Amino side chain, charged

Amino Acid 3- 1-Letter Letter Side chain polarity Side chain charge (pH 7.4) Hydropathy Absorbance index kmax(nm) max (xlO ... 

Short chains of amino acid residues are known as di-, tri-, tetrapeptide, and so on, but as the number of residues increases the general names oligopeptide and polypeptide are used. When the number of chains grow to hundreds, the name protein is used. There is no definite point at which the name polypeptide is dropped for protein. Twenty common amino acids appear regularly in peptides and proteins of all species. Each has a distinctive side chain (R in Figure 45.3) varying in size, charge, and chemical reactivity. 

EIectrosta.tlcs. Electrostatic interactions, such as salt bridges, result from the electrostatic attraction that occurs between oppositely charged molecules. These usually involve a single cation, eg, the side chain of Lys or Arg, or the amino terminus, etc, interacting with a single anion, eg, the side chain of Glu or Asp, or the carboxyl terminus, etc. This attractive force is iaversely proportional to the distance between the charges and the dielectric constant of the solvent, as described by Coulomb s law. 

Wool has a complex chemical stmcture, composed mainly of a large number of different proteins (87). It is amphoteric in character because of the presence of basic amino and acidic carboxyl groups in the side chains of some of the component amino acids. In an aqueous acidic dyebath, protonation of the amino and carboxyl groups results in a net positive charge on the fiber. 

The amino acids are usually divided into three different classes defined hy the chemical nature of the side chain. The first class comprises those with strictly hydrophobic side chains Ala (A), Val (V), Leu (L), He (1), Phe (F), Pro (P), and Met (M). The four charged residues, Asp (D), Glu (E), Lys (K), and Arg (R), form the second class. The third class comprises those with polar side chains Ser (S), Thr (T), Cys (C), Asn (N), Gin (Q), His (H), Tyr (Y), and Trp (W). The amino acid glycine (G), which has only a hydrogen atom as a side chain and so is the simplest of the 20 amino acids, has special properties and is usually considered either to form a fourth class or to belong to the first class. 

Each amino acid has atoms in common, and these form the main chain of the protein. The remaining atoms form side chains that can be hydrophobic, polar, or charged. 

Figure 2.4 The helical wheel or spiral. Amino acid residues are plotted every 100° around the spiral, following the sequences given in Table 2.1. The following color code is used green Is an amino acid with a hydrophobic side chain, blue is a polar side chain, and red is a charged side chain. The first helix is all hydrophobic, the second is polar on one side and hydrophobic on the other side, and the third helix is all polar.

Electrophoresis is used primarily to analyze mixtures of peptides and proteins, rather than individual amino acids, but analogous principles apply. Because they incorporate different numbers of amino acids and because their side chains are different, two peptides will have slightly different acid-base properties and slightly different net charges at a particular pH. Thus, their mobilities in an electric field will be different, and electrophoresis can be used to separate them. The medium used to separate peptides and proteins is typically a polyacrylamide gel, leading to the term gel electrophoresis for this technique. 

FIGURE 27.19 Proposed mechanism of hydrolysis of a peptide catalyzed by carboxypeptidase A. The peptide is bound at the active site by an ionic bond between its C-terminal amino acid and the positively charged side chain of arginine-145. Coordination of Zn to oxygen makes the carbon of the carbonyl group more positive and increases the rate of nucleophilic attack by water. 

John.son, L. N., and Barford, D., 1994. Electro.static effects in die control of glycogen pho.sphoryla.se by pho.sphorylation. Protein Science 3 1726-1730. Di.scn.s.sion of die pho.sphate group s ability to deliver two negative charges to a protein, a property that no amino acid side chain can provide. 

What about tertiary structure Why does any protein adopt the shape it does The forces that determine the tertiary structure of a protein are the same forces that act on ail molecules, regardless of size, to provide maximum stability. Particularly important are the hydrophilic (water-loving Section 2.13) interactions of the polar side chains on acidic or basic amino acids. Those acidic or basic amino acids with charged side chains tend to congregate on the exterior of the protein, where they can be solvated by water. Those amino acids with neutral, nonpolar side chains tend to congregate on the hydrocarbon-like interior of a protein molecule, away from the aqueous medium. 

Also important for stabilizing a protein s tertiary stmcture are the formation of disulfide bridges between cysteine residues, the formation of hydrogen bonds between nearby amino acid residues, and the presence of ionic attractions, called salt bridges, between positively and negatively charged sites on various amino acid side chains within the protein. 

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