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Unit 2 1 U NIT 2 P ART A: P ROTEIN S TRUCTURE P ART B: P ROTEIN P URIFICATION AND A NALYSIS P ART A: L EVELS OF S TRUCTURE IN P ROTEIN A RCHITECTURE Assignment: Nelson & Cox, review pp. 43 - 51 (stop at "Solutes affect..."), 84 - 85, 92 - 93, 113 - 123, 129 - 131, 135 - 138, 140 - 148. The biological activity of a protein depends on its three-dimensional structure and its interaction with other molecules. Detailed knowledge of protein structure contributes greatly to our understanding of exactly how a protein functions. We have learned in Unit 1 that proteins are made up of linear polymers of amino acids. In this unit we will learn how the amino acid sequence dictates the three dimensional structure of proteins and how hydrophobic interactions and secondary structures are involved in the folding of proteins to produce the tertiary structure. 1. What is a prosthetic group (p. 84)? 2. There are 20 common amino acids found in proteins. Many of these amino acids can be modified after synthesis of the polypeptide chain. List several of these modification types. (Table 3-4, pp. 85).
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Unit 2 2 3. Levels of Structure in Proteins (p. 92). Distinguish between each of the four levels of protein structure. For secondary structure, a better definition states simply that the secondary structure of a protein consists of regularly repeating conformations of the polypeptide backbone such as α helices and β pleated sheets. These always involve hydrogen (H) -bonds in a regular pattern. A more complete definition of the tertiary structure of a globular protein is that it consists of the completely folded, 3-dimensional, biologically active (or native) conformation of a single polypeptide protein. In tertiary structure the nature of the amino acid side chains is an important factor. 4. Atomic forces, interactions, or bonds Proteins are held together and all interactions between molecules are caused by hydrogen bonds, ionic bonds or interactions, hydrophobic interactions, and van der Waals interactions. Discuss these weak non-covalent interactions that stabilize a protein's conformation (review pp. 43 - 51, pp. 114 - 115). 5. Polypeptide chains are flexible but the peptide bond does not rotate. Referring to Fig. 4-2 (p. 116), explain the following: a. The peptide unit is rigid and planar: the N and C atoms of each peptide bond and the atoms attached to them all lie in one plane. b. There is no freedom of rotation about the bond between the carbonyl carbon atom and the nitrogen atom of the peptide unit. c. The hydrogen of the amino group is nearly always trans (opposite) to the oxygen of the carbonyl group because the cis form is sterically hindered. d. The link between the α -carbon atom and the carbonyl carbon atom is a pure single bond. The bond between the α -carbon atom and the peptide nitrogen atom is also a pure single bond. Thus there is a large degree of rotational freedom about each of these bonds. But there are restrictions as shown by the Ramachandran plot (Fig. 4-3, p. 117).
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