Nucleotides and Nucleic Acids Nucleotides have a wide variety of functions One major function is to provide the thermodynamic driving force for a number of chemical reactions This is especially well known for ATP but GTP is also used for a variety of reactions UTP is used in glycogen and complex carbohydrate biosynthesis and CTP is used in complex lipid synthesis Nucleotides are used to form intracellular signaling molecules such as cAMP and cGMP In addition ATP ADP and AMP act as signals to modulate energy metabolism Nucleotides form parts of some cofactors including NAD FAD and coenzyme A Finally nucleotides are the monomer units that comprise the nucleic acids RNA and DNA Cells maintain pools of free nucleotides for a variety of purposes Adenosine derivatives are the most common free nucleotides because ATP is used in the largest number of reactions In addition ATP is converted into S adenosylmethionine and a number of other molecules involved in metabolic reactions As mentioned above pools of other free nucleotides are also important in some types of reactions although these pools tend to be much smaller than those of ATP Synthesis of nucleic acids and especially synthesis of DNA requires synthesis of nucleotides because the cellular pools of the required free nucleotides are insufficient to provide all of the monomer units required Nucleotide nomenclature and structure Nucleotides are comprised of a nitrogen containing molecule called a base attached to a ribose ring The bases are derivatives of two possible ring structures purine and pyrimidine and are numbered according to their parent compound The bases all contain significant conjugated systems which absorb ultraviolet light 16 6 1 N 2 5 7 N 5 N 6 2 8 N 4 N 3 Purine 9 3 N 1 Pyrimidine HO CH2 O Base 5 4 O P O CH2 O O 1 4 3 HO 2 1 HO Nucleoside O 4 3 OH Base 5 2 OH Nucleotide Monophosphate O O Base 5 O P O CH2 O 1 4 3 2 HO 2 Deoxyribonucleotide Monophosphate The base and ribose ring together are termed a nucleoside the suffix oside means a compound covalently bonded to carbohydrate The base and the ribose with one or more phosphate attached are termed a nucleotide The ribose ring numbering is 16 DNA and RNA exhibit a maximum absorption at about 260 nm due to the absorbance of the nucleotide bases Most proteins have a maximum absorption at 280 nm due to the absorbance of tryptophan and tyrosine One method for assessing the relative amount of protein and nucleic acid in a sample is to measure the A260 A280 ratio a ratio of above 1 8 indicates that the solution contains nucleic acid with little protein Copyright 2000 2011 Mark Brandt Ph D 71 from 1 to 5 The prime modifier to the ribose ring number designates the ribose carbons as distinct from the atoms of the purine or pyrimidine ring Nucleotides all have the base attached to the 1 carbon Deoxyribonucleotides the nucleotides present in DNA lack the 2 hydroxyl The base in the nucleoside can have one of two possible conformations syn and anti Both are present although the anti conformation is more common physiologically due both to the lower steric strain and to that fact that this conformation is required for nucleic acid structure The rotation about the base ribose bond is restricted by steric hindrance so the nucleotide must be synthesized in one form or the other For purines the syn structure is drawn most frequently this is not a reflection of the common conformation but instead merely allows the drawing to occupy less space on the page NH2 syn O P O CH2 anti N N O NH2 N O N O N N O P O CH2 O N N O O HO OH HO OH The most common bases are the two purine and three pyrimidine derivatives shown below Purines NH2 N N Base Adenine N Pyrimidines NH2 Nucleotide H2N N H N H Cytosine Cytidine Uracil Uridine Thymine Thymidine O O NH N Guanine N Nucleotide N Adenosine O HN Base Guanosine N H N H O O H3C NH N H Copyright 2000 2011 Mark Brandt Ph D 72 O These are not the only bases used in physiology Others include xanthine and hypoxanthine intermediates in purine metabolism a methylated version of adenine with the methyl group attached to the nitrogen attached to C6 a methylated version of cytosine 5 methyl cytosine pseudouridine which has the ribose attached to C5 instead of N1 of uracil and 1 3 7 trimethylxanthine better known as caffeine Uric acid is a major excretion product following purine degradation accumulation of uric acid in tissues results in gout O O N N N N H Hypoxanthine O N HN N H N H O HN Xanthine O Uric acid H3C NH HN N H N H O O O H N O O CH3 N N N N CH3 1 3 7 Trimethyl xanthine Pseudouracil The phosphates in nucleotide triphosphates are most commonly attached to the 5 carbon If the site of phosphate attachment is not given it is assumed to be at the 5 position while other sites of attachment must be stated explicitly Thus AMP is 5 AMP while 3 AMP has to be written out NH2 AMP N O N O P O CH2 NH2 3 AMP N N N N HO CH2 O O N N O O HO O P O OH OH O RNA contains adenosine cytidine guanosine and uridine commonly abbreviated as A C G and U DNA contains deoxyadenosine deoxycytidine deoxyguanosine and deoxythymidine commonly abbreviated as A C G and T Note that in nucleic acids thymine is therefore only present in DNA and uracil is only present in RNA In humans most purines and pyrimidines present as nucleotides the major exceptions are xanthine and uric acid Some organisms use purines for other purposes and maintain the purines in the free form An example of this is provided by the series of methylated xanthine derivatives produced in plants that have biological activity in humans 1 3 dimethylxanthine theophylline an active ingredient in chocolate 3 7 dimethylxanthine theobromine found in tea and 1 3 7 trimethylxanthine caffeine Copyright 2000 2011 Mark Brandt Ph D 73 The structure and role of nucleic acids Nucleic acids are polymers of nucleotides in which the phosphate from the 5 position of one nucleotide is attached to the 3 hydroxyl of the preceding nucleotide This phosphodiester link is created using the energy from the triphosphate form of the nucleotide being added driven by the release of inorganic pyrophosphate Because of this intrinsic directionality nucleic acid sequences are typically written from 5 to 3 unless otherwise specified Ribonucleic acid RNA is synthesized from ribonucleotide triphosphates while deoxyribonucleic acid is synthesized from deoxyribonucleotides as shown below Additional DNA O Additional DNA 5 carbon O O P O 5 O G O CH2 O P O C O O O