PURINES AND PYRIMIDINES
JOURNAL OF CELLULAR PHYSIOLOGY (). The Relationship Between Purines, Pyrimidines,. Nucleosides, and Glutamine for Fibroblast. J Cell Physiol. Aug;(2) The relationship between purines, pyrimidines, nucleosides, and glutamine for fibroblast cell proliferation. Engström W. Base-pairing takes place between a purine and pyrimidine: namely, A pairs with T, They are approximately nm in width, and are found in association with.
Beta-alanine from cytosine or uracil may either be excreted or incorporated into the brain and muscle dipeptides, carnosine his-beta-ala or anserine methyl his-beta-ala. General Comments Purine and pyrimidine bases which are not degraded are recycled - i. This recycling, however, is not sufficient to meet total body requirements and so some de novo synthesis is essential.
There are definite tissue differences in the ability to carry out de novo synthesis. De novo synthesis of purines is most active in liver. Non-hepatic tissues generally have limited or even no de novo synthesis. Pyrimidine synthesis occurs in a variety of tissues. For purines, especially, non-hepatic tissues rely heavily on preformed bases - those salvaged from their own intracellular turnover supplemented by bases synthesized in the liver and delivered to tissues via the blood.
The bases generated by turnover in non-hepatic tissues are not readily degraded to uric acid in those tissues and, therefore, are available for salvage.
The liver probably does less salvage but is very active in de novo synthesis - not so much for itself but to help supply the peripheral tissues. De novo synthesis of both purine and pyrimidine nucleotides occurs from readily available components.
De Novo Synthesis of Purine Nucleotides We use for purine nucleotides the entire glycine molecule atoms 4, 5,7the amino nitrogen of aspartate atom 1amide nitrogen of glutamine atoms 3, 9components of the folate-one-carbon pool atoms 2, 8carbon dioxide, ribose 5-P from glucose and a great deal of energy in the form of ATP.
In de novo synthesis, IMP is the first nucleotide formed. PRPP Since the purines are synthesized as the ribonucleotides, not as the free bases a necessary prerequisite is the synthesis of the activated form of ribose 5-phosphate. The enzyme is heavily controlled by a variety of compounds di- and tri-phosphates, 2,3-DPGpresumably to try to match the synthesis of PRPP to a need for the products in which it ultimately appears. Commitment Step De novo purine nucleotide synthesis occurs actively in the cytosol of the liver where all of the necessary enzymes are present as a macro-molecular aggregate.
The first step is a replacement of the pyrophosphate of PRPP by the amide group of glutamine. The product of this reaction is 5-Phosphoribosylamine. The amine group that has been placed on carbon 1 of the sugar becomes nitrogen 9 of the ultimate purine ring.
What is the difference between a purine and a pyrimidine?
This is the commitment and rate-limiting step of the pathway. The enzyme is under tight allosteric control by feedback inhibition. This is a fine control and probably the major factor in minute by minute regulation of the enzyme.
The nucleotides inhibit the enzyme by causing the small active molecules to aggregate to larger inactive molecules.
Normal intracellular concentrations of PRPP which can and do fluctuate are below the KM of the enzyme for PRPP so there is great potential for increasing the rate of the reaction by increasing the substrate concentration.
The kinetics are sigmoidal. The enzyme is not particularly sensitive to changes in [Gln] Kinetics are hyperbolic and [gln] approximates KM. Very high [PRPP] also overcomes the normal nucleotide feedback inhibition by causing the large, inactive aggregates to dissociate back to the small active molecules. Purine de novo synthesis is a complex, energy-expensive pathway. It should be, and is, carefully controlled. Formation of IMP Once the commitment step has produced the 5-phosphoribosyl amine, the rest of the molecule is formed by a series of additions to make first the 5- and then the 6-membered ring.
The whole glycine molecule, at the expense of ATP adds to the amino group to provide what will eventually be atoms 4, 5, and 7 of the purine ring The amino group of 5-phosphoribosyl amine becomes nitrogen N of the purine ring. One more atom is needed to complete the five-membered ring portion and that is supplied as 5, Methenyl tetrahydrofolate.
Before ring closure occurs, however, the amide of glutamine adds to carbon 4 to start the six-membered ring portion becomes nitrogen 3. This addition requires ATP. Another ATP is required to join carbon 8 and nitrogen 9 to form the five-membered ring. The next step is the addition of carbon dioxide as a carboxyl group to form carbon 6 of the ring.
The amine group of aspartate adds to the carboxyl group with a subsequent removal of fumarate. The amino group is now nitrogen 1 of the final ring. This process, which is typical for the use of the amino group of aspartate, requires ATP. The final atom of the purine ring, carbon 2, is supplied by Formyl tetrahydrofolate.
Ring closure produces the purine nucleotide, IMP. Note that at least 4 ATPs are required in this part of the process. At no time do we have either a free base or a nucleotide. The oxygen at position 2 is substituted by the amide N of glutamine at the expense of ATP. The amino group is provided by aspartate in a mechanism similar to that used in forming nitrogen 1 of the ring. Removal of the carbons of aspartate as fumarate leaves the nitrigen behind as the 6-amino group of the adenine ring.
The monophosphates are readily converted to the di- and tri-phosphates. Control of De Novo Synthesis Control of purine nucleotide synthesis has two phases. Each one stimulates the synthesis of the other by providing the energy. One could imagine the controls operating in such a way that if only one of the two nucleotides were required, there would be a partial inhibition of de novo synthesis because of high levels of the other and the IMP synthesized would be directed toward the synthesis of the required nucleotide.
If both nucleotides were present in adequate amounts, their synergistic effect on the amidotransferase would result in almost complete inhibition of de novo synthesis. De Novo Synthesis of Pyrimidine Nucleotides Since pyrimidine molecules are simpler than purines, so is their synthesis simpler but is still from readily available components. Glutamine's amide nitrogen and carbon dioxide provide atoms 2 and 3 or the pyrimidine ring.
They do so, however, after first being converted to carbamoyl phosphate. The other four atoms of the ring are supplied by aspartate. As is true with purine nucleotides, the sugar phosphate portion of the molecule is supplied by PRPP.
Carbamoyl Phosphate Pyrimidine synthesis begins with carbamoyl phosphate synthesized in the cytosol of those tissues capable of making pyrimidines highest in spleen, thymus, GItract and testes. This uses a different enzyme than the one involved in urea synthesis. Formation of Orotic Acid Carbamoyl phosphate condenses with aspartate in the presence of aspartate transcarbamylase to yield N-carbamylaspartate which is then converted to dihydroorotate. In man, CPSII, asp-transcarbamylase, and dihydroorotase activities are part of a multifunctional protein.
Oxidation of the ring by a complex, poorly understood enzyme produces the free pyrimidine, orotic acid.
What is the Difference Between Purines and Pyrimidines?
This enzyme is located on the outer face of the inner mitochondrial membrane, in contrast to the other enzymes which are cytosolic. Note the contrast with purine synthesis in which a nucleotide is formed first while pyrimidines are first synthesized as the free base. OMP is then converted sequentially - not in a branched pathway - to the other pyrimidine nucleotides. Control The control of pyrimidine nucleotide synthesis in man is exerted primarily at the level of cytoplasmic CPS II.
Other secondary sites of control also exist e. These are probably not very important under normal circumstances. In bacteria, aspartate transcarbamylase is the control enzyme. There is only one carbamoyl phosphate synthetase in bacteria since they do not have mitochondria. Carbamoyl phosphate, thus, participates in a branched pathway in these organisms that leads to either pyrimidine nucleotides or arginine. Interconversion of Nucleotides The monophosphates are the forms synthesized de novo although the triphosphates are the most commonly used forms.
But, of course, the three forms are in equilibrium. There are several enzymes classified as nucleoside monophosphate kinases which catalyze the general reaction: Similarly, the diphosphates are converted to the triphosphates by nucleoside diphosphate kinase: One can legitimately speak of a pool of nucleotides in equilibrium with each other.
Purines and Pyrimidines
Salvaging of purine and pyrimidine bases is an exceedingly important process for most tissues. There are two distinct pathways possible for salvaging the bases. Salvaging Purines The more important of the pathways for salvaging purines uses enzymes called phosphoribosyltransferases PRT: As a salvage process though, we are dealing with purines.
A-PRT is not very important because we generate very little adenine. Remember that the catabolism of adenine nucleotides and nucleosides is through inosine. This enzyme salvages guanine directly and adenine indirectly.
Lesch-Nyhan Syndrome HG-PRT is deficient in the disease called Lesch-Nyhan Syndrome, a severe neurological disorder whose most blatant clinical manifestation is an uncontrollable self-mutilation. Lesch-Nyhan patients have very high blood uric acid levels because of an essentially uncontrolled de novo synthesis. It can be as much as 20 times the normal rate. Both of these factors could lead to an increase in the activity of the amidotransferase. Salvaging Pyrimidines A second type of salvage pathway involves two steps and is the major pathway for the pyrimidines, uracil and thymine.
Formation of Deoxyribonucleotides De novo synthesis and most of the salvage pathways involve the ribonucleotides. Exception is the small amount of salvage of thymine indicated above. Deoxyribonucleotides for DNA synthesis are formed from the ribonucleotide diphosphates in mammals and E. A base diphosphate BDP is reduced at the 2' position of the ribose portion using the protein, thioredoxin and the enzyme nucleoside diphosphate reductase.
Because purines always bind with pyrimidines — known as complementary pairing — the ratio of the two will always be constant within a DNA molecule.
In other words, one strand of DNA will always be an exact complement of the other as far as purines and pyrimidines go. This complementary pairing occurs because the respective sizes of the bases and because of the kinds of hydrogen bonds that are possible between them they pair more favorably with bases with which they can have the maximum amount of hydrogen bonds. There are two main types of purine: One strategy that may help you remember this is to think of pyrimidines like pyramids that have sharp and pointy tops.
Which purines pair with which pyrimidines is always constant, as is the number of hydrogen bonds between them: C with three hydrogen bonds One way to remember which bases go together is to look at the shapes of the letters themselves.
The letters made up of only straight lines A and T are paired with each other, while the letters that are made up of curves G and C also go together.
The number of adenines in a DNA molecule will always be equal to the number of thymines. The same goes for guanines and cytosines. Expect a question asking you to calculate something similar to this on the exam.