Biochemistry PhD Program
Message From the Director
Blake Hill, PhD
Professor of Biochemistry
Director, Graduate Program in Biochemistry
Amazing discoveries in biomedical research rely on Biochemistry. Name your favorite scientific discovery in biology and it likely derived from biochemical investigations. DNA replication, GPCR signaling, DNA structure, PCR, CRISPR/Cas9, Next Gen DNA sequencing, Proteomics, other "omics": These amazing advances were made by biochemists that developed a deep understanding of the underlying mechanism behind these processes to revolutionize our thinking. At MCW Biochemistry, you will hone your critical thinking skills to solve complex problems by dissecting them into fundamental, indivisible components. You will also learn outstanding communication and presentation skills. Such critical thinking and presentation skills are useful in a wide variety of careers including scientific research. We invite you to explore the exciting, NIH-funded research of our faculty that seeks to understand the basis of a host of human illnesses from diabetes, cancer, neurodegeneration, inflammation, heart, lung, and metabolic diseases. Come join our family and see why research from MCW Biochemistry is featured in textbooks!
Biochemistry PhD Program
About the Program
02222 – Advance Protein Chemistry – 3 credits
With complete sequences for the genomes of human and many other species now available, much of the attention in molecular biological research is rapidly turning to the characterization of organism-wide collections of gene products, often referred to as functional genomics or proteomics. These efforts magnify the importance of a biochemical reductionist approach to understanding the function and activity of newly identified gene products. Just as the human genome project catalyzed generational advances in DNA sequencing technology, current trends demand improved methods for efficient cloning, production and physical characterization of recombinant proteins. Many of these proteins represent undiscovered targets for intervention in human disease, and thermodynamic and kinetic analyses of their structure, activity, and function will enable translational research in medicine and drug discovery. This course will focus on the practical aspects protein chemistry including production, identification and functional characterization with a focus on steps most commonly encountered in the development of targets for three-dimensional structural characterization and functional assays. Literature examples will be emphasized including new methods and optimization of standard approaches for high-throughput applications. Where applicable, their application to the design or discovery of novel ligands, inhibitors and lead compounds will be emphasized.
02301 – Biochemistry Seminar – 1 credit
This course gives students practice in presenting and evaluating their research data. Solutions to research problems encountered are also discussed. This course is required beginning in the second semester of the second year and continues throughout each student’s program.
02207 - Enzyme Kinetics and Receptor Binding – 1 Credit
This course covers both the theoretical framework and practical aspects of enzyme kinetics and receptor binding studies. Topics covered include basic steady state kinetics including the determination and meaning of Km and Vmax values for simple and multi-substrate reactions, determination of the binding properties and kinetic consequences of common reversible inhibitors (competitive, non-competitive, uncompetitive, mixed), slow-on, slow-off inhibitors, and irreversible inactivators. Dissociation constants and procedures for determining them will be discussed for both enzymes and macromolecular receptors. Practical methodologies for determining presteady state kinetics will be presented. Practical aspects of designing kinetic studies will be discussed and later sessions of the course will involve reading and student-led discussions of studies in the literature that illustrate ways in which studies of enzyme kinetics or receptor binding advanced the study of particular enzymes and other macromolecules. Over the 6-week duration of the course each student will prepare a short project report in which they describe the design of a series of kinetic or receptor binding studies that draw on the teachings of the course and are related to the work they propose to carry out for their dissertation.
02226A - Biophysical Techniques in Biochemistry – 3 credits
This course will introduce the basic theory and practical applications of an array of biophysical techniques commonly used in biochemical research. Optical, fluorescence, and magnetic resonance spectroscopies, x-ray crystallography, mass spectrometry and kinetics techniques are just a sampling of the topics covered in this comprehensive course.
02230A – Biomolecular NMR: Structure and Molecular Recognition – 1 credit
Nuclear magnetic resonance spectroscopy (NMR) is a powerful tool for the interrogation of biomolecular structure and interactions at atomic resolution. Structural genomics efforts have produced refinements in the methodology for three-dimensional protein structure determination, such that new structures can be solved in a matter of weeks using increasingly automated processes. This course begins with a description of the quantum mechanical basis for multidimensional NMR using the product operator formalism. This powerful operator algebra rigorously predicts the propagation of the nuclear spin wavefunction under a time-independent Hamiltonian operator governing interactions between nuclear spins and between spins and static or transient magnetic fields, enabling the development of increasingly complex pulse sequences for multidimensional, multinuclear NMR measurements of biomolecules. Simple pulse sequences for magnetization transfer and isotope editing are described using product operators and combined into more complex two- and three-dimensional pulse schemes for triple-resonance correlation of nuclei in proteins. Systematic application of these NMR methods to the sequence-specific assignment of isotopically-enriched proteins will then be linked to the interpretation of other of types NMR data (nuclear Overhauser effect; scalar and dipolar couplings) that report directly on tertiary structure. The balance of the course will consist of practical, hands-on training in basics of 2D/3D NMR data acquisition, processing and analysis, as well as interactive computer tutorials on the chemical shift assignment and 3D structure determination processes.
Pre-requisite: Biochemistry 02222 Encouraged
02235 – Biomolecular NMR: Protein Dynamics and Binding – 1 credit
NMR spectroscopy is one of the most powerful tools of contemporary structural biology. Multiple NMR applications will enable the student to do structural, thermodynamic and kinetic analyses of proteins and nucleic acids under physiological conditions with site-specific resolution. The course "Biomolecular NMR: Structure and Molecular Recognition" provides a general foundation of NMR spectroscopy and is a pre-requisite. The current course "Biomolecular NMR: Protein Dynamics and Binding" extends discussion of NMR to topics of protein dynamics, conformational transitions and ligand binding as monitored by NMR methods to extract site-specific thermodynamic and kinetic parameters.
Pre-requisite: Biochemistry 02222
02240 – Contemporary X-Ray Crystallography – 1 credit
X-ray crystallography is the main method that is used to elucidate 3-dimensional structures of macromolecules and biomolecular complexes, and capable of revealing structural details at high resolutions. Powered by modern synchrotron-based light sources and state-of-the-art computer programs, contemporary crystallographic research has provided mechanistic insights into complex cellular functions such as gene transcription and translation. While crystallographic computer programs are openly available, the use of these packages by biologists who do not have a theoretical comprehension of crystallography can be unproductive. This course is designed to teach non-crystallographers the capability to intelligently use crystallographic programs that are available in the form of bundled software. Attendees will learn systematically the central theory behind the crystallographic tools in use today, and hence grow an appreciation of the physical process that takes place during an experiment to determine the structure of a protein or nucleic acid. A central aim of this is to generate stimulating discussions that will help the students to grasp the essence of macromolecular crystallography.
02248 – Structural Basis of Macromolecular interactions – 1 credit
Biochemical functions of macromolecules are dependent on the three-dimensional (3-D) structures of such molecules. The determination of 3-D structures of proteins, nucleic acids and their complexes is therefore a necessary step in understanding mechanisms of any biomolecular system. X-ray crystallography is the main method for 3-D structure determination, capable of either low (e.g. subdomain) or high (atomic) resolution analysis. This course teaches the working knowledge necessary for carrying out X-ray diffraction experiments and uses hands-on exercises as the main format. Students will crystallize a well-known protein, practice X-ray data collection and data processing using contemporary computer programs.
02276A – Special Topics in Biochemistry: Redox Signaling and Metabolism in Cancer – 1 credit
This course will focus on the role of redox-sensitive signaling and metabolic mechanisms/pathways in neoplastic transformation. Major areas to be covered include: (a) reactive oxygen and reactive nitrogen species (ROS, RNS) as second messengers; (b) metabolic vs. non-metabolic ROS/RNS sources; (c) cellular targets of oxidative attack or modification; (d) preventative and reparative antioxidant defenses; (e) activation and regulation of redox signaling cascades; (f) proliferative vs. apoptotic signaling under oxidative pressure; (g) dysregulated redox metabolism in cancer and (h) signaling events in oxidant-based tumor therapies. Students are expected to develop an advanced understanding of various aspects of redox signaling ad metabolism in tumorigenesis through introductory lectures, outside readings, and in-class discussions.
02276A – Special Topics in Biochemistry: Mass Spectrometry in Biomedical Research – 1 credit
The overall goal of the course is to provide a comprehensive overview of how mass spectrometry can be used in modern biomedical research. This course is designed for students without prior mass spectrometry experience and will introduce fundamental concepts regarding instrumentation, experimental design, and analysis of peptides, proteins, small molecules, lipids, metabolites, and glycans.
Those interested in pursuing education and research within the Department of Biochemistry should pursue admission through either the Interdisciplinary Program in Biomedical Sciences (IDP) and/or Neuroscience Doctoral Program (NDP) as well as the Medical Scientist Training Program (MD/PhD).
After completion of the first year curriculum of that program, students who choose to complete their dissertation work with faculty of the Biochemistry Department will have the opportunity to continue their graduate studies by selecting from among a wide range of courses that are offered within the Biochemistry Department as well as other programs at MCW. Courses to be taken are based on the student's interests in consultation with the student's dissertation committee.
The Department of Biochemistry offers diverse research opportunities leading to a PhD for students interested in doing biomedical research at a molecular level.
A Bachelor’s degree (either completed or in the process of completing) is required for admission to any MCW graduate program. Applicants will ideally have a 3.0 or higher grade point average (GPA), as well as quantitative and verbal reasoning GRE scores at or above the 50th percentile (3.5 or higher writing score). Personal statements and letters of recommendation from professors, advisors, research supervisors, etc. who know you well are highly regarded in the admission process. Prior research experience is also strongly considered.
The MCW Graduate School operates on a rolling admissions basis. However, applications accepted by the priority application deadline of December 15th will receive first priority for admission the following Fall. Students are admitted once per year.
Tuition and Fees
If you have questions regarding tuition or your account, please contact the Office of Student Accounts, at (414) 955-8172 or email@example.com. Please refer to the All Student Handbook (PDF) for tuition payment policies and information.
All full-time PhD students receive a full tuition remission, health insurance and stipend.
2018-2019 Stipend: $30,011
Masters, Certificate & Non-Degree Students
Students seeking financial aid for MPH, MS or MA degree programs, visit the Financial Aid Office website.
Current MCW Employees
Tuition Course Approval Form - Human Resources (PDF)
There will be a $100 late registration fee for anyone not completing registration by the date indicated on the schedule each semester.
There is also a $250 late payment fee for tuition not paid on time according to the Tuition Payments policy in the All Student Handbook (PDF).
Late payment fee is in addition to any late registration fee.
MCW Graduate School
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