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 R₁ looks like: -CH- H₂N CH₂ CH₂ CH₂ NH NH₂ Could R, form a salt bridge with R, at physiological pH, if R₂ were the right kind of residue? O yes Ono If you said R, could form a salt bridge with Ry, 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.

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 R₁ looks like: -CH- H₂N CH₂ CH₂ CH₂ NH NH₂ Could R, form a salt bridge with R, at physiological pH, if R₂ were the right kind of residue? O yes Ono If you said R, could form a salt bridge with Ry, 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.

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 R, and R, come close to each other. Here's what R looks like: -CH- CH HO CH O yes Could R, form a salt bridge with R, at physiological pH, if R₂ were the right kind of residue? O no If 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 the 3-letter code of any of them. Explanation Check Z X E all option H cmd H N J 0 O P cmd option
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)
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
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 here (Identify the following amino acid (at pH = 7.0): (COO-)–CH(NH3+)–CH2–CH2–CH2–CH2–(NH3+)) (at pH = 7.0). it is a polar, negatively-charged amino acid it is a non-polar, negatively-charged amino acid it is a polar, positively-charged amino acid it is a non-polar, positively-charged amino acid it is a non-polar, uncharged amino acid
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.
A sample of the amino acid tyrosine is barely soluble in water. Would a polypeptide containing only Tyr residues, poly(Tyr), be more or less soluble, assuming the total number of Tyr groups remains constant?
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?
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 following are structural diagrams of a selection of newly discovered amino acids. OH -の-CHs NH HO C-OH NH, AN-CH CH2 CH2 OH Ho NH, C=0 a) Select 1 amino acid. Redraw it. Label the alpha carbon and circle/highlight the entire backbone of the amino acid. b) The amino acids are part of a channel protein embedded in the cell membrane. Choose 2 amino acids (from above) that you would expect to find within the interior/middle of the cell membrane. Draw the formation of the dipeptide using the 2 amino acids you selected. Identify the other products formed in the reaction.
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
The major difference between a protein molecule in its native state and inits denatured state lies in the number of conformations available. To a firstapproximation, the native, folded state can be thought to have one conformation. The unfolded state can be estimated to have three possible orientations about each bond between residues.(a) For a protein of 100 residues, estimate the entropy change per moleupon 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 increasingtemperature?