Sandbox Reserved 470: Difference between revisions

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'''[[Glyceraldehyde-3-phosphate Dehydrogenase]]'''

<Structure load='3gpd' size='400' frame='true' align='right' caption='Glyceraldehyde-3-phosphate Dehydrogenase' scene='Insert optional scene name here' />(abbreviated as GAPDH or the less common G3PDH) (EC 1.2.1.12) ~37kDa catalyzes the sixth step of [glycolysis], a reversible cytosolic process in [eukaryotes] which involves the breakdown of glucose for energy and carbon molecules. Along with its role in glycolysis and [gluconeogenesis], recent research has determined that GAPDH is actually a multifunctional protein, as it has numerous defined, non-metabolic functions involved in multiple subcellular processes including [transcription] activation, ER to Golgi transportation, transcriptional control of histone [gene expression], nuclear membrane fusion, neuronal initiation of [apoptosis], recognizing fraudulently incorporated nucleotides in DNA, and maintaining [telomere] structures. Research also shows that it possibly has a direct involvement in cellular phenotype of human [neurodegenerative] disorders, especially those characterized by expansion of [CAG repeats].

<Structure load='3gpd' size='400' frame='true' align='right' caption='Glyceraldehyde-3-phosphate Dehydrogenase' scene='Insert optional scene name here' />(abbreviated as GAPDH or the less common G3PDH) (EC 1.2.1.12) ~37kDa is a well-known [enzyme] which catalyzes the sixth step of [glycolysis], a reversible cytosolic process in [eukaryotes] which involves the breakdown of glucose for energy and carbon molecules. Along with its role in glycolysis and [gluconeogenesis], recent research has determined that GAPDH is actually a multifunctional protein, as it has numerous defined, non-metabolic functions involved in multiple subcellular processes including [transcription] activation, ER to Golgi transportation, transcriptional control of histone [gene expression], nuclear membrane fusion, neuronal initiation of [apoptosis], recognizing fraudulently incorporated nucleotides in DNA, and maintaining [telomere] structures. Research also shows that it possibly has a direct involvement in cellular phenotype of human [neurodegenerative] disorders, especially those characterized by expansion of [CAG repeats].

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'''Role in Glycolysis:'''

*The Steps:

:In two coupled steps,

[[Image:GAPDH_PGK-rxn.gif]]

*The Steps:

GAPDH catalyzes the conversion of [glyceraldyhyde-3-phosphate] at carbon 1 to [1,3-bisphosphoglycerate] (1,3-BPG).

~~:In three coupled steps,~~ GAPDH catalyzes the conversion of [glyceraldyhyde-3-phosphate] at carbon 1 to [1,3-bisphosphoglycerate] (1,3-BPG)~~, by combining~~ phosphorylation with oxidation in an overall [endergonic] reaction (ΔG°'=+6.3 kJ/mol (+1.5 kcal/mol)). First, the oxidation of glyceraldyhyde-3-phosphate to D-glycerate 1,3-bisphosphate takes place, in which an aldehyde is converted to carboxylic acid ((ΔG°'=-50 kJ/mol (-12 kcal/mol))and NAD+ ([Nicotinamide adenine dinucleotide]), an important co-factor and [ligand] found bound to the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene> of GAPDH, is simultaneously reduced endergonically to NADH. This oxidation reaction is required for the initiation of the second reaction because it is highly [exergonic] and thus drives the endergonic second reaction ((ΔG°'=+50 kJ/mol (+12 kcal/mol)). In the second reaction a molecule of inorganic phosphate is transferred to a GAP intermediate to form a product with a high potential to transfer phosphates, 1,3-bisphosphoglycerate. ~~Without~~ GAPDH's use of covalent catalysis ~~in the second step~~, the energy barrier of the reaction would be too high and the reaction would be too slow for living organisms.

*The Reactions:

:The reaction involving the GAPDH enzyme combines phosphorylation with oxidation in an overall [endergonic] reaction. (ΔG°'=+6.3 kJ/mol (+1.5 kcal/mol)) First, the oxidation of glyceraldyhyde-3-phosphate to D-glycerate 1,3-bisphosphate takes place, in which an aldehyde is converted to carboxylic acid ((ΔG°'=-50 kJ/mol (-12 kcal/mol))and NAD+ ([Nicotinamide adenine dinucleotide]), an important co-factor and [ligand] found bound to the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene> of GAPDH, is simultaneously reduced endergonically to NADH. This oxidation reaction is required for the initiation of the second reaction because it is highly [exergonic] and thus drives the endergonic second reaction ((ΔG°'=+50 kJ/mol (+12 kcal/mol)). In the second reaction a molecule of inorganic phosphate is transferred to a GAP intermediate to form a product with a high potential to transfer phosphates, 1,3-bisphosphoglycerate.

*The Mechanism:

:The mechanism of GAPDH is mainly dependent the thiol functional group on a cysteine residue which lies within the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene>. This important thiol group acts as a [nucleophile], attacking the carbon on the aldehyde functional group of the [substrate], glyceraldehyde 3-phosphate, after it binds to GAPDH. The creation of a thiohemiacetal intermediate occurs from this oxidative reaction, which then loses a hydride to NAD+, which is also bound nearby, forming NADH and a carboxyl group from the aldehyde. Conservation of energy is maintained through this thioester linkage to the active site cysteine. The GAP intermediate is then used in the second step, where it is important to notice that without GAPDH's use of covalent catalysis, the energy barrier of the reaction would be too high and the reaction would be too slow for living organisms.

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'''Other roles:'''

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 '''[[Glyceraldehyde-3-phosphate Dehydrogenase]]'''
-<Structure load='3gpd' size='400' frame='true' align='right' caption='Glyceraldehyde-3-phosphate Dehydrogenase' scene='Insert optional scene name here' />(abbreviated as GAPDH or the less common G3PDH) (EC 1.2.1.12) ~37kDa catalyzes the sixth step of [glycolysis], a reversible cytosolic process in [eukaryotes] which involves the breakdown of glucose for energy and carbon molecules.  Along with its role in glycolysis and [gluconeogenesis], recent research has determined that GAPDH is actually a multifunctional protein, as it has numerous defined, non-metabolic functions involved in multiple subcellular processes including [transcription] activation, ER  to Golgi transportation, transcriptional control of histone [gene expression], nuclear membrane fusion, neuronal initiation of [apoptosis], recognizing fraudulently incorporated nucleotides in DNA, and maintaining [telomere] structures.  Research also shows that it possibly has a direct involvement in cellular phenotype of human [neurodegenerative] disorders, especially those characterized by expansion of [CAG repeats].
+<Structure load='3gpd' size='400' frame='true' align='right' caption='Glyceraldehyde-3-phosphate Dehydrogenase' scene='Insert optional scene name here' />(abbreviated as GAPDH or the less common G3PDH) (EC 1.2.1.12) ~37kDa  is a well-known [enzyme] which catalyzes the sixth step of [glycolysis], a reversible cytosolic process in [eukaryotes] which involves the breakdown of glucose for energy and carbon molecules.  Along with its role in glycolysis and [gluconeogenesis], recent research has determined that GAPDH is actually a multifunctional protein, as it has numerous defined, non-metabolic functions involved in multiple subcellular processes including [transcription] activation, ER  to Golgi transportation, transcriptional control of histone [gene expression], nuclear membrane fusion, neuronal initiation of [apoptosis], recognizing fraudulently incorporated nucleotides in DNA, and maintaining [telomere] structures.  Research also shows that it possibly has a direct involvement in cellular phenotype of human [neurodegenerative] disorders, especially those characterized by expansion of [CAG repeats].
 ----
 '''Role in Glycolysis:'''
+*The Steps:
+:In two coupled steps,
 [[Image:GAPDH_PGK-rxn.gif]]
-*The Steps:
+GAPDH catalyzes the conversion of [glyceraldyhyde-3-phosphate] at carbon 1 to [1,3-bisphosphoglycerate] (1,3-BPG).
-:In three coupled steps, GAPDH catalyzes the conversion of [glyceraldyhyde-3-phosphate] at carbon 1 to [1,3-bisphosphoglycerate] (1,3-BPG), by combining phosphorylation with oxidation in an overall [endergonic] reaction (ΔG°'=+6.3 kJ/mol (+1.5 kcal/mol)).  First, the oxidation of glyceraldyhyde-3-phosphate to D-glycerate 1,3-bisphosphate takes place, in which an aldehyde is converted to carboxylic acid ((ΔG°'=-50 kJ/mol (-12 kcal/mol))and NAD+ ([Nicotinamide adenine dinucleotide]), an important co-factor and [ligand] found bound to the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene> of GAPDH, is simultaneously reduced endergonically to NADH.  This oxidation reaction is required for the initiation of the second reaction because it is highly [exergonic] and thus drives the endergonic second reaction ((ΔG°'=+50 kJ/mol (+12 kcal/mol)).  In the second reaction a molecule of inorganic phosphate is transferred to a GAP intermediate to form a product with a high potential to transfer phosphates, 1,3-bisphosphoglycerate.  Without GAPDH's use of covalent catalysis in the second step, the energy barrier of the reaction would be too high and the reaction would be too slow for living organisms.
+*The Reactions:
+:The reaction involving the GAPDH enzyme combines phosphorylation with oxidation in an overall [endergonic] reaction.   (ΔG°'=+6.3 kJ/mol (+1.5 kcal/mol)) First, the oxidation of glyceraldyhyde-3-phosphate to D-glycerate 1,3-bisphosphate takes place, in which an aldehyde is converted to carboxylic acid ((ΔG°'=-50 kJ/mol (-12 kcal/mol))and NAD+ ([Nicotinamide adenine dinucleotide]), an important co-factor and [ligand] found bound to the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene> of GAPDH, is simultaneously reduced endergonically to NADH.  This oxidation reaction is required for the initiation of the second reaction because it is highly [exergonic] and thus drives the endergonic second reaction ((ΔG°'=+50 kJ/mol (+12 kcal/mol)).  In the second reaction a molecule of inorganic phosphate is transferred to a GAP intermediate to form a product with a high potential to transfer phosphates, 1,3-bisphosphoglycerate.
+*The Mechanism:
+:The mechanism of GAPDH is mainly dependent the thiol functional group on a cysteine residue which lies within the <scene name='Sandbox_Reserved_470/Active_site_gapdh/1'>active site</scene>.  This important thiol group acts as a [nucleophile], attacking the carbon on the aldehyde functional group of the [substrate], glyceraldehyde 3-phosphate, after it binds to GAPDH.  The creation of a thiohemiacetal intermediate occurs from this oxidative reaction, which then loses a hydride to NAD+, which is also bound nearby, forming NADH and a carboxyl group from the aldehyde.  Conservation of energy is maintained through this thioester linkage to the active site cysteine.  The GAP intermediate is then used in the second step, where it is important to notice that without GAPDH's use of covalent catalysis, the energy barrier of the reaction would be too high and the reaction would be too slow for living organisms.
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 '''Other roles:'''