98-99 University Bulletin Entry for:


(file last updated: [8/10/1998 - 15:21:11])


Undergraduate Concentration

The biochemistry major is designedto equip students with a broad understanding of the chemical andmolecular events involved in biological processes. The biochemistryconcentration 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 biochemistryleading to the degree of doctor of philosophy is designed to providestudents with a deep understanding of the chemical principlesgoverning the workings of biological macromolecules and to trainstudents to carry out independent original research. Major emphasisin this program is placed upon experimental research work. However,students are required to complete formal course work in advancedbiochemistry, molecular biology, and physical biochemistry. Additionalcourses and seminars are available in a wide range of subjects,including enzyme regulation, neurobiology, immunology, structuralbiochemistry, membrane biology, and molecular genetics. Studentsare encouraged to choose advanced courses and seminars accordingto their particular interests. Doctoral research topics are chosenin areas under investigation by the faculty; these include problemsin macromolecular structure and function, enzyme function andregulation, RNA processing, gene regulation, membrane transportand receptor function, molecular pharmacology, mechanisms of cellmotility, microbial metabolism, and the biochemistry of cellularelectrical excitability. A theme running through this researchis the relationship of biochemical functions to underlying molecularstructures and mechanisms.

The graduate program in biochemistryleading to the degree of master of science is designed to givestudents a substantial understanding of the chemical and molecularevents in biological processes and experience in research. Theprogram is divided among formal course work, biochemical techniques,and a research project. Additional courses and seminars are availablein a wide range of subjects, as described above.

How to Become an UndergraduateConcentrator

The general aim of the concentrationis to ensure that the students first learn the necessary chemicaland physical chemical background and then the basic principlesand observations of biochemistry and molecular biology. The departmentalso offers a variety of introductory and advanced courses inmore specialized subjects such as neurobiology, X-ray crystallography,and physical biochemistry. These courses sample the range of subjectsthat can be studied by biochemical methods and from a biochemicalpoint of view.

How to Be Admitted tothe Graduate Program

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


Daniel Oprian, Chair

Structure-function studiesof visual pigments and other cell surface receptors.

Jeff Gelles

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

Nicolaus Grigorieff

High resolution electron cryo-microscopyof membrane proteins and channels.

Lizbeth Hedstrom

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

Thomas Hollocher

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

Dorothee Kern

Dynamics of enzymes. Magneticresonance methods.

Irwin Levitan

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

John Lowenstein

Role of phospholipids in hormoneaction. Regulation of lipogenesis. Regulation and function ofthe purine nucleotide cycle. Regulation and function of adenosineproduction in heart. Techniques include cloning and high levelexpression of proteins concerned.

Christopher Miller

Structure and function of ionchannel proteins. Membrane transport and mechanisms of electricalexcitation.

Melissa Moore

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

Gregory Petsko (Director,Rosenstiel Center)

X-ray crystallographic analysisof protein structure and enzyme mechanisms.

Alfred Redfield (RosenstielCenter)

Magnetic resonance in biopolymers.Physical biochemistry. Macromolecular structure.

Dagmar Ringe (RosenstielCenter)

Structures of enzymes and enzyme-substratecomplexes. X-ray crystallography.

Helen Van Vunakis

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

Pieter Wensink (RosenstielCenter)

Structure and function of proteinsthat regulate transcription.

Requirements for the UndergraduateConcentration

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

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

A student may graduate witha double concentration in biochemistry and biology, or in biochemistryand chemistry, if the concentration requirements in each departmentare fully met.

Honors Program

Courses required of all candidateslisted above plus one year each of BCHM 101 and 99, submissionof an acceptable research dissertation, and a grade point averageof 3.00 in the sciences and mathematics. BCHM 99 may not exceedthree semester course credits. Petition for this program is madeat the beginning of the senior year.

Combined B.A./M.S. Program

This program requires completionof 38 courses, including the courses required of all candidateslisted above, plus a summer research residency and four one-semester100-level courses beyond any such courses used to fulfill minimalrequirements for the concentration in biochemistry. These additional100-level courses are approved by the department and would normallyinclude a year of BCHM 101 and one or two semesters of researchunder BCHM 150. Not less than three nor more than four semestersof research credit total (BCHM 99 plus 150) are required for theresearch component of the B.A./M.S. Program. A candidate musthave 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-levelsemester courses counted under the graduate part of the B.A./M.S.Program. Application to this program is made to the departmentand 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 requiredand, if a thesis is found unacceptable under this program, itwill automatically be considered under the Honors Program. Itis advisable, in order to complete the Honors Program or the combinedB.A./M.S. Program, to gain exemption where possible from introductorycourses in science and mathematics. This is especially importantfor the premedical student who must also fulfill requirementsimposed by medical schools.

Requirements for the Degreeof Master of Science

Program of Study

Students must successfullycomplete an approved program of at least eight courses. Thesecourses would normally include five graduate-level courses inbiochemistry and related areas with the remaining courses beingthesis research. The five graduate-level courses would normallyinclude advanced biochemistry (BCHM 101a and b) and three of thefollowing four courses: physical biochemistry (BCHM 104b); molecularbiology (BIBC 105b); biochemical techniques (BCHM 200a and b).Students who complete the program and thesis with distinctionmay 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 requirementis one year.

Language Requirement

There is no language requirement.


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

Requirements for the Degreeof Doctor of Philosophy

Program of Study

Each doctoral candidate mustsatisfactorily 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). Afterthese core courses are completed, the faculty will evaluate eachstudent's performance to decide whether the student should continueworking toward the Ph.D. or the M.S. degree. In addition to thecore courses, the Ph.D. program requires the completion of fourbiochemistry seminars and one advanced course from outside thedepartment.

Residence Requirement

The minimum residence requirementis three years.

Language Requirements

There is no foreign languagerequirement.

Financial Support

Students may receive financialsupport (tuition and stipend) throughout their participation inthe Ph.D. program. This support is provided by a combination ofUniversity funds, training grants, and individual research grants.


As a part of the graduate trainingprogram, Ph.D. students are required to participate as teachingassistants for two terms.

Qualifying Examinations

An oral qualifying examinationmust be taken generally at the beginning of the second year. Inthis examination, the student will be asked to defend or refutetwo propositions. One proposition will be assigned in an areaof research outside the student's immediate area of specialization,and one will be an original proposition put forth by the studentfor a research problem in his or her area of interest (this isnot necessarily a problem upon which he or she will carry outresearch).

In addition, the student mustsuccessfully pass a comprehensive examination administered atthe end of the second year of study.

Dissertation and Defense

A dissertation will be requiredthat summarizes the results of an original investigation of anapproved subject and demonstrates the competence of the candidatein independent research. This dissertation will be presented ina departmental lecture and defended in a Final Oral Examination.

Courses of Instruction

(1-99) Primarily for UndergraduateStudents

BCSC 1a The Brain: FromMolecules to Perception

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Does NOT meet the concentrationrequirements in biochemistry.

Describes the structure andfunction of individual brain cells and interactions among themin multicellular networks. The organization of the brain and highercognitive functions, including perception, will also be discussed.Usually offered every year.

Messrs. Levitan (BCHM) andSekuler (PSYC)

BCSC 1b Biotechnology: ItsOrigins, Scientific Basis, and Impact

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Does NOT meet the concentrationrequirements in biochemistry. Enrollment limited to 35.

Genetic engineering and otherforms of biotechnology have had and will have a profound impacton our understanding of the living cell and on human health. Ithas led to the development of new strains of plants and animals.The course describes the basics of this technology. Examples ofpresent and future applications will be used to illustrate thenew technology. Usually offered in odd years.

Mr. Lowenstein

BCSC 3b Dinosaur Paleobiology

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Prerequisite: High schoolbiology. Does NOT meet the concentration requirements in biochemistryor biology. Enrollment limited to 35.

Discusses the origins, anatomy,evolution, biology, environment, and extinction of dinosaurs basedon modern evidence. When and where did they live? Were dinosaurshot 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 includestwo one-day field trips. Will be offered in the spring of 1998.

Mr. Hollocher

BCSC 7b Drug Discovery andDevelopment

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

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

Messrs. Oprian and Gelles

BIBC 22a Genetics and MolecularBiology

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Prerequisites: CHEM 10a,bor 11a,b or 15a,b. CHEM 25a and BIOL 18a must be taken beforeor concurrently with this course

An introduction to the currentunderstanding of hereditary mechanisms and the cellular and molecularbasis of gene transmission and expression. Usually offered everyyear.

Mr. Wensink (Sec. 1) and Ms.Sengupta (Sec. 2)

BCHM 98a Readings in Biochemistry

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

Directed scholarship on selectedtopics in biochemistry for outstanding juniors or seniors. Regularlyscheduled discussion and written assignments leading to a substantiveterm paper. The tutorial is arranged only by mutual agreementbetween 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 chemistrywith laboratory. Requirement of BCHM 100a may be waived. Enrollmentlimited. Signature of department chair required.

Undergraduate research. A maximumof three course credits may be taken as BCHM 99a and/or 99b. Atthe discretion of the department, one semester may be taken fordouble credit (99e). Offered every year.


BCHM 99b Research for Undergraduates

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


BCHM 99e Research for Undergraduates

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


(100-199) For Both Undergraduateand Graduate Students

BCHM 100a Introductory Biochemistry

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

Topics include chemistry, reaction,and metabolism of biologically important compounds; formationand utilization of "energy-rich" compounds; introductionto enzyme mechanisms; interrelation and comparison of basic biochemicaland chemical processes; and metabolic regulation. Usually offeredevery year. Multiple sections.

Mr. Lowenstein (fall-section1), Ms. Moore (fall- section 2)

Mr. Petsko (spring)

BCHM 101a Advanced BiochemistryI

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Prerequisites: One yearof 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. Metabolismof carbohydrates, lipids, amino acids, nucleic acids, vitaminsand coenzymes, and hormones and inorganic substances. Coupledenzyme reactions and the synthesis of macromolecules. Regulatedenzymes and the regulation of metabolism. Usually offered everyyear.

Ms. Hedstrom

BCHM 101b Advanced BiochemistryII

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

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

Mr. Oprian

BCHM 104b Physical Chemistryof Macromolecules

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

The course illustrates principlesby which biological macromolecules behave in aqueous solution.Topics include linkage between ligand binding and conformationschanges, protein folding, protein-DNA recognition, hydrophobicforces, single-molecule behavior. Protein, nucleic acid, and membranestructural principles will also be disussed. Offered every year.

Mr. Gelles

BIBC 105b Molecular Biology

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

Examination of molecular processesin replication and expression of genetic information and techniquesby which this understanding has been achieved. Topics includerecombinant DNA and other molecular biological techniques, structureand organization of DNA in chromosomes, DNA replication, transcriptionand 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 Biophysicsand Biochemistry

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Prerequisite: One year ofcollege chemistry and one year of calculus or permission of theinstructor.

Biochemists and molecular biophysicistsseek to understand the behavior of living systems in terms ofthe properties of individual molecules. Because molecular motionsare random, molecular properties are often best thought of instatistical terms. This course will give an introduction to thetools of probability theory and molecular statistics. We willthen apply these tools to a variety of interesting biologicalproblems, including: molecular diffusion, binding of ligands tocell surface receptors, bacterial chemotaxis, single-channel kinetics,and biochemical separation methods. Usually offered in even years.

Messrs. Gelles and Miller

BCHM 136b Protein-DNA Recognition

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Prerequisite: BIBC 105bor permission of the instructor.

Many important biological phenomenadepend on proteins that bind non-specifically to the DNA helixor that bind specifically to particular DNA sequences or structures.This course surveys the structures, DNA binding mechanisms andfunctions of such proteins. Usually offered every third year.Last offered in the spring of 1994.

Mr. Wensink

NBCH 148b Advanced Topicsin Neuroscience

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Prerequisite: NBIO 140bor permission of the instructor. May be taken concurrently withNBIO 140b.

A discussion of cellular andmolecular mechanisms that generate endogenous electrical propertiesof nerve cells. The regulation of endogenous patterns of neuronalactivity by external influences including neurotransmitters, hormones,and sensory input will also be discussed. Usually offered in evenyears.

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 chemistryand laboratory; BCHM 99d. Enrollment limited and signature ofdepartment chair required.

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

Mr. Lowenstein and Staff

BCHM 150b Research for theB.A./M.S. Candidates

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

Mr. Lowenstein and Staff

BCHM 151b Ion Channel Proteins

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This course considers the molecularproperties of ion channels, the most basic element of molecularhardware in the nervous system. We examine the molecular architectureof channels and the mechanisms of channel activity. The mechanismsof voltage-dependence, ion selectivity, and channel gating willbe emphasized. Usually offered in odd years.

Mr. Miller

BCHM 171b Protein X-rayCrystallography

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Prerequisites: Familiaritywith computing is necessary and a basic biochemistry course isrecommended.

A practical guide to the determinationof three dimensional structures of proteins and nucleic acidsby X-ray diffraction. Students will learn theory behind diffractionfrom macromolecular crystals and will carry out all of the calculationsnecessary to solve a protein structure at high resolution. Usuallyoffered in even years.

Mr. Petsko and Ms. Ringe

(200 and above) Primarilyfor Graduate Students

BCHM 200a and b BiochemistryTechniques

Prerequisite: BCHM 101.May be taken concurrently.

Usually offered every year.

Mr. Gelles and Staff

BCHM 202b Chemistry of Enzyme-CatalyzedReactions

Deals with reaction mechanismsof catalysis in aqueous solution, some of which are relevant toenzymic catalysis. Usually offered in even years.

Mr. Abeles


One or two seminars are giveneach term. Each student presents oral or written reports on variousaspects of the announced seminar topic. Topics are repeated usuallyat two-to three-year intervals.

BCHM 219b Enzyme Mechanisms

Ms. Hedstrom

BCHM 222a Protein Kinasesand Phosphatases

Mr. Lowenstein

BCHM 223a Signal Transduction

Mr. Oprian

BCHM 224a Microtubule-BasedMechanoenzymes

Mr. Gelles

BIBC 224b The RNA World

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

This course employs seminarsand 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 everyyear.

Ms. Moore

BCHM 233b Mechanisms ofTranscription and Transcriptional Regulation

Mr. Wensink

Graduate Research

BCHM 401d Biochemical ResearchProblems

Independent research for theM.S. and Ph.D. degrees. Specific sections for individual facultymembers as requested.


Journal Club, Colloquia,and Research Clubs

In addition to the formal coursesannounced above, all graduate students are expected to participatein the department's Research Clubs and Colloquia. Colloquia aregeneral meetings of the department in which department and guestspeakers present their current investigations. Research clubsare organized by various research groups of the department.

CONT 300b Ethical Practicein Health-Related Sciences

Required of all first-yeargraduate students in health-related science programs. Not forcredit.

Scientists are becoming increasinglyaware of the importance of addressing ethical issues and valuesassociated with scientific research. This course, taught by Universityfaculty from several graduate disciplines, will cover major ethicalissues germane to the broader scientific enterprise, includingareas or applications from a number of fields of study. Lecturesand relevant case studies will be complemented by two public lecturesduring the course. Usually offered every year.

Ms. Ringe

Cross-Listed Courses

CHEM 235b

Advanced NMR Spectroscopy