R group amino acid

Hydrophobic interactions make a large contribution to the stability of protein structures. Burial of hydrophobic amino acid R groups so as to exclude water requires at least two layers of secondary structure. Two simple motifs, the /3-a-/3 loop and the a-a comer (Fig. 4—20a), create two layers. 

Specificity Each of these enzymes has a different specificity for the amino acid R-groups adjacent to the susceptible peptide bond (Figure 19.5). For example, trypsin cleaves only when Ihe carbonyl group of the peptide bond is contributed by arginine or lysine. These enzymes, like pepsin described above, are synthesized and secreted as inactive zymogens. 

Proteins may be fibrous or globular. The structure and polarity of the particular amino acid R groups and their sequence affect the solubility properties and tertiary structure of proteins. Quaternary structure refers to the aggregation of similar protein subunits. 

Most nonfibrous proteins have a very precise and compact three-dimensional or tertiary structure formed when the a-helix and random coil of the polypeptide chain bends, twists, and folds over and back upon itself. The tertiary structure is stabilized by interactions of amino acid R-groups (Fig. 2-4a), and thus, is dictated by the primary structure. The biochemical function of a protein is intimately tied to its tertiary structure. That is, to function in a certain way, a protein must have the correct tertiary structure. Stated conversely only one specific tertiary structure will permit a protein to serve optimally a specific function (see also Figs. 4-3 and 4-4). 

Figure 4-4 The active site (shaded area) occupies only a small region of the enzyme. A, B, and C are the amino acid R-groups responsible for substrate binding and catalytic activity.

The two classes of amino acids that exist are based on whether the R-group is hydrophobic or hydrophilic. Hydrophobic or nonpolar amino acids tend to repel the aqueous environment and are located mostly in the interior of proteins. They do not ionize or participate in the formation of hydrogen bonds. On the other hand, the hydrophilic or polar amino acids tend to interact with the aqueous environment, are usually involved in the formation of hydrogen bonds, and are usually found on the exterior surfaces of proteins or in their reactive centers. It is for this reason that certain amino acid R-groups allow enzyme reactions to occur. 

Some proteins are composed of more than one peptide. They are said to have quaternary structure. Weak attractions between amino acid R groups hold the peptide subunits of the protein together. Some proteins require an attached, nonprotein prosthetic group. 

If an enzyme catalyzed a reaction by modifying the local pH, what kind of amino acid R groups would you expect to find in the active site ... 

Protein shapes are maintained by a variety of forces that arise from interactions between the amino-acid R groups. Name the amino acid that possesses each R group and the force that could arise in each of the following interactions ... 

Secondary structure largely depends on hydrogen bonding involving the peptide bonds, whereas tertiary structure (Chapter 8) depends on bonds involving the amino acid R-groups. 

How does the R group in proline differ from the other amino acid R groups in Table 22.1 ... 

The combination of an enzyme (E) and a substrate (S) within the active site forms an enzyme-substrate (ES) complex that provides an alternative pathway for the reaction with lower activation energy. Within the active site, the amino acid R groups catalyze the reaction to give an enzyme-product (EP) complex. Then the products are released, and the enzyme is available to bind to another substrate molecule. 

In the induced-fit model, substrates induce the active site to change structure to give an optimal fit by the substrate. In the enzyme—substrate complex, catalysis takes place when the amino acid R groups react with a substrate. 

Further folding of the protein molecules held in place by attractive forces between amino acid side chains is determined by the nature of the amino acid R groups. 

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