Course Descriptions

Core Curriculum – Genes
Fall 1st half
2.0 credit hours
Instruction includes molecular genetics of model organisms; DNA replication, repair and recombination; transcription; RNA catalysis, processing and interference; translation; protein turnover; developmental biology; and genomics.

Core Curriculum – Proteins
Fall 1st half
2.0 credit hours
Instruction includes the energetic basis of protein structure; stability; ligand binding and regulation; enzyme mechanics and kinetics; methods of purification; and analysis by spectroscopic methods.

Protein Structure and Folding
Fall 2nd half
2.0 credit hours
This course is an overview of the basic principles governing protein structure and folding. Topics include stereochemical mechanisms by which protein secondary and tertiary structures are generated and stabilized, methods of prediction of tertiary structure from amino acid sequence, and the organization of folding motifs into protein structures. Instruction will be based on didactic material, discussion of the primary literature, and student projects utilizing computer graphics.

Quantitative Biology I
Spring 1st half
1.5 credit hours
This course explores the quantitative understanding of biological regulatory networks by considering (1) their experimental analysis, (2) their depiction by creation of explicit physical models, (3) reduction of the physical models of mathematical models, and (4) the use of the mathematical models to provide mechanistic understanding and drive new and more effective experiments.

The course deals mostly with strategy of modeling process and analysis of simple reactions (first- and second-order chemical reactions, diffusion, equilibrium, and steady-state systems) and their combination into small signaling modules, with some underlying techniques for working with quantitative data. This course is a prerequisite for Quantitative Biology II.

Professionalism, Responsible Conduct of Research, and Ethics I
Fall full semester
1.0 credit hour
Topics covered through lectures and small group discussions: goals of education in RCR; professionalism; collaboration; teambuilding and professional behaviors; everyday practice of ethical science; mentorship; data management and reproducibility; animal research; genetics and human research.

Professionalism, Responsible Conduct of Research, and Ethics II
Spring full semester
1.0 credit hour
Topics covered through lectures and small group discussions: codes of ethics and misconduct; building inter-professional teams; conflict of interest; sexual boundaries and professional behavior; applications of genetic testing; technology transfer and intellectual property; plagiarism, authorship, and citation; Peer review; image and data manipulation.

Recommended

Core Curriculum – Cells
Fall 2^nd half
2.0 credit hours
Instruction includes cell structure; membrane biology; intracellular membrane and protein trafficking; energy conversion; signal transduction and second messengers; cytoskeleton; cell cycle; and introductory material in microbiology, immunology, and neurobiology.

Electives

See degree plan (page 2) for specific elective requirements.

Modern Methods in Structural Biology
Spring 1st half
1.5 credit hours
Much of modern structural biology is based on results obtained with two high-resolution methods (X-ray crystallography, NMR spectroscopy), often complemented by several lower-resolution approaches (EM, scattering, FRET, among others). We assert that the successful union of these general approaches is absolutely critical in modern structural biology, particularly as biophysical methods are applied to larger, multicomponent systems that are often dynamic in their composition. This course provides the foundation for students to understand these techniques, extending the introduction provided in the first year Core Course. A central focus for the course will be discussions of both the theory and application of X-ray crystallography and NMR spectroscopy, with the aim to establish the physical bases of both methods using instruction that covers theory and application. Combined with introductions into the lower-resolution methods, this course will provide students with the ability to critically evaluate the relative strengths and weaknesses of each technique and how they can be combined to provide insight into biological systems.

Spectroscopy
Spring 2nd half
1.5 credit hours
Covers optical spectroscopy with emphasis on applications in biomedical research. including interaction of light and matter, absorption spectroscopies (UV/vis and infrared), fluorescence, and circular dichroism.

Computational Approaches in Protein Science
Spring 1st half
1.5 credit hours
The basics of computational methods used to analyze protein sequences and structures. Topics include sequence similarity searches using profile-based tools, functional prediction, structure prediction and threading, homology modeling, energy-based simulations, protein classification, and evolutionary concepts: homology inference and tree reconstruction.

Advanced NMR Spectroscopy
Spring 2nd half
1.5 credit hours
This course is designed to provide a strong background on biomolecular NMR spectroscopy. Topics covered include diverse practical aspects on the application of one-dimensional and multidimensional NMR techniques, protein structure determination, analysis of protein dynamics, product operator formalism, design of pulse sequences and studies of large proteins/systems. Prerequisite for this course: Modern methods in structural biology.

Quantitative Analysis of High Content/High Complexity Data Sets
Spring 2nd half
1.5 credit hours
The goal of this course is to teach students about how high content / high complexity data sets are generated and analyzed to extract information, and how the information is analyzed and integrated to generate knowledge. The course will begin with an overview of the types of high content data sets generated from a variety of discovery platforms (i.e., genomics, proteomics, metabolomics, imaging, structure), the information they include, and their architecture. Additional introductory lectures will cover data preprocessing (focusing on quality control and reproducibility) and the basics of high content data set analyses. Once the student has had a solid introduction, specific examples of the types of data and analyses associated with the various discovery platforms will be studied and discussed. The course will conclude with specific approaches to data analysis and integration. During the course, the students will be exposed to programming languages, such as R and its statistical packages, as well as a variety of bioinformatic tools that are available on the internet. The course material will include theoretical and conceptual, as well as practical and applied, presentations.

Physical Biochemistry I
Fall 2nd half
2.0 credit hours
This course will provide an advanced look at multiple aspects of biochemistry, including protein analysis, mass spectrometry, equilibria, specificity, cooperativity, and regulation of macromolecular interactions, sedimentation velocity and equilibrium analysis, and related topics. These principles will be illustrated by the study of well-characterized examples from the literature. The course emphasizes quantitative analysis and reading and discussion of the primary literature.

Physical Biochemistry II
Spring 1st half
1.5 credit hours
This course is designed to provide students with a basic understanding of enzyme mechanism and enzyme kinetic analysis. Topics to be covered include basic Michaelis-Menten kinetics, multisubstrate reactions and inhibitor studies ranging from the methods to analyze simple competitive inhibitors to suicide or tight binding inhibitors. These principles will be illustrated for a series of classic well-characterized enzyme reactions. The course emphasizes quantitative analysis through a series of problem sets and through reading and discussion of the primary literature.

Practical X-Ray Crystallography
Spring 2nd half
1.5 credit hours
Practical X-ray Crystallography will mix lectures and hands-on tutorials, with the goal of providing beginners in the discipline the tools to move forward confidently on crystallographic projects of their own. In the tutorial section, students will grow protein crystals, collect and process X-ray diffraction data, solve the phase problem using both molecular replacement and anomalous diffraction, build protein models, refine the model, analyze the model, and learn effective model presentation. Students will be tutored in the use of state-of-the-art crystallographic software. In the lectures, the principles behind the methods will be discussed. Prerequisite for this course: Modern methods in structural biology. Recommended prerequisite: Protein Structure and Folding.

Quantitative Biology II
Spring 2nd half
1.5 credit hours
Quantitative Biology I is a prerequisite to this course. The course includes approaches to dealing with larger, complex and/or non-linear systems: building complex behaviors from simple components, appearance of non-linear systems and their analysis, some theoretical approaches to complex systems and to parameterizing large, complex and/or non¬linear models. This section includes some teleological discussion of the biological (functional and evolutionary) utilities of complex or non-linear systems.