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Structure of Nucleic Acids (2011)

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Structure of Nucleic Acids (2011) Nucleic Acids (Structure) Nucleic acids determine and control the functioning of cells. DNA – deoxyribonucleic acid and RNA – ribonucleic acid. Both nucleic acids are polymers of nucleotides. Nucleotides contain a phosphate group, a sugar and a nitrogen base. You already know the structure of the phosphate group. Notice that in this nucleotide the sugar (β-D-ribose, found in RNA) is an aldopentose. If you wanted to draw the sugar found in DNA, then you have to remove the Oxygen atom from C-2’ (keep in mind that the C atoms in the sugar are numbered in a clockwise direction). β-D-ribose 2-deoxy -D-ribose (ribose) (deoxyribose) The nitrogen bases, which are heterocyclic rings containing nitrogen, can be divided in two classes according to the number of rings they have. They are: PURINES PYRIMIDINES NH2 O NH2 O O Both nucleic acids contain the C N C N C C H3C C C N C N H HC N HC NH C NH nitrogen bases: Adenine, HC HC Guanine and Cytosine, but C CH C C HC C N N HC C HC C N N NH2 N O N O N O Thymine appears only in H Adenine (A) H Guanine (G) Uracil (U) Thymine (T) H Cytosine (C) H H DNA, whereas Uracil in RNA. (Don’t need to memorize them!) If the structure contains just the carbohydrate and the nitrogen base, it is known as a nucleoside. The names of nucleosides are given according to the type of N-base. If the nucleoside contains a purine (two rings), the name of the structure will end with “_____osine”. (Adenosine, Guanosine) On the other hand, if the N-base is a pyrimidine (one ring), the name will end with “_____idine”. (Cytidine, Thymidine, Uridine) The name of this nucleoside is: “Adenosine”, but if we change the carbohydrate for deoxyribose, then the name would be “Deoxyadenosine”. The following table (next page) summarizes the composition of the nucleosides, and the way in which the names are abbreviated. Reyes free to copy for educational purposes Chem 30B Nucleosides Name Composition Abbreviation Adenosine Adenine-ribose A Deoxyadenosine Adenine-deoxyribose dA Guanosine Guanine-ribose G Deoxyguanosine Guanine-deoxyribose dG Cytidine Cytosine-ribose C Deoxycytidine Cytosine-deoxyribose dC Thymidine Thymine-ribose T Deoxythimidine Thymine-deoxyribose dT Uridine Uracil-ribose U Deoxyuridine Uracil-deoxyribose dU Nucleotides have a phosphate group on C-5’. To give the name to the nucleotide we simply need to consider the new structure added, which is one phosphate group on C-5’. The name of this nucleotide would be: Guanosine 5’-monophosphate or GMP (Notice that we use the nucleoside name.) Any nucleotide can bond to additional phosphate groups: Look at the following examples with ribose and deoxyribose respectively: O O O NH NH NH O O O O O O - N O O P O -O P O P O N O -O P O P O P O N O O O O - H H - - O O O H H O- O- O- H H H H H H H H OH OH OH OH OH OH Uridine 5’-monophosphate, Uridine 5’-diphosphate, Uridine 5’-triphosphate, UMP UDP UTP O O O NH NH NH O O O O O O - N O - N O O P O O P O P O -O P O P O P O N O O O O - H H - - H H - - - O O O O O O H H H H H H H H OH H OH H OH H Deoxythymidine 5’- Deoxythymidine 5’-diphosphate, Deoxythymidine 5’-triphosphate, monophosphate, dTMP dTDP dTTP Note: You must be able to draw any nucleotide given the name or abbreviation. (E.g. Guanosine 5’-monophosphate, dCDP, ATP, etc.) Reyes free to copy for educational purposes Chem 30B Primary structure of DNA As we mentioned before, nucleic acids (DNA, RNA) are polymers of these nucleotides. The sequence of nucleotides forms the primary structure of DNA. O Notice three points: NH Thym ine 1) The phosphate and the carbohydrate form a backbone. NH2 O N O 5' end N O P O CH N 2 O A denine 2) The chain has a ‘free’ phosphate group at the 5’ end O H H N N and a ‘free’ hydroxide group H 3' H O H NH2 at the 3’ end. 5' O P O CH2 O N Cyt osine 3) The nucleotides are O- H H bonded together by a H 3' H O H N O phosphodiester group. O Phosphodiester 5' O P O CH Bond 2 O N NH O- H H H 3' H O H N N N H2 5' Guanine O P O CH 2 O - H H O H H H 3' end OH Secondary structure of DNA – The double helix Double helix – two strands twisted together (“Twisted ladder”) [Watson & Crick 1953] The two chains are oriented in opposite directions, and held in place by means of H-bonds between Nitrogen bases. Reyes free to copy for educational purposes Chem 30B Hydrogen bonds between N-bases: A=T (2 H-bonds) G≡C (3-H bonds) As we can see, a purine will H-bond to a pyrimidine. This situation results in a constant width for the ladder and it is known as “complementary base pairing”. ‘A’ can not pair with ‘G or ‘C’, ‘G’ can not pair with ‘A’ or ‘T’. If one strand is: 5’—A-T-G-T-C-C-A—3’ The other strand would be: 3’—T-A-C-A-G-G-T—5’ Reyes free to copy for educational purposes Chem 30B Types of RNA Differences between DNA and RNA: Ø The Carbohydrate: RNA uses ribose instead of deoxyribose. Ø Nitrogen base: Uracil instead of Thymine. Ø RNA is single stranded. Ø RNA is not as long as DNA. There are three main types of RNA: Messenger RNA (mRNA) – carries the genetic information from DNA in the nucleus to the ribosomes where protein synthesis occurs. Ribosomal RNA (rRNA) – is present in the ribosomes (cellular organelles made of RNA and proteins), which in turn are made of two subunits (one small and one large). Transfer RNA (tRNA) – “interprets” the genetic code and delivers amino acids to the ribosome. Reyes free to copy for educational purposes Chem 30B Acknowledgments: “Twisted ladder” [Watson & Crick 1953] fundamentals of General, Organic and Biologival Chemistry. McMurry, et Al., Sixth Edition, page. 817. H-bonds formed by nitrogen bases fundamentals of General, Organic and Biologival Chemistry. McMurry, et Al., Sixth Edition, page. 818. Base pairing: http://en.wikipedia.org/wiki/DNA Transfer RNA http://www.tutorvista.com/biology/types-of-dna-and-rna Reyes free to copy for educational purposes Chem 30B .
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