Proteins common amino acids

Short chains of amino acid residues are known as di-, tri-, tetrapeptide, and so on, but as the number of residues increases the general names oligopeptide and polypeptide are used. When the number of chains grow to hundreds, the name protein is used. There is no definite point at which the name polypeptide is dropped for protein. Twenty common amino acids appear regularly in peptides and proteins of all species. Each has a distinctive side chain (R in Figure 45.3) varying in size, charge, and chemical reactivity. 

Amino acids are the molecular building blocks of peptides and proteins. About 20 common amino acids are known. 

Iteration of the reaction shown in Figure 4.2 produces polypeptides and proteins. The remarkable properties of proteins, which we shall discover and come to appreciate in later chapters, all depend in one way or another on the unique properties and chemical diversity of the 20 common amino acids found in proteins. 

The structures and abbreviations for the 20 amino acids commonly found in proteins are shown in Figure 4.3. All the amino acids except proline have both free a-amino and free a-carboxyl groups (Figure 4.1). There are several ways to classify the common amino acids. The most useful of these classifications is based on the polarity of the side chains. Thus, the structures shown in Figure 4.3 are grouped into the following categories (I) nonpolar or hydrophobic... 

The tendencies of the amino acids to stabilize or destabilize a-helices are different in typical proteins than in polyamino acids. The occurrence of the common amino acids in helices is summarized in Table 6.1. Notably, proline (and hydroxyproline) act as helix breakers due to their unique structure, which fixes the value of the —N—C bond angle. Helices can be formed from either... 

Table 26.1 The 20 Common Amino Acids in Proteins (continued) Name Abbreviations MW Stricture...

Humans can synthesize 12 of the 20 common amino acids from the amphiboHc intermediates of glycolysis and of the citric acid cycle (Table 28-1). While nutritionally nonessenrial, these 12 amino acids are not nonessential. AH 20 amino acids are biologically essential. Of the 12 nutritionally nonessential amino acids, nine are formed from amphibolic intermediates and three (cysteine, tyrosine and hydroxylysine) from nutritionally essential amino acids. Identification of the twelve amino acids that humans can synthesize rested primarily on data derived from feeding diets in which purified amino acids replaced protein. This chapter considers only the biosynthesis of the twelve amino acids that are synthesized in human tissues, not the other eight that are synthesized by plants. 

It is possible to calculate whether a particular sequence of amino acids present in a protein is consistent with a transmembrane location. This can be done by consulting a table that hsts the hydrophobicities of each of the 20 common amino acids and the free energy val-... 

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. 

In all, there are 2 —16 different ways to combine two amino acids in chains of four units. The 20 common amino acids combine to give 20 tetrapeptides, which is 1.6x10 different molecules. Each time the chain adds an amino acid, the number of possibilities is multiplied by 20, so a set of n amino acids can form 20 different pol q)eptides. Because proteins can contain hundreds of amino acids, each of which can be any of the 20... 

C13-0087. The smallest proteins contain about 50 amino acids. How many different proteins containing 50 amino acids can be formed from the 20 common amino acids Express your answer in power of 10 notation. 

If the environmental temperature is constant, the racemization process takes place at a uniform rate, which is determined, at any time during the process, by the relative amounts of / and d forms of the amino acid can be measured. As the racemization proceeds and the concentration of the / form amino acid decreases, the rate of racemization gradually slows down. When there is a mixture of 50% of each of the d and / forms, the racemization process stops altogether. The half-life of the racemization of aspartic acid, for example, a common amino acid in proteins, at 20°C is about 20,000 years. This half-life makes it possible to date proteins as old as about 100,000 years. So far, however, the dates obtained with the technique have proved somewhat inconsistent, probably because of the difficulty in verifying whether the temperature of the amino acids has been constant. 

In addition to the 20 common amino acids, some modified amino acids are also found in several proteins. These amino acids are normally altered via a process of post-translational modification (PTM) reactions (i.e. modified after protein synthesis is complete). Almost 200 such modified amino acids have been characterized to date. The more common such modifications are discussed separately in Section 2.5. 

There are 20 common amino acids in the human body. All amino acids contain a carboxylic acid group and an amino group. Amino acids can be linked by amide bonds to form proteins. Each amino acid has a different side chain, which is attached to the centre carbon atom. Figure 2.16, below, shows the structure of an amino acid. The letter G represents the side chain of the amino acid. Examples of side chains include —CH3 (for the amino acid alanine), —CH2CH2CONH2 (for glutamine), and —CH2OH (for serine). 

The functionalization of folded motifs is based on an understanding of secondary and tertiary structures (Fig. 2) and must take into account the relative positions of the residues, their rotamer populations and possible interactions with residues that do not form part of the site. For example, glutamic acid in position i has a strong propensity for salt-bridge formation, and thus reduced reactivity, if there is a Lys residue available i-4 in the sequence, but the probabihty is much less if the base is i-3 [60]. Fortunately, there is a wealth of structural information on the structural properties of the common amino acids from studies of natural proteins that provides considerable support for the design of new proteins. The naturally occurring amino acids have so far been used to construct reactive sites for catalysis [11-13], metal- and heme-binding sites [14,15,19,21,22] and for the site-selective functionalization of folded proteins [24,25]. 

Of the 20 amino acids that commonly occur in proteins, glycine has no side chain and alanine has the simplest side chain, a methyl group. Side chains for all the common amino acids of proteins are collected in figure 10.1. These are grouped into three categories. 

Enzymes dependent on folic acid as coenzyme include participants in the synthesis of thymine, an essential component of DNA, and methionine, a common amino acid in proteins, among other important metabolites. A deficiency of folic acid results in the disease megaloblastic anemia. 

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