Amino acid ionizable

The amino acids in question are the basic amino acids lysine, arginine, and histidine, and the acidic amino acids aspartic acid and glutamic acid. The side-chain functions of these amino acids, ionized at pH 7 (see Box 4.7), act as acids or bases. In a reverse sequence, protons may be acquired or donated to regenerate the conjugate acids and conjugate bases. 

In proteins, three amino acids, tryptophan, tyrosine and phenylalanine, are responsible for the U.V. absorption, c in proteins is detemiined at the maximum (278 nm) (Fig. 1.13) and thus, concentrations of proteins are calculated by measuring the absorbance at this wavelength. Cystine and the ionized sulfhydryl groups of cysteine absorb also in this region but much weakly than the three aromatic amino acids. Ionization of the sulfhydiyl group induces an increase in the absorption and an appearance of a new peak around 240 nm. The imidazole group of histidine absorbs in the 185-220 nm region. Finally, important absorption of the peptide bonds occurs at 190 nm. 

It can be seen from Table 2 that the intrinsic values of the pK s are close to the model compound value that we use for Cys(8.3), and that interactions with surrounding titratable residues are responsible for the final apparent values of the ionization constants. It can also be seen that the best agreement with the experimental value is obtained for the YPT structure suplemented with the 27 N-terminal amino acids, although both the original YPT structure and the one with the crystal water molecule give values close to the experimentally determined one. Minimization, however, makes the agreement worse, probably because it w s done without the presence of any solvent molecules, which are important for the residues on the surface of the protein. For the YTS structure, which refers to the protein crystallized with an SO4 ion, the results with and without the ion included in the calculations, arc far from the experimental value. This may indicate that con-... 

Amino acid Three- letter code One- letter code Mass of residue in. b proteins Accessible surface area, 2 nm Hydrophobicity index ionizable side chain Occurrence in n/ proteins, /o Relative mutabihty... 

Chemical Properties. Hydrogen cyanide is a weak acid its ionization constant is of the same magnitude as that of the natural amino acids (qv). Its stmcture is that of a linear, triply bonded molecule, HC=N. 

From a chemical point of view, the common amino acids are all weak polyprotic acids. The ionizable groups are not strongly dissociating ones, and the degree of dissociation thus depends on the pH of the medium. All the amino acids contain at least two dissociable hydrogens. 

FIGURE 4.6 The ionic forms of the amino acids, shown without consideration of any ionizations on the side chain. The cationic form is the low pH form, and the titration of the cationic species with base yields the zwitterion and finally the anionic form. (Irving Geis)... 

Typical values for pAlg are in the range of 9.0 to 9.8. At physiological pH, the a-carboxyl group of a simple amino acid (with no ionizable side chains) is completely dissociated, whereas the a-amino group has not really begun its dissociation. The titration curve for such an amino acid is shown in Figure 4.7. 

Separation methods based on size include size exclusion chromatography, ultra-filtration, and ultracentrifugation (see Chapter Appendix). The ionic properties of peptides and proteins are determined principally by their complement of amino acid side chains. Furthermore, the ionization of these groups is pH-dependent. 

The 20 natural amino acids differ from each other by the nature of their sidechains. Differences involve overall size, hydrophobic or hydrophilic character and, perhaps most importantly, ionization state. While the sidechains are normally written in terms of neutral structures, some may also exist in either protonated or deprotonated forms depending on pH. 

A selection of amino acids (acid A, acid B,...) terminated at both ends by amide functionality, i.e., MeNHCO-CHR-NHCOMe, are provided. These are given in the ionization states found at neutral pH. For each, first identify the amino acid, and then the ionization state (neutral, protonated or deprotonated). Next compare electrostatic potential maps among the different amino acids. Which amino acids would prefer hydrophobic environments Hydrophilic environments Explain your reasoning. 

With the identities and amounts of amino acids known, the peptide is sequenced to find out in what order the amino acids are linked together. Much peptide sequencing is now done by mass spectrometry, using either electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI) linked to a time-of-flight (TOF) mass analyzer, as described in Section 12.4. Also in common use is a chemical method of peptide sequencing called the Edman degradation. 

Experimentation showed that the protein was not glycosylated and that the sequence at the iV-amino acid terminus corresponded to that expected. The C-terminus sequence, however, did not correspond to that predicted and these data were interpreted in terms of the presence of a heterogeneous, truncated, protein. A study of the tryptic digest fragments from this protein with matrix-assisted laser desorption ionization (MALDI) with post-source decay enabled the authors to suggest the positions at which the parent protein had been truncated. 

Molecules that contain an equal number of ionizable groups of opposite charge and that therefore bear no net charge are termed zwitterions. Amino acids in blood and most tissues thus should be represented as in A, below. 

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