### Characterization of Membrane-Spanning Proteins*Membrane-spanning proteins* are notoriously difficult to characterize by x-ray crystallography.#### a. Detection of Membrane-Spanning Proteins**Question:** 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.**Diagram Explanation:** - The diagram depicts an alpha helix structure with an amino terminus.- It shows the repeating structure of an alpha helix with spacing marked as 5.4 Å, which corresponds to 3.6 residues per turn.**Analysis:** This information assists in identifying proteins that can span the lipid bilayer. Given the typical thickness of 30 Å for the lipid bilayer, the periodic nature of the alpha helix structure can be used to calculate how many turns or residues of an alpha helix are necessary to span the membrane.#### b. Features of Transmembrane Proteins with β-Sheets**Question:** Identify and briefly describe how the features of a transmembrane protein composed of β-sheets differ from that above.**Analysis:**- β-sheets differ in structure from alpha helices as they involve extended strands that can form broader sheets through hydrogen bonding.- In the context of transmembrane proteins, β-sheets will form a barrel-like structure (β-barrel) to traverse the lipid bilayer, differing from the cylindrical helices of alpha helices.- These sheets provide a different mode of spanning the membrane due to their distinct arrangement and bonding, affecting how they fit within the lipid bilayer.### ConclusionUnderstanding these structural differences is crucial for characterizing the membrane-spanning regions of proteins, which has implications for their functional roles and for biotechnological applications.

The biological membranes consist of a bi-layer of phospholipid molecules.In addition, there membrane…

Answered: Membrane-spanning proteins are…

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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which in is the best method for separating proteins A and B that have the properties below: Protein A: a tetramer of identical 80kDa subunits with a pl of 6.4 Protein B: a monomeric protein with a MW of 80kDa and a pl of 9.2 A.) Anion exchange chromatography at pH 11 B.) Gel exclusion chromatography C.) Cation exchange chromatography at pH 4 D. Cation exchange chromatography at pH 11 E.) SDS-PAGE
(a) 1 Normalized fluorescence 0.8 0.6 0.4 0.2 0 1.7.0- 50 55 OM 0.100 M 0.200 M 0.300 M 0.500 M 1.00 M 2.00 M Where is fully folded protein? • Where is fully unfolded protein? • Where is partially folded protein? 60 A 65 Temp. (°C) 70 75 80 To what does SYPRO orange bind? • Why does fluorescence increase as a function of temperature? • Define a melting temperature for a protein. • Demonstrate how an estimated melting temperature of the protein in zero molar ligand can be determined. • What is the effect of increasing the molar concentration on melting temperature for this protein? Why is melting temperature a useful measurement to make for a protein especially if you are interested in protein aggregation?
The amide hydrogen atoms of peptide bonds within proteins can exchange with protons in the solvent. In general, amide hydrogen atoms in buried regions of proteins and protein complexes exchange more slowly than those on the solvent-accessible surface do. Determination of these rates can be used to explore the proteinfolding reaction, probe the tertiary structure of proteins, and identify the regions of protein–protein interfaces. These exchange reactions can be followed by studying the behavior of the protein in solvent that has been labeled with deuterium ( ²H), a stable isotope of hydrogen. What two methods described in this chapter could be readily applied to the study of hydrogen– deuterium exchange rates in proteins?
Hydrogen bonds are usually 2.7-3.3 angstrom long. According to this information, do you think there is a direct hydrogen bonding between H840 and the phosphodiester bond that links dG13 and dT14 (Chain C)? If not, what is the key role of H840 in Cas9?
Is there more than one subunit shown? Is your protein bound to anything else? Describe the secondary structures you see.
Describe how you might extract membrane proteins from a mouse cell culture without using a commercial kit. Your proposal should take into account that the membrane protein sample extracted should be compatible with a subsequent purification step involving ion exchange chromatography. Justify your choices of extraction steps and reagents that you might use.
Which of the peptide sequences below best matches the hydropathy plot shown? L 10 Residue Number 4 2 Hydropathy value -2 0 セー RAFLILFMTYFLILFLI ILYYAGSREDHSGYLIL OLHGDQNRERDGHSQERD EQSDTERNQHGALIYLI 01 5 15
PLEASE have the following and help D:. What i need for the chosen of 2/3 choices. 2) Illustrate detailed chemical scheme for how you will functionalize your biomolecule to the surface of the sensor (e.g. if you wanted to functionalize a protein to a gold SPR chip, you should could show the assembly of an amine-terminated SAM, followed by carbodiimide coupling of. the protein). These schemes should be drawn using a chemical illustration software package (ChemDraw / ChemSketch).Your chemical schemes should be as detailed as necessary to accurately depict the chemical design of your system, DO NOT INCLUDE a step-wise mechanism, it is not necessary. You should include at least one literature reference to support your conjugation strategy.3) Include an illustration of the functional sensor, and describe whether the sensor is label-free or not, what signal is observed, and how you would detect the interaction (i.e. if a labeled antibody is required, you should describe what label would…
Which positions can tolerate conservative substitution?
a and b please
Please help with part 3 and 4
Peptide 1: QAMGRAGDLKYLGLHSV Peptide 2: ALMALFMVMALVLVSVLFIA Peptide 3: MVEDLLKQIARYLISE Which of these peptides would be most likely to be found as an a helix in a soluble (cytoplasmic) protein? Which would be most likely to be found as an a helix in a transmembrane protein? Which would be least likely to form an a helix of any kind? Briefly explain your answers.

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