Instructors: Guo-Liang Wang and Eric Stockinger

Click below to download handouts and reference papers as PDF files

One slides/page lecture notes

Four slides/page lecture notes

Reference paper 1

Reference paper 2

Course Video

Printed copies of handouts will not be provided in class. Please print out your own handouts.

Study questions

1. What are the differences between protein domains and protein motifs?

2. List two methods used to separate proteins from complex mixtures of proteins.

3. In two-dimensional polyacrylamide gel electrophoresis what physical properties of proteins allow them to be separated proteins in: (a) the first dimension and (b) the second dimension? What is the isoelectric point of a protein?

4. Using chromatography and a polar stationary phase matrix, which molecules separate in the matrix, the polar ones or the nonpolar ones?

5. Name three technologies that could be used to find the interacting partner protein of your favorite protein. Outline the key steps in an experiment using one of those three technologies to find the partner or target of your favorite protein.

6. At what residues does trypsin cleave the peptide bond? What does it mean to translate all ETS into conceptual protein? Is it possible to predict where trypsin would cleave a conceptual protein? Is it possible to predict the masses of trypsin-digested conceptual proteins? Can you explain how you might find the gene encoding a protein for a peptide that you identified by mass spec?

7. What is an epitope tag? What is the main advantage of the two step TAP-Tag purification scheme over that of a single tag, single step purification scheme? (Explained in Gavin et. al., 2010)

8. In the simplest of terms, state what a protein-protein hub is and what a protein-protein bottleneck is (explained in Dietz et. al, 2011).