PURINES AND PYRIMIDINES
A summary of Bases, Sugars, and Phosphates in 's Structure of Nucleic Acids. The bases come in two categories: thymine and cytosine are pyrimidines, while. Purines and pyrimidines are the two families of nitrogenous bases that make up There are two main types of purine: Adenine and Guanine. outline the relationship between nucleic acids, nucleotides and The five bases that are found in nucleotides are often represented by their Pyrimidines are heterocyclic amines with two nitrogen atoms in a Unlike proteins, which have 20 different kinds of amino acids, there are only 4 different kinds of.
Nitrogenous base - Wikipedia
Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other, the grooves are unequally sized. The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove.
As a result, proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove. This situation varies in unusual conformations of DNA within the cell, but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form .
Chargaff's rules - Wikipedia
Chargaff's rules was given by Erwin Chargaff which state that DNA from any cell of all organisms should have a 1: This pattern is found in both strands of the DNA.
They were discovered by Austrian chemist Erwin Chargaff. In molecular biology, two nucleotides on opposite complementary DNA strands that are connected via hydrogen bonds are called a base pair often abbreviated bp. Alternate hydrogen bonding patterns, such as the wobble base pair and Hoogsteen base pair, also occur—particularly in RNA—giving rise to complex and functional tertiary structures.
He synthesized it for the first time in by uric acid which had been isolated from kidney stones by Scheele in Purine itself, has not been found in nature, but it can be produced by organic synthesis.
- Purine and Pyrimidine Metabolism
- What is the Difference Between Purines and Pyrimidines?
- 28.1: Nucleotides and Nucleic Acids
A purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Adenine[ edit ] Adenine is one of the two purine nucleobases the other being guanine used in forming nucleotides of the nucleic acids DNA or RNA. In DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. Adenine forms adenosine, a nucleoside, when attached to ribose, and deoxyadenosine when attached to deoxyribose.
It forms adenosine triphosphate ATPa nucleotide, when three phosphate groups are added to adenosine. In DNA, guanine is paired with cytosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine-imidazole ring system with conjugated double bonds. Guanine has two tautomeric forms, the major keto form and rare enol form.
Bases to Uric Acid Both adenine and guanine nucleotides converge at the common intermediate xanthine.
Hypoxanthine, representing the original adenine, is oxidized to xanthine by the enzyme xanthine oxidase. Guanine is deaminated, with the amino group released as ammonia, to xanthine. If this process is occurring in tissues other than liver, most of the ammonia will be transported to the liver as glutamine for ultimate excretion as urea. Xanthine, like hypoxanthine, is oxidized by oxygen and xanthine oxidase with the production of hydrogen peroxide. In man, the urate is excreted and the hydrogen peroxide is degraded by catalase.
Xanthine oxidase is present in significant concentration only in liver and intestine. The pathway to the nucleosides, possibly to the free bases, is present in many tissues. Gouts and Hyperuricemia Both undissociated uric acid and the monosodium salt primary form in blood are only sparingly soluble. Hyperuricemia is not always symptomatic, but, in certain individuals, something triggers the deposition of sodium urate crystals in joints and tissues.
In addition to the extreme pain accompanying acute attacks, repeated attacks lead to destruction of tissues and severe arthritic-like malformations. The term gout should be restricted to hyperuricemia with the presence of these tophaceous deposits.
Principles of Biochemistry/Nucleic acid I: DNA and its nucleotides
In gouts caused by an overproduction of uric acid, the defects are in the control mechanisms governing the production of - not uric acid itself - but of the nucleotide precursors.
The only major control of urate production that we know so far is the availability of substrates nucleotides, nucleosides or free bases. One approach to the treatment of gout is the drug allopurinol, an isomer of hypoxanthine. Allopurinol is a substrate for xanthine oxidase, but the product binds so tightly that the enzyme is now unable to oxidized its normal substrate. Uric acid production is diminished and xanthine and hypoxanthine levels in the blood rise.
These are more soluble than urate and are less likely to deposit as crystals in the joints. Another approach is to stimulate the secretion of urate in the urine. Summary In summary, all, except ring-methylated, purines are deaminated with the amino group contributing to the general ammonia pool and the rings oxidized to uric acid for excretion. Since the purine ring is excreted intact, no energy benefit accrues to man from these carbons.
Pyrimidine Catabolism In contrast to purines, pyrimidines undergo ring cleavage and the usual end products of catabolism are beta-amino acids plus ammonia and carbon dioxide. Pyrimidines from nucleic acids or the energy pool are acted upon by nucleotidases and pyrimidine nucleoside phosphorylase to yield the free bases. The 4-amino group of both cytosine and 5-methyl cytosine is released as ammonia. Atoms 2 and 3 of both rings are released as ammonia and carbon dioxide.
The rest of the ring is left as a beta-amino acid. Beta-amino isobutyrate from thymine or 5-methyl cytosine is largely excreted. 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. 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. 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.