Biomolecules,

Biomolecules are molecules found in living things. The major classes of biomolecules are proteins, carbohydrates, fats, and nucleic acids. All biomolecules contain carbon, hydrogen, and oxygen. Proteins also contain nitrogen and sometimes sulfur, and nucleic acids contain nitrogen and phosphorus. Other types of atoms may also be found in these compounds. 

Proteins are organic polymers made up of amino acids. They have both structural and functional roles in living organisms. For example, proteins are a major part of the structures of skin, hair, and nails. Special proteins within the cells of the body that are called enzymes are necessary for all the chemical reactions of life. Without enzymes, the chemical reactions inside cells would happen too slowly to support life. 

The R group, which can consist of varying numbers and kinds of atoms, is different in each of the twenty amino acids. The rest of the structure is the same. 

This structure is called a dipeptide because it shows a peptide bond linking two amino acids. However, the chain could have been made up of fifty or more amino acids, all linked by peptide bonds. 

Such a chain is called a polypeptide because it is made up of many amino acids. 

Biomolecules are organic compounds found in bioiogicai systems. Many are relatively small, with molecular weights of less than 1000 g/mol. There are four main families of these small molecules—simple sugars, amino acids, lipids, and nucleotides. Many simple biomolecules are used to synthesize larger compounds that have important cellular functions. 

The biomolecules that constitute matter in living organisms are often polymers with molecular masses of the order of a million or even larger. As discussed later in this chapter, these biomolecules may be divided into the categories of carbohydrates, proteins, lipids, and nucleic acids. Proteins and nucleic acids consist of macromolecules, lipids are usually relatively small molecules, and carbohydrates range from relatively small sugar molecules to high-molecular-mass macromolecules such as those in cellulose. 

The behavior of a substance in a biological system depends to a large extent upon whether the substance is hydrophilic ( water-loving ) or hydrophobic ( water-hating ). Some important toxic substances are hydrophobic, a characteristic that enables them to traverse cell membranes readily. Part of the detoxification process carried on by living organisms is to render such molecules hydrophilic, and therefore water-soluble and readily eliminated from the body. 

Application of IR-SEC to biomolecules brings additional challenges and these are mostly related to the availability of material, its maximum concentration, interference from other vibrational modes of the macromolecule, and the need to work in highly absorbing solvents such as water. The water solubility of most salt window materials means that studies must be conducted using insoluble 

Chemists are likely to be familiar with certain biomolecules such as carbohydrates and lipids from their organic chemistry lectures. However, many do not have a clear understanding of the composition and function of other biomolecules such as proteins andDNA. This chapter introduces the biomolecules, which are the target of the analytical methods described in the following chapters. 

The gases usually postulated to have been present in the atmosphere of the early Earth include NH, H S, GO, GO, GH, N, H, and (in both liquid and vapor forms) H O. However, there is no universal agreement on the relative amounts of these components, from which biomolecules ultimately arose. Many of the earlier theories of the origin of life postulated GH as the carbon source, but more recent studies have shown that appreciable amounts of GO must have existed in the atmosphere at least 3.8 billion (3.8 x 10 ) years ago. 

This conclusion is based on geological evidence The earliest known rocks are 3.8 billion years old, and they are carbonates, which arise from GO. Any NHj originally present must have dissolved in the oceans, leaving in the atmosphere as the nitrogen source required for the formation of proteins and nucleic acids. 

How were biomolecules likely to have formed on the early Earth  

Experiments have been performed in which the simple compounds of the early atmosphere were allowed to react under the varied sets of conditions that might have been present on the early Earth. The results of such experiments indicate that these simple compounds react abiotically or, as the word indicates (a, not, and bios, life ), in the absence of life, to give rise to biologically important compounds such as the components of proteins and nucleic acids. Of historic interest is the well-known Miller-Urey experiment, shown schematically in Eigure 1.4. In each trial, an electric discharge, simulating lightning, is 

Each abundance is given as the number of atoms relative to a thousand atoms of carbon. 

Nitrogen is closely concerned with many or most vital processes. With 95%-99% bioenrichment, which can be achieved with relatively cheap materials such as NH salts, N is several times more NMR sensitive than naturally-abundant C, and can give useful labeling information. Sensitivity enhancement methods such as DEPT or INEPT are of great value, with or without N-enrichment. ° ° Also useful, particularly for in vivo work, is indirect detection of N by double quantum proton NMR. Applications of solid state techniques to biomolecules in N or N resonance were described in Section 1.3. 

The use of N in highly symmetrical locations, as in RNH, in which internal rotation is possible, should not be neglected. The metabolism of inorganic nitrogen in roots has been studied by N NMR, and in vivo studies of metabolism in algae, fungi, and higher plants by C, N and N NMR have been reviewed.  

Lichter, R. L. Nitrogen-15 NMR Spectroscopy Wiley-Interscience New York, 1979, 1-221. 

Roberts, J. D. In Bloch Festschrift Rice University Press Houston, Texas, 1980. 

Lippmaa, E. Saluvere, T. Laisaar, S. Chem. Phys. Lett. 1971, 11, 120-123. 

If one or more of the hydrogen atoms of a non-metal hydride are replaced formally with another group, R—e.g., alkyl residues—then derived compounds of the type R-XHn-i, R-XHn-2-R, etc., are obtained. In this way, alcohols (R-OH) and ethers (R-O-R) are derived from water (H2O) primary amines (R-NH2), secondary amines (R-NH-R) and tertiary amines (R-N-R R ) amines are obtained from ammonia (NH3) and thiols (R-SH) and thioethers (R-S-R ) arise from hydrogen sulfide (H2S). Polar groups such as -OH and -NH2 are found as substituents in many organic compounds. As such groups are much more reactive than the hydrocarbon structures to which they are attached, they are referred to as functional groups. 

New functional groups can arise as a result of oxidation of the compounds mentioned above. For example, the oxidation of a thiol yields a disulfide (R-S-S-R). Double oxidation of a primary alcohol (R-CH2-OH) gives rise initially to an aldehyde (R-C(O)-H), and then to a carboxylic acid (R-C(O)-OH). In contrast, the oxidation of a secondary alcohol yields a ketone (R-C(O)-R). The carbonyl group (C=0) is characteristic of aldehydes and ketones. 

The addition of an amine to the carbonyl group of an aldehyde yields—after removal of water—an aldimine (not shown see p. 178). Aldimines are intermediates in amino acid metabolism (see p. 178) and serve to bond aldehydes to amino groups in proteins (see p. 62, for example). The addition of an alcohol to the carbonyl group of an aldehyde yields a hemiacetal (R-O-C(H)OH-R). The cyclic forms of sugars are well-known examples of hemi- 

Very important compounds are the carboxylic acids and their derivatives, which can be formally obtained by exchanging the OH group for another group. In fact, derivatives of this type are formed by nucleophilic substitutions of activated intermediate compounds and the release of water (see p. 14). Carboxylic acid esters (R-O-CO-R ) arise from carboxylic acids and alcohols. This group includes the fats, for example (see p.48). Similarly, a carboxylic acid and a thiol yield a thioester (R-S-CO-R ). Thioesters play an extremely important role in carboxylic acid metabolism. The best-known compound of this type is acetyl-coenzyme A (see p. 12). 

Carboxylic acids and primary amines react to form carboxylic acid amides (R-NH-CO-R ). The amino acid constituents of peptides and proteins are linked by carboxylic acid amide bonds, which are therefore also known as peptide bonds (see p. 66). 

The functions of materials in these three groups may overlap. 

The lipid part of the membrane is essentially a two-dimensional liquid in which the other materials are immersed and to which the cytoskeleton is anchored. This last statement is not totally correct, as some membrane bound enzymes require the proximity of particular lipids to function properly and are thus closely bound to them. Simple bilayers formed from lipids in which both hydrocarbon chains are fully saturated can have a highly ordered structure, but for this reason tend to be rigid rather than fluid at physiological temperatures. Natural selection has produced membranes which consist of a mixture of different lipids together with other amphiphilic molecules such as cholesterol and some carboxylic acids. Furthermore, in many naturally occurring lipids, one hydrocarbon chain contains a double bond and is thus kinked. Membranes formed from a mixture of such materials can retain a fluid structure. The temperature at which such membranes operate determines a suitable mixture of lipids so that a fluid but stable structure results at this temperature. It will be seen that the lipid part of a membrane must, apart from its two-dimensional character, be disordered to do its job. However, the membrane bound proteins have a degree of order, as will be discussed below. 

The plasma membrane totally encloses the interior of a cell but clearly many different molecules must be able to cross this barrier if the cell is 

71 Bonds create nucleophilic sites and are more easily broken than a bonds. 

Problem 3.13 Label the electrophilic and nucleophilic sites in each molecule. 

By identifying the nucleophilic and electrophilic sites in a compound you can begin to understand how it will react. In general, electron-rich sites react with electron-deficient sites  

At this point we don t know enough organic chemistry to draw the products of many reactions with confidence. We do know enough, however, to begin to predict if two compounds might react together based solely on electron density arguments, and at what atoms that reaction is most likely to occur. 

For example, alkenes contain an electron-rich C-C double bond and so they react with electrophiles, E. On the other hand, alkyl halides possess an electrophilic carbon atom, so they react with electron-rich nucleophiles. 

It is noteworthy that bovine mucosal heparin and porcine mucosal heparin can be distinguished by H and C NMR spectra [10], [11], [12], Since they differ in the extent of sulfation, they show a different fingerprint . In addition, the chemical shift of HI and H5 in iduronic acid as well as the magnitude of separation of the glucosamine/iduronic acid HI pair are appropriate to discriminate between the counter-ion sodium or calcium. [10] In a similar manner, the extent and site of sulfation of dextran sulfate could be described by 300-MHz H NMR spectra. Additionally, the manufacturer could be determined [13], [14] by comparison of the pattern. 

As can be concluded from the examples described above, further applications of NMR spectroscopy can be expected to be introduced to the Ph. Eur. and national European pharmacopoeias as well as the JP and the USP in the future. The high potential of NMR spectroscopy in terms of identification and quantification of drugs and their impurities resulting from the synthesis pathway or degradation will be demonstrated in the following sections. 

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Weiss S 1999 Fluorescence spectroscopy of single biomolecules Science 283 1676-83... 

The variety of molecules used to prepare LB films is enonnous. and only a small selection of examples can be presented here. Liquid crystals and biomolecules such as phospholipids, for example, can also be used to prepare LB films. The reader is referred to tire literature for infonnation about individual species. 

Wolynes P G 1996 Symmetry and the energy landscape of biomolecules Proc. Natl Acad. Sci. (USA) 93 14 249-55... 

Apart from the sheer complexity of the static stmctures of biomolecules, they are also rather labile. On the one hand this means that especial consideration must be given to the fact (for example in electron microscopy) that samples have to be dried, possibly stained, and then measured in high vacuum, which may introduce artifacts into the observed images [5]. On the other, apart from the vexing question of whether a protein in a crystal has the same stmcture as one freely diffusing in solution, the static stmcture resulting from an x-ray diffraction experiment gives few clues to the molecular motions on which operation of an enzyme depends [6]. 

The most recently introduced optical teclmique is based on the retardation of light guided in an optical waveguide when biomolecules of a polarizability different from that of the solvent they displace are adsorbed at the waveguide surface (optical waveguide lightmode spectroscopy, OWLS) [H]. It is even more sensitive than ellipsometry, and the mode... 

The reactions of biopolymers at interfaces fonn tire basis of some extremely important industrial processes. The primary process in all cases is tire adsorjDtion of biomolecules, usually proteins. If ultimately living cells are adsorbed, tliis always takes place onto a preadsorbed protein layer (which may be secreted by tire cells themselves [130]). These processes can be classified into tliree categories ... 

A salient feature of natural surfaces is tliat tliey are overwhelmingly electron donors [133]. This is tlie basis for tlie ubiquitous hydrophilic repulsion which ensures tliat a cell can function, since massive protein-protein aggregation and protein-membrane adsorjition is tliereby prevented. In fact, for biomolecule interactions under typical physiological conditions, i.e. aqueous solutions of moderately high ionic strengtli, tlie donor-acceptor energy dominates. 

Peyrard M (ed) 1995 Nonlinear Excitations in Biomolecules Les Ulis Editions de Physique)... 

Newton M D 1999 Electron transfer from isolated molecules to biomolecules Advanced Chemicai Physics vol 106, ed J Jortner and M Bixon (New York Wiley) pp 303-75... 

Wynne K and Hochstrasser R M 1999 Coherence and adiabaticity in ultrafast electron transfer Adv. Chem. Phys. 107 (Electron transfer from isolated molecules to biomolecules) part 2, 263-309... 

Experimental techniques based on the application of mechanical forces to single molecules in small assemblies have been applied to study the binding properties of biomolecules and their response to external mechanical manipulations. Among such techniques are atomic force microscopy (AFM), optical tweezers, biomembrane force probe, and surface force apparatus experiments (Binning et al., 1986 Block and Svoboda, 1994 Evans et ah, 1995 Israelachvili, 1992). These techniques have inspired us and others (see also the chapters by Eichinger et al. and by Hermans et al. in this volume) to adopt a similar approach for the study of biomolecules by means of computer simulations. 

Miyazawa, T. Conformational aspects and biological functions of biomolecules. J. Mol. Struct. 126 (1985) 493-508... 

Gascoyne, P.R.C., Pethig, R. Experimental and theoretical aspects of hydration isotherms for biomolecules. J. Chem. Soc. Faradey Trans. 1 (1977) 171-180... 

The last part of this account will be devoted to protein kinases and protein phosphatases and some recent results we have obtained for them. Protein kinases and phosphatases are signaling biomolecules that control the level of phosphorylation and dephosphorylation of tyrosine, serine or threonine residues in other proteins, and by this means regulate a variety of fundamental cellular processes including cell growth and proliferation, cell cycle and cytoskeletal integrity. 

Since the stochastic Langevin force mimics collisions among solvent molecules and the biomolecule (the solute), the characteristic vibrational frequencies of a molecule in vacuum are dampened. In particular, the low-frequency vibrational modes are overdamped, and various correlation functions are smoothed (see Case [35] for a review and further references). The magnitude of such disturbances with respect to Newtonian behavior depends on 7, as can be seen from Fig. 8 showing computed spectral densities of the protein BPTI for three 7 values. Overall, this effect can certainly alter the dynamics of a system, and it remains to study these consequences in connection with biomolecular dynamics. 

The IE scheme is nonconservative, with the damping both frequency and timestep dependent [42, 43]. However, IE is unconditionally stable or A-stable, i.e., the stability domain of the model problem y t) = qy t), where q is a complex number (exact solution y t) = exp(gt)), is the set of all qAt satisfying Re (qAt) < 0, or the left-half of the complex plane. The discussion of IE here is only for future reference, since the application of the scheme is faulty for biomolecules. 

The LIN method (described below) was constructed on the premise of filtering out the high-frequency motion by NM analysis and using a large-timestep implicit method to resolve the remaining motion components. This technique turned out to work when properly implemented for up to moderate timesteps (e.g., 15 Is) [73] (each timestep interval is associated with a new linearization model). However, the CPU gain for biomolecules is modest even when substantial work is expanded on sparse matrix techniques, adaptive timestep selection, and fast minimization [73]. Still, LIN can be considered a true long-timestep method. 

In order to apply the techniques discussed above to the MD simulation o biomolecules, one takes the Liouville operator for a macromolecule in vacuo containing N atoms to be... 

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