Life: The Science of Biology
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Author: David E. Sadava, David M. Hillis, H. Craig Heller, Sally D. Hacker
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Chapter 3.2, Problem 2R
Summary Introduction
To review:
The most probable explanation for the observations that replacement of glycine (G) with alanine (A) or serine (S) does not change the shape of a protein, while replacement of G with valine (V) results in the change in the protein’s shape.
Introduction:
A change in the protein shape takes place with even a small change in its amino acid sequence. For example, the glycine resides at a particular location in a protein and makes certain interactions with other amino acids. Replacement of glycine with arginine (R) or glutamic acid (Q) results in a considerable change in the shape of protein near the amino acid change.
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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?
a. which amino acid can form a covalent bond with its side chain?
b. which amino acid can contribute to protein tertiary and quarternary structure by forming a covalent bond?
Residues such as valine, leucine, isoleucine, methionine, andphenylalanine are often found in the interior of proteins,whereas arginine, lysine, aspartic acid, and glutamic acid areoften found on the surface of proteins. Suggest a reason forthis observation. Where would you expect to find glutamine,glycine, and alanine?
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- A portion of a polypeptide chain contains the following sequence of amino acids: (-Met, -Leu, -Ala, -Cys, -Asp-) a.) Which amino acid can form a disulfide bond? b.) Which amino acids are likely to make the polypeptide more soluble in water? c.) Which amino acids are likely to make the polypeptide less soluble in water? d.) How does the primary structure of a protein affect its tertiary structure?arrow_forwardProteins can be precipitated out of aqueous solution bythe addition of an electrolyte; this process is called “saltingout” the protein. (a) Do you think that all proteins wouldbe precipitated out to the same extent by the same concentrationof the same electrolyte? (b) If a protein has beensalted out, are the protein–protein interactions stronger orweaker than they were before the electrolyte was added?arrow_forwardValine is an amino acid with a nonpolar side chain and serine is one with a polar side chain. Draw the two amino acids.(a) Why is the side chain for valine nonpolar, whereas the side chain for serineis polar?(b) Which amino acid has a hydrophilic side chain and which has a hydrophobic sidechain?arrow_forward
- Globular proteins are water-soluble, whereas fibrous proteins are insoluble in water. Indicate whether you expect the following amino acids to be on the surface of a globular protein or on the surface of a fibrous protein.(a) Ala (b) Glu(c) Leu (d) Phe(e) Ser (f) Valarrow_forwardWhen an amino acid's side chain, such as aspartic acid, has a pKa, that pKa is not the same if the amino acid occurs on the interior of a protein. Why would the pKa of a side chain of an Asp occuring on the inside of a protein be different from an Asp on the outside of a protein?arrow_forwardAmong these amino acid combinations listed above, only the combination of Lys and Glu have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein. Explain by drawing (a) why Lys and Glu side chain interaction stabilizes the tertiary structure of a protein (b) why the pairs of Glu and Asp & Arg and Pro cannot provide the stability to the protein structure.arrow_forward
- Our understanding of how proteins fold allows us to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence :a)Where might bends or βturns occur? b)Where might intrachain disulphide cross-linkages be formed? c)Assuming that this sequence is part of a bigger globular protein, indicate the probable location (on the surface or interior of the protein) of the following amino acid residues: Asp, Ile, Thr, Ala, Gln and Lys. Explain your reasoningarrow_forwardWhen an inappropriate amino acid is substituted in place of another, as occurs in certain genetic disorders, the resulting protein is either poorly functional or non-functional. Since proteins contain hundreds if not thousands of amino acids, why should the change of a single amino acid be so critical?arrow_forwardOur growing understanding of how proteins fold allows researchers to make predictions about protein structure based on primary amino acid sequence data. Consider the following amino acid sequence.(a) Where might bends or β turns occur?(b) Where might intrachain disulfide cross-linkages be formed?(c) Assuming that this sequence is part of a larger globular protein, indicate the probable location (external surface or interior of the protein) of the following amino acid residues: Asp, Ile, Thr, Ala, Gln, Lys. Explain your reasoning.arrow_forward
- If a Cys residue in a protein was replaced with either Ser or Phe amino acid, which substitution would you expect to result in the greatest structural change and why?arrow_forwardAre amino acids other than the usual 20 amino acidsfound in proteins? If so, how are such amino acids incorporatedinto proteins? Give an example of such an amino acid and a protein in which it occurs.arrow_forwardA particular amino acid contains a -CH2NH3+ group. Is this amino acid more likely to be found on the inside or outside of the folded protein? Briefly explain.arrow_forward
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Biomolecules - Protein - Amino acids; Author: Tutorials Point (India) Ltd.;https://www.youtube.com/watch?v=ySNVPDHJ0ek;License: Standard YouTube License, CC-BY