Decarboxylation and Carboxylation

2007 ◽  
Author(s):  
Perry A. Frey ◽  
Adrian D. Hegeman
Keyword(s):  
Carbon Dioxide ◽  
Tricarboxylic Acid Cycle ◽  
Pyruvate Dehydrogenase Complex ◽  
Radical Center ◽  
Ribulose Bisphosphate Carboxylase ◽  
Carboxylate Group ◽  
Leaving Group ◽  
Acetoacetate Decarboxylase ◽  
Metal Cofactor ◽  
Ketoacid Dehydrogenase

Decarboxylation is an essential process in catabolic metabolism of essentially all nutrients that serve as sources of energy in biological cells and organisms. The most widely known biological process leading to decarboxylation is the metabolism of glucose, in which all of the carbon in the molecule is oxidized to carbon dioxide by way of the glycolytic pathway, the pyruvate dehydrogenase complex, and the tricarboxylic acid cycle. The decarboxylation steps take place in thiamine pyrophosphate (TPP)–dependent α-ketoacid dehydrogenase complexes and isocitrate dehydrogenase. The latter enzyme does not require a coenzyme, other than the cosubstrate NAD+. Many other decarboxylations require coenzymes such as pyridoxal-5'-phosphate (PLP) or a pyruvoyl moiety in the peptide chain. Biological carboxylation is the essential process in the fixation of carbon dioxide by plants and of bicarbonate by animals, plants, and bacteria. Carboxylation by enzymes requires the action of biotin or a divalent metal cofactor, and it requires ATP when the carboxylating agent is the bicarbonate ion. The most prevalent enzymatic carboxylation is that of ribulose bisphosphate carboxylase (rubisco), which is responsible for carbon dioxide fixation in plants. The basic chemistry of decarboxylation is illustrated by mechanisms A to D in fig. 8-1. The mechanisms all require some means of accommodation for the electrons from the cleavage of the bond linking the carboxylate group to the α-carbon. In mechanism A, an electron sink at the β-carbon provides a haven for two electrons. Acetoacetate decarboxylase functions by this mechanism (see chap. 1), as well as PLP- and TPP-dependent decarboxylases (see chap. 3). In mechanism B, a leaving group at the β-carbon departs with two electrons. Mevalonate-5-diphosphate decarboxylate functions by mechanism B and is discussed in a later section. In mechanism C, a leaving group replaces the α-carbon and departs with a pair of electrons. A biological example is formate dehydrogenase, in which the leaving group is a hydride that is transferred to NAD+. In mechanism D, a free radical center is created adjacent to the α-carbon and potentiates the homolytic scission of the bond to the carboxylate group. Mechanism D requires secondary electron transfer processes to create the radical center and quench the formyl radical.

THE METABOLISM OF VALERATE-2-C14 BY UREDOSPORES OF WHEAT STEM RUST

1963 ◽  
Vol 41 (1) ◽  
pp. 1-7 ◽  
Author(s):  
H. Reisener ◽  
A. J. Finlayson ◽  
W. B. McConnell
Keyword(s):  
Carbon Dioxide ◽  
Glutamic Acid ◽  
Specific Activity ◽  
Tricarboxylic Acid Cycle ◽  
High Specific Activity ◽  
Water Soluble ◽  
Buffer Solution ◽  
Wheat Stem Rust ◽  
Carbon 14 ◽  
Water Soluble Extract

When uredospores of Puccinia graminis var. tritici race 15B were shaken in a medium containing M/30 phosphate buffer, pH 6.2, and valerate-2-C14, about 88% of the radioactivity was removed from the buffer solution in a period of 3 hours. About 40% of the carbon-14 taken from the buffer was found in a water-soluble extract of the spores and about 15% was respired as carbon dioxide. The result is compared with an earlier report that carbon 1 of valerate is more extensively released as carbon dioxide and less extensively incorporated into spore components. Glutamic acid, glutamine, γ-aminobutyric acid, and alanine of high specific activity were isolated. It was estimated from partial degradation that more than one-half of the carbon-14 of glutamic acid occurred in position 4 and that carbon 5 was very weakly labelled. Citric acid was also of high specific activity and was labelled predominantly in the internal carbons.It is concluded that respiring rust spores utilize externally supplied valerate by β-oxidation, which releases carbons 1 and 2 in a form which is metabolized as acetate by the tricarboxylic acid cycle.

Aktivierung von CO2 an Übergangsmetallzentren: Struktur und Reaktivität eines C-C-Kopplungsproduktes von CO2 und 2.3-Dimethylbutadien am elektronenreichen Nickel(O) / Activation of CO2 at Transition Metal Centers: Structure and Reactivity of a C-C-Coupling Product of CO2 and 2,3-Dimethylbutadiene at Electron-Rich Nickel(O)

1983 ◽  
Vol 38 (7) ◽  
pp. 835-840 ◽  
Author(s):  
Dirk Walther ◽  
Eckhard Dinjus ◽  
Joachim Sieler ◽  
Nguyen Ngoc Thanh ◽  
Wolfgang Schade ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Transition Metal ◽  
Carboxylic Acids ◽  
Coordination Sphere ◽  
Oxidative Coupling ◽  
Central Atom ◽  
Carboxylate Group ◽  
Metal Centers ◽  
X Ray ◽  
Unsaturated Carboxylic Acids

Carbon dioxide reacts with 2,3-dimethylbutadiene and bis-cyclooctadiene(1,5)-nickel(O) in the presence of N,N′-tetramethyl-ethylendiamine (tmeda) to form [(3,4,5-η3)-3,4-dimethyl-3-pentenylato](N,N′-tetramethyl-ethylendiamine)-nickel(II) as the product of the oxidative coupling of CO2 and the diene. The deep red complex crystallizes in the rhombic space group Pbca. The structure was determined by an X-ray analysis. The monodendate carboxylate group, the π-allyl system and a N-atom of tmeda form a planar coordination sphere around the central atom. The distance between Ni and the second N-atom of tmeda is very long (2.314 Å). Reaction of the complex with R−X (R: H, CH3) yield 3-unsaturated carboxylic acids; tmeda can be substituted by 2,2′-bipyridine.

The anaerobic end-products of helminths

Parasitology ◽  
1984 ◽  
Vol 88 (1) ◽  
pp. 179-198 ◽  
Author(s):  
J. Barrett
Keyword(s):  
Carbon Dioxide ◽  
Tricarboxylic Acid Cycle ◽  
Metabolic Cost ◽  
Product Formation ◽  
Carbon Dioxide Fixation ◽  
Functional Adaptation ◽  
Catabolic Pathways ◽  
Parasitic Helminths ◽  
Wide Range ◽  
End Products

Parasitic helminths belong to 3 separate phyla and there is always the danger of over-generalization. The various routes of anaerobic carbohydrate breakdown in parasitic helminth differ in their efficiencies and in their power output. The choice of end-product represents a compromise between these two conflicting forces. In addition, anaerobic pathways must satisfy the redox requirements of the tissues and provide a source of intermediates for synthetic reactions. Other considerations include the metabolic cost of excretion and the effect of end-products on protein structure and function. The different end-products may fulfil additional functions such as pH control, nitrogenous excretion, osmotic regulation, intracellular signalling and the suppression of host responses.A complicating factor in parasitic helminths is the existence of strains with different biochemical characteristics, including marked variation in end-product formation. The various tissues of the same parasite can also produce different end-products and the pattern of end-product formation is influenced by a variety of extrinsic and intrinsic factors such as age, sex, length of incubation, pO2 and availability of substrates. The catabolic pathways of helminths thus show considerable functional adaptation.There is, as yet, no satisfactory explanation as to why helminths do not make the maximum use of any oxygen available to them; and the contribution of oxidative processes to the overall energy balance of parasites probably varies from species to species.The catabolic pathways of adult helminths are derived from the anaerobic pathways present in their free-living relatives. Two main trends are evident, homolactic fermentation and carbon dioxide fixation, the latter involving a partial reverse tricarboxylic acid cycle. In general, homolactic fermentation is found in blood and tissue parasites, carbon dioxide fixation in gut parasites. These two types of metabolism are, of course, in no way absolute, most homolactic fermentors fix carbon dioxide to a certain extent and many parasites which fix carbon dioxide also produce lactate. Parasitic helminths possess a wide range of different catabolic pathways, superimposed upon which is a high degree of functional plasticity.

RESPIRATION OF INTACT CELLS OF A LOW-TEMPERATURE BASIDIOMYCETE

1966 ◽  
Vol 44 (8) ◽  
pp. 1077-1086 ◽  
Author(s):  
E. W. B. Ward
Keyword(s):  
Carbon Dioxide ◽  
Low Temperature ◽  
Oxygen Uptake ◽  
Respiratory Quotient ◽  
Tricarboxylic Acid Cycle ◽  
Carbon Sources ◽  
Endogenous Respiration ◽  
Starvation Period ◽  
Intact Cells ◽  
Exogenous Glucose

Conventional manometric procedures were used to measure oxygen uptake and carbon dioxide evolution by cells of a low-temperature basidiomycete. Total respiration was lowest and, relatively, endogenous respiration was highest in old cells. During starvation, endogenous respiration decreased but did so most rapidly in young cells. Maximum response to exogenous glucose was obtained from young cells after starvation. The respiratory quotient of endogenous respiration fell from 1.0 to approximately 0.7 during starvation, indicating a change in endogenous substrate. Conversely the respiratory quotient for exogenous respiration of added glucose increased with the starvation period. The level of oxidative assimilation of glucose was shown to be high (80-90%) and evidence was obtained that exogenous glucose did not suppress endogenous respiration.The optimum temperature for oxygen uptake was 25 °C, below which the Q10 was approximately 2. At 30 °C the rate, while initially highest, decreased during the 6-hour incubation period.The fungus utilized various compounds as carbon sources, but not sucrose in short-term experiments. Glucose, but not xylose was fermented, although the ratio of carbon dioxide to ethanol was not 1:1. Inhibition by fluoride, arsenite, iodoacetate, fluoroacetate, and malonate suggested that both glucose and xylose are respired at least in part by the Embden-Meyerof pathway and the tricarboxylic acid cycle. Endogenous respiration was only slightly affected by these inhibitors.

scholarly journals Enhancing Bioethanol Production by Deleting Phosphoenolpyruvate Synthase and ADP-Glucose Pyrophosphorylase, and Shunting Tricarboxylic Acid Cycle In Synechocystis Sp. PCC 6803

2021 ◽  
Author(s):  
E-Bin Gao ◽  
Penglin Ye ◽  
Haiyan Qiu ◽  
Junhua Wu ◽  
Huayou Chen
Keyword(s):  
Carbon Dioxide ◽  
Ethanol Production ◽  
Atmospheric Carbon Dioxide ◽  
Metabolic Flux ◽  
Tricarboxylic Acid Cycle ◽  
Tricarboxylic Acid ◽  
Acid Cycle ◽  
Photosynthetic Production ◽  
Engineered Strain ◽  
Pcc 6803

Abstract Background: The outstanding ability of directly assimilating carbon dioxide and sunlight to produce biofuels and chemicals impels photosynthetic cyanobacteria to become attractive organisms for the solution to the global warming crises and the world energy growth. The cyanobacteria-based method for ethanol production has been increasingly regarded as alternatives to food biomass-based fermentation and traditional petroleum-based production. Therefore, we engineered the model cyanobacterium Synechocystis sp. PCC 6803 to synthesize ethanol and optimized the biosynthetic pathways for improving ethanol production under photoautotrophic conditions.Results: In this study, we successfully achieved the photosynthetic production of ethanol from atmospheric carbon dioxide by an engineered mutant Synechocystis sp. PCC 6803 with over-expressing the heterologous genes encoding Zymomonas mobilis pyruvate decarboxylase (PDC) and Escherichia coli NADPH-dependent alcohol dehydrogenase (YqhD). The engineered strain was further optimized by an alternative engineering approach to improve cell growth, and increase the intracellular supply of the precursor pyruvate for ethanol production under photoautotrophic conditions. This approach includes blocking phosphoenolpyruvate synthetic pathway from pyruvate, removing glycogen storage, and shunting carbon metabolic flux of tricarboxylic acid cycle. Through redirecting and optimizing the metabolic carbon flux of Synechocystis, a high ethanol-producing efficiency was achieved (248 mg L-1 day-1) under photoautotrophic conditions with atmospheric CO2 as the sole carbon source. Conclusions: The engineered strain SYN009 (∆slr0301/pdc-yqhD, ∆slr1176/maeB) would become a valuable biosystem for photosynthetic production of ethanol and for expanding our knowledge of exploiting cyanobacteria to produce value chemicals directly from atmospheric CO2.

Structure, Carbon Dioxide Fixation and Metabolism of Stomata

1974 ◽  
Vol 1 (2) ◽  
pp. 221 ◽  
Author(s):  
CJ Pearson ◽  
FL Milthorpe
Keyword(s):  
Carbon Dioxide ◽  
Organic Acid ◽  
Co2 Fixation ◽  
Tricarboxylic Acid Cycle ◽  
Guard Cells ◽  
Tricarboxylic Acid ◽  
Light Illumination ◽  
Acid Cycle ◽  
Free Air ◽  
Positive Correlations

Studies were made of the structure and rates of CO2 fixation of epidermis and of changes in organic metabolites in Commelina cyanea during transition to light and dark in both normal and CO2-free air. Guard cells of C. cyanea and Vicia faba contain numerous highly developed mitochondria and starch-forming chloroplasts (mitochondria: chloroplast ratios of 3 : 1) in comparison to other epidermal cells with few mitochondria and rudimentary plastids without starch. Their rates of photosynthesis per chloroplast appeared to be at least as high as those of the mesophyll, but circumstantial evidence suggested that about half of current photosynthate was respired. The rate of CO2 fixation in the dark was about 0.2–0.4% of that in the light. Illumination caused an increase, and darkening a decrease, of aperture, malate, and organic acid 1% within the epidermis of C. cyanea. Darkening in CO2-free air was accompanied by only slight decreases in aperture and malate. There were close positive correlations between aperture and concentration of malate and between aperture and organic acid 14C. During opening, the rise in organic acid 14C was associated with a decline in amino acid 14C. It is suggested that organic acids may be formed through aspartate and possibly also from sugars and other amino acids entering the tricarboxylic acid cycle. Concentrations of sugars were not related to aperture although they increased on illumination and declined about 2 h after darkening. Polysaccharide concentrations in the epidermis of darkened leaves were similar to those in illuminated leaves.

Addition and Elimination

2007 ◽  
Author(s):  
Perry A. Frey ◽  
Adrian D. Hegeman
Keyword(s):  
Carboxylic Acid ◽  
Tricarboxylic Acid Cycle ◽  
The Body ◽  
Addition Reactions ◽  
Divalent Metal Ions ◽  
Major Barrier ◽  
Body Of Knowledge ◽  
Leaving Group ◽  
Leaving Groups ◽  
The Many

Most elimination and addition reactions in biochemistry proceed by α,β-elimination/addition mechanisms. In the case of elimination, the leaving group is β to an activating functional group in the substrate. The activating group may be the carbonyl group of a ketone or aldehyde, the iminium group derived from an aldehyde or ketone, or the acyl-carbonyl of a carboxylic acid or ester, and the proton is α to the activating group. Addition reactions in this class are the same reactions in reverse, and they follow the course of the Michael addition in organic chemistry. The generic process is illustrated in scheme 9-1. Substituents among the activating and leaving groups are diverse and are presumed to account for the significant variations among enzymes in the class. A few enzymes in this class catalyze elimination/addition without the assistance of a coenzyme or cofactor. They presumably incorporate sufficiently acidic (A—H) or basic (:B) amino acid side chains to catalyze the proton transfer processes, or they may stabilize carbanionic intermediates by low-barrier hydrogen bonding. Others employ divalent metal ions, pyridoxal-5'-phosphate (PLP), [4Fe–4S] centers, or NAD+ to facilitate the reactions. Cofactors and coenzymes increase the acidity of Cα—H or improve the propensity of the leaving group Y to depart. In most cases, the major barrier consists of increasing the acidity of the Cα—H group, which decreases the pKa. In a few cases, as when the leaving group is a carboxylic acid or a phosphate, no catalysis is required for it to depart. Limited space prevents discussion of the many enzymes that catalyze cofactor-independent α, β-eliminations. We address the actions of fumarase and crotonase because of the historic emphasis on the biochemical significance of these enzymes. Many other dehydratases and ammonia lyases also belong in this group. In the tricarboxylic acid cycle, fumarate arises from the action of succinate dehydrogenase, and fumarase (EC 4.2.1.2) catalyzes the addition of water to form S-malate. The reaction can be monitored in either direction, and in various studies, the kinetic parameters may be quoted as such (e.g., fumarate formation, or malate formation). The body of knowledge about the action of fumarase is surprisingly incomplete, given the importance of the enzyme in metabolism.

Sign in / Sign up

Export Citation Format

Share Document