Proteins Polypeptide bonds

FeMoco can be extracted from the MoFe protein into A(-methylfor-mamide (NMF) solution 32) and has been analyzed extensively using a wide range of spectroscopic techniques both bound to the protein and in solution after extraction from it (33). The extracted FeMoco can be combined with the MoFe protein polypeptides, isolated from strains unable to synthesize the cofactor, to generate active protein. The structure of the FeMoco is now agreed 4, 5, 7) as MoFeTSg homocitrate as in Fig. 4. FeMoco is bound to the a subunit through residues Cys 275, to the terminal tetrahedral iron atom, and His 442 to the molybdenum atom (residue numbers refer to A. vinelandii). A number of other residues in its environment are hydrogen bonded to FeMoco and are essential to its activity (see Section V,E,2). The metal... 

Figure 1.1 Rigid peptide bonds link amino acid residues together to form proteins. Other bonds within the polypeptide structure may exhibit considerable freedom of rotation.

Noncovalent interactions play a key role in biodisciplines. A celebrated example is the secondary structure of proteins. The 20 natural amino acids are each characterized by different structures with more or less acidic or basic, hydrophilic or hydrophobic functionalities and thus capable of different intermolecular interactions. Due to the formation of hydrogen bonds between nearby C=0 and N-H groups, protein polypeptide backbones can be twisted into a-helixes, even in the gas phase in the absence of any solvent." A protein function is determined more directly by its three-dimensional structure and dynamics than by its sequence of amino acids. Three-dimensional structures are strongly influenced by weak non-covalent interactions between side functionalities, but the central importance of these weak interactions is by no means limited to structural effects. Life relies on biological specificity, which arises from the fact that individual biomolecules communicate through non-covalent interactions." " Molecular and chiral recognition rely on... 

Through the formation of polypeptide bonds between amino acids, very long chains of sequences are obtained. Generally, proteins consist of hundreds and thousands of amino acids. For example, human hemoglobin has four polypeptide chains, of which two are cf-chains and two are j3-chains. There are 141 amino acids in each a-chain with a sequence of... 

When amino acids are linked together by acid-amide bonds, linear macromolecules (peptides) are produced. Those containing more than ca. 100 amino acid residues are described as proteins (polypeptides). Every organism contains thousands of different proteins, which have a variety of functions. At a magnification of ca. 1.5 million, the semischematic illustration shows the structures of a few intra and extracellular proteins, giving an impression of their variety. The functions of proteins can be classified as follows. 

Linus Pauling and Robert Corey examined the structures of crystals formed by amino acids and short peptides before they ventured into the world of proteins. From their crystallographic investigations of amino acids and peptides, they formulated two rules that describe the ways in which amino acids and peptides interact with one another to form nonco-valently bonded crystalline structures. These rules laid the foundations for our understanding of how amino acids in protein polypeptide chains interact with one another. 

In polypeptides and proteins, hydrogen bonds are of polar origin and are usually stronger than other noncovalent bonds. Both backbone amides and... 

The repair and replication of cells involves metabolism - interconversions of hundreds of low molecular weight metabolites that ultimately yield the precursors for much larger, more complex macromolecules such as phospholipids (based on phosphatidic. acids or long chain fatty acid esters of glycerol phosphate), polynucleotides such as RNA and DNA (polymers of nucleotide monomers), proteins (polypeptides or amino acid monomers linked by peptide bonds) and polysaccharides (polymers of simple sugars or monosaccharides). 

Some of the important substances in which H bonds are formed are proteins, polypeptides, sugars, lignins, gelatin, starch, and other substances from living tissues. This area shares with polymer formation a prominent position among the most intriguing chemical problems. The... 

Copper has a marked tendency to form complexes with organic substances, especially proteins, polypeptides, and amino acids. In complexed form, copper may not react with reagents or may not be extracted quantitatively. Special care must therefore be taken to free copper from these bonds quantitatively before its determination. This often cannot be achieved without dry or wet ashing. 

Ramachandran s stereochemical plot diagram) of dipeptides has been widely used to predict the secondary structures of proteins [306-309]. It is well known that the calculations on the polypeptides are limited by the number of atoms and hence high level ab initio and DFT calculations have been possible recently only. Several theoretical calculations with different levels of accuracy have been made on the polypeptides to study the < )- 1> plot distribution, H-bonding interactions, and stability [1-4, 308-322]. In the stability of polypeptides and proteins, H-bond plays an important role in the formation of the secondary structures such as the a-helix, (3-sheet, etc., and higher-order structures [1-4]. Quantum chemical calculations on some of the secondary structures in peptides and proteins ((3-sheets, (3-turns, and y-turns) at the HF and MP2 levels have been performed with special emphasis to the H-bonded structures... 

If the number of amino acids forming polypeptide bonds is more than 12.000, the polypeptides are called PROTEINS. 

Through the formation of polypeptide bonds between amino acids, very long chains of sequences are obtained. Generally, proteins consist of... 

Studies of intramolecular ET in oxidases provide interesting examples of how pulse radiolysis is employed to obtain insights into both (1) these enzymes respective mechanisms of action and (2) electron transfer along protein polypeptide matrices that were most probably selected by evolution (9,10, 30-32). Thus, early attempts to study the electron uptake mechanism by the blue oxidase, ceruloplasmin, showed that a diffusion-controlled decay process of the eaq in solutions of this protein is paralleled by the formation of transient optical absorptions due to electron adducts of protein residues, primarily of cystine disulfide bonds (30). The monomolecular decay of the latter absorption was found to have the same rate constant as that at which the type 1 Cu(II) absorption band was reduced. These results were interpreted as being the combined result of the high reactivity of the e q and the relatively inaccessible type 1 Cu(II) site, yielding an indirect, intramolecular electron transfer pathway from surface-exposed residues (30). 

After cross-linking, the experimenter analyzes the solution on an SDS gel. Thick gels (3 to 1.5 mm instead of 0.75 mm) allow us to load a lot of protein per pocket and thus enhance the signal of the ligand/binding polypeptide bond in the autoradiogram or fluorogram. 

There are probably however, in proteins other types of bonds apart from the polypeptide bond. An argument in favour of this is that the enzyme pepsin can destroy proteins but not polypeptides. 

As we have seen from the overview of chemistry of polypeptides, three levels of the structure of proteins can be discerned. The first level is the primary structure of proteins (polypeptides) which is simply the linear order of amino acids in the chain starting from the N-terminus up to the C-terminus. Formation of a-helices and p-sheets is the secondary structure of proteins and it is responsible for the shape of the polypeptide molecule. Aggregation of these polypeptides into the final molecule of the protein is its tertiary structure (as shown in the figure above). The most common way by which polypeptides are interconnected into the tertiary structure includes the disulfide bonds between the cysteine residues (amino acids). 

Some of the proteins involved in the formation of the polypeptide bond have now been identified. 

The names of many great chemists are associated with the study of proteins. The famous organic chemist Baron Justus von Liebig maintained for a long time that all proteins stemmed from only one type of molecule, and all variations had the same radical. But the composition of these large molecules was to remain mysterious until Emil Fisher established that proteins were made of up to 20 different amino acid residues linked by polypeptide bonds. 

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