Amino acid residues found In proteins

A FIGURE 3-12 Common modifications of internal amino acid residues found in proteins. These modified residues and numerous others are formed by addition of various chemical groups (red) to the amino acid side chains after synthesis of a polypeptide chain. 

Table IV. Hydroxylated Amino Acid Residues Found in Proteins...

Asparagine and glutamine are the amides of two other amino acids also found in proteins, aspartate and glutamate, respectively, to which asparagine and glutamine are easily hydrolyzed by acid or base. Cysteine is readily oxidized to form a covalently linked dimeric amino acid called cystine, in which two cysteine molecules or residues are joined by a disulfide bond (Fig. 3-7). The disulfide-linked residues are strongly hydrophobic (nonpolar). Disulfide bonds play a special role in the structures of many proteins by forming covalent links between parts of a protein molecule or between two different polypeptide chains. 

Transfer RNAs (tRNAs), the smallest of the three major species of RNA molecules (4S), have between 74 and 95 nucleotide residues. There is at least one specific type of tRNA molecule for each of the twenty amino acids commonly found in proteins. Together, tRNAs make up about fifteen percent of the total RNA in the cell. The tRNA molecules contain unusual bases (for example, pseudouracil, see Figure 22.2, p. 290) and have extensive intrachain base-pairing (Figure 30.3). Each tRNA serves as an "adaptor molecule that carries its specific amino acid—covalently attached to its 3-end—to the site of protein synthesis. There it recognizes the genetic code word on an mRNA, which specifies the addition of its amino acid to the growing peptide chain (see p. 429). 

Many amino acids, such as citrulline and ornithine (which are found in the urea cycle), are not building blocks of proteins. Other nonstandard amino acids, such as hydroxyproline, are formed after translation by posttranslational modification. When discussing amino acids and translation, the magic number was always 20. Only 20 standard amino acids were put onto tRNA molecules for protein synthesis. In the late 1980s, another amino acid was found in proteins from eukaryotes and prokaryotes alike, including humans. It is selenocysteine, a cysteine residue in which the sulfur atom has been replaced by a selenium atom. 

Proteins (and enzymes) consist of amino acids that are linked together by peptide (or amide) bonds (-CO-NH-) between the a-carboxyl (COOH) group of one residue and the a-amino (NH2) group of the next. The 20 amino acids usually found in proteins are listed in Tables 1.2 and 1.3. They differ only in their side... 

In the light of the structure of the enzyme (Chapter 6), we can see which parts of the amino-acid sequence of the protein have essential functions such as binding of the metal centres. Sure enough, these same amino acids are found in equivalent positions in the sequence of other [NiFe] hydrogenases they are said to be conserved. The regions of sequence that contain these conserved residues are known as motifs. By looking for these motifs, we can learn about possible structure and function of hydrogenases for which we have sequences but no X-ray structures. 

Another major effect, found in PGA, is optical inversion of L-glutamate to D-glutamate residues. One implication of the radiation-induced optical inversion in proteins is that some modification of amino acids may pass undetected by the usual chemical analyses which do not distinguish between l- and D-isomers. Furthermore, introducing a D-amino acid residue into a protein could have a far-reaching effect on the secondary and tertiary structures, and this could have a more serious effect on the functional properties of the molecule than changes in the side chains. One biological property of PGA which is affected by irradiation in solution is its hydrolysis by proteolytic enzymes. The conformation of the polymer has a marked effect on its susceptibility to hydrolysis by certain enzymes 27), and we have... 

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