Hydrogen atoms, amino acids

Amino acids possess a carboxyl group and an amino or imino group. Most widespread are (X-amino acids, which have the general formula R—CHNHg—COOH. If R does not represent a hydrogen atom (%-amino acids are asymmetric. The primary metabolic amino acids belong to the L-series [2(S)-amino acids] ... 

Figure 2.32. Nitrogenase Mo-Fe protein from Azotobacter vinelandii. Hydrogen and amino acid atoms are not shown. Based on Protein Data Bank ID IMlN (Einsle et al, 2002). There are four sets of FegS and MoFe7S9N clusters, with one enlarged in Fig...

Primary and secondary amines possess replaceable amino hydrogen atoms. With acid chlorides (RCOCl) or anhydrides, (RCO)jO, they yield crystalline derivatives which are very useful in their separation and identification. Benzoyl derivatives are often preferred to acetyl derivatives because the former are less soluble and have higher melting points further, benzoyl chloride, unlike acetyl chloride, is not ea.sily hydrolyzed in water, and hence the acylation can be carried out in aqueous solutions. Tertiary amines do not react and therefore can be obtained unchanged. 

Numerous biphosphines appear to be good chiral ligands for the near-quantitatively enantioselective hydrogenation of amino acid precursors The two phosphorus atoms are connected by a chiral backbone having one asymmetric center or two. The general structure is easily prepared by alkylation of a disubstituted phosphide ... 

An a-amino acid contains an amino group a carboxyl group, a hydrogen atom and a distinctive R group - all of these are bound to an a-carbon atom. Amino acids in solution at neutral pH are in their zwitterionic form i.e., the -NH2 is present in the form of -NHa and the -C(X)H is present in the form of a deprotonated COO. This may be represented in the wedge and Fisher projection forms (Fig. 2.1). 

It is important to notice that the united-atom simplification cannot be applied to functional hydrogens which are involved in the formation of a hydrogen hond or a salt bridge. This would destroy interactions important for the structural integrity of the protein. Removing the hydrogen at the u-carbon of the peptide backbone is also dangerous, because it prevents racemization of the amino acid. 

With active methylene compounds, the carbanion substitutes for the hydroxyl group of aHyl alcohol (17,20). Reaction of aHyl alcohol with acetylacetone at 85°C for 3 h yields 70% monoaHyl compound and 26% diaHyl compound. Malonic acid ester in which the hydrogen atom of its active methylene is substituted by A/-acetyl, undergoes the same substitution reaction with aHyl alcohol and subsequendy yields a-amino acid by decarboxylation (21). 

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

All of the 20 amino acids have in common a central carbon atom (Co) to which are attached a hydrogen atom, an amino group (NH2), and a carboxyl group (COOH) (Figure 1.2a). What distinguishes one amino acid from another is the side chain attached to the Ca through its fourth valence. There are 20 different side chains specified by the genetic code others occur, in rare cases, as" the products of enzymatic modifications after translation. 

Figure 1.2 Proteins are built up by amino acids that are linked by peptide bonds to form a polypeptide chain, (a) Schematic diagram of an amino acid. Illustrating the nomenclature used in this book. A central carbon atom (Ca) is attached to an amino group (NH2), a carboxyl group (COOH), a hydrogen atom (H), and a side chain (R). (b) In a polypeptide chain the carboxyl group of amino acid n has formed a peptide bond, C-N, to the amino group of amino acid + 1. One water molecule is eliminated in this process. The repeating units, which are called residues, are divided into main-chain atoms and side chains. The main-chain part, which is identical in all residues, contains a central Ca atom attached to an NH group, a C =0 group, and an H atom. The side chain R, which is different for different residues, is bound to the Ca atom.

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 1.3 The "handedness" of amino acids Looking down the H-Ca bond from the hydrogen atom, the L-form has CO, R, and N substituents from Cq going In a clockwise direction. There is a mnemonic to remember this for the L-form fhe groups read CORN in clockwise direcfion.

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