What would you predict about the ratio of hydrophilic to hydro-phobic amino acid residues in a series of monomeric globularproteins that range in size from a molecular weight of 10,000g/mole to a molecular weight of 100,000 g/mole?Note that the volume of a sphere is 4/3nr³, while the sur-face area of the outside of a sphere is 4nr².How would your prediction change if the monomeric proteins werefibrous instead of globular?

Globular protein has a spherical topography. The fraction of hydrophilic amino acid residues in a…

Answered: What would you predict about the ratio…

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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What is the molecular basis for the observation that the overall charge on a protein becomes increasingly positive as pH drops and more negative as pH increases?
In a 0.1 M lysine solution, what are the individual concentrations of the protonated C-terminus form of the amino acid versus the non- protonated at pH 4 (pKa = 2.16)
Approximate molecular weight for an unknown protein from gel-filtration experiment is 130 kDa. Thirty six mg of this pure protein was treated with excess of fluorodinitrobenzene. After the reaction and complete acid hydrolysis the mixture was found to contain 356 µg of dinitrobenzene derivative of methionine (free acid) and no other amino acid-dinitrobenzene derivatives. Is this protein consisting of single polypeptide chain or multiple subunits? If it consists of multiple subunits, then how many? From these data, can you calculate the molecular weight of the protein more precisely?
You are given a protein solution with a concentration of 0.15 mg/ml. Suppose that we want to prepare a solution containing 100 μg of the protein at a concentration of 1 mg/ml. To achieve this, we will first dry down enough protein solution to obtain 100 μg of proteins. How much solution do we need for drying down? How much volume of H2O do we need to add to the dried protein to obtain the desired concentration?
Consider the phenolic hydroxyl group of a particular Tyr residue in a protein. Suppose the hydroxyl group in the unfolded protein in aqueous solution, where the group is exposed to H2O, has a pKa of 10.0. If that group is found in a hydrophobic environment in the interior of the protein when the protein is folded into its native tertiary structure, would you expect the pKa of the phenolic hydroxyl to be higher or lower in the folded protein interior than in H2O? Explain your reasoning.
a) The pl of a protein is 9.0. What will be the net charge (positive, negative or neutral) on the protein under the following conditions: A buffer with pH 9.0: A buffer with pH 7.0: A buffer with pH 10.0: b) Your protein is present in a sample buffer which has a pH 7.0. The sample is applied to an ANION EXCHANGE column. Will protein 1 bind to the beads on the column? Yes/No
You have discovered a novel protein that has a pl = 5.5. To study the functional properties of this new protein, your research group has made a mutant that contains two amino acid changes: a surface phenylalanine residue in the normal protein has been replaced by histidine (side chain pK, = 6.1), and a surface glutamine has been replaced by glutamic acid (side chain pK, = 6.0). Is the pl of the mutant protein predicted to be greater than, less than, or the same as the pI of normal protein? Support your answer with the appropriate calculation.
Consider the following peptide to answer the questions below: A M A K K E S H I F T A I D E What is the total charge of this peptide at pH = 5? What is the N terminal amino acid (full name)? C terminal amino acid? How many fragments would result if this peptide underwent proteolytic cleavage with V-8 protease and what are these fragments (list them)? Would this peptide be a candidate to form an alpha helix? Why or why not
Hello, I am trying to understand how to calculate the overall charge of a peptide at pH = 7. Please show your work and explain how you got the answer. Here are two peptide examples (assume it consists of 20 residues): 1) 10% Gly, 20% Leu, 15% Lys, 15% Phe, 15% Gln, 25% Glu 2) 10%Gly, 15% Leu, 20% Lys, 15% Met, 15% Thr, 25% Arg
A protein of unknown structure has been purified. Size-exclusion chromatography reveals that the native protein has a MW of 240,000. Chromatography in the presence of 6 M guanidine hydrochloride yields a single peak corresponding to a protein of MW 60,000. Chromatography in the presence of 6 M guanidine hydrochloride and 10 mM B-mercaptoethanol yields peaks for proteins of MW 34,000 and 26,000. Explain what can be determined about the structure of this protein from these data.
Using the quarternary structure of hemoglobin shown inFigure 9-3(d), explain in structural terms how a mutation in the β subunit protein could be suppressed by amutation in the a subunit gene.
Amino acids project from each polypeptide backbone in a β-sheet in an alternating fashion (oneabove the plane and the next below the plane – see Fig 3.8B). Consider the following proteinsequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg-Leu-Lys-Ile-Arg-Phe-Glu.a. Is there a pattern to these amino acids? If so, what is it? b. What does this sequence of amino acids mean for the hydrophobicity/hydrophilicity of theresulting β-sheet? c. Can you make a prediction about how the β-sheet will be arranged in higher levels of protein structure? If so, what prediction would you make?

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