Graph the given clearly and answer the question 2. Roughly sketch the hydropathy plot for the given hypothetical membrane protein. Follow the colorassignments of the helical domains and properly label your plot and axes (NB: Only a rough sketch isbeing asked. No need be exact with the hydropathy indices and residue numbers). Hydropathy Plots10501001502002503↑HydrophobicHydrophilicAminoterminusOutside-31050100150200250Residue numberBacteriorhodopsinInsideCarboxylterminusHydropathy index

The amino acids can be classified based on the polarity of the side chains to form a scale called…

Answered: 2. Roughly sketch the hydropathy plot…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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Create a ROUGH SKETCH (no need for exact hydropathy indices and residue numbers) of the hydropathy plot for the given membrane protein. -coo Please follow the color assignment of the helical domains and properly label the plot and axes. Here is an example: Amino Outside terminus Transmembrane helices are predicted by hydrophobic stretches of 20-25 aa residues 10 50 100 150 200 250 Hydrophobic Inside Hydrophilic Carboxyl terminus -3 10 50 100 150 200 250 Residue number Bacteriorhodopsin Hydropathy index
Bacteriorhodopsin is an integral membrane protein containing 248 amino acids. X- ray analysis of this protein reveals that it consists of seven parallel a-helical segments, each of which traverses the bacterial cell membrane. Calculate the minimum number of amino acid residues necessary for a single a-helical segment to completely traverse the bacterial cell membrane (assume the membrane has a thickness of 4.1 nm). (a) (b) Estimate the fraction of the bacteriorhodopsin protein that is involved in membrane-spanning helices.
Membrane-spanning proteins are notoriously difficult to characterize by x-ray crystallography. Hollonut of VISA Toplon a. Explain how the information in the diagrams below can be used in the detection of membrane- spanning proteins consisting of alpha helices, given that the lipid portion of a typical bilayer is approximately 30 Å thick. Amino terminus 5.4 A (3.6 residues) b. Identify and briefly describe how the features of a transmembrane protein composed of ß-sheets differ from that above.
1. In Gel filtration chromatography, when will you stop collecting eluents if sample is not colored? 2. How does SDS-PAGE separate proteins and peptides from each other? Explain. 3. Explain the Donnan Membrane Phenomenon. Why is it important for the homeostasis of the cell?
1. The CFTR protein is a chloride channel in the cell membrane. Use your understanding of the biochemical properties/categories of amino acids and how they interact with membrane phospholipids to predict the distribution of charged/polar, and non-polar amino acids within the domains of CFTR listed below. Consider one category to include the charged amino acids and the polar amino acids and the other category to include the non-polar amino acids. For each domain, predict which category of amino acids is likely to be most abundant. Also, explain the rationale behind your prediction. Protein domain Prediction (Charged/Polar or Non-Polar amino acids?) Explanation for prediction TMD1 and TMD2 (transmembrane domains, parts 1-12) ECLs and ICLs (extracellular and intracellular loops) NBD1 and NBD2 R
4. Deducing quaternary structure via SDS-PAGE. SDS-PAGE is a convenient method for separating polypeptides solely on the basis of size. Small polypeptides travel faster than large ones; rate of migration through the gel is inversely proportional to the logarithm of molecular weight. The subunit structure of a multimeric protein often can be deduced using this technique in conjunction with a protein cross-linking agent. Cross-linking agents react with amino acid residues of two polypeptides that are in contact, thereby linking them by covalent bonds. After limited treatment with the reagent, so that some but not all subunits become cross-linked to their neighbors, the protein is subjected to SDS-PAGE and the molecular weights of the resulting proteins (bands) are estimated. The results of such experiments on two proteins (Protein A and Protein B) are shown below. What is the most likely subunit structure of each protein? Protein A SDS-PAGE cross-linking agent MW 105,000 70,000 35,000…
7. Specificity of membrane transporters. A protein that transports amino acids across the cell membrane was found to bind only a few amino acids efficiently. To find the specificity, many different amino acids and substrate analogs were used as competitive inhibitors in transport studies at pH 5.9 with L-histidine (Km = 10 μM). The Ki values calculated from Lineweaver-Burk plots are shown in the table below. Comparing the structures of L-histidine and the competitive inhibitors (for which most of them, you should know their structures!), what can you conclude about the characteristics of molecules that this transport protein binds at its active site? K; (10-€ M) Amino acid or analog L-Lys L-Arg Gly L-Asp D-His Histamine Dehydrourocanate D-Arg 2 3 285 450 340 390 285 355 HN- + HN + Structure -ΝΗ -NH3 histamine ΝΗ -COO™ dehydrourocanate
Researchers have discovered a new membrane protein that has three transmembrane domain αhelixes that span the lipid bilayer.a. If the lipid bilayer is 30 Å thick, what is the smallest number of amino acid residues thatcan be in each α-helixes for them to be long enough to span the bilayer?
1. Consider the following α helix from myoglobin at pH 7. Gln-Gly-Ala-Met-Asn-Lys-Ala-Leu-Glu-His-Phe-Arg-Lys-Asp-Ile-Ala-Ala-Lys-Tyr(a) Label amino acids in the polypeptide above as follows: p for polar and uncharged, np for non polar, – for negatively charged, and + for positively charged.(b) How many complete turns are there in this helix?(b) Which side chains are likely to be on the side of the helix that faces the aqueous solvent? Why?(c) Which side chains are likely to face the interior of the protein? Why?
1 Among the given statements, which ones describe an alpha helix? Select the correct response(s): a. Ten turns of the helix will have 40 amino acid residues. b. It has a corkscrew shape that is sinistral in nature. c. It is represented by an arrow in protein caricature. d. It has a corkscrew shape that is dextral in nature. e. Ten turns of the helix will cover a distance of 5.4 nanometers. f. It is represented by an looped string in protein caricature. g. Ten turns of the helix will have 10 H-bonds
4. The table below describes a procedure in preparing standard solutions of a protein sample with different concentrations. (A) Determine the concentrations of each tube if the starting concentration of the protein is 500 mg ml (B) Determine the equation of the line if the concentration (x-axis) was plotted vs the absorbance (y-axis). (C) What is the concentration, in mg ml of the diluted unknown protein sample if the absorbance at 595 nm is 0.333? Tube Volume of protein, Volume of water, Final concentration, Absorbance mL mL mg ml [at 595 nm) 1 0.00 5.00 0.113 2 0.70 4.30 0.184 3 1.40 3.80 0.251 14 2.10 2.90 0.329 2.80 2.20 0.385 3.50 1.50 0.454 7 4.20 0.80 0.503 5.00 0.00 0.577
Your research advisor would like you to measure the movement of a protein X using FRAP. The results of your FRAP experiment are shown below. What can you conclude? Fluorescence Intensity (Arbitrary Units) Time (Seconds) Time point of exposure to an intense laser Protein X appears to be completely immobilized in the membrane Protein X appears to be partially immobilized in the membrane You cannot make predictions about the mobility of Protein X with these data Protein X appears to be completely mobile in the membrane

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2. Roughly sketch the hydropathy plot for the given hypothetical membrane protein. Follow the color assignments of the helical domains and properly label your plot and axes (NB: Only a rough sketch is being asked. No need be exact with the hydropathy indices and residue numbers). CO-