3. When you think about the primary structure of the mannose-6-P receptor, assuming that it is anintegral membrane protein with one membrane-spanning domain and assuming that it has a ERSS, whatare all of the different protein domains that must be present in this protein's primary structure to get itto where it needs to go and to carry out all of the functions/activities? (Draw a schematic of the proteinstructure/sequence and explain each region).

The internal amino acid sequences in the membrane protein carries the information that determines…

Answered: 3. When you think about the primary…

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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Would an extracellular signal receptor protein mostly likely consist of type 1 or type 2 alpha helices? Explain your reasoning
3. Consider a transmembrane protein that spans the inner nuclear membrane. Suggest a pathway by which such a protein could reach its destination. In your scheme, describe how the proposed mechanism would ensure that specific proteins are stably localized to the inner nuclear membrane whereas others are not.
5.. A sample of cells has a total receptor concentration of 25 mM. Ninety percent of the receptors have bound ligand and the concentration of free ligand is 125 µM. Calculate the K for the receptor ligand interaction. (a) What is the AG° for binding for this interaction at 25°C?
AAA is a protein found in both the cytosol as well as the nucleus. In its active state, it helps to facilitate the movement of proteins into and out of the nucleus. Specifically, AAA-alpha and AAA-beta binds to receptors on the nucleus and allows for materials to enter or exit through the channels associated with the receptors. They also play a role in dropping off cargo that import and export receptors hold onto. AAA functions are controlled by two other proteins: BBB and CCC. BBB binds onto AAA, while CCC removes BBB from AAA when they are bound. As a result, there is a BBB and CCC concentration gradient that forms between the cytosol and nucleus. During prophase I, is there a concentration gradient for BBB and CCC between the cytosol and the nucleus? Why? Is this also the case during the other phases of meiosis or the cell cycle?
6. Define a receptor tyrosine kinase and distinguish it from a serine/threonine kinase. (As we discuss ANY kinase in signalling pathways, pay close attention to what type of kinase it is...does it phosphorylate serene/threonine resides or tyrosine residues?)
9. Shown below is a binding pocket for a protein with a ligand bound. The ligand interacts with a serine and a valine side chain. ligand a. Briefly explain, in terms of Ka, the effect of a mutation that replaces the serine residue with a valine residue. b. Briefly explain, in terms of Kd, the effect of a mutation that alters the ligand (as seen below) binding to the original, unmutated, binding site. :0: ligand 2
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
1. You are working on identifying novel proteins associated with the plasma membrane and you isolate XYZ1. Protein sequencing shows XYZ1 is comprised of: MGASSCSELRSSAFALSERSDKSSAVLLIVLGVMAVGIYLLVTMVLIIGTSANRASGSKD SESMSTLECAAPNDSAA a. Based on the sequence. Do you predict this is a peripheral membrane protein or an integral membrane protein? (Hint: use the Hydropathy plot generator on Expasy using default settings to help answer this question.) b. You decide to conduct an experiment to further assess how the protein is connected to the PM. The experiment is conducted by either 1) treating intact cells with chymotrypsin, 2) by disrupting the plasma membrane such that chymotrypsin has access to both sides of the plasma membrane, or 3) by using detergents to remove all lipid bilayers and treating the proteins such that chymotrypsin will have access to -Chym. Cond. 1 - +Chym. Cond. 2 Cond. 3 the entire length of the protein. The treatments are run on an SDS-PAGE gel (together with an…

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