Nucleotide rates

These were originally prepared by Khorana as selective protective groups for the 5 -OH of nucleosides and nucleotides. They were designed to be more acid-labile than the trityl group because depurination is often a problem in the acid-catalyzed removal of the trityl group. Introduction of p-methoxy groups increases the rate of hydrolysis by about one order of magnitude for each p-methoxy substituent. For 5 -protected uridine derivatives in 80% AcOH, 20°, the time for hydrolysis was... 

The renaturation rate of DNA is an excellent indicator of the sequence complexity of DNA. For example, bacteriophage T4 DNA contains about 2 X 10 nucleotide pairs, whereas Escherichia coli DNA possesses 4.64 X 10 . E. coli DNA is considerably more complex in that it encodes more information. Expressed another way, for any given amount of DNA (in grams), the sequences represented in an E. coli sample are more heterogeneous, that is, more dissimilar from one another, than those in an equal weight of phage T4 DNA. Therefore, it will take the E. coli DNA strands longer to find their complementary partners and reanneal. This situation can be analyzed quantitatively. 

The overall direction of the reaction will be determined by the relative concentrations of ATP, ADP, Cr, and CrP and the equilibrium constant for the reaction. The enzyme can be considered to have two sites for substrate (or product) binding an adenine nucleotide site, where ATP or ADP binds, and a creatine site, where Cr or CrP is bound. In such a mechanism, ATP and ADP compete for binding at their unique site, while Cr and CrP compete at the specific Cr-, CrP-binding site. Note that no modified enzyme form (E ), such as an E-PO4 intermediate, appears here. The reaction is characterized by rapid and reversible binary ES complex formation, followed by addition of the remaining substrate, and the rate-determining reaction taking place within the ternary complex. 

By structural complementarity, dicationic l,4-diazabicyclo[2.2.2]octane (VII) provides an appropriate recognition site for phosphate ions and two stearyl side chains attached to the amines add lipophilic properties 59,60). Such a carrier model can selectively extract nucleotides from aqueous solution to chloroform solution via lipophilic salt formation. The order of nucleotide affinity is ATP > ADP > AMP. The selectivity ratios were 45 for ADP/AMP and 7500 for ATP/AMP at pH 3. The relative transport rate was ATP > ADP > AMP. The ratios were 60 for ATP/AMP and 51 for ADP/AMP. The modes of interaction of ADP and ATP are proposed to be as shown in Fig. 6. 

The facile and selective oxidation of both primary and secondary hydroxy groups with certain nucleotides led Pfitzner and Moffatt (48) to explore the scope of the carbodiimide-methyl sulfoxide reagent with steroid and alkaloid alcohols. Relatively minor differences were apparent in the rate of oxidation of epimeric pairs of 3- and 17- hydroxy steroids whereas the equatorial lLx-hydroxyl group in several steroids was readily oxidized under conditions where the axial epimer was unreactive [cf. chromic oxide oxidation (51)]. 

Phalloidin and phallacidin are cyclic peptides from the mushroom Amanita phalloides that stabilize F-actin. Phalloidin binds to residues 114-118 of an actin protomere and blocks nucleotide exchange without interfering with nucleotide hydrolysis. It enhances the rate of nucleation as well as that of elongation. It slowly penetrates the cell membrane and is used for immunocytochemical localization of F-actin. 

Polymer growth J(c) showed nonlinear monomer concentration dependence in the presence of ATP (Carrier et al., 1984), while in the presence of ADP, the plot of J(c) versus monomer concentration for actin was a straight line, as expected for reversible polymerization. The data imply that newly incorporated subunits dissociate from the filament at a slower rate than internal ADP-subunits in other words, (a) the effect of nucleotide hydrolysis is to decrease the stability of the polymer by increasing k and (b) nucleotide hydrolysis is uncoupled from polymerization and occurs in a step that follows incorporation of a ATP-subunit in the polymer. Newly incorporated, slowly dissociating, terminal ATP-subunits form a stable cap at the ends of F-actin filaments. 

Because ATP hydrolysis on F-actin takes place with a delay following the incorporation of ATP-subunits, and because in the transient F-ATP state filaments are more stable than in the final F-ADP state, polymerization under conditions of sonication can be complete, within a time short enough for practically all subunits of the filaments to be F-ATP. At a later stage, as Pj is liberated, the F-ADP filament becomes less stable and loses ADP-subunits steadily. The G-ADP-actin liberated in solution is not immediately converted into easily polymerizable G-ATP-actin, because nucleotide exchange on G-actin is relatively slow, and is not able to polymerize by itself unless a high concentration (the critical concentration of ADP-actin) is reached. Therefore, G-ADP-actin accumulates in solution. A steady-state concentration of G-ADP-actin is established when the rate of depolymerization of ADP-actin (k [F]) is equal to the sum of the rates of disappearance of G-ADP-actin via nucleotide exchange and association to filament ends. [G-ADP]ss in this scheme is described by the following equation (Pantaloni et al., 1984) ... 

Kinosian, H.J., Selden, L.A., Estes. J.E., Gershman, L.C. (1993). Nucleotide binding to actinication dependence of nucleotide dissociation and exchange rates. J. Biol. Chem. 268, 8683-8691. 

In both intermediate and maximum rates of respiration, control is distributed between several different steps, including the activity of the adenine nucleotide translocator (Groen et al., 1983). It is now recognized that the idea of a simple rate-limiting step for a metabolic pathway is simplistic and that control is shared by all steps although to different extents (Kacserand Bums, 1978 Fell, 1992). Each step in a pathway has a flux control coefficient (FCC) defined as ... 

Human tissues can synthesize purines and pyrimidines from amphibolic intermediates. Ingested nucleic acids and nucleotides, which therefore are dietarily nonessential, are degraded in the intestinal tract to mononucleotides, which may be absorbed or converted to purine and pyrimidine bases. The purine bases are then oxidized to uric acid, which may be absorbed and excreted in the urine. While little or no dietary purine or pyrimidine is incorporated into tissue nucleic acids, injected compounds are incorporated. The incorporation of injected [ H] thymidine into newly synthesized DNA thus is used to measure the rate of DNA synthesis. 

Since biosynthesis of IMP consumes glycine, glutamine, tetrahydrofolate derivatives, aspartate, and ATP, it is advantageous to regulate purine biosynthesis. The major determinant of the rate of de novo purine nucleotide biosynthesis is the concentration of PRPP, whose pool size depends on its rates of synthesis, utilization, and degradation. The rate of PRPP synthesis depends on the availabihty of ribose 5-phosphate and on the activity of PRPP synthase, an enzyme sensitive to feedback inhibition by AMP, ADP, GMP, and GDP. 

A number of different DNA polymerase molecules engage in DNA replication. These share three important properties (1) chain elongation, (2) processivity, and (3) proofreading. Chain elongation accounts for the rate (in nucleotides per second) at which polymerization occurs. Processivity is an expression of the number of nucleotides added to the nascent chain before the polymerase disengages from the template. The proofreading function identifies copying errors and corrects them. In E coli, polymerase III (pol III) functions at the... 

In mammahan cells, the polymerase is capable of polymerizing about 100 nucleotides per second, a rate at least tenfold slower than the rate of polymerization of deoxynucleotides by the bacterial DNA polymerase complex. This reduced rate may result from interference by nucleosomes. It is not known how the rephcation complex negotiates nucleosomes. 

B. Studies of Equilibria and Reactions.—N.m.r. spectroscopy is being increasingly employed to study the mode and course of reactions. Thus n.m.r. has been used to unravel the mechanism of the reaction of phosphorus trichloride and ammonium chloride to give phosphazenes, and to follow the kinetics of alcoholysis of phosphoramidites. Its use in the study of the interaction of nucleotides and enzymes has obtained valuable information on binding sites and conformations and work on the line-widths of the P resonance has enabled the calculation of dissociation rate-constants and activation energies to be performed. 

Rate Coefficients for the Decomposition of N -n-Butyl-N -nitroso acetamide by Nucleotide-5 -monophosphates in 0.1M Phosphate... 

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