Amino acids

Amino acids cannot be analysed by GC unless suitable derivatives are prepared, which obviously is a disadvantage over other methods, such as paper, thin-layer and ion-exchange chromatography. On the other hand, the GC analysis of derivatives of amino acids is rapid, instrumentation can be used for a wide range of applications, the sensitivity of the analysis if high and there is the possibility of working with small amounts of samples. 

One-step procedures, advantageous as they may seem owing to their simplicity, have not been completely successful owing to the different reactivities of the various groups 

These derivatives for the analysis of amino acids have been widely investigated and various combinations of acyl and alkyl groups have been tested in order to find the properties most suitable from the viewpoint of chromatography, the reaction yields and the reaction time for the whole group of amino acids. Their preparation is based on the first, i.e., esterification step, when common esterification reactions are applied with minor modifications, and the second step, when amino and other functional groups are acylated with anhydrides, chlorides or other acylating agents. 

Esterification with higher diazoalkanes [205] has also been suggested. A 2-ml volume of 50% potassium hydroxide solution was added to 5 ml of diethyl ether in a small flask. N-n-Butyl(or propyl)-N-nitrosoguanidine (1 g) was suspended in diethyl ether and added to the flask through a separating funnel. The reaction was carried out in a water-bath at 45°C. The diazo compound have been passed through a cooler, was trapped in diethyl ether. Hydrochlorides of amino acids (about 5 mg) were dissolved in 4 ml of methanol 

The above esterification reagent, however, decomposes Trp considerably (up to 75% after 1 h) and therefore it is essential not to exceed the optimal time in order to obtain reproducible yields. 

Amino acids. Because of their zwitterionic nature, amino acids are soluble in water. Their solubility in organic solvents rises as the fat-soluble portion of the molecule increases. The likeliest impurities are traces of salts, heavy metal ions, proteins and other amino acids. Purification of these is usually easy, by recrystallisation from water or ethanol/water mixtures. The amino acid is dissolved in the boiling solvent, decolorised if necessary by boiling with Ig of acid-washed charcoal/lOOg amino acid, then filtered hot, chilled, and stood for several hours to crystallise. The crystals are filtered off, washed with ethanol, then ether, and dried. 

Amino acids have high melting or decomposition points and are best examined for purity by paper or thin layer chromatography. The spots are developed with ninhydrin (see Lederer and Lederer, p.44). Customary methods for the purification of small quantities of amino acids obtained from natural sources (i.e. l-5g) are ion-exchange chromatography (see p. 20) or countercurrent distribution (see p. 28). For general treatment of amino acids see Greenstein and Winitz [The Amino Acids, Vols 1-3, J.Wiley Sons, New York 1961]. 

A useful source of details such as likely impurities, stability and tests for homogeneity of amino acids is Specifications and Criteria for Biochemical Compounds, 3rd edn, 1972, National Academy of Sciences, USA]. 

Amino acids are the building blocks of proteins. A single protein consists of one or more chains of amino adds strung end to end by peptide bonds Hence the name polypeptide. You must be able recognize the structure of an amino acid and a polypeptide. A peptide bond creates the functional group known as an amide (an amine connected to a carbonyl carbon). It is formed via condensation of two amino acids. The reverse reaction is the hydrolysis of a peptide bond. 

Amino acids used by the human body are a-amino acids. They are called alpha-amino adds bt cause the amine group is attached to the carbon which is alpha to the carbonyl carbon, similar to a-hydrogens of ketones and aldehydes. 

Notice the R group on each amino acid. The R group is called the side chain of the amino acid. Nearly all organisms use the same 20 a-amino acids to synthesize proteins. Many amino acids and amino acid derivatives, such as hydroxyprotine and cystine, can be created by post-translational modifications after the polypeptide is formed. Ten amino acids are essential. ( Essential means that they cannot be synthesized by the body, so they must be ingested. Some books list 8 or 9 amino acids as essential. The discrepancy involves whether or not to list as essential those amino acids that are derivatives of other essential amino acids.) Each amino acid differs only in its R group. The R groups have different chemical properties. These proper- 

Polar side groups are hydrophilic and will turn to face an aqueous solution such as cytosol. Nonpolar side groups are hydrophobic and will turn away from an aqueous solution. These characteristics affect a proteiiTs tertiary structure. 

Electrophoresis can separate amino acids by subjecting them to an electric field. The electric field applies a force whose strength and direction is dependent upon the net chaise of die amino acid. If a solution of amino acids at a pH of f underwent electrophoresis, which of the following would most likely move the furthest toward the anode  

Amino acids, one of four kinds of small biomolecules that have important biological functions in the cell (Section 3.9), also undergo proton transfer reactions. 

Chapter 28 discusses the synthesis of amino acids and their conversion to proteins. 

Humans can synthesize only 10 of the 20 amino acids needed for protein synthesis. The remaining 10, called essential amino acids, must be obtained from the diet and consumed on a regular, almost daily basis. Diets that include animal products readily supply all the needed amino acids. Because no one plant source has sufficient amounts of all the essential amino acids, vegetarian diets must be carefully balanced. Grains—wheat, rice, and corn—are low in lysine, and legumes— beans, peas, and peanuts— are low in methionine, but a combination of these foods provides all the needed amino acids. Thus, a diet of corn tortillas and beans, or rice and tofu, provides all essential amino acids. A peanut butter sandwich on wheat bread does, too. 

The 20 amino acids that occur naturally in proteins differ in the identity of the R group bonded to the a carbon. The simplest amino acid, called glycine, has R = H. When the R group is any other substituent, the a carbon is a sterer enic center, and there are two possible enantiomers. 

Amino acids exist in nature as only one of these enantiomers. Except when the R group is CH2SH, the stereogenic center on the a carbon has the S configuration. An older system of nomenclature names the naturally occurring enantiomer of an amino acid as the L isomer, and its unnatural enantiomer the D isomer. 

Amino acids were first studied as their esters by mass spectrometry in the late 1950 s and early 1960 s [136-138]. Although many free amino acids can be directly sublimed and give useful spectra, some decompose on heating while others, most noteably arginine and cystine, pyrolyse. These undesirable features prompted the search for derivatives which would permit either direct or reservoir introduction into the mass spectrometer of as many of the biological amino acids as possible. This was prior to the 

The mass spectral fragmentation reactions of a number of derivatives used in GC-MS have been reported including a series of esters of the JV-trifluoroacetates [152] and the pertrimethylsilyl derivatives [153-155] and their carbon-13- [156] and deuterium-containing analogues [157]. General reviews of the mass spectra of the common amino acids and their derivatives are also available [151,158]. 

An example of the sensitivity range which can be achieved by GC-MS is illustrated by the detection and semiquantitative determination of N-e-monomethyllysine and lysine in myosin hydrolysates isolated from heart cultures [159]. There are 620 residues of lysine to one of methyl-lysine in myosin. Operating in the selected ion mode these two compounds as their TFA-butyl derivatives can be estimated in a single run of injected sample from 4pmol of myosin. 

The procedure has been applied to the analysis of control urine and that from a patient with maple-syrup-urine disease. The results from 5 separate analyses in each case gave standard deviations of less than 10% of the mean. This was routinely achieved where the level of an amino acid was about 1 ng. 

Most work to date on the mass spectrometry of amino acids has employed electron impact ionization. Although this process gives spectra with adequate structural information for most applications in many instances the molecular ions are of very low intensity. As intense M +1 ions are given by all amino acids using chemical ionization, e.g. [161,162] there is little doubt that this process will find wide application in the future [163]. 

Amino acids can be classified according to their substituent R groups (Fig. 1.2 to Fig. 1.8) in basic amino acids, R contains a further amino group, whereas in acidic amino acids, R contains a further carboxyl group. In addition, there are aliphatic, aromatic, hydroxyl containing and sulfur containing amino acids according to the nature of the substituent, as well as a secondary amino acid. 

For convenience, the names for amino acids are often abbreviated to either a three symbol or a one symbol short form. For example. Arginine can be referred 

Amino acids can also be classified according to their polarity and charge at pH 6 to 7, which corresponds to the pH range found in most biological systems. This is often referred to as the physiological pH. Non-polar amino acids with no 

In addition to the 20 natural amino acids, there are other amino acids, which occur in biologically active peptides and as constituents of proteins. These will not be covered in this textbook. 

For every amino acid, there is a specific pH value at which it exhibits no net charge. This is called the isoelectric point, pi. At its isoelectric point, an amino acid remains stationary in an applied electric field, i.e. it does not move to the positive or negative pole. The isoelectric point can be estimated via the Henderson-Hasselbalch equation  

Amino acids have an aliphatic or aromatic chain that bears both the amine group NH2 and the carboxylic acid group COOH. These acids are more or less water-soluble. They are very important in biochemistry. 

Protein hydrolysis leads to amino acids. These amino acids, when heated, will decompose into carbon dioxide and ammonia. The aerobic or anaerobic decomposition of proteins and amino acids will always release more or less complex amines, which have a putrid smell, and carbon dioxide and ammonia if the decomposition is pursued further. 

Glycocol (aminoacetic acid) NH2CH2COOH, the simplest amino acid, has no action on aluminium. 

Aluminium resists putrefying organic matter well, which releases large amounts of carbon dioxide, ammoniac and amines. 

1 Amino Acids Detection of the molecular ion peaks of amino acids can be difficult. If we examine the mass spectra of amino acids, as well as of steroids and triglycerides, by a variety of ionization techniques, we can appreciate their relative merits. 

The El spectra of amino acids (Fig. 2.17a) or their esters give weak or nonexistent molecular ion peaks, but Cl and FD (Fig. 2.11b and c) give either molecular or quasimolecular ion peaks. The weak molecular ions in the El spectra arise since amino acids easily lose their carboxyl group and the esters easily lose their carboal-koxyl group upon electron impact. 

FIGURE 2.17. Mass spectra of leucine, (a) Electron impact (El). (b) Chemical ionization (Cl), (c) Field desorption (FD). 

The FD fragmentation pattern for leucine shows an MH+ (m/z 132) ion, that readily loses a carboxyl group 

2 Amino Acids. - In MAS NMR spectra of highly and uniformly C, N-enriched amino acids and proteins, homonuclear coupling interactions contribute significantly to the C linewidths, particularly for moderate applied magnetic 

Solid state NMR spectroscopy was applied to measure the isotropic chemical shifts, chemical shift anisotropies and asymmetry parameters of three phosphorylated amino acids, O-phospho-L-serine, O-phospho-L-threonine and O-phospho-L-tyrosine. The CP buildup rates and longitudinal relaxation times of P and H were determined and compared with the values measured for a triphosphate bound to a crystalline protein. It was shown that the phosphorylated amino acids are well-suited model compounds, e.g. for the optimisation of experiments on crystalline proteins. In addition, from 2D exchange experiments on O-phospho-L-tyrosine the existence of an exchange between the two different conformations of the molecule was deduced. 

Chan and Tycko have reported a new technique suitable for the determination of the backbone torsion angle i ) in peptides with isolated uniformly labelled residues.  

CD and X-ray crystallography have been applied to study the conformational properties of peptides of p -aminoxy acids (NH2OCHRCH2COOH) having different side chains on the P carbon atom. Theoretical studies on a series of model diamides were also used to rationalise the experimentally observed conformational features of the p -aminoxy peptides. 

The fully extended peptide conformation has been investigated for the first time in the solid state by CP MAS NMR. The compounds examined were members of a terminally protected, homo-oligopeptide series (from monomer through hexamer) based on C ,C -didehydroalanine. 

The amino acids like the hydroxy acids and the halogen acids belong to the class of substituted acids. In them an amino group (—NH2) is substituted in the non-carboxyl part of the acid. They were not discussed with the other substituted acids because we wished to consider at one time both the amino acids derived from mono-basic acids and those derived from di-basic acids in connection with the proteins which we shall find are related compounds. 

Synthesis from Halogen Acids.—The simplest method for the synthesis of amino acids is by the action of ammonia on the halogen acids and is exactly analogous to the formation of alkyl amines from alkyl halides. 

From Aldehydes.— Aldehydes and ketones by the hydrogen cyanide reaction yield cyan-hydrine compounds which are nitriles of hydroxy acids. When such an hydroxy acid nitrile is treated with ammonia the hydroxyl group is replaced by the amino group forming the nitrile of the amino acid, the amino acid itself being obtained on hydrolysis of the nitrile. 

By this synthesis, it will be noticed that the alpha- immo acids result as the amino group is always linked to the carbon to which the carboxyl is also linked. The amino acid will also contain one more carbon than the aldehyde or ketone due to the addition of the cyanide radical, i.e.y acetic aldehyde yields amino propionic acid and propanone (acetone) yields amino iso-butyric acid. 

From Oximes and Hydrazones.—The oximes and hydrazones obtained from ketone acids yield amino acids on reduction with sodium amalgam and glacial acetic acid. 

In a-amino acids, the L-compounds are those in which the NH2 group is on the left-hand side of the Fischer projection in which the COOH group appears at the top. 

For all the amino acids in the table, except for cysteine, the L-form has the -configuration. For cysteine, the L-form has the f -configuration, because the -CH2SH group has higher priority than -COOH according to the sequence rule (see Chapter 7). 

Other abbreviations that may be encountered in the literature include those listed in Table 5.5. 

Name Abbreviations R Group (Side Chain) Molecular Formula 

Note Nonprotein amino acids are marked. Three-letter codes in brackets are not recommended.  

Simple amino acids are the basic building blocks of proteins. Their structures contain both an amino group, usually a primary amine, and a carboxylic acid. The relative positions of these groups vary, but for most naturally occurring 

Fundamentals of Medicinal Chemistry, Edited by Gareth Thomas 

-y etc. depending on the relative positions of the amine and carboxylic acid groups. 

The structures of amino acids can also contain other functional groups besides the amine and carboxylic acid groups (Table 1.1). Methionine, for example, contains a sulphide group, whilst serine has a primary alcohol group. 

CH3CHCH2CH(NH2)COOH H2NCH2CH2CH 2CH2CH(NH 2)COOH Lysine Lys K 9.7 

Acidic amino acids (aspartic acid + glutamic acid) predominate in tree nuts (Table 2.5). Similar to other plant proteins, tree nut proteins are incomplete proteins. When compared to the Food and Agricultural Organization (FAO) and World Health Organization (WHO)-recommended pattern for essential amino acids for a 2-5 year old, ttyptophan is the first limiting amino acid in all tree nuts except macadamia, where lysine is the first. However, compared to the FAO- and WHO-reconunended essential amino acid pattern for an adult, only almond is deficient in sulfur amino acids (methionine -I- cysteine), whereas all others contain adequate amounts of all of the essential amino acids. 

Several amino acids, such as glycine and gamma-aminobutyric acid (GABA), are important inhibitory transmitters in the brain and spinal cord. Glycine seems to be the inhibitory transmitter used by certain interneurons located throughout the spinal cord, and this amino acid also causes inhibition in certain areas 

The history of amino acids begins four billion years ago. The Earths atmosphere then consisted of water vapour, carbon dioxide, nitrogen, carbon monoxide, hydrogen, methane and ammonia. It was hot, and for millions of years lightning flashes discharged across the sky (Fig. 4.1). Under these conditions initially aldehydes and hydrogen cyanide originated, and therefrom amino adds were produced (by Strecker reaction). 

2 By using Stanley Miller s apparatus, it became possible to prove that the building blocks of life had their origin in the prebiotic atmosphere. 

Even more convincing than the spectroscopic proof of amino acids in the imiverse is the chemical analysis of chondrites (meteorites). Seventeen amino acids were discovered in the Murchison chondrite, which was found in Australia ten of these do not occur in Nature (on Earth). In terms of the total amino acid content of the Murchison chondrite, about one third consists of glycine. 

3 The Great Orion Nebula M42 is located in the so-called sword area underneath the star Alnitak in Orion s Belt. 

The Orion nebula contains dust, and it may be assumed that new stars can be formed in this area. 

Tamura, M. Kagotani, Y. Furukawa, Y. Amino, and Z. Yoshida, Tetrahedron Lett., 1981, 22, 3413. 

Heidelberger, A. Guggisberg, E. Stephanou, and M. Hesse, Helv. Chim. Acta, 1981, 64, 399. 

Reagents i, Ph3P=CHC02Mej ii, Hj-Pt iii, HCl-AcOH iv, EtOH-SOjCl 

Reagents i, MeMgl ii, KDA iii, RCHO iv, ClSiMe3 v, MeC02H-H20 vi, BOC-s-reagent 

Schdilkopf, H. Hausberg, M. Segal, U. Reiter, I. Hoppe, W. Saenger, and K. Lindner, Liebigs Ann. Chem., 1981, 439. 

The complexes of amino acids with copper are formed according to the general reaction shown in Equation 7.14 [47]. The formation constants for the copper-amino acid complexes are generally greater than that for copper ammonia complex [48]. Therefore, it is anticipated that amino acids should be more effective than ammonia in assisting the dissolution of oxidized copper during CMP. 

Carboxylic acids which contain the amino group (— NH2) are called amino acids. 

Amino acids show basic properties because of the amino group (— NH2) and acidic properties because of the carboxyl group (— COOH), so they are amphoteric compounds. Amino acids act as a base when they react with an acid and act as an acid when they react with a base, in both cases a salt is formed. 

Proteins are polymers of amino acids. Proteins are extremely important since they have a wide range of biological significance. They serve as nutrients, enzymes, cellular products of genes by translation (reflects the hereditary information), building material of muscles and other biologically important structures. 

Amino acids are the monomeric units of proteins. The general structure of an amino acid is as follows  

In the above diagram representing an amino acid, the characteristic amino and carboxyl groups are indicated by the arrows. Amino acids combine with other amino acids to form peptides. 

All proteins are composed of amino acids linked into a linear sequence by peptide bonds between the amino group of one amino acid and the carboxyl group of the preceding amino acid. The amino acids found in proteins are all a-amino acids i.e., the amino and carboxyl groups are both attached to the same carbon atom (the a-carbon atom Fig. 3-1). The a-carbon atom is a potential chiral center, and except when the —R group (or side chain) is H, amino acids display optical activity. All amino acids found in proteins are of the l configuration, as indicated in Fig. 3-1. 

There are 20 different amino acids used in the synthesis of proteins these amino acids are listed in Table 3.1, which also contains the two commonly used symbols for each amino acid. The three-letter symbols are easier to remember, but the single-letter symbols are often used in writing long sequences. In many proteins some of the amino acids are modified after incorporation into proteins e.g., in collagen, a hydroxyl group is added to each of several proline residues to yield hydroxyproline residues. With the exception of proline, the a-amino acids that are incorporated into proteins can be represented by the formula shown in Fig. 3-1. 

The side chains of the amino acids do not form a natural series, and thus, there is no easy way to learn their structures. It is useful to classify them according to whether they are polar or nonpolar, aromatic or aliphatic, or acidic or basic, although these classifications are not mutually exclusive. Tyrosine, for example, can be considered to be both aromatic and polar, although the polarity introduced by a single hydroxyl group in this aromatic compound is somewhat feeble. 

The Greek symbols indicate the nomenclature of the carbon chains in certain amino acids. The carbon atom carrying (i.e.. next to) the carboxyl group is labeled a. 

Given that the molar absorbance coefficient of tyrosine in water is 1,420 L mol 1 cm-1 at 275 nm. what is the concentration of tyrosine in a solution of path length 1 cm for which the absorbance is 0.71  

A useful source of details such as likely impurities, stability and tests for homogeneity of amino acids is 

Specifications and Criteria for Biochemical Compounds, 3rd edrt. National Academy of Sciences, USA, 1972. 

Twenty-five known naturally occurring amino acids were isolated from various proteins by hydrolysis. All but one of them, glycine, possess an asymmetric carbon. Table 8.1 hsts the naturally occurring amino acids and gives their structures [26, 28, 31]. 

Among the above shown amino acids, a certain number are known as essential amino acids. They are not synthesized by human bodies and must be ingested for human metabolism. 

All the optically active amino acids (that means aU except glycine) have an l configuration. In addition, all amino acids exist as zwitterions. 

Correlations between the structures of amino acids and peptides and their I3C chemical shifts are of general interest for bio-, enzyme- and peptide chemists, since these compounds occur in all cells of living organisms. 

The results of several investigations of amino acids by 13C NMR can be summarized as follows [97, 785-793] (Table 5.25)  

For the synthesis of peptides, amino acid derivatives with protected amino or carboxy groups are used as starting materials. The application of 13C NMR spectroscopy for the control of the synthesis of those protected amino acids has ben reported in the literature [791, 792, 794]. 

The carbon atoms of some important protecting groups resonate in the following ranges [791,792,794] (Table 5.25) The carbonyl carbon of the t-bulyloxycarbonyl groups is found at 150 to 160, the quaternary carbon atom between 77 and 82 and the methyl group at 28 to 30 ppm. The aromatic carbons of benzyloxycarbonyl and benzyl groups 

Compound Amino acid moiety Protecting groups  

Although most of the biologically important amino acids are available commercially in tonne quantities, only a handful (Table 6.10) are manufac- 

Amino acid Method of manufacture Annual production (tonnes) 

Other compounds which interfere with the synthesis of the cellular membranes, for example some antibiotics such as penicillin and some surfactants, have a similar effect even when the concentration of biotin is not limiting. This manipulation of the conditions under which the organism grows to ensure the efficient excretion of the L-glutamic acid is reminiscent of the control of citric acid synthesis in A. niger (section 6.2.2.2). 

Some other organisms can produce L-glutamate from other substrates. Brevibacterium flavum will use acetate efficiently if copper (II) ions (25-250jUgl ) are added to the medium, while Nocardia erythropolis and Arthrobacter paraffineus will use hydrocarbons, although the yields are lower (60gl- ). 

After the fermentation the L-glutamate is precipitated at acid pH. The cells are separated from the fermentation broth and hydrochloric acid is added to the cleared broth to lower the pH to 3.2. This is close to the isoelectric point of glutamate, that is, the pH at which it has no net charge, and it precipitates as a crude solid. This can be further purified by ion-exchange chromatography. 

We first discuss the packing properties of a-amino acids containing non-polar residue groups which make only van der Waals intermolecular contacts. The 

(S)-Norleucine. The hydrogen-bonding arrangement a Molecular layer b Bilayer of molecules 

Main structural molecular characteristics of amino acids are a carboxylic acid and an amino group in one molecule. They can be coupled in a huge variation but only 22 of over 500 known amino acids are proteinogenic, that is, needed for the buildup of polypeptides and proteins. Selected proteinogenic amino acids are discussed in the following with respect to single-molecule detection and the effects of connecting two or more amino acids to a peptide. 

TERS experiments on amino acid monolayers have demonstrated that nanocrystalline gold plates provide an excellent substrate [63]. These plates show a surface roughness of 100-200 pm, which is essentially atomically flat. The hexagonal and triangular gold plates have a height of about 20 5 nm and 

The next step toward understanding TER spectra of proteins was the investigation of small peptides. In those experiments, the detection of the peptide bond was of particular interest. In a comparative Raman, SERS, and STM- TERS studies of dipeptides, a tripeptide, and a protein, results were presented by Blum et al. in 2012 [65]. Experiments were performed with an STM—TERS setup, which enables a precise sample-tip distance control, which can be applied to either conductive samples or very thin ( l-2 nm) samples on a conductive substrate. In contrast to AFM-based experiments, some additional effects regarding the actual voltage bias between tip and sample must be carefully considered [68]. Using the dipeptides 

In conclusion, TERS allows a clear characterization and distinction of selected amino acids and small peptides. The observed orientation effects could be explained by the small number of molecules contributing to a TERS signal. 

The four nucleobases guanine (G), adenine (A), thymine (T), and cytosine (C) are the essential molecules in the biomacromolecules DNA and RNA. 

There is a very large difference in reactivity between a-amino acids and small peptides derived from them. Even the presence of functional sidechains on amino acids has minimal influence on their reactivity. In contrast, with peptides the sidechains on the amino acid residues can strongly influence reactivity and lead to a variety of different complexes. The sidechains are critically important in vanadiumbinding enzymes, where they are essential to the binding process. Furthermore, judicious use of appropriate groups in affinity chromatography can provide exceedingly effective methods for isolation and purification of enzymes [64], 

The identities of the two VL complexes are not known with certainty, but the available evidence suggests the -557 ppm-type products arise from monodentate reaction at the carboxylate group, whereas the -544 ppm products derive from monodentate reaction at the nitrogen functionality. Additional products from amino acids with reactive sidechains, as found in serine or aspartic acid, have not been reported.51V chemical shifts for products formed with histidine are similar to those observed for other amino acids, except that an additional signal (-571 ppm) has been observed [66], 

Proteins are naturally occurring polyamides, polymers of a-amino acids. The structure can be illustrated as follows  

In this section, the structure, function, and reactivity of amino acids, peptides, and proteins will be discussed with the goal of providing a foundation for successful derivatization. The interplay of amino acid functionality and the three-dimensional folding of polypeptide chains will be seen as forming the basis for protein activity. Understanding how the attachment of foreign molecules can affect this tenuous relationship, and thus alter protein function, ultimately will create a rational approach to protein chemistry and modification. 

The side chains do not participate in polypeptide formation and are thus free to interact and react with their environment. 

All of the aliphatic and aromatic hydrophobic residues often are located at the interior of protein molecules or in areas that interact with other non-polar structures such as lipids. They usually form the hydrophobic core of proteins and are not readily accessible to water or other hydrophilic molecules. 

Unprotonated Primary Amine Containing Molecule (a-amine or lysine e-amines of proteins) 

Tyrosine contains a phenolic side chain with a pKa of about 9.7-10.1. Due to its aromatic character, tyrosine is second only to tryptophan in contributing to a protein s overall absorptivity at 275-280nm. Although the amino acid is only sparingly soluble in water, the ionizable nature of the phenolic group makes it often appear in hydrophilic regions of a protein—usually 

Peptides and proteins are composed of amino acids polymerized together through the formation of peptide (amide) bonds. The peptide bonded polymer that forms the backbone of polypeptide structure is called the a-chain. The peptide bonds of the a-chain are rigid planar units formed by the reaction of the a-amino group of one amino acid with the a-carboxyl group of another (Fig. 1). The peptide bond possesses no rotational freedom due to the partial double bond character of the carbonyl-amino amide bond. The bonds around the a-carbon atom, however, are true single bonds with considerable freedom of movement. 

The sequence and properties of the amino acid constituents determine protein structure, reactivity, and function. Each amino acid is composed of an amino group 

FigutG 1 Rigid peptide bonds link amino acid residues together to form proteins. Other bonds within the polypeptide structure may exhibit considerable freedom of rotation. 

Rgure 2 Individual ammo acids consist of a primary (a) amine, a carboxylic acid group, and a unique side chain structure (R). At physiological pH the amine is protonated and bears a positive charge, while the carboxylate is ionized and possesses a negative charge. 

A typical protein chain is formed by the peptide repeating unit (—CO—NH— —C HR—) where R is an aliphatic or aromatic substituent of the amino acid and often referred to as the amino acid side chain . Most of the observed Raman bands 

Baldwin and coworkers reported strong complexing properties of certain amino acids such as tyrosine, tryptophan, methionine and cysteine with copper ions, due 

The geometric structure of the chelation on Cu is also essential as Cu 0 is less free on the electrode surface than the Cu metal ion in aqueous solution. Based on these mechanisms, the free amino acids would be more steadily accessible to the Cu 0 reachon site than would peptides and proteins and the density of functional -COO and -N termini, size and geometric folding of which could stericaUy hinder the Cu A2 structure at the Cu SPE surface. Although not related directly to any medical diagnosis, this application may prove to be valuable in the diagnosis of congenital amino acid-associated disorders of tyrosine and phenylalanine metabolism. 

The classical work of Dawson and Pritchard [40] on the determination of a-amino acids uses a standard amino acid analyser modified to incorporate a fluorometric detection system. In this method the samples are desalinated on cation exchange resins and concentrated prior to analysis. The output of the fluorometer is fed through a potential divider and low-pass filter to a compensation recorder. 

An example of a chromatogram obtained from a saline sample and the mole percentage of each amino acid in the sample is depicted in Fig. 4.5. 

The Miller-Urey reaction has been quite successful in duplicating these results. All 20 amino acids identified in meteorites, and 12 others, were produced by electric discharges on CH4-NH3-H2O-H2 mixtures, in the presence of an aqueous phase (Ring et al., 1972 Wolman et al., 1972). Even the proportions of the various amino acids resemble those in Murchison to within 1-2 orders of magnitude. 

The FTT synthesis has given less impressive results, having produced only 11 definite and 8 tentative matches (Yoshino et al., 1971 Hayatsu et al., 1971). Total yields were 0.01-0.1%, much less than in the Miller-Urey synthesis (2%), though similar to the abundance in meteorites ( 0.1% of the organic carbon). The product. distribution again was fairly similar to that in meteorites, but also included aromatic or heterocyclic amino acids such as tyrosine and histidine that cannot be made by conventional Miller-Urey syntheses. In the present context, that is a liability rather than an asret, since these amino acids have not been found in meteorites either. 

These differences may reflect mainly the effort expended on the two methods, rather than their intrinsic merits. The FTT work was done before the meteorite results became available, and so many of the non-protein amino acids simply were not looked for. Also, both syntheses persumably involve the same two steps (Miller et al., 1976) formation of unstable intermediates at high T, and rapid quenching and hydrolysis of the reaction products. The standard Miller-Urey flask, with its small spark zone and large liquid phase, is an optimal configuration for this purpose, in contrast to the FTT flask, where the hot and cold zones are in reverse ratio. If the intermediates and reaction paths indeed are similar (Miller et al., 1976), then it should be possible to improve yields in the FTT synthesis merely by changing the configuration of the apparatus, to provide a larger cold zone and faster quench. 

The close match of the amino acid distributions in meteorites and the Miller-Urey synthesis suggests that the meteoritic amino acids were produced by the essential steps of the Miller-Urey synthesis. It is not yet clear what these essential steps would be in a nebular setting. Synthesis of intermediates obviously does not require an electric discharge, but can also be achieved from CO, NHj, and H2. The required 

The chemical state of the amino acids in Murchison has been studied in great detail. About 80% exist in water-soluble form (Kvenvolden et al., 1971), but only in part as free amino acids. When extracted with D O, some amino acids become partially deuterated whereas others do not (Lawless and Peterson, 1975). This suggests that some amino acids either have labile H atoms, or are produced by hydrolysis of precursors . 

During the 1980s, advances in fermentation technology allowed the economic production of a number of amino acids from starch hydrolyzates. Examples are lysine, threonine, tryptophan, methionine and cysteine. Starch-derived amino acids are generally used as animal nutrition supplements, enabling animal nutritionists to formulate 

Because of this partial double bond char- acter, the amide group is essentially planar. In addition, it is stiff and rotation around the amide C-N bond is highly restricted. Accord- ingly, rotations can only occur around two of the three bonds in each amino acid residue in a polypeptide chain and, as we will see, these rotations are limited by steric factors. But we are getting shead of ourselves here. What is the nature of the different groups, R, that determine the properties of each amino acid Besides, what is an amino acid So far we have only showed you amino acid segments that have been incorporated into chains. 

Amino acids have the general structure HOOC-CHR-NH2. There is a carboxylic acid on one end and an amine on the other. In-between there is a carbon atom that is attached to a hydrogen atom and a group we have simply labeled R. As we have already mentioned, it is the nature of this group that varies from one amino acid to another. 

Australian barnacles (Courtesy Keith Davy—www. mesa. edu.au). 

FIGURE 9-7 Schematic diagram of an L-amino acid group in a polypeptide chain. 

Primary amines are introduced here because they are one of the root compounds of the important series of compounds called the amino acids . 

If one or more of the hydrogen atoms on a carbon atom of an amine is replaced by a carboxylic acid group , COOH, as in NH2CH2COOH, then the series is called an amino acid because its members contain both an amine group and a carboxylic acid group. 

This unusual type of molecule is essential to all living things. It has a basic group (i.e. NH2) at one end and an acidic group (i.e. COOH) at the other end. This means that the molecules can have dual basic and acidic properties, depending on what environment it is in. This is an important property for molecules so vital for our body cells, which are subject to many changes of acidity. 

The acidity of a solution is more quantitatively defined as a pH value. This is a term that expresses the hydrogen ion concentration on a 1-14 scale. Solutions with pH 1-6 show acidic properties, pH 7 is neutral and solutions with pH 8-14 are basic. The lower the acidic scale is, the more acidic the solution alternatively, above 7, the more basic a solution is, the greater the value. 

For the biosynthesis of cell components a microorganism must be supplied with appropriate low molecular weight compounds such as sugars, organic acids, amino acids etc. Many of 2-, 3-, 4- and 5-carbon compounds are formed in catabolic reactions. In propionic acid bacteria these reactions comprise the propionic acid fermentation, TCA cycle and hexose monophosphate shunt. The latter supplies the cell with erythrose-phosphate, ribose-5-phosphate and reducing equivalents (NADPH) needed for many syntheses. Erythrose-4-phosphate is used in the formation of aromatic amino acids phenylalanine, tryptophane, tyrosine. Ribose-5-phosphate is incorporated into nucleic acids. The pentose cycle and propionic acid fermentation, as mentioned before, have a number of common precursors and enzymes. The inclusion of common precursors into one or another pathway is regulated by the level of ATP (Labory, 1970), and this regulation in fact determines the ratio of catabolic and anabolic processes in the cell. 

Protein synthesis in propionibacteria is accompanied by the generation of a pool of 16 amino acids cysteine, histidine, arginine, aspartic and glutamic acids, glycine, serine, threonine, alanine, tyrosine, valine, methionine. 

In other raw materials, too, protein enrichment occurs for various reasons protein concentration in the raw material may be too low for certain purposes, the sensory characteristics of the material (color, taste) may not be acceptable, or undesirable constituents may be present. Some products rich in protein also result from other processes, e.g., in oil and starch production. Enrichment results from the extraction of the con- 

Kirk-Othmer Encyclopedia of Chemical Technology (4th Edition) 

Amino acids are the main components of proteins. Approximately twenty amino acids are common constituents of proteins (1) and are called protein amino acids, or primary protein amino acids because they are found in proteins as they emerge from the ribosome in the translation process of protein synthesis (2), or natural amino acids. In 1820 the simplest amino acid, glycine, was isolated from gelatin (3) the most recendy isolated, of nutritional importance, is L-threonine which was found (4) in 1935 to be a growth factor of rats. The history of the discoveries of the amino acids has been reviewed 

Hydroxylated amino acids (eg, 4-hydroxyproline, 5-hydroxylysine) and A/-methylated amino acids (eg, /V-methylhistidine) are obtained by the acid hydrolysis of proteins. y-Carboxyglutamic acid occurs as a component of some sections of protein molecules it decarboxylates spontaneously to L-glutamate at low pH. These examples are formed upon the nontranslational modification of protein and are often called secondary protein amino acids 

The presence of many nonprotein amino acids has been reported in various living metaboUtes, such as in antibiotics, some other microbial products, and in nonproteinaceous substances of animals and plants (7). Plant amino acids (8) and seleno amino acids (9) have been reviewed. 

The asterisk signifies an asymmetric carbon. AH of the amino acids, except glycine, have two optically active isomers designated D- or L-. Isoleucine and threonine also have centers of asymmetry at their P-carbon atoms (1,10). Protein amino acids are of the L-a-form (1,10) as illustrated in Table 1. 

An element is a pure substance that cannot be broken down into simpler substances by ordinary chemical techniques. Elements combine with one another in different amounts to form everything from air, to food, to tools, to the human body. 

There are some 118 known elements, but only 4 elements make up 99% of living organisms. These elements are hydrogen (H), oxygen (0), nitrogen (N), and carbon (C), and they are special because they are widely available everywhere and also suitable for the chemistry of life. 

The table shows a lis names, which can be called Ala or simpl of the 20 standard amino acids and the abbreviations of their a 3-letter code or a single letter. For example, alanine can be IT A.  

AMINO ACID 3-LETTER CODE 1-LETTER CODE R GROUP 

Like all other amino acids, the alpha carbon has a bond to a COOH group and another to a NH2 group. But unlike the others, 

L-glutamic acid or its salt, monosodium glutamate (MSG), is used as an additive to human food to enhance the taste. Although seaweed had been used in Asia to enhance food flavor for over 1000 years, it was not 

The fermentation uses glucose-containing organic feedstock it is aerobic and the L-glutamic acid is excreted by the cell into the surrounding liquid medium. The glutamic acid is separated from the fermentation broth by filtration the filtrate is concentrated and the acid is allowed to crystallize. MSG is manufactured on a large scale in many countries and is an additive in many food items. The worldwide production is estimated to be 800,0001. 

Amino acid Starting material Microorganism Remarks 

L-aspartic acid Fumaric acid Escherichia coli (aspartase)  

L-Dopa L-tyrosine o-Catechol or phenol, ammonia, pyruvate Erwinia herbicola  

The glyoxylate-ene reaction, promoted by the Ti-BINOL complex, produces chiral a-hydroxy esters, which provide an easy access to the corresponding carboxylic acid derivatives bearing a chiral center at the a position. The adduct between the glyoxylate and exo olefin is proposed as a key intermediate of the collagenase-selective inhibitor, Trocade (Hoffmann-La Roche) [20]. This remarkable process has been developed for large-scale production. 

60% ) are obtained in alkylations of related Schiff s bases derived 

Other than glycine can be resolved with ee s of up to 63% by asymmetric protonation of the derived enolates using a chiral amine 

The Schollkopf bis-lactim ether method can be used to prepare (D)-glutamic acid and a number of substituted homologues with 

An alternative to the bis-lactim ether approach is based on condensations of saturated five-membered heterocycles such as imidazolidinone (532) which can now be obtained in an optically pure state by a straightforward classical resolution/ The related oxazolidinone (533) has been obtained from methionine and used to prepare (R)-amino-acids [cf. (528) ] as well as the vinyl substituted derivatives(534) by oxidation and elimination of the sulphur group. Yet more general routes to chiral amino—acids have been reported using a variety of asymmetrically substituted ester enolate equivalents (535) in combination with the electrophilic nitrogen source di-t-butyl 

All give excellent enantiomeric enrichments in the final products [(523) or (528)] and generally, but not always, excellent chemical yields for many targets there seems to be little to choose between the individual sequences. Similarly excellent asymmetric inductions have been achieved in condensations between imines [e.g. (537)] and 

The best and most efficient pharmacy is within your own system. 

Amino acids are extremely important to living systems because they form the bases of the many proteins necessary for life. There are 20 common amino acids that function as protein building blocks (Table 3.6.2). There are at least 31 additional amino acids not commonly part of natural proteins among these are some hormones and neurotransmitters (Garrett and Grisham, 1999). 

FIGURE 15.8 Two moisturizing lotions, one with a water-in-oii emuision (Nivea) and the other an oii-in-water emuision (Keri). 

The hydrocarbon end of a soap or detergent molecule is (hydrophilic, hydrophobic) while the polar end is (hydrophilic, hydrophobic). 

Which is more likely to precipitate the hard-water ions (Ca, Mg +, Fe ) as a sticky precipitate (a) Traditional soaps (b) Synthetic detergents. 

All proteins are condensation polymers of amino acids. A large number of 

000 different proteins. It is amazing that all these proteins are derived alpha-amino group and a carboxyl from only 20 different amino acids (Table 15.5). Even more amazing is group building blocks of proteins 

Nucleophilic attack of azide provides the potentially useful azide derivative (457). High asymmetric inductions occur in condensations of the lithium carbanion (452 R =H) or the corresponding titanium derivative with glyceraldehydes or 

A new route to racemic a-amino-acids in general consists of an overall a-amination of simple carboxylic acid esters in a relative of the Japp-Klingermann reaction, a method which is usually only successful with active methylene compounds such.as malonates. Thus, 0-silyl-enolates of esters (464) condense with benzenediazonium tetrafluoroborate to give, after isomerization, 

Presumably dipole stabilization by the adjacent amido carbonyl group is the key to this reaction, which is certainly more economical than related methods in which the dianion of the ester 

Most of the general methods for preparing a-amino-acids are 

Nucleophiles potentially can attack a-imino-esters at three sites the ester group, the imine carbon, or the imine nitrogen. 

Proteins are complex organic compounds of high molecular weight. In common with carbohydrates and fats they contain carbon, hydrogen and oxygen, but in addition they aU contain nitrogen and generally sulphur. 

Proteins are foimd in aU living cells, where they are intimately connected with all phases of activity that constitute the life of the cell. Each species has its own specific proteins, and a single organism has many different proteins in its cells and tissues. It follows therefore that a large number of proteins occur in nature. 

Amino acids are produced when proteins are hydrolysed by enzymes, acids or alkalis. Although over 200 amino acids have been isolated from biological materials, only 20 of these are commonly found as components of proteins. 

The exception is proline, which has an imino ( NH) instead of an amino group. The nature of the R group, which is referred to as the side chain, varies in different amino acids. It may simply be a hydrogen atom, as in glycine, or it may be a more complex radical containing, for example, a phenyl group. 

The chemical structures of the 20 amino acids commonly found in natural proteins are shown in Table 4.1. 

Analyte Analyzed sample HPLC mode Electrochemical detection References 

Secondary amino acids Gelatine HPAEC IPAD (Au) [85] 

carnosine, anserine, and glutamine Ostrich meat RP-HPLC Amperometric detection (CuNP) [95] 

D-Ala Fruit concentrate or purees HPCEC ER-amperometric detection (Pt) [96] 

Proteins are the workhorses of living organisms. Biological chemistry is all about proteins. 

Protein molecules are composed of long chains of amino acids strung together in a highly specific order. One end of an amino acid has a nitrogen (amino) group, usually shown as -NH. The other end has a -COOH group, which you may recall 

When we eat foods that contain protein, digestive enzymes break the protein molecules apart into their component amino acid molecules. One of two things can happen to the amino acid molecules after they are absorbed into the body through the walls of the small intestine. Either they can be used to synthesize other amino acids that the body needs but which were not in the original protein molecules, or, they can remain unchanged. Either way, a reservoir of amino acids is present in the body s cells that can be used to produce new protein molecules. 

Essential amino acids are those that the human body cannot synthesize, so they have to come from foods that we eat. A diet that includes any animal products provides all of the 

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X-alanine, 2-aminopropanoic acid, C3H7NO2, CH3.CH(NH2)C00H. M.p. 297X. One of the amino-acids obtained by the hydrolysis of proteins. 

Certain other amino-acids occur in a few proteins, and others, not necessarily a- or l-amino-acids, are found naturally in the free state or as constituents of peptides. 

The amino-acids are colourless, crystalline substances which melt with decomposition. They are mostly soluble in water and insoluble in alcohol. 

As constituents of proteins the amino-acids are important constituents of the food of animals. Certain amino-acids can be made in the body from ammonia and non-nitrogenous sources others can be made from other amino-acids, e.g. tyrosine from phenylalanine and cystine from methionine, but many are essential ingredients of the diet. The list of essential amino-acids depends partly on the species. See also peptides and proteins. 

M.p. 207°C. The naturally occurring substance is dextrorotatory. Arginine is one of the essential amino-acids and one of the most widely distributed products of protein hydrolysis. It is obtained in particularly high concentration from proteins belonging to the prolamine and histone classes. It plays an important role in the production of urea as an excretory product. 

H2N (CH2]5 NH2. a syrupy fuming liquid, b.p. 178-180 - C. Soluble in water and alcohol. Cadaverine is one of the ptomaines and is found, associated with pulrescine, in putrefying tissues, being formed by bacterial action from the amino-acid lysine. It is found in the urine in some cases of the congenital disease cystinuria. The free base is poisonous, but its salts are not. 

Decarboxylases, which are highly specific for individual amino-acids, decarboxylale these to amines. 

M.p. 246-250°C (decomp.). A dipeptide present in mammalian muscle. Like anserine it contains the amino-acid -alanine which is not found in proteins. 

Copper III) is known in complex oxides and fluorides and in amino-acid complexes. 

Crystalline solid m.p. 35-36 "C, b.p. 154--156 C, prepared by oxidizing A,A -dicycIo-hexylthiourea with HgO in carbon disulphide solution, also obtained from cyclohexylamine and phosgene at elevated temperatures. Used as a mild dehydrating agent, especially in the synthesis of p>eptides from amino-acids. Potent skin irritant. 

CgHiiNO. M.p. 282 C (decomp.). The naturally occurring substance is laevorotatory. It is an amino-acid isolated from various plant sources, but not found in the animal body. It is formed from tyrosine as the first stage in the oxidation of tyrosine to melanin. It is used in the treatment of Parkinson s disease. 

C4H6N2O2. Sublimes 260"C sparingly soluble in water hydrolysed by alkalis or mineral acids to glycylglycine. It and substituted dike-topiperazines are formed by the condensation of amino-acids, and are obtained in small quantities on the hydrolysis of proteins. 

CfiHqNaO . M.p. 277 C. The naturally occurring substance is laevorotatory. Histidine is one of the basic amino-acids occurring in the hydrolysis products of proteins, and particularly of the basic proteins, the protamines and histones. It is an essential constituent of the food of animals. 

Insulin is built up of two polypeptide chains. A of 21 amino-acids and B of 30 amino-acids, linked by two disulphide bridges. 

C(,Hi3N02, CH3 CH2-CHMe-CHNH2-COOH. Colourless crystals, m.p. 284 C (decomp.). The naturally occurring substance is dextrorotatory. An amino-acid, occurring with leucine as a product of protein hydroly-... 

H2N-CH2 [CH2j3.CH(NH2) COOH. Colourless needles, m.p. 224 C (decomp.), very soluble in water, insoluble in alcohol. L-(-H)-Lysine is one of the basic amino-acids occurring in particularly large quantities in the protamine and histone classes of proteins. It is an essential amino-acid, which cannot be synthesized by the body and must be present in the food for proper growth. It can be manufactured by various fermentation processes or by synthesis. 

M.p. 283 C (decomp.). Soluble in water and alcohol. The naturally occurring substance is laevorotatory. Methionine is one of the natural sulphur-containing amino-acids, and is present in small quantities in the hydrolysis pro-... 

Transfer or soluble RNAs are specific carrier molecules for amino-acids during protein synthesis on ribosomes with ribosomal RNA as the template. There is at least one t-RNA molecule for each amino-acid. 

The same nomenclature has been adopted for amino-acids, the configurational family to which the a-carbon atom belongs being denoted by the prefixes d- and L-. 

M.p. 140°C. An amino-acid occasionally formed in the hydrolysis products of proteins and occurring in the urine of some birds as dibenzoylornithine. Ornithine is a precursor of arginine in plants, animals and bacteria. 

An important laboratory use involves the Gabriel synthesis of a-amino-acids. 

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