Bonds amide

The backbone of polypeptides and, more generally, proteins is made up of a linear sequence of amino acids. 

Two of the three single bonds involved in each unit are flexible, and their detailed conformation dictates overall polypeptide structures and (ultimately) function. The amide bond is generally assumed to be rigid. Why (See also Chapter 10, Problem 1.) 

Examine the geometry of formamide. Is the CN bond shorter than expected for a normal single bond (in methylamine), and closer to that expected for a full double bond (in methyleneimine) Is the CO bond longer than that expected in a carbonyl compound (in formaldehyde), perhaps closer to that appropriate for a single bond (in methanol) Also, compare the electrostatic potential map for formamide with those of formaldehyde and methylamine. Is the CO bond in formamide more or less polar than that in formaldehyde Is the CN bond in formamide more or less polar than that in methylamine Draw whatever Lewis structures are needed to properly describe the geometry and charge distribution of formamide. 

Electrostatic potential map for formamide shows negatively-charged regions (in red) and positively-charged regions (in blue). 

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One starts with individual amino adds or with peptides and tries to achieve the regioselective formation of a new amide bond. In its most general form such syntheses of peptides involve the following stages ... 

This difference m reactivity especially toward hydrolysis has an important result We 11 see m Chapter 27 that the structure and function of proteins are critical to life Itself The bonds mainly responsible for the structure of proteins are amide bonds which are about 100 times more stable to hydrolysis than ester bonds These amide bonds are stable enough to maintain the structural integrity of proteins m an aqueous environment but susceptible enough to hydrolysis to be broken when the occasion demands... 

Amides are the least reactive caiboxyhc acid deiivative and the only nucleophilic acyl substitution reaction they undeigo is hydrolysis Amides are fanly stable m water but the amide bond is cleaved on heating m the presence of strong acids 01 bases Nomi nally this cleavage produces an amine and a caiboxyhc acid... 

The acid-base reactions that occur after the amide bond is broken make the overall hydrolysis irreversible m both cases The amine product is protonated m acid the car boxylic acid is deprotonated m base... 

The leader of DuPont s effort was Wallace H Carothers who reasoned that he could reproduce the properties of silk by constructing a polymer chain held together as is silk by amide bonds The neces sary amide bonds were formed by heating a dicar boxylic acid with a diamine Hexanedioic acid adipic acid) and 1 6 hexanediamme hexamethylenedi-amine) react to give a salt that when heated gives a polyamide called nylon 66 The amide bonds form by a condensation reaction and nylon 66 is an example of a condensation polymer... 

The product of this reaction is an imide (Section 20 16) a diacyl derivative of an amine Either aqueous acid or aqueous base can be used to hydrolyze its two amide bonds and liberate the desired primary amine A more effective method of cleaving the two amide bonds is by acyl transfer to hydrazine... 

Ammo acids are carboxylic acids that contain an amine function An amide bond between the carboxylic acid function of one ammo acid and the ammo nitrogen of another is called a peptide bond... 

A key biochemical reaction of ammo acids is their conversion to peptides polypeptides and proteins In all these substances ammo acids are linked together by amide bonds The amide bond between the ammo group of one ammo acid and the carboxyl of another IS called a peptide bond Alanylglycme is a representative dipeptide... 

Whereas acid catalyzed hydrolysis of peptides cleaves amide bonds indiscriminately and eventually breaks all of them enzymatic hydrolysis is much more selective and is the method used to convert a peptide into smaller fragments... 

Acid hydrolysis cleaves the amide bonds of the 2 4 dimtrophenyl labeled peptide giving the 2 4 dimtrophenyl labeled N terminal ammo acid and a mixture of unlabeled ammo acids... 

A major advance was devised by Pehr Edman (University of Lund Sweden) that has become the standard method for N terminal residue analysis The Edman degrada tion IS based on the chemistry shown m Figure 27 12 A peptide reacts with phenyl iso thiocyanate to give a phenylthwcarbamoyl (PTC) denvative as shown m the first step This PTC derivative is then treated with an acid m an anhydrous medium (Edman used mtromethane saturated with hydrogen chloride) to cleave the amide bond between the N terminal ammo acid and the remainder of the peptide No other peptide bonds are cleaved m this step as amide bond hydrolysis requires water When the PTC derivative IS treated with acid m an anhydrous medium the sulfur atom of the C=S unit acts as... 

Only the N terminal amide bond is broken m the Edman degradation the rest of the peptide chain remains intact It can be isolated and subjected to a second Edman procedure to determine its new N terminus We can proceed along a peptide chain by beginning with the N terminus and determining each ammo acid m order The sequence is given directly by the structure of the PTH derivative formed m each successive degradation... 

Couple the two protected ammo acids by amide bond formation between them... 

FIGURE 27 13 The mechanism of amide bond formation by W W dicyclohexylcarbodiimide promoted condensation of a carboxylic acid and an amine... 

Hydrazine cleaves amide bonds to form acylhydrazides according to the general mechanism of nucleophilic acyl substitution discussed in Chapter 20... 

Dipeptide (Section 27 7) A compound in which two a amino acids are linked by an amide bond between the amino group of one and the carboxyl group of the other... 

Peptide (Section 27 7) Structurally a molecule composed of two or more a ammo acids joined by peptide bonds Peptide bond (Section 27 7) An amide bond between the car boxyl group of one a amino acid and the ammo group of another... 

Polyamide (Section 20 17) A polymer in which individual structural units are joined by amide bonds Nylon is a syn thetic polyamide proteins are naturally occurring polyamides... 

An alternative approach to peptide sequencing uses a dry method in which the whole sequence is obtained from a mass spectrum, thereby obviating the need for multiple reactions. Mass spec-trometrically, a chain of amino acids breaks down predominantly through cleavage of the amide bonds, similar to the result of chemical hydrolysis. From the mass spectrum, identification of the molecular ion, which gives the total molecular mass, followed by examination of the spectrum for characteristic fragment ions representing successive amino acid residues allows the sequence to be read off in the most favorable cases. 

However, interpretation of, or even obtaining, the mass spectrum of a peptide can be difficult, and many techniques have been introduced to overcome such difficulties. These techniques include modifying the side chains in the peptide and protecting the N- and C-terminals by special groups. Despite many advances made by these approaches, it is not always easy to read the sequence from the mass spectrum because some amide bond cleavages are less easy than others and give little information. To overcome this problem, tandem mass spectrometry has been applied to this dry approach to peptide sequencing with considerable success. Further, electrospray ionization has been used to determine the molecular masses of proteins and peptides with unprecedented accuracy. 

Deamidation of soy and other seed meal proteins by hydrolysis of the amide bond, and minimization of the hydrolysis of peptide bonds, improves functional properties of these products. For example, treatment of soy protein with dilute (0.05 A/) HCl, with or without a cation-exchange resin (Dowex 50) as a catalyst (133), with anions such as bicarbonate, phosphate, or chloride at pH 8.0 (134), or with peptide glutaminase at pH 7.0 (135), improved solubiHty, whipabiHty, water binding, and emulsifying properties. 

The mechanism for photodegradation at short wavelengths is generaUy beUeved to be initiated by the photolytic cleavage of the amide bond (eq. 17), which has the lowest bond strength in aUphatic polyamides (220 kj/mol (53 kcal/mol))... 

The ability of lipases to synthesize the amide bond has been shown (26). Mucor miehei lipase (NOVO tipozyme) has been used in the reaction of laurylamine and oleic acid at 60°C. Water was shown to inhibit the synthesis of this Ai-lauryloleamide (27). 

Ansamacrolides. Antibiotics ia the ansamacroHde family ate also referred to as ansamycias. They are benzenoid or naphthalenoid aromatic compounds ia which nonadjacent positions are bridged by an aliphatic chain to form a cycHc stmcture. One of the aliphatic—aromatic junctions is always an amide bond. Rifampin is a semisyntheticaHy derived member of this family and has clinical importance. It has selective antibacterial activity and inhibits RNA polymerase. 

Polymers, metals, ceramics, and glasses may be utilized as biomaterials. Polymers (see Ppolymerprocessing), an important class of biomaterials, vary gready in stmcture and properties. The fundamental stmcture may be one of a carbon chain, eg, in polyethylene or Tedon, or one having ester, ether, sulfide, or amide bond linkages. PolysiHcones, having a —Si—O—Si— backbone, may contain no carbon. 

Alitame (trade name Adame) is a water-soluble, crystalline powder of high sweetness potency (2000X, 10% sucrose solution sweetness equivalence). The sweet taste is clean, and the time—intensity profile is similar to that of aspartame. Because it is a stericaHy hindered amide rather than an ester, ahtame is expected to be more stable than aspartame. At pH 2 to 4, the half-life of aUtame in solution is reported to be twice that of aspartame. The main decomposition pathways (Fig. 6) include conversion to the unsweet P-aspartic isomer (17) and hydrolysis to aspartic acid and alanine amide (96). No cyclization to diketopiperazine or hydrolysis of the alanine amide bond has been reported. AUtame-sweetened beverages, particularly colas, that have a pH below 4.0 can develop an off-flavor which can be avoided or minimized by the addition of edetic acid (EDTA) [60-00-4] (97). 

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