Ph.D. in Chemical Biology Curriculum

Chemical Biology trainees follow an interdisciplinary course of preparation not available in most departmental settings. The classroom component of the Chemical Biology curriculum is comprised of several high-level courses and is designed to provide students with rigorous training in modern aspects of chemical biology. First, all students take Chemical Biology 501/502, which is a two-semester course that discusses the structure, function and chemistry of biological macromolecules including proteins, nucleic acids and carbohydrates. Topics include mechanistic enzymology, the interactions of proteins and small molecules with RNA and DNA, macromolecular folding, combinatorial methods including SELEX and gene shuffling, combinatorial organic synthesis, high throughput screening and chemical genetics. All students will also complete Chemical Biology 601/602, which is also a two-semester long course. In this class, students are taught critical thinking and analysis through weekly discussion of the primary research literature.

Based on individual interests, the remaining course requirements of the Program can be fulfilled from a variety of chemistry, biochemistry or biology classes taught on campus. Hence, a major advantage of the Chemical Biology Program is that it allows students maximum flexibility in their training program. A partial listing of additional courses is presented below.

During the first year in the program, students are required to conduct two semester-long research rotations in different laboratories of their choosing. These rotations are important for many reasons: they provide an opportunity for students to meet the faculty and other graduate students; they provide a basis to select a research advisor; they give students the chance to experience different types of research; and they acclimate students to the research environment at the University.

Upon satisfactory completion of course and research rotation requirements, students undertake the Preliminary Qualifying Examination. Upon successful completion of the examination, a student becomes a candidate for the Ph.D. degree and focuses exclusively on thesis research. Once research results are deemed to be suitable for writing a thesis by the advisor and thesis committee, students begin to write a thesis and then defend it. The expected time needed to obtain the Ph.D. degree is approximately five years.

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M.S. in Cancer Chemical Biology Curriculum

The Master of Science in Cancer Chemical Biology program requires the completion of 24 credits over the course of two semesters. All students will complete a core of Chemical Biology courses (Chemical Biology 501 and 502; 6 credits total), Ethics Training (Fall term; 1 credit), and Critical Analysis in Chemical Biology (Chemical Biology 601 002 and 602 002; 4 credits total which includes a capstone writing project).



Additional Courses

Bioinformatics 524/525: Foundations in Bioinformatics and Systems Biology
This course provides an introduction to the principles and practical approaches of bioinformatics as applied to genes and proteins. The complete course is comprised of three modules covering (1) Foundations of Bioinformatics; (2) Statistics in Bioinformatics; and (3) Systems Biology. [Students may register for all modules as a single three credit course (under course code BIOINF524), or each one credit module separately (under course code BIOINF525)].

Bioinformatics 527: Introduction to Bioinformatics & Computational Biology
This course introduces students to the fundamental theories and practices of Bioinformatics and Computational Biology via a series of integrated lectures and labs.  These lectures and labs will focus on the basic knowledge required in this field, methods of high-throughput data generation, accessing public genome-related information and data, and tools for data mining and analysis.  The course is divided into four areas:  Basics of Bioinformatics, Computational Phylogeny (includes sequence analysis), Systems Biology and Modeling.

Bioinformatics 528: Advanced Applications of Bioinformatics
This course introduces fundamental concepts and methods for bioinformatics and the advanced applications. The topics covered include bioinformatics databases, sequence and structure alignment methods, Monte Carlo simulation methods, protein folding and protein structure prediction methods, and modeling of protein-protein interactions. Emphasis is place on the understanding of the concepts taught and on their practical utilization, with the objective of helping students use the bioinformatics tools to solve problems in their own research.

Bioinformatics 545 / Statistics 545: High Throughput Molecular Genomic and Epigenomic Data Analysis
This course will cover statistical methods used to analyze data in experimental molecular biology, with an emphasis on gene and protein expression array data. Topics: data acquisition, databases, low level processing, normalization, quality control, statistical inference (group comparisons, cyclicity, survival), multiple comparisons, statistical learning algorithms, clustering visualization, and case studies.

Bioinformatics 551 / Biological Chemistry 551: Proteome Informatics.
Introduction to proteomics, from experimental procedures to data organization and analysis.  Basic syllabus: sample preparation and separations, mass spectrometry, database search analysis, de novo sequence analysis, characterizing post translational modifications, medical applications. Further topics may include, e.g.: 2-D gels, protein-protein interactions, protein microarrays. Research literature seminars required.

Biological Chemistry 528 / Chemistry 528 / Medicinal Chemistry 528: Biology & Chemistry of Enzymes.
This course will cover the chemical and catalytic mechanisms of enzyme-catalyzed reactions, with an emphasis on organic and organometallic cofactors in biology and mechanisms of group transfer reactions, redox reactions, rearrangements, decarboxylations, carboxylations, and methylation.

Biological Chemistry 640: Post-transcriptional Gene Regulation
A discussion based course that will cover the mechanisms and the biological roles of post-transcriptional gene regulation in eukaryotes. Topics will include RNA interference, microRNAs, regulated polyadenylation, subcellular regulation of translation, and others. The class will focus on reading and discussion of the recent literature, but topics will be introduced by short lectures.

Biological Chemistry 650: Eukaryotic Gene Expression.
This course seeks to develop the students’ understanding of recent progress in the investigation of gene expression that is based on advances in biochemical, structural, molecular, cellular and genomic approaches. Topics will cover eukaryotic RNA polymerases, general transcriptional factors, mechanisms of transcriptional regulation, and chromatin structure and modification/remodeling. An emphasis will be placed on structural aspects of transcription and polymerase function.

Biological Chemistry 660: Molecules of Life: Protein Structure, Function, and Dynamics.
This is an advanced, primarily literature-based course for graduate students and upper level undergraduates with previous background in protein structure and function. It will introduce select biological systems to illustrate how modern protein biochemistry advances our understanding of biological mechanisms. Topics include protein structure, function, and dynamics; protein folding/misfolding and how this relates to disease; the impact that protein modification, processing, and trafficking has on cellular processes. The emphasis will be on proteins as non-static structures and how structural changes modulate their functions.

Biological Chemistry 673 / Chemistry 673: Kinetics & Mechanism of Enzymes.
This course will cover the investigation of enzyme mechanisms with an emphasis on kinetic and thermodynamic methodology, including: ligand binding to macromolecules, transient kinetics, steady-state kinetics, and kinetic isotope effects. The key kinetic and thermodynamic concepts that govern the action of enzymes, and the thought processes required to deduce catalytic and kinetic mechanisms will be explored. Topics will be treated from both a "gut-feeling" and a mathematical perspective, and applications to real systems, including experimental methods, data analysis, and common errors/fallacies/abuses, will be considered in detail. Because computer methods for analyzing and simulating data have taken a prominent place in the field, the use of software from kinetics research will be emphasized through numerous "hands-on" exercises. 

Biophysics 520 / Chemistry 520: Theory and Methods of Biophysical Chemistry I.
This course provides an overview of key methodologies of contemporary biophysics and biophysical chemistry. Principles of structure determination by X-ray diffraction, solution and solid-state NMR and electron microscopy will be covered. A variety of optical spectroscopic techniques, including UV/Vis, fluorescence, circular dichroism and cell imaging will be discussed. Methods for the separation and study of biological macromolecules and membranes including ultracentrifugation, chromatography, electrophoresis, mass spectrometry and calorimetry will be introduced. This course is the first of a two term biophysical chemistry series BIOPHYS 520/521.

Biophysics 521 / Chemistry 521: Biophysical Chemistry II.
This course discusses protein and nucleic acid structure and dynamics, the nature of underlying forces and interactions that control biopolymer processes, and aspects of dynamics in the context of function. Emphasis will be laid on theories from thermodynamics and statistical mechanics that form the basis of physical models for processes and processing in these systems. The first half of the course will deal with the establishment of a natural "language" for the description of chemical and biological processes through statistical mechanics. In the latter half of the course we will discuss current problems and questions for which physical and statistical mechanical models have been developed. A partial list of areas to be addressed include energy landscape theory and its applications to folding of proteins and nucleic acids, mechanical and statistical models for molecular machines and methods and applications of molecular dynamics and simulations of proteins, nucleic acids and their complexes.

Biophysics 602 / Chemistry 602: Protein Crystallography.
Principles of Macromolecular Crystallography: Fundamental of the methods for determining 3-dimensional structures of large molecules by x-ray crystallography. Aimed at students who expect to use crystallography as a major tool for their research, and at those who want in-depth knowledge of the methods in order to analyze structure data.

Cell and Developmental Biology 530: Cell Biology.
This graduate course is designed to present basic information as well as the most recent developments in key areas of cell biology, including membranes, protein synthesis, folding and trafficking, epithelial polarity, cytoskeleton, cell-cell and cell-substrate interactions, and signal transduction. Participating faculty are drawn from various campus and medical school departments and provide lectures in areas of their expertise. Lecturers are encouraged to provide a part of the lecture material in the context of actual experiments so that students are exposed to current experimental approaches in cell biology, as well as basic information. In addition to a highly recommended cell biology textbook, reading lists are provided, and 1-2 papers are generally put on reserve in the library for each lecture. Students will be expected to demonstrate their knowledge of course material by examinations.

Chemistry 507: Inorganic Chemistry.
Structural and mechanistic concepts relating to inorganic and organometallic compounds, inorganic stereochemistry, crystal chemistry, point symmetry, ligand field theory, MO theory, catalysis, bioinorganic chemistry, and generalizations about the periodic table.

Chemistry 515 / 538: Organometallic Chemistry.
Systematic consideration of modern aspects of organometallic chemistry including main group and transition metal complexes. The structure and bonding in organometallic compounds are covered. Particular emphasis is placed on applications of homogeneous organometallic catalysis in polymer synthesis, industrial processes, and synthetic organic chemistry.

Chemistry 540: Organic Principles.
Mechanisms of organic chemical reactions, stereochemistry, and conformational analysis. The important types of organic reactions are discussed. Basic principles are emphasized; relatively little attention is paid to the scope and synthetic applications of the reactions.

Chemistry 541: Advanced Organic Chemistry.
Synthetic organic chemistry. The scope and limitations of the more important synthetic reactions are discussed within the framework of multistep organic synthesis.

Chemistry 542: Applications of Physical Methods to Organic Chemistry.
Applications of infrared, ultraviolet and nuclear magnetic resonance spectroscopy, optical rotary dispersion, mass spectrometry and other physical methods to the study of the structure and reactions of organic compounds.

Chemistry 543: Organic Mechanisms.
Students will learn to propose and write reasonable mechanisms for organic reactions, including complex multi-step processes. Knowledge of the details of the fundamental organic reaction processes will also be gained.

Chemistry 616: Advanced Inorganic Chemistry.
The application of theoretical principles to the experimental observations of modern inorganic chemistry: ligand field and molecular orbital theory of complex ions, structural chemistry, magnetic properties, ESR, Mossbauer spectra, NQR.

Epidemiology 460: Introduction to Bacterial Pathogenesis.
This course covers the basics of the biochemistry, molecular biology, and genetics of chemotaxis and flagella, pili and adhesins, extracellular proteases, bacterial toxins, invasion and intracellular growth, phase and antigenic variation, gene transfer, LPS, iron, M-proteins, capsules, chemotherapy, antibiotic resistance and global regulation of virulence elements.

Epidemiology 560: Mechanisms of Bacterial Pathogenesis.
Microbial structures and their relation to basic mechanisms of bacterial pathogenesis; structure, function, and genetics of bacterial toxins; and host resistance and immunity. Discussions of pathogenic organisms of major public health importance, diseases caused, and their epidemiology.

Human Genetics 541: Gene Structure & Regulation.
This course explores how the information content of the DNA genome is (i) organized, propagated, and altered, and (ii) functionally expressed by regulated transcription into RNA - the core molecular properties and processes of genetic systems that underlie all further investigations of organismal, clinical, and population genetics. As a graduate level course, it is expected that students will enter HG541 with a basic understanding of the nature of biological systems, DNA, RNA, replication, and transcription. HG541 will focus on developing an advanced modern understanding of these molecules and reactions. We will explore what experimental research in model organisms and humans has taught us about the molecular encoding of genetic information while simultaneously exposing gaps in our understanding. Throughout, attention will be given to newer genome-wide analysis methods that are dramatically increasing our understanding of the extent of genetic variation and the many modes of gene expression. Also, students will be introduced to recombinant DNA technologies as one important way that molecular genetic insight is reduced to practice in biological research. Upon completion of HG541, students will appreciate the directions research in molecular genetics is heading and be able to draw on this insight as they pursue further studies and research in diverse areas of genetics and biology.

Human Genetics 630 / Cellular and Molecular Biology 630: Genetics Short Course.
Topic: Frontiers in Gene Regulation

Medicinal Chemistry 532: Bioorganic Principles of Medicinal Chemistry.
A mechanistic organic chemistry/biochemistry approach to medicinal chemistry, emphasizing macromolecular targets of drug action. The first of four sections focuses on enzymes as drug targets, with emphasis on inhibitors of enzyme action. Section 2 covers nucleic acids as targets for drug action and includes agents that interact with nucleic acids directly and those that inhibit nucleic acid biosynthesis. Section 3 explores metabolic pathways and mechanisms for xenobiotic transformation. Section 4 discusses the rationale behind drug delivery and prodrug approaches as well as design strategies based on routes of bioactivation.

Microbiology and Immunology 553: Cancer Biology.
This course will cover a broad range of subjects relating to cancer biology. Emphasis is on the relationship between basic science and clinical aspects of cancer. Topics to be covered include carcinogenesis, cancer progression, tumor pathology, oncogenes, cellular growth control, tumor suppressor genes, oncogenic viruses, apoptosis, tumor immunology, clinical oncology, and therapeutics.

Microbiology and Immunology 607: Microbial Pathogenesis I
This first module will emphasize functional and ecological aspects of microbial pathogenicity.

Microbiology and Immunology 615: Molecular and Cellular Determinants of Viral Pathogenesis I
This course will cover basic concepts in viral replication, entry, assembly and pathogenesis. The readings will be from the primary literature, with suggested background readings from a textbook, Principles of Virology (2nd ed.)

Microbiology and Immunology 619: Special Topics in Microbiology and Immunology
Didactic overview and critical analysis of the literature focused on a specific timely topic in current microbiology and immunology research.  Students will read and discuss the primary literature as well as complete assignments that further explore the topic.

Microbiology and Immunology 640: Molecular and Cellular Immunology.
This course will be focused upon molecular and cellular aspects of the mammalian immune system. Topics include: Mechanisms of antigen recognition in innate and adaptive immunity; antigen processing and presentation; the MHC; generation of diversity in immune receptors; B and T cell development, activation, differentiation and effector function; phagocytes; NK cells and other innate immune cell types, immunological tolerance and its breakdown; microbial immunity; and signal transduction in the immune system. The course will include both didactic lectures and discussion-type seminars based upon contemporary research papers.

Neuroscience 601 / Molecular, Cellular, and Developmental Biology 610: Principles of Neuroscience I.
This course represents the first half of a year long, graduate-level survey of neuroscience. The goals for NEUROSCI 601 and 602 are: 1) To provide our students with a sense of the state of current knowledge in molecular, cellular, developmental, integrative and cognitive neuroscience. Considerable emphasis is put on pulling together information obtained from different types of investigations (anatomical, physiological, behavioral, biochemical, genetic) to gain a balanced view of neuroscience. 2) To provide our students with a sense of how knowledge was obtained, by reading and discussing "classic papers." 3) To provide our students with a sense of where the current frontier is, by reading and discussing very recent papers. Each week this class meets for 3-5 hours, with a mix of lectures and discussion. The major topics treated in NEUROSCI 601 and 602 are: I) Excitable Membranes, II) Molecular Neuropharmacology, and III) Developmental Neurobiology.

Pharmacology 601: From Molecules to Patients: Basic Quantitative Principles of Pharmacology.
This is a graduate level course that examines the fundamental principles of pharmacology and their quantitative treatment as a basis for understanding the properties and mechanism of action of drugs. The course is aimed at, but not limited to students of Pharmacology, Medicinal Chemistry, Chemical Biology, Toxicology, Bioinformatics or Biological Chemistry. Topics include: Structure and physical properties of drugs; quantitative structure-activity and dose-response relationships; receptors as determinants of drug action; concepts, analysis and modeling of agonists, antagonists, and receptor mechanisms; signal amplification, selectivity, and regulation; drug absorption, distribution and metabolism; modern approaches to drug design.

Pharmacology 612: Antimicrobial and Anticancer Pharmacology.
This course uses a combination of textbook and literature reference to provide students with an understanding of the different classes of drugs and used to treat infectious diseases and cancer.  The course will focus on the mechanisms of drug action, the basis of selectivity and therapeutic applications.  Traditional as well as novel approaches to therapeutics will be discussed, as well as the role of drug resistance and strategies for its management.

Pharmacology 615: Molecular Neuropharmacology.
Pharmacology 615 uses a combination of textbook and literature readings and class discussions to present students with a study of central nervous system molecular neuropharmacology and neurochemistry. Topics will include neurotransmitters in the central nervous system and drugs used therapeutically in the central nervous system. (Cross-listed with Neuroscience 612.)

Pharmacology 616: Seminar in Cardiovascular Pharmacology.
This course consists of seminar presentations along with the use of self-instructional, computer assisted learning modules in the Learning Resource Center.  Emphasis will be placed on pharmacologic interventions used in the management of disorders affecting the cardiovascular system.  Major topics of discussion will focus on the following drug categories:  Drugs affecting the Autonomic Nervous System; Vasoactive Substances; Water, Electrolyte Metabolism and Diuretic Drugs, Antihypertensive Drugs; Calcium Channel Blockers, Cardiac Glycosides and other Cardioactive Agents; Antianginal Drugs; Antiarrhythmic Agents.

Pharmacology 621: Translational Pharmacology: From Drug Discovery to Therapeutics.
Experts from academic and industry will take you on a journey from bench science to new therapeutic agents. Students will learn how to translate preclinical studies to clinical trials and FDA approval. Critical evaluation of clinical trials, patent issues and pharmacoeconomics will also be taught.

Physics 511: Quantum Theory and Atomic Structure I.
This course will focus on the explanation of fundamental concepts, mathematical structure, and calculation methods of quantum mechanics. The course covers the following topics: fundamental concepts of quantum mechanics and its mathematical structure, exactly solvable quantum systems, symmetries in quantum mechanics, approximation methods, atomic and Molecular structure, scattering theory, quantum many-particle systems, and relativistic wave equations.

Physiology 577: Membrane and Cell Physiology.
This course specifically focuses on the molecular, structural and functional properties of membranes and of their relationship to cell physiology. Topics include membrane structure and trafficking, water and solute transport across membranes/cells, mechanisms of ion channel gating and conduction, the basis of membrane/cell electrical excitability, propagation of electrical signals through cell networks, and the activation and dynamics of calcium signaling. The course emphasizes a quantitative approach to understanding cell and membrane physiology. The subject matter of the course is addressed through lectures, as well as via a number of problem sets that illustrate quantitative analysis of membrane and cell physiology and enhance appreciation and understanding of the subject material. The molecular and functional aspects of membrane and cell physiology are also discussed within the framework of tissue and organ physiology and pathology. When relevant, clinical correlations are incorporated in the lecture material to illustrate the importance of the information to biomedical science research.