Biochemistry (BIOC)

BIOC 0003. Scientific Writing: Development and Defense of a Research Proposal. 2 Credit Hours.

The course consists of writing a progress report describing research results during the last year. The course is required of all graduate students beginning the first semester after selection of a supervising professor.

BIOC 4000. Special Topic. 4 Credit Hours.

This is a self-designed course created by both the student and the department to cover a specific topic. A Course Approval Form must be completed along with documentation of the designed course description.

BIOC 5083. Hydrodynamic Methods. 2 Credit Hours.

This course is intended to provide students with the opportunity to gain a solid understanding of hydrodynamics and macromolecular transport processes, such as sedimentation and diffusion. The focus will be on hydrodynamic methods involving analytical ultracentrifugation and light scattering. Topics in sedimentation velocity, sedimentation equilibrium, buoyant density sedimentation, as well as static and dynamic light scattering and the complementarity of these approaches will be discussed. Macromolecular interactions involving mass action, concentration dependent nonideality and reaction rates are covered. This course will also cover a range of data analysis approaches including the van Holde-Weischet method, the second moment method, direct boundary fitting by finite element modeling, the C(s) method, the 2-dimensional spectrum analysis, genetic algorithm optimization and nonlinear least squares fitting approaches to user-defined models. Statistical analysis using Monte Carlo and bootstrap methods will also be covered. Open for Cross Enrollment on Space Available Basis.

BIOC 5085. Biophysical Methods In Biology. 2 Credit Hours.

This course is required for all students enrolled in the Molecular Biophysics and Biochemistry track. The course covers modern biophysical methods for studying biological macromolecules in sufficient detail to understand the current literature. Topics to be covered include macromolecular structure determination by X-ray crystallography and NMR spectroscopy; absorbance, fluorescence, and EPR spectroscopy; circular dichroism; light scattering; mass spectrometry; and hydrodynamics, including diffusion, electrophoresis, sedimentation velocity, and sedimentation equilibrium. Open for Cross Enrollment on Space Available Basis.

BIOC 5087. Molecular Genetics And Biotechnology. 1 Credit Hour.

This course is required for all students enrolled in either Molecular Biophysics & Biochemistry Track. The objective of this course is to provide comprehensive treatment approaches to experimental biochemistry and biophysics rooted in genetics, recombinant DNA technology, and genomics.

BIOC 5091. Special Topics In Biochemistry: Hydrodynamic Methods. 1 Credit Hour.

This course is intended to provide students with the opportunity to gain a solid understanding of hydrodynamics and macromolecular transport processes, such as sedimentation and diffusion. The focus will be on hydrodynamic methods involving analytical ultracentrifugation and light scattering. Topics in sedimentation velocity, sedimentation equilibrium, buoyant density sedimentation, as well as static and dynamic light scattering and the complementarity of these approaches will be discussed. Macromolecular interactions involving mass action, concentration dependent nonideality, and reaction rates are covered. This course will also cover a range of data analysis approaches including the van Holde-Weischet method, the second moment method, direct boundary fitting by finite element modeling, the C(s) method, the 2-dimensional spectrum analysis, genetic algorithm optimization, nonlinear least squares fitting approaches to user-defined models. Statistical analysis using Monte Carlo and bootstrap methods also will be covered.

BIOC 5092. Nuclear Magnetic Resonance Spectroscopy For Biochemists. 2 Credit Hours.

This course provides a working knowledge of the basic underlying theory of modern pulsed Nuclear Magnetic Resonance methods in the study of the structures and internal dynamics of biological macromolecules in solution. The theoretical concepts to be covered include an overview of pulse excitation, digital sampling, and Fourier transformation. The product operator formalism will be used to describe how modern multinuclear multidimensional pulse methods function to yield the desired signals. The practical concepts to be covered will include an overview of modern methods for obtaining sequential resonance assignments, determining high-resolution three-dimensional structures, and analyzing internal dynamics.

BIOC 5093. Data Analysis In Biochemistry And Biophysics. 1 Credit Hour.

This course is required for all students enrolled in either Molecular Biophysics & Biochemistry Track, or the Diabetes & Metabolic Disorders Track, and is open to all students enrolled in the Integrated Multidisciplinary Graduate Program. The course covers statistical and mathematical analysis of typical biochemical data. Topics to be discussed include: enzyme kinetics, first and second order chemical reactions, ligand binding, scintillation counting of radioactivity, UV-VIS difference and derivative spectra, analytical ultra-sedimentation, and solution of multiple simultaneous equations using matrix algebra. Emphasis is placed upon the use of computers to analyze experimental data using programs running under Windows, or Linux platforms. Students will also become familiar with file transfers between these two platforms and the use of VNC viewer to enable their PC computers to be used as a Linux terminal.

BIOC 5094. Research Presentations and Career Opportunities. 1 Credit Hour.

The goal of the course is to provide students with continuous experience in (1) formal presentation of their ongoing research progress; (2) exposure to various career opportunities through guest speakers; and (3) discussion and critical analysis of current scientific literature should time allow. The course meets weekly with all second-year students cycling through to make research presentations, with interspersed guest presentations on career opportunities and student presentations of journal articles by 1st-year students selected from the student's area of research interest, but also of relevance to the whole class.

BIOC 6010. Gene Expression and Omics. 2 Credit Hours.

This course presents 1) the principles of gene expression, including transcription, epigenetic regulation (histone modifications and DNA methylation), mRNA processing and degradation, translation, post-translational modifications, and protein degradation, and 2) the omics approaches for collective characterization and quantification of different aspects of gene expression, including genomics, epigenomics, proteomics, and metabolomics. Two main teaching formats are used in this course: 1) Didactic lectures in which information is delivered to the class, and 2) Paper presentations and discussions, in which students present assigned papers and lead discussions by the entire class. Although one student will present each paper, all students will be expected to read each paper and to be prepared to discuss it in the form of comments and questions. Prerequisites: Permission of the Course Director and IBMS 5000 (or equivalent).

BIOC 6015. Metabolic Disorders. 2 Credit Hours.

This course will present an introduction to dysfunctions in normal metabolic processes that lead to major human disorders and pathologies. Major topics to be covered include the causes and pathogenesis associated with Type 2 diabetes, obesity, and related hormonal signaling pathways. Other topics will focus on lipid and protein metabolic disorders, and on dysfunctions associated with mitochondrial and extracellular matrix defects.

BIOC 6029. MBB Journal Club and Student Research Presentations. 2 Credit Hours.

To be taken by all graduate students in the MBB track each semester starting with the second year. Students will each make one presentation per semester. Presentations will typically be of a recent journal article in the area of biochemistry or biophysics. Journal articles for presentations must be approved by the instructor. With permission, a student may present a summary of his or her doctoral research. In the Spring semester of their third year, students will present a review of literature relevant to their doctoral research. Grading will be based on both the presentation and involvement in class discussion.

BIOC 6033. Cell Signaling Mechanisms. 2 Credit Hours.

This course covers the molecular mechanisms of action of various extracellular mediators including hormones, neurotransmitters, growth factors, cytokines, etc., and cell signaling events. Several areas will be discussed including: (1) mechanisms of mediator synthesis; (2) interaction of mediators with specific receptors; (3) modulation by mediators of various second messenger systems including cyclic nucleotides, inositol phospholipids, calcium, protein phosphorylation, ion flux, etc.; and (4) intra- and intercellular mechanism for regulating mediator action. Open for Cross Enrollment on Space Available Basis.

BIOC 6035. Target Identification and Hit/Lead Discovery. 2 Credit Hours.

This course provides students with an understanding of the overall process of drug discovery and development. It covers the principles of target identification and validation, the basic methods of drug development, the physical biochemistry of how drugs interact with their biological targets, the role of protein structures in drug-protein interactions, the application of medicinal chemistry in lead optimization, and the development of biologicals like antibodies, vaccines, and RNAs for therapeutics. Focused lectures on specific therapeutic areas will include anti-parasite drug development and drug development for cancer. Prerequisites for the course is at the discretion of the course directors, based on adequate undergraduate courses in chemistry, biochemistry and mathematics. Open for Cross Enrollment on Space Available Basis.

BIOC 6036. Macromolecular Structure & Mechanism. 2 Credit Hours.

This course will cover the fundamentals of protein and nucleic acid structure and of enzyme catalysis. The course is required of students in the Molecular Biochemistry and Biophysics Track. Topics to be covered include: DNA and RNA structure, protein structure, protein folding, ligand binding by proteins, and enzyme catalysis. Open for Cross Enrollment on Space Available Basis.

BIOC 6037. Integration Of Metabolic Pathways. 2 Credit Hours.

The course is required of students in the Molecular Biophysics and Metabolic Pathways track. The objective is to provide an understanding of the individual reactions in intermediary metabolism and how the reactions are integrated by regulatory mechanisms. Topics include carbohydrate, lipid, and nitrogen metabolism and mechanisms of regulation of individual enzymes and metabolic pathways. Open for Cross Enrollment on Space Available Basis.

BIOC 6038. Surface Plasmon Resonance Workshop. 0.5 Credit Hours.

Surface plasmon resonance can be used to measure the equilibrium and rate constants of a variety of biomolecular interactions, including protein-protein, protein-small molecule, protein-nucleic acid and protein-phospholipid. In this laboratory intensive workshop, students will be exposed to the principles of experimental design, data collection, and data analysis utilizing state of the art instrumentation and model interactions.

BIOC 6043. Structure & Function Of Membrane Proteins. 2 Credit Hours.

This is a course targeted at students within any of the Graduate Tracks. The objective is to provide a broad view, allowing for in depth consideration in selected areas, of the structure and diverse functions of proteins within a membrane environment. Specific topics covered will include: ion selective channels, large membrane pores, membrane transporters, membrane pumps, and membrane receptors. The format of the course will be didactic lecture followed by student presentations of relevant topics. Open for Cross Enrollment on Space Available Basis.

BIOC 6069. Contemporary Biochemistry Student Review. 1 Credit Hour.

The course has two aspects. In the first, students will have the opportunity to put together a didactic lecture on a biochemical topic, essentially an oral review. Alternatively, students who attend a scientific meeting may pick a theme that was presented at that meeting in any of multiple venues (symposia, platform presentations, posters) and develop it as a presentation equivalent to an oral review. In each case, students will research the background of the material and present the latest findings. This is not intended to be a journal club but rather a didactic or teaching lecture. The course Director will work with the students ahead of time to assist them in preparing their presentation. The second aspect is that students who are not themselves presenting are required to attend the presentations. Biochemistry students must present at least once in years 3.5 of their matriculation in order to graduate with the Ph.D. degree. May be repeated for credit.

BIOC 6071. Supervised Teaching. 1-9 Credit Hours.

This course consists of teaching medical or dental biochemistry under close supervision of instructors. Management of small conference teaching groups as well as formal lecture presentations will be included.

BIOC 6098. Thesis. 1-12 Credit Hours.

Registration for a least one term is required of M.S. candidates.