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Showing 31 - 40 of 49833 pathways
SMPDB ID Pathway Chemical Compounds Proteins

SMP0000035

Pw000145 View Pathway
Metabolic

Bile Acid Biosynthesis

A bile acids life begins as cholesterol is catabolized, as bile acid is a derivative of cholesterol. This pathway occurs in the liver, beginning with cholesterol being converted to 7a-hydroxycholesterol through the enzyme cholesterol-7-alpha-monooxygenase, after being transported into the liver cell. 7a-hydroxycholesterol then becomes 7a-hydroxy-cholestene-3-one, which is made possible by the enzyme 3-beta-hydroxysteroid dehydrogenase type 7. 7a-hydroxy-cholestene-3-one then is used in two different chains of reactions. The first, continuing in the liver, uses the enzyme 3-oxo-5-beta-steroid-4-deydrogenase to become 7a-hydroxy-5b-cholestan-3-one. After that, aldo-keto reductase family 1 member C4 is used to create 3a,7a-dihydroxy-5b-cholestane. In the mitochondria of the cell, sterol 26-hydroxylase converts 3a,7a-dihydroxy-5b-cholestane to 3a,7a,26-trihydroxy-5b-cholestane, which is then converted to 3a,7a-dihydroxy-5b-cholestan-26-al by the same enzyme used in the previous reaction. This enzyme is used another time, to create 3a,7a-dihydroxycoprostanic acid. Then, bile acyl-CoA synthetase teams up with 3a,7a-dihydroxycoprostanic acid to create 3a,7a-dihydroxy-5b-cholestanoyl-CoA. 3a,7a-dihydroxy-5b-cholestanoyl-CoA remains intact while alpha-methylacyl-CoA racemase moves it along through the peroxisome. Peroxisomal acyl coenzyme A oxidase 2 converts 3a,7a-dihydroxy-5b-cholestanoyl-CoA into 3a,7a-dihydoxy-5b-cholest-24-enoyl-CoA. With the help of water, peroxisomal multifunctional enzyme type 2 turns 3a,7a-dihydoxy-5b-cholest-24-enoyl-CoA into 3a,7a,24-trihydoxy-5b-cholestanoyl-CoA. This compound then uses peroxisomal multifunctional enzyme type 2 to create chenodeoxycholoyl-CoA. From there, propionyl-CoA and chenodeoxycholoyl-CoA join forces and enlist the help of non-specific lipid transfer protein to further chenodeoxycholoyl-CoAâ€TMs journey in the peroxisome. It is then transported back into intracellular space, where after its used in 3 different reactions, its derivatives interact with intestinal microflora in the extracellular space to become lithocholyltaurine, lithocholic acid glycine conjugate, and lithocholic acid. Revisiting 7a-hydroxy-cholestene-3-one, the second chain of reactions it is involved in follows a similar path as the first, moving through the mitochondria, endoplasmic reticulum and peroxisome until choloyl-CoA is formed, which then is used in three reactions so that its derivatives may leave the cell to interact with intestinal microflora and become taurodeoxycholic acid, deoxycholic acid glycine conjugate and deoxycholic acid. There are two more important components of this pathway, both depicting the breakdown of cholesterol into bile acid. These components of the pathway occur in the endoplasmic reticulum membrane, although 2 enzymes, 25-hydroxycholesterol 7-alpha-hydroxylase and sterol 26 hydroxylase, are found in the mitochondria. Bile acids play a very important part in the digestion of foods, and are responsible for the absorption of water soluble vitamins in the small intestine. Bile acids also help absorb fats into the small intestine, a crucial part of any vertebrates diet.

SMP0000036

Pw000019 View Pathway
Metabolic

D-Arginine and D-Ornithine Metabolism

D-Amino acids have been show to be present in high concentrations in humans and play a role in biological functions. D-Amino may have negative effects as they can be found in some bacteria or form spontaneously in certain reactions. D-Amino acid oxidase (DAAO) is one of the main enzymes that metabolize D-Amino acids via deamination. DAAO is highly specific towards D-amino acids and favours free neutral D-amino acids or those with hydrophobic, polar or aromatic groups. Acidic amino acids are not catalyze by DAOO.

SMP0000037

Pw000029 View Pathway
Metabolic

Lysine Degradation

The degradation of L-lysine happens in liver and it is consisted of seven reactions. L-Lysine is imported into liver through low affinity cationic amino acid transporter 2 (cationic amino acid transporter 2/SLC7A2). Afterwards, L-lysine is imported into mitochondria via mitochondrial ornithine transporter 2. L-Lysine can also be obtained from biotin metabolism. L-Lysine and oxoglutaric acid will be combined to form saccharopine by facilitation of mitochondrial alpha-aminoadipic semialdehyde synthase, and then, mitochondrial alpha-aminoadipic semialdehyde synthase will further breaks saccharopine down to allysine and glutamic acid. Allysine will be degraded to form aminoadipic acid through alpha-aminoadipic semialdehyde dehydrogenase. Oxoadipic acid is formed from catalyzation of mitochondrial kynurenine/alpha-aminoadipate aminotransferase on aminoadipic acid. Oxoadipic acid will be further catalyzed to form glutaryl-CoA, and glutaryl-CoA converts to crotonoyl-CoA, and crotonoyl-CoA transformed to 3-hydroxybutyryl-CoA. 3-Hydroxybutyryl-CoA will form Acetyl-CoA as the final product through the intermediate compound: acetoacetyl-CoA. Acetyl-CoA will undergo citric acid cycle metabolism. Carnitine is another key byproduct of lysine metabolism (not shown in this pathway).

SMP0000039

Pw000144 View Pathway
Metabolic

Glycerolipid Metabolism

The glycerolipid metabolism pathway describes the synthesis of glycerolipids such as monoacylglycerols (MAGs), diacylglycerols (DAGs), triacylglycerols (TAGs), phosphatidic acids (PAs), and lysophosphatidic acids (LPAs). The process begins with cytoplasmic 3-phosphoglyceric acid (a product of glycolysis). This molecule is dephosphorylated via the enzyme glycerate kinase to produce glyceric acid. Glyceric acid is then transformed to glycerol (via the action of aldehyde dehydrogenase and aldose reductase). The free, cytoplasmic glycerol can then be phosphorylated to glycerol-3-phosphate through the action of glycerol kinase. Glycerol-3-phosphate can then enter the endoplasmic reticulum where glycerol-3-phosphate acyltransferase (GPAT) may combine various acyl-CoA moieties (which donate acyl groups) to form lysophosphatidic (LPA) or phosphatidic acid (PA). The resulting phosphatidic acids can be dephosphorylated via lipid phosphate phosphohydrolase (also known as phosphatidate phosphatase) to produce diacylglycerols (DAGs). The resulting DAGs can be converted into triacylglycerols (TAGs) via the addition of another acyl group (contributed via acyl-CoA) and the action of 1-acyl-sn-glycerol-3-phosphate acyltransferase. Extracellularly, the triacylglycerols (TAGs) can be converted to monoacylglycerols (MAGs) through the action of hepatic triacylglycerol lipase. In addition to this cytoplasmic route of glycerolipid synthesis, another route via mitochondrial synthesis also exists. This route begins with glycerol-3-phosphate, which can be either derived from dihydroxyacetone phosphate (DHAP), a product of glycolysis (usually in the cytoplasm of liver or adipose tissue cells) or from glycerol itself. Glycerol-3-phosphate in the mitochondria is first acylated via acyl-coenzyme A (acyl-CoA) through the action of mitochondrial glycerol-3-phosphate acyltransferase to form lysophosphatidic acid (LPA). Once synthesized, lysophosphatidic acid is then acylated with another molecule of acyl-CoA via the action of 1-acyl-sn-glycerol-3-phosphate acetyltransferase to yield phosphatidic acid. Phosphatidic acid is then dephosphorylated to form diacylglycerol. Specifically, diacylglycerol is formed by the action of phosphatidate phosphatase (also known as lipid phosphate phosphohydrolase) on phosphatidic acid coupled with the release of a phosphate. The phosphatase exists as 3 isozymes. Diacylglycerol is a precursor to triacylglycerol (triglyceride), which is formed in the addition of a third fatty acid to the diacylglycerol by the action of diglyceride acyltransferase. Since diacylglycerol is synthesized via phosphatidic acid, it will usually contain a saturated fatty acid at the C-1 position on the glycerol moiety and an unsaturated fatty acid at the C-2 position. When the body uses stored fat as a source of energy, glycerol and fatty acids are released into the bloodstream. Fatty acids, stored as triglycerides in humans, are an important and a particularly rich source of energy. The energy yield from a gram of fatty acids is approximately 9 kcal/g (39 kJ/g), compared to 4 kcal/g (17 kJ/g) for carbohydrates. Since the hydrocarbon portion of fatty acids is hydrophobic, these molecules can be stored in a relatively anhydrous (water-free) environment. Fatty acids can hold more than six times the amount of energy than sugars on a weight basis. In other words, if you relied on sugars or carbohydrates to store energy, then you would need to carry 67.5 lb (31 kg) of glycogen to have the energy equivalent to 10 lb (5 kg) of fat.

SMP0000040

Pw000146 View Pathway
Metabolic

Glycolysis

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.

SMP0000041

Pw000040 View Pathway
Metabolic

Sulfate/Sulfite Metabolism

This pathway illustrates the conversion of sulfite to sulfate (via sulfate oxidase) and subsequent generation of adenylylsulfate (APS) via 3'-phosphoadenosine 5'-phosphosulfate synthase 2. APS is converted to phosphoadenylyl-sulfate (PAPS) via adenylylsulfate kinase. APS can also be regenerated from PAPS by 3'(2'), 5'-bisphosphate nucleotidase 1. PAPS is eventually converted to adenosine bisophosphate (PAP) through the action of several different enzymes including aryl sulfotransferase, chondroitin 4-sulfotransferase 13 and estrone sulfotransferase. The metabolism pathway in question is important for many reasons. Recall, that the sulfite ion is in fact the conjugate base of sulfurous acid. Moreover, this ion is found naturally in one of the worlds most popular beverages, wines. Beyond its natural occurence, sulfite ion had the property of stopping fermentation. As such, the addition of it to products such as wine can be used either as a preservative or to stop the fermentation process at a moment which is of interest. Finally, this preservation property goes beyond merely wines, and finds utility in dried fruits, potatoes, etc.

SMP0000043

Pw000159 View Pathway
Metabolic

Galactose Metabolism

This pathway depicts the conversion of galactose into glucose, lactose, and other sugar intermediates that may be used for a range of metabolic process. Dietary sources of galactose are numerous, but some of the primary sources in the human diet can be found in milk and milk derivative products. This is because during digestion milk sugars and lactose are hydrolyzed into their molecular constituents (e.g. base monosaccharides). In milk, such monosaccharides include glucose and galactose. The metabolism of the sugar Galactose is occurs almost entirely in the liver, and its metabolism is the consequence of three steps or reactions. First, the phosphorylation of galactose is induced by a special enzyme with the predictable name, galactokinase, and produces galactose 1-phosphate. Second, this biproduct and a second molecule, UDP-glucose, undergo a reaction which leads to the formation of UDP-galactose and glucose 1-phosphate. Thus, this reaction produces 1 molecule of glucose 1-phosphate per molecule of galactose. This is mediated by the enzyme galactose-1-phosphate uridylyltransferase (GALT). The resulting UDP-galactose undergoes epimerization to form UDP-glucose via the enzyme UDP-galactose-4 epimerase (GALE). The UDP-glucose can be used in glucuronidation reactions and other pentose interconversions. In a reaction shared with other pathways, glucose 1-phosphate can be converted into glucose 6-phosphate. There are other pathways associated with galactose metabolism. For instance, galactose can be converted into UDP-glucose by the sequential activities of GALK, UDP-glucose pyrophosphorylase 2 (UGP2), and GALE. Galactose can also be reduced to galactitol by NADPH-dependent aldose reductase. Also shown in this pathway is the conversion of glucose to galactose vis a vis a different process to the ones described earlier. This pathway, called hexoneogenesis, allows mammary glands to produce galactose. It should be noted however, that despite the existence of this pathway of galactose production, the vast majority of galactose in breast milk is actually the result of direct uptake up from the blood, whereas only a small fraction, ~35%, is the result of this de novo process hexoneogenesis. Also depicted in this pathway are the conversions of other dietary di and tri-saccharides (raffinose, manninotriose, melibiose, stachyose) into galactose, glucose and fructose as well as and dietary sugar alcohols (melibitol, galactinol, galactosylglycerol) into sorbitol, myo-inositol, and glycerol.

SMP0000044

Pw000043 View Pathway
Metabolic

Histidine Metabolism

Histidine, an amino acid, plays an important role in the creation of proteins. It is unique as an amino acid as it is needed for nucleotide formation. The biosynthesis of histidine in adults begins with the condensation of ATP and PRPP (phosphoribosyl pyrophosphate) to form n-5-phosphoribosyl 1-pyrophosphate (phosphoribosyl-ATP). It is also worth noting that PRPP is the beginning compound for purine and pyrimidine creation. Subsequent histidine biosynthetic steps (from phosphoribosyl-ATP onwards) are likely to occur in the intestinal microflora. Elimination of the phosphate and the opening of the ring in phosphoribosyl-ATP forms phosphoribosyl-forminino-5-aminoimidazole-4-carboxamide ribonucleotide(phosphoribosyl-forminino-AICAR-phosphate). This is subsequently converted to 5-phosphoribulosyl-forminino-5-aminoimidazole-4-carboxamide ribonucleotide. Cleavage of this compound creates imidazole glycerol phosphate and AICAR (aminoimidazolecarboxamide ribonucleotide) with glutamine being involved as an amino group donor. AICAR is used again through the purine pathway while the imidazole glycerol phosphate is converted to imidazole acetal phosphate. Transamination yields histidinol phosphate which is then turned into histidinol, and then, finally, to histidine. L-histidine is catalyzed by histidine ammonia-lyase into urocanic acid. This acid is then converted to 4-imidazolone-5-propionic acid by urocanate hydratase. 4-imidazolone-5-propionic acid is then converted to formiminoglutamic acid, using the enzyme probable imidazolonepropionase. One last reaction occurs to allow for glutamate metabolism, as formiminoglutamic acid is converted to l-glutamic acid through the use of formimidoyltransferase-cyclodeaminase. Histidine is also a precursor for carnosine biosynthesis(via carnosine synthase), with beta-alanine being the rate limiting precursor. Anserine can be synthesized either from carnosine via carnosine N-methyltransferase or from 1-methylhistidine via carnosine synthase. Inversely, cytosolic non-specific dipeptidase catalyzes the synthesis of 1-methylhistidine from anserine. Histidine is found in meat, seeds, nuts and whole grains. It is a very important amino acid in keeping a pH of 7 in the body, as it acts as a shuttle for protons to maintain a balance of acids and bases in the blood and different tissues.

SMP0000045

Pw000008 View Pathway
Metabolic

Amino Sugar Metabolism

Amino sugars are sugar molecules containing an amine group. They make up many polysaccharides including, glycosaminoglycans or mucopolysaccharides.

SMP0000046

Pw000160 View Pathway
Metabolic

Pyrimidine Metabolism

A group of heterocyclic aromatic organic compound, pyrimidines are similar in structure to benzene and pyridine and count the nucleic acids cytosine, thymine, and uracil as structural derivatives. The following pathway illustrates a many pyrimidine-associated processes such as nucleotide biosynthesis, degradation, and salvage. This pathway depicts a number of pyrimidine-related processes such as nucleotide biosynthesis, degradation, and salvage. For pyrimidine nucleotide biosynthesis, carbamoyl phosphate derived from the action of carbamoyl phosphate synthetase II (CPS-II) on glutamine and bicarbonate is converted into carbamoyl aspartate by aspartate transcarbamoylase, ATCase. Dihydroorotic acid is subsequently generated by the action of carbamoyl aspartate dehydrogenase on carbamoyl aspartate. Dihydroorotate dehydrogenase then converts dihydroorotic acid to orotic acid. From this point, orotate phosphoribosyltransferase incorporates phosphoribosyl pyrophosphate into (PRPP) to produce orotidine monophosphate. Orotidine-5’-phosphate carboxylase subsequently converts orotidine monophosphate into uridine monophosphate (UMP). UMP is further phosphorylated twice to form UTP; the first instance by uridylate kinase and the second instance by ubiquitous nucleoside diphosphate kinase. UTP moves into the CTP synthesis pathway with the action of CTP synthase which aminates the molecule. The uridine nucleotides are also feedstock for the de novo thymine nucleotides synthesis pathway. DeoxyUMP which is derived from UDP or CDP metabolism is transformed by the action of thymidylate synthase into deoxyTMP of which the methyl group is sourced from N5,N10-methylene THF. THF is subsequently regenerated from DHF via dihydrofolate reductase (DHFR) which is essential for the continuation of thymidylate synthase activity. Serine hydroxymethyl transferase then acts on THF to regenerate N5,N10-THF. Pyrimidine synthesis is a comparatively simpler process than purine synthesis due to a couple of factors; pyrimidine ring structure is assembled as a free base rather being derived from PRPP and there is no branch in the pyrimidine synthesis pathway as opposed to the purine synthesis pathway. For thymidine, the action of thymidine kinase on it (or alternatively deoxyuridine) plays an important role in what is referred to as the salvage pathway to dTTP synthesis. However to form dTMP, the action of thymine phosphorylase and thymidine kinase is required. For deoxycytidine, deoxycytidine kinase is required (deoxycytidine also acts on deoxyadenosine and deoxyguanosine). For uracil, UMP can be formed by the action of uridine phosphorylase and uridine kinase on uracil. Pyrimidine catabolism ultimately results in the formation of the waste products of urea, H2O, and CO2. The product of cytosine breakdown, uracil, can be broken down to N-carbamoyl-β-alanine which can be catabolized into β-alanine. The product of thymine breakdown is β-aminoisobutyrate. The transamination of α-ketoglutarate to glutamate requires both of these breakdown products (β-alanine and β-aminoisobutyrate) to act as amine group donors. The products of this transamination can move through a further reaction that produces malonyl-CoA or methylmalonyl-CoA, a precursor for succinyl-CoA which is used in the Krebs cycle.
Showing 31 - 40 of 49833 pathways