Protein Description A 35 kDa monomer Disulfide-linked homodimer comprised of 19 kDa monomers homodimer of 38 kDa monomers B C homotrimer of 25 kDa subunits
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Given the description of four different proteins above: Which protein will have the highest mobility in an SDS-PAGE gel?
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- Protein-4YU4 is given, choose a part of it (containing at least 30 amino acid residues), find the amino acid sequence (sequence in it), identify what functional groups the amino acid substitutes contain (carboxyl group and 2-position the Nitro group will form amide bonds, forming the covalent basic structure of the protein). What different interactions can occur between these functional groups? How will it relate to the spatial structure of the protein?Hydropathy & Amphipathicity 2 -1 -2- 110 210 310 410 510 Residue Number C. Draw the topology of this membrane protein in the bilayer and indicate the range of residues forming transmembrane a-helices.CENTRAL DOGMA & STRUCTURE-FUNCTION RELATIONSHIPS IN PROTEINS You are a bacteriologist studying a pathogenic protein (the "BAD" protein) that contributes to diseases caused by Staphylococcus aureus. BAD functions as an aß heterodimer, and the a subunit (25kD) and ß subunit (75KD) are held together by an electrostatic interaction between K in the a subunit and D in the B subunit. You are trying to dissociate the BAD subunits to prevent pathogenesis in the bacteria. Which mutation would you make to prevent the BAD subunits from forming a dimer? Assume neutral pH. (A) introduce AAA → AGA point mutation in the a subunit gene (B) introduce GAC → GAG point mutation in the ß subunit gene (C) introduce GAT → CGT point mutation in the ß subunit gene (D) introduce two point mutations: AAG → GTG in the a subunit gene & GAC → CTC in the B subunit gene (E) introduce two point mutations: AAA → TGC in the a subunit gene & GAT → TGT in the B subunit gene second base in codon A TGT Cys TGC Cys TTT Phe…
- SDS-AGE analysis of protein for subunit composition: A protein has a molecular mass of 400 kDa when measured by size-exclusion chromatography (gel filtration). When subjected to gel electrophoresis in the presence of SDS only and SDS plus 2-ME, the following pattern of SDS-PAGE is observed. MM - molecular standard proteins with known molecular weight (in kDa) as shown on the left of the gel are used to determine the size of unknown proteins. a) Determine the subunit composition of this protein (i.e., how many subunits are in its quaternary structure?). MM SDS SDS 2-ME kDa 180- 160- 100- 90- 60- 50-Given: Cryo-EM structure of PCoV_GX spike glycoprotein 1. What can you tell me about the identity of the protein? 2. What is the importance of this protein?GABA (B) protein Need help answering questions about the GABA(B) protein. What is the primary structure Describe secondary structure (alpha-helix, beta sheet, and how many of each and what percent of the total protein)What is the tertiary structure (which should also show secondary structure)Does the protein have a quaternary structure, if so what is it?
- Purification of a new unknown protein that you isolated from tissue and Assume that you have reached the following data during the characterization; Gel filtration: Gel filtration in protein native conformation When chromatographed, it has a molecular weight of 240000 daltons (240 kDa) is detected to be around. Gel filtration: The same protein is first denatured with 6 M guanidinium hydrochloride subjected to gel filtration chromatography again under denatured conditions. is retained, and the only column from the column with a molecular weight of about 60000 daltons (60 kDa) a protein is obtained. SDS-PAGE: Protein finally SDS-PAGE in the presence of beta-mercaptoethanol (Sodium dodecyl-sulphate polyacrylamide gel electrophoresis) analysis being held. As a result of SDS-PAGE analysis, their weight in the gel is approximately 40000 daltons. Two protein bands corresponding to (40 kDa) and 20000 daltons (20 kDa) is observed. In the light of these findings, the quaternary/quaternary…Shape and dimension. (a) Tropomyosin, a 70-kDa muscle protein, is a two-stranded α-helical coiled coil. Estimate the length of the molecule. (b) Suppose that a 40-residue segment of a protein folds into a two-stranded antiparallel β structure with a 4-residue hairpin turn. What is the longest dimension of this motif?TERTIARY STRUCTURE (A) (B) (C) Fg Eet Galand Sen 20e Figure 6. Examples of the arrangement of a-helices and B-sheets in folded protein domains. Copyright 2013 from Essential Cell Biology, 4th Edition by Alberts et al. Reproduced by permission of Garland Science/ Taylor & Francis LLC. Figure 6 shows three examples of how secondary structure elements can be arranged in relation to one another in the functional, folded form of a complete protein or one compact portion of a protein. The overall three-dimensional shape (or conformation) of a protein is its tertiary structure. • What do you think holds together the various secondary structural elements in a particular three-dimensional pattern? (Hint: Look back at Figure 5 - what is sticking out from the sides of the a-helices and B-strands?)
- Hierarchical Organization of Protein Structure Q3.1 Describe the properties of an amphipathic alpha helix and identify numbered amino acids in a dodecamer polypeptide that contribute to the chemical properties of this secondary protein structure (see the amphipathic alpha helix described in chapter 4). Where are amphipathic alpha helices found in a globular cytosolic protein?2. Subunit Composition of a Protein. A protein has a molecular mass of 400 kDa when measured by size-exclusion chromatography ( F). When subjected to gel electrophoresis in the presence of sodium dodecyl sulfate (SDS), the protein gives three bands with molecular masses of 180, 160, and 60 kDa. When electrophoresis is carried out in the presence of SDS and dithiothreitol (=), three bands are again formed, this time with molecular masses of 160, 90, and 60 kDa. Determine the subunit composition of the protein. Note: dithiothreitol is a reagent to beak down the disulfide bonds.Ala-Arg-Val-His-Asp-Gln Given the polypeptide chain above Estimate the net charge of the polypeptide chain at physiological pH (7.4) and at pH 5.0 . How many peptide bonds are there? What kind of polypeptide is it?
