Structure representation sugars

Even though Haworth formulas give a sound representation of the ring structures of sugars, the real structure conformation can be most accurately represented by the chair forms of cyclohexane as shown in... 

Figure 3.4. Structural representations of glucose, the major sugar and the primary source of energy of higher animals that gives rise to 36 ATP molecules during its oxidation to carbon dioxide and water. In the Fischer projection, the central structure, carbon atoms 2, 3, 4, and 5 each contains four different substituents, making them asymmetrical centers.

Figure 17.3 Anatomy of a redox enzyme representation of the X-ray crystallographic structure of Trametes versicolor laccase III (PDB file IKYA) [Bertrand et al., 2002]. The protein is represented in green lines and the Cu atoms are shown as gold spheres. Sugar moieties attached to the surface of the protein are shown in red. A molecule of 2,5-xyhdine that co-crystallized with the protein (shown in stick form in elemental colors) is thought to occupy the broad-specificity hydrophobic binding pocket where organic substrates ate oxidized by the enzyme. Electrons from substrate oxidation are passed to the mononuclear blue Cu center and then to the trinuclear Cu active site where O2 is reduced to H2O. (See color insert.)...

FIGURE 11-43 Structure of the lactose transporter (lactose permease) of E. coli. (a) Ribbon representation viewed parallel to the plane of the membrane shows the 12 transmembrane helices arranged in two nearly symmetrical domains shown in different shades of blue. In the form of the protein for which the crystal structure was determined, the substrate sugar (red) is bound near the middle of the membrane where it is exposed to the cytoplasm (derived from PDB ID 1 PV7). (b) The structural changes postulated to take place during one transport... 

A more realistic representation for the hemiacetal ring structure is the Haworth projection formulas. The formulas for a-D-glucose are shown in Figure 4.3. The shorthand form of the Haworth projection eliminates the Hs and indicates OHs by dashes. Five- and six-membered cyclic sugars are called furanose and pyranose, respectively.3... 

Figure 8.1 The two sugars, five nitrogenous bases, and phosphate that occur in nucleic acids. Each fundamental unit of nucleic acid is a nucleotide, an example of which is shown. The single letter beside the structural formula of each of the nitrogenous bases is used to denote the base in shorthand representations of the nucleic acid chains.

Fig. 1. Two ribbon representations of the crystal structure of the DNA decamer d(CCTCG -CTCTC/GAGAG CGAGG) containing a unique cisplatin interstrand cross-link at d(GpC)-d(GpC) site (asterisks indicate the chelated bases in the adduct). A front view (A) allows to see the structure with the lesion in the minor groove. A side view (B) shows the chicane of the backbone with the helix-sense reversal. Ptn atom, yellow ammine groups, navy blue sugars, pink guanines, navy blue adenines, red thymines, yellow cytosines, hght blue phosphodiester backbone, green.

Among the first attempts to model the structural perturbation of DNA following complexation with platinum were those by Jankowski and co-workers [66-68], who represented each base, sugar, and phosphate of a DNA strand as a point. This representation ignores the specific energetics of stacking, base... 

Natural sialic acids (Schauer 1982 1991) are derivatives of 5-amino-3,5-dideoxy- D-glycero-D-galacto-nonu osonic acid 12.1. This awkward name has been replaced by neuraminic acid . The most common derivative is N-acetyl-neuraminic acid 12.2 whose configuration is easy to memorize because, in the Fischer representation, 12.3, it is presented as an aldolic condensation product of N-acetylmannosamine (2-acetamido-2-deoxy-D-mannose) and pyruvic acid. When the expression sialic acid is used without any other precision, it is in reference to derivative 12.2. It exists in the free state or glycosidated in the d-conformation, which allows an equatorial disposition of the three-carbon side chain. Structure 12.2 represents the stable /3-anomer of the free sugar with an axial anomeric hydroxyl group and all-equatorial non-anomeric substituents. An X-ray spectrum of this crystallized /3- anomer confirms this conformation and reveals, moreover, that the side chain has the zig-zag conformation with two... 

Scheme 17. A representation of the chiral columnar aggregates formed by d(pG), d(GpG), d(GpGpG), and d(GpGpGpGpGpG). The filled circles represent the sugar units (for clarity, only one sugar per tetramer is shown). The screw thread is obtained by joining the filled circles the screw pitches are in the order d(GpG) > d(GpGpG) > d(GpGpCpGpG), indicating parallel unwinding of the helical structure. Reproduced from ref. 362 (Gottarelli et al., Comprehensive Supramolecular Chemistry 1996, Vol. 9, p. 483) with permission from Elsevier Science.

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