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Nucleotide Metabolism

Nisa RachmaniaMubarikMajor MicrobiologyDepartment ofBiology,IPB

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Microbial Physiology (Nisa RM)

ATP, are the sources of energy that drive most of ourreactions.

ATP is the most commonly used source but GTP is used inprotein synthesis as well as a few other reactions.

UTP is the source of energy for activating glucose andgalactose.

CTP is an energy source in lipid metabolism.

AMP is part of the structure of some of the coenzymes likeNAD and Coenzyme A. And, of course, the nucleotides arepart of nucleic acids

Microbial Physiology (Nisa RM)

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Nomenclature

Nitrogen BasesThere are two kinds of nitrogen-containing bases - purines andpyrimidines.

Purines consist of a six-membered and a five-memberednitrogen-containing ring, fused together.

Pyridmidines have only a six-membered nitrogen-containingring. There are 4 purines and 4 pyrimidines that are of concernto us.

PurinesAdenine and guanine are found in both DNA and RNA.Hypoxanthine and xanthine are not incorporated into the nucleicacids as they are being synthesized but are importantintermediates in the synthesis and degradation of the purinenucleotides.

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Adenine = 6-amino purine

Guanine = 2-amino-6-oxypurine

Hypoxanthine =6-oxy purine

Xanthine = 2,6-dioxy purine

Microbial Physiology (Nisa RM)

PURINES

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Pyrimidines

Uracil = 2,4-dioxypyrimidine

Thymine = 2,4-dioxy-5-methylpyrimidine

Cytosine = 2-oxy-4-aminopyrimidine

Orotic acid = 2,4-dioxy-6-carboxypyrimidine

Cytosine is found in both DNA and RNA. Uracil is found only inRNA. Thymine is normally found in DNA. Sometimes tRNA will

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contain some thymine asMicrobial Physiology (Nisa RM)

NucleosidesIf a sugar, either ribose or 2-deoxyribose, is added to anitrogen base, the resulting compound is called a nucleoside.Carbon 1 of the sugar is attached to nitrogen 9 of a purine baseor to nitrogen 1 of a pyrimidine base. The names of purinenucleosides end in -osine and the names of pyrimidinenucleosides end in -idine. The convention is to number the ringatoms of the base normally and to use l', etc. to distinguish thering atoms of the sugar. Unless otherwise specificed, the sugar isassumed to be ribose. To indicate that the sugar is 2'-deoxyribose, a d- is placed before the name.-Adenosine-Guanosine-Inosine - the base in inosine is hypoxanthine-Uridine-Thymidine-Cytidine

Microbial Physiology (Nisa RM)

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Nucleotides

Adding one or more phosphates to the sugar portion of anucleoside results in a nucleotide.The phosphate is in ester linkage to carbon 5' of the sugar. Ifmore than one phosphate is present, they are generally in acidanhydride linkages to each other. If such is the case, no positiondesignation in the name is required. If the phosphate is in anyother position, however, the position must be designated. Forexample, 3'-5' cAMP indicates that a phosphate is in esterlinkage to both the 3' and 5' hydroxyl groups of an adenosinemolecule and forms a cyclic structure.Some representative names are:

-AMP = adenosine monophosphate = adenylic acid-CDP = cytidine diphosphate-dGTP = deoxy guanosine triphosphate-dTTP = deoxy thymidine triphosphate

(more commonly designated TTP)-cAMP = 3'-5' cyclic adenosine monophosphate

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Microbial Physiology (Nisa RM)

PolynucleotidesNucleotides are joined together by 3'-5' phosphodiester bondsto form polynucleotides. Polymerization of ribonucleotides willproduce an RNA while polymerization of deoxyribonucleotidesleads to DNA.

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Hydrolysis of Polynucleotides

Most, but not all, nucleic acids in the cell are associated withprotein. After dissociation of the protein and nucleic acid, theprotein is metabolized like any other protein.

The nucleic acids are hydrolyzed randomly by nucleases to yield amixture of polynucleotides. These are further cleaved byphosphodiesterases (exonucleases) to a mixture of themononucleotides.The nucleotides are hydrolyzed by nucleotidases to give thenucleosides and Pi. The nucleosides undergo phosphorolysis withnucleoside phosphorylases to yield the base and ribose 1-P (ordeoxyribose 1-P). Since R 1-P and R 5-P are in equilibrium, thesugar phosphate can either be reincorporated into nucleotides ormetabolized via the Hexose Monophosphate Pathway. The purineand pyrimidine bases released are either degraded or salvaged forreincorporation into nucleotides. There is significant turnover of allkinds of RNA as well as the nucleotide pool. DNA doesn't turnoverbut portions of the molecule are excised as part of a repair process.

Microbial Physiology (Nisa RM)

Microbial Physiology (Nisa RM)

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nucleobase of IMP (hypoxanthine) is shown. (Nisa RM)

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Purine and pyrimidines from tissue turnover which are notsalvaged are catabolized and excreted. Little dietary purine isused and that which is absorbed is largely catabolized as well.

Catabolism of purines and pyrimidines occurs in a less usefulfashion than did the catabolism of amino acids in that we donot derive any significant amount of energy from thecatabolism of purines and pyrimidines.

Pyrimidine catabolism, however, does produce beta-alanine,and the endproduct of purine catabolism, which is uric acid inman, may serve as a scavenger of reactive oxygen species.

http://web.indstate.edu/thcme/mwking/nucleotide-metabolism.html

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Synthesis of the first fully formed purine nucleotide, inosine monophosphate, IMP beginswith 5-phospho--ribosyl-1-pyrophosphate, PRPP. Through a series of reactions utilizingATP, tetrahydrofolate (THF) derivatives, glutamine, glycine and aspartate this pathway yieldsIMP. The two indicated enzymes (A and B) are those catalyzing the rate limiting step and thereaction necessary for the purine nucleotide cycle, respectively. The structure of the

Microbial Physiology

The purine nucleotide cycle serves an important function within exercising muscle. The generation of fumarate provides skeletalmuscle with its' only source of anapleurotic substrate for the TCA cycle. In order for continued operation of the cycle during exercise,muscle protein must be utilized to supply the amino nitrogen for the generation of aspartate. The generation of asparate occurs bythe standard transamination reactions that interconvert amino acids with -ketoglutarate to form glutamate and glutamate withoxaloacetate to form aspartate. Myoadenylate deaminase is the muscle-specific isoenzyme of AMP deaminase, and deficiencies inmyoadenylate deaminase lead to post-exercise fatigue, cramping and myalgias.

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Synthesis of UMP from carbamoyl phosphate. Carbamoyl phosphate utilized in pyrimidinenucleotide synthesis differs from that synthesized in the urea cycle; it is synthesized fromglutamine instead of ammonia and is synthesized in the cytosol. The reaction is catalyzed bycarbamoyl phosphate synthetase II (CPS-II). Subsequently carbamoyl phosphate isincorporated into the pyrimidine nucleotide biosynthesis pathway through the action ofaspartate transcarbamoylase (ATCase) which is the rate limiting step in pyrimidinebiosynthesis. Following completion of UMP synthesis it can be phosphorylated to UTP and

utilized as a substrate for CTPMicrobial Physiologysynthesis of CTP. Uridine nucleotides aresynthase for the (Nisa RM)also the precursors for de novo synthesis of the thymine nucleotides.

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