Chem 271 Problem Set 2 - Spring 2010

Chem 271 Problem Set 2 - Spring 2010 - Chem 271/MCB 212...

Info iconThis preview shows pages 1–5. Sign up to view the full content.

View Full Document Right Arrow Icon
Chem 271/MCB 212 Problem Set #2 Due by 5pm on February 19, 2010 1. In 2005, Jack Taunton reported a highly selective inhibitor for two kinases, RSK1 and RSK2. These kinases transfer the gamma-phosphoryl group from ATP to the hydroxyl group of ser, thr, or tyr residues. This is a particularly significant finding because it is very difficult to distinguish between the 491 kinases in the human genome using small molecules. a. The inhibitor was proposed to react with a cysteine residue that is close to the active site. Propose two different products for this reaction. b. Interestingly, the reactive cysteine residue was not part of the catalytic machinery that transfers the phosphate group. In this instance, why is it advantageous to target an ancillary amino acid instead of one that is directly involved in the catalytic reaction?
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
c. In order to find other kinases that are targeted by these compounds, a fluorescent version of the substrate was prepared. After exposing live cells to this compound, any kinases that possess the reactive cysteine would be labeled covalently and could be detected visually using gel electrophoresis. This approach was somewhat successful, but the bulky fluorescent group interfered with binding and rendered the inhibitor insoluble. As an alternative, design an approach that uses a [3+2] “Click” reaction to attach a fluorescent reporter to an inhibitor after incubation with the cells. Provide the specific structures of the compounds that you would use and the conditions under which you would carry out the conjugation reaction. d. Using similar logic, provide the structures of the inhibitor and the appropriate fluorescent reagent(s) that you would use to detect the modified kinases with the Staudinger ligation.
Background image of page 2
2. Amino acid 1 has been incorporated into proteins using the Schultz in vitro method. a. Starting with the amino acid, outline the steps that you would take to accomplish this. For the purposes of this question, assume that the artificial amino acid is not toxic and that all of the functional groups are stable in living cells and in the presence of common buffers used in biology. b. How would you incorporate this amino acid into a protein using the Residue-Specific technique (aka the Tirrell method? c. Briefly state the advantages and disadvantages of each method with respect to quantity of protein, specificity, and experimental ease.
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
d. Once this residue has been incorporated into proteins, it can be used to attach additional peptides wherever it is located. The resulting branched structures are practically impossible to prepare using traditional protein expression methods. Provide any structural features that a peptide would need to possess in order to couple to this site in high yield. e. Starting with your peptide and the protein with the artificial amino acid, provide the
Background image of page 4
Image of page 5
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 02/19/2010 for the course CHEM 271 taught by Professor Mattfrancis during the Spring '09 term at University of California, Berkeley.

Page1 / 12

Chem 271 Problem Set 2 - Spring 2010 - Chem 271/MCB 212...

This preview shows document pages 1 - 5. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online