Imagine the main chain of a protein bends back on itself, so that two amino acid residues R, and R, come close to each other. Here's what Rlooks like:-CH-CHHOCHO yesCould R, form a salt bridge with R, at physiological pH, if R₂ were the right kind of residue?O noIf you said R, could form a salt bridge with R₂, what would R, have to be?If there's only one possibility, write its 3-letter code. If there is more than one possibility, write the3-letter code of any of them.ExplanationCheckZXEalloptionHcmdHNJ0OPcmdoption

Salt bridge is a bond between amino acids which carry opposite charges. The opposite charges exert…

Answered: Imagine the main chain of a 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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Imagine the main chain of a protein bends back on itself, so that two amino acid residues R₁ and R₂ come close to each other. Here's what R₁ looks like: -CH- CH₂ CH₂ CH₂ CH₂ 1 NH3 Could R₁ form a salt bridge with R₂ at physiological pH, if R₂ were the right kind of residue? O yes O no If you said R₁ could form a sal bridge with R₂, what would R₂ have to be? 0 If there's only one possibility, write its 3-letter code. If there is more than one possibility, write the 3-letter code of any of them. X ? BEET 号图 Ar
Indicate which of the amino acid residues in the following peptide sequence contains a group that has a positive charge for its most likely charge state at pH 10. Asp-Tyr-Lys-GIn-Thr-Ile-Phe-Met-Ser (If none of the amino acids fit the criterion, select "none".) Asp Tyr ооооооооо Lys Gln Thr lle Phe Met Ser none
If an oligosaccharide is attached to a protein via an O-glycosidic linkage which amino acid residue(s) are likely to be involved? O Glutamine O Serine O Histidine O Threonine O Both (b) and (d)
Which of the following amino acids would you least expect to find on the surface of a water-soluble protein? Explain I Serine Glutamat Lysime Threonine
Based upon your knowledge of protein folding, which of the following statements would you expect to be FALSE: O The native state is the protein conformation with the most negative Gibbs free energy value. O The hydrophobic effect causes non-polar side chains to pack into the interior of a protein away from solvent. Proteins are likely to try out every possible conformation before folding into the native state. O A protein incubated in hexane (C6H14) is likely to denature and unfold. O Detergents can interact with the side chains of valine, leucine and phenylalanine.
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?
The major difference between a protein molecule in its native state and in its denatured state lies in the number of conformations available. To a first ap- proximation, the native, folded state can be thought to have one conforma- tion. The unfolded state can be estimated to have three possible orientations about cach bond between residues. (a) For a protein of 100 residues, estimate the entropy change per mole upon denaturation. (b) What must be the enthalpy change accompanying denaturation to allow the protein to be half-denatured at 50 °C? (c) Will the fraction denatured increase or decrease with increasing temperature?
Which of the following amino acids are more likely to be on the interior of the protein? And which are more likely to be exposed to the surface? L I D E W A V K H M Q Y
Imagine the main chain of a protein bends back on itself, so that two amino acid residues R, and R, come close to each other. In the table below are four possibilities for what R, and R, might be. In each case, decide whether a specific interaction could form between the residues. If a specific interaction could form, give the name of the interaction. R₁ R₂ threonine cysteine glutamine arginine cysteine tyrosine phenylalanine glutamate specific interaction? Oyes no yes O no O yes O no Oyes O no name of specific interaction 0 0 0 0 X
Describe the amino acid illustrated above (at pH = 7.0). (the following amino acid at pH = 7 (aqueous form): (COO-)–CH(NH3+)–CH2–(COO-)) it is a non-polar, positively-charged amino acid it is a polar, positively-charged amino acid it is a polar, uncharged amino acid it is a polar, negatively-charged amino acid it is a non-polar, negatively-charged amino acid
Which intermolecular forces are important in acetic acid, CH3 –(C=0)-oh? A particular amino acid contains a- CHNH3+ group. Is this amino acid more likely to be found on the inside or the outside of the folded protein? Briefly explain. The addition of ethanol, CH3CHOH, t an aqueous solution lowers the surface tension of the solution. Predict whether adding ethanol to an aqueous protein solution will tend to stabilize or unfold the protein. Briefly explain.
An oligopeptide has the following amino acid sequence: NH2-Ala-Glu–Leu–Trp–Tyr-Ser–Gly–Lys–Leu-Ala–Arg-Ala-Phe-Ile-Pro–Gly-COOH a) Estimate the net electric charge of the molecule at pH 8.0 and pH 11.0. b) If the above peptide is passed through a cation exchange chromatographic column (that is, the matrix of the column has negative charges) stabilized at pH 8.0, would you expect it to be retained on the column? c) Indicates the number of fragments, and the sequence of each of them, that would be obtained when treating the peptide in question with: i) trypsin, ii) chymotrypsin.

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