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Intelligent Design, the best explanation of Origins » Molecular biology of the cell » Metabolism » Glycolysis

Glycolysis

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1 Glycolysis on Sun Jun 29, 2014 7:22 am

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Glycolysis

http://reasonandscience.heavenforum.org/t1796-glycolysis

Cells require ATP to manufacture enzymes before glycolysis can even occur. (The old adage of “it takes money to make money” is applicable here—it takes energy to produce energy!) As such, proponents of evolution have an enormous chicken-egg problem. Which came first, glycolysis to make energy or energy from glycolysis needed to make enzymes? Without the enzymes, glycolysis could not occur to produce ATP. But without the ATP those enzymes could not be manufactured. This is strong evidence that the process of cellular respiration is not the product of evolution.

http://reasonandscience.heavenforum.org/t2158-glucose-and-its-importance-for-life

Glycolysis is the most ubiquitous pathway in all energy metabolism, occurring in almost every living cell. 4 The glycolytic pathway is multifunctional. Thus it provides the cell with energy [adenosine triphosphate (ATP)] from glucose catabolism and also can serve an anabolic function by yielding C-3 precursors for the synthesis of amino acids, fatty acids, and cholesterol. The 10-step glycolytic pathway is illustrated in Fig. 1. Glycolysis involves the splitting of the C-6 hexose into two molecules. The splitting occurs in step 4 (starting from glucose). At this point, a six-carbon sugar is cleaved to yield 2 three-carbon compounds, one of which, glyceraldehyde-3-phosphate, is the only oxidizable molecule in the entire pathway. After the cleavage in step 4, two successive ATPgenerating steps occur: one at step 7 and the other at step 10.

Remarkably, of all these alternatives, we find that the trunk pathway observed in nature carries the highest biochemical flux in both the glycolytic and gluconeogenic directions, for parameters that represent typical intracellular physiological conditions. 5






Carbohydrate catabolism supplies the energy and the carbohydrate skeletons for biosynthesis. Carbohydrate catabolism is handled differently in typical anaerobes and in typical aerobes. Anaerobes catabolize glucose and other carbon compounds that can be converted into the three-carbon compound pyruvate. This results in the net production of two ATPs for every glucose molecule that is catabolized.


Cells cannot survive without a source of energy and a source of chemical “building blocks”—the small molecules from which macromolecules such as proteins, nucleic acids, and
polysaccharides are synthesized. In many organisms, including you and me, these two requirements are related. The desired energy and small molecules are both present in
the food molecules that these organisms produce or ingest. We will consider how chemotrophs, such as animals and most microorganisms, obtain energy from the food they engulf or ingest, focusing especially on the oxidative breakdown of sugar molecules. Remember that oxidation reactions involve the loss of electrons and hydrogens and release energy. We will discuss the process by which phototrophs, such as green plants, algae, and some bacteria, tap the solar radiation that is the ultimate energy source for almost all living organisms. They will use this energy to reduce carbon dioxide (add electrons and hydrogens) in order to produce sugar molecules. Keep in mind that the reactions whereby cells obtain energy also can provide the various small molecules that cells need for synthesis of macromolecules and other cellular constituents.


Glycolysis Is a Central ATP-Producing Pathway

The major process for oxidizing sugars is the sequence of reactions known as glycolysis—from the Greek glukus, “sweet,” and lusis, “rupture.” Glycolysis produces ATP without the involvement of molecular oxygen (O2 gas). It occurs in the cytosol of most cells, including many anaerobic microorganisms.  During glycolysis, a glucose molecule with six carbon atoms is converted into two molecules of pyruvate, each of which contains three carbon atoms. For each glucose molecule, two molecules of ATP are hydrolyzed to provide energy to drive the early steps, but four molecules of ATP are produced in the later steps. At the end of glycolysis, there is consequently a net gain of two molecules of ATP for each glucose molecule broken down. Two molecules of the activated carrier NADH are also produced.







Glycolysis involves a sequence of 10 separate reactions, each producing a different sugar intermediate and each catalyzed by a different enzyme. Like most enzymes, these have names ending in ase—such as isomerase and dehydrogenase—to indicate the type of reaction they catalyze. Although no molecular oxygen is used in glycolysis, oxidation occurs, in that electrons are removed by NAD+ (producing NADH) from some of the carbons derived from the glucose molecule. The stepwise nature of the process releases the energy of oxidation in small packets, so that much of it can be stored in activated carrier molecules rather than all of it being released as heat (see Figurebelow)



Schematic representation of the controlled stepwise oxidation of sugar in a cell, compared with ordinary burning.
(A) If the sugar were oxidized to CO2 and H2O in a single step, it would release an amount of energy much larger than could be captured for useful purposes.
(B) In the cell, enzymes catalyze oxidation via a series of small steps in which free energy is transferred in conveniently sized packets to carrier molecules—most often ATP and NADH. At each step, an enzyme controls the reaction by reducing the activation-energy barrier that has to be surmounted before the specific reaction can occur. The total free energy released is exactly the same in (A) and (B).





Thus, some of the energy released by oxidation drives the direct synthesis of ATP molecules from ADP and Pi, and some remains with the electrons in the electron carrier NADH. Two molecules of NADH are formed per molecule of glucose in the course of glycolysis. In aerobic organisms, these NADH molecules donate their electrons to the electron-transport chain, and the NAD+ formed from the NADH is used again for glycolysis

Glycolysis Illustrates How Enzymes Couple Oxidation to Energy Storage

The formation of ATP during glycolysis provides a particularly clear demonstration of how enzymes couple energetically unfavorable reactions with favorable ones, thereby driving the many chemical reactions that make life possible. Two central reactions in glycolysis (steps 6 and 7) convert the three-carbon sugar intermediate glyceraldehyde 3-phosphate (an aldehyde) into 3-phosphoglycerate (a carboxylic acid), thus oxidizing an aldehyde group to a carboxylic acid group. The overall reaction releases enough free energy to convert a molecule of ADP to ATP and to transfer two electrons (and a proton) from the aldehyde to NAD+ to form NADH, while still liberating enough heat to the environment to make the overall reaction energetically favorable .



Energy storage in steps 6 and 7 of glycolysis. (A) In step 6, the enzyme glyceraldehyde 3-phosphate dehydrogenase couples the energetically favorable oxidation of an aldehyde to the energetically unfavorable formation of a high-energy phosphate bond. At the same time, it enables energy to be stored in NADH. The formation of the high-energy phosphate bond is driven by the oxidation reaction, and the enzyme thereby acts like the “paddle wheel” coupler, see below :




In step 7, the newly formed high-energy phosphate bond in 1,3-bisphosphoglycerate is transferred to ADP, forming a molecule of ATP and leaving a free carboxylic acid group on the oxidized sugar. The part of the molecule that undergoes a change is shaded in blue; the rest of the molecule remains unchanged throughout all these reactions. (B) Summary of the overall chemical change produced by reactions 6 and 7.

The figure above outlines this remarkable feat of energy harvesting. The chemical reactions are precisely guided by two enzymes to which the sugar intermediates are tightly bound. The first enzyme (glyceraldehyde 3-phosphate dehydrogenase) forms a short-lived covalent bond to the aldehyde through a reactive –SH group on the enzyme, and catalyzes its oxidation by NAD+ in this attached state. The reactive enzyme–substrate bond is then displaced by an inorganic phosphate ion to produce a high-energy phosphate intermediate, which is released from the enzyme. This intermediate binds to the second enzyme (phosphoglycerate kinase), which catalyzes the energetically favorable transfer of the high-energy phosphate just created to ADP, forming ATP and completing the process of oxidizing an aldehyde to a carboxylic acid. Note that the C–H bond oxidation energy in step 6 drives the formation of both NADH and a high-energy phosphate bond. The breakage of the high-energy bond then drives ATP formation. We have shown this particular oxidation process in some detail because it provides a clear example of enzyme-mediated energy storage through coupled reactions





“If metabolic pathways evolved by the sequential addition of new enzymatic reactions to existing ones, the most ancient reactions should, like the oldest rings in a tree trunk, be closest to the center of the “metabolic tree”, where the most fundamental of the basic molecular building blocks are synthesized. This position in metabolism is firmly occupied by the chemical processes that involve sugar phosphates, among which the most central of all is probably the sequence of reactions known as glycolysis, by which glucose can be degraded in the absence of oxygen (that is, anaerobically). The oldest metabolic pathways would have had to be anaerobic because there was no free oxygen in the atmosphere of the primitive earth.” 1

Most proponents of evolution believe that glycolysis process started by fermentation. 3 From this, allegedly more complex forms of respiration evolved that require catalyzation by a large number of complex enzymes. But that is where a major problem arises. In order to break down the six-carbon sugar of glucose enzymes are required. Each step within the chemical reaction of gly­colysis is further catalyzed by specific enzymes, whose origin is still unexplainable by evolutionary assumptions. Enzymes are proteins that are made within the cell—but their production requires energy. Thus, cells require ATP to manufacture enzymes before glycolysis can even occur. (The old adage of “it takes money to make money” is applicable here—it takes energy to produce energy!) As such, proponents of naturalism have an enormous chicken-egg problem. Which came first, glycolysis to make energy or energy from glycolysis needed to make enzymes? Without the enzymes, glycolysis could not occur to produce ATP. But without the ATP those enzymes could not be manufactured. This is strong evidence that the process of cellular respiration is not the product of evolution. As John Maina and John West observed: “Molecular oxygen is vital for generation of energy that in turn is fundamental to life”

The critical role oxygen plays in providing cellular energy can be seen in the following equation. If one were to add oxygen to a glucose molecule (a simple sugar), the result would be carbon dioxide and water—with an overall yield of 36 aden­o­sine triphosphate (ATP) molecules! Cells utilize ATP as the energy currency for most reactions in the cell that require energy.

C6H12O6 + 6O2 + 6CO2 + 6H20
(with a typical energy yield of 36 ATP)

This cellular process is known as gly­col­y­sis. Most proponents  of evolution believe this process started by fermentation. From this, allegedly more complex forms of respiration evolved that require catalyzation by a large number of complex enzymes. But that is where a major problem arises. In order to break down the six-carbon sugar of glucose enzymes are required. Each step within the chemical reaction of gly­colysis is further catalyzed by specific enzymes, whose origin is still unexplainable by evolutionary assumptions. Enzymes are proteins that are made within the cell—but their production requires energy. Thus, cells require ATP to manufacture enzymes before glycolysis can even occur. (The old adage of “it takes money to make money” is applicable here—it takes energy to produce energy!) As such, evolutionists have an enormous chicken-egg problem. Which came first, glycolysis to make energy or energy from glycolysis needed to make enzymes? Without the enzymes, glycolysis could not occur to produce ATP. But without the ATP those enzymes could not be manufactured. This is strong evidence that the process of cellular respiration is not the product of evolution. As John Maina and John West observed: “Molecular oxygen is vital for generation of energy that in turn is fundamental to life” (2005, 85:838).


The other point that should not be missed is that glucose and other sugars are only present within living things in nature. This would require plant material or other life forms in existence as a food source. So how does this requirement affect the evolutionary timeline? Why would organisms evolve cellular respiration if glucose or other sugars were not available? This necessity puts restrictions on evolution and the alleged evolutionary appearance of plants.

Finally, we must ask the question of how the first living cells survived if they were still evolving a mechanism to produce and store energy in the form of ATP? If a cell is unable to make proteins, get rid of waste, or successfully divide, then how long would it survive? The obvious answer is that cells have always possessed the ability to manufacture and store energy. Our bodies were designed in such a way that complex cascades of chemical reactions occur continuously in cells throughout the body without any conscious effort on our part. We know today that the absence of one of the steps involved in these complex cascades can have dire effects on cellular growth. The only logical explanation is that a Master Architect laid out these complex steps, and we are slowly uncovering the handiwork of that Designer.

One of life's most important metabolic pathways, glycolysis, plays a key  role in harvesting energy for use in most cells. 2 This biochemical process releases energy from glucose (a six-carbon sugar) by fracturing it into two molecules of pyruvate (a three-carbon compound). The cell captures a portion of this liberated chemical energy and stores it in the chemical bonds of special molecules for later use.
The glycolytic pathway traps energy from glucose breakdown by using it to form ATP (adenosine triphosphate). This molecule has two high-energy chemical bonds. When broken, the energy stored in the high-energy bonds is made available for the cell to use. The forming and breaking of the high energy bonds is like recharging and discharging a battery. The cell couples the breakdown of ATP's high-energy bonds to energy-requiring biochemical processes and activities. In this way, energetically unfavorable processes in the cell become feasible by using the energy stored in ATP
The use of ATP to power the cell's operations displays elegant chemical logic. Biochemists refer to ATP as the cell's energy currency. Instead of inefficiently coupling the breakdown of a large number of different high-energy compounds to a wide range of energetically unfavorable processes in the cell (like a barter-based economy), the cell uses only a few high-energy compounds (like a currency-based economy) to satisfy the multifarious energy  demands of the cell. From an energetics standpoint, the net output of glycolysis is two molecules of ATP for each molecule of glucose broken apart. (Two molecules of NADH [nicotinamide adenine dinucleotide] are also generated for each molecule of glucose. NADH, like ATP, is also an energy-currency molecule  that mediates the transfer of electrons between biomolecules in the cell.) Biochemists have long considered glycolytic ATP production to be opti- mal. The prevailing view has been that the rate of ATP production is just right  at two ATP molecules/glucose. According to this model, at faster rates the energy yield would fall below two ATP molecules. At slower rates, more ATP molecules/glucose would be generated, but ATP amounts would fall below the minimum level needed to satisfy the cell's energy demands.

Recent work indicates that the prevailing view of glycolytic optimization is not entirely correct. The production rate of ATP is not optimal in glycolysis, but the amount of ATP produced is. If that's the case, then why isn't the  yield of ATP in glycolysis higher? This research demonstrates that any output other than two ATP molecules/glucose negatively impacts the biochemical  processes that use ATP.
This molecule sits at the center of a complex web of activities within the cell. For example, in addition to providing energy for cell operations, ATP also regulates metabolic pathways. Production rates that exceed two ATP  molecules/glucose would create havoc with other cell processes that use ATP. Production rates that fall short of two ATP molecules/glucose would  fail to yield the maximum amount of energy possible from each glucose molecule. The performance of the glycolytic pathways finds balance between the amount of ATP produced and its global use throughout the cell.

1) http://creation.com/origin-of-life-critique
2) Fazale Rana, Cells design : Glycolysis
3) http://www.apologeticspress.org/ApPubPage.aspx?pub=1&issue=574&article=594
4) Origins of Life on the Earth and in the Cosmos pg. 194
5) http://www.nature.com/articles/ncomms9427



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2 Re: Glycolysis on Fri Aug 28, 2015 6:10 pm

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Enzymes of Glycolysis 1

PHASE I:  The enzymes in detail

keggs
 
The different enzymes involved in glycolysis act as kinases, mutases, and dehydrogenases, cleaving enzymes, isomerases or enolases.  They act in concert to split or rearrange the intermediates, to add on phosphate groups, and to move those phosphate groups onto ADP to make ATP. Several of the reactions involve the phosphorylation of intermediates, which is important not only for the production of ATP from ADP, but also as a useful handle on the substrate for enzyme binding, to trap intermediates within the cell, and to drive pathways in one direction by making phosphorylation and dephosphorylation reactions irreversible.  The different enzymes have been split into two groups, those in phase I and those in phase II, simply for convenience.
 
Hexokinase (EC 2.7.1.1)
 
Catalyses: a-D-Glucose + ATP à Glucose-6-phosphate (G6P) + ADP
 
The first step in glycolysis is a priming reaction, where a phosphate group is added to glucose using ATP.  This reaction is important for its ability to trap glucose within the cell.  Whereas glucose can easily traverse the plasma membrane, the negatively charged phosphate group prevents G6P from crossing, so cells can stock up on glucose while levels are high.  However, the hexokinase reaction is highly regulated, with G6P providing a feedback inhibition of the enzyme, thereby preventing excessive stockpiling until glycolysis depletes G6P levels.
            In mammals, there are four isozymes of hexokinase: types I, II, III and IV (glucokinase).  These isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues.  Type I, II and III hexokinases can phosphorylate a variety of hexose sugars, including glucose, fructose and mannose, and as such are involved in a number of metabolic pathways.  It is thought that type I hexokinase may have a catabolic function, producing G6P for energy production in glycolysis, whereas types II and III may have an anabolic function, providing G6P for glycogen or lipid synthesis.  Type I hexokinase binds to the mitochondrial membrane, thereby enabling the coordination of the rate of glycolysis with that of the TCA cycle.  Type IV hexokinase (glucokinase) is a liver/pancreatic b-cell enzyme that is specific for a-D-glucose, and whose level is controlled by insulin, not G6P.  Due to the lack of inhibition by G6P, during times of high blood glucose levels the liver can stockpile G6P, converting it to glycogen for later use.  In pancreatic b cells, type IV hexokinase acts as a glucose sensor to modify insulin secretion.  Mutations in type IV hexokinase have been associated with diabetes mellitus.
 
Phosphoglucose isomerase (EC 5.3.1.9)
 
Catalyses:  Glucose-6-phosphate (G6P) à Fructose-6-phosphate (F6P)
 
Phosphoglucose isomerase (PGI) catalyses the interconversion of G6P and F6P during glycolysis and gluconeogenesis.  The shift of the carbonyl oxygen from the C1 position in G6P to the C2 position in F6P is necessary in order to add another phosphate group at the C1 position in a later reaction.
PGI is a multi-functional enzyme that moonlights as neuroleukin (a neurotrophic factor that mediates the differentiation of neurons), as autocrine motility factor (a tumour-secreted cytokine that regulates cell motility), as differentiation and maturation mediator, and as myofibril-bound serine proteinase inhibitor.  Therefore, inside the cell PGI functions in glucose metabolism, while outside the cell it acts as a nerve growth factor and cytokine.       
Mutations in PGI are associated with nonspherocytic haemolytic anaemia.
 
Phosphofructokinase (EC 2.7.1.11)
 
Catalyses:  Fructose-6-phosphate (F6P) + ATP à Fructose-1,6-bisphosphate (F1,6PP) + ADP
 
The third step in glycolysis is another priming reaction, adding a second phosphate group to F6P.  This reaction is unidirectional, committing the cell to glycolysis, as opposed to energy storage, or producing a different sugar.  A different enzyme, fructose bisphosphatase, is required to catalyse the reverse reaction.  The cellular levels of phosphofructokinase (PFK) and fructose bisphosphatase help drive metabolism towards glycolysis or gluconeogenesis, respectively. 
PFK is an inducible, highly regulated, allosteric enzyme that is a key regulator of glycolysis.  PFK is activated by AMP, ADP, Pi, and fructose-2,6-bisphosphate (F2,6PP), and is inhibited by ATP, citrate, H+ and possibly F1,6PP. In resting muscle, ATP levels are high, while AMP levels are relatively low, contributing to the inhibition of PFK.  This inhibition of PFK is reinforced by citrate, an intermediate in the TCA cycle that signals the availability of substrate for aerobic ATP production.  By contrast, in working muscle, ATP levels remain fairly constant, while AMP levels rise as ATP and AMP are made from two ADP molecules, signalling the need to activate PFK, and consequently glycolysis.  F2,6PP is produced as a metabolic signal, and is not an intermediate in any metabolic pathway.  F2,6PP functions as an activator of PFK (glycolysis) and a concomitant inhibitor of fructose bisphosphatase (gluconeogenesis). 
Deficiencies in PFK lead to Tauri disease (glycogen storage disease VII), an autosomal recessive disorder characterised by severe nausea, vomiting, muscle cramps and myoglobinuria in response to bursts of intense or vigorous exercise.
 
Fructose-bisphosphate aldolase (EC 4.1.2.13)
 
Catalyses:  Fructose-1,6-bisphosphate (F1,6PP) à dihydroxyacetone phosphate (DHAP) + Glyceraldehyde-3-phosphate (G3P)
 
Fructose-bisphosphate aldolase (aldolase) catalyses the reversible cleavage of F1,6PP to two triose phosphates, both of which continue through glycolysis.
There are two classes of aldolases, which have different catalytic mechanisms: class I enzymes are found in animals, do not require a metal ion, and are characterised by the formation of a Schiff base intermediate between an active site lysine and a substrate carbonyl group, while the class II enzymes are produced in bacteria and fungi, and require an active-site divalent metal ion.  Isozymes are found for each class of enzyme, and in vertebrates the genes encoding each isozyme show tissue-specific expression.  For example, class I aldolase A is expressed in muscle, aldolase B in liver, kidney, stomach and intestine, and aldolase C in brain, heart and ovary.  The different isozymes have different catalytic functions: aldolases A and C are mainly involved in glycolysis, while aldolase B is involved in both glycolysis and gluconeogenesis.  Defects in aldolase B result in hereditary fructose intolerance.
 
Triosephosphate isomerase (EC 5.3.1.1)
 
Catalyses:  Dihydroxyacetone phosphate (DHAP) à Glyceraldehyde-3-phosphate (G3P)
 
            Triosephosphate isomerase (TIM) catalyses the reversible interconversion of G3P and DHAP.  Only G3P can be used in glycolysis, therefore TIM is essential for energy production, allowing two molecules of G3P to be produced for every glucose molecule, thereby doubling the energy yield. 
            Deficiencies in TIM are associated with haemolytic anaemia coupled with a progressive, severe neurological disorder.
 
            This brings us to the end of the first phase of glycolysis, where a molecule of glucose has produced two molecules of glyceraldehde-3-phosphte, at the cost of two ATP molecules.

PHASE II:  The enzymes in detail
 
            The second phase of glycolysis involves the extraction of energy in the form of 4 ATP per molecule of glucose, a net gain of 2 ATP molecules.  The product of glycolysis, pyruvate, can then be further broken either aerobically ( to carbon dioxide and water through the TCA cycle) or anaerobically (to lactate or alcohol).
 
Glyceraldehyde 3-phosphate dehydrogenase  (EC 1.2.1.12)
 
Catalyses:  Glyceraldehyde-3-phosphate (G3P) +NAD+ + Pi à 1,3-Bisphosphoglycerate (1,3BPG) + NADH + H+
 
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis by reversibly catalysing the oxidation and phosphorylation of G3P to the energy-rich intermediate 1,3BPG.  NAD+ is a co-substrate for this reaction. 
GAPDH displays diverse non-glycolytic functions as well, its role depending upon its subcellular location.  For instance, the translocation of GAPDH to the nucleus acts as a signalling mechanism for programmed cell death, or apoptosis.  The accumulation of GAPDH within the nucleus is involved in the induction of apoptosis, where GAPDH functions in the activation of transcription.  The presence of GAPDH is associated with the synthesis of pro-apoptotic proteins like BAX, c-JUN and GAPDH itself.
GAPDH has been implicated in certain neurological diseases: GAPDH is able to bind to the gene products from neurodegenerative disorders such as Huntington’s disease, Alzheimer’s disease, Parkinson’s disease and Machado-Joseph disease through stretches encoded by their CAG repeats.  Abnormal neuronal apoptosis is associated with these diseases.  Propargylamines such as deprenyl increase neuronal survival by interfering with apoptosis signalling pathways via their binding to GAPDH, which decreases the synthesis of pro-apoptotic proteins.
 
Phosphoglycerate kinase (EC 2.7.2.3)
 
Catalyses:  1,3-Bisphosphoglycerate (1,3BPG) + ADP à 3-Phosphoglycerate (3PG) + ATP
 
            Phosphoglycerate kinase (PGK) is an enzyme that reversibly catalyses the formation of ATP to ADP, using one of the high-energy phosphate groups from 1,3BPG.  The reaction forms two ATP molecules per glucose (one per 1,3BPG molecule), which compensates for the expenditure of 2 ATP in phase I of glycolysis.  The ATP is made by substrate-level phosphorylation, where a phosphate group is transferred from 1,3BPG directly to ADP.  This reaction is essential in most cells for the generation of ATP in aerobes, for fermentation in anaerobes and for carbon fixation in plants.
Deficiencies in PGK are associated with haemolytic anaemia, myopathy, central nervous system disorder and growth retardation.
 
Phosphoglycerate mutase (EC 5.4.2.1)
 
Catalyses:  3-Phosphoglycerate (3PG) à 2-Phosphoglycerate (2PG)
 
Phosphoglycerate mutase (PGAM) catalyses the transfer of the phospho group from the C3 position to the C2 position, in preparation for the synthesis of ATP.  PGAM enzymes from different sources exhibit different reaction mechanisms.  For instance, some PGAM enzymes (vertebrates, fungi, certain bacteria) use 2,3-bisphophoglycerate as a cofactor to phosphorylate a serine residue to prime the reaction, whereas other PGAM enzymes (plants, certain invertebrates, algae, certain bacteria) carry out intramolecular phosphoryl group transfer via an active site residue without the need of a cofactor.
            Deficiencies in PGAM can cause acute muscle dysfunction with exercise intolerance and muscle breakdown.
 
Enolase (EC 4.2.1.11)
 
Catalyses:  2-Phosphoglycerate (2PG) à Phosphoenolpyruvate (PEP) + H2O
 
Enolase (phosphopyruvate hydratase) is an essential glycolytic enzyme that catalyses the reversible dehydration of 2-phosphoglycerate to the high-energy intermediate phosphoenolpyruvate.  Enolase is strongly inhibited by fluoride ions, which forms a fluorophosphate complex with magnesium at the active site.  In vertebrates, there are 3 different, tissue-specific isozymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue.  The functional enzyme exists as homo- or hetero-dimers of the different isozymes.  In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer.
Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke.  Several tumour cells have also been found positive for neuron-specific enolase.  Beta-enolase deficiency is associated with glycogenosis type XIII defect.
 
Pyruvate kinase (EC 2.7.1.40)
 
Catalyses:  Phosphoenolpyruvate (PEP) + ADP à Pyruvate + ATP
 
Pyruvate kinase (PK) catalyses the final step in glycolysis, the conversion of PEP to pyruvate with the concomitant transfer of the high-energy phosphate group from PEP to ADP, thereby generating ATP.  PK requires both magnesium and potassium for activity.  In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes.
PK helps control the rate of glycolysis, along with phosphofructokinase and hexokinase.  PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions.  The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted.  L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme.  M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver.
The pyruvate produced by PK feeds into a number of different metabolic pathways.  Under aerobic conditions, pyruvate can be transported to the mitochondria, where it enters the TCA cycle and is further broken down to produce considerably more ATP through oxidative phosphorylation.  Alternatively, pyruvate can be anaerobically reduced to lactate in cells lacking mitochondria, or under hypoxic conditions, such as found in hard working muscle tissues.  Other by-products of anaerobic breakdown of pyruvate include ethanol during fermentation by yeast

2

1) http://www.ebi.ac.uk/interpro/potm/2004_2/Page2.htm
2) http://www.kois.sk/bioorg/bioorganicka_chemia/BIOORG1/kniha%20o%20metabolickych%20drahach_2012.pdf



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3 Re: Glycolysis on Sat Aug 29, 2015 5:13 pm

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Glycolysis and Alcoholic Fermentation

by Jean Sloat Morton, Ph.D

Evidence for Creation

When the oxygen supply runs short in heavy or prolonged exercise, muscles obtain most of their energy from an anaerobic (without oxygen) process called glycolysis. Yeast cells obtain energy under anaerobic conditions using a very similar process called alcoholic fermentation. Glycolysis is the chemical breakdown of glucose to lactic acid. This process makes energy available for cell activity in the form of a high-energy phosphate compound known as adenosine triphosphate (ATP). Alcoholic fermentation is identical to glycolysis except for the final step (Fig. 1). In alcoholic fermentation, pyruvic acid is broken down into ethanol and carbon dioxide. Lactic acid from glycolysis produces a feeling of tiredness; the products of alcoholic fermentation have been used in baking and brewing for centuries.
Both alcoholic fermentation and glycolysis are anaerobic fermentation processes that begin with the sugar glucose. Glycolysis requires 11 enzymes which degrade glucose to lactic acid (Fig. 2). Alcoholic fermentation follows the same enzymatic pathway for the first 10 steps. The last enzyme of glycolysis, lactate dehydrogenase, is replaced by two enzymes in alcoholic fermentation. These two enzymes, pyruvate decarboxylase and alcoholic dehydrogenase, convert pyruvic acid into carbon dioxide and ethanol in alcoholic fermentation.
The most commonly accepted evolutionary scenario states that organisms first arose in an atmosphere lacking oxygen. Anaerobic fermentation is supposed to have evolved first and is considered the most ancient pathway for obtaining energy. There are several scientific difficulties, however, with considering fermentations as primitive energy harvesting mechanisms produced by time and chance.
First of all, it takes ATP energy to start the process that will only later generate a net gain in ATP. Two ATPs are put into the glycolytic pathway for priming the reactions, the expenditure of energy by conversion of ATP to ADP being required in the first and third steps of the pathway (Fig. 2). A total of four ATPs are obtained only later in the sequence, making a net gain of two ATPs for each molecule of glucose degraded. The net gain of two ATPs is not realized until the tenth enzyme in the series catalyzes phosphoenolpyruvate to ATP and pyruvic acid (pyruvate). This means that neither glycolysis nor alcoholic fermentation realizes any gain in energy (ATP) until the tenth enzymatic breakdown.


Fig. 1. A comparison of two anaerobic energy-harvesting mechanisms.



It is purely wishful thinking to suppose that a series of 10 simultaneous, beneficial, additive mutations could produce 10 complex enzymes to work on 10 highly specific substances and that these reactions would occur in sequence. Enzymes are proteins consisting of amino acids united in polypeptide chains. Their complexity may be illustrated by the enzyme glyceraldehyde phosphate dehydrogenase, which is the enzyme that catalyzes the oxidation of phosphoglyceraldehyde in glycolysis and alcoholic fermentation. Glyceraldehyde phosphate dehydrogenase consists of four identical chains, each having 330 amino acid residues. The number of different possible arrangements for the amino acid residues of this enzyme is astronomical.


To illustrate, let us consider a simple protein containing only 100 aim acids. There are 20 different kinds of L-amino acids in proteins, and each can be used repeatedly in chains of 100. Therefore, they could be arranged in 20^100 or 10^130 different ways. Even if a hundred million billion of these (10^17) combinations could function for a given purpose, there is only one chance in 10^113 of getting one of these required amino acid sequences in a small protein consisting of 100 amino acids.
By comparison, Sir Arthur Eddington has estimated there are no more than 10^80 (or 3,145 x 10^79) particles in the universe. If we assume that the universe is 30 billion years old (or 10^18 seconds), and that each particle can react at the exaggerated rate of one trillion (10^12) times per second, then the total number of events that can occur within the time and matter of our universe is 10^80 x 10^12 x 10^18 = 10^110. Even by most generous estimates, therefore, there is not enough time or matter in our universe to "guarantee" production of even one small protein with relative specificity.


If probabilities involving two or more independent events are desired, they can be found by multiplying together the probability of each event. Consider the 10 enzymes of the glycolytic pathway. If each of these were a small protein having 100 amino acid residues with some flexibility and a probability of 1 in 10^113, the probability for arranging the amino acids for the 10 enzymes would be:  1 in 10^1,130.
And 1 in 101,130 is only the odds against producing the 10 glycoytic enzymes by chance. It is estimated that the human body contains 25,000 enzymes. If each of these were only a small enzyme consisting of 100 amino acids with a probability of 1 in 10-113, the probability of getting all 25,000 would be (10-113)25,000, which is 1 chance in 102,825,000. The actual probability for arranging the amino acids of the 25,000 enzymes will be much slimmer than our calculations indicate, because most enzymes are far more complex than our illustrative enzyme of 100 amino acids.
Mathematicians usually consider 1 chance in 10^50 as negligible. In other words, when the exponent is larger than 50, the chances are so slim for such an event ever occurring, that it is considered impossible. In our calculations, 10-110 was considered the total number of events that could occur within the time and matter of our universe. The chances for producing a simple enzyme-protein having 100 amino acid residues was I in 10^113. The probability for 25,000 enzymes occurring by chance alone was 1 in 102,825,000. It is preposterous to think that even one simple enzyme-protein could occur by chance alone, much less the 10 in glycolysis or the 25,000 in the human body!



Fig. 2. Notice that ATP is formed at two different locations above (steps 7 & 10). Because there are 2 molecules of the substrates, there will be 2 molecules of ATP formed at both locations, making a total of 4 molecules of ATP. Two molecules of ATP were necessary for priming the original breakdown of glucose (step 1). Therefore, a net of 2 molecules of ATP are recognized from the entire breakdown of glucose pyruvate. (4 ATP formed - 2 ATP primers = 2 ATP net overall gain.) Notice also that this MW net gain In ATP is not recognized until phosphoenolpyruvate is broken down by pyruvate kinase to form 2 molecules of pyruvate. This means that 10 enzymatic reactions must proceed in sequence, before energy in the form of ATP is obtained.

There are still other problems with the theory of evolution for alcoholic fermentation and glycolytic pathways. It is necessary to account for the numerous complex regulatory mechanisms which control these chemical pathways. For example, phosphofructokinase is a regulatory enzyme which limits the rate of glycolysis. Glycogen phosphorylase is also a regulatory enzyme; it converts glycogen to glucose-1-phosphate and thus makes glycogen available for glycolytic breakdown. In complex organisms there are several hormones such as somatotropin, insulin, glucagon, glucocorticoids, adrenaline thyroxin and a host of others which control utilization of glucose. No evolutionary mechanism has ever been proposed to account for these control mechanisms.


In addition to the regulators, complex cofactors are absolutely essential for glycolysis. One of the two key ATP energy harvesting steps in glycolysis requires a dehydrogenase enzyme acting in concert with the "hydrogen shuttle" redox reactant, nicotinamide adenine dinucleotide (NAD+). To keep the reaction sequence going, the reduced cofactor (NADH + H +) must be continuously regenerated by steps later in the sequence (Fig. 2), and that requires one enzyme in glycolysis (lactic dehydrogenase) and another (alcohol dehydrogenase) in alcoholic fermentation. In the absence of continuously cycled NAD+, "simple" anaerobic ATP energy harvest would be impossible.
And there are further difficulties yet for evolutionary theory to surmount. At one point, an intermediate in the glycolytic pathway is "stuck" with a phosphate group (needed to make ATP) in the low energy third carbon position. A remarkable enzyme, a "mutase" (Step 8 ), shifts the phosphate group to the second carbon position—but only in the presence of pre-existent primer amounts of an extraordinary molecule, 2,3-diphosphoglyceric acid. Actually, the shift of the phosphate from the third to the second position using the "mutase" and these "primer" molecules accomplishes nothing notable directly, but it "sets up" the ATP energy-harvesting reaction which occurs two steps later!


In summary, the following items make an evolutionary origin for glycolysis and alcoholic fermentation totally untenable: (1) the extreme improbability of getting even one simple enzyme by random processes; (2) the fact that the overall net gain in energy (ATP) is not recognized until pyruvate formation suggests that the chemical reaction must proceed through at least 10 enzymatic steps and that these steps of necessity must be in sequence; (3) the complex regulatory mechanisms, cofactors, and "primers" necessary for glucose utilization cannot be explained by evolutionary speculation.


On the other hand, the tight fit among complex and interdependent steps—especially the way some reactions take on meaning only in terms of reactions that occur much later in the sequence—seems to point clearly to creation with a teleological purpose, by an Intelligence and Power far greater than man's.


References

A.I. Oparin, Origin of Life, New York: Dover Pub., lnc., 1965, pp. 225-26.(Jark and Synge (eds.), The Origin of Life on the Earth, New York: Pergamon Press, 1959, p. 52.Ernil Borel, Probabilities and Life, New York: Dover Pub., Inc., 1962, p. 28.[/list]






http://www.icr.org/article/glycolysis-alcoholic-fermentation/

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4 Re: Glycolysis on Sat Aug 29, 2015 5:49 pm

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Glycolysis and the Citric Acid Cycle: The Control of Proteins and Pathways 1


Automobiles have incredible engines, cooling systems, drive trains, and so forth, but all of this must be controlled. The accelerator, gears and brakes are essential in automobile design. This is even more true in biology where regulation and control at all levels is crucial and incredibly complex, particularly since so much of the control is performed automatically. At the cellular level, the cell’s machines—the proteins—are controlled at several levels. As one leading textbook describes:

A living cell contains thousands of enzymes, many of which operate at the same time and in the same small volume of the cytosol. By their catalytic action, these enzymes generate a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs.

Regulation occurs at many levels. At one level, the cell controls how many molecules of each enzyme it makes by regulating the expression of the gene that encodes that enzyme. The cell also controls enzymatic activities by confining sets of enzymes to particular subcellular compartments, enclosed by distinct membranes. The rate of protein destruction by targeted proteolysis represents yet another important regulatory mechanism. But the most rapid and general process that adjusts reaction rates operates through a direct, reversible change in the activity of an enzyme in response to specific molecules that it encounters.


So the cell controls its proteins by controlling how many it creates and destroys, and by confining them to certain compartments. But most directly it controls them directly, as one controls an automobile with the accelerator and brake.

Glycolysis and the citric acid cycle

A great example of all this is the nearly universal glycolysis pathway and citric acid cycle which team up to process food intake. In the glycolysis pathway about a dozen protein enzymes break down the six-carbon sugar known as glucose into two three-carbon molecules. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. If just one of the enzymes is not present or otherwise not functioning then the entire process doesn’t work.

In addition to breaking down glucose, glycolysis also produces energy-carrying molecules called ATP. These are in constant demand in the cell as they are used wherever energy is needed. Like most pathways, glycolysis is interconnected with other pathways within the cell. The molecular products of glycolysis are used elsewhere and so the rate at which the glycolysis pathway proceeds is important. Too fast and its products won’t be useful, too slow and other pathways have to slow down.

Glycolysis is regulated in a number of ways. The first enzyme in the glycolysis pathway is regulated by its own product. This enzyme alters glucose to form an intermediate product, but if the rest of the pathway is not keeping up then the intermediate product will build up, and this will cause the enzyme to shut down temporarily. The enzyme is designed to be controlled by the presence of its product.

Two other enzymes in the pathway have even more sophisticated regulation. They are sensitive to a number of different molecules which either increase or decrease the enzyme activity. For example, these enzymes are partly controlled by the energy level of the cell. This makes sense since glycolysis helps supply energy to the cell. A good indicator of the cell’s energy level is the relative concentrations of ATP and spent ATP. High levels of ATP indicate a strong energy supply. Hence the enzyme activity is inhibited (and therefore the glycolysis pathway is slowed) when ATP is abundant. But high levels of spent ATP counteract this effect.

How do these molecules control enzyme activity? The molecules are tiny compared to the big enzymes they control. Just as a small key is used to start up and turn off a big truck, so too these small molecules have big effects on their target enzyme. And just as the truck has an ignition lock that can be turned only by the right key, so too the enzyme has several docking sites that are just right for a particular small molecule, such as ATP.

Not only does ATP fit just right into its docking site, but it perturbs the enzyme structure in just the right way so as to diminish the enzyme activity. There is another docking site that only a spent ATP will fit into. And if this occurs then the enzyme structure is again perturbed just right so as to encourage activity and reverse the ATP docking effect.

Glycolysis and the rest of the cell

Glycolysis and the citric acid cycle do not merely create energy for the cell. Just as an oil refinery also produces a range of petroleum products, glycolysis and the citric acid cycle, in addition to producing energy, spin off a series of essential biochemical components needed by the cell. This figure illustrates how these pathways produce nucleotides, lipids, amino acids, cholesterol and other molecules.


In fact glycolysis and the citric acid cycle exist within a complex web of chemical pathways within the cell. These many pathways interaction with each other in many ways, as shown in this wire chart (glycolysis and the citric acid cycle are shown in red).



Sometimes a three dimensional view, that can be rotated, helps to understand the interactions between these many pathways.


This design is complex at many levels. At the molecular level, there is the precise control of the protein enzymes. At the pathway level, there is the interaction between the enzymes. And at the cellular level there is interactions between the different pathways. And all of this has nothing in common with evolution’s naïve, religiously-driven, dogma that biology must be one big fluke. As one evolutionist admitted (one of the textbook authors):


We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naive as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB—and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. … But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. […]

Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts. Within each protein assembly, intermolecular collisions are not only restricted to a small set of possibilities, but reaction C depends on reaction B, which in turn depends on reaction A—just as it would in a machine of our common experience. […]

We have also come to realize that protein assemblies can be enormously complex. … As the example of the spliceosome should make clear, the cartoons thus far used to depict protein machines vastly underestimate the sophistication of many of these remarkable devices. [Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell 92 (1998): 291-294.]


But the dogma remains. Evolutionists insist that evolution must be a fact and they use dozens of religious arguments to make their case. In the next moment they turn around and insist it is all about science. The result is pathetic science, such as the journal paper that tried to explain the citric acid cycle as “evolutionary opportunism.” Religion drives science, and it matters.

1) http://darwins-god.blogspot.com.br/2011/07/glycolysis-and-citric-acid-cycle.html

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5 Re: Glycolysis on Sun Aug 30, 2015 4:26 pm

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Glycolysis 1

One of life’s most important metabolic pathways, glycolysis, plays a key role in harvesting energy for use in most cells. This biochemical process releases energy from glucose (a six-carbon sugar) by fracturing it into two molecules of pyruvate (a three-carbon compound). The cell captures a portion of this liberated chemical energy and stores it in the chemical bonds of special molecules for later use.
The glycolytic pathway traps energy from glucose breakdown by using it to form ATP (adenosine triphosphate). This molecule has two high-energy chemical bonds. When broken, the energy stored in the high-energy bonds is made available for the cell to use. The forming and breaking of the high energy bonds is like recharging and discharging a battery. The cell couples the breakdown of ATP’s high-energy bonds to energy-requiring biochemical processes and activities. In this way, energetically unfavorable processes in the cell become feasible by using the energy stored in ATP .
The use of ATP to power the cell’s operations displays elegant chemical logic. Biochemists refer to ATP as the cell’s energy currency. Instead of inefficiently coupling the breakdown of a large number of different high-energy compounds to a wide range of energetically unfavorable processes in the cell (like a barter-based economy), the cell uses only a few high-energy compounds (like a currency-based economy) to satisfy the multifarious energy demands of the cell.
From an energetics standpoint, the net output of glycolysis is two molecules of ATP for each molecule of glucose broken apart. (Two molecules of NADH [nicotinamide adenine dinucleotide] are also generated for each molecule of glucose. NADH, like ATP, is also an energy-currency molecule that mediates the transfer of electrons between biomolecules in the cell.) Biochemists have long considered glycolytic ATP production to be optimal. The prevailing view has been that the rate of ATP production is just right at two ATP molecules/glucose. According to this model, at faster rates the energy yield would fall below two ATP molecules. At slower rates, more ATP molecules/glucose would be generated, but ATP amounts would fall below the minimum level needed to satisfy the cell’s energy demands.
Recent work indicates that the prevailing view of glycolytic optimization is not entirely correct. The production rate of ATP is not optimal in glycolysis, but the amount of ATP produced is. If that’s the case, then why isn’t the yield of ATP in glycolysis higher? This research demonstrates that any output other than two ATP molecules/glucose negatively impacts the biochemical processes that use ATP.
This molecule sits at the center of a complex web of activities within the cell. For example, in addition to providing energy for cell operations, ATP also regulates metabolic pathways. Production rates that exceed two ATP molecules/glucose would create havoc with other cell processes that use ATP. Production rates that fall short of two ATP molecules/glucose would fail to yield the maximum amount of energy possible from each glucose molecule. The performance of the glycolytic pathways finds balance between the amount of ATP produced and its global use throughout the cell.

1) Fazale Rana's Cell's design pg.: 137

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6 Glycolisis at LUCA on Mon Aug 31, 2015 4:26 pm

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Astrobiology: An Evolutionary Approach 1

METABOLISM IN THE LAST COMMON ANCESTOR

It is generally held that all life on Earth today is descended from a common ancestor. The similarity of the biochemical machinery and the genetic material among all known organisms lends powerful support to this theory, even though 3 billion years worth of evolution has resulted in a wide variety in the details of genetic organization and biomolecular structure and function. Before we can look at the possible metabolic functions of the earliest
biochemical systems on Earth, we need to consider what we know about the last common ancestor of modern biochemistry.

The composition of the last universal common ancestor of all life on Earth, which we will refer to as LUCA, can only be inferred from available current data. Those data include primarily phylogenetic, but also some geochemical, evidence. The phylogenetic evidence lies in the evolutionary trees that can be constructed using the similarity (homology) between nucleotide sequences of genes, or amino acid sequences of the proteins coded for by genes, in modern species both closely and distantly related. The geochemical evidence is contained, for the most part, in stable isotope ratios of biologically important elements in ancient rocks. In both cases, the evidence is somewhat fragmentary and difficult to interpret. Our picture of the metabolic functions of LUCA is thus really only a model, or a set of models, based on inference.

Metabolic Functions
The percentage of inferred LUCA genes that code for metabolic enzymes varies from study to study. One analysis comparing genomes of bacteria, archaea, and yeast resulted in a putative LUCA genome in which 45 out of 115 genes are metabolic. Thirty-three of these 45 genes involve either sugar or nucleotide metabolism. Another phylogenetic study identified approximately 300 highly conserved protein-coding genes, with about 100 of those
coding for metabolic enzymes. Of these, the metabolically related genes were again primarily involved in sugar and nucleotide metabolism. Consensus LUCA genomes based on compilation of data from several studies that took sequence-, structure-, and function-based approaches included several classes of enzymes. One such class is oxidoreductases, which catalyze redox reactions. Also included are glycosyl transferases, which act on sugars; phosphotransferases, which catalyze addition of phosphate groups; and amino acid ligases. Analysis of the occurrence of various protein folding domains across modern species resulted in the identification of five particularly
ancient domains. These include domains that hydrolyze nucleoside triphosphates, bind nucleic acids, bind nucleotide cofactors, and interact with Fe–S clusters. It has also been pointed out that the glycerol derivatives used in both bacteria and archaea to synthesize membrane phospholipids are made from dihydroxyacetone phosphate (DHAP), a key intermediate in glycolysis. This suggests, assuming LUCA had phospholipid membranes similar to those of modern bacteria and eukaryotes, that DHAP was available within the cell. This, in turn, indirectly suggests that most of the glycolytic pathway was operational in LUCA. Overall, the bulk of central metabolism has been inferred to have been strongly conserved in most model LUCA genomes. This includes amino acid and nucleotide synthesis, lipid and coenzyme synthesis, as well as most glycolysis and TCA cycle enzymes. The results of phylogenetic comparisons like these are not always unambiguous, however. In one putative genome, for example, the glycolytic enzymes enolase, pyruvate kinase, and phosphoglycerate kinase were all present, while phosphoglyceromutase and glyceraldehyde-3-phosphate dehydrogenase were absent. Phosphoglyceromutase is the enzyme that sits in the middle of the second phase of glycolysis (the energy-producing phase). How LUCA would How LUCA would have managed to carry out glycolysis without this step in the pathway is unclear.

Minimum Requirements for a Metabolic System
Much of our understanding of the minimum requirements for a metabolic system comes from endosymbiotic microorganisms that inhabit the blood or digestive tract of higher organisms. These species, including members of the genera Mycoplasma, Rickettsia, and Chlamydia, absorb many necessary compounds from their hosts. They have around 150–180 essential genes that are common to them. These include genes for enzymes in the glycolysis and pentose phosphate pathways, as well as enzymes that synthesize nucleotides, phospholipids, and a number of coenzymes. However, these organisms do not synthesize fatty acids, amino acids, or most purine and pyrimidine bases. These compounds are obtained from the environment inside the host.

It has also been pointed out that not all extant metabolic pathways are chemically minimal. In other words, in some cases, it is possible to envision pathways from one intermediate to another that would be chemically possible but contain fewer steps than those that have evolved over time. A few such shortcut pathways exist in some modern organisms, in fact. One example is the Entner–Doudoroff pathway. This alternate pathway is activated
in some microorganisms under certain conditions and converts glucose-6-phosphate to glyceraldehyde phosphate and pyruvate in only four steps. This is in contrast to glycolysis, which uses nine steps for the same transformation. It seems possible, then, that FIMS could have carried out the same general catabolic and anabolic functions we see in biology today but with fewer pathway steps and thus fewer required enzymes. However, any metabolic system that we would recognize as such would appear to require roughly 100 genes/ enzymes/pathway steps in order to function.

1. https://books.google.com.br/books?id=oWzSBQAAQBAJ&pg=PA129&lpg=PA129&dq=glycolysis+was+present+in+luca&source=bl&ots=XQPTA_2Agn&sig=1j3K1B81mCg_wTo1xOuld6rImjw&hl=en&sa=X&ved=0CB0Q6AEwAGoVChMI6IzGkq7UxwIVyCKQCh3kyA9k#v=onepage&q&f=false



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7 Re: Glycolysis on Wed Sep 09, 2015 1:27 pm

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Clearly, the evolution of anaerobic glycolysis is a muddy question. As more genomic data becomes available from diverse eukaryotic taxa, determining the evolutionary history of this pathway should be both fruitful and exciting.
http://ec.asm.org/content/5/12/2138.full


http://sandwalk.blogspot.com.br/2015/08/a-little-learning-of-biochemistry.html?showComment=1441047935909#c5341427346574111548

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The odds of forming the glycolysis or the gluconeogenesis pathway by chance

We note that Stanley Miller's experiments only produced 13 of the 21 basic (amino acid) building blocks of protein molecules. 2 To put this in perspective, lets assume that a modern computer running Windows Vista, with Monitor and Printer, and plugged into an electric source of power is comparable to the most basic self-replicating bacterium. Let's also assume that the Computer system consists of 21 basic materials (i.e. gold, silver, aluminum, tin, lead, silicon, plastic, etc...). Then what Miller found is equivalent to finding 13 of the 21 basic materials with which "computers" are made of. But even if we had all 21, we still need to order them ALL into the correct pieces (i.e. wire, solder, plastic frame, screws, circuit boards, Integrated Circuits, fan, Power Supply, smooth glass, etc..) --- something that simply WILL NOT happen all by itself. This is one of the many reasons why more and more people today are turning to Intelligent Design, as the evidence clearly indicates that God (or an outside Intelligent Influence) must have intervened in the Creation/Origin of Life on this Planet.

Proteins, for example, consist of long chains of 400 or more amino acids in a specific sequence. 1 Each of the amino acids in the sequence is one of 20 different kinds, and if the sequence is altered slightly, the protein will not be functional.  Moreover, 19 of the 20 kinds of amino acids[2] come in two forms—a left-handed and a right-handed form—but living things consist only of left-handed molecules.  Outside of living things, amino acids occur only in a 50-50 ratio of right-handed and left-handed forms.  Even if we artificially create a sample where one form or the other predominates, the sample will, with time, return to a 50-50 ratio through a process called racemation.

The odds of 400 left-handed amino acids linking up by chance is less than (0.5)380, and, since the simplest cell would need over 120 proteins, the combined probability would be less than (0.5)380x120 = 1.08x10-13,727.  This is an impossibly small probability, and we have not yet accounted for the specific sequences of amino acids needed, which would reduce the probability far more.[3]

The probability of getting heads in a single flip of a fair coin is 1 in 2. The probability of getting four heads in a row is 1/2 × 1/2 × 1/2 × 1/2, that is, (1/2)4 or 1/16.

For the occurrence of two particular nucleotide bases, the odds are 1/4 × 1/4. For three, 1/4 × 1/4 × 1/4, or 1/64, or (1/4),3 and so on.  The information-carrying capacity of a sequence of a specific length n can then be
calculated using Shannon’s familiar expres​sion(I =–log2p) once one computes a probability value (p) for the occurrence of a particular sequence n nucleotides long where p = (1/4)n. The p value thus yields a corresponding measure of information-carrying capacity or syntactic information for a sequence of n nucleotide bases.

Lets apply the same calculation to glycolysis:

1.Hexokinase 915 amino acids : (0.5)732 
http://www.brenda-enzymes.info/sequences.php?f[stype_ec]=1&f[ec]=2.7.1.1&f[stype_accession_code]=1&f[accession_code]=Q91W97
2.Phosphoglucose isomerase 569 amino acids (0.5)455
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=5.3.1.9&f[stype_accession_code]=1&f[accession_code]=P29333
3.Phosphofructokinase 941 amino acids (0.5)752
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=2.7.1.11&f[stype_accession_code]=1&f[accession_code]=C4QXA5
4.Fructose-bisphosphate aldolase 364 amino acids (0.5)291
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=4.1.2.13&f[stype_accession_code]=1&f[accession_code]=Q8JH71
5.Triosephosphate isomerase 241 amino acids (0.5)193
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=5.3.1.1&f[stype_accession_code]=1&f[accession_code]=B0CEX1
6.Glyceraldehyde 3-phosphate dehydrogenase 336 amino acids (0.5)269
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=1.2.1.12&f[stype_accession_code]=1&f[accession_code]=P17729
7.Phosphoglycerate kinase 417 amino acids (0.5)334
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=2.7.2.3&f[stype_accession_code]=1&f[accession_code]=P00559
8.Phosphoglycerate mutase 404 amino acids (0.5)323
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=5.4.2.1&f[stype_accession_code]=1&f[accession_code]=Q2Y4T5
9.Enolase 432 amino acids (0.5)345
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=4.2.1.11&f[stype_accession_code]=1&f[accession_code]=Q74K78
10. Pyruvate kinase 508 amino acids (0.5)406
http://www.brenda-enzymes.org/sequences.php?f[stype_ec]=1&f[ec]=2.7.1.40&f[stype_accession_code]=1&f[accession_code]=Q6FV12

So the average size of each protein is about 512 amino acids. (0.5)512 x 10  or (0.5)5120  or one to 10^10240




While most steps in gluconeogenesis are the reverse of those found in glycolysis, three regulated and strongly exergonic reactions are replaced with more kinetically favorable reactions.

1. Hexokinase/glucokinase, ====  glucose-6-phosphatase,
3. phosphofructokinase, =====  fructose-1,6-bisphosphatase,
10. pyruvate kinase enzymes ======  PEP carboxykinase


This system of reciprocal control allow glycolysis and gluconeogenesis to inhibit each other and prevent the formation of a futile cycle.

That means, both exist in parallel, together.

The majority of the enzymes responsible for gluconeogenesis are found in the cytoplasm; the exceptions are mitochondrial pyruvate carboxylase and, in animals, phosphoenolpyruvate carboxykinase. The latter exists as an isozyme located in both the mitochondrion and the cytosol.

Than means, mitochondria is required by the gluconeogenesis pathway. 

According to your story, Larry,  first there was Gluconeogenesis in some bacterial cells, and - two or three new enzymes arose to replace and  make it to an efficient glycolysis pathway after millions of years of evolution. You admitted of not knowing  how this transition or replacement could have happened naturally ( humm.. genetic drift ?! ) . Further, you have not explained  how Gluconeogenesis emerged in the first place.  You failed to mention that a parallel initial precursor Glycolysis pathway would have been necessary, and you  did not explain how it could have emerged either.  This precursor system of Glycolysis had to be in place  to synthesize the products required in a hypothetical proto cell ( supposed there were other complex chemical cellular reactions required already, somehow through natural pressure/self assembly of chemicals ( humm, did they have  a inborn drive to become alive and start self replication , somehow ??! ....).

As i have mentioned  at my library, there is a HUDGE UNBRIDGEABLE GAP between  unspecified metal catalysts  performing glucose or similar substrate  production,  as the  paper " The widespread role of non-enzymatic reactions in cellular metabolism " asserts - , and parallel another identical system ( convergence development already at this stage ? - amazing !! ) as precursor of Glycolysis, to a transition  to the highly complex specific enzymes required in both pathways. How could  unguided , random chemical reactions provide a compelling explanation to that question ?  Both pathways, Gluconeogenesis, and Glycolysis, use about ten highly specified complex enzymes, each exercising very different tasks. Since there was no evolution at this stage, the emergence  would have had to happen by random chance. There was no energy to form polypeptide assemblage and interlinking  without these enzymes. Lets assume that the average size of each enzime was 500 amino acids. In some miraculous way, they would have had to be all selected to be only left handed, the 20 different amino acids used for life would have had to be selected amongst many others, ( how they were available, amongst fixed nitrogen etc etc. is another story ) and then assemble in the right sequence through peptide bonds . There is a hudge gap that has to be filled between " modern " polypeptide formation through ribosomes, mRNA, and tRNA's, and supposed primordial amino chain formations without this advanced machinery. How could the gap be closed ? Not only are prebiotic mechanisms unlikely, but the transition would have required the emergence of a prebiotic specific mechanism and afterwards transition from one mechanism to the other extant today.

Laurent Boiteau Prebiotic Chemistry: From Simple Amphiphiles to Protocell Models, page 3:
Spontaneous self-assembly occurs when certain compounds associate through noncovalent hydrogen bonds, electrostatic forces, and nonpolar interactions that stabilize orderly arrangements of small and large molecules.  The argument that chemical reactions in a primordial soup would not act upon pure chance, and that  chemistry is not a matter of "random chance and coincidence , finds its refutation by the fact that the information stored in DNA is not constrained by chemistry. Yockey shows that the rules of any communication system are not derivable from the laws of physics.  He continues : “there is nothing in the physicochemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” In other words, nothing in nonliving physics or chemistry obeys symbolic instructions. So, to find functional enzymes in sequence space is not determined by chemical reactions.

A short protein molecule of 150 amino acids, the probability of building a 150 amino acids chain in which all linkages are peptide linkages would be roughly 1 chance in 10^45.
Lets assume a average size of each enzyme in both pathways  of about 500 amino acids. That would result in the possibility to get all these enzymes after one of  10^10000 trial and error attempts. That is ten with 10.000 zeroes. If we add the odds to get the right interlinking of the enzymes to get a functional  metabolic network, the picture  becomes even  less remotely possible. It should be evident that chance is not a capable mechanism to come up with just one of the several metabolic pathways required for a first organism.

http://www.doesgodexist.org/NovDec09/Information-Function.html
Literature from those who posture in favor of creation abounds with examples of the tremendous odds against chance producing a meaningful code. For instance, the estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143. Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.

1. http://members.toast.net/puritan/Articles/HowOldIsTheEarth_A.htm
2. http://creationwiki.org/The_odds_of_life_forming_are_incredibly_small_(Talk.Origins)



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9 Carbohydrate Metabolism on Sun Feb 05, 2017 1:05 pm

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Carbohydrate Metabolism

Glycolysis

Glycolysis is the central pathway of carbohydrate metabolism and makes comparative analysis of variants of this pathway all the more interesting.

Glucokinase (EC 2.7.1.2)
Fermentation of glucose starts with its phosphorylation, which is catalyzed by glucokinase. Although many bacteria bypass the glucokinase step by phosphorylating glucose concomitantly with its uptake by the PEPdependent
phosphotransferase system, some of them, including E. coli, encode a glucokinase (COG0837) that shares little sequence similarity with yeast and human enzymes. There is also another bacterial form, found in S. coelicolor, Bacillus megaterium, and other bacteria [32,795]. Recently, P. furiosus has been reported to encode an ADP-dependent glucokinase [435]. This enzyme has no detectable sequence similarity to any  other glucokinase, but shows significant structural similarity to enzymes of the ribokinase family [383]. In retrospect, several conserved motifs were detected in this new glucokinase and the ribokinase family proteins, which indicates of a homologous relationship. Thus, a c1ear-cut case of nonorthologous gene displacement is observed: a ribokinase family enzyme has been recruited to replace the typical glucokinase. So far, the ADP-dependent glucokinase has been found only in M. jannaschii and in pyrococci. The existence of at least three distinct forms of glucokinase is remarkable, especially given that this is apparently not an essential component of glycolysis. Moving down the glycolytic pathway, we find similar examples of non-orthologous gene displacement for several other, essential enzymes.


COMPARATIVE GENOMICS, MINIMAL GENE-SETS AND THE LAST UNIVERSAL COMMON ANCESTOR 1




1. http://www.cbs.dtu.dk/CBS/courses/brazilworkshop/files/koonin_NRM_2003.pdf

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