SDS-PAGE separates proteins based primarily on which of the following characteristics: O a. their intrinsic charges O b. their three-dimensional shapes C. their sizes in basepairs O d. their expression levels e. their molecular weights Of. their His-tags
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- 22. Some tRNAs contain inosine, which can base pair with A, C, and U. Why might this be advantageous with ate but not ambiguous? olyp min 33. What is required for molecular surfaces/interfaces to interact with one another for a sufficient amount of time (such as an antibody/antigen)?Shown below is a portion of primary sequence of a very large protein. -Gly-Pro-Arg-Gly-Pro-Hyp-Gly-Ser-Ala-Gly-Ser-Hyp-Gly-Lys-Asp--- Which of the following structures is most likely formed from this protein sequence? D A. A О В. В OC.C O D. D OE. E B.HN, NH. NH H2N° А. В. Consider the 3 structures shown. Which of these is (normally) NOT present in either DNA or RNA? (select all that apply) А В none of the above ZI C.
- . Some naturally occurring polynucleotide sequences are palindromic; that is, they are self-complementary about an axis of symmetry. Such a sequence is TCAAGTCCATGGACTTGG AGTTCAGGTACCTGAACC Show how this structure might form a double hairpin, or cruciform, conformation. Indicate the center of symmetry in the sequence and the bounds of the cruciform.. A protein has been sequenced after cleavage of disulfide bonds. The protein is known to contain 3 Cys residues, located as shown below. Only one of the Cys has a free - SH group and the other two are involved in an -s-s- bond. A Phe Cys « N-terminus Cys- - Met Cys- C-terminus The only methionine and the only aromatic amino acid (Phe) in this protein are in the positions indicated. Cleavage of the intact protein (i.e., with disulfide bonds intact) by either cyanogen bromide or chymotrypsin does not break the protein into two peptides. Where is the -s-s- bond (i.e., AB, BC, or AC)?-novel protein is described that functions best at pH 10.5, and contains a beta strand on one side. The authors report that at pH 10.5 this beta strand's interaction with an alpha helix is stabilized by an ionic interaction. a. Beneath each pair of amino acid names, draw out the structures for the two amino acids at pH 10.5 Asp-Arg Asn-Gln Cys-Glu b. Which of these pairs would be the best candidates for the ionic interaction at pH 10.5? (circle your choice): Asp-Arg Asn-Gln Leu-Gly C. Explain your choice in part b (25 words or less)
- 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…Tt O 8. What are the driving forces that promotes tertiary -3D and quaternary -4D structure formation of proteins. Provide specific examples of the interactions that drive the formation of 3D and 4D structures?1CFD CALCIUM-FREE CALMODULIN How long is the protein’s primary sequence?Does this protein have any secondary, tertiary and/or quaternary structures present?Are there any molecular additions to this protein that are not amino ac
- 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?Understanding the Relevance of Chaperones in Protein Folding Protein molecules, like all molecules, can be characterized in terms of general properties such as size, shape, charge, solubility/hydrophobicity. Consider the influence of each of these general features on the likelihood of whether folding of a particular protein will require chaperone assistance or not. Be specific regarding just Hsp7O chaperones or Hsp7O chaperones and Hsp60 chaperonins.GT 3 A. Write the structure of the pentapeptide GLDSC. B. What is the complete name of this pentapeptide? 1. Show a tertiary structure of ACGGC after a disulfide bond forms. A sample of an unknown peptide was divided into two aliquots. One aliquot was treated with trypsin; the other was treated with cyanogen bromide. Given the following sequences (N-terminal to C-terminal) of the resulting fragments, deduce the sequence of the original peptide. 2. 3. Trypsin treatment Asn-Thr-Trp-Met-lle-Lys Gly-Tyr-Met-GIn-Phe Val-Leu-Gly-Met-Ser-Arg Cyanogen bromide treatment Gln-Phe Val-Leu-Gly-Met lle-Lys-Gly-Tyr-Met Ser-Arg-Asn-Thr-Trp-Met