Biochemistry (BIOC)

Combined Campus Program (UMBC and UMB) University of Maryland, Baltimore County (UMBC), Department of Chemistry and Biochemistry

RICHARD KARPEL, Chair
MICHAEL F. SUMMERS, Graduate Program Co-Director
GERALD WILSON, Graduate Program Co-Director

Professors
BUSH, C. ALLEN, Ph.D., University of California, Berkeley; Chemical structure and three-dimensional conformation of complex carbohydrates of glycoproteins and polysaccharides of the cell surface using biophysical methods such as NMR spectroscopy, circular dichroism and molecular modeling
FISHBEIN, JAMES C., Ph.D., Brandeis University; Mechanisms of organic reactions in aqueous solutions; generation and study of reactive intermediates, particularly those involved in nitrosamine and nitrosamide carcinogenesis; chemical toxicology
KARPEL, RICHARD L., Ph.D., Brandeis University; Nucleic acid helix-destabilizing proteins, protein-nucleic acid interactions, retroviral structural proteins
SUMMERS, MICHAEL F., Ph.D., Emory University, Howard Hughes Medical Investigator; NMR and biophysical studies of retroviral genome recognition, virus assembly and macro-molecular interactions

Associate Professors
CULLUM, BRIAN M., Ph.D., University of South Carolina; Development of optical sensors and optical-sensing techniques for biomedical and environmental research
KELLY, LISA A., Ph.D., Bowling Green University; Mechanistic investigations of visible-light-induced redox reactions using laser flash photolysis techniques, with particular emphasis on developing synthetic chemical assemblies that efficiently undergo chemical redox reactions with biological substrates
SMITH, PAUL J., Ph.D., University of Pittsburgh; Bio-organic and physical organic chemistry; biomimetic catalysis, DNA structure and DNA binding by small molecules
RADTKE-SELEY, KATHERINE., Ph.D., Auburn University; The discovery, design and synthesis of nucleoside/nucleotide and heterocyclic enzyme inhibitors for use as medicinal agents with chemotherapeutic emphasis in the areas of anticancer, antiviral, antibiotic and antiparasitic targets.

Assistant Professors
GARCIN, ELSA., Ph.D., Universite Joseph Fourier, Grenoble (France); The mechanisms by which nitrogen oxide affect catalytic activity and dynamic association with regulatory proteins.
THORPE, IAN., Ph.D., University of Utah; To understand the fundamental physical principles that govern the interplay between protein structure, function and dynamics.
KANN, MARICEL., Ph.D., University of Michigan; The availability of genomic data derived from hundreds of genome projects has generated a great challenge: to understand the complexity of biological process and to decipher the mechanisms that lead to healthy or diseased organisms.

University of Maryland, Baltimore (UMB), School of Medicine; Department of Biochemistry and Molecular Biology (MBIC) and *affiliated faculty

RICHARD ECKERT, Chair
GERALD WILSON, Graduate Program Co-Director
MICHAEL F. SUMMERS, Graduate Program Co-Director

Professors
ANIL, JAISWAL, Ph.D.,Lucknow University, India; Oxidative Stress: Nrf2:INrf2 (Keap1) Signaling in Cell Survival and Death BASHIRELAHI, NASIR (School of Dentistry), Ph.D., University of Louisville; Steroid hormone action
BLACK, LINDSAY W., Ph.D., Stanford University; Bacteriophage morphogenesis and DNA packaging
BLOCH, ROBERT, Ph.D., Harvard University; Cell and Molecular Biology, Muscle Physiology, Biacore and Surface Plasmon Resonance
CIVIN, CURT, M.D., National Cancer Institute; Hematopoietic Stem Cells for Transplantation, MicroRNA Regulation of Adult and Embryonic Human Hematopoietic Development
DAVID KAETZEL, Ph.D., Washington College, Chestertown; The NM23 Family of Metastasis Suppressor Genes DONNENBERG, MICHAEL, M.D., Columbia University, College of Physicians and Surgeons; Interactions between pathogenic Escherichia coli and host cells; Combined molecular biology, cell biology and biochemical approaches are used to gain insight into the processes by which pathogenic E. coli cause disease
ENWONWU, CYRIL (Research), Ph.D., University of Bristol, U.K.
KAPER, JAMES B., Ph.D., University of Maryland, College Park; Bacterial virulence factors
LAKOWICZ, JOSEPH R., Ph.D., University of Illinois; Biophysical applications of fluorescence spectroscopy
LU-CHANG, A-LIEN, Ph.D., University of North Carolina at Chapel Hill; Enzymology of DNA mismatch repair
MONTEIRO, MERVYN J., Ph.D., University of London, England; Biochemistry, molecular biology
ROGERS, TERRY B., Ph.D., University of California, Davis; Signaling mechanisms in the heart and brain
SCHNEIDER, MARTIN F., Ph.D., Duke University; Intra-cellular calcium movements during muscle activation
VARMA, SHAMBHU D., Ph.D., University of Rajasthan, India; Afflications on lens metabolism and cataract formation
WEBER, DAVID, Ph.D., University of North Carolina, Chapel Hill; Structural and mechanistic studies of enzymes, NMR< /p>

Associate Professors
THOMPSON, RICHARD B., Ph.D., University of Illinois, Urbana; Fiber-optic biosensors and fluorescence spectroscopy
WILSON, GERALD M., Ph.D., Queen’s University, Canada; RNA-binding proteins, RNA structure, mRNA turnover, oncogenes, cytokines, regulation of gene expression
PANCER, ZEEV, D.Sc., Isreal Institute of Technology; Unique biomedicine-important antibodies from ancient fish

Assistant Professors
CARRIER, FRANCE, Ph.D., Montreal University, Canada; Genotoxic stress response in mammalian cells
GARTENHAUSE, RONALD,M.D., Employing translational profiling methodology, we were able to demonstrate that MCT-1 was able to upregulate the translation of a subset of cancer-related mRNAs involved in cell growth regulation, proliferation and apoptosis

SONGON, AN, Ph.D., Pennsylvania State University; Cellular Biochemistry of Metabolic Multienzyme Complexes in Living Cells
NURMINSKAYA. MARIA, Moscow State University, Russia
Degrees Offered

M.S. and Ph.D. (combined Biochemistry graduate program, UMBC and UMB). Contact departments for further information.

Program Description

This is an inter-campus program, combining two departments: the Department of Chemistry and Biochemistry at UMBC and the Department of Biochemistry and Molecular Biology in the School of Medicine at UMB. The two departments together offer a single course of study leading to the doctoral in Biochemistry. Students entering this joint program have the benefit of the extensive facilities and resources of the departments on both campuses, and they have the chance to interact with a large pool of scientists with a wide spectrum of research interests.

The doctoral program is administered by a graduate committee consisting of eight faculty members. Committee members for the 2008-present term are M.F. Summers (chair), D.J. Weber (co-chair), F. Carrier, D. Fabris, E. Garcine, M. Monteiro, T.B. Rogers and G. Wilson.

Program Specialties

The following is a list of some of the research specialties available within both of the participating departments.

In the Department of Chemistry and Biochemistry (UMBC), research areas include structure-function studies of nucleic acid helix-destabilizing proteins, model systems for enzyme mechanisms, development of synthetic methods for synthesis of natural products and nucleosides, reactions of carcinogenic polycyclic aromatic hydrocarbon epoxides, infrared and Raman spectroscopy of phospholipid membrane systems, structures of complex carbohydrates, molecular modeling, NMR of metallobiomolecules, gene regulation, DNA binding by small molecules, drug interactions with metalloproteins, mechanisms of drug resistance, photochemistry of nucleic acids, bioanalytical and biomedical applications of mass spectrometry, and relationship studies between molecular geometry and reactivity in biological systems.

The Department of Biochemistry and Molecular Biology (School of Medicine, UMB) offers a wide range of research interests, with particular strengths in molecular biology, protein structure and function, membrane biochemistry and physical biochemistry. These areas include molecular genetics of bacterial transformation genes, phage molecular biology, DNA packaging and morphogenesis, enzymology of DNA mismatch repair, fidelity of transcription, gene expression in muscle development, molecular biology of drug resistance, protein targeting and translocation in eukaryotic cells, molecular energy transduction within enzymes, hemoglobin structure function and blood-substitute design, structure of membrane and contractile proteins, membrane signal transduction mechanisms and proteins, receptor-mediated signaling in heart and brain cells, ion pores and enzymatic catalysis, biochemistry of reproduction in ovarian cells, intra- cellular calcium movements during muscle activation, molecular mechanism of muscle contraction, molecular physiology of allosteric systems and biophysical applications of fuorescence spectroscopy.

Degree Requirements

Upon matriculation in the program, each student will be assigned to a member of the program faculty by the UMB-UMBC graduate committee. The role of the faculty member who serves as an interim advisor is to assist the student in all procedures relative to registration and early course selection until the time when the student has a research advisor and an advisory committee.

Students normally will choose their research advisor from among the graduate faculty members of the program at the end of the first academic year of graduate study. The choice will depend on mutual agreement between the student and the participating faculty member. The choice of advisor must be approved by the UMB-UMBC graduate committee. To form the student’s advisory committee, the student and the research advisor will designate two additional faculty members from the program whose interests are consistent with the student’s research interests and one other program member or other faculty member whose interests are related to the student’s research. The membership of the advisory committee must include representatives from both the UMB and UMBC campuses, and its membership must be approved by the UMB-UMBC graduate committee. The research advisor will serve as the chair of the student’s advisory committee and as chair of the student’s final oral examination committee.

The advisory committee assists in the selection of courses for the student’s program, approves dissertation research plans and is available to the student for consultation. This committee reviews the student’s progress annually throughout the whole of the program of study and advises the student of the results of these reviews. Each entering student who has not demonstrated proficiency in the areas of organic chemistry and either physical chemistry or biology is required to correct the deficiency prior to matriculation. The student normally is accepted on a provisional status until this time.

During the initial year, each entering student will be required to take a research orientation rotation course. This can be either of the following: GPLS 609, Laboratory Rotations (UMB), or CHEM 602, Introduction to Laboratory Research (UMBC). This course consists of six to eight weeks of laboratory work in each of three laboratories in at least two research areas.

Each student is required to take a comprehensive course in biochemistry. This requirement can be met by CHEM 437 and CHEM 638 (UMBC) or GPLS 601, 602 and 603 (UMB).

All students receive a comprehensive and rigorous education in biochemistry by participating in formal courses representing principal areas of biochemistry and molecular biology. In addition to the general biochemistry rotation and laboratory research courses, each student will be required to register for advanced biochemistry courses until passing with a grade of “B” or better in one course in each of three of the following five subject areas: molecular biology, enzymology and bio-organic chemistry, physical biochemistry, metabolism and regulation, and biochemistry of structure and function. One additional course also is required in one of the three chosen areas. In addition to these advanced courses, a minimum of three credits of a further course in a related area, but not necessarily within the program, is required. These advanced courses in biochemistry and related areas are to be approved by the student’s advisory committee.

In addition to the above courses, graduate students in the program are required to enroll in an approved seminar course each semester until they have been admitted to candidacy. During the first two years, students must register for the GPLS 608 seminar course (UMB) or CHEM 713 (UMBC). Even after completion of this requirement, attendance at weekly seminars is strongly encouraged. A minimum of 12 credit hours of dissertation research must be taken for credit, i.e., either GPLS 899 (UMB) or CHEM 899 (UMBC).

Effective September 1, 2005, for a student to be admitted to candidacy, the following qualifications must be met to advance to candidacy:

  1. Successful completion of program course requirements with at least a 3.0 grade point average.
  2. Must have an advisory committee chosen and approved by the director.
  3. Students will be required to pass an oral qualifier exam no later than six months following the completion of their course requirements. Two weeks prior to the oral qualifier exam, each student will be required to submit an NIH-style research proposal to his or her thesis committee that is based on his or her proposed doctoral research. The format of this proposal will follow the page limits and any other rules and regulations of an actual NIH pre-doctoral fellowship proposal. Students may submit this proposal to the NIH or another appropriate granting agency (i.e. American Cancer Society, American Heart Association, etc.); although, this is not required (sample site: grants1.nih.gov/grants/guide/pa-files/PA-03-067.html The research proposal will be presented orally to the student’s committee as part of the oral qualifier exam. During the oral qualifier exam, the student will be rigorously tested on his or her general knowledge of biochemistry and molecular biology, including:
    1. Molecular biology
    2. Enzymology and bio-organic chemistry
    3. Physical and structural biochemistry
    4. Metabolism and regulation

At the end of the oral exam, the committee will meet and determine that (1) the student passes and is recommended to be admitted to candidacy, (2) the student fails and must retake the exam within three months or (3) the student fails and cannot retake the exam. In the third case, it will also be determined whether the student qualifies for a terminal master’s degree.

Prior to the meeting, the research advisor and/or the student should receive a packet of the student's record, including the courses taken and grades learned while in the program. It is the student's responsibility to send a current transcript of their grades and an updated CV to Foyeke Daramola at least two weeks prior to the date of the exam.

There are two requirements for performance in courses. First, a student must achieve at least an overall “B” average during the first two years of enrollment. Second, a student must have a “B” average or better in major courses alone. If either requirement is not met, the student may be dismissed from the program. At the discretion of the UMB-UMBC graduate committee, the student may be allowed an additional one or two semesters to achieve the “B” average in either of the above categories. If the student still has an average below “B” in either category, the student will be dismissed. In the latter case, no exceptions are allowed. Upon completion of the dissertation and its approval by the student’s advisory committee, the research advisor will select members of the advisory committee, as well as at least one other faculty member and/or an outside reviewer to serve as examiners on the final oral examination.

Program Admission Requirements

Students wishing to enter the Ph.D. program in biochemistry will be required to meet the basic minimum standards for admission to the University of Maryland, Baltimore Graduate School, and to receive the approval of the UMB-UMBC graduate committee. Such approval normally will be based upon undergraduate grades, letters of recommendation, Graduate Record Examination scores and, wherever possible, personal interviews. Previous success in graduate education will be taken into consideration. All original application documents must be sent directly to the Graduate School, not to the graduate program. Each entering student will be expected to satisfy minimum requirements in the fields of organic chemistry and either physical chemistry or introductory biology. If the undergraduate record of the student does not demonstrate to the satisfaction of the UMB-UMBC graduate committee that all these requirements have been met, the student will be given a choice of taking a placement examination in the deficient area(s) or taking the appropriate course(s) from among the following (or their equivalent): CHEM 351, 352, Organic Chemistry [3,3]; CHEM 301, 302, Physical Chemistry [4,3]; BIOL 100, Concepts of Biology [4]; BIOL 303, Cell Biology [3]. Students with deficiencies in all these areas will not ordinarily be considered for admission.

Facilities and Special Resources

UMBC students are offered hands-on access to an extensive array of tools for modern chemical and biochemical research. The department's specialized research instrumentation includes calorimetry, chromatography, stopped-flow and temperature-jump kinetics, transient laser spectroscopy (including nano-second laser flash photolysis, pico-second and femto-second pump-probe, and pico-second fluorescence systems), nuclear magnetic resonance spectroscopy (including one 200-, one 400-, one cryoprobe-equipped 500-, two 600- and one 800-MHz instruments), X-band CW electron paramagnetic resonance spectrometry, circular dichroism, X-ray diffraction, infrared spectroscopy, atomic absorption- and gas chromatography-mass spectrometry and Fourier transform ion cyclotron resonance mass spectrometry apparatus, as well as extensive molecular modeling and computational chemistry facilities.

In addition to TOF/FT, a laser desorbtion mass spectrometer, and both 500- and 600- MHz NMRs, the department houses one of the few 12 T FTICR mass spectrometers located in academic institutions worldwide. The Howard Hughes Medical Institute suite houses a second 600- and an 800-MHz NMR instrument, both of which are used for high-dimensional studies of HIV proteins, metallobiomolecules and macromolecular interactions. Access to principal journals is available in the Albin O. Kuhn Library and Gallery.

The Department of Biochemistry and Molecular Biology (School of Medicine, UMB) is an extensive research facility located in the Biomedical Research Facility. Equipment within the department includes analytical and preparative ultra-centrifuges; spectro-polarimetry facilities; automated amino acid analyzers; protein-sequencing and peptide- synthesizing equipment; photon-counting spectrofuorometry instrumentation; milli- and nanosecond spectrofuorometer; phase- modulation lifetime fuorometer; rapid-quench and stopped-flow kinetic instrumentation; multiple high-performance liquid chromatography facilities; full facilities for analytical electron microscopy; controlled environment rooms and extensive radioactive counting, cell culture and other centralized facilities. The Center for Fluorescence Spectroscopy is located in the Department of Biochemistry and Molecular Biology, Biomedical Research Facility, as well as in an NMR Facility that is located in the Health Sciences Facility. The students also have access to the Molecular Graphics Facility located in the Biomedical Research Facility.

Outplacement Success

Graduates of the program continue their training with post-doctoral appointments or obtain employment at such competitive and prestigious institutions or corporations as Scripps Institute (CA), Howard Hughes Medical Institutes, NIH, Cornell University and E.I. Lilly, as well as at many local and national biotechnology firms.

Financial Assistance

Financial assistance is available on a competitive basis to students accepted into the program. Qualified first-year students usually are offered teaching or research assistantships on a competitive basis. Research assistantships are often available for students actively engaged in thesis research. In addition, students are encouraged to apply for nationally awarded graduate fellowships, such as those offered by the National Science Foundation and National Institutes of Health.

COURSE LISTING

See CHEMISTRY program and BIOLOGICAL SCIENCES program for additional courses

CHEM 401
Chemical and Statistical Thermodynamics [3]

Intended for first-year graduate students and advanced undergraduates, this course is a treatment of chemical and statistical thermodynamics at a more sophisticated level than that encountered in CHEM 301/302. Emphasis is placed on the use of thermodynamic data available in the chemical literature and experimental methods of obtaining these data. (Spring) Prerequisite: CHEM 302.

CHEM 405
Inorganic Chemistry [3]

Basic theoretical concepts of inorganic chemistry, including a study of the periodic table, its elements, and their physical and chemical properties. Several theories of bonding are discussed, as well as the mechanisms of inorganic reactions, coordination chemistry and the chemistry of transition metals. (Fall) Prerequisite: CHEM 302.

CHEM 410
Quantum Chemistry [3]

Introduction to the principles of quantum mechanics and their application to chemical systems. The postulatory basis of quantum mechanics; approximate methods; vibrational, rotational, electronic, nuclear magnetic and electron spin spectroscopy; atomic structure; the chemical bond; valence bond and molecular orbital theory. Prerequisite: CHEM 302.

CHEM 437
Comprehensive Biochemistry I [4]

The first semester of a two-semester sequence providing a thorough introduction to the principles of modern biochemistry. Major topics include enzyme kinetics and the structures and properties of proteins, nucleic acids, carbohydrates and lipids. (Fall) Prerequisite: BIOL 100 and CHEM 352 or equivalent.

CHEM 437L
Biochemistry Laboratory [4]

Modern methods of biochemical research. Laboratory experiments are designed to provide experience in working with biologically active materials and familiarity with standard biochemical techniques. These include spectrophotometry; chromatography; isotope tracer techniques; ultra-centrifugation; enzyme kinetics; isolation, purification and characterization of proteins, nucleic acids and subcellular organelles. (Fall) Note: Two laboratory sessions per week. Corequisite: CHEM 437 and consent of the instructor.

CHEM 601
Current Topics in Chemistry [1-4]

A discussion of specialized topics in areas of chemistry currently in a state of rapid evolution. The format of the course will be tutorial. May include varied topics such as applications of mass spectrometry in biochemistry and pharmacology, advanced NMR techniques. Prerequisite: Consent of instructor.

CHEM 602
Introduction to Laboratory Research [1-3]

The purpose of this course is to familiarize graduate students with the different areas of research within the Department of Chemistry and Biochemistry to expand their knowledge of experimental techniques and to provide the basis for a more informed selection of an advisor for thesis research. Note: For the joint Biochemistry program, a student enrolling in the course will work for periods of about six weeks in the laboratories of three faculty members, at least one of whom should be engaged in an area of research different from the preferred area of the student’s specialization.

CHEM 606
Bioinorganic Chemistry [3]

The functions of metals in biology, biochemistry and medicine are presented with emphasis on the structural and catalytic properties of metal centers in metalloproteins. Topics include catalysis, metalloenzyme mechanisms, inorganic co-factors and co-enzymes, and metal chemotherapeutic agents. Prerequisite: CHEM 405 or consent of instructor.

CHEM 610
Special Topics in Theoretical Chemistry [3]

Discussions of current approaches to problems in theoretical chemistry will be presented in the form of lectures and seminars. Topics to be discussed will include molecular orbital theory; statistical mechanics of non-ideal systems; cooperative systems, phase transitions and critical phenomena; non-equilibrium thermodynamics and rate theory; scattering theory and molecular spectra. Prerequisite: Consent of instructor.

CHEM 615
Statistical Mechanics and Theory of Rate Processes [3]

Introduction to statistical mechanics and theoretical aspects of absolute reaction rate theory. Statistical definition of entropy; compounding of systems; combinatorial problems; the methods of Gibbs; quantum statistics; partition functions; applications in equilibrium states of gases, solids and liquids; partition formulation of the theory of absolute reaction rates. Prerequisite: CHEM 302.

CHEM 631
Chemistry of Proteins [3]

An advanced treatment of the chemistry of proteins and protein-containing supramolecular structures. Topics include isolation and purification of proteins, structure of proteins and relation of structure to biological function. Prerequisite: BIOL 430, CHEM 137 or equivalent, and consent of instructor.

CHEM 632
Advanced Biochemistry [3]

The topics presented would not normally be covered in any other biochemical courses and may include an advanced treatment of enzyme kinetics, with emphasis upon two substrate systems; allosteric control mechanisms; replication and transcription and the biochemistry of specialized tissues. Prerequisite: Consent of instructor.

CHEM 633
Biochemistry of Nucleic Acids [3]

A survey of nucleic acid structure and function, with emphasis on chemical aspects. Topics will include DNA and RNA structure, packaging of nucleic acids, chemical and physical properties of nucleic acids, proteins and enzymes of DNA replication, fidelity of nucleic acid synthesis, biochemistry of DNA recombination, enzymology of transcription and RNA processing. Prerequisite: CHEM 437 or equivalent or consent of instructor.

CHEM 635
Biochemistry of Complex Carbohydrates [3]

This course will address the structure and function of the carbohydrates of glycoproteins, glycolipids, proteoglycans and bacterial polysaccharides. Topics also will include carbohydrates as informational macromolecules and decoding by lectins, biosynthesis, structure, engineering of glycoproteins, bacterial adhesion and virulence and tumor antigens. Prerequisite: CHEM 437 or equivalent.

CHEM 638
Comprehensive Biochemistry II [4]

This course is intended primarily for first year graduate students who have completed CHEM 437, Comprehensive Biochemistry I. The student will be required to attend the undergraduate lecture course in biochemistry (CHEM 138, Comprehensive Biochemistry II), which covers metabolic pathways and selected topics in nucleic acid and membrane biochemistry. In addition, the student will be assigned reading in the research literature in one or more of the above areas and be required to write a paper based on this reading.

CHEM 640
Special Topics in Molecular Structure [3]

Discussions of the major physical methods for determination of molecular structure will be presented. Emphasis will be placed on the application of theoretical principles to experimental problems and to computational methods required for interpretation of data. Topics to be discussed may include X-ray, electron and neutron scattering; molecular spectroscopy (infrared, ultraviolet and microwave); nuclear magnetic and electron spin resonance; dipole moment determination; and dielectric relaxation. Prerequisite: Consent of the instructor.

CHEM 641
Physical Chemistry of Macromolecules [3]

Introduction to the physical chemistry of macromolecules. Emphasis will be placed on the development of broad general concepts applicable to the study of all types of macromolecules, e.g. synthetic and biological. Topics considered include determination of molecular weight distributions; conformational properties of high polymers; and thermodynamics and transport properties of polymer solutions, polyelectrolytes and polymerization processes. Techniques such as sedimentation analysis, light scattering, osmometry and viscometry will be discussed. Prerequisite: CHEM 301 and consent of the instructor.

CHEM 642 Physical Biochemistry [3]
Structural determination of proteins and nucleic acids in the solid state and in solution. Transitions between and stability of secondary and tertiary structure. Ligand binding and association processes. Interpretation of spectra, titration curves and multi-component equilibria, hydrodynamic properties and fluorescence polarization. Prerequisite: Consent of instructor, CHEM 301 and CHEM 437 or equivalents.

CHEM 643
Molecular Spectroscopy and Biopolymers [3]

Team-taught course covering theory and applications of advanced spectroscopic techniques used to study the structure and function of biomacro-molecules (polysacharides, DNA, co-enzymes and co-factors). Aspects of modem Fourier Transform NMR, including one- and two-dimensional methods (COSY, NOESY, HOHAHA) will be presented. Principles of mass spectrometry and examples of the potential, limitations and applications of electron impact, desorption ionization, high-resolution tandem mass spectrometry and interfaced chromatography-mass spectrometry will be discussed. Theory and applications of other spectroscopic techniques, including molecular vibrational (Raman, resonance Raman and infrared), electron spin resonance (ESR), and laser fluorescence spectroscopies also will be presented. Prerequisite: Consent of instructor.

CHEM 644
Molecular Modeling [3]

Survey of theoretical methods for simulation of biopolymer conformation. Force fields, energy maps, energy minimization and molecular dynamics simulation. Influence of solvents. Applications to proteins, nucleic acids, etc. Laboratory section will emphasize practical calculations on biopolymers and use of databases of structural biochemistry. Prerequisite: CHEM 301 and CHEM 437 or equivalent.

CHEM 650
The Chemistry of Heterocyclic Compounds [3]

An in-depth survey of the properties, reactions and synthesis of heterocyclic compounds containing the heteroatoms of oxygen, sulfur and/or nitrogen. The course will consist of lectures based on readings from monographs and current literature. Prerequisite: Consent of instructor.

CHEM 651
Mechanisms of Organic Reactions. [3]

Advanced treatment of the study of organic reaction mechanisms, with emphasis on the development of broad principles governing various organic reactions. Description of metastable intermediates, such as carbonium ions, carbanions, carbenes and free radicals; kinetic effects in relation to structure; conformational analysis; and stereochemistry. Prerequisite: CHEM 352.

CHEM 652
Physical Organic Chemistry [3]

Introduction to theoretical aspects of organic chemistry. Molecular orbital approximations, linear free-energy relationships, general theory of acid-base catalysis, medium effects and isotope effects. Prerequisite: CHEM 451 and consent of instructor.

CHEM 653
Organic Chemistry of Nucleic Acids [3]

A survey of organic chemical principles governing structure, properties and reactions of nucleic acids, including synthesis of nucleic acid bases, nucleosides, nucleotides and polynucleotides, and their important synthetic analogues possessing anti-viral and anti-tumor properties. Study of reactivity of nucleic acid building blocks, including addition and substitution reactions, ring openings and rearrangements, hydrolysis of glycosidic and phosphodiester bonds, and photochemical reactions. Study of primary structure, acid-base property, tautomerism and conformation of nucleic acids. Review of secondary structure, base-pairing and stacking interactions, helical structure, stability, conformation, denaturation, renaturation and crosslinking. Prerequisite: CHEM 352.

CHEM 654
Organic Synthetic Chemistry [3]

A survey of the basic principles of reactions and strategies in organic synthesis. The course will focus on reactions leading to new bond formation, functional group transformation and the combination of these reactions in the synthesis of complex organic molecules. Lectures will be based on readings from monographs and current literature. Prerequisite: Consent of instructor.

CHEM 655
Introduction to Biomedicinal Chemistry [3]

A survey of (a) principles and methods of drug design, including modem rational approach aided by computers, disease models, natural products, analogue synthesis and pharmacophore identification; (b) physiochemical principles of drug action, including solubility, partition co-efficients, surface interactions, stereochemical, electronic and quantum chemical factors, chemical bonding and quantitative structure-activity relationships (QSAR); (c) receptor concept of drug action, including nature, definition, characterization, models and classical theories of receptor function; (d) mechanisms of drug action, including enzyme stimulation, inhibition and regulation; (e) drug distribution, metabolism and inactivation, including bioavailability, biotransformations, chemical and metabolic stability, pharmacokinetic variability and design of pro-drugs; (f) case studies selected from a list of anti-tumor, analgetic, anti-microbial, anticholinergic, anti-adrenergic, psycho-active and cardiovascular drugs and (g) curentstatus and future impact in drug development, including protein therapeutics, gene therapy, anti-sense drugs, cytokines and drug resistance. Prerequisite: BIOL 100 and CHEM 352.

CHEM 657
Total Synthesis of Natural Products [3]

The course will cover the total syntheses of selected natural products from animal, plant, marine, bacterial and fungal sources, including vitamins, alkaloids, hormones, terpenoids and antibiotics. Both historically significant total syntheses of landmark, such as those of cholesterol, morphine, strychnine and vitamin B12, and the more modern total syntheses, such as those as taxol, bleomycin and enediyne antibiotics will be elaborated. Students who opt to take the course for graduate credits (CHEM 657) will be required to write an additional term paper and/or make an oral presentation on the total synthesis of a selected natural product. Prerequisite: CHEM 352 or equivalent.

CHEM 660
Special Topics in Analytical Chemistry [3]

A course of lectures and seminars devoted to modern methods in analytical chemistry. Two of the following topics will be considered: instrumental methods in spectroscopic analysis, scattering and diffraction methods, electroanalytical and polarographic techniques, chromatography, separation and purification methods and tracer methods. Readings from current literature will be the basis of both lectures and seminars. Prerequisite: Consent of instructor.

CHEM 661
Advanced Instrumental Methods of Analysis [4]

A lecture-laboratory course devoted to the theory, instrumentation and application of modem electrochemical, spectroscopic and chromatographic techniques. Advantages and limitations of different instrumental methods are discussed using selected topics of environmental, clinical and toxicological analyses. Journal articles will be used to review recent advances and new trends in development of analytical techniques. Laboratory experiments may include polarography and pulse voltammetry, anodic stripping analysis, potentiometry with ion-selective electrodes, flame and electrothermal atomic absorption, UV-VIS spectrophotometry, Raman spectroscopy, electrophoresis, capillary gas chromatography and high-performance liquid chromatography (HPLC) and gas chromatography/mass spectroscopy. (Spring) Prerequisite: Consent of instructor or CHEM 300 and CHEM 311L or equivalent.

CHEM 662
Analytical Spectroscopy [3]

An advanced course in spectroscopic methods of qualitative and quantitative analysis, with emphasis on instrumental design, construction and operation. Topics will include atomic spectroscopy, light scattering, electronic and vibrational molecular spectroscopy. The role of lasers in modern spectroscopic methods will be explored.

CHEM 663
Analytical Separations [3]

An advanced course in separation science, with emphasis on chromatographic techniques. This course will cover the theory of chemical separations, physical description and operation of various chromatographic instruments and general application of these techniques. Readings from current literature will supplement the lectures.

CHEM 664
Electronics for Chemists [3]

A lecture-laboratory course designed to introduce chemists to a wide range of electronic principles from electron theory to digital computer technology. This course will cover alternating and direct current electronics, semiconductor technology and signal processing. Emphasis will be placed on circuits and electronic applications commonly found in chemical research laboratories.

CHEM 670
Special Topics in Dynamics and Mechanisms [3]

Discussions of the major methods and approaches to the study of chemical kinetics and other rate processes as applied to the elucidation of mechanisms of organic, inorganic and biochemical reactions. One of two of the following topics may form the basis of a semester’s work in this course: rapid reaction techniques; stopped flow, pressure and temperature jump methods; ultrasonics; inorganic reaction mechanisms-solvation; electron and proton transfer; substitution reactions; biocatalysis-inhibition; activation; allosteric effects; kinetics of structural transitions and phase transformation; gas phase kinetics and heterogeneous catalysis. Prerequisite: Consent of instructor.

CHEM 672
Enzyme Reaction Mechanisms [3]

The mechanism of enzyme action will be examined, with emphasis on the following topics: three-dimensional structure of enzymes, chemical catalysis, methods of determining enzyme mechanisms, stereochemistry of enzymatic reactions, detection of intermediates, affinity labels and suicide inhibitors, transition state analogs, energy relationships, evolutionarily “perfect” enzymes, genetic engineering and enzymes and use of binding energy in catalysis. Instruction will be in both lecture and seminar format, with emphasis on recent literature. Prerequisite: CHEM 352 and CHEM 457 or consent of instructor. Recommended: CHEM 451.

CHEM 680
Seminar in Biophysical Chemistry [3]

A series of weekly lectures and seminars dealing with current developments in the field of biophysical chemistry.

CHEM 682
Special Topics in Biochemistry [3]

A series of weekly lectures and seminars dealing with topics of current research interest in the field of biochemistry. A single area in which advances of major significance have been made may be chosen.

CHEM 684
Special Topics in Chemistry [3]

A series of weekly lectures and seminars dealing with recent or current important developments in chemistry. A single area in which advances of major significance have been made, or a given term, e.g., physical, organic or inorganic chemistry, will be selected.

CHEM 690
Chemistry Seminar [1]

A series of weekly seminars devoted to a wide range of topics encompassing the current literature in all fields of chemistry. Note: Each student will be required to present an extensive written paper based on the seminar and on collateral readings from current literature. Enrollment will be limited to ensure that participating student has an opportunity to present at least one major seminar. Prerequisite: Consent of instructor.

CHEM 710
Research Tutorial in Chemistry [1]

Intensive tutorial seminar on current topics of research actively pursued by the faculty member directing the course.

CHEM 713
Biochemistry/Chemistry Seminar [1]

This core course is required for first- and second-year graduate students. A varied background in the biochemistry/chemistry current research fields will be presented. Note: Students will be required to attend eight seminars in the semester, either at the UMB Department of Biochemistry and Molecular Biology or the UMBC Department of Chemistry and Biochemistry. Course is linked with MBIC 713.

CHEM 715
Issues at the Chemistry/Biology Interface [1]

This course is specifically tailored for CBI students. The class is designed to introduce CBI students to areas of research at the interface that they might not otherwise encounter.

CHEM 799
Master's Thesis Research [1-6]

Master's thesis research conducted under the direction of a faculty member. Note: Six credit hours are required for the M.S. degree.

CHEM 899
Doctoral Dissertation Research [1-6]

Research on doctoral dissertation conducted under the direction of a faculty advisor. Note: A minimum of 12 credit hours are required for the Ph.D. degree.

UMB Department of Biochemistry and Molecular Biology, School of Medicine (MBIC)

GPLS 608
Seminar [1]

This course requires that students attend eight research seminars during the semester either at the UMB Department of Biochemistry and Molecular Biology or the UMBC Department of Chemistry and Biochemistry. Research seminars will be given by local, national and international speakers, and synopses of the seminars are prepared by each student and turned in to the instructor.

GPLS 609
Lab Rotations [1]

Students gain experience in a variety of techniques and become familiar with the faculty members and their research. Doctoral students generally complete two or three rotations in different laboratories in the program. Rotations usually last six to eight weeks.

GPLS 616
Molecular Mechanisms of Signal Transduction [3]

This twice-weekly literature, discussion and lecture course covers mechanisms of hormone action upon target cells, with emphasis on the molecular mechanisms by which hormones mediate their cellular effects. Prerequisites: Completion of GPLS core curriculum, GPLS 601, GPLS 602 and GPLS 603.

GPLS 618
Readings/Special Topics [1]

GPLS 622
Intro to Biostatistics [3]

This course is designed to develop an understanding of statistical principles and methods as applied to human health and disease. Topics include: research design; descriptive statistics; probability; distribution models; binomial, Poisson and normal distribution; sampling theory and statistical inference.

GPLS 625
Fundamentals of Membrane Transport: Ion Channels [3]

Covers the role of voltage- and receptor-gated ion channels in cell function. Although the emphasis is on structure and function of channels in excitable tissues such as nerve and muscle, students gain insight into the rapidly developing field of ion channel function in non-excitable cells such as lymphocytes, transformed cells and glial cells and the roles of ion channels in development.

GPLS 635
Bacterial Genetics [4]

Covers induction, expression and selection of mutants; molecular basis of mutations; transfer of genetic information by transformation, transduction and conjugation; complementation and recombination in phage and bacteria; plasmids; and recombinant DNA. Two lectures and two laboratory periods per week deal with the genetics of bacteria and bacterial viruses.

GPLS 665
Special Topics in Cancer Biology

This three-credit course has been designed to introduce students to both the biology of specific cancers and how patients with these diseases are managed and treated. The course will consist of twice weekly lectures in which a basic or translational scientist will be paired with a clinician to describe a specific disease and the major questions that need to be answered to improve treatments.

GPLS 701
Advanced Molecular Biology [3]

This core course for the biochemistry program covers advanced topics in molecular biology and genetics, taught principally from current primary literature. A combination of lectures and student-directed seminars address recent developments in DNA/RNA metabolism and regulation of gene expression, while additional sessions explore genetics and molecular contributions to control of cellular function and disease.

GPLS 709
Advanced Biochemistry [3]

This advanced core course for the biochemistry program emphasizes protein structure and function, including the following topics: protein folding and stability; thermodynamics; allosteric interactions; protein structure/dynamics, the chemistry of enzyme mechanisms; steady-state and pre-steady state kinetics; and methods used for characterizing proteins and enzymes, including circular dichroism, nuclear magnetic resonance, X-ray diffraction, protein fluorescence and stopped-flow techniques. The course includes problem sets and two exams.

GPLS 713
Graduate Biochemistry Seminar [2]

Student taking this required course will examine and then present research seminars on current topics in biochemistry and molecular biology. Special topics will vary each semester and are chosen in advance by the instructor. In addition to the quality of the scientific presentation, the course will also stress the critical evaluation of the scientific work by the presenter and the members of the class; thus, participation in weekly discussions by all students is an essential aspect of the course.

GPLS 714
Muscle: Contractility and Excitation [3]

This course offers a comprehensive description of the basic physiology, biochemistry and biophysics of cardiac, skeletal and smooth muscle. Topics include: ultrastructure of skeletal muscle, mechanical and biochemical features of the crossbridge cycle in contraction, excitation-contraction coupling, calcium-induced calcium release in cardiac muscle, physiology and pharmacology of smooth muscle.

GPLS 715
Muscle Cell Biology and Development [3]

This course considers the developmental biology of muscle, including its innervation and plasticity. The course begins with a discussion of the factors controlling the proliferation and differentiation of myoblasts. Next is a consideration of fiber type determination, its relationship to use, and the effects of hypertrophy and atrophy on muscle. The structure, function and formation of the neuromuscular junction and its relationship to the organization of structures in the extra-junctional region form the next set of topics. Emphasis is placed on the extra-cellular matrix and the cytoskeleton. The last part of the course deals with the relationship of activity and hormonal influences to the biochemical properties of muscle. The course meets twice weekly and consists of one lecture and one session for student oral presentations and discussion of assigned research pertinent to the lecture topic.

GPLS 720
Fluorescence Spectroscopy [2]

An intensive introduction to the techniques of time- and frequency-domain fluorescence spectroscopy with emphasis on applications in biochemistry and biophysics. The course lasts four-and-a-half days in January. Topics may include time- and frequency-domain measurement techniques, time-resolved anisotropy, data analysis including global analysis, instrumental design, fluorescence energy transfer, transient effects in quenching, excited-state reactions, fluorescence-based sensing including fiber-optics, fluorescence lifetime imaging, fluorometry with two-photon excitation and near-infrared fluorometry.

GPLS 799
Master’s Research [2-9]

GPLS 899
Doctoral Research [9]