Ph.D. Courses

Graduate Biochemistry
5 semester hours
3 lectures/week

 Fall  

This is an 8 week introduction to fundamental topics in biochemistry and physical biochemistry. Topics include: protein structure, folding, and function, nucleic acid structure and protein-DNA interactions, carbohydrates & glycoproteins, lipids & membranes, enzymology, energetics & allostery, posttranslational modification of protein function, transcription, translation, and DNA replication. The course also covers some aspects of basic metabolism (glycolysis and the citric acid cycle). The material is presented in formal lectures in conjunction with a structure-based macromolecules project that includes an oral presentation, discussion sessions, and reading of the literature.

Dr. Jon Lai

Human Metabolism: Regulation & Disease 

3 semester hours
2 lectures/week

Spring  

The goal of Human Metabolism: Regulation and Disease is to provide students with an understanding of the principles of the interrelated pathways of human metabolism and the ability to apply those principles to discussion of the pathophysiology and the design of new therapies for human disease. The course combines lecture, self-study and weekly small group student-led discussions of contemporary literature relevant to the lecture topics. 

Dr. Maureen Charron

Computational Biology of Protein 
3 semester hours
2 lectures/week

 

An introductory course to Protein Bioinformatics. We provide a systematic introduction to the major techniques, algorithms and tools used in Bioinformatics (for sequence alignments, classifications, secondary and tertiary structure predictions, modeling, sampling of conformations, energy functions, prediction of various functional and structural features of proteins, docking etc.).

Dr. Andras Fiser 

NMR for Chemistry & Enzymology  

3 Semester hours 

2 Lectures/week 

The course will provide a gentle introduction to basic NMR theory, and a more thorough treatment of the application of NMR to solving biochemical problems. Topics will include one-, two-, and possibly 3-dimensional methods applied to: the covalent structure and conformation of small molecules and macromolecules, ligand binding and exchange rates, pKa values, and enzyme mechanisms. Three weekly discussion sessions based on assigned readings will be combined with hands-on sessions in the NMR lab, where students will be assigned projects to be completed on the NMR spectrometers. 

Dr. David Cowburn
Dr. Sean Cahill 

Gene Expression: Beyond the Double Helix 
3 semester hours
2 lectures/week

Fall  

This course deals with molecular mechanisms of biological information content. Specifically, the course will tackle the question of how the information contained within DNA, RNA, and chromatin is stored and used in different biological contexts. The major focus is on the molecular mechanisms of the regulation of gene expression and their impact on cellular functions. Topics include: the genome and DNA, the biochemistry of DNA transcription into RNA, biochemistry of chromatin and the histone code, regulation of transcription and of chromatin structure, its modification and role in epigenetic phenomena; metabolism of the major cellular classes of RNA, emphasizing transcription, processing, 

stability/degradation, and translation of messenger RNA into protein and control at each of these steps; the role of RNA-mediated catalysis in biology and evolution; the biology and biochemistry of non-coding RNA and the use of RNAi as an experimental and therapeutic tool. 

Dr. David Shechter
Dr. Matt Gamble 

Mechanisms of Enzymes Targeted by Drugs 
3 semester hours
2 lectures/week

Spring  

Methods used to probe the chemical mechanisms of enzyme-catalyzed reactions; mechanistic dissection of specific enzymes targeted by drugs; new enzyme targets with therapeutic potential; drug discovery and drug design 

Dr. John Blanchard
Dr. Vern Schramm