Amino acids side-chain solubilities

Milk contains a range of groups which are effective in buffering over a wide pH range. The principal buffering compounds in milk are its salts (particularly soluble calcium phosphate, citrate and bicarbonate) and acidic and basic amino acid side-chains on proteins (particularly the caseins). The contribution of these components to the buffering of milk was discussed in detail by Singh, McCarthy and Lucey (1997). 

The relative orientation of polar and nonpolar amino acid side chains in integral membrane proteins is inside-out relative to that of the amino acid side chains of water-soluble globular proteins. Explain. 

Frequently enzymes act in concert with small molecules, coenzymes or cofactors, which are essential to the function of the amino acid side chains of the enzyme. Coenzymes or cofactors are distinguished from substrates by the fact that they function as catalysts. They are also distinguishable from inhibitors or activators in that they participate directly in the catalyzed reaction. Chapter 10, Vitamins and Coenzymes, starts with a description of the relationship of water-soluble vitamins to their coenzymes. Next, the functions and mechanisms of action of coenzymes are explained. In the concluding sections of this chapter, the roles of metal cofactors and lipid-soluble vitamins in enzymatic catalysis are briefly discussed. 

C is correct The solubilities of amino acids differ based upon the R group. Phenylalanine has a benzene R group and is the least polar amino acid listed. The carboxylic acid and amines on the other R groups increase solubility. You may have also memorized the four groups of amino acid side chains as either nonpolar, polar, acidic, or basic. Acidic, basic, and polar amino adds have greater water sohibility than nonpolar amino acids. 

Proteins are large polypeptides with molecular weights ranging from a few thousand into the millions. They contain 16% N on the average. Because some 20 amino acids are present in most proteins and there is no limitation to the size and amount of each amino acid a protein may contain, the number and types of proteins found in nature are almost limitless. Each protein has certain physical and chemical properties that are uniquely suited to its role in the living organism. The properties a protein may exhibit are ultimately a result of its amino acid content. Amino acid side chains determine whether the protein is water soluble, whether it is acidic or basic, and the shape it assumes. It is thus extremely important to study the amino acid content and sequences in proteins, as well as to ascertain their shapes and sizes. To exhibit a specific biologic property, a protein must not only contain the correct amino acid sequence but it must also have the appropriate size and shape. 

In their native conformation, globular proteins have non-polar amino acid side chains oriented towards the interior of the protein and polar side chains oriented outwards, towards the solvent. The stability of the native conformation is determined by hydrophobic interactions within the interior of the molecule, and electrostatic interactions and hydrogen bond interactions at the protein-water interface. Disturbing these interactions can alter the balance between the intra- and intermole-cular interactions, which are responsible for maintaining the protein in soluble... 

Fig. 9. Structures of soluble fragments of retrovirus TM proteins. Murine leukemia virus (MLV Fass et al, 1996) and filovirus (Weissenhom et al, 1998 Malashkevich et at, 1999) TM subunits are represented on the left by the HTLV TM structure (Kobe et at, 1999), with which they share remarkable similarity. Human and simian lentivirus TM subunits (Weissenhom etat, 1997 Chan etat, 1997 Caffrey etat, 1998) are represented by the structure of SIV TM on the right. Both structures are hairpins containing central three-stranded coiled coils surrounded by buttressing regions that pack into the grooves on the outsides of the coiled coils. The amino acid side chains in the conserved cysteine-rich motif of HTLV TM are shown as space-filling atoms and labeled according to their positions in the motif.

Figure 1 Tabulated data for amino acid side chains commonly targeted in chemical modification reactions. As a specific example, a space-filling model of a soluble celulase domain from C. cellulolyticum (PDB ID 11A7) shows the relative abundance and surface accessibility of these residues. Examples of commonly used modification reagents are also listed.

The development of chemoselective reactions to give a native peptide bond at the site of hgation allows the synthesis of proteins with little or no modification to the covalent structure. A native structure at the ligation site is often desirable in the middle of protein structural domains (amino acid 60-120). The challenge of this approach is to form an amide bond chemoselectively in the presence of free amine side chains (Lys) and carboxylate side chains (Glu/Asp). Ideally, no protecting groups should be used for any of the amino acid side chains as they limit peptide solubility and require additional deprotection steps that can severely reduce the yield and convenience of the synthesis. 

In this report, these concepts are applied to real proteins to collagen, an important structural material in tendons, bones, teeth, and skin, and to gelatin, the denatured product of collagen that is so important industrially. These materials are complex because of their 18 different, component amino acid side chains in addition, they present experimental difficulties because of their water solubility— they cannot be washed (e.g., with an aqueous detergent) to assure surface cleanliness. Furthermore, they are often of unknown purity. They do have the common polyamide backbone, and it is possible to transform the molecular configuration. The data are indicative of the potential utility of contact angle measurements of important, natural materials. No claim is made for adequate attention to the complex biochemistry of these materials. 

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