Graduate Faculty
Associate Biochemistry Faculty
Special Departmental Requirements
Master of Science Degree
Doctor of Philosophy Degree
Courses

INDIANAPOLIS PROGRAM
(DEPARTMENT OF BIOCHEMISTRY AND MOLECULAR BIOLOGY)

School of Medicine

Chairperson
Professor Robert A. Harris

Departmental e-mail:
biochem@iupui.edu

Departmental URL:
http://www.biochemistry.iu.edu

Graduate Faculty

Showalter Professors
David M. Gibson (Emeritus), Robert A. Harris

Professors
David Allmann, William Bosron, Donald Bowman (Emeritus), Anna DePaoli-Roach, Howard Edenberg, Rose Fife (Medicine), Mark Goebl, Jean Hamilton-Steinrauf, Edwin Harper, Maureen Harrington, Hiremagalur N. Jayaram, Peter Roach, Roger Roeske, Arthur Schulz (Emeritus)

Associate Professors
Thomas Hurley, Suk-Hee Lee,* Ronald Wek

Assistant Professors
John W. Hawes,* Lawrence Quilliam,* David Timm*

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Associate Biochemistry Faculty

Distinguished Professors
Morris Aprison (Emeritus, Neurobiology), Ting Kai Li (Medicine)

Professors
W. Marshall Anderson (Northwest Center for Medical Education), Walter Balcavage (Emeritus, Terre Haute Center for Medical Education), Martin Bard (Biology), Philip Breitfeld (Pediatrics), David Crabb (Medicine), Rose Fife (Medicine), Theodore Gabig (Medicine), Ruth Gurd (Emerita, Medical Sciences, Bloomington), George Guthrie (Emeritus, Evansville Center for Medical Education), Larry Jones (Medicine), Mark Kelley (Pediatrics), Lawrence Lumeng (Medicine), William McBride Jr. (Neurobiology), Byron Olson (Dentistry), Barth Ragatz (Fort Wayne Center for Medical Education), John Richardson (Bloomington), Jay Simon (Neurobiology), Godfrey Tunnicliff (Evansville Center for Medical Education), Mervin Yoder Jr. (Pediatrics)

Adjunct Professor
Robert Blickenstaff, Renee C. Lin (Medicine)

Associate Professors
Simon Atkinson* (Medicine), Dring Crowell (Biology), David Daleke (Bloomington), Donald L. Durden, Shao-Ling Fong (Ophthalmology), Robert Hromas (Medicine), Michael W. King (Terre Haute Center for Medical Education), Edward McKee (South Bend Center for Medical Education), Stephen Randall (Biology), Kent Redman* (Fort Wayne Center for Medical Education), David Skalnik (Pediatrics), Theodore Widlanski (Bloomington)

Adjunct Associate Professor
Robert A. Dean* (Pathology), Thomas Stephens (Affiliate Graduate Faculty Status), Terry Vik* (Medicine)

Assistant Professors
Kristin Chun,* Mark Deeg* (Medicine), Joseph Dynlacht* (Radiation Oncology), Harikrishna Nakshatri* (Medicine), Simon Rhodes* (Biology), James Walsh* (Medicine)

Assistant Scientist
Dan Spandau* (Medicine)

Adjunct Assistant Professor
Ronald R. Bowsher (Affiliate Graduate Faculty Status)

Graduate Advisor
Professor Mark Goebl, Medical Science Building 4071, (317) 274-2055

Degrees Offered
Master of Science and Doctor of Philosophy

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Special Departmental Requirements

(See also general University Graduate School requirements and departmental brochure.)

Admission Requirements
Two semesters of calculus and organic chemistry are required for admission. These courses or their equivalent can be taken during the first year of graduate study. It is strongly recommended that students take an introductory course in biochemistry prior to enrollment. The General Test of the Graduate Record Examination is required; the subject test in biochemistry, chemistry, or biology is recommended.

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Master of Science Degree

Course Requirements
A minimum of 30 credit hours, including the core curriculum courses B807, B810, G817, and G865 or any three core courses plus G841, G890 or G910; and at least 6 credit hours, but not more than 9 credit hours, in research. Participation in student seminar, B890, is required.

Final Examination
Oral, covering thesis and course work.

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Doctor of Philosophy Degree

Course Requirements
A total of 90 credit hours, of which a minimum of 32 credit hours must be in courses other than research, including the core curriculum courses B807, B810, G817, and G865. Participation in student seminar, B890, is required every semester of residence.

Grades
A minimum grade point average of 3.0 (B) must be maintained in all nonresearch course work.

Minor
A minimum of 12 credit hours in one of the following programs: life science, physical science, anatomy, biomathematics, biophysics, chemistry, computer science, mathematics, medical genetics, microbiology, neurobiology, pathology, pharmacology, physics, physiology, or toxicology.

Minor in Molecular Biology
See entry under “Microbiology and Immunology”.

Minor in Life Science
A minimum of 12 credit hours outside the student’s major department, chosen from the biological sciences or from the following departments: anatomy, biochemistry, biophysics, dental sciences, medical genetics, microbiology, pathology, pharmacology, physiology, toxicology. At least 6 credit hours must be taken in one of the listed departments or in the biological sciences. The minor program must be approved by the student’s advisory committee, the minor representative on which must be selected from one of the departments in which courses for the minor are taken.

Ph.D. Minor in Biomathematics
The minor in biomathematics is designed to provide graduate students in the programs in biological science with sufficient formal training in mathematics to prepare them to work in an area of biological research that is mathematically oriented. The prerequisites for the minor are: (1) 10 credits of calculus (MATH 163,¹ MATH 164, or equivalent); and (2) CSCI 2201 and CPT 360,² CSCI 300,¹ CSCI 320,¹ or the equivalent. The minor requires at least 15 credits chosen from the following courses: MATH 262,¹ MATH 511,¹ MATH 519,¹ CSCI 461,¹ CSCI 512,¹ CSCI 543,¹ EE 583,² G650,³ G651,³ Q652,³ Q653,³ F704,³ and B848. The minor must include MATH 262¹ or equivalent.

Qualifying Examinations
Students meet once every six months with their advisory committee to review progress in course work and the dissertation research proposal. Usually, at the completion of the second semester of study, students sit for a written qualifying examination. The final examination in the series is an oral defense of a written research proposal. The nature of the examination over the minor is determined by the member of the advisory committee representing that area. It may consist of a separate examination but is usually part of the written and oral examinations. Continuation of a student in the program depends upon satisfactory performance and progress in each phase of the program.

Dissertation
A minimum of 45 credit hours in research, completed with a grade point average of 3.0 (B) or above. It is expected that the dissertation will qualify for publication in a recognized journal.

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

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Courses

B500 Introductory Biochemistry (3 cr.) P: C341 or equivalent. Structures of carbohydrates, proteins, lipids, and nucleic acids. Basic principles of enzyme catalysis, protein synthesis, intermediary metabolism, and nutrition.
B800 Medical Biochemistry (3 cr.) P: one semester of organic chemistry. Structure and function of biological molecules, regulation of cellular processes by nutrients and hormones, biochemical and molecular basis of disease.
B803 Advanced Biochemistry (cr. arr., max. of 3 cr.) Tutorial instruction in biochemistry.
B807 Protein Structure and Function (3 cr.) P: two semesters of organic chemistry; one semester of biochemistry. Physical forces stabilizing protein structure; protein folding. Essential features of macromolecular interactions. Introduction to enzyme kinetics and chemical mechanism in enzyme reactions.
B808 Physical Biochemistry (3 cr.) P: two semesters of physical chemistry; two semesters of calculus; one semester of biochemistry. Thermodynamics and biophysical chemistry of protein, enzymes, nucleic acids, and membranes.
B809 Advanced Organic Chemistry (1-3 cr.) P: two semesters of organic chemistry; two semesters of physical chemistry; B807 or consent of instructor. Tutorial instruction in organic chemistry, as applied to biochemistry.
B810 Cellular Biochemistry and Regulation (3 cr.) P: two semesters of organic chemistry; one semester of biochemistry. Fundamental pathways of metabolism, with emphasis on the mechanisms of metabolic regulation. Mechanisms of signal transduction and the control of cellular function by hormones, growth factors, and other extracellular regulators.
B811 Advanced Intermediary Metabolism (1-3 cr.) P: B810. Tutorial instruction in specialized areas of metabolism.
B813 Chemistry of Steroids (3 cr.) P: two semesters of organic chemistry. Isolation, structure, and determination. Chemical properties and synthesis of the steroids.
B814 Advanced Enzymology (1-3 cr.) P: B807 or B810. Tutorial instruction in enzyme isolation and kinetics.
B830 Biochemical Nutrition (3 cr.) P: two semesters of organic chemistry; one semester of biochemistry. Metabolic utilization of biological fuels. Components required in animal nutrition; essential amino and fatty acids, vitamins, and trace elements. Biochemical derangements in nutritional deficiencies, metabolic disease states, and starvation.
B835 Neurochemistry (3 cr.) P: two semesters of organic chemistry; one semester of biochemistry, or consent of instructor. Metabolism of nervous system tissue. Neurochemical techniques.
B836 Advanced Topics in Neurochemistry (2 cr.) P: B835 or equivalent. Selected topics in neurochemistry dealing with specialized functions of the nervous system.
B842 Instrumentation and Methods of Analysis II (3 cr.) P: two semesters of organic chemistry; one semester of biochemistry.
B848 Mathematics for Biochemistry (3 cr.) Differential equations and topics in advanced calculus.
B854 Introduction to Research (1 cr.) P: two semesters of organic chemistry; two semesters of physical chemistry, one semester of biochemistry, or consent of instructors. Tutorial and laboratory instruction in biochemistry. Purpose is to introduce students in biochemistry to three different research programs.
B855 Research (cr. arr.)
B857 Biochemistry of Exercise (3 cr.) P: B800, B810, or consent of instructors. Study of the biochemical and physiological changes in the human body due to exercise and consequence of long-term exercise programs.
B858 Physical Chemistry (3 cr.) P: one year of physical chemistry. Quantum chemistry and molecular spectra. Statistical mechanics and thermodynamics. Kinetics. Liquid state.
B859 Advanced Physical Chemistry (1-3 cr.) P: B808 or B858. Tutorial instruction in physical chemistry as an extension of either B808 or B858.
B860 Biophysical Protein Chemistry (3 cr.) P: two semesters of physical chemistry; two semesters of calculus. Physical chemistry of particular interest to the biologist. Chemical and physical properties of protein. Multiple equilibria, radiation interactions, transport phenomena.
B868 Advanced Molecular Biology (1-3 cr.) P: G865 or equivalent. Tutorial instruction in specialized area of molecular biology.
B890 Seminar (1 cr.)
G804 Cellular and Molecular Biology (3 cr.) P: One semester of organic chemistry. Cellular and molecular biology that emphasizes the structural organization, biochemistry and molecular biology of cells. Includes cellular processes, development and differentiation and their relationship to medicine.
G817 Eukaryotic Cell Biology (2 cr.) P: one semester of biochemistry. Organization and function of subcellular structures. Intracellular coordination of cell activity: protein and RNA trafficking, chromatin dynamics, and intracellular processing of receptor mediated signals.
G841 Methods of Protein Chemistry (3 cr.) P: B500 or equivalent. Discussion and laboratory instruction in modern methods for protein purification, analysis of purity, peptide mapping, and amino acid sequencing.
G865 Fundamental Molecular Biology (3 cr.) P: B800 or equivalent. Principles of molecular structure, function, and biosynthesis; core information regarding procaryotic and eukaryotic gene continuity and metabolic coordination; introduction to multicellular systems and problems. (Joint program: biochemistry, medical genetics, microbiology.)
G890 Methods in Molecular Biology and Pathology (3 cr.) P: G865 and/or J838, and consent of instructor. Basic principles and techniques in molecular biology and pathology. Particular emphasis will be on molecular techniques that can be used to study problems related to biochemistry and pathology.
G910 Advanced Molecular Biology Methods (3 cr.) P: G865 and/or G890 and consent of instructor. Advanced theory and techniques in molecular biology. The focus of the course will be on techniques related to manipulation of cloned DNA to study their expression, structure and function.

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