are also required for the Ph.D. program described below.

Residence Requirement

The minimum residence requirement is one year.

Language Requirement

There is no language requirement.


M.S. thesis describing original research carried out in the laboratory of the research advisor.

Requirements for the Degree of Doctor of Philosophy

Program of Study

Each doctoral candidate must satisfactorily complete the following core courses: advanced biochemistry (BCHM 101a and b), molecular biology (BIBC 105b), physical biochemistry (BCHM 104b), and biochemical techniques (BCHM 200a and b). After these core courses are completed, the faculty will evaluate each student's performance to decide whether the student should continue working toward the Ph.D. or the M.S. degree. In addition to the core courses, the Ph.D. program requires the completion of four biochemistry seminars and one advanced course from outside the department.

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 Ph.D. program. This support is provided by a combination of University funds, training grants, and individual research grants.


As a part of the graduate training program, Ph.D. students are required to participate as teaching assistants for two terms.

Qualifying Examinations

An oral qualifying examination must be taken generally at the beginning of the second year. In this examination, the student will be asked to defend or refute two propositions. One proposition will be assigned in an area of research outside the student's immediate area of specialization, and one will be an original proposition put forth by the student for a research problem in his or her area of interest (this is not necessarily a problem upon which he or she will carry out research).

In addition, the student must successfully pass a comprehensive examination before the research dissertation can be defended.

Dissertation and Defense

A dissertation will be required that summarizes 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.

Courses of Instruction

(1-99) Primarily for Undergraduate Students

BCSC 1a The Brain: From Molecules to Control of Movement

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Does NOT meet the concentration requirements in biochemistry.

Describes the structure and function of individual brain cells and interactions among them in multicellular networks. The organization of the brain and higher cognitive functions, including the control of motor activity, will also be discussed. Usually offered every year.

Messrs. Levitan (BCHM) and Lackner (PSYC)

BCSC 1b Biotechnology: Its Origins, Scientific Basis, and Impact

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Does NOT meet the concentration requirements in biochemistry. Enrollment limited to 35.

Genetic engineering and other forms of biotechnology have had and will have a profound impact on our understanding of the living cell and on human health. It has led to the development of new strains of plants and animals. The course describes the basics of this technology. Examples of present and future applications will be used to illustrate the new technology. Usually offered in odd years.

Mr. Lowenstein

BCSC 3b Dinosaur Paleobiology

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Prerequisite: High School biology. Does NOT meet the concentration requirements in biochemistry or biology. Enrollment limited to 35.

Discusses the origins, anatomy, evolution, biology, environment, and extinction of dinosaurs based on modern evidence. When and where did they live? Were dinosaurs hot or cold, fast or slow, good parents or poor, bright or stupid, social or not, noisy or silent? How are they related to birds? Where and how does one dig for dinosaurs? The course includes two one-day field trips. Will be offered in the spring of 1998.

Mr. Hollocher

BCSC 6b How Muscles Contract and Cells Move

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Does NOT meet the concentration requirements in biochemistry.

This course will describe how muscles work, the role of exercise, and the nature of muscle disease. We will start with a description of muscle at the light microscope level and proceed down to the molecular level. An understanding of the contractile mechanism will require some discussion of elementary biochemistry, cell biology, and physical techniques. It will be shown how basic principles underlying muscle movement apply to non-muscle cells in both the animal and plant kingdom. Usually offered in odd years.

Ms. Lowey

BCSC 7b Drug Discovery and Development

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Prerequisite: High school chemistry. Does NOT meet the concentration requirements in biochemistry. Enrollment limited to 50.

The drugs commonly used in today's society for control of sickness and disease have a rich and varied history. This course will trace the cultural origins and serendipitous discoveries of several pharmaceuticals, placing emphasis on the development of their current usage and mode of action. Topics to be covered include antibiotics, antitumor agents, psychotropic drugs, and treatments and vaccines for AIDS. We will also discuss how our body copes with foreign chemicals like drugs, pesticides, and cigarette smoke, and what unintended side effects on people and the environment accompanies the widespread use of these compounds. Usually offered in even years.

Messrs. Oprian and Gelles

BIBC 22a Genetics and Molecular Biology

(Formerly BIOL 21b)

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Prerequisites: CHEM 10a,b or 11a,b or 15a,b. CHEM 25a and BIOL 18a must be taken before or concurrently with this course. This course may not be repeated for credit by students who have taken BIOL 21b in previous years.

An introduction to the current understanding of hereditary mechanisms and the cellular and molecular basis of gene transmission and expression. Usually offered every year.

Mr. Fulton (Sec. 1) and Mr. Wensink (Sec. 2)

BCHM 98a Readings in Biochemistry

Prerequisites: BIBC 22a (formerly BIOL 21b); BCHM 100a or 102a; and one year of organic chemistry with laboratory. Enrollment limited. Signatures of the concentration advisor and mentor required. Does NOT satisfy the concentration requirement 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.


BCHM 99a Research for Undergraduates

Prerequisites: BIBC 22a (formerly BIOL 21b); and BCHM 100a; one year of organic chemistry with laboratory. Requirement of BCHM 100a or 102a may be waived. Enrollment limited. Signature of department chair required.

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.


BCHM 99b Research for Undergraduates

See BCHM 99a for special notes and course description. Offered every year.


BCHM 99e Research for Undergraduates

See BCHM 99a for special notes and course description. Offered every year.


(100-199) For Both Undergraduate and Graduate Students

BCHM 100a Introductory Biochemistry

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Prerequisites: One year of organic chemistry with laboratory. Enrollment limited to 50.

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. Multiple sections.

Mr. Lowenstein (fall-section 1), Ms. Lowey (spring-section 1), and

Ms. Moore (spring-section 2)

BCHM 101a Advanced Biochemistry I

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Prerequisites: One year of organic chemistry with laboratory and

BCHM 100a or their equivalent. Enrollment limited to 50.

A discussion of enzyme reactions, including energetics, kinetics, and reaction mechanisms. Metabolism of carbohydrates, lipids, amino acids, nucleic acids, vitamins and coenzymes, and hormones and inorganic substances. Coupled enzyme reactions and the synthesis of macromolecules. Regulated enzymes and the regulation of metabolism. Usually offered every year.

Ms. Hedstrom and Mr. Oprian

BCHM 101b Advanced Biochemistry II

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Prerequisite: BCHM 101a or permission of instructor. Enrollment limited to 50.

See BCHM 101a for course description. Usually offered every year.

Ms. Hedstrom and Mr. Oprian

BCHM 104b Physical Chemistry of Macromolecules

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Prerequisite: CHEM 41a (Physical Chemistry, Lectures I) and either BCHM 100a or BCHM 101a.

The course illustrates principles by which biological macromolecules behave in aqueous solution. Topics include linkage between ligand binding and conformations changes, protein folding, protein-DNA recognition, hydrophobic forces, single-molecule behavior. Protein, nucleic acid, and membrane structural principles will also be disussed. Offered every year.

Mr. Miller

BIBC 105b Molecular Biology

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Prerequisites: BIBC 22a (formerly BIOL 21b) and BIOL 22b (formerly BIOL 20a).

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.

Messrs. Haber and Sen

BCHM 128b Statistical Biophysics and Biochemistry

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Prerequisite: One year of college chemistry and one year of calculus or permission of the instructor.

Biochemists and molecular biophysicists seek to understand the behavior of living systems in terms of the properties of individual molecules. Because molecular motions are random, molecular properties are often best thought of in statistical terms. This course will give an introduction to the tools of probability theory and molecular statistics. We will then apply these tools to a variety of interesting biological problems, including: molecular diffusion, binding of ligands to cell surface receptors, bacterial chemotaxis, single-channel kinetics, and biochemical separation methods. Usually offered in even years.

Messrs. Gelles and Miller

BCHM 134b Advanced Biophysical Methods

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Prerequisite: BCHM 104b.

Several useful methods will be presented including solid-state NMR, EPR, EXAFS, and resonance raman spectroscopy. Applications of these methods to interesting biologically relevant problems will be discussed. Usually offered in odd years.

Mr. Redfield

BCHM 135a Redox Enzymology

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Prerequisite: BCHM 100a; BIBC 22a (formerly 21b).

This course includes lectures and student seminars and is open to senior and graduate students. The course focuses on the structure and mechanisms of redox enzymes. Organisms use three different classes of redox centers in enzymes. One class consists of organic cofactors, such as NAD+ and flavins; a second, of metal centers; and a third, of sulfhydryl groups of the protein. All three kinds of enzymes will be discussed. Usually offered in even years.

Mr. Hollocher

BCHM 136b Protein-DNA Recognition

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Prerequisite: BIBC 105b or permission of the instructor.

Many important biological phenomena depend on the binding of specific DNA sequences by regulatory proteins. The course will survey work on the structure of sequence-specific DNA binding proteins and their complexes with DNA, to study the mechanisms of specific DNA binding. The biological significance of different binding mechanisms will also be discussed. Usually offered every third year. Last offered in the spring of 1994.

Mr. Wensink

BCHM 142b Cell Motility

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Prerequisite: Biochemistry and Cell Biology or signature of the instructor.

Muscle and non-muscle myosins form a large family of molecular motors. We will discuss how these mechanoenzymes play fundamental roles in muscle contraction, cell locomotion, phagocytosis, and vesicle transport. Usually offered in even years.

Ms. Lowey

NBCH 148b Advanced Topics in Neuroscience

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Prerequisite: NBIO 140b or permission of the instructor. May be taken concurrently with NBIO 140b.

A discussion of cellular and molecular mechanisms that generate endogenous electrical properties of nerve cells. The regulation of endogenous patterns of neuronal activity by external influences including neurotransmitters, hormones, and sensory input will also be discussed. Usually offered in even years.

Mr. Lisman

BCHM 150a Research for B.A./M.S. Candidates

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Prerequisites: BIBC 22a (formerly BIOL 21b) and BCHM 100a; one year of organic chemistry and laboratory; BCHM 99d. Enrollment limited and signature of department chair required.

The final semester(s) of laboratory research under the B.A./M.S. Program, to be pursued under the supervision of a faculty advisor. Usually offered every year.

Mr. Hollocher and Staff

BCHM 150b Research for the B.A./M.S. Candidates

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See BCHM 150a for special notes and course description. Usually offered every year.

Mr. Hollocher and Staff

BCHM 151b Ion Channel Proteins

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This course considers the molecular properties of ion channels, the most basic element of molecular hardware in the nervous system. We examine the molecular architecture of channels and the mechanisms of channel activity. The mechanisms of voltage-dependence, ion selectivity, and channel gating will be emphasized. Usually offered in odd years.

Mr. Miller

BCHM 171b Protein X-ray Crystallography

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Prerequisites: Familiarity with computing is necessary and a basic biochemistry course is recommended.

A practical guide to the determination of three dimensional structures of proteins and nucleic acids by X-ray diffraction. Students will learn theory behind diffraction from macromolecular crystals and will carry out all of the calculations necessary to solve a protein structure at high resolution. Usually offered in even years.

Mr. Petsko and Ms. Ringe

(200 and above) Primarily for Graduate Students

BCHM 200a and b Biochemistry Techniques

Prerequisite: BCHM 101. May be taken concurrently.

Usually offered every year.

Mr. Gelles and Staff

BCHM 202b Chemistry of Enzyme-Catalyzed Reactions

Deals with reaction mechanisms of catalysis in aqueous solution, some of which are relevant to enzymic catalysis. Usually offered in even years.

Mr. Abeles


One or two seminars are given each term. Each student presents oral or written reports on various aspects of the announced seminar topic. Topics are repeated usually at two to three year intervals.

BCHM 219b Enzyme Mechanisms

Ms. Hedstrom

BCHM 222a Protein Kinases and Phosphatases

Mr. Lowenstein

BCHM 224a Microtubule-based Mechanoenzymes

Mr. Gelles

BIBC 224b The RNA World

Prerequsites: BCHM 100a, BIBC 105b, or permission of the instructor.

This course employs seminars and lectures to approach a wide range of topics in RNA research. Topics include RNA enzymes, RNA structure, protein-RNA interactions, pre-MRNA splicing, and RNA localization. Usually offered every year.

Ms. Moore

BCHM 233b Mechanisms of Transcription and Transcriptional Regulation

Mr. Wensink

Graduate Research

BCHM 401d Biochemical Research Problems

Independent research for the M.S. and Ph.D. degrees. Specific sections for individual faculty members as requested.


Journal Club, Colloquia, and Research Clubs

In addition to the formal courses announced above, all graduate students are expected 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.

CONT 300b Ethical Practice in Health-Related Sciences

Required of all first-year graduate students in health-related science programs. Not for credit.

Scientists are becoming increasingly aware of the importance of addressing ethical issues and values associated with scientific research. This course, taught by University faculty from several graduate disciplines, will cover 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 will be complemented by two public lectures during the course. Usually offered every year.

Mr. Jones

Cross-Listed Courses

CHEM 235b

Advanced NMR Spectroscopy