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Chapter 3 http://courses.cm.utexas.edu/kbrowning/ch369/private/chapter3/chapt... 1 of 10 9/7/07 3:45 PM Nucleotides, DNA and the Central Dogma NOTE: if you cannot see images in the boxes, do not worry about it, they are eye candy, just structures of the molecules in 3D. To view them requires a plug-in called C H I M E . Getting it working is sometimes more trouble that it is worth as the plug-in is not compatible with all or newer versions of browsers (firefox) and operating systems (eg mac osX). monomers connected by covalent bond to form polymers DNA and RNA monomers also function in catalysis, energy transfer, hormone signal mediation note that many of the co-substrates have a nucleotide portion--NAD, FAD, etc. purine or pyrimidine ring nitrogen containing, weak base--hence the term "bases" when referring to the nucleotides nitrogens can also ionize at different pHs free bases are rarely found in nature--extremely insoluble double bonds absorb UV--used to quantitate nucleotides/nucleic acids Purines--2 rings; G and A found in RNA and DNA guanine G adenine A Pyrimidines--one ring--C found in RNA and DNA; U in RNA; T in DNA thymine T cytosine C uracil U Many other types of purines and pyrimidines are important in tRNAs and as molecules with biological effects (caffeine and theophylline)
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Chapter 3 http://courses.cm.utexas.edu/kbrowning/ch369/private/chapter3/chapt... 2 of 10 9/7/07 3:45 PM caffeine--coffee theophylline--tea Nucleosides --contain ribose (RNA-ribonucleosides) or deoxyribose (DNA-deoxyribonucleosides), no phosphate glycosidic bond--C1' carbon of sugar to N-1 of pyrimidines or N9 of purines adenosine-ribo guanosine-ribo cytidine-ribo uridine-ribo thymidine-deoxy Nucleoside Derivatives--mimics that lack the ability to be incorporated into DNA--no 3' OH group used to treat AIDS--inhibits replication of HIV virus used to treat Herpes, shingles, chicken pox AZT--3'-azido-3'-deoxythymidine Acyclovir--Zovirax Nucleotides --OH group of ribose esterified with phosphate monophosphates are dibasic acids with pKa of ~1 and 6
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Chapter 3 http://courses.cm.utexas.edu/kbrowning/ch369/private/chapter3/chapt... 3 of 10 9/7/07 3:45 PM AMP-ribo GMP-ribo CMP-ribo UMP-ribo TMP--deoxy Diphosphates and triphosphates --ATP is given as an example the phosphate groups are given the designation α ( alpha closest to ribose), β ( beta, middle), γ (gamma, farthest from ribose) di- and tri-phosphates always complexed with Mg ++ di- and tri-phosphates are used in many metabolic reactions di- and tri-phosphates are synthesized from the monophosphates by kinases using ATP as the source of phosphate ATP (triphosphate) Polynucleotides--DNA, RNA Deoxyribonucleic acids (DNA) backbone of alternating units of 2-deoxy-ribose and phosphate in which the 3’-OH of one deoxy-ribose is joined by a phosphodiester bond to the 5’-OH of another deoxy-ribose unit Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule (or an RNA molecule) 5’ end to the 3’ end--directionality
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Chapter 3 http://courses.cm.utexas.edu/kbrowning/ch369/private/chapter3/chapt...
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