Acidic polar side chains

Ammo acids with polar but nonwmzed side chains Among ammo acids with polar side chains serine is the smallest it is not much larger than alanine With a —CH2OH side chain serine participates well m hydrogen bonding and often occurs m regions of a peptide that are exposed to water... 

The amino acids are usually divided into three different classes defined hy the chemical nature of the side chain. The first class comprises those with strictly hydrophobic side chains Ala (A), Val (V), Leu (L), He (1), Phe (F), Pro (P), and Met (M). The four charged residues, Asp (D), Glu (E), Lys (K), and Arg (R), form the second class. The third class comprises those with polar side chains Ser (S), Thr (T), Cys (C), Asn (N), Gin (Q), His (H), Tyr (Y), and Trp (W). The amino acid glycine (G), which has only a hydrogen atom as a side chain and so is the simplest of the 20 amino acids, has special properties and is usually considered either to form a fourth class or to belong to the first class. 

Figure 2.4 The helical wheel or spiral. Amino acid residues are plotted every 100° around the spiral, following the sequences given in Table 2.1. The following color code is used green Is an amino acid with a hydrophobic side chain, blue is a polar side chain, and red is a charged side chain. The first helix is all hydrophobic, the second is polar on one side and hydrophobic on the other side, and the third helix is all polar.

What about tertiary structure Why does any protein adopt the shape it does The forces that determine the tertiary structure of a protein are the same forces that act on ail molecules, regardless of size, to provide maximum stability. Particularly important are the hydrophilic (water-loving Section 2.13) interactions of the polar side chains on acidic or basic amino acids. Those acidic or basic amino acids with charged side chains tend to congregate on the exterior of the protein, where they can be solvated by water. Those amino acids with neutral, nonpolar side chains tend to congregate on the hydrocarbon-like interior of a protein molecule, away from the aqueous medium. 

Of the 20 amino acids, 11 have polar side chains (color screened), and 9 have nonpolar side chains. One, proline, has a unique ring structure. Under the name of each amino acid is its three-letter abbreviation. 

Amino acids with uncharged polar side chains... 

Based on the properties of the side chains, the 20 amino acids can be put into six general classes. The first class contains amino acids whose side chains are aliphatic, and is usually considered to include glycine, alanine, valine, leucine, and isoleucine. The second class is composed of the amino acids with polar, nonionic side chains, and includes serine, threonine, cysteine, and methionine. The cyclic amino acid proline (actually, an imino acid) constitutes a third class by itself. The fourth class contains amino acids with aromatic side chains tyrosine, phenylalanine, and tryptophan. The fifth class has basic groups on the side chains and is made up of the three amino acids lysine, arginine, and histidine. The sixth class is composed of the acidic amino acids and their amides aspartate and asparagine, and glutamate and glutamine. 

Amino acids with nonpolar (hydrophobic) R-groups are generally found in the interior of proteins that function in an aqueous environment, and on the surface of proteins (such as membrane proteins) that interact with lipids. Amino acids with polar side chains are gener ally found on the outside of proteins that function in an aqueous environment, and in the interior of membrane-associated proteins. 

To summarize, the binding sites of lysozyme and the serine proteases are approximately complementary in structure to the structures of the substrates the nonpolar parts of the substrate match up with nonpolar side chains of the amino acids the hydrogen-bonding sites on the substrate bind to the backbone NH and CO groups of the protein and, for lysozyme, to the polar side chains of amino acids. The reactive part of the substrate is firmly held by this binding next to acidic, basic, or nucleophilic groups on the enzyme. 

The primary, secondary, and tertiary structures of the macromolecule surrounding the metal ion, however, make possible an enormous variation in the microenvironment of the metal ion. The microenvironment also consists of amino acids whose side chains (and also perhaps the peptide backbone) can assume a role in a given catalytic reaction in addition to the metal ion. Such variation is not readily achieved in small molecular systems, but many variations in solvent polarity, pH, etc., can be applied to homogeneous catalysts. 

The first 11 residues at the N-terminal end of the K+ channel are predominantly hydrophobic in nature. When individual residues in this region were replaced by amino acids with polar side chains, inactivation of the channel was slowed relative to the rate in the wild-type protein. Following the hydrophobic residues, the protein has a cluster of five positively charged residues. Mutations that deleted... 

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