Amides biochemistry

Y.P, Zhang, R.N.A.H. Lewis, R.S. Hodges, andR.N. McElhaney. Peptide models of helical hydrophobic transmembrane segments of membrane proteins. 1. Studies of the conformation, intrabilayer orientation and amide hydrogen exchangeability of Ac-K2-(LA)i2-K2-amide. Biochemistry, 34 (1995) 2348-2361. 

Chi Z H, Chen X G, Holtz J S W and Asher S A 1998 UV resonance Raman-selective amide vibrational enhancement quantitative methodology for determining protein secondary structure Biochemistry 27 2854-64... 

Boyd DB. Beta-lactam antibacterial agents Computational chemistry investigations. In Greenberg A, Breneman CM, Liebman JF, editors. The amide linkage Structural significance in chemistry, biochemistry, and materials science. New York Wiley, 2000. p. 337-75. 

As in the case of esters, hydrolysis of amides is also a fundamental reaction in organic chemistry and plays a key role in biological systems. The reaction has been covered extensively in organic chemistry and biochemistry textbooks. 

A first review of our work in this field was published under the title Syntheses Using Heterocyclic Amides (Azolides) in Angewandte Chemie in 1962 an updated version co-authored by W. Rohr was included in Vol. V of the series Newer Methods of Preparative Organic Chemistry (Verlag Chemie, Weinheim 1967). Since then, however, azolide reactions, due to their versatility, ease of handling, and mild reaction conditions, have become widely used in very diverse fields of chemistry and biochemistry, as will be shown in this book. 

Hypermodified nucleosides that contain an attached amino acid at C(6) are important in the biochemistry of RNAs. The Ni11 complex with N-[(9-/3-D-ribofuranozylpurin-6-yl)-carbamoyl]-threonine (699) forms a very stable complex involving N(l) of the purine ring, the amide-N and the carboxylate of the attached threonine as donors.1837... 

Selective cleavage of peptides and proteins is an important procedure in biochemistry and molecular biology. The half-life for the uncatalyzed hydrolysis of amide bonds is 350 500 years at room temperature and pH 4 8. Clearly, efficient methods of cleavage are needed. Despite their great catalytic power and selectivity to sequence, proteinases have some disadvantages. Peptides 420,423,424,426 an(j proteins428 429 can be hydrolytically cleaved near histidine and methionine residues with several palladium(II) aqua complexes, often with catalytic turnover. 

Greenberg, A., Breneman, C. and Liebman, J.F. (2000). The Amide Linkage Structural Significance in Chemistry, Biochemistry and Material Science. Wiley Sons, Inc, New York... 

Zhang Z, Li Y, Stearns RA, et al. Cytochrome P450 3A4-mediated oxidative conversion of a cyano to an amide group in the metabolism of pinacidil. Biochemistry 2002 41(8) 2712-2718. 

Acyl-transfer reactions are some of the most important conversions in organic chemistry and biochemistry. Recent work has shown that adjacent cationic groups can also activate amides in acyl-transfer reactions. Friedel-Crafts acylations are known to proceed well with carboxylic acids, acid chlorides (and other halides), and acid anhydrides, but there are virtually no examples of acylations with simple amides.19 During studies related to unsaturated amides, we observed a cyclization reaction that is essentially an intramolecular acyl-transfer reaction involving an amide (eq 15). The indanone product is formed by a cyclization involving the dicationic species (40). To examine this further, the related amides 41 and 42 were studied in superacid promoted conversions (eqs 16-17). It was found that amide 42 leads to the indanone product while 41... 

The amino acids link together by the reaction of an amino group of one amino acid with the carboxylic acid group of another amino acid. This forms a peptide bond. (For the sake of clarity the + signs in the reaction have been omitted.) A peptide bond is an amide group in molecules that are not biochemical. Many functional groups have different names in organic chemistry and in biochemistry. 

J. L. Huot C. Baig D. Jahn J. Moser A. tmond S. P. Blais R. Chenevert J. Lapointe, Biochemistry 2007, 46, 13190-13198. M. Bailly, Nouveaux aspect des voles indirectes de formation des aa-ARNt amides. Ph.D. Thesis, Universite Louis Pasteur,... 

Zhang Z., Post C.B., Smith D.L. Amide hydrogen exchange determined by mass spectrometry application to rabbit muscle aldolase. Biochemistry 1996, 35, 779—791. 

In biochemistry, the amide linkage is traditionally referred to as a peptide bond. Whether the resultant polymer is classified as a peptide or a protein is not clearly defined generally, a chain length of more than 40 residues confers protein status, whereas the term polypeptide can be used to cover all chain lengths. 

Amino acids link to form amides and create a polyamide. In biochemistry, the amide gets replaced with a peptide, making the proteins polypeptides. The sequence of the amino acids dictates the primary structure of the protein. 

S. Yamada, in The Amide Linkage. Structural Significance in Chemistry, Biochemistry and Materials Science (Eds. A. Greenberg, C. M. Breneman and J. F. Liebman), Wiley, New York, 2000, p. 215. 

A.F. Spatola, Peptide backbone modifications A structure-activity analysis of peptides containing amide bond surrogates, conformational constraints, and related backbone replacements, in B. Weinstein(Ed.), Chemistry and Biochemistry of Amino Acids, Peptides and Proteins, Marcel Dekker, New York, 1983, pp. 267-357. 

Esters and amides hydrolyze much more slowly, and for useful rates require a catalyst. The hydrolysis of amides is of exceptional importance in biochemistry and will be discussed in more detail in Chapters 24 and 25. 

N. A. Kocharova, O. V. Shcherbakova, A. S. Shashkov, Y. A. Knirel, N. K. Kochetkov, E. V. Kholodkova, and E. S. Stanislavsky, Structure of the O-specific polysaccharide of the bacterium Providencia alcalifaciens serogroup 023 containing a novel amide of D-glucuronic acid with A -(l-carboxyethyl)lysine, Biochemistry (Moscow), 62 (1997) 501-508. 

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