RNA, DNA and

A cyclic five-carbon (pentose) sugar deoxynbose for DNA, and nbose for RNA. 

A phosphate attached to the 5 carbon of the sugar by phosphoester linkage. 

2 The name genetic engineering should not mislead the readers that it is a field of engineering it is a field of biological science. 

3 Macromolecules a polymer, especially one composed of more than 100 repeated monomers. 

The nucleotides of DNA are called deoxyribonucleotides, since they contain the sugar deoxyribose, whereas, those of RNA are called nbonucleotides since they contain nbose instead. Each nucleotide contains both a specific and a nonspecific region. The phosphate and sugar groups are the nonspecific portion of the nucleotide, while the purine and pyrimidine bases make up the specific portion. 

In order to understand the mechanisms of pathogen disinfection by UV light, it is necessary first to be familiar with the structure of DNA and RNA, as they play key roles in two important aspects of reproduction of microorganisms protein synthesis and the replication of chromosomes. 

The subunits of nucleotides are finked together to form a long polymer chain in nucleic acids. The linkages are formed between the phosphate group of one subunit and the sugar group of the next. This matrix forms a sugar-phosphate backbone to the molecule of nucleic acid. 

The structure of DNA is much more complex than that of RNA. It is enormously long and composed of millions of nucleotides. Unlike RNA, DNA is always double-stranded 

The gully complementary nature of the base pairs in DNA means that each strand can act as a blueprint for the other. Assisted by the enzyme DNA polymerase, the DNA molecule can be unzipped and replicate itself exactly by the assemblage of new nucleotides from the cell s pool. This process is known as semiconservative replication because the two identical DNA molecules produced consist of one original and one new strand of DNA. DNA is able to replicate itself, which is essential to the process of cell division. As a result, an exact copy of the cell s genetic instructions can be handed on to the next generation of cells. 

The long molecules of DNA occur within the nucleus of individual cells. It is thought that each DNA molecule corresponds to a single chromosome. There are a characteristic number of chromosomes for individual species. These carry the hereditary information of the individual on a series of shorter sections of the nucleic acid known as genes. The nucleic acid within the nucleus of most cells, such as bacteria and protozoa, is composed of double-stranded DNA. DNA contains the information necessary for the synthesis of ribosomal, transfer, and messenger RNA, which are responsible for synthesis of enzymes, which drive metabolic processes within the cell. The genetic material of viruses may either be DNA or RNA and can be single- or double-stranded (3). 

Two different types of DNA occur in distinct locations in the living cell nuclear DNA in the cell s nucleus and mitochondrial DNA (mt-DNA) in the mitochondria (see Textbox 50). RNA occurs in several types messenger RNA, transfer RNA, ribosomal RNA, and others, all in the cytoplasm of the cells (see Table 85) (Bloomfield et al. 2000). 

Archaeological Chemistry, Second Edition By Zvi Goffer Copyright 2007 John Wiley Sons, Inc. 

DNA Deoxyribonucleic acid Carries genetic instructions for maldng living organisms 

RNA Ribonucleic acid Transfers genetic information from DNA to proteins synthesized by the cell 

The nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), which carry embedded in their complex molecules the genetic information that characterizes every organism, are found in virtually all living cells. Their molecules are very large and complex biopolymers made up basically of monomeric units known as nucleotides. Thus DNA and RNA are said to be polynucleotides. The nucleotides are made up of three bonded (linked) components a sugar, a nitrogenous base, and one or more phosphate groups  

The illustration opposite shows selected nucleic acid molecules. Fig. A shows various conformations of DNA, and Fig. B shows the spatial structures of two small RNA molecules. In both, the van der Waals models (see p. 6) are accompanied by ribbon diagrams that make the course of the chains clear. In all of the models, the polynucleotide backbone of the molecule is shown in a darker color, while the bases are lighter. 

A-DNA arises when B-DNA is dehydrated. It probably does not occur in the cell. 

In the Z-conformation (3), which can occur within GC-rich regions of B-DNA, the organization of the nucleotides is completely different. In this case, the helix is left-handed, and the backbone adopts a characteristic zig-zag conformation (hence Z-DNA ). The Z double helix has a smaller pitch than B-DNA. DNA segments in the Z conformation probably have physiological significance, but details are not yet known. 

Investigations of synthetic DNA molecules have shown that DNA can adopt several different conformations. All of the DNA segments shown consist of 21 base pairs (bp) and have the same sequence. 

By far the most common form is B-DNA (2). As discussed on p. 84, this consists of two antiparallel polydeoxynucleotide strands intertwined with one another to form a right-handed double helix. The backbone of these strands is formed by deoxyribose and phosphate residues linked by phosphoric acid diester bonds. 

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The model suggested can be easily extended to the case of inhomogeneous NAs by means of introducing the dependence of the model parameters on the number of the NA unit in the chain and solving (4) and (7) for every NA unit. This seems important as natural NAs such as DNA and RNA are inhomogeneous. The extension of the model on the case of more than three conformations also can be done easily. 

Having settled on a definition of chemoinformatics, it is time for us to reflect on the distinction between chemoinformatics and bioinformatics. The objects of interest of bioinformatics are mainly genes and proteins. But genes, DNA and RNA, and proteins are chemical compounds They are objects of high interest in chemistry, Chemists have made substantial contributions to the elucidation of the structure and function of nucleic adds and proteins. The message is dear there is no clearcut distinction between bioinfonnatics and chemoinformatics I... 

With the increase in hardware and software, larger systems can be handled with higher accuracy. Much work will continue to be devoted to the study of proteins and polynucleotides (DNA and RNA), and particularly their interactions with more sophisticated methods. Remember proteins and genes are chemical compounds and sophisticated theoretical and chemoinformatics methods should be applied to their study - in addition to the methods developed by bioinfor-maticians. 

Firefly lucifenn is an example of an azole that contains a benzene ring fused to the five membered ring Such structures are fairly common Another example is benzimidazole present as a structural unit m vitamin B12 Some compounds related to benzimidazole include purine and its ammo substituted derivative adenine one of the so called het erocychc bases found m DNA and RNA (Chapter 28)... 

These relationships are general Hydroxyl substituted purines and pyrimidines exist in their keto forms ammo substituted ones retain structures with an ammo group on the ring The pyrimidine and punne bases m DNA and RNA listed m Table 28 1 follow this general rule Beginning m Section 28 7 we 11 see how critical it is that we know the cor rect tautomeric forms of the nucleic acid bases... 

A virus is a species containing DNA and RNA that can reproduce itself, but to do this, it needs to hijack the metabolism (cells) of a host organism, since it has no information itself with which to build cells. 

Intoxication by aflatoxkis is referred to as aflatoxicosis. Edema and necrosis of hepatic and renal tissues seem characteristic of aflatoxicosis, and hemorrhagic enteritis accompanied by nervous symptoms often appear ki experimental animals. The mode of action of aflatoxkis kivolve an kiteraction with DNA and inhibition of the polymerases responsible for DNA and RNA synthesis (96). 

The methylphosphonates differ from the phosphodiesters and phosphorothiolates in that the methyl derivatives are uncharged and are thus less water soluble. Moreover, compared to the naturally occurring phosphodiesters, the methylphosphonates form slightly less stable duplexes with complementary DNA and RNA sequences. This effect has been ascribed to the iaevitable chiraUty problem that is, if one isomer biads less well, the overall binding is decreased. Methylphosphonates can enter cell membranes by a passive mechanism and are completely resistant to nucleases. 

Proteias are metabolized coatiauously by all living organisms, and are ia dyaamic equilibrium ia living cells (6,12). The role of amino acids ia proteia biosyathesis has beea described (2). Most of the amino acids absorbed through the digestioa of proteias are used to replace body proteias. The remaining portioa is metabolized iato various bioactive substances such as hormones and purine and pyrimidine nucleotides, (the precursors of DNA and RNA) or is consumed as an energy source (6,13). 

Mechanism of Action. THie earliest studies on the mechanism of action of lincomycin showed that lincomycin had the immediate effect on Staphjlococcus aureus of complete inhibition of protein synthesis (23). TThis inhibition results from the blocking of the peptidyltransferase site of the SOS subunit of the bacterial ribosome (24). Litde effect on DNA and RNA synthesis was observed. 

Although experimental studies of DNA and RNA structure have revealed the significant structural diversity of oligonucleotides, there are limitations to these approaches. X-ray crystallographic structures are limited to relatively small DNA duplexes, and the crystal lattice can impact the three-dimensional conformation [4]. NMR-based structural studies allow for the determination of structures in solution however, the limited amount of nuclear overhauser effect (NOE) data between nonadjacent stacked basepairs makes the determination of the overall structure of DNA difficult [5]. In addition, nanotechnology-based experiments, such as the use of optical tweezers and atomic force microscopy [6], have revealed that the forces required to distort DNA are relatively small, consistent with the structural heterogeneity observed in both DNA and RNA. 

Computational studies of nucleic acids offer the possibility to enliance and extend the infonnation available from experimental work. Computational approaches can facilitate the experimental detennination of DNA and RNA structures. Dynamic information. 

TABLE 4.10 Recommended TSK-GEL SW and TSK-GEL PW Columns for Separating Double-Stranded DNA and RNA Fragments... 

Adenine (6-amino purine) and guanine (2-amino-6-oxy purine), the two common purines, are found in both DNA and RNA (Figure 11.4). Other naturally occurring purine derivatives include hypoxanthlne, xanthine, and uric acid (Figure 11.5). Flypoxanthine and xanthine are found only rarely as constituents of nucleic acids. Uric acid, the most oxidized state for a purine derivative, is never found in nucleic acids. 

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