Biochemistry, Interdisciplinary

Bloomington Program
Biology, Chemistry, Medical Sciences, Optometry, Psychology

College of Arts and Sciences
Bloomington

Director
Professor Carl Bauer

Departmental E-mail
bchem@indiana.edu

Departmental URL
www.indiana.edu/~bchem

Graduate Faculty
Degrees Offered
Special Program Requirements
Master of Science Degree
Doctor of Philosophy Degree
Courses
Cross-Listed Courses

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Graduate Faculty

(An asterisk [*] denotes associate membership in University Graduate School faculty.)

Carlos Miller Chair
Mark Estelle (Biology)

Clyde Culbertson Professor of Biology
Carl Bauer (Biology)

Lilly Chemistry Alumni Chair
Milos Novotny (Chemistry)

Linda and Jack Gill Chairs of Biomolecular Sciences
Richard DiMarchi (Chemistry), J. Michael Walker (Psychology)

Robert and Marjorie Mann Chair
David Clemmer (Chemistry)

Distinguished Professors
Milos Novotny (Chemistry), Peter Ortoleva (Chemistry)

Professors
Joseph Bonanno (Optometry), Jose Bonner (Biology), Yves Brun (Biology), Peter Cherbas (Biology), David Clemmer (Chemistry), Richard DiMarchi (Chemistry), Thomas Donahue (Biology), Mark Estelle (Biology), Patricia Foster (Biology), Elizabeth Raff (Biology), James Reilly (Chemistry), John P. Richardson (Emeritus, Chemistry), Milton Taylor (Biology), J. Michael Walker (Psychology), Theodore Widlanski (Chemistry), Malcolm Winkler (Biology), Jeffrey Zaleski (Chemistry)

Associate Professors
David Daleke (Biochemistry, Molecular Science, Medical Sciences), Jim Drummond (Biology), John Foley* (Anatomy and Cell Biology, Medical Sciences), Joseph Near (Pharmacology and Toxicology, Medical Sciences), Kenneth Nephew (Cellular and Integrative Physiology, Medical Sciences), Martha Oakley (Chemistry), Martin Stone (Chemistry), Claire Walczak* (Molecular Biology, Medical Sciences)

Assistant Professors
Lingling Chen* (Biology), Bogdan Dragnea* (Chemistry), Joseph Duffy* (Biology), Viola Ellison* (Biology), Andrew Feig* (Chemistry), Clay Fuqua* (Biology), Richard Hardy* (Biology), David Kehoe (Biology), Scott Michaels (Biology), Christine Quirk (Pharmacology and Toxicology, Medical Sciences), Anne Prieto* (Psychology), Thomas J. Tolbert* (Chemistry), Kelly Williams (Biology), Joel Ybe* (Biology)

Graduate Advisor
Professor Carl Bauer, Myers Hall 150C, (812) 856-0192

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Degrees Offered

Master of Science and Doctor of Philosophy

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Special Program Requirements

(See also general University Graduate School requirements.)

Admission Requirements
Undergraduate course work must include two semesters of organic chemistry and one semester of biochemistry. Though not required, one semester of molecular biology and two semesters of biology are recommended. One semester of (bio)physical chemistry is strongly recommended. Deficiencies in required courses must be removed during the first year of graduate study.

Master of Science Degree

Course Requirements
A minimum of 30 credit hours, of which 18 credit hours must be in course work other than research, including 12 credit hours in biochemistry and 6 credit hours in graduate-level courses.

Thesis
Required.

Final Examination
Oral, covering thesis and major.

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Doctor of Philosophy Degree

Course Requirements
A total of 90 credit hours, of which 18 credit hours, satisfied by the core courses (B501, B502, B503 and B504, B580), and three semesters of B600. The sequence of courses comprising the major must be approved by the student's advisory committee.

Minor
A doctoral student in biochemistry may minor in any appropriate discipline, following the requirements specified by the minor department. The sequence of courses comprising the minor must be approved by the student's advisory committee. The core Biochemistry courses (B501, B502, B503, B504) may be used to fulfill the minor requirement, but a single course may not be credited to both the major and minor requirement.

Qualifying Examinations
In the fifth semester, students meet with their examination committee to review past performance and to evaluate plans for completing the Ph.D. oral and written presentations of research progress are required.

Final Examination
Oral, covering dissertation, major, and minor.

Ph.D. Minor in Biochemistry
Students from other programs who wish to minor in biochemistry must complete at least 6 credit hours of graduate course work in biochemistry, excluding B502, B580, and B600, with an average of B (3.0) or above. At least one of the courses must be B501, B503, or B504.

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Courses

Biochemistry

B501 Integrated Biochemistry (4.5 cr) P: Undergraduate biochemistry (equivalent to C483 or C484) or consent of instructor. Basic principals and methodologies of biochemistry; essentials of macromolecular biosynthesis; mechanism-based examination of biochemical aspects of cell biology; material is presented with an integrative approach designed to illustrate the inter-relationship of biochemical processes.

B502 Analysis of Biochemical Literature (1.5 cr.) P: Concurrent enrollment in B501 or consent of instructor. Critical evaluation of the biochemical literature, using selected papers as examples; development of written and oral communication skills in the context of literature analysis.

B503 Macromolecular Structure and Interaction (3 cr.) P: B501 or undergraduate biochemistry (equivalent to C483 or C484), one semester of undergraduate organic chemistry (equivalent to C341) or consent of instructor. Undergraduate (bio)physical chemistry (equivalent to C481 or C361) is strongly recommended. Principals of inter-and intra-molecular interactions; structural stability of proteins and nucleic acids; thermodynamic and kinetic analysis of complex binding; experimental methods for analysis of macromolecular structure and binding.

B504 Biomolecular Catalysis (3 cr.) P: Undergraduate organic chemistry (equivalent to C342), undergraduate biochemistry (equivalent to C483 or C484) or consent of instructor. Theory and analysis of biochemical catalysis; enzyme kinetics; cofactors; regulation of enzymatic reactions.

B580 Introduction to Biochemical Research (3 cr.) P: graduate standing. Objectives and techniques of biochemical research.

B600 Seminar in Biochemistry (1 cr.) P: B502 or consent of instructor. Advanced critical analysis of the current scientific literature and scientific presentations. Attendance and participation in the weekly Biochemistry Program seminar series is required.

B601 Advanced Nucleic Acid Biochemistry (1.5 cr.) P: B501 or consent of instructor. Mechanistic analysis of nucleic acid metabolism; specificity and role of DNA polymerases and repair pathways; DNA replication and recombination mechanisms; RNA structural motifs and physical properties; RNA synthesis and processing in gene expression; catalytic RNA molecules; applications of RNA molecules.

B602 Advanced Protein Biosynthesis and Processing (1.5 cr.) P: B501 or consent of instructor. Detailed analysis of protein synthesis, post-translational modification, and macromolecular assembly, including the role these modifications play in mature protein function; byosynthesis, structure, function, and analysis of complex oligosaccharides.

B603 Advanced Macromolecular Structure and Interactions (1.5 cr.) P: B503 or consent of instructor. Supplements and extends B503: emphasis on stability and folding mechanisms of proteins and nucleic acids and detailed thermodynamic analysis of binding interactions.

B604 Structural Methods (1.5 cr.) P: B503 or consent of instructor. Fundamental principles of circular dichroism, nuclear magnetic resonance and X-ray crystallography in the study of protein and nucleic acid structures. Theoretical and practical aspects will be presented, with particular emphasis on application strategies.

B605 Structure and Function of Biological Membranes (1.5 cr.) P: B501, B503 or consent of instructor. Biochemistry and biophysics of lipids, membranes and membrane proteins; fundamentals of membrane transport; interfacial catalysis; transmembrane signal transduction.

B680 Special Topics in Biochemistry (1.5-3 cr.) P: Consent of instructor. Topics vary yearly and include the following: Physico-chemical techniques in the study of macromolecules; experimental methods in enzymology; organic chemistry of enzymatic reactions and enzyme models; conformational properties and macromolecules. Can be retaken for credit.

B880 Research: Biochemistry (cr. arr.)**

**This course is eligible for a deferred grade.

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Cross-Listed Courses

Biology

L529 Bioinformatics in Molecular Biology and Genetics: Practical Applications (4 cr.) P: I501, I502, L519 or consent of instructor. Practical experience in a range of data analysis and software engineering methods applied to molecular biology data.

L585 Molecular Genetics (3 cr.) P: L364 and C483 or equivalent. The molecular basis of genetic interactions, with emphasis on microbial systems. The course covers the molecular mechanisms of mutation, suppression, recombination, complementation, etc., as well as mechanisms for gene transfer in bacteria and bacteriophage. The application of genetic analysis to a variety of molecular biological topics is emphasized.

L586 Molecular Analysis of Cell Biology (3 cr.) Critical analysis of recent advances in our understanding of molecular organization of cellular structures and of their mode of function. The primary interest of this course concerns the eukaryotic cell.

M525 Topics in Microbial Biochemistry and Physiology (3 cr.) P: graduate standing and C483 or M350 or equivalent. The course will consider topics in physiology and biochemistry of eukaryotic and prokaryotic microorganisms. Subjects include membrane physiology and regulatory networks in metabolism and gene expression.

Chemistry

C615 Bioanalytical Chemistry (1.5-3 cr.) P: C511, C512. Survey of modern analytical techniques, including spectrochemical, electrochemical, and separation methods used in biochemical analysis and their applications. (May be given in alternate years).

C632 Structure, Function, and Spectroscopy of Metal Ions in Biological Systems (3 cr.) Introduction to the field of bioinorganic chemistry and spectroscopic methods for determining structure/function relationship of metal ions in biology. Emphasis on oxygen carriers, metal ion transport and storage, as well as oxidoreductases involved in oxygen, hydrogen and nitrogen metabolism. A discussion of electron transfer proteins, photosystems, and the role of metals in medicine will also be included.

Medical Sciences

B801 Molecular and Cellular Biochemistry (3 cr.) P: Graduate standing and consent of instructor. Biochemistry for medical students, emphasizing structure-function relationships of cellular components, biosynthesis of nucleic acids and proteins, degradation of simple and complex cell constituents, and regulation of cell growth.

B802 Metabolism and Signal Transduction (3 cr.) P: Graduate standing and consent of instructor. Biochemistry for medical students, including signaling pathways, membrane biochemistry, and the metabolism of macromolecules in health and disease with emphasis on clinical applications.

Physics

P575 Introductory Biophysics (3 cr.) P: Two out of three from the following: (1) P221/P222 and P301 or equivalent, (2) C105/C106 or equivalent, and (3) L221 and L312 or equivalent; or consent of instructor. Overview of cellular components; basic structures of proteins, nucleotides, and biological membranes; solution physics of biological molecules, mechanics and motions of biopolymers; physical chemistry of binding affinity and kinetics; physics of transport and signal transduction; biophysical techniques such as microscopy and spectroscopy; mathematical modeling of biological systems.

Neural Sciences

N612 Ion Channels and Receptors (3 cr.) P: Graduate status and consent of instructor. Molecular, biophysical, and biochemical analysis of the major molecules responsible for neural excitability and synaptic transmission: receptor-coupled ion channels, voltage-dependent ion channels, G-protein coupled receptors, transporters, signal transduction pathways, synaptic vesicle-associated proteins, cytoskeletal proteins, classical and novel neurotransmitters and modulators.

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