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Nucleotides: Their Synthesis and Degradation

 

Nucleotides: Nitrogenous base + pentose sugar + phosphate group(s)

     (1) The Nitrogenous Bases:

         Planar, aromatic, heterocyclic

        Structural derivatives of purine or pyrimidine

        Note that numbers on the atoms are "unprimed"

 

        The parent compounds are shown below:

                                                                            

                                                                                 

                                      

               

                The structures of the two most common purines are:

 

                                                

                                                                                     

                  The structures of the three most common pyrimidines are:

                                            

                                                             

 

               * Note: We will soon see other important purines and pyrimidines.

          (2) Sugars: D-ribose and 2'-deoxyribose

                Pentoses: 5-C sugars

                "Primes" refer to numbering of the atoms of the ribose 

                                       

 The "2'-deoxy-" notation means that there is no -OH group on the 2' carbon atom

                Purines bond to the C1' of the sugar at their N9 atoms

                Pyrimidines bond to the sugar C1' atom at their N1 atoms

 

                                                     

                                                                               

                   A "nucleoside" results from the linking of one of these 2 sugars  with one of the purine-  or  pyrimidine-derived bases through an N-glycosidic linkage.                 

                        The chemical bond linking them is an "N- glycosidic bond"

                                                           

                                                                

       (3) Phosphate Group(s)

            Mono-, di-, and triphosphates

            Phosphate can be bonded to either C3' or C5' atoms of sugar

                     A "nucleotide" is a 5'-phosphate ester of a nucleoside.

 

                                       

                                                                                             

            RNA (ribonucleic acid) is a polymer of ribonucleotides

            DNA (deoxyribonucleic acid) is a polymer of deoxynucleotides

            Deoxy- and ribonucleotides contain adenine, guanine and cytosine

            Ribonucleotides also contain uracil

            Deoxynucleotides also contain thymine

 

The Naming Conventions

There's a logic to the naming of the nucleosides and nucleotides, if you can remember a few rules.

            The purine NSs  end in "-sine" :   adenosine and guanosine

            The pyrimidine NSs end in "-dine" : cytidine, uridine, deoxythymidine

            To name the NTs, use the NS name, followed by "mono-", "di-" or "triphosphate":

                    adenosine monophosphate, guanosine triphosphate, deoxythymidine monophosphate

 

Nucleotides have a number of roles. Most notably they are  the monomers for nucleic acid polymers. Nucleoside triphosphates, like ATP and GTP, are energy carriers in metabolic pathways. Nucleotides are also components of some important coenzymes, like FAD, NAD+ and Coenzyme A.

 

Exercise: View the various nucleotide structures

   

Exercise: Take the Nucleotide Identification Quiz

 

The Metabolism of Nucleotides

Before we look at nucleic acid structure, we need to study the synthesis of the purine and pyrimidine ribonucleotides and the subsequent synthesis of the deoxyribonucleotides, followed by their catabolic and recycling pathways. The synthetic pathways are particularly detailed, and I suggest that you review my introduction to the study of biochemical pathways so that you can break the information down into manageable pieces. Along the way, we will correlate the information, where appropriate, to disease states. In such instances, I will use the header  "Clinical Correlate".

 

Purine Ribonucleotide Synthesis

Surprisingly, the purine ribonucleotides are formed as such de novo, and the bases themselves are derived from them. The first purine ribonucleotide to be synthesized in an organism is inosine monophosphate (IMP), and AMP and GMP are subsequently derived from them. The purine base of IMP is hypoxanthine:

 

                                             

                                                                           

We will see that all purine nucleotides are ultimately degraded to uric acid, which is itself a purine. Studies by Buchanan in the mid 1900s established the origin of the individual atoms in uric acid, and it's helpful to mention these now, as we will soon see how they are incorporated into the molecule. Using the numbering convention as described, we will see the following:

 

                                                           

                                                                    

        N1 :  Aspartate Amine                                

        C2 , C8 : Formate

        N3 , N9 : Glutamine

        C4 , C5 , N7 : Glycine 

        C6 : Bicarbonate ion  

A survey of the biosynthesis of IMP shows that there are 11 individual steps and 7 types of enzymes involved:

        kinases (1)

        transferases (1)

        synthetases (4)   (Remember the difference between synthetases and synthases)

        transformylases (2)

        carboxylases (1)

        lyases (1)

        cyclohydrolases (1)

 

ATP is involved in 6 of the steps, but we will see that an additional ATP is needed to form a-D-Ribose-5-phosphate, the first molecule in the pathway. That's a lot of ATPs, and therefore, so as not to be wasteful, nature very effectively salvages derivatives of purines in recycling pathways.The ribose-5-phosphate is produced in the pentose phosphate pathway, which you have already studied.

The 5-Phosphoribosyl-a-pyrophosphate (PRPP) formed in the first step is also a precursor of pyrimidine synthesis, and it is also a precursor of the synthesis of Trp and His. Because it is part of so many important pathways, it is highly regulated. The role of ATP in this step is different from that of the other steps in this pathway in which it is found. ATP activates the ribose-5-phosphate by adding a pyrophosphate group (PPi) to C1 of the sugar (i.e., there is a group transfer).  All of the other ATP-involving steps that follow harness the energy of hydrolysis of a phosphate bond of ATP (exergonic) to drive an endergonic reaction. In these steps, one can talk about "coupling" of two reactions, such that the exergonic one drives the endergonic one with the result that the overall DG' is negative. 

IMP Biosynthesis

 

 

 

Reaction Mechanism for Purine Biosynthesis

Digression: "Coupling" of Reactions

You have frequently heard ATP referred to as the "universal energy currency" of the cell, and this is true for all organisms. Why ATP ended up being such a pivotal coenzyme, and not GTP, UTP, etc., is probably just a matter of chance. The free energy of biological oxidation reactions can be stored in the bonds of ATP (chemical energy). It's relatively easy to hydrolyze pyrophosphate linkages in ATP, with the result that a considerable amount of free energy is released (DGo' = -30.5 kJ/mol for ATP hydrolysis to ADP and Pi ).If this were released into the cell as heat, it would serve no useful purpose as far as making an endergonic chemical reaction proceed, since there's no way for the cell to transduce heat energy into work. But, if two reactions are "coupled" such that the product of an endergonic reaction is the reactant of an exergonic one (and the magnitude of the free energy change of the exergonic one is greater than that of the endergonic) then the exergonic reaction pulls the endergonic one through an intermediate. In other words, for chemical energy to be so coupled, there must be an intermediate common to both reactions in the set.

When ATP appears as a reactant, it can generally participate in two ways: part of the ATP molecule can be transferred to an acceptor molecule or ATP hydrolysis can drive an otherwise unfavorable reaction. The Pi, PPi, adenyl or adenosinyl groups can be transferred, as in the first step in the purine biosynthetic pathway. In such instances, the substrate is said to be "activated" by the transfer. When the free energy of ATP hydrolysis drives an endergonic reaction, the overall mechanism must involve transfer of a Pi group somewhere along the way, even though, in the final analysis, it will appear as Pi in the reaction ATP + H20 --> ADP  +  Pi. Otherwise, there would be no way to couple the reactions. 

You might want to think about the possibility of transducing heat energy or electrical energy into chemical energy in the cell.

Back to the Purine Biosynthetic Pathway:

Notice that, in the second step, the notation on the C1 changes from a to b. These two forms are "anomers" and they specify the position of the -OH group on the C1 carbon with respect to the -CH2OH group on C4 . From step 3 to the end of the pathway, the anomeric form is b .Also in this step, the pyrophosphate produced is hydrolyzed to 2Pi , an irreversible step that commits the pathway in its direction toward the production of IMP. This, then, is the flux-controlling step.

In the two steps involving lyases, notice that fumarate is one of the products. Fumarate has the structure:

           

and you now can see where the double bond is.

In the transformylase steps, there are group transfers, namely the "formyl" group  (-CH=O) donated by the cofactor N10 -formyl-THF, where THF stands for tetrahydrofolate. Sulfonamides can inhibit the steps involving THF because they are structural analogs of the PABA component of THF.

Finally, in this pathway, many of the enzymes are grouped together on single polypeptide chains. This serves to organize and control the processing of a substrate from one step to the next. Such "chanelling" increases the overall rate of a pathway and protects intermediates from degradation. In animals, the enzymes of the IMP synthesis pathway are grouped as follows:

        Reactions 3,4,5

        Reactions 7,8

        Reactions 10,11

In Class Exercise: Calculate how many ATP equivalents are needed to synthesize IMP.

IMP is rapidly converted to AMP and GMP in the following set of two-step reactions::

                                      

Note that GTP hydrolysis drives the first step and that the lyase in the second step is the same lyase that we saw in reaction 9 in the IMP synthesis pathway.

  

 

        

The subsequent hydrolysis of PPi to 2Pi , an irreversible reaction, drives the last step. You will also recognize that the purine base on XMP is a new one to us, namely xanthine.Other than the C8 keto group, it is identical to uric acid.

Note that a guanine nucleotide (GTP) is involved in the AMP pathway and that an adenine nucleotide (ATP) is involved in the GMP pathway. This reciprocity is fundamental to the control of production of both AMP and GMP and their di- and triphosphates.

The subsequent phosphorylation of the nucleoside monophosphates, AMP and GMP, leads to formation of the nuclcleoside di- and triphosphates:

 

Regulatory Control of Purine Nucleotide Biosynthesis

The basic idea here is that there is exquisite control of the amounts of purine nucleotides available for synthesis of nucleic acids, and that the pathways are individually regulated at the cellular level. Furthermore, the relative amounts of ATP and GTP are also controlled at the cellular level.

We expected that the first step, in which PRPP is synthesized, would be subject to regulation because of the prominence of PRPP in other biosynthetic reactions, including that of pyrimidine nucleotides. Increasing levels of ADP and GDP have a negative feedback effect on the enzyme Ribose phosphate pyrophosphokinase. The enzyme catalyzing the second step of the pathway, Amidophosphoribosyl transferase, is inhibited by all of the adenine and guanine nucleotides, the adenine nucleotides binding to one inhibitory site on the enzyme and the guanine nucleotides to another separate site. This enzyme is also "activated" by the increase in the level of PRPP and this is called a "feedforward activation".

IMP is also subject to regulation at points after its production. AMP and GMP each competitively inhibit their own production. Also, each AMP synthesized requires one GTP and each GMP synthesized requires one ATP, in a reciprocal fashion as mentioned above. As about equal amounts of AMP and GMP are needed in nucleic acid synthesis, this reciprocity provides for that. The rate of production of AMP increases with increasing concentrations of GTP, and that of GMP with increasing concentrations of ATP.

 

Purine Catabolism and Salvage

All pathways of purine nucleotide and deoxynucleotide degradation in all animals lead to uric acid.

Both cellular and ingested nucleic acids are degraded, their products being turned over, or salvaged, or excreted from the body. An organism is able to produce most of the nucleotides that it needs in the de novo pathways that we are now studying, so most of the nucleotides, bases, etc. that are catabolic products of ingested nucleic acids are excreted after further degradation.

Ingested nucleic acids are degraded to nucleotides in the intestine by:

            pancreatic nucleases

            intestinal phosphodiesterases

Specific nucleotidases and nonspecific phosphatases further degrade nucleotides to nucleosides. These can either be absorbed into intestinal mucosa or degraded in the intestine by nucleosidases and nucleoside phosphorylases As follows:

            Nucleoside + H2O -->  base + ribose

            Nucleoside + Pi --> base + ribose-1-phosphate

Although we haven't yet shown how to get deoxyribonucleotides from ribonucleotides, whatever we say about the purine ribonucleotide degradation pathways will hold for the purine deoxyribonucleotides.

The 4 purine nucleotides that we have studied are AMP, IMP, XMP and GMP and each one of these can be degraded to its corresponding nucleoside by the action of  5'-nucleotidase, which catalyzes cleavage of the phosphate group from the 5' C of the ribose. Notice that these are hydrolysis reactions. Nucleosides are degraded to the bases xanthine, hypoxanthine and guanine by the action of purine nucleoside phosphorylase (PNP) and ultimately all three are degraded to uric acid through the common intermediate, xanthine. Note that the base adenine is not an intermediate in these pathways. That's because there's a detour from  adenosine to inosine, which is the first product in the degradation of IMP, rather than a degradation of adenosine to adenine by the action of PNP. Also, AMP can be deaminated (loss of an NH4+ group) by AMP deaminase to IMP:

 

                       

 

The nucleosides inosine, xanthosine and guanosine are degraded respectively to hypoxanthine, xanthine and guanine and, in the process, the ribose sugar, which was attached by its C1 to the base is phosphorylated:

 

                

 

What's really interesting here is that the ribose sugar is recycled in the form of ribose-1-phosphate, which can be incorporated into PRPP which, as we now know, is integral to the biosynthesis of purines, pyrimidines, histidine and tryptophan. That's a really efficient way to run a cell!

Hypoxanthine and guanine are each converted to xanthine by the actions of xanthine oxidase and guanine deaminase respectively. The xanthine is converted to uric acid in a reaction again catalyzed by xanthine oxidase. 

Xanthine oxidase contains a number of agents involved in the transport of electrons ultimately to dioxygen. It is a dimeric protein that contains FAD,  a molybdenum complex alternately in its +4 and +6 oxidation states, and two Fe-S clusters. The O2 is converted to H2O2 in the process, and this, in turn, is reacted to H2O and O2 by catalase, as the H2O2  can react to form other harmful oxidizind species.

You might have noticed that AMP is deaminated to IMP in one reaction while IMP is the precursor of AMP in a two-step reaction series previously studied. Look at these reactions separately :

        AMP  +  H2O  -->  IMP  +  NH4+         (AMP deaminase)

         IMP  +  Aspartate  +  GTP   -->  AMP  +  fumarate  +  GDP  +  Pi    (adenylosuccinate synthetase                                                                                                                       adenylosuccinate lyase)

Adding the two, we have:

        Aspartate  +  H2O +  GTP  -->  Fumarate  +  GDP  +  Pi  +  NH4+

What this shows is that the overall effect of combining these two reactions is a net result of deaminating an aspartate to a fumarate at the expense of a GTP molecule. This cycle of reactions is know as the "purine nucleotide cycle" and it is of physiologic importance in muscle metabolism. Muscle tissue replenishes its citric acid cycle intermediates via the purine nucleotide cycle rather than through the usual "replenishing reactions", the most important of which is the generation of oxaloacetate from pyruvate catalyzed by pyruvate carboxylase. The fumarate generated in the purine nucleotide cycle feeds into the citric acid cycle to regenerate malate, oxaloacetate, and so forth.

 

 

 

 

AMP Deaminase Deficiency

 

 

 

 

Adenosine deaminase (1ADA - see Chime below), the enzyme catalyzing the deamination of adenosine to inosine, is an example of an enzyme that contains the a/b domain structure, which is the most frequently encountered and most regular domain structure. We will take a small detour here and examine the structure of a/b barrels in general and of adenosine deaminase in particular.

There are two types of a/b structures:

        (1) the "central parallel" structure and (2) a mixed b-sheet surrounded by a-helices.

These structures are found in all glycolytic enzymes and in proteins that bind and transport metabolites. ADA has the central barrel structure in which eight twisted,parallel b-strands (the "staves" of the barrel) are connected by eight a-helical loops. Each loop connects the carboxyl end of a b-strand with the amino end of an a-helix, the helices being found on the outside of the "barrel" and stabilized by hydrophobic interactions between hydrophobic side chains of the a-helices and hydrophobic side chains of the b-sheet. Because this structure was first described in triosephosphate isomerase (TIM), it is also know as the "TIM barrel".

In all of the double-barrel structures, the active site is at the bottom of a funnel-shaped pocket comprised of the eight loops described above.The residues that are involved in binding and in catalytic activity are in the loop regions. 

       

  

2ADA: Adenosine Deaminase

             

 

Humans excrete uric acid into the urine as insoluble crystals. So do birds, terrestrial reptiles and some insects, but they excrete it as a paste of uric acid crystals, and thereby conserve water. In other organisms, uric acid is further modified prior to excretion as follows:

        Uric acid --> Allantoin --> Allantoic acid --> Urea --> Ammonia

 

 

 

 

 

Gout

 

 

Xanthine oxidase inhibitors can inhibit the production of uric acid and thereby be used to treat gout. Allopurinol, an analog of hypoxanthine, binds to xanthine oxidase where it is hydroxylated to alloxanthine. The enzyme is thereby inactivated because of tight binding of the alloxanthine to it. As a result, uric acid production decreases and, consequently, hypoxanthine and xanthine levels increase. Fortunately, these are more soluble than uric acid. Compare the molecule of allopurinol shown below to a molecule of hypoxanthine to see how similar they are:

                                                           

In another example of the efficiency of cellular mechanisms, we will look at the turnover or salvage of  adenine, guanine and hypoxanthine that result from the degradation of nucleic acids. These purines are salvaged by two enzymes in mammals:

            Adenine phosphoribosyl transferase (APRT):      Adenine  +  PRPP  == AMP  + PPi

            Hypoxanthine-guanine phosphoribosyl transferase: Hypoxanthine + PRPP == IMP + PPi                          

                            (HGPRT)                                              Guanine + PRPP == GMP  +  PPi

Rather than having to resynthesize AMP and GMP  (and IMP) from scratch, these bases are recycled into their nucleotides by simple one-step reactions.

 

 

Defective HGPRT Production: Lesch-Nyhan Syndrome

 

 

 

 

 

 

 

 

Purine Autism

 

 

Pyrimidine Ribonucleotide Synthesis

The various atoms of the pyrimidine ring are derived as follows:

        N1,C4,C5,C6 :    all derived from Aspartate

        C2 : from HCO3-

        N3 :  from the Glutamine amide nitrogen

The key molecule in the synthesis of the pyrimidine ribonucleotides is uridine monophosphate (UMP), as it is the final product of the six-step synthesis pathway and from which  CTP is subsequently derived. The pyrimidine ring, in the form of dihydroorotate, is formed first (note that this is not the case for the pyrimidine bases) following attachment to ribose-5-phosphate.

Some of the highlights of the reactions involved in the synthesis of UMP are:

(1) Two ATP molecules are needed for each UMP molecule produced, and these are both used in the first     step, in which carbamoyl phosphate is produced from glutamine, bicarbonate and a phosphate from one of the ATPs. The other ATP is hydrolyzed to ADP and Pi , providing free energy to drive the reaction. The enzyme, carbamoyl phosphate synthetase II, is found in the cytosol; carbamoyl phosphate is also produced in the urea cycle, but the enzyme involved there is the intramitochondrial carbamoyl phosphate synthetase I.

(2) There are two condensation reactions in this pathway, the first resulting in the formation of carbamoyl aspartate and the second in dihydroorotate. The latter is an intramolecular condensation reaction.

(3) Dihydroorotate dehydrogenase is the only intramitochondrial enzyme in this pathway (in eukaryotes), and the oxidizing power is provided by the reduction of quinones.

(4) The attachment of the pyrimidine base to the ribose phosphate ring is catalyzed by orotate phosphoribosyl transferase (OPRT) and PRPP provides the ribose-5-phosphate moeity. Hydrolysis of the PPi that is split off of the PRPP makes this reaction irreversible.

(5) The same "channeling" phenomenon is seen in the pyrimidine pathway that we saw in the purine pathway. The enzymes in steps 1,2 and 3 are on the same polypeptide chain, while the last two (reactions 5 and 6) are on another single chain.

Exercise: Calculate the number of ATP equivalents needed to synthesize UMP.

Pyrimidine Ribonucleotide Synthesis

Going from UMP to UTP and CTP:

A nucleoside monophosphate kinase catalyzes the transfer of a Pi from ATP to UMP to form UDP. A nucleoside diphosphate catalyzes the same kind of reaction, transferring a Pi from ATP to UDP to form UTP.

CTP is synthesized from UTP via an amination reaction catalyzed by CTP synthetase. Here, the hydrolysis of ATP drives the reaction and glutamine provides its amide nitrogen (in animals) to the pyrimidine base at the C4 position.

           

 

Regulatory Control of Pyrimidine Nucleotide Biosynthesis

Regulatory control differs in bacteria and in animals. In bacteria, regulation occurs at the level of ATCase. In animals, the regulation occurs at the level of carbamoyl phosphate synthetase II. We will focus on regulatory control in animals.

UDP and UTP inhibit carbamoyl phosphate synthetase II while ATP and PRPP activate it.

UMP (and CMP) competitively inhibit OMP decarboxylase.

We saw that the purine synthesis pathway was inhibited by ADP and GDP at the level of the ribose  phosphate pyrophosphokinase step, thus controlling the level of PRPP. This, in turn, has implications for the production of pyrimidines, since the production rate of orotate depends upon the amount of PRPP.

 

 

 

Orotic Aciduria

 

 

Degradation of Pyrimidines

CMP and UMP are degraded to their respective bases in a series of reactions similar to what we saw in the degradation of purines. Specifically, these are dephosphorylation, deaminase and  phosphorylation reactions, the latter resulting in cleavage of a glycosidic bond. Reduction of  uracil (and thymine, a methyl derivative of uracil that occurs in DNA) occurs in the liver and b-alanine (b-aminoisobutyrate) result. These are converted to malonyl-CoA (and methylmalonyl-CoA). Malonyl-CoA is a precursor of fatty acid synthesis, so the breakdown of pyrimidine nucleotides contributes in a small way to cellular energy metabolism. Methylmalonyl-CoA enters the citric acid cycle after being converted to succinyl-CoA.

Deoxyribonucleotide Formation

With the exception of the discussions of purine and pyrimidine nucleotide degradation, which are generalized to ribonucleotides and deoxyribonucleotides, the biosynthetic pathways that we have looked at were specific to ribonucleotides and, therefore, to RNA. Now we want to build upon this to discuss the components of DNA, the deoxyribonucleotides.

DNA differs from RNA:

(1) It is composed of deoxyribonucleotides

(2) The ribose sugar in a deoxyribonucleotide  is does not have a hydroxyl group at the 2' carbon position.

(3) Uracil does not appear (normally) as a base in DNA; instead thymine (5-methyluracil) appears.

The transition from a ribonucleotide to a deoxyribonucleotide looks simple enough; just replace the -OH group on the 2' carbon atom with a hydrogen atom. This is certainly more efficient than synthesizing the deoxyribonucleotides de novo. The reduction of the 2' carbon is accomplished by means of a free radical mechanism, catalyzed by ribonuclease reductases. There are a few different such reductases, and we will study E.coli ribonucleotide reductase as a representative.Ribonucleotide reductases reduce ribonucleoside diphosphates (NDPs) to their deoxyribonucleoside diphosphates (dNDPs)

A study of this enzyme, its structure, mechanism of action and regulation is a glimpse of the beauty of the workings of nature. First, the entire enzyme is composed of two subunits, denoted R1 and R2 , each one being a homodimer. The R1 subunit can be represented as a2 and the R2 as b2 . So the whole enzyme is a tetramer, a2b2 . The a subunit has a substrate binding site containing about five thiol (-SH) groups and two different effector binding sites, the "specificity site" and the catalytic "activity site". The structure of the b subunit has been determined by xray crystallography.

       

 

 R1 and R2 subunits of E. coli Ribonucleotide Reductase

 

    

The iron prosthetic group is particularly interesting because it is binuclear (it has two iron ions), each one octahedrally coordinated to various groups. The two ions are bridged by an O2- on one side and by the carboxyl group of Glu 115. In close proximity to one of the iron ions is Tyr 122 and they interact forming a tyrosyl free-radical. It is likely that the transfer of an electron from the substrate (oxidation of the substrate) to the tyrosyl radical is mediated by the thiyl radical (-S) of Cys 439, located in R1 .

During the reduction of the NDPs,a sulfhydryl pair from 2 Cys residues in R1 reduces the 2'-C of the ribose, and a disulfide bond is formed between the two sulfurs of this pair. This, in turn, is reduced by two other sulfhydryl groups of Cys residues in R1 and these are ultimately reduced by external reducing agents.

Thioredoxin is a physiologic reducing agent of ribonucleotide reductase and its pair of Cys residues can swap H atoms with the disulfide formed, thus regenerating the original enzyme. In the process, thioredoxin is oxidized to a disulfide:

           

The oxidized thioredoxin is reduced in a reaction catalyzed by thioredoxin reductase and mediated by NADPH, the final electron acceptor in the overall process of the reduction of NDPs to dNDPs.Glutaredoxin, another disulfide-containing protein, can also reduce ribonucleotide reductase.

The phosphorylation of the dNDPs to dNTPs is catalyzed by nucleoside diphosphate kinase with any NTP or dNTP donating the phosphate group.

Thymine Formation

We did not discuss the formation of the pyrimidine nucleotide thymine in the section of pyrimidine nucleotide biosynthesis because it was necessary to first talk about the production of the deoxyribonucleotides. Thymine is formed by methylating deoxyuridine monophosphate (dUMP) rather than by the reduction at the C 2' position of a nucleoside diphosphate that would correspond to TDP. Although UTP is needed for RNA production, dUTP is not needed for DNA production and, in fact, if there were appreciable amounts of  dUTP in the cell, there would be many substitution errors of dUTP for dTTP. That is the reason for the following roundabout way that thymine is produced.

dUTP is hydrolyzed in the presence of dUTP diphosphohydrolase to dUMP and pyrophosphate. The dUMP is then methylated at C 5 on the pyrimidine ring to produce dTMP, which is then rephosphorylated to dTTP.

       

         

1DUD: dUTPase

 

  

The enzymatic methylation of the dUMP is catalyzed by thymidylate synthase and in the reaction the cofactor,N5,N10 - methylene tetrahydrofolate, is oxidized to dihydrofolate. This is the only known biochemical reaction in which the net oxidation state of THF is changed.

The coenzyme, tetrahydrofolate, is regenerated by a recycling of the DHF as follows:

   DHF  +  NADPH  +  H+  --> THF  +  NADP+       (enzyme: dihydrofolate reductase, DHFR)

   THF  +  serine   --> N5,N10 - Methylene-THF  +  glycine  (enzyme: serine hydroxymethyl transferase)

 

 

 

Anti-Folate Drugs

 

 

 

Regulation of the Amounts of the dNTPs Needed for DNA Synthesis:

It is of extreme importance to the organism that the dNTPs are highly regulated and this regulation is feedback-controlled at the level of ribonucleotide reductase. Some highlights of this regulation are as follows:

        ATP binding at the "activity site" on the R1 subunit activates ribonucleotide reductase toward whatever effector is bound at the "specificity site" while dATP is inhibitory.

        If ATP or dATP bind at the specificity site while ATP is bound at the activity site, then CDP and UDP reduction are stimulated.

        If dTTP binds at the specificity site and ATP is bound to the activity site, then GDP reduction is stimulated while CDP and UDP reduction are inhibited.

        If dGTP binds to the specificity site while ATP is bound to the activity site, then ADP reduction is stimulated while CDP, UDP and GDP reduction are inhibited.

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