Course Descriptions

Instructor: DGS-Kuehn
Fall and Spring Semesters (Years 1 and 2)
In year one, you will rotate through and conduct faculty/mentor-approved research in different Biochemistry labs. If you’re in your 2^nd year, you’ll be in a thesis lab. Students are expected to be performing research when they are not in class, attend departmental seminars, keep up-to-date lab notebooks, and present oral and written summaries of their ongoing research, as appropriate for each laboratory.

Instructor: Richardsons
Not Offered Spring Semester 2023
You will learn how to get the most out of experimental and computational 3D structures including:

• 3D Molecular Literacy: computer and physical molecular models of proteins and nucleic acids, worksheets, and hands-on exploration.
• Data bases and the data itself: gaining familiarity with the Protein Data Bank (PDB); the Electron Density Server (EDS); and the peculiarities, caveats, and reliabilities of different categories of molecular data.
• Computational methods for studying and depicting macromolecules including:
  • Model building in structural biology
  • Molprobity and all-atom contact analysis and methodologies for multiple conformations, ensembles, and mobility

Projects include: interactive 3D illustrations about macromolecules using kinemages or other molecular graphics programs, often with short, non-interactive introduction. 

Instructors: Lee, Bennett, Kuehn, Rajagopal, and Yang
2^nd ½ Spring Semester
This course will highlight modern topics regarding biological membranes and membrane proteins that are important for human physiology and disease. Topics include:

• Structure and dynamics of biological membranes
• Structure, and function of membrane proteins that play critical roles in cell signaling
• Diseases related to dysfunction of membrane and membrane proteins
• Current efforts on drug discovery

Major techniques used in membrane research will also be covered. The format will be a combination of lectures and discussions of primary literature. Students will be evaluated based on their class participation and performance at the final presentations. 

Instructor: Beese
1^st ½ Fall Semester
Structure of Macromolecules – This class teaches the principles of modern structural biology including protein-nucleic acid recognition, enzymatic reactions, viruses, immunoglobulins, signal transduction, and structure-based drug design—described in terms of the atomic properties of biological macromolecules. There will be discussions on the methods of structure determination, with particular emphasis on macromolecular X-ray crystallography, Nuclear Magnetic Resonance (NMR) methods, homology modeling, and bioinformatics. You will use molecular graphics tutorials and Internet databases to view and analyze structures.

Instructor: Zhou
2^nd ½ Fall Semester
Molecular Biology I – As a continuation of BCH 658, this introductory course teaches how to use quantitative methods to understand biological structure and function. You’ll study the:

• Structure/function analysis of proteins as enzymes
• Kinetics of binding
• Catalysis and allostery
• Protein folding
• Stability
• Design protein-protein interactions

Instructor: Schumacher
Not Offered Spring Semester 2023
A major emphasis of this course is on the reading and in-depth discussion of primary research papers. You will explore how new nucleic acid biology concepts have been developed and what types of experiments have made advances possible. Each course section will consist of background lecture material presented by the faculty member, followed by several sessions to discuss paradigm papers selected by the faculty. You will do oral presentations using figures from the papers and explanatory background as needed and prepare an 8-10 page research paper or an oral talk to demonstrate proficiency in the topics of DNA and Genome Stability—Chromatin and chromosome structure, replication, repair, genetic recombination, mutation, and chromosome rearrangement.

Instructor: Meyer
Spring Semester
This course explores various aspects of RNA biology and function. Topics include:

• Splicing
• Translation
• RNA: Protein interactions
• Non-coding RNAs
• RNA modifications
• Viral RNA regulation
• RNA structure-function relationships
• RNA-targeted drug discovery

You will also learn about major techniques in RNA research, including in vitro and in vivo methods for understanding global RNA regulation. The format will be a combination of weekly lectures and discussions of primary scientific literature. You will be evaluated on your participation and performance during in-class presentations and will write a short mock research grant on a topic of your choosing.

Instructor: Oas
Fall Semester
You’ll survey the theory and application of biological techniques—based on physical principles—to understand their application in primary scientific literature. Methods covered include:

• Optical Spectroscopy
• Fluorescence
• Binding
• Light Microscopy
• Electron Microscopy
• Hydrodynamics
• Kinetic Methods
• Electrophysiology
• Magnetic Resonance
• Mass Spectrometry

Lectures on each method are presented by an expert. 

Instructor: Bartesaghi
Fall Semester
This Advanced Topics course will focus on the image analysis aspects of cryo-electron microscopy (EM), including image enhancement, reconstruction, classification, and movie processing used to determine the high-resolution structure of proteins from cryo-EM images. The course will provide an overview of the cryo-EM structure determination pipeline, focusing primarily on the data analysis aspects of the technique and covering the full breadth of reconstruction strategies.

Prerequisites: Students should have a background in either protein structure/molecular biology or computer vision/image processing.

Instructor: Al-Hashimi
Spring Semester (alternating years with BCH 696)
Aimed for students with some familiarity in high-resolution NMR, you will deepen your understanding of how NMR experiments actually work and be introduced to quantum mechanical tools that help explain pulse sequences. You’ll study advanced biomolecular NMR experiments that enable the structural and dynamic characterization of biomolecules. Roughly half the course follows online lectures that accompany the textbook, with class meetings emphasizing concepts, group discussion, and problem-solving. Instructor consent is required.

Instructor: Schumacher and Staff
Spring Semester (alternating years with BCH 695)
This course teaches the theoretical and practical principles of macromolecular X-ray crystallography. Topics include:

• Crystal symmetry
• Space group theory and determination
• Diffraction theory
• Practical understanding of crystallization
• X-ray intensity data collection and data processing
• Phase determination
• Refinement and model validation

Instructor consent is required.

Instructor: Brennan
Fall/Spring Semester
This course is a requirement of all first-, second-, and third-year biochemistry graduate students to learn how to clearly and concisely present the background, data, conclusions, and future prospects of your research in both oral and written formats. First-year students will present their rotation projects. Second and third-year students will annually present their research. All students will provide feedback so each presenter can improve presentation content and style.

Instructor: Kuehn
Fall Semester
This is a discussion-based course that includes introductory lectures and the critical reading of select topics in Biochemistry literature. Topics and instructors are announced each semester. 

Instructor: Noor
1^st ½ Fall Semester
This course is a great introduction to understanding the graduate student mindset. Weekly talks and Q&As will focus on choosing a thesis advisor, writing a grant proposal, the scientific manuscript peer review processes, and other topics related to transitioning to and being successful in graduate school. 

Instructor: Oas
Fall and Spring Semester
Each week, a student will present a paper on their research. Attendance is open to all graduate and postdoctoral students and faculty who have an interest in structural biology. All SBB certificate students are required to attend.

Instructor: McCafferty
Spring Semester
This course covers:

• Basic enzymology
• Mechanisms of enzymatic reactions
• Cofactors
• Oxidoreductases
• C1 chemistry
• Carbon-carbon bond formation
• Carboxylation/decarboxylation
• Heme
• Pyridoxal enzymes
• Thiamine enzymes

Instructor: Caron
First 1/3 Spring Semester
This module covers the basic mechanism of signal transduction through G protein-coupled receptors (GPCR) and how they control a wide array of biological functions—from vision to reproduction—and how they are the largest targets of therapeutic interventions. You will study how new concepts of signal transduction mechanisms are leading to the development of new and improved therapies for various disorders.

Instructor: McDonnell
Mid 1/3 Spring Semester
This module covers how ion channels and intracellular nuclear receptors control cellular functions, mediated through transcription or calcium signaling, to regulate physiological processes in health and disease.

Instructor: Pendergast
Last 1/3 Spring Semester
This module focuses on signaling pathways induced by extracellular factors that regulate growth, survival, and development—and their deregulation in diseases including cancer. Topics include those regulated by ligand-activated Receptor Tyrosine Kinases, Wnt/beta-catenin signaling, Notch signaling, and Hedgehog signaling.