Pentose Phosphate Pathway PDF

Tymoczko Berg Gatto Stryer Biochemistry: A Short Course Fourth Edition CHAPTER 26 The Pentose Phosphate Pathway © 2019 W. H. Freeman and Company. Learning Objectives When we have finished this section, you should be able to do the following: 1. Summarize the biological objectives of the PPP. 2. Reca...

Tymoczko Berg Gatto Stryer Biochemistry: A Short Course Fourth Edition CHAPTER 26 The Pentose Phosphate Pathway © 2019 W. H. Freeman and Company. Learning Objectives When we have finished this section, you should be able to do the following: 1. Summarize the biological objectives of the PPP. 2. Recall reactions, enzymes and intermediates of the PPP. 3. Outline the molecules generated by the PPP and their contribution to other metabolic processes. 4. Recall the mechanisms of regulation of the PPP. 5. Explain the functional relationship between glycolysis and the PPP. The Pentose Phosphate Pathway (PPP) In this section, we explore another pathway that is linked to glycolysis through several intermediates. As will be seen, a central role of the pentose phosphate pathway (PPP) is to produce NADPH, a molecule that serves as the currency of reducing power for most reductive biosynthetic reactions. The PPP also generates ribose 5-phosphate (a five-carbon sugar, and behind the name of the pathway) which provides the sugar component for nucleotides and thus for DNA and RNA. The PPP shares key intermediates with glycolysis, and as such the regulation of these pathways are coordinately regulated. The PPP Yields NADPH and Five-Carbon Sugars The synthesis of biomolecules often requires reduction reactions. In all organisms, NADPH is used as the currency for reducing power. In animals, this pathway is active in tissues where the synthesis of biomolecules occurs at high rates. All reactions in this pathway are carried out in the cytosol. The Pentose Phosphate Pathway Consists of an Oxidative Phase and a Non-Oxidative Phase This pathway has two phases. 1. In the first part, the oxidative phase, glucose-6-P is oxidized and in the process, NADP+ gets reduced to NADPH. 2. In the second phase, the non-oxidative phase, ribulose-5-P is converted to ribose-5-P which is the second major product of this pathway. Also occurring in this phase of the pathway is the interconversion of 3-, 4-, 5-, 6-, and 7-carbon sugars. These interconversions provide a way for the excess 5-carbon sugars to be converted to intermediates of glycolysis. This is important since the need for NADPH in the cell is much greater than the need for ribose-5-P. Thus, the PPP has a mechanism whereby to divert the excess ribose-5-P to glycolysis where it can be metabolized into useful components and/or to produce ATP. Phase 1: Oxidative Phase The reactions that take place in the first phase: Figure: Reactions in the oxidative phase of the PPP. The two NADPH produced are highlighted in yellow. Source: Tymoczko, J., Berg, J. & Stryer, L. (2007). Biochemistry: A Short Course (6th ed.). New York, NY: W. H. Freeman and Company, Fig. 20-20. Permission: This material has been reproduced in accordance with the University of Saskatchewan Fair Dealing Guidelines, an interpretation of Sec.29.4 of the Copyright Act. Important things to note. The pathway starts with glucose-6-P, which is an intermediate of both glycolysis and gluconeogenesis. The first enzyme in the pathway is glucose-6-P dehydrogenase, which by its name indicates that it is catalyzing an oxidation-reduction reaction. Indeed, one NADPH is produced in this reaction. There is a second NADPH formed by the last enzyme in this phase. So for every glucose-6-P molecule that enters the pathway, two NADPH are produced. Ribulose-5-P, a 5-carbon sugar, is the end-product of this phase that is converted to ribose-5-P (as well as other sugars) in phase 2 of this pathway. Phase 2: Non-Oxidative Phase In phase 2 of the pathway, no NADPH is formed and thus is referred to as the non-oxidative portion. The major goal of this phase is to convert ribulose-5-P to ribose-5-P, which is catalyzed by an isomerase. Ribulose 5phosphate isomerase Figure 4-2: The conversion of ribulose-5-P to ribose-5-P is catalyzed by an isomerase. Source: Tymoczko, J., Berg, J. & Stryer, L. (2015). Biochemistry: A Short Course (3rd ed.). New York, NY: W. H. Freeman and Company, p. 474. Permission: Courtesy of MacMillan Learning. Important Point Excess ribose-5-P formed in the PPP can be completely converted to glycolytic intermediates. Borrowed from: https://www.chegg.com/homework-help/questionsand-answers/2-five-tanks-linked-pipes-shown-fig-1mass-flow-rate-constituent-pipe-computed-productvol-q109496440 Figure 4-3: The reactions in the non-oxidative phase of the PPP. Source: Fig. 1 in https://thediaryof5biochemians.wordpress.com/2014/04/13/pentose-phosphate-pathway-and-gluconeogenesis %E2%80%8F/ Permission: This material has been reproduced in accordance with the University of Saskatchewan interpretation of Sec.30.04 of the Copyright Act. Pentose Phosphate Pathway Is Primarily Regulated by Levels of NADP+ It is important to remember that glucose-6-P can be metabolized by both glycolysis and the PPP, since both pathways take place in the cytosol. There is only one pool of glucose-6-P in the cytosol, from which it is funneled into one pathway or the other. It is unlikely to be all or nothing, but rather a shift in which pathway is used more. The most important point to remember about the regulation of the PPP is that it is the cytosolic concentration of NADP+ which plays the biggest role. Pentose Phosphate Pathway Is Primarily Regulated by Levels of NADP+ First step of this pathway is catalyzed by glucose-6-P dehydrogenase. This reaction is the rate-limiting step i.e., the slowest step, which is often a point of regulation in any pathway. This is also one of two steps where NADPH is produced. Consider a situation where there is a lot of NADPH in the cell; this means that NADP+ is low since most is in the reduced form (NADPH). Since NADP+ is a substrate for glucose-6-P dehydrogenase, a low concentration of NADP+ will result in a low rate through this step. This step is further inhibited by the fact that NADPH competes for NADP+ for binding to the enzyme glucose-6-P dehydrogenase i.e., NADPH is a competitive inhibitor of NADP+. So when NADPH levels are high (and correspondingly NADP+ is low), there is no need for the oxidative portion of the PPP to be highly active. Pentose Phosphate Pathway Is Primarily Regulated by Levels of NADP+ Additionally NADP+ ALSO binds an separate allosteric site that positively regulates glucose-6-P-dehyrdrogensase activity – Thus stimulating the enzyme when needed and failing to stimulate when NADP+ is depleted through conversion and accumulation of NADPH+ Bound at allosteric site only Bound at both the allosteric site and the active site X. Wei et al. 2022. Allosteric role of a structural NADP+ molecule in glucose-6-phosphate dehydrogenase activity. PNAS 119. 1-9 https://doi.org/10.1073/pnas.2119695119 Glycolysis and the PPP Are Coordinately Regulated Obviously then, the fate of glucose-6-P is highly dependent on the cell’s need for NADPH. If the need is low, then more will be metabolized through glycolysis. If there is high demand for NADPH, more glucose-6-P will be metabolized through the PPP. Because glucose-6-P can be metabolized either through glycolysis or by the PPP, we need to consider what will determine the fate of this biomolecule. It turns out that the decision as to whether glucose-6-P will be metabolized by glycolysis or the PPP is also guided by the need of the cell for ribose-5-P and ATP which are important products of the PPP and glycolysis, respectively. It is easiest to explain this by considering four different metabolic conditions. Figure: Four modes of the PPP. Source: Tymoczko, J., Berg, J. & Stryer, L. (2015). Biochemistry: A Short Course (3rd ed.). New York, NY: W. H. Freeman and Company, Fig. 26.3, p. 479. Permission: Courtesy of MacMillan Learning. Mode 1: Need for Ribose-5-P is Greater Than the Need for NADPH Mode 1: The need for ribose-5-P is greater than the need for NADPH - This situation can arise in cells that are rapidly dividing and have to synthesize a lot of DNA. In this case, most of the glucose-6-P is metabolized through glycolysis to fructose6-P and glyceraldehyde-3-P. These two molecules can then be used by the nonoxidative portion of the PPP, using the reversible reactions catalyzed by transketolase and transaldolase, to produce ribose-5-P. This emphasizes the interplay between these two pathways and the various entry points for metabolites. Mode 2: The need for NADPH and ribose-5-P are about the same Mode 2: The need for NADPH and ribose-5-P are about the same - In this case, glucose-6-P is metabolized through the oxidative portion of the PPP where NADPH is produced. The ribulose-5-P that is produced is converted to ribose-5-P. This results in the replenishment of both NADPH and ribose-5-P. Mode 3: The Need for NADPH is Greater Than That for Ribose-5-P Mode 3: The need for NADPH is greater than that for ribose-5-P. In this scenario, which occurs in liver, there are three sets of reactions that in the end result in the complete oxidation of glucose-6-P to CO2 with the formation of NADPH. First, glucose-6-P is converted to ribulose-5-P by the oxidative portion of the PPP which results in NADPH production. The ribulose-5-P that is produced is easily and rapidly converted to ribose-5-P, which is then converted to fructose-6-P and glyceraldehyde-3-P by the nonoxidative reactions of the PPP. These two metabolites can then be used in gluconeogenesis to produce glucose-6P. If one writes out the stoichiometry of all three of these reaction sets, one finds that every glucose-6-P is oxidized to 6CO2 with 12 NADPH produced. Mode 4: Both NADPH and ATP are required Mode 4: Both NADPH and ATP are required. In this scenario, glucose-6-P needs to be oxidized through the PPP in order to obtain NADPH. But ATP is produced by glycolysis, not by the PPP. So how does this happen? Glucose-6-P is metabolized through the oxidative portion of the PPP which produces NADPH. The ribulose-5-P produced is converted to fructose-6-P and glyceraldehyde-3-P by the nonoxidative portion of the PPP. Both of these metabolites can then enter glycolysis and be metabolized to pyruvate, which produces ATP. As we will see later, pyruvate can be oxidized further to produce even more ATP; conversely, pyruvate can also be used as a building block for the synthesis of other biomolecules.