Lecture 32 & 33: Pyruvated Dehydrogenase & the TCA Cycle
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Amphibolic Nature of Krebs Cycle
Amphibolic nature of Krebs Cycle How what we are is what we eat • In aerobic organisms, the citric acid cycle is an amphibolic pathway, one that serves in both catabolic and anabolic processes. • Since the citric acid does both synthesis (anabolic) and breakdown (catabolic) activities, it is called an amphibolic pathway • The citric acid cycle is amphibolic (i.e it is both anabolic and catabolic in its function). • It is said to be an AMPHIBOLIC pathway, because it functions in both degradative or catabolic and biosynthetic or anabolic reactions (amphi = both) A central metabolic pathway or amphibolic pathway is a set of reactions which permit the interconversion of several metabolites, and represents the end of the catabolism and the beginning of anabolism • The KREBS CYCLE or citric acid cycle is a series of reactions that degrades acetyl CoA to yield carbon dioxide, and energy, which is used to produce NADH, H+ and FADH. • The KREBS CYCLE connects the catabolic pathways that begin with the digestion and degradation of foods in stages 1 and 2 with the oxidation of substrates in stage 3 that generates most of the energy for ATP synthesis. • The citric acid cycle is the final common pathway in the oxidation of fuel molecules. In stage 3 of metabolism, citric acid is a final common catabolic intermediate in the form of acetylCoA. • This is why the citric acid cycle is called a central metabolic pathway. Anaplerosis and Cataplerosis Anaplerosis is a series of enzymatic reactions in which metabolic intermediates enter the citric acid cycle from the cytosol. Cataplerosis is the opposite, a process where intermediates leave the citric acid cycle and enter the cytosol. -
Tbamitchodral L Alizaion of the 4Aminobutyrate-2-&Oxoglutarate
5d.em. J. (lWg77) 161,9O.-307 3O1 Printed in Great Britain Tbamitchodral L alizaion of the 4Aminobutyrate-2-&Oxoglutarate Transminase from Ox Brait By INGER SCHOUSDOE,* BIRGIT 1MO* and ARNE SCHOUSBOEt Department ofBDahemistry At andC*, University ofCopenhagen, 2200 Copenhagen M, Denark (Receved 4 June 1976) In order to determine the intramitochondrial location of 4-aminobutyrate transaminase, mitochondria were prepared from ox brain and freed from myelin and syiaptosomes by using conventional demitygradient-centrifugation techniques, and the purity was checked electron-microscopically. Iner and outer mimbrenes and matrix were prepared from the mitochondria by large-amplitude sweling and subsequent density-gradient centrfugationt The fractions were characterized by using both electron microscopy and differnt marker enzymes. From the specific activity of the 4-aminobutyrate transaminase in the submitochondrial fractions it was concluded that this enzyme is associated with the inner mitochondrial membrane. It is generally agreed that the 4-aminobutyrate-2- pyridoxal phosphate were from Sigma Chemical oxoglutarate transaminase (EC2.6.1.19) from brain is Co., St. Louis, MO, U.S.A. Ficoll was from mainly associated with free mitochondria (Salganicoff Pharmacia, Uppsala, Sweden, and crystallized & De Robertis, 1963, 1965; van den Berget al., 1965; bovine serum albumin was from BDH Biochemicals, van Kempen et at., 1965; Balazs et al., 1966; Poole, Dorset, U.K. 4-Amino[1-'4C]butyrate (sp. Waksman et al., 1968; Reijnierse et al., 1975), radioactivity 50mCi/mmol) and [1-14qtyramine (sp. and a preparation of a crude mitochondrial fraction radioactivity 9mCi/mmol) were obtained from was used by Schousboe et al. (1973) and Maitre et al. -
Alternative Acetate Production Pathways in Chlamydomonas Reinhardtii During Dark Anoxia and the Dominant Role of Chloroplasts in Fermentative Acetate Productionw
This article is a Plant Cell Advance Online Publication. The date of its first appearance online is the official date of publication. The article has been edited and the authors have corrected proofs, but minor changes could be made before the final version is published. Posting this version online reduces the time to publication by several weeks. Alternative Acetate Production Pathways in Chlamydomonas reinhardtii during Dark Anoxia and the Dominant Role of Chloroplasts in Fermentative Acetate ProductionW Wenqiang Yang,a,1 Claudia Catalanotti,a Sarah D’Adamo,b Tyler M. Wittkopp,a,c Cheryl J. Ingram-Smith,d Luke Mackinder,a Tarryn E. Miller,b Adam L. Heuberger,e Graham Peers,f Kerry S. Smith,d Martin C. Jonikas,a Arthur R. Grossman,a and Matthew C. Posewitzb a Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305 b Colorado School of Mines, Department of Chemistry and Geochemistry, Golden, Colorado 80401 c Stanford University, Department of Biology, Stanford, California 94305 d Clemson University, Department of Genetics and Biochemistry, Clemson, South Carolina 29634 e Colorado State University, Proteomics and Metabolomics Facility, Fort Collins, Colorado 80523 f Colorado State University, Department of Biology, Fort Collins, Colorado 80523 ORCID ID: 0000-0001-5600-4076 (W.Y.) Chlamydomonas reinhardtii insertion mutants disrupted for genes encoding acetate kinases (EC 2.7.2.1) (ACK1 and ACK2) and a phosphate acetyltransferase (EC 2.3.1.8) (PAT2, but not PAT1) were isolated to characterize fermentative acetate production. ACK1 and PAT2 were localized to chloroplasts, while ACK2 and PAT1 were shown to be in mitochondria. -
Exam #2 Review
Exam #2 Review Exam #2 will cover all the material that has been presented in class since Exam #1 and up through the metabolism introduction. This includes eukaryotic cell structure / function, transport, the closed system growth curve, enzymes and the introduction to metabolism. As always, it is best to begin by studying your notes and then after you feel your study is complete, take some time to look through this review. I. Eukaryotic cell structure / function A. There is a great deal of variance among eukaryotic cells - from protozoan cells to yeast cells to human cells. Fungi and protists (classically split into algae and protozoa) are eukaryotic representatives of the microbial world. B. Structure of the eukaryotic cell. 1. Cytoskeleton - provides structure and shape of cell, three components: a. Microtubules - largest element of cytoskeleton, composed of hollow cylinders of tubulin, form mitotic spindles, cilia and flagella and cell “highways”. b. Microfilaments - smallest element of cytoskeleton, composed of actin, involved in motion (pseudopod formation). c. Intermediate filaments - very stable structural element, play a supportive role, composed of proteins including keratin. Practice: Microfilaments a. are a component of the cytoskeleton. b. are long, twisted polymers of a protein called actin. c. form eukaryotic flagella. d. are made of tubulin. e. a and b f. c and d 2. Nucleus a. Bound by both an inner and outer membrane. The space between the two membranes is called the perinuclear space. The membrane has large nuclear pores through which proteins can pass (Why is this important?) b. Linear pieces of DNA are packaged by wrapping one and three quarters times around a histone octamer to form a core particle. -
Altered Expression and Function of Mitochondrial Я-Oxidation Enzymes
0031-3998/01/5001-0083 PEDIATRIC RESEARCH Vol. 50, No. 1, 2001 Copyright © 2001 International Pediatric Research Foundation, Inc. Printed in U.S.A. Altered Expression and Function of Mitochondrial -Oxidation Enzymes in Juvenile Intrauterine-Growth-Retarded Rat Skeletal Muscle ROBERT H. LANE, DAVID E. KELLEY, VLADIMIR H. RITOV, ANNA E. TSIRKA, AND ELISA M. GRUETZMACHER Department of Pediatrics, UCLA School of Medicine, Mattel Children’s Hospital at UCLA, Los Angeles, California 90095, U.S.A. [R.H.L.]; and Departments of Internal Medicine [D.E.K., V.H.R.] and Pediatrics [R.H.L., A.E.T., E.M.G.], University of Pittsburgh School of Medicine, Magee-Womens Research Institute, Pittsburgh, Pennsylvania 15213, U.S.A. ABSTRACT Uteroplacental insufficiency and subsequent intrauterine creased in IUGR skeletal muscle mitochondria, and isocitrate growth retardation (IUGR) affects postnatal metabolism. In ju- dehydrogenase activity was unchanged. Interestingly, skeletal venile rats, IUGR alters skeletal muscle mitochondrial gene muscle triglycerides were significantly increased in IUGR skel- expression and reduces mitochondrial NADϩ/NADH ratios, both etal muscle. We conclude that uteroplacental insufficiency alters of which affect -oxidation flux. We therefore hypothesized that IUGR skeletal muscle mitochondrial lipid metabolism, and we gene expression and function of mitochondrial -oxidation en- speculate that the changes observed in this study play a role in zymes would be altered in juvenile IUGR skeletal muscle. To test the long-term morbidity associated with IUGR. (Pediatr Res 50: this hypothesis, mRNA levels of five key mitochondrial enzymes 83–90, 2001) (carnitine palmitoyltransferase I, trifunctional protein of -oxi- dation, uncoupling protein-3, isocitrate dehydrogenase, and mi- Abbreviations tochondrial malate dehydrogenase) and intramuscular triglycer- CPTI, carnitine palmitoyltransferase I ides were quantified in 21-d-old (preweaning) IUGR and control IUGR, intrauterine growth retardation rat skeletal muscle. -
82870547.Pdf
ORIGINAL RESEARCH published: 06 March 2017 doi: 10.3389/fpls.2017.00291 Integrated Transcriptome and Metabolic Analyses Reveals Novel Insights into Free Amino Acid Metabolism in Huangjinya Tea Cultivar Qunfeng Zhang 1, 2, Meiya Liu 1, 2 and Jianyun Ruan 1, 2* 1 Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China, 2 Key Laboratory for Plant Biology and Resource Application of Tea, The Ministry of Agriculture, Hangzhou, China The chlorotic tea variety Huangjinya, a natural mutant, contains enhanced levels of free amino acids in its leaves, which improves the drinking quality of its brewed tea. Consequently, this chlorotic mutant has a higher economic value than the non-chlorotic Edited by: varieties. However, the molecular mechanisms behind the increased levels of free amino Basil J. Nikolau, Iowa State University, USA acids in this mutant are mostly unknown, as are the possible effects of this mutation Reviewed by: on the overall metabolome and biosynthetic pathways in tea leaves. To gain further John A. Morgan, insight into the effects of chlorosis on the global metabolome and biosynthetic pathways Purdue University, USA Vinay Kumar, in this mutant, Huangjinya plants were grown under normal and reduced sunlight, Central University of Punjab, India resulting in chlorotic and non-chlorotic leaves, respectively; their leaves were analyzed *Correspondence: using transcriptomics as well as targeted and untargeted metabolomics. Approximately Jianyun Ruan 5,000 genes (8.5% of the total analyzed) and ca. 300 metabolites (14.5% of the total [email protected] detected) were significantly differentially regulated, thus indicating the occurrence of Specialty section: marked effects of light on the biosynthetic pathways in this mutant plant. -
A New Mode of B Binding and the Direct Participation of A
Research Article 997 A new mode of B12 binding and the direct participation of a potassium ion in enzyme catalysis: X-ray structure of diol dehydratase Naoki Shibata1, Jun Masuda1, Takamasa Tobimatsu2, Tetsuo Toraya2*, Kyoko Suto1, Yukio Morimoto1 and Noritake Yasuoka1* Background: Diol dehydratase is an enzyme that catalyzes the adenosylcobalamin Addresses: 1Department of Life Science, Himeji (coenzyme B ) dependent conversion of 1,2-diols to the corresponding Institute of Technology, 1475-2 Kanaji, Kamigori, 12 Ako-gun, Hyogo 678-1297, Japan and 2Department aldehydes. The reaction initiated by homolytic cleavage of the cobalt–carbon bond of Bioscience and Biotechnology, Faculty of α β γ of the coenzyme proceeds by a radical mechanism. The enzyme is an 2 2 2 Engineering, Okayama University, Tsushima-Naka, heterooligomer and has an absolute requirement for a potassium ion for catalytic Okayama 700-8530, Japan. activity. The crystal structure analysis of a diol dehydratase–cyanocobalamin *Corresponding authors. complex was carried out in order to help understand the mechanism of action of E-mail: [email protected] this enzyme. [email protected] Results: The three-dimensional structure of diol dehydratase in complex with Key words: B12 enzyme, diol dehydratase, radicals, cyanocobalamin was determined at 2.2 Å resolution. The enzyme exists as a reaction mechanism, TIM barrel αβγ dimer of heterotrimers ( )2. The cobalamin molecule is bound between the Received: 16 March 1999 α and β subunits in the ‘base-on’ mode, that is, 5,6-dimethylbenzimidazole of Revisions requested: 7 April 1999 the nucleotide moiety coordinates to the cobalt atom in the lower axial position. -
Nutritional Vitamin B6 Deficiency Impairs Lipid Me Tabolism and Leads
J Nutr Sci Vitaminol, 47, 306-310, 2001 Xanthurenic Acid Inhibits Metal Ion-Induced Lipid Peroxidation and Protects NADP-Isocitrate Dehydrogenase from Oxidative Inactivation Keiko MURAKAMI,Masae ITO and Masataka YOSHINO* Department of Biochemistry, Aichi Medical University School of Medicine,Nagakute, Aichi 480-1195, Japan (ReceivedJanuary 26, 2001) Summary Vitamin B6 deficiency increases the lipid peroxidation and the synthesis of xanthurenic acid from tryptophan. Antioxidant properties of xanthurenic acid were exam ined in relation to the coordination of transition metals. Xanthurenic acid inhibited the for mation of thiobarbituric acid-reactive substances as a marker of iron-mediated lipid peroxi dation and copper-dependent oxidation of low density lipoprotein. NADP-isocitrate dehydro genase (EC 1.1.1.42), a principal NADPH-generating enzyme for the antioxidant defense system, was inactivated by reduced iron and copper, and xanthurenic acid protected the en zyme from the Fe2+-mediated inactivation. Xanthurenic acid may participate in the en hanced regeneration of reduced glutathione by stimulating the NADPH supply. Xanthurenic acid further enhanced the autooxidation of Fe2+ ion. Other tryptophan metabolites such as kynurenic acid and various quinoline compounds did not inhibit the lipid peroxidation and the inactivation of NADP-isocitrate dehydrogenase, and they showed little or no effect on the Fe2+ autooxidation. The antioxidant properties of xanthurenic acid are related to the metal-chelating activity and probably to the enhanced oxidation of reduced transition met als as a prooxidant, and this action may be due to the electron deficient nature of this com pound. Key Words xanthurenic acid, antioxidant, LDL, NADP-isocitrate dehydrogenase, reactive oxygen species Nutritional vitamin B6 deficiency impairs lipid me Lipid peroxidation. -
ATP-Citrate Lyase Has an Essential Role in Cytosolic Acetyl-Coa Production in Arabidopsis Beth Leann Fatland Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2002 ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis Beth LeAnn Fatland Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Molecular Biology Commons, and the Plant Sciences Commons Recommended Citation Fatland, Beth LeAnn, "ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis " (2002). Retrospective Theses and Dissertations. 1218. https://lib.dr.iastate.edu/rtd/1218 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. ATP-citrate lyase has an essential role in cytosolic acetyl-CoA production in Arabidopsis by Beth LeAnn Fatland A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Plant Physiology Program of Study Committee: Eve Syrkin Wurtele (Major Professor) James Colbert Harry Homer Basil Nikolau Martin Spalding Iowa State University Ames, Iowa 2002 UMI Number: 3158393 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. -
Decarboxylation What Is Decarboxylation?
Decarboxylation What is decarboxylation? Decarboxylation is the removal of a carboxyl group when a compound is exposed to light or heat. A carboxyl group is a grouping of carbon, oxygen, and hydrogen atoms in the form of COOH. When a compound is decarboxylated, this group is released in the form of carbon dioxide. Decarboxylation of cannabinoids When considering the decarboxylation of cannabinoids, it is important to note that this reaction is what causes the neutral acidic cannabinoids to turn into the active cannabinoids found in most products on the market. Both the neutral and acidic cannabinoids are naturally found in the cannabis plant. The active cannabinoids that have psychoactive properties are what occur after decarboxylation. Below is the mechanism for the conversion of THCA to THC. https://www.leafscience.com/2017/04/13/what-is-thca/ Heating THCA converts it to THC by kicking off the carboxyl group seen on the right side of the THCA molecule. Once the carboxyl group is released from the THCA it forms carbon dioxide and the THC compound. The THC is now ready for use in different products and will provide the psychoactive effects that popularized this compound. This simple reaction is all it takes to convert the acidic cannabinoids to their active counterparts. Cannabinolic acid (CBDA) and CBD are both another example of this process. Decarboxylation process Light can start the decarboxylation process after a period of time, but heat is the more common element used. There are different methods to decarboxylate cannabis depending on user preference. In the industry, dabs, vapes and joints decarboxylate instantly when heat is applied to the product. -
Isocitrate Dehydrogenase Activity Assay Kit (MAK062)
Isocitrate Dehydrogenase Activity Assay Kit Catalog Number MAK062 Storage Temperature –20 C TECHNICAL BULLETIN Product Description Developer 1 vl Isocitrate dehydrogenase (IDH) catalyzes the Catalog Number MAK062E conversion of isocitrate to -ketoglutarate. In eukaryotes, there are three isozymes of IDH, the IDH Positive Control (NADP+) 20 L mitochondrial IDH2 and IDH3, and the cytoplasmic/ Catalog Number MAK062F peroxisomal IDH1. All three IDH family members require the presence of a divalent cation (Mg2+ or Mn2+) NADH Standard, 0.5 mole 1 vl and either the electron-accepting cofactor NADP+ (IDH1 Catalog Number MAK062G and IDH2) or NAD+ (IDH3) for their enzymatic activity. IDH1 and IDH2 mutations resulting in neomorphic Reagents and Equipment Required but Not enzymatic activity are found in certain cancers such as Provided. glioblastoma, acute myeloid leukemia, and colon 96 well flat-bottom plate – It is recommended to use cancer. This neoactivity shows a change in the clear plates for colorimetric assays. substrate specificity resulting in the conversion of Spectrophotometric multiwell plate reader -ketoglutarate to 2-hydroxyglutarate. Mutations in IDH family members are also associated with Ollier disease Precautions and Disclaimer and Maffucci syndrome. This product is for R&D use only, not for drug, household, or other uses. Please consult the Material The Isocitrate Dehydrogenase Activity Assay kit Safety Data Sheet for information regarding hazards provides a simple and direct procedure for measuring and safe handling practices. + + + NADP -dependent, NAD -dependent, or both NADP + and NAD -dependent IDH activity in a variety of Preparation Instructions samples. IDH activity is determined using isocitrate as Briefly centrifuge vials before opening. -
Optimization of the Decarboxylation Reaction in Cannabis
APPLICATION NOTE FT-IR Spectroscopy Authors: Dr. Markus Roggen1 Antonio M. Marelli1 Doug Townsend2 Ariel Bohman2 1Outco SanDiego, CA 2PerkinElmer, Inc. Shelton, CT. Optimization of the Decarboxylation Reaction Introduction The production of cannabis in Cannabis Extract extracts and oils for medicinal and recreational products has increased significantly in North America. This growth has been driven by both market demand in newly legalized states and patient demand for a greater diversity in cannabis products.1,2,3 Most cannabis extraction processes, independent of solvent or instrument choice, undergo a decarboxylation step whereby the carboxylic acid functional group is removed from the cannabinoids. The decarboxylation reaction converts the naturally occurring acid forms of the cannabinoids, e.g. tetrahydrocannabinolic acid (THCA) and cannabidiolic acid (CBDA), to their more potent neutral forms, e.g. tetrahydrocannabinol (THC) and cannabidiol (CBD). Because the carboxylic acid group is thermally labile, the industry typically applies a heat source, and at times a catalyst, to decarboxylate the cannabinoids. The heat-promoted decarboxylation reaction has been Decarboxylation Reaction discussed at length within the industry, but an extensive Decarboxylation was achieved by heating the cannabis extract in 4, 5, 6 literature search reveals very few papers on the process. a oil bath with a programmable hot plate. An overhead stirrer The data available represents a large spectrum of reaction was utilized to promote even heat distribution throughout the conditions, including a range in reaction temperature, time experiment. Oil bath and extract temperatures were recorded and instrumental setup. As such, there is a lack of universal every five minutes throughout the 80-minute heating process.