6. You discover a new transmembrane ion channel and upon structural characterization you demonstrate that it is a homo-tetramer, in which each subunit possess 2 transmembrane a- perpendicular to the plane of the membrane and 20 amino acid residues are embedded in the lipid bilayer. a. Estimate the thickness of the membrane lipid bilayer. b. If the homotetramer has MW of 70 KDa, what percent of its mass would reside in the membrane-spanning portion? c. Upon conformational change one of the two helices in each subunit tilts to 45 degrees within the membrane in respect to the plane. How many amino acids in this helix are embedded in the membrane after the transition? d. What percent of the ion channel mass reside in the membrane-spanning portion after the conformational change occurs? e. Transmembrane pores and channels can also be formed by proteins that form B-barrel structures. B-barrels are constituted by ß-strands that spans the entire membrane. Assuming that these B-strands are perpendicular to the plane of the membrane, how many residues must a B-strand have to span the lipid bilayer? "

6. You discover a new transmembrane ion channel and upon structural characterization you demonstrate that it is a homo-tetramer, in which each subunit possess 2 transmembrane a- perpendicular to the plane of the membrane and 20 amino acid residues are embedded in the lipid bilayer. a. Estimate the thickness of the membrane lipid bilayer. b. If the homotetramer has MW of 70 KDa, what percent of its mass would reside in the membrane-spanning portion? c. Upon conformational change one of the two helices in each subunit tilts to 45 degrees within the membrane in respect to the plane. How many amino acids in this helix are embedded in the membrane after the transition? d. What percent of the ion channel mass reside in the membrane-spanning portion after the conformational change occurs? e. Transmembrane pores and channels can also be formed by proteins that form B-barrel structures. B-barrels are constituted by ß-strands that spans the entire membrane. Assuming that these B-strands are perpendicular to the plane of the membrane, how many residues must a B-strand have to span the lipid bilayer? "

Biology: The Dynamic Science (MindTap Course List)

4th Edition

ISBN:9781305389892

Author:Peter J. Russell, Paul E. Hertz, Beverly McMillan

Publisher:Peter J. Russell, Paul E. Hertz, Beverly McMillan

Chapter5: Membranes And Transport

Section: Chapter Questions

Problem 3TYK: The freeze-fracture technique demonstrated: a. that the plasma membrane is a bilayer with individual...

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1. 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 that can be in each α-helixes for them to be long enough to span the bilayer? b. If one of the three α-helixes is titled at a 32° angle relative to an axis perpendicular to the surface of the lipid bilayer, what is the smaller number of amino acid helixes required for that helix to still span the lipid bilayer? c. How many hydrogen bonding interactions would there be in the smallest possible tilted transmembrane α-helix? d. If the tilted α-helix was a 310 helix instead how many amino acid residues would be required to span the lipid bilayer? How many amino acid residues would be required if it was a π-helix?
Distinguish between transmembrane proteins, integral proteins, and peripheral proteins. 7. Integral proteins are often found spanning the membrane of a cell or organelle. These proteins serve as channels for specific molecules to travel through the membrane, either into or out of the cell. Indicate on the picture of the integral protein where you would most likely find amino acids with hydrophobic R-groups. Next, indicate on the picture of the integral protein where you would most likely find amino acids with hydrophilic R-groups. Explain your reasoning.
The lipid portion of a typical bilayer is about 30 Å thick. (a) Calculate the minimum number of residues in an a-helix required to span this distance. (b) Calculate the minimum number of residues in a B-strand required to span this distance. (c) Explain why a-helices are most commonly observed in transmembrane protein sequences when the distance from one side of a membrane to the other can be spanned by significantly fewer amino acids in a B-strand conformation. (d) The epidermal growth factor receptor has a single transmembrane helix. Find it in this partial sequence: .RGPKIPSIATGMVGALLLLVVALGIGILFMRRRH..
3. Some proteins are membrane bound and have segments (called transmembrane domains) that pass through the membrane and anchor the protein to the lipid bilayer. Predict which amino acid residues are likely found in the transmembrane domains of proteins, and which amino acid residues are likely found just at the membrane surface on the interior and exterior of the cell. Succinctly explain your rationale.
+H₂N-CH-COO™ 1 CH₂ I CH₂ 1 CH₂ I +H₂N-CH₂ A. amino acid D O amino acid B amino acid C O amino acid A +H₂N-CH-COO™ 1 amino acid E C=O B. Of the four amino acids shown, this amino acid would most likely be located in the transmembrane domain of an integral membrane protein. +H₂N-CH-COO™ 1 CH₂ 1 OH C. +H₂N-CH-COO™ I CH H₂C CH₂ D.
Name the three major assumptions made by the "Cell theory". (i) The lipid membrane is composed of lipid molecules. Explain the principle of membrane formation highlighting the role of the physical properties of the lipids. (ii) Comparing dimensions and length scales is often a first step in an analysis. Give an approximate value for the thickness of a lipid bilayer and the linear length of a helical turn of a DNA double helix. A technician wants to amplify DNA from a patient sample. However, the lab is not equipped with a thermocycler. (i) (ii) Name two methods for DNA amplification that can be operated at constant temperature and give their acronyms. Explain these two methods in detail using a schematic and name all necessary components that are required to perform the amplification. Describe the main function of the middle ear. Highlight the role of the ossicles and the tympanic membrane.
The lipid portion of a typical bilayer is about 30 Å thick. (a) Calculate the minimum number of residues in an α-helix required tospan this distance. (b) Calculate the minimum number of residues in a β-strand required to span this distance. (c) Explain why α-helices are most commonly observed in transmembrane protein sequences when the distance from one side of a membrane to the other can be spanned by significantly fewer amino acids in aβ-strand conformation. (d) The epidermal growth factor receptor has a single transmembrane helix. Find it in this partial sequence: . . . RGPKIPSIATGMVGALLLLVVALGIGILFMRRRH . .
Ion channels are formed by a particular kind of membrane protein that allows the passage of a specific ion (or ions) under certain conditions. This type of protein is most likely a(n) a. peripheral membrane protein with additional hydrophobic domains b. integral membrane protein with a transmembrane domain c. a cholesterol-like molecule that is positioned in the phospholipid bilayer d. membrane phospholipid with hydrophilic head group e. soluble enzyme anchored to a scaffolding protein on the cytoplasmic side of the plasma membrane
10. As described by the fluid mosaic model, biological membranes contain not only phospholipids but also a variety of other molecules, particularly proteins. The overarching question I want you to consider is how proteins are structured to fulfill their interactions with and functions in cell membranes. A. First, let's just consider a single-pass transmembrane protein, which has just a single region (also called domain) crossing through the phospholipid bilayer, as diagrammed to the right. Describe which regions of this transmembrane protein are likely to be hydrophilic vs. hydrophobic. B. Briefly explain the reasoning for your responses. Outside of cell (aqueous) Inside of cell (aqueous)
Explain how the amphipathic (containing both hydrophobic and hydrophilic sides) protein (shown; left)would be anchored in the phospholipid bilayer (shown; right); which portion do you predict would besticking out towards the water? Which portion would be hiding inside the membrane?
Drawn below is a schematic of a transmembrane protein. Extracellular Cell membrane Cytosolic side (a) From the list below, select the amino acid(s) that might by more common in the extracellular domain of this membrane protein and whose side- chain can form hydrogen bonds with the surrounding water molecules. Explain why you selected this option(s). Lysine Serine Phenylalanine Methionine (b) From the list below, select the amino acid(s) that would likely be found in the transmembrane/ membrane spanning domain of this protein and whose side- chain interacts with the lipid bilayer. Lysine Serine Phenylalanine Methionine
Sequence analysis of a membrane protein shows four 20-amino acid long stretches of residues that are predominantly hydrophobic. Between each of these stretches of hydrodophobic residues, a stretch of predominantly hydrophilic residues is found. From this observation one can reasonably postulate that: A. this is a peripheral membrane protein which interacts with the membrane via hydrophobic interactions B. this protein has 4 alpha helical segments that span the membrane C. this protein can be removed from the membrane by dramatically increasing the salt concentration. D. this is a 4 stranded beta barrel which spans the membrane E. this is a glycoprotein Facilitated diffusion (passive transport) through a biological membrane is A. driven by a concentration gradient. B. generally irreversible. C. endergonic. D. driven by the ATP to ADP conversion