Barry L. Stoddard
Overview of general principles of protein structure, including forces that contribute to folding and stabilization, followed by an extended coverage of the means by which protein structure and function are modified and regulated. Examples from recent developments in protein folding, processing, and allosteric regulation. Prerequisite: introductory biochemistry and cell biology.
Offered first five weeks of winter quarter (in 2010: T/Th Jan. 5 to Feb. 4)
As undergraduates, we all learned the basic 'Central Dogma' of biology: DNA --> RNA --> Proteins. However, this pathway serves as the initial foundation for a subsequent, massive diversification of protein structures, biochemical properties and activities, allowing the eventual development of complex single-cell and multicellular organisms from a relatively small number of genes (typically somewhere between 2 to 5 thousand for prokaryotes; 6 to 30 thousand for eukaryotes). This diversification is particularly critical for the assembly of cells into functional tissues and organs and complex biological systems. In this ConJoint module, we discuss a variety of strategies for the modification, diversification and regulation of protein structure and activity, including alteration of backbone connectivities and primary sequence, elaboration of protein folds, alteration of side chain chemistries, and regulation via ligand binding.
The course will assume knowledge at the level of an advanced undergraduate biochemistry course. Background and understanding in the areas we will discuss at the level of Stryer, Biochemistry or Alberts, Molecular Biology of the Cell will be assumed.
Student learning goals
Principles of protein fold classification, protein stability and dynamics, and protein chemical modifications
Application of web-based tools of protein structural analysis to current problems in protein structure/function analyses
Analysis and discussion of current primary literature for several problems in protein structure/function relationships
General method of instruction
Discussion of chosen papers from the primary literature
Question and answer times
Discussion of in-class and/or out-of-class problems and assignments
Undergraduate class in basic biochemistry
Understanding of basic chemical principles of protein structure (peptide bonds, side chain chemistries, steric principles of noncovalent interactions)
Class assignments and grading
A series of take-home problems involving use of web-based analytical tools and a single final take-home assignment involving the use of these tools and of the topics discussed during the class for the purpose of assigning functional roles to uncharacterized protein sequences.
In class participation, preparedness and completion of all assignments