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Showing 71 - 80 of 48700 pathways
SMPDB ID Pathway Chemical Compounds Proteins


Pw000026 View Pathway

Glycerol Phosphate Shuttle

The glycerol phosphate shuttle also known as the glycerophosphate shuttle. It shuttles electrons to mitochondrial carriers in the oxidative phosphorylation pathway from cytosolic NADH. This shuttle relies on mitochondrial glycerol-3-phosphate dehydrogenase (mGPDH). This is also a common process for the cell to regenerate cytosolic NAD+ for other processes.


Pw000014 View Pathway

Butyrate Metabolism

Butyrate metabolism (Butanoate metabolism) describes the metabolic fate of a number of short chain fatty acids or short chain alcohols that are typically produced by intestinal fermentation. Many of these molecules are eventually used in the production of ketone bodies, the creation of short-chain lipids or as precursors to the citrate cycle, glycolysis or glutamate synthesis. The molecule for which this pathway is named, butyric acid, is a four-carbon fatty acid that is formed in the human colon by bacterial fermentation of carbohydrates (including dietary fiber). It is found in rancid butter, parmesan cheese, and vomit, and has an unpleasant odor and acrid taste, with a sweet aftertaste (similar to ether).


Pw000038 View Pathway

Taurine and Hypotaurine Metabolism

There is an organic acid known as Taurine, which is a derivative product of sulfhydryl amino acid (which contains sulfur), as well as cysteine. The synthesis or metabolism in mammalian systems of this acid transpires within the pancreas in such a fashion that it utilizes a pathway known as the cysteine sulfinic acid pathway. To put this process in context, its occurrence is often seen in vivo, in hepatocytes, and is fundamental in the cyclical process of recovering bile acids from the intenstine, turning them back into salts and returning them to the bile. In essence the cysteine pathway induces a sulfhydryl group to be oxidized, creating cysteine sulfinic acid, by utilizing the appropriate enzymes (ie cysteine dioxygenase). This new acid undergoes decarboxylation creating a new compound: hypotaurine. This process goes on as Taurine now is subjected to conjugation vis a vis its amino terminal group. This includes acids such as chenodeoxycholic acid and cholic acid, and in turn the formation of bile salts occurs. Moreover, this entire process can be catalyzed via bile acid and a special amino acid N-acetyltransferase.


Pw000033 View Pathway

Phenylacetate Metabolism

Phenylacetate (or phenylacetic acid) metabolism involves two steps. The first step is the conversion of phenylacetate into phenylacetyl-CoA which is catalyzed by acyl-coenzyme A synthetase ACSM1 or acyl-coenzyme A synthetase ACSM2B. Coenzyme A and ATP are also involved in this first step and AMP and pyrophosphate will be generated during the first step of metabolism. In the second step, phenylacetyl-CoA and L-glutamine interacts with glycine N-acyltransferase to generate coenzyme A as well as phenylacetylglutamine, of which the latter will be excreted in the urine. Phenylacetate metabolism provides a route that facilitates the excretion of nitrogen for patients with urea cycle defects; hence, it is important for clinical purposes.


Pw122277 View Pathway

Kidney Function - Ascending Limb of The Loop of Henle

The loop of Henle of the nephron can be separated into an ascending limb and the descending limb. The descending limb is highly impermeable to solutes such as sodium, but permeable to water. Conversely, the ascending limb is highly impermeable to water, but permeable to solutes. Chloride, potassium, and sodium are co-transported across the apical membrane (closest to the lumen) via transporters from the filtrate. The transporter requires all three ions present to be effective and to maintain electroneutrality. In addition, the three ions are transported across the basolateral membrane (closest to the renal interstitium) via other means such as the sodium potassium ATPase transports and the chloride channels in the membrane. As these solutes are being actively transported out of the ascending limb and into the renal interstitium/capillary network without water following (due to the lack of water permeability), the filtrate becomes more diluted. Furthermore, these ions simultaneously causes an increase in osmotic pressure that contributes to water reabsorption in the descending limb. This effect can be magnified with the help of vasopressin, which is a hormone that is typically involved with water reabsorption. However, when it acts on the ascending limb, it aids in increasing sodium reabsorption which will increase water reabsorption in the latter parts of the nephron (the distal tubule and collecting duct).


Pw122328 View Pathway

Kandutsch-Russell Pathway (Cholesterol Biosynthesis)

The Kandutsch-Russell pathway is the alternative pathway stemming from the mevalonate pathway completing cholesterol biosynthesis. The Bloch pathway and the Kandutsch-Russell pathway are both key to a functioning human body as cholesterol aids in the development of many important nutrients and hormones, such as vitamin D. Starting in the endoplasmic reticulum, lanosterol is the first compound used in this pathway, and when catalyzed by delta(24)-sterol-reductase, becomes 24,25-dihydrolanosterol. 24,25-Dihydrolanosterol is quickly converted to 4,4-dimethyl-14a-hydroxymethyl-5a-cholesta-8-en-3b-ol with the help of the enzyme lanosterol 14-alpha demethylase. This same enzyme, lanosterol 14-alpha demethylase, is also responsible for the conversion of 4,4-dimethyl-14a-hydroxymethyl-5a-cholesta-8-en-3b-ol into 4,4-dimethyl-14a-formyl-5a-cholest-8-en-3b-ol. Lanosterol 14alpha demethylase is used once more here, to push the pathway into the inner nuclear membrane, converting 4,4-dimethyl-14a-formyl-5a-cholest-8-en-3b-ol into 4,4-dimethyl-5a-cholesta-8,14-dien-3b-ol. Now located in the inner nuclear membrane, 4,4-dimethyl-5a-cholesta-8,14-dien-3b-ol is converted into 4,4-dimethyl-5a-cholesta-8-en-3b-ol through the help of a lamin-b receptor. Entering the endoplasmic reticulum membrane, methylsterol monooxygenase 1 is used to convert 4,4-dimethyl-5a-cholesta-8-en-3b-ol into 4a-hydroxymethyl-4b-methyl-5a-cholesta-8-en-3b-ol. 4a-Hydroxymethyl-4b-methyl-5a-cholesta-8-en-3b-ol then uses methylsterol monooxygenase 1 to become 4a-formyl-4b-methyl-5a-cholesta-8-en-3b-ol. Once again, methylsterol monooxygenase 1 is used to convert 4a-formyl-4b-methyl-5a-cholesta-8-en-3b-ol into 4a-carboxy-4b-methyl-5a-cholesta-8-en-3b-ol. Now using sterol-4-alpha-carboxylate 3-dehydrogenase, 4a-carboxy-4b-methyl-5a-cholesta-8-en-3b-ol is turned into 4a-methyl-5a-cholesta-8-en-3-one. This puts the pathway in the cell membrane, where a 3-keto-steroid reductase is used to convert 4a-methyl-5a-cholesta-8-en-3b-one into 4a-methyl-5a-cholesta-8-en-3-ol. Moving back into the endoplasmic reticulum membrane, methylsterol monooxygenase 1 converts 4a-methyl-5a-cholesta-8-en-3-ol into 4a-hydroxymethyl-5a-cholesta-8-en-3b-ol. Methylsterol monooxygenase is used twice more in this pathway, first converting 4a-hydroxymethyl-5a-cholesta-8-en-3b-ol into 4a-formyl-5a-cholesta-8-en-3b-ol, then converting 4a-formyl-5a-cholesta-8-en-3b-ol into 4a-carboxy-5a-cholesta-8-en-3b-ol. Now using sterol-4-alpha-carboxylate 3 dehydrogenase, 4a-carboxy-5a-cholesta-8-en-3b-ol becomes 5a-cholesta-8-en-3-one and brings the pathway back to the cell membrane. 5a-Cholesta-8-en-3-one teams up with a 3-keto-steroid reductase to create 5a-cholest-8-en-3b-ol. Then, stepping back into the endoplasmic reticulum membrane, 5a-cholest-8-en-3b-ol enlists the help of 3-beta-hydroxysteroid-delta(8),delta(7)-isomerase to produce lathosterol. Lathosterol and lathosterol oxidase work together to make 7-dehydrocholesterol . Finally, 7-dehydrocholesterol partners with 7-dehydrocholesterol reductase to create cholesterol, completing the final step in cholesterol biosynthesis.


Pw000146 View Pathway


Glycolysis is a metabolic pathway with sequence of ten reactions involving ten intermediate compounds that converts glucose to pyruvate. Glycolysis release free energy for forming high energy compound such as ATP and NADH. Glycolysis is consisted of two phases, which one of them is chemical priming phase and second phase is energy-yielding phase. As the starting compound of chemical priming phase, D-glucose can be obtained from galactose metabolism or imported by monosaccharide-sensing protein 1 from outside of cell. D-Glucose is catalyzed by probable hexokinase-like 2 protein to form glucose 6-phosphate which is powered by ATP. Glucose 6-phosphate transformed to fructose 6-phosphate by glucose-6-phosphate isomerase, which the later compound will be converted to fructose 1,6-bisphosphate, which is the last reaction of chemical priming phase by 6-phosphofructokinase with cofactor magnesium, and it is also powered by ATP. Before entering the second phase, aldolase catalyzing the hydrolysis of F1,6BP into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Dihydroxyacetone phosphate and glyceraldehyde 3-phosphate can convert to each other bidirectionally by facilitation of triosephosphate isomerase. The second phase of glycolysis is yielding-energy phase that produce ATP and NADH. At the first step, D-glyceraldehyde 3-phosphate is catalyzed to glyceric acid 1,3-biphosphate by glyceraldehyde-3-phosphate dehydrogenase with NAD, which also generate NADH. ATP is generated through the reaction that convert glyceric acid 1,3-biphosphate to 3-phosphoglyceric acid. Phosphoglycerate mutase 2 catalyze 3-phosphoglyceric acid to 2-Phospho-D-glyceric acid, and alpha-enolase with cofactor magnesium catalyzes 2-Phospho-D-glyceric acid to phosphoenolpyruvic acid. Eventually, plastidial pyruvate kinase 4 converts phosphoenolpyruvic acid to pyruvate with cofactor magnesium and potassium and ADP. Pyruvate will undergo pyruvate metabolism, tyrosine metabolism and pantothenate and CoA biosynthesis.


Pw000172 View Pathway

Mitochondrial Beta-Oxidation of Medium Chain Saturated Fatty Acids

Beta-oxidation is the major degradative pathway for fatty acid esters in humans. Fatty acids and their CoA esters are found throughout the body, playing roles such as components of cellular lipids, regulators of enzymes and membrane channels, ligands for nuclear receptors, precursor molecules for hormones, and signalling molecules. Beta-oxidation occurs in the peroxisomes and mitochondria, the latter of which is depicted here. Whether beta-oxidation starts in the mitochondria or the peroxisome depends on the length of the fatty acid. Medium to long chain fatty acids go directly to the mitochondria, whereas very long chain fatty acids (>22 carbons) may be first metabolized down to octanyl-CoA in the peroxisomes and then transported to the mitochondria for the remainder of the oxidation. Beta-oxidation begins with activation of fatty acids by an acyl-coenzyme A synthetase. ATP is used to produce reactive fatty acyl adenylate that can then react with coenzyme A to produce a fatty acyl-CoA. Short and medium chain fatty acids can enter the mitochondria directly via diffusion where they are activated in the mitochondrial matrix by acyl-coenzyme A synthetases. In the first step of the beta-oxidation cycle, a double bond between C-2 and C-3 is formed, producing a trans-Δ2-enoyl-CoA. This is catalyzed by acyl-CoA-dehydrogenases in the mitochondria, which have forms specific to the different lengths of fatty acids. In the second step, enoyl CoA hydratase hydrates the newly formed double bond between C-2 and C-3, producing an L-beta-hydroxyacyl CoA. Next, L-beta-hydroxyacyl CoA dehydrogenase converts the hydroxyl group into a keto group, producing a beta-ketoacyl CoA. In the fourth and final step, the enzyme beta-ketothiolase cleaves the β-ketoacyl CoA and inserts the thiol group of another CoA between C-2 and C-3, reducing the acyl-CoA by 2 carbons and generating acetyl-CoA. The final two steps also have enzymatic forms specific to short chain fatty acids. Additionally, there is a trifunctional protein complex with enzymatic activity capable of performing all of the final 3 steps (hydratase, dehydrogenase, thiolase) in medium to very long chain fatty acids. This four step cycle repeats, removing 2 carbons from the fatty acid each time until it becomes acetyl-CoA. Acetyl-CoA is necessary for the citric acid cycle, among other cellular processes.


Pw000456 View Pathway

DNA Replication Fork

DNA is composed of two long and complementary strands, with a backbone on the outside and nucleotides in the middle. During replication the two strands of DNA separate; the resulting structure is called the replication fork. The replication fork forms because enzymes called helicases surround the DNA strands and break the hydrogen bonds which hold them together. The result is that two long branches, almost like fork prongs, each of which is a DNA strand. Replication of DNA has two main different processes. Because DNA is replicated in the 5' to 3' direction, and because both DNA strands in the replication fork are negative mirror images of each other, and because the replication fork is created on only one direction down the length of the DNA, two types of replication strands are formed: the leading and the lagging strand. These strands are so named by the way in which DNA polymerase reads the original DNA strand and attaches the complementary nucleotides as it makes its way along the chain. Because the direction of the movement of the replication fork, and the direction of the addition of nucleotides in the leading strand is the same, the process is continuous.That is, a polymerase is able to read the DNA and add the matching nucleotide bases to it continuously. In prokaryotes DNA polymerase III is responsible for creating the leading strand. The lagging strand is oriented in the opposite direction to the leading strand. Thus, replication of the lagging strand occurs in the opposing direction to that of the leading strand and the replication fork. As a result, replication of the lagging strand is a slower and more complicated process than that of the leading strand. Thus it is seen to lag behind the leading strand (hence the name).


Pw000153 View Pathway

Lactose Degradation

Lactose degradation (Lactose metabolism) shows the breakdown of alpha lactose into its constituent sugars, which are then utilized by the body as an energy source. Alpha-Lactose is the major sugar present in milk and the main source of energy supplied to the newborn mammalian in its mother’s milk. Lactose is also an important osmotic regulator of lactation. It is digested by the intestinal lactase, an enzyme expressed in newborns. Its activity declines following weaning. Lactase hydrolyzes alpha lactose into D-glucose and D-galactose, which are actively transported into the intestinal epithelial cells via the SGLT1 (GLUT1) cotransporter. GLUT1 actively transports glucose and galactose with 2 sodium ions. A sodium/potassium ATPase makes ATP by moving three sodium ions to the blood per two potassium ions that cross into the epithelial cell, giving the GLUT1 transporter energy to work. D-glucose and D-galactose diffuse into the blood, facilitated by the SLC2A2 transporter on the basolateral membrane on the intestinal epithelial cells. The sugars are then transported to liver.
Showing 71 - 80 of 48700 pathways