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Biochemistry : HBondingDNA (9 Variations) The structure and replication of DNA are strongly dependent on the hydrogen bonding system present in the double helix. How many functional groups in thymine can participate in hydrogen bonding? (This means all the groups, not just the ones that actually participate in hydrogen bonding in the double helix.)
Biochemistry : ComplementaryDNA (20 Variations)
Determine the sequence of the complementary DNA strand for the following sequence. (Note: Complementary strands match up 5' ends to 3' ends.)
5'-TAATGAGT-3'
Glycosyltransferases A and B: Four Critical Amino Acids Determine Blood TypeNatisha L. Rose, Monica M. Palcic, and Stephen V. Evans Human A, B, and O blood type is determined by the presence or absence of distinct carbohydrate structures on red blood cells. In this review the chemistry of the blood group ABO system and the role of glycosyltransferase A, glycosyltransferase B, and the four amino acids critical to determining blood group status are discussed. Rose, Natisha L.; Palcic, Monica M.; Evans, Stephen V. J. Chem. Educ.2005, 82, 1846.
Carbohydrates |
Enzymes |
Kinetics |
Bioorganic Chemistry |
Crystals / Crystallography |
Molecular Biology |
X-ray Crystallography |
Amino Acids
Testing for Ultraviolet Toxicity Using FungiMarcelo Vital and Patricia Esperón In this article, we describe a laboratory project quantifying the effects of UV radiation on a suspension of living cells. This laboratory experiment was designed for undergraduate students in biochemistry. The experiment was carried out employing different fungi strains, changing the dosage of radiation, the distance to the UV source, and the exposure period to the UV radiation. The quantity of viable spores was calculated and the doseresponse curves were drawn. Students were able to prove that 100% of mortality was achieved with the longest time of exposure. Vital, Marcelo; Esperón, Patricia. J. Chem. Educ.2005, 82, 926.
Nucleic Acids / DNA / RNA |
UV-Vis Spectroscopy |
Medicinal Chemistry |
Molecular Biology |
Photochemistry
A 3D Model of Double-Helical DNA Showing Variable Chemical DetailsSusan G. Cady A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance the basic helical frame to show the shapes and sizes of the nitrogenous base rings, 3' and 5' chain termini, and base pair hydrogen bonding. Students can incorporate random or real gene sequence data into their models. Cady, Susan G. J. Chem. Educ.2005, 82, 79.
Molecular Models of DNAWilliam F. Coleman The featured molecules this month come from the paper by David T. Crouse on the X-ray determination of the structure of DNA. Given that most students are aware of the double helix, it seems appropriate to back up a little and examine the components that give rise to this structure. Accordingly, the molecule collection includes: Purine and pyrimidine, structural precursors of the four bases found in DNA: cytosine (C), thymine (T), adenine (A), and guanine (G) The four corresponding deoxyribonucleosides The four deoxyribonucleotides (the nucleoside monophosphates) A two-base-pair fragment showing the AT and GC hydrogen-bonded complements Several small 24-base-pair DNA fragments polyAT, polyGC, and a random array of bases. The DNA fragments provide a good opportunity to have students explore features of the Jmol and Chime menus. Using the Jmol menu as an example (right-click on the structure to bring up the menu) students can use the measuring tools to get an idea of the length of a complete turn in the DNA, the relative widths of the major and minor grooves, and the diameter of the helix. They can use the coloring schemes to detect the various base pair combinations, and learn to read the code for the random sequence. In Chime they can use the Shapely coloring scheme for this same purpose. Exploring other aspects of the menu will allow students to present the molecules in the various forms, including ribbon and cartoon views. In RNA, thymine is replaced by uracil, and the sugar moiety has an axial hydroxyl group on the carbon atom adjacent to the base binding site (the 2? carbon). The structures of uracil and of uridine monophosphate are included in the molecule collection. Students can use the Web to download and examine more complex DNAs using a site such as the Nucleic Acid Database at Rutgers University.
Nucleic Acids / DNA / RNA
Molecular Models of DAPIWilliam F. Coleman This month's Featured Molecule is DAPI (4′,6-diamidino-2-phenylindole), from the paper by Eamonn F. Healy (1). The utility of DAPI is a consequence of its being a minor-groove binder to DNA. A crystal structure of DAPI binding to the minor groove of a synthetic DNA has been determined, and the structure file made available through the RCSB Protein Data Bank (2, 3). That structure is also included in the Featured Molecules Collection, with the water molecules removed for the sake of clarity. For many students this may be their first encounter with the binding of small molecules to DNA. Another example of such binding is the intercalation of the antibiotic actinomycin into DNA. The Department of Biology at the University of Hamburg maintains an excellent Web site showing both crystal and NMR structures of actinomycin intercalation (4). Observant students will also note in the structure of DAPI a theme that has appeared several times in our Featured Molecules, and that is the non-planarity of adjacent delocalized ring systems. In DAPI, it is a five-membered ring adjacent to a six-membered ring, and the observed departure from planarity is less than that in biphenyl. Students might be asked to explain that difference.
