Biochemistry acid-base properties

Proton transfer reactions (proton association and dissociation) in the excited state of aromatic compounds are elementary processes in both chemistry and biochemistry. The acid-base properties in the excited state of aromatic compounds are closely related to electronic structure, which is considerably different from that in the ground state. A large number of studies on the acidity constants pK in the excited state of aromatic compounds have shown that the pK values are markedly different from the acidity constants pK in the ground state [1-31]. 

For the studies of the excited-state proton transfer reactions of aromatic compounds, kinetic analyses by means of fluorimetry, single-photon counting, and laser photolysis methods are very important to obtain the exact data. Their acid-base properties in the excited states can be understood on the bases of thermodynamic analyses and electronic structures. Large changes in the acidity constant of organic compounds upon electronic excitation may be applicable to various fields, especially to biochemistry. 

Another important drug physicochemical phenomenon is the ionization of Bronsted acids and bases in aqueous solution that plays a central role in much of chemistry and biochemistry and that also affects drug in vitro stability and in vivo metabolism activity. The extent of ionization can be represented by the pKg or ionization constant, which often is used in predicting drug-drug interaction because of the change of acid or base properties. For example, given a weak acid HA, its dissociation in water is subject to the chemical equilibrium ... 

Based on our current understanding of ribosomal protein synthesis, several strategies have been developed to incorporate amino acids other than the 20 standard proteinogenic amino acids into a peptide using the ribosomal machinery . This allows for the design of peptides with novel properties. On the one hand, such a system can be used to synthesize nonstandard peptides that are important pharmaceuticals. In nature, such peptides are produced by nonribosomal peptide synthetases, which operate in complex pathways. On the other hand, non-natural residues are a useful tool in biochemistry and biophysics to study proteins. For example, incorporation of non-natural residues by the ribosome allows for site-specific labeling of proteins with spin labels for electron paramagnetic resonance spectroscopy, with... 

Knowledge of the chemical properties of the common amino acids is central to an understanding of biochemistry. The topic can be simplified by grouping the amino acids into five main classes based on the properties of their R groups (Table 3-1), in particular, their polarity, or tendency to interact with water at biological pH (near pH 7.0). The polarity of the R groups varies widely, from nonpolar and hydrophobic (water-insoluble) to highly polar and hydrophilic (water-soluble). 

Lipids are made up of many classes of very different molecules that all show solubility properties in organic solvents. Mass spectrometry plays a key role in the biochemistry of lipids. Indeed, mass spectrometry allows not only the detection and determination of the structure of these molecules but also their quantification. For practical reasons, only the fatty acids, acylglycerols and bile acids are discussed here, although other types of lipids such as phospholipids, [253-256] steroids, [257-259] prostaglandins, [260] ceramides, [261,262] sphingolipids [263,264] and leukotrienes [265,266] have been analysed successfully by mass spectrometry. Moreover, the described methods will be limited to those that are based only on mass spectrometry, even if the majority of these methods generally are coupled directly or indirectly with separation techniques such as GC or HPLC. A book on the mass spectrometry of lipids was published in 1993. [267]... 

Proton transfer reactions play very important role in chemistry and biochemistry [1-3]. Considerable attention has been focused on the gas phase reactions in the last decades, since they are free of the solvent pollution thus being related to the intrinsic reactivity [4 6]. In particular, investigations of gas-phase acidities and basicities were some of the major undertakings in the field [7,8]. The proton affinity (PA), on the other hand is an interesting thermodynamic property by itself. It gives useful information on the electronic structure of base in question and serves as an indicator of the electrophilic substitution susceptibility of aromatic compounds [9]. It is the aim of this article to describe some recent advances in theoretical calculations of the proton affinities of substituted aromatics. We shall particularly dwell in more detail on the additivity rules, which enable simple and quick estimates of PAs in heavily substituted benzenes and naphthalenes. Some prospects for future developements will be briefly discussed too. 

This chapter focuses on computational techniques that allow for hiological discovery based on the protein sequence itself ov on their comparison to protein families. Unlike nucleotide sequences, which are composed of four bases that are chemically rather similar (yet distinct), the alphabet of 20 amino acids found in proteins allows for much greater diversity of structure and function, primarily because the differences in the chemical makeup of these residues are more pronounced. Each residue can influence the overall physical properties of the protein because these amino acids are basic or acidic, hydrophobic or hydrophilic, and have straight chains, branched chains, or are aromatic. Thus, each residue has certain propensities to form structures of different types in the context of a protein domain. These properties, of course, are the basis for one of the central tenets of biochemistry that sequence specifies conformation (Anflnsen et al., 1961). 

Dolinnaya NG, Braswell EH, Fosella JA, Klump H, Fresco JR (1993) Molecular and thermodynamic properties of d(A -G)10, a single-stranded nucleic acid helix without paired or stacked bases. Biochemistry 32 10263-10270... 

As already mentioned, charge-transfer complexing between the stacked bases may also make a contribution to the stability of the nucleic acids. In fact, the general problem of the occurrence of charge-transfer complexes between biomolecules and the intimately connected electron-donor and electron-acceptor properties of these compounds, are amongtypical problems of quantum biochemistry, the elucidation of which is to a large extent dependent on the success of the relevant calculations. 

Bunemann, H. Dattagupta, N. Schuetz, H. J. MuUer, W. Synthesis and properties of acrylamide-substituted base pair specific dyes for deoxyribonucleic acid template mediated synthesis of dye polymers. Biochemistry 1981, 20, 2864-2874. 

Noting that the amino acids do have acidic properties, it is of interest to compare these with typical organic acids and bases. Remembering that the pXa of a dissociable function is the pH at which it is half-ionized (see any biochemistry text for the mathematical expression that relates pH and pK, the Henderson-Hasselbalch equation), the pK values of any compound may serve as index of that compound s acidity. 

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