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 Protein B SDS-PAGE cross-linking agent MW 55,000 40,000 15,000

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 Protein B SDS-PAGE cross-linking agent MW 55,000 40,000 15,000

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter31: Completing The Protein Life Cycle: Folding, Processing, And Degradation

Section: Chapter Questions

Problem 3P: Understanding the Relevance of Chaperones in Protein Folding Protein molecules, like all molecules,...

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3 Common Databases on Protein Study (Peptide Sequence to Structural Analysis).A tool provided before 2020 and after 2020? Your task is to find : 1) Disadvantage/limitation of the mentioned database Common Databases on Protein Study (Peptide Sequence to Structural Analysis).A tool provided before 2020 and after 2020?
2. A ligand binds more tightly to the folded state (N) of a protein than to the unfolded state (U). Show that the ligand stabilizes the protein and calculate by how much (ΔΔGfold = ?). Please help me find out deltadelta G fold.
2 If a protein is predominantly made up of aliphatic and aromatic amino acids, which of the following is most likely true about such protein? Select the correct responses): a. It is a protein with a net negative charge b. It is most probably a structural protein. c. It is a protein that is cationic in nature. d. It is a protein that is hydrophobic in nature. e. It is most probably a catalytic protein. f. It is a water-solube protein. g. It is most probably a carrier protein.
1. Use the info of this molecule as well as the attached addendum to demonstrate the flow of genetic information to protein sequence as described by the so-called “Central Dogma” . Clearly indicate the direction of your polynucleotide strands and peptide/protein. ATG GCA TGC AAT AGC TCA TGC 2. What would happen to the amino acid sequence if the underlined nucleotide (C) would change to an A?
SDS-PAGE gels are used to study changes in protein primary structure. Which of the following statements about SDS-PAGE gels is correct? A. The negatively charged proteins will move towards the negatively charged electrode in the SDS-Page chamber B. A detergent is needed to disrupt protein secondary, tertiary, and quaternary structure before a gel can be run C. No "stains" or other treatments are needed to "see" the protein bands on a gel D. Long polypeptides move a further distance from the loading well in a SDS-PAGE gel than short polypeptides
. Pick all that are TRUE regarding analysis of quaternary structures of proteins using polyacrylamide electrophoresis:I. The added β-mercaptoethanol disrupts S--S bonds bridging the polypeptide chains causing the appearance of higher Rf bands compared to the native protein run. II. Heating up any protein before subjecting to SDS-PAGE will always result in the formation of more than one band.III. A good asymmetrical gel layout would be : (Lane 1) MW ladder, (2) native protein, (3) protein + β-ME, (4) protein + HCL, (5) protein + β-ME + HCl.IV. Formation of a single band in the protein + β-ME + HCl run, whose Rf is lower than the native run, could be indicative that the protein is a homodimer.A. I onlyB. I and IIC. II and IIVD. None is true
What is the function of sodium dodecyl sulfate (SDS) in SDS-PAGE? stabilizes the gel matrix, improving resolution during electrophoresis SDS solubilizes proteins to give them uniformly negative charges, so the separation is based purely on size. SDS raises the pH of the gel, separating multiunit proteins into individual subunits. SDS solubilizes proteins to give them uniformly positive charges, so separation is based purely on pH.
SDS-PAGE gels separate proteins by charge. Therefore proteins that are 10,000 daltons (g/mol) will move the same distance as proteins that are 80,000 daltons (g/mol). This statement is: True or False (And why)
Some proteins migrate anomalously in SDS-PAGE gels. For instance, the molecular weight determined from an SDS-PAGE gel is sometimes very different from the molecular weight determined from the amino acid sequence. Suggest an explanation for this discrepancy.
3 Common Databases on Protein Study (Peptide Sequence to Structural Analysis).A tool provided before 2020 and after 2020? Your task is to find : 1) Advantage on mentioned databases Common Databases on Protein Study (Peptide Sequence to Structural Analysis).A tool provided before 2020 and after 2020?
1) What are the four levels of protein folding. How do you distinguish those different levels? What can denature a protein? 2) What are detergents and why are they useful? How do they basically work? 3) What is meant by amphipathic? What is an example of this?
SDS gel electrophoresis can be used to determine a.) The molecular mass of denatured protein subunits b.) Whether subunits in a protein complex have the identical sequence c.) The molecular mass of a native protein complex d.) The overall charge on a polypeptide