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Syllabus for The Biogenesis and Cell Biology of Proteins

           

 

Time: Second semester          

Designed for: undergraduate students (2nd and 3rd year)  in biology (3 points - one 2hr lecture a week + tirgul).

                       

Significance:

Every facet of cellular life and function is dependent on the proper biogenesis, directed folding, and vigilant quality control of proteins. Despite their multitude of functions, structures, and electrostatic properties, all proteins have a common feature - the necessity of maintaining "native" structural integrity enabling proper function.

Structure: The introductory part of the course will detail the cellular pathways that ensure correct protein biogenesis, starting from the basic building blocks of amino acids. We will then learn about the significant efforts expended by the cell to maintain protein folding homeostasis over the course of its lifetime. The problematic consequences of protein misfolding, and resultant protein aggregation, will also be discussed; as well as how these processes may contribute to human disease. Finally, the super-structure of protein organization in living cells will be discussed in the context of protein folding and aggregation.

Grades will be assigned based on an exam at the end of the course.




Topics that will be covered include: 


Protein Building Blocks – Amino Acids
          Functional groups of organic biomolecules
          Hydrophobic and Hydrophilic interactions
          Condensation and Hydrolysis
          The flow of genetic information

 The Basis for Protein Folding
          The Anfinsen experiment
          The Hydrophobic effect
          Cysteins and di-sulfide bonds       
           Exiting the Ribosome

 Protein Folding in the Cell
          Chaperones and Chaperonins
          Post-translational modification
          Protein folding in the ER
          Molecular crowding
          Co-translational folding and degradation

Protein Synthesis and Destruction
          The Ubiquitin-Proteasome system
          The role of protein degradation in cellular regulation (cell cycle, immune response)
          Ubiquitination of misfolded proteins

Chaperones
          Chaperone systems: CLiPs and HSPs, Hsp70, Hsp90, Hsp40, Hsp104, sHsps
          Chaperones as buffers of function
          Protein super-structures and folding together as a heteroligomeric structure




Protein Folding Quality Control
          Function of Chaperone systems in Quality Control
          Quality Control in Compartments (Cytosol, Nucleus, ER)


Cellular response to protein folding stress
           ER stress response
           Cytosolic stress response
            Oxidative stress




Proteostasis
          Global folding and marginal stability
          Folding buffers

Aggregation and Inclusions
          All proteins can aggregate
           Amyloids
            Inclusions
            Neurodegenerative Diseases
            Are inclusions toxic or protective?




Prions
           Protein fibers and functional aggregates
            Yeast prions
             Protective or harmful?




Spatial Organization of Protein Folding Quality Control
           The role of compartmentalization in quality control and survival




Techniques for Studying Proteins - Live Cell Imaging
          What can imaging do for you?
          Why live cell imaging
          Molecular dynamics imaging (FRAP, FLIP, FRET, PhAc)
          Different approaches in microscopy (Confocality, EM, Spinning Disk, Deconvolution)
          Breaking the diffraction limit

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