Amino acids group 1- nonpolar side chains

Many amino acids have nonpolar side chains. Such groups cannot fit into the structure of water and so they tend to aggregate in aqueous solution to minimize the area of interaction with water. This tendency is called a hydrophobic interaction. 

Which amino acids have nonpolar side chains (Group 1)... 

In the following group, identify the amino acids with nonpolar side chains and those with basic side chains alanine, serine, arginine, lysine, leucine, and phenylalanine. 

Which amino acids have nonpolar side chains (Group 1) One group of amino acids has nonpolar side chains. The side chains are mosdy aliphatic or aromatic hydrocarbons or their derivatives. 

Among the common amino acids, eleven have side chains that contain polar functional groups that can form hydrogen bonds, such as —OH, —NH2, and — CO2 H. These hydrophilic amino acids are commonly found on the outside of a protein, where their interactions with water molecules increase the solubility of the protein. The other nine amino acids have nonpolar hydrophobic side chains containing mostly carbon and hydrogen atoms. These amino acids are often tucked into the inside of a protein, away from the aqueous environment of the cell. 

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. 

Theoretically, there are 20 x 20 possible different combinations of amino acid residues adjacent to one another in a polypeptide. If each possible combination were needed a specific protease, then 400 different proteolytic enzymes would be required. However, the proteolytic enzymes have broad specificities, largely confined to groups of amino acids with similar side-chain characteristics (e.g., basic or nonpolar), and therefore only a few different types of enzymes are encountered. 

The properties of a part of a polypeptide chain depend on the properties of the side chains present. For example, the side chain of glutamic acid is acidic. The side chain of histidine is basic. The side chains of asparagine and several other amino acids are strongly polar. On the other hand, amino acids with nonpolar side groups, such as valine, are nonpolar. 

Figure 1. The twenty common amino acids found in proteins. The zwitterionic forms of the amino acids are shown as they exist in solution at pH 7. Amino acids, except for proline, differ only in their side-chains. Amino acids with similar side-chains are grouped together. They are also roughly organized according to polarity, from the most polar (lower left) to the most nonpolar (upper right). The polarity of the side-chains is a major determinant of the folded structure of a protein.

Because amino acids have both a basic (the amine) and an acidic (the carboxylic acid) functional group, the state of protonation of the molecule varies with pH as shown in Equation 24.1. The presence of a functional group in the side chain may have considerable influence upon the position of this equilibrium at different pHs. The pH at which the vast majority of the molecules are in the zwitterionic form, and therefore have a net charge of zero, is referred to as the isoelectric point, pi. An amino acid is least soluble in water at its isoelectric point, which is different for each amino acid. If the side chain bears an ionizable group such as a carboxylic acid or an amine, the state of protonation of that functional group will also vary as a function of pH. However, the amino acids used in the exjjeriments in this chapter are nonpolar, so we will not concern ourselves with the complexities associated with ionizable side chains. 

Each amino acid has a different R group, or side chain. The side chains of the amino acids in a protein determine the protein s properties. In Table 25.2 the side chains of the amino acids are shown within a color screen. Nine of the amino acids have nonpolar, or hydrocarbon, side chains (left side of table). The remaining 11 amino acids have polar side chains (right side of table), capable of ionizing or forming hydrogen bonds with other amino acids or with water. 

The structures of the two peptides are similar, so it might seem surprising that their functions are so different. However, closer inspection shows that there is one small difference and one major difference in their amino acid composition. Both have a neutral, nonpolar side chain at residue 3, but residue 8 in oxytocin is the nonpolar amino acid leucine, whose side chain is a sec-butyl group, but residue 8 in vasopressin is arginine, whose side chain has a positive charge. As a result, the for oxytocin has a very low affinity for vasopressin and the receptor for vasopressin has a very low affinity for oxytocin. Since they bind different receptors, they have different functions. 

HYDROPHOBIC INTERACTIONS. These bonding interactions arise from the tendency of nonpolar side chains of amino acids (or lipids) to reside in the interior, nonaqueous environment of a protein (or membrane/ micelle/vesicle). This process is accompanied by the release of tightly bound water molecules from these apolar side-chain moieties. The hydrophobic effect is thermodynamically driven by the increased disorder i.e., A5 > 0) of the system, thereby overcoming the unfavorable enthalpy change i.e., AH < 0) for water release from the apolar groups. 

Nonpolar, Aliphatic R Groups The R groups in this class of amino acids are nonpolar and hydrophobic. The side chains of alanine, valine, leucine, and isoleucine... 

In both carboxypeptidase A and thermolysin the active site Zn2+ is chelated by two imidazole groups and a glutamate side chain (Fig. 12-16). In carboxypeptidase A, Arg 145, Tyr 248, and perhaps Arg 127 form hydrogen bonds to the substrate. A water molecule is also bound to the Zn2+ ion. The presence of the positively charged side chain of Arg 145 and of a hydro-phobic pocket accounts for the preference of the enzyme for C-terminal amino acids with bulky, nonpolar side chains. The Zn2+ in thermolysin is also bound to two imidazole groups and that in D-alanyl-D-alanyl carboxypeptidase to three. 

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 term lyophobic interactions is intended to generalize the expres sion hydrophobic interactions to other solvents than water. Hydro-phobic interactions have been prominently implicated in determining the native configuration of proteins in aqueous solution. These interactions are actually not of a single relatively well-defined character, as are electrostatic or hydrogen bond interactions, but are rather a set of interactions responsible for the immiscibility of nonpolar substances and water. Proteins contain a substantial proportion of amino acids such as phenylalanine, valine, leucine, etc., with nonpolar side-chain residues. These nonpolar groups should tend, therefore, other factors permitting, to cluster on the... 

The amino acids with nonpolar, aliphatic side chains, Ala, lie. Leu, Met, and Val, are sufficiently hydro-phobic that they are most often buried in the generally hydrophobic core of non-membrane-embedded proteins. Note that lie and Val have particularly sterically hindered P-carbons. Of the aromatic amino acids. His, with a pK of around 6, will mostly be in the uncharged form at physiological pH values (therefore more often hydrophobic than polar), and will be a likely choice for reactions which involve proton transfer. Phe and Trp are clearly hydrophobic. Despite having a polar hydroxyl group, if we consider the free energy required to transfer... 

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