You have discovered a novel protein that has a pl = 5.5. To study thefunctional properties of this new protein, your research group hasmade a mutant that contains two amino acid changes: a surfacephenylalanine residue in the normal protein has been replaced byhistidine (side chain pK, = 6.1), and a surface glutamine has beenreplaced by glutamic acid (side chain pK, = 6.0). Is the pl of themutant protein predicted to be greater than, less than, or the same asthe pI of normal protein? Support your answer with the appropriatecalculation.

In this mutation process, hydrophobic phenylalanine is replaced by the Histidine residue. Histidine…

Answered: You have discovered a novel protein…

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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Jacqueline isolated an interesting new protein from the broth of a yeast culture. After purification of the protein, she requested an amino acid analysis and found that the protein contained 0.57% tryptophan by weight (tryptophan Mr-204). Calculate the minimum molecular weight of the protein (i.e., assuming there is only one tryptophan residue per protein molecule).
You are given an equimolar (0.10 mM) mixture of Ubiquitin protein that is free/pure of any other macromolecules (e.g. nucleic acids) in a pH 7.0 phosphate buffer How can you purify Ubiquitin? Propose a 2-step minimum plan to purify their protein. Basic rules: Affinity chromatography (e.g. His Tag purification) is not an allowed step because these proteins are in their native state (i.e. – do not have a polyhistidine tag). Also, you are not allowed to rely solely on the color of certain proteins (e.g. cytochrome C and GFP) in your characterization/proposal. You are allowed to buffer exchange (i.e. – switch buffers) but try to keep your pH’s in a reasonable range (5.5 – 8.5) or you risk denaturing your protein! Assume you can only separate proteins under 50.0 kDa with a 5.0 kDa difference using SEC. Otherwise, assume proteins greater than 50.0 kDa are unable to be separated. Assume proteins with the same charge (positive or negative) are not easily separated using IEC. Assume all…
You have discovered a novel protein that has a pI = 5.5. To study the functional properties of this new protein, your research group has made a mutant that contains two amino acid changes—namely, a surface Phe residue in the normal protein has been replaced by His (side chain pKa = 6.1) and asurface Gln has been replaced by Glu (side chain pKa = 6.0). Is the pI of themutant protein predicted to be greater than, less than, or the same as the pIof the normal protein? Support your answer with the appropriate calculation
Fluorescent proteins like the green fluorescent protein (GFP) found in jellyfish are a class of colorful proteins that shine a particular color when exposed to ultraviolet light. These proteins, despite exhibiting a wide range of diverse colors, have nearly identical secondary structure across organisms and phenotypes. Each GFP-like protein has a few alpha-helices as well as a characteristic beta-barrel composed of 11 beta-sheets that shields the inside of the protein from solvent (i.e., water). The GFP- like protein shown below is a green fluorescent protein from the great star coral Montastraea cavernosa and contains two alpha-helices in its structure (labeled A and B and colored cyan). A B 1. Helix A contains 6 amino acids, including a phenylalanine and an aspartic acid. Which position (1 or 2, colored in red) would you more likely expect aspartic acid to be located? [Select] 2. If you were to compare helix A to helix B, would you expect the ratio of polar:non-polar residues to be…
Marker Proteins Molecular Weight (daltons) Distance 132,000 66,000 43,000 14,400 Serum Albumin (Dimer) Serum Albumin (Monomer) 23mm 32mm Ovalbumin 39mm 60mm Lysozyme Unknown 1 26mm Unknown 2 58mm Rabbit serum (albumin) 33mm 1.On semilog paper (provided below) plot the distance migrated by each standard protein as a function of molecular weight. Determine the molecular weight of the unknown proteins and the major protein found in rabbit serum (albumin) from this calibration curve. ii) Interferon is a protein of 25,000 Dalton. How far would it have migrated, land it been included in this experiment? iii) The average amino acid residue in a protein has a molecular weight of 120 Daltons. Assuming that your unknowns are average, how many amino acid residues do they contain
Using the letter “R" to indicate amino acid side chain, draw the following: A. The backbone atoms and bonds of a parallel ß-sheet with two B-strands of 5 amino acid each (use slide 23 of Chapter 6 for guidance). B. The backbone atoms and bonds of an antiparallel B-sheet with two B-strands of 5 amino acid each (use slide 23 of Chapter 6 for guidance). C. Draw the hydrogen bonds connecting the two B-strands in each B-sheet.
Shown in the following table are several amino acid substitutionsin the a and b chains of human hemoglobin. determine how many of them can occur as a result of a single nucleotide change.
1) You are studying the toxic protein called ectatomin, a major component of ant venom (specifically from the species Ectatomma tuberculatum), that embeds into cell membranes and creates pores that cause cells to lyse. Ectatomin is a small dimer, meaning the protein is comprised of two polypeptides; the sequences of the two polypeptides are given in the table with single-letter abbreviations. polypeptide sequences of ectatomin monomers polypeptide |protein sequence polypeptide 1 GVIPKKIWETVCPTVEPWAKKCSGDIATYIKRECGKL polypeptide 2 WSTIVKLTICPTLKSMAKKCEGSIATMIKKKCDK You could use absorbance at 280nm or colorimetric assays like the Bradford assay or bicinchoninic acid assay (BCA) assay to quantify the amount of ectatomin you have for your experiment. Why might you choose to use a colorimetric method instead of absorbance at 280nm? Select the best answer. a) Measuring absorbance at higher wavelengths, like 595nm or 562nm, is more accurate than measuring absorbance at 280nm. b) The Bradford…
The figure shows an example of a thermal denaturation plot. The melting temperature (Tm) is the midpoint of the temperature range over which denaturation occurs. Percent unfolded 100 80 60 40 20 0 20 Tm 40 60 Temperature (°C) 80 100
3) You are working on a protein with the following sequence in an area of interest. -Asp-Leu-Leu-Gln-Glu-Glu-Asp-Glu-Ser-Arg a. The current structure, solved at pH 7.4, of this segment has an alpha helix that is disrupted a er the Gln. Why might the alpha helix stop at this residue? b. This protein is involved in Lysosomes in vivo. The secondary structure of this region is expected to change into a complete alpha helix. Why might this change into a complete helix? ( Hint: Lysosomes are acidic!)
Two proteins are discovered, and both are shown to have a potential in treating fatty liver disease. The structural differences of the proteins require them to be delivered using spherical nanoparticles made of different polymers. The scientists are trying to decide which protein will be more efficient to use in applications where a faster drug release is more favorable. Protein 1 is loaded into spherical nanoparticles made of polymer 1 which has R=100 nm at a concentration of 50 nM. Protein 2 is loaded into spherical nanoparticles made of polymer 2 which has R=250 nm, at a concentration of 50 nM. The partition coefficient of polymer 1 is 0.01 and is known to be half of partition coefficient of polymer 2. The diffusion coefficient of protein 1 in polymer 1 is 2x10-6 cm2/s, and diffusion coefficient of protein 2 in polymer 2 is 3.4x10-6 cm2/s. Determine which treatment will be selected for treatment of fatty liver disease.
Assume that the translational error frequency, δ, is 1 x 10–4.(a) Calculate the probability of making a perfect protein of 100 residues.(b) Repeat for a 1000-residue protein.

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