ACTIVE FIGURE 6.4 A Ramachandran diagram showing the sterically reasonable values of the angles  and . The shaded regions indicate particularly favorable values of these angles. Dots in purple indicate actual angles measured for 1000 residues (excluding glycine, for which a wider range of angles is permitted) in eight proteins. The lines running across the diagram (numbered +5 through 2 and -5 through -3) signify the number of amino acid residues per turn of the helix; “+” means right-handed helices; “-” means left-handed helices. (After Richardson, J. S., 1981. The anatomy and taxonomy of protein structure. Advances in Protein Chemistry 34:167–339.) Test yourself on the concepts in this figure at http://chemistry. brookscole.com/ggb3 Fig. 6-04, p.157

FIGURE 6.8 The arrangement of NXH and CUO groups (each with an individual dipole moment) along the helix axis creates a large net dipole for the helix. Numbers indicate fractional charges on respective atoms. Fig. 6-08, p.160

FIGURE 6.10 A “pleated sheet” of paper with an antiparallel -sheet drawn on it. (Illustration: Irving Geis. Rights owned by Howard Hughes Medical Institute. Not to be reproduced without permission.) Fig. 6-10, p.163

FIGURE 6.11 The arrangement of hydrogen bonds in (a) parallel and (b) antiparallel -pleated sheets. Fig. 6-11, p.163

FIGURE 6.27 (a) The natural right-handed twist exhibited by polypeptide chains, and (b) the variety of structures that arise from this twist. Fig. 6-27, p.177

FIGURE 6.12 The structures of two kinds of  -turns (also called tight turns or  -bends). (Illustration: Irving Geis. Rights owned by Howard Hughes Medical Institute. Not to be reproduced without permission.) Fig. 6-12, p.165

loop FIGURE 6.25 The three-dimensional structure of bovine pancreatic trypsin inhibitor. Note the stabilization of the  -helix by a hydrogen bond to Ser47 and the stabilization of the -sheet by Asn43. Beta-turn Fig. 6-25, p.175

FIGURE 6.23 The three-dimensional structure of bovine ribonuclease A, showing the  -helices as ribbons. (Jane Richardson.) Fig. 6-23a, p.173

(b) Domain 2 of phosphoglycerate kinase, composed of a -sheet layer between two layers of helix, three layers overall. Fig. 6-28b, p.178

(b) The two helices (yellow and blue) in the interior of the citrate synthase dimer (residues 260–270 in each monomer) are mostly hydrophobic. Fig. 6-24b, p.174

FIGURE 6.30 Parallel -array proteins—the eightstranded -barrels of triose phosphate isomerase (a, side view, and b, top view) and (c) pyruvate kinase. (Jane Richardson.) Fig. 6-30, p.180

(side-view) Fig. 6-30a, p.180

(b) metal-rich proteins. Fig. 6-35b, p.184

FIGURE 6.39 The transition state model for the folding of globular proteins. (a) A single free energy barrier separates the unfolded or denatured (D) state and the folded or native (N) state. (b) A model with a single folding pathway with sequential transition states along the folding pathway. (c) A model in which there are multiple, similar transition states, and a variety of folding pathways. (Adapted from Myers, J. K., and Oas, T. G., 2002. Mechanisms of fast protein folding. Annual Review of Biochemistry 71:783–815.) Fig. 6-39, p.189