The Anomeric Effect Paul Krawczuk
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Stereoelectronic Effects in Nucleosides and Nucleotides and Their Structural Implications
Stereoelectronic Effects in Nucleosides and Nucleotides and their Structural Implications (including Appendix on literature up to 2005) Christophe Thibaudeau, Parag Acharya and Jyoti Chattopadhyaya* *To whom correspondence should be addressed. E-mail: [email protected] F +4618554495 T +46184714577 www.boc.uu.se Department of Bioorganic Chemistry Biomedical Center, Uppsala University, Sweden 2 Christophe Thibaudeau, Parag Acharya and Jyoti Chattopadhyaya* Dept of Bioorganic Chemistry Uppsala University Biomedical Center, Box 581 S-751 23 Uppsala Dr C. Thibaudeau has completed his Ph.D in Feb, 1999 at the Dept of Bioorganic Chemistry under the supervision of Prof J. Chattopadhyaya Dr P. Acharya has completed his Ph.D in Dec, 2003 at the Dept of Bioorganic Chemistry under the supervision of Prof J. Chattopadhyaya Dr J. Chattopadhyaya is professor of Bioorganic Chemistry at the Uppsala University Use the following for citation in your reference: Uppsala University Press First Edition: 1999; Second Edition, 2005 Copyright © May, 1999 by J. Chattopadhyaya, C. Thibaudeau and P. Acharaya ISBN 91-506-1351-0 pp 166 Chattopadhyaya et al, "Stereoelectronic Effects in Nucleosides & Nucleotides and their Structural Implications", Dept of Bioorganic Chemistry, Box 581, Uppsala University, S-75123 Uppsala, Sweden, Ver 160205 [email protected] 3 The intrinsic flexibility of pentoses in natural PREFACE nucleosides and nucleotides, owing to their lower energy barrier for interconversions compared to the The three essential components of DNA and RNA are hexopyranoses, is dictated by the energetics of the aglycone, the pentofuranose sugar in β-D stereochemistry stereoelectronic effects, which simply can be tuned and the phosphodiester. The phosphates at the backbone and modulated by choice of substituents and their makes DNA/RNA to behave as polyelectrolyte, the pentose ionization state as well as by their complexation with sugar gives the intrinsic flexibility with relatively low energy potential ligands present in the medium. -
Carbohydrates: Structure and Function
CARBOHYDRATES: STRUCTURE AND FUNCTION Color index: . Very important . Extra Information. “ STOP SAYING I WISH, START SAYING I WILL” 435 Biochemistry Team *هذا العمل ﻻ يغني عن المصدر المذاكرة الرئيسي • The structure of carbohydrates of physiological significance. • The main role of carbohydrates in providing and storing of energy. • The structure and function of glycosaminoglycans. OBJECTIVES: 435 Biochemistry Team extra information that might help you 1-synovial fluid: - It is a viscous, non-Newtonian fluid found in the cavities of synovial joints. - the principal role of synovial fluid is to reduce friction between the articular cartilage of synovial joints during movement O 2- aldehyde = terminal carbonyl group (RCHO) R H 3- ketone = carbonyl group within (inside) the compound (RCOR’) 435 Biochemistry Team the most abundant organic molecules in nature (CH2O)n Carbohydrates Formula *hydrate of carbon* Function 1-provides important part of energy Diseases caused by disorders of in diet . 2-Acts as the storage form of energy carbohydrate metabolism in the body 3-structural component of cell membrane. 1-Diabetesmellitus. 2-Galactosemia. 3-Glycogen storage disease. 4-Lactoseintolerance. 435 Biochemistry Team Classification of carbohydrates monosaccharides disaccharides oligosaccharides polysaccharides simple sugar Two monosaccharides 3-10 sugar units units more than 10 sugar units Joining of 2 monosaccharides No. of carbon atoms Type of carbonyl by O-glycosidic bond: they contain group they contain - Maltose (α-1, 4)= glucose + glucose -Sucrose (α-1,2)= glucose + fructose - Lactose (β-1,4)= glucose+ galactose Homopolysaccharides Heteropolysaccharides Ketone or aldehyde Homo= same type of sugars Hetero= different types Ketose aldose of sugars branched unBranched -Example: - Contains: - Contains: Examples: aldehyde group glycosaminoglycans ketone group. -
Structural Features
1 Structural features As defined by the International Union of Pure and Applied Chemistry gly- cans are structures of multiple monosaccharides linked through glycosidic bonds. The terms sugar and saccharide are synonyms, depending on your preference for Arabic (“sukkar”) or Greek (“sakkēaron”). Saccharide is the root for monosaccha- rides (a single carbohydrate unit), oligosaccharides (3 to 20 units) and polysac- charides (large polymers of more than 20 units). Carbohydrates follow the basic formula (CH2O)N>2. Glycolaldehyde (CH2O)2 would be the simplest member of the family if molecules of two C-atoms were not excluded from the biochemical repertoire. Glycolaldehyde has been found in space in cosmic dust surrounding star-forming regions of the Milky Way galaxy. Glycolaldehyde is a precursor of several organic molecules. For example, reaction of glycolaldehyde with propenal, another interstellar molecule, yields ribose, a carbohydrate that is also the backbone of nucleic acids. Figure 1 – The Rho Ophiuchi star-forming region is shown in infrared light as captured by NASA’s Wide-field Infrared Explorer. Glycolaldehyde was identified in the gas surrounding the star-forming region IRAS 16293-2422, which is is the red object in the centre of the marked square. This star-forming region is 26’000 light-years away from Earth. Glycolaldehyde can react with propenal to form ribose. Image source: www.eso.org/public/images/eso1234a/ Beginning the count at three carbon atoms, glyceraldehyde and dihydroxy- acetone share the common chemical formula (CH2O)3 and represent the smallest carbohydrates. As their names imply, glyceraldehyde has an aldehyde group (at C1) and dihydoxyacetone a carbonyl group (at C2). -
• for an Anomer, the OH Is Drawn Down. • for a Anomer, the OH Is
How to draw a Haworth projection from an acyclic aldohexose Example: Convert D-mannose into a Haworth projection. CHO HO H HO H H OH H OH CH2OH D-mannose Step [1]: · Draw a hexagon and place the oxygen atom in the upper right corner. O O in upper right corner Step [2]: · Place the anomeric carbon on the first carbon clockwise from the oxygen. · For an anomer, the OH is drawn down. · For a anomer, the OH is drawn up. This C becomes the anomeric C. 1CHO O H O OH HO H 1 1 HO H OH H H OH anomer anomer H OH anomeric carbon - CH2OH first C clockwise from O · Always keep in mind that the anomeric carbon comes from the carbonyl carbon in the acyclic form. Step [3]: · Add the substituents of the three chiral carbons closest to the C=O. · The substituents on the right side of the Fischer projection are drawn down. · The substituents on the left are drawn up. CHO HO 2 H add H O H O H 3 C2 - C4 H HO H 4 OH OH 4 OH OH H 4 OH HO OH HO OH 3 2 3 2 H H H OH H H anomer anomer CH2OH Haworth convention - 2 Step [4]: · For D sugars the CH2OH group is drawn up. For L sugars the CH2OH group is drawn down. CHO CH2OH CH2OH HO H H O H H O H H HO H H OH OH OH OH H OH HO OH HO OH H H H OH H H anomer anomer CH2OH This OH on the right side CH OH is drawn up. -