Erik's handout #4

Erik's handout #4 - 1.) Beta-Sheets often have one side...

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1.) Beta-Sheets often have one side facing the surface of the protein and one side facing the interior, giving rise to an amphiphillic sheet with one hydrophobic surface and one hydrophilic surface. From the sequences listed below pick the one that could form a strand in a amphiphillic beta-sheet. a. A-L-S-C-D-V-E-T-Y-W-L-I b. D-K-L-V-T-S-I-A-R-E-F-M c. T-L-N-I-S-F-Q-M-E-L-D-V Correct answer is c. Beta-sheets R groups are alternating from the top to the bottom of the sheet. 2.)(T/F) Christian Anfinsen studied the protein urease, and determined that the 1° amino acid sequence contained all the information needed for the proper folding of the native 3° structure. False, he studied ribonuclease A, the denaturant he used was urea. 3.)(T/F) -Mercaptoethanol is a strong Β detergent , which can break disulfide bonds. Not a detergent 4.)(T/F) When running an SDS-PAGE analysis the smaller proteins always migrate faster towards the negative electrode on the bottom. Positive on the bottom . 5 .) (T/F) When running a 2-D gel analysis the first step is always to set up a pH gradient and then add you SDS plus your proteins. False, if you were to add sds before running your separation based on pI , you would get not results b/c you ruin the intrinsic charge of the peptide. 6.)(T/F) Detergents are amphiphillic molecules. True 7.) You are working in a lab and you isolate the lysate from a cancer cell and a non-cancer cell, you would like to determine what proteins are being expressed in the non cancer cell and you want to determine there structure. What methods could you use? Design an experiment. 2-D gel w/control, find spots that do not match -> trypsin digest, Mass Spectrometry, find fragment masses and get peptide sequence from data base -> NMR or X-ray crystallography. 8.) Name the two protein folding models and which one is correct? Hydrophobic collapse and hierarchical.both I. Free energy funnel
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a. Represents the folding pathway of a protein as it assumes its native state. b. The folding funnel hypothesis is closely related to the hydrophobic collapse hypothesis, under which the driving force for protein folding is provided by the stabilization associated with the sequestration of hydrophobic amino acid side chains in the interior of the folded protein c. The depressions on the side represent a semi-stable folding intermediate. d.
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This note was uploaded on 04/29/2010 for the course PSYCH PSYCH 179 taught by Professor Koob during the Fall '09 term at UCSD.

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Erik's handout #4 - 1.) Beta-Sheets often have one side...

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