BIOC30090

Part 1: This module builds on material covered in stage 2 to further understand the structure and function of proteins and enzymes. Lectures 1-6: Basic concepts of protein structure are discussed. The use of 1D and 2D NMR to determine the structure of peptides and proteins is explained. The relative merits of NMR spectroscopic approaches are assessed. The 1D, 2D, COSY, TOCSY, DQFCOSY and other related NMR methods will be discussed in detail. Biochemical methods for examining protein-protein, protein-ligand and protein-DNA interactions are explained.

Part 2: Lectures 1-4: Protein Post-translational Modifications (PTMs) and Protein Trafficking: Students will be taught about the different types of protein PTMs performed in eukaryotic and prokaryotic cells, the enzymes responsible, cellular locations, function and role in disease in drug development.       
Lecture 1: Overview of Eukaryotic and Prokaryotic PTMs (e.g., lipidation (lipoproteins), glycosylation (glycoproteins), phosphorylation, acetylation, methylation, proteolysis). The different types and functions of PTMs in eukaryotic and prokaryotic organisms (e.g. localization, activity, stability, structure/folding, epigenetic regulation, signaling, degradation)
Lecture 2: PTM specificity (e.g. signal peptides, cleavage sites and motifs), location (e.g. ribosome, membranes, cytoplasm, ER, Golgi) and enzyme cascades (e.g.  protein kinases/phosphatases, acetyltransferases/methyltransferases, proteases) 
Lecture 3: Marking proteins for degradation. Ubiquitination - Ubiquitin protein, types of ubiquitination, enzyme cascade, proteasome, p97) 
Lecture 4: PTMs in disease and drug development (cancer, infections, chemotherapeutics, antibiotics) 
Lectures 5-7: Protein Engineering and biotechnology (What is it? How is it done? Why?) Students will be taught about protein engineering in biotechnology, why we perform protein engineering, the different types and methodologies and how protein engineering can be utilized to solve problems,   
Lecture 5: What properties can be engineered and why (Thermostability, pH stability/optimization, catalysis, specificity
Lecture 6: How are proteins engineering? (Directed evolution, rational design, de novo protein design, fusion proteins)
Lecture 7: Examples of and bottlenecks in novel protein design (Designing new proteins with unique functions)

Part 3: Lectures 1-6: The following aspects of enzymology are introduced: Catalysts & enzymes (Enzymes as catalysts, Energy balance & thermodynamics); Enzyme kinetics (How do me measure reaction rate? Reaction order); Transition State Theory & the Michaelis-Menten equation); Enzyme inhibitors (Inhibitors as research tools and therapeutic agents; Competitive, Uncompetitive, and Non-competitive inhibition; Inhibition constant & IC50 values); Influence of pH on enzyme chemistry (Intermolecular bonds in proteins, Types of catalytic mechanisms, A detailed look at the mechanism of chymotrypsin)

Part 4: Lectures 7-9: The following aspects of protein interactions are introduced: Protein-protein interactions (Bonding in protein interactions; Measuring protein interactions); Protein-ligand interactions (Drug and inhibitor molecules; Measuring protein-ligand affinity); Protein-DNA interactions (Transcription factors & protein folding); Antibodies & therapy (Antibody structure, function, & uses)