Ph.D. Curriculum

Basic methods of DNA manipulation, library construction, cloning

An integrated approach to the applications of NMR, X-ray crystallography, and mass spectrometry in structural biology.

An integrated approach to the applications of NMR, X-ray crystallography, and mass spectrometry in structural biology.

Discussion, lecture.

Survey of the most important preparative reactions in organic synthesis. Emphasis is placed on mechanism and stereochemistry where appropriate. Introduction to retrosynthetic analysis. Reading assignments from primary and review literature.

Mechanistic organic chemistry for first-year graduate students; weekly homework problems; extensive use of handouts and literature materials.

Preparation of grant applications and process of grant review.

Ethics in scientific research for graduate students.

Formal seminars and informal presentations of current research results.  Includes a tutorial in presentation methods.

Doctoral thesis research.

Natural products and related synthetic compounds; biogenesis, metabolic pathways, structure elucidation and synthesis of alkaloids and other heterocycles, steroids, and terpenes.

Approaches to the chemical preparation and delivery of bioconjugates of pharmaceuticals and biophysical probes to selected cellular targets. Biochemical studies of affinity probes, immunoconjugates, prodrugs, liposomes, membrane mimetics, and chemically-modified polysaccharides, peptides, and nucleic acids are included.

Summary: This survey course, including a hands-on computational component, will cover computational and simulation methods for understanding the structure, dynamics and interactions of biological molecules with an emphasis on topics relevant to therapeutic design, delivery and disposition. Possible topics will include molecular modeling, atomistic simulation, molecular docking, drug design, ADME, homology modeling, high performance computing, and protein structure prediction. We will first review fundamental principles of molecular interaction and then survey various modeling approaches to highlight their ranges of applicability and limitations. Experience with computers will be very helpful for the laboratory component.

Design of synthetic approaches to complex organic molecules; retrosynthetic analysisand functional group compatibility is stressed; numerous examples of syntheticstrategies from the literature are presented and analyzed.

Discussion, lecture. Continuation of CHEM 7240.

Solution of complex organic structural problems using UV, IR, MS and NMR.Emphasis is placed on NMR.

Discussion, lecture. Continuation of CHEM 7270.

Discussion, lecture.

Discussion, lecture.  Continuation of CHEM 6460.

Fundamental aspects of drug transport and effects from a systems physiology to a cellular level. Pharmacokinetics is taught with emphasis on understanding compartmental and non-compartmental modeling, physiologic modeling, and cellular drug transport to characterize the effectiveness of drug delivery systems.

Physicochemical fundamentals of dosage form design. Molecular thermodynamics approach to establishing principles of solutions, structures of liquids and solids, complexation, ion-solvent interactions, and multiple equilibria of organic solutes. Physiochemical examination of peptides and proteins, and protein structures. Thermodynamics of nucleic acids including temperature effects, cooperativity and hybridization equilibria. Principles of colloid and interfacial sciences applied to pharmaceutical dosage formulations.

Introduction to polymers in pharmaceutics and drug delivery. Transport phenaoena in drug delivery sytsems. Macromolecular and vesicular carriers. Biorecognition and drug targeting. Protein, oligonucleotide, and gene delivery systems.

Principles of kinetics and mechanisms of organic reactions and structure-reactivity relationships applied to phermceutical systems. Mechanisms of the degradation and stabilization of drugs, proteins, and DNA.

Biochemical mechanisms involved in, and factors affecting, metabolism and toxicities of drugs, food additives, pesticides, industrial chemicals, and naturally occurring toxic agents.

Mechanisms by which extracellular signals, through receptors, regulate transmembrane signaling systems that control production of second messengers within target cells.

General principles, testing procedures, toxic responses, and target organ toxicities.

Mechanisms of chemically induced injury to living systems. Biologically reactive chemical intermediates, cellular responses to chemical injury, and carcinogenesis and genetic toxicity.

Enzyme nomenclature, distribution, properties and characteristics; physiological and xenobiotic regulation of activity and pharmacological and toxicological consequences of enzyme activation, induction, and inhibition.

Advanced topics in prokaryotic and eukaryotic gene expression including transcription, RNA processing and export and translation. Core courses for the molecular biology graduate program.

Advanced topics in cell biology including topics in cell structure and methods, membrane, protein trafficking, cell growth and differentiation, and signal transduction; core course for molecular biology graduate program.

Statistical methods in Biology

Principles of and topics in developmental biology. The course is based on reading and discussion of primary literature. Registration is limited to 20 students.