Objectives

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.

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

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 track 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. However, students are required to complete formal course work in advanced biochemistry and physical biochemistry. Students in the bioorganic chemistry track 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, as described above.

How to Become an Undergraduate Concentrator

Students who are interested in concentrating in biochemistry should speak with the department advising head.

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.

Faculty

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

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

High resolution electron cryo-microscopy of membrane proteins and channels.

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

Dynamics of enzymes. Magnetic resonance methods.

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

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

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

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

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

Requirements for the Undergraduate Concentration

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 15a,b) with laboratory; BIOL 22a-Formerly BIBC 22a with laboratory (Genetics and Molecular Biology); BIOL 22b with laboratory (Cell Structure and Function) (the above courses must be taken prior to the senior year); BCHM 100a (Introductory Biochemistry); one year of physical chemistry, CHEM 41a (Physical Chemistry, Lectures I) and either BCHM 104b (Physical Chemistry of Macromolecules) or CHEM 41b (Physical Chemistry, Lectures II); and one elective from any 100-level course (excluding research courses) offered in the biochemistry and biology departments. With advance approval from the biochemistry department advising head, an upper-level course offered by another department (e.g., chemistry or physics) may also fulfill the elective requirement. The laboratory associated with CHEM 41a is optional.

In addition to the degree requirements listed above for the Bachelor of Arts degree, the Bachelor of Science degree requires one year of BCHM 101a and b (Advanced Biochemistry).

Required of all students: No course offered for concentration requirements may be taken pass/fail. Grades below C- in upper- level courses (CHEM 41a and b, and any course numbered 100 or above) cannot be used to fulfill the requirements of the concentration. Furthermore, no more than one D will be allowed in any other course required for the concentration.

In addition to the degree requirements listed above, departmental honors require completion of two semesters of BCHM 99 (Research for Undergraduates), submission of an acceptable research thesis, and a final grade point average of 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.

In addition to all courses requires for the Bachelor of Science degree, the B.S./M.S. degree required completion of one additional elective (excluding research courses) approved in advance by the biochemistry department 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 coursework) summer research residency lasting at least 10 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 100-level biochemistry and biology courses. This program requires completion of 38 courses; no more than four semesters of research (BCHM 99 or 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 B.S. is awarded. To qualify for the B.S./M.S. degree, the thesis must constitute a significant research contribution; if a thesis is found unacceptable under B.S./M.S program, it will automatically be considered under the Honors program.

In order to complete the Honors Program or the combined B.S./M.S. 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

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 BCHM 101a and b (Advanced Biochemistry) and three of the following four courses: BCHM 104b (Physical Chemistry of Macromolecules); BIOL 105b-Formerly BIBC 105b (Molecular Biology); BCHM 200a and b (Biochemical Techniques). 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.

The minimum residence requirement is one year.

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

Students must successfully complete the core curriculum defined below. Biochemistry students will typically complete the core curriculum in the first year.

BCHM 101a,b Advanced Biochemistry

BCHM 102a? Quantitative Analysis of Biochemical Systems

BCHM 104b Physical Chemistry of Macromolecules

BCHM 200a,b Biochemical Techniques (Lab rotations)

CONT 300b Ethical Practices in Health-Related Sciences

Four other advanced courses (100-level or above) from the Biochemistry, Biology, Biophysics, Chemistry, or Neuroscience Programs. These courses must include at least two courses selected from BCHM 219-250.

In order to receive a Ph.D. in biochemistry with a specialization in bioorganic chemistry, students must complete:

A. The core curriculum defined above.

B. Two rotations dealing with problems in organic chemistry as part of BCHM 200a,b.

C. CHEM 134a (Advanced Organic Chemistry: Synthesis). (Bioorganic track students have the option of substituting CHEM 134a for BCHM 102a or BCHM 104b in the first year and completing the core curriculum in the second year.)

D. Two courses selected from BCHM 219-250.

E. One other advanced chemistry course, chosen from:

CHEM 111a Computational Chemistry

CHEM 130a Advanced Organic Chemistry: Structure

CHEM 131a Advanced Organic Chemistry: Topics in Structure and Reactivity

CHEM 132b Advanced Organic Chemistry: Spectroscopy

CHEM 137b The Chemistry of Organic Natural Products

CHEM 229b Introduction to X-Ray Structure Determination

CHEM 235b Advanced NMR Spectroscopy

As a part of their Ph.D. training, students are required to assist with the teaching of two one-semester courses.

The minimum residence requirement is three years.

There is no foreign language requirement.

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.

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 administered at the end of the second year of study.

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

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

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

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

Staff

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

Staff

(100-199) For Both Undergraduate and Graduate Students

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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. Grigorieff (fall), Mr. Lowenstein (spring)

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Describes the principles of biological catalysts and the chemical logic of metabolic pathways. Representative enzymes from each reaction class are discussed with an emphasis on understanding how mechanisms are derived from experimental evidence. Topics include serine proteases, phosphatases, isomerases, carboxylases and dehydrogenases. Usually offered every year.

Ms. Kern

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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.

Ms. Moore and Mr. Oprian

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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. The physical bases of spectroscopic and diffraction methods commonly used in the study of proteins and nucleic acids will also be discussed. Will be offered in the fall of 2001.

Mr. Gelles

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Illustrates the basic principles on which biological macromolecules are constructed and by which they function. Overall structures of proteins, nucleic acids, and membranes are described 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. Miller

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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.

Ms. Moore and Staff

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

Ms. Moore and Staff

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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 every second year.

Mr. Miller

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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 every second year.

Mr. Petsko and Ms. Ringe

(200 and above) Primarily for Graduate Students

Usually offered every year.

Mr. Gelles and Staff

Topics are repeated usually at two- to three-year intervals.

Ms. Kern

Ms. Hedstrom

Mr. Lowenstein

Messrs. Miller and Oprian

Mr. Gelles

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

A continuation of BCHM 271b. Offering dependent on BCHM 271a class interest.

Mr. Petsko

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. Last offered the fall of 2000.

Mr. Petsko

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

Staff

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.

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. Lowenstein

Cross-Listed Courses

Advanced NMR Spectroscopy