Amino acids group 4- basic side chains

Amino acids with basic side chains Basic amino acids are the opposite of acidic amino acids. Their most important role is to form ionic bonds to negative ions—phosphate and the like. Lysine is a simple example. The side chain contains four CH2 groups and terminates in —NH3 +. Arginine has an even more basic, if somewhat more complicated and larger, side chain. Conversely, the side chain of histidine is not as basic as that of lysine and the concentrations of the unprotonated and protonated forms of histidine are almost equal at biological pH. Strong Lewis acid-Lewis base complexes between the unprotonated form of histidine and metal ions is very common in proteins. Histidine side chains are also involved in moving protons from one atom to another. 

The isoelectric point of utt amino acid depends on its structure, with values for the 20 common amino acids given in T le 26.1. The 15 amino acids with neutral or veakly acidic side chains- have i.soelectTic points near neutrality, in the pH rar S.O-6.5.The two- ankino acids with, more strongly acidic side chains have isoelectric points at lower pH, so that dissoctatim of the extra -COOll in the side chair, is suppressed und the three amino acids with basic side chains have isoelectric points at higher pH. so that protonation of the extra amino group is suppressed. 

Which amino acids have basic side chains (Group 4)... 

Reactive amino acid groups. The side chains of amino acids contain a variety of reactive residues. For example, histidine can accept and/or donate a proton to or from a substrate. In hydrolysis reactions, an acyl group can be bound to a serine side chain before it reacts with water. Having enzymes with these catalytic functions close to a substrate increases the rate of the reactions that use them. For example, a proton bound to histidine can be donated directly to a basic group on a substrate. 

Several amino acids have basic side chains. This essentially means that the R group in 50 has an amine unit attached to it. Lysine (67 R = [CH214NH2) has a primary amine, tryptophan (68 R = CH2-indole) has the indole unit, and histidine (69 R = CH2-imidazole) has an imidazole unit. All three of these amino acid side chains have a basic nitrogen. Arginine (70 R = [CH2] NHC[=NH]NH2) has a guanidine unit. Guanidine (71) is essentially the imine derivative of urea (72), and the NH2 unit is basic. 

The total of amino acids with basic side chains slightly exceeds those with free carboxyl groups. Collagen is thus a basic protein with an isoelectric point in the region of pH 9-4. 

It is interesting to note that the amino acid side chains may be either neutral as in valine, acidic as in glutamic acid or basic as in lysine. The presence of both acidic and basic side chains leads to proteins such as casein acting as amphoteric electrolytes and their physical behaviour will depend on the pH of the environment in which the molecules exist. This is indicated by Figure 30.2, showing a simplified protein molecule with just one acidic and one basic side group. 

Peptides and proteins are composed of a-amino acids linked by amide bonds (see Section 13.1). Their properties, for example the ability of enzymes to catalyse biochemical reactions, are dependent upon the degree of ionization of various acidic and basic side-chains at the relevant pH. This aspect will be discussed in more detail in Section 13.4, but, here, let us consider a simple amino acid dissolved in water at pH 7.0. An a-amino acid has an acidic carboxylic acid group and a basic amine group. Both of these entities need to be treated separately. 

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. 

The other amino acids are considered neutral, with no strongly acidic or basic side chains. Their isoelectric points are slightly acidic (from about 5 to 6) because the —NH3" group is slightly more acidic than the —COO- group is basic. 

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. 

Some amino acids, such as aspartic acid and lysine, have acidic or basic side chains. These additional ionizable groups complicate somewhat the acid—base behavior of these amino acids. Table 28.1 lists the pAT values for these acidic and basic side chains as well. 

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. 

Let us consider first an amino acid with a side chain that contains neither acidic nor basic groups— an amino acid, for example, such as alanine. 

If an amino acid contains a side chain that has an acidic or basic group, the equilibria become more complex. Consider lysine, for example, an amino acid that has an additional — NH2 group on its e carbon. In strongly acidic solution, lysine is present as a dication because both amino groups are protonated. The first proton to be lost as the pH is raised is a proton of the carboxyl group = 2.2), the next is from the a-aminium group... 

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