1. Chap. 3 Problem 1 See Fig. 3.1a & 3.2 for basic information about structure classifications. More on the definitions of primary, secondary, tertiary, and quaternary structure can be found in the text on p. 61-68. Examples of secondary structures are the  helix, ß sheet, and ß turns. Secondary structures are stabilized primarily by H-bonds. All three types of noncovalent interactions (H-bonds, ionic interactions, and van der Waals forces) stabilize tertiary and quaternary structure. The hydrophobic effect also is generally important in the folding of protein structure elements.

2. Chap. 3 Problem 2 Molecular chaperones and chaperonins play important roles in the folding of newly synthesized proteins in cells. By binding to an unfolded protein and promoting folding, its aggregation and targeting to the proteasome for degradation are prevented. Although many proteins can fold spontaneously, chaperones reduce the time required for folding and decrease the likelihood that the protein will become trapped in a partially folded state. Molecular chaperones (e.g., Hsp70, Fig. 3.16) act as monomers to promote folding, whereas chaperonins (e.g., GroELS, Fig. 3.17) are large multisubunit machines. Both chaperonins and molecular chaperones use ATP to catalyze folding. Fig. 3.17a

3. Chap. 3 Problem 3 Enzymes accelerate chemical reactions by stabilizing and thereby lowering the energy of the transition state (Fig. 3.20). The active site is where the substrate binds and the chemical reaction occurs. The turnover number (k cat ) is the rate constant for the reaction. It is 1/2 V max equivalent to the number of substrate molecules that can be converted to product at a single active site per second. The K m is a reflection of an enzyme ’ s affinity for the substrate and is mathematically equal to the substrate concentration at which the reaction rate is 1/2 V max (Fig. 3.22b, below). The lower the K m, the higher the affinity of the enzyme for substrate. The V max of an enzyme-catalyzed reaction is the reaction rate attained when the active sites of all enzyme molecules are bound to substrate (saturation conditions). The rate constant is a proportionality constant that when multiplied by the concentration of the ES complex, gives the reaction rate, V. V becomes equivalent to V max when [ES] = [E total ].

4. Chap. 3 Problem 6 Many cellular proteins are degraded by a large protein complex known as the proteasome (p. 85-88). Ubiquitin is a protein tag that targets proteins to the proteasome for degradation (Fig. 3.29). Degradation requires polyubiquitination as shown in the figure. The degraded protein is cleaved to small peptides, and the ubiquitin monomers are recycled. Proteasome inhibitors that block degradation of tumor suppressor proteins are being investigated as cancer therapeutics.

5. Chap. 3 Problem 7 Cooperativity refers to a change in ligand binding affinity or enzymatic activity in a protein or enzyme that results from conformational changes caused by the binding of a regulatory molecule. Binding of regulatory molecules fine tunes the activity of the protein often by changing its affinity for ligand/substrate. Enzymes and binding proteins that exhibit cooperativity have distinctive sigmoidal shaped activity/binding curves (Fig. 3.30 hemoglobin). Protein phosphorylation and proteolytic cleavage also are used to modulate the function and activity of proteins and enzymes. Ultimately these modifications change the conformation and activity of the protein.