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Chapter_03_Solutions - Chapter 3 Proteins THE SHAPE AND...

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DEFINITIONS 3–1 Quaternary structure 3–2 a helix 3–3 Primary structure 3–4 Binding site 3–5 Tertiary structure 3–6 Polypeptide backbone 3–7 b sheet 3–8 Protein domain 3–9 Secondary structure TRUE/FALSE 3–10 True. In both states—stretched like a string and properly folded—a protein has a highly ordered arrangement of its atoms. A folded protein is stable at a near entropy minimum because the entropic cost is more than balanced by the contributions of weak bonds. A stretched out protein, however, is not stable at this entropy minimum and will assume a more disordered state; that is, it will maximize its entropy. 3–11 True. In a b sheet the amino acid side chains in each strand are alternately positioned above and below the sheet. This relationship can be seen in Fig- ure 3–38 (see Answer 3–19), which shows that the carbonyl oxygens alternate from one side of the strand to the other. Thus, each strand in a b sheet can be viewed as a helix in which each successive amino acid is rotated 180 ° . 3–12 True. Chemical groups on such protruding loops can often surround a molecule, allowing the protein to bind to it with many weak bonds. THOUGHT PROBLEMS 3–13 Free amino acids have an amino group and a carboxylate group, both of which are charged at neutral pH. In proteins these groups are involved in peptide bonds, which are uncharged. Thus, the hydrophobicity/hydro- philicity of a free amino acid is not the same as that of its side chain in a pro- tein. To measure the hydrophobicity/hydrophilicity of the side chains, it is common to assess the properties of side-chain analogs. Thus, for alanine one would use methane, for threonine, ethanol, for aspartic acid, acetic THE SHAPE AND STRUCTURE OF PROTEINS In This Chapter THE SHAPE AND A45 STRUCTURE OF PROTEINS PROTEIN FUNCTION A53 A45 Chapter 3 3 Proteins
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A46 Chapter 3: Proteins acid, and so on. To assess hydrophilicity, one can measure the solubility of the side-chain analogs in water. In general, this is done by determining how the side-chain analog partitions between a vapor of the analog and water. Hydrophobicity can be measured in an analogous way by assessing how a side-chain analog partitions between water and a nonpolar solvent such as cyclohexane. One might imagine that the rank order for hydrophilicity would be the reverse of that for hydrophobicity. From the rank order lists in Figure 3–34, that is mostly true, but there are differences, most notably tyro- sine (Y) and tryptophan (W). Reference: Creighton TE (1993) Proteins, 2nd ed, pp 153–155. New York: WH Freeman. 3–14 Hydrogen bonds, electrostatic attractions, van der Waals attractions, and the hydrophobic force. 3–15 A. Heating egg-white proteins denatures them, allowing them to interact with one another in ways that were not possible at the lower temperature of the hen’s oviduct. This process forms a tangled meshwork of polypeptide chains.
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