Munkácsy E. & Rea, S. L. the Paradox Of
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Catabolism Iii
Nitrogen Catabolism Glycogenolysis Protein Fat catabolism Catabolism Fatty Acid Amino-acid GlycolysisDegradation catabolism Pyruvate Oxidation Krebs' Cycle Phosphorylation Oxidative CATABOLISM III: Digestion and Utilization of Proteins • Protein degradation • Protein turnover – The ubiquitin pathway – Protein turnover is tightly regulated • Elimination of nitrogen – By fish, flesh and fowl – How is the N of amino acids liberated and eliminated? • How are amino acids oxidized for energy 1 Protein Catabolism Sources of AMINO ACIDS: •Dietary amino acids that exceed body’s protein synthesis needs •Excess amino acids from protein turnover (e.g., proteolysis and regeneration of proteins) •Proteins in the body can be broken down (muscle wasting) to supply amino acids for energy when carbohydrates are scarce (starvation, diabetes mellitus). •Carnivores use amino acids for energy more than herbivores, plants, and most microorganisms Protein Catabolism The Digestion Pathway • Pro-enzymes are secreted (zymogens) and the environment activates them by specific proteolysis. • Pepsin hydrolyzes protein into peptides in the stomach. • Trypsin and chymotrypsin hydrolyze proteins and larger peptides into smaller peptides in the small intestine. • Aminopeptidase and carboxypeptidases A and B degrade peptides into amino acids in the small intestine. 2 Protein Catabolism The Lysosomal Pathway • Endocytosis, either receptor-mediated, phagocytosis, or pinocytosis engulfs extra- cellular proteins into vesicles. • These internal vesicles fuse as an early endosome. • This early endosome is acidified by the KFERQ Substrates vATPase (“v” for vesicular). • Components that are recycled, like receptors, HSPA8 are sequestered in smaller vesicles to create Co-chaperones the multivesicular body (MVB), sometimes called a late endosome. • If set for degradation, it will fuse with a KFERQ primary lysosome (red) which contains many cathepsin-type proteases. -
Proteomic and Metabolomic Analyses of Mitochondrial Complex I-Deficient
THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 24, pp. 20652–20663, June 8, 2012 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Proteomic and Metabolomic Analyses of Mitochondrial Complex I-deficient Mouse Model Generated by Spontaneous B2 Short Interspersed Nuclear Element (SINE) Insertion into NADH Dehydrogenase (Ubiquinone) Fe-S Protein 4 (Ndufs4) Gene*□S Received for publication, November 25, 2011, and in revised form, April 5, 2012 Published, JBC Papers in Press, April 25, 2012, DOI 10.1074/jbc.M111.327601 Dillon W. Leong,a1 Jasper C. Komen,b1 Chelsee A. Hewitt,a Estelle Arnaud,c Matthew McKenzie,d Belinda Phipson,e Melanie Bahlo,e,f Adrienne Laskowski,b Sarah A. Kinkel,a,g,h Gayle M. Davey,g William R. Heath,g Anne K. Voss,a,h René P. Zahedi,i James J. Pitt,j Roman Chrast,c Albert Sickmann,i,k Michael T. Ryan,l Gordon K. Smyth,e,f,h b2 a,h,m,n3 David R. Thorburn, and Hamish S. Scott Downloaded from From the aMolecular Medicine Division, gImmunology Division, and eBioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, the bMurdoch Childrens Research Institute, Royal Children’s Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia, the cDépartement de Génétique Médicale, Université de Lausanne, 1005 Lausanne, Switzerland, the dCentre for Reproduction and Development, Monash Institute of Medical Research, Clayton, Victoria 3168, Australia, the hDepartment of Medical Biology -
Supplementary Materials
Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented. -
Effect of Dietary Protein on Lipid and Glucose Metabolism: Implications for Metabolic Health
Effect of dietary protein on lipid and glucose metabolism: implications for metabolic health Annemarie Rietman 34334 Rietman.indd 1 09-07-15 09:32 Thesis committee Promotors Prof. Dr F.J. Kok Professor of Nutrition and Health Wageningen University Prof. Dr D. Tomé Professor of Nutrition and Protein Metabolism AgroParisTech, France Co-promotor Dr M. Mensink Assistant professor, Division of Human Nutrition Other members Prof. Dr W.H. Hendriks, Wageningen University Prof. Dr E. Blaak, Maastricht University, The Netherlands Prof. L. Tappy, Université de Lausanne, Switzerland Dr R. Heiligenberg, Hospital ‘De Gelderse Vallei’, Ede, The Netherlands This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences). 34334 Rietman.indd 2 09-07-15 09:32 Effect of dietary protein on lipid and glucose metabolism: implications for metabolic health Annemarie Rietman Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 11 September 2015 at 4 p.m. in the Aula. 34334 Rietman.indd 3 09-07-15 09:32 Annemarie Rietman Effect of dietary protein on lipid and glucose metabolism: implications for metabolic health 160 pages PhD thesis, Wageningen University, Wageningen, NL (2015) With references, with summaries in English and Dutch ISBN 978-94-6257-348-2 34334 Rietman.indd 4 09-07-15 11:15 Abstract Background: Diet is an important factor in the development of the Metabolic Syndrome (Mets) and type 2 Diabetes Mellitus. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Gluconeogenesis 1
GLUCONEOGENESIS It is the process by which glucose molecules are produced from non- carbohydrate precursors, which include lactate, glucogenic amino acids, glycerol part of fat and propionyl CoA derived from odd chain fatty acids. Gluconeogenesis occurs mainly in the liver, and to a lesser extent in the kidney. The pathway is partly mitochondrial and partly cytoplasmic. 4 3 2 ! 1 Gluconeogenesis involves several enzymes of glycolysis, but it is not a reversal of glycolysis. The irreversible steps in glycolysis are circumvented by four enzymes which are designated as the key enzymes of gluconeogenesis, these enzymes are: 1. Pyruvate Carboxylase 1 http://cden.tu.edu.iq Tikrit University College of Dentistry Pyruvate in the cytoplasm enters the mitochondria. Then, carboxylation of pyruvate to oxaloacetate is catalysed by a mitochondrial enzyme, Pyruvate carboxylase. It needs the co-enzymes biotin and ATP. 2. Phosphoenol Pyruvate Carboxy Kinase (PEPCK) In the cytoplasm, PEPCK enzyme converts oxaloacetate to phosphoenol pyruvate by removing a molecule of CO2. GTP donates the phosphate. The net effect of these two reactions is the conversion of pyruvate to phosphoenol pyruvate. This circumvents the irreversible step 9 of glycolysis. Partial Reversal of Glycolysis The phosphoenol pyruvate undergoes further reactions catalyzed by the glycolytic enzymes to form fructose-1,6-bisphosphate (see glycolysis steps 8,7,6,5 and 4; all these reactions are freely reversible). 3. Fructose-1, 6-bisphosphatase Fructose-1, 6-bisphosphate is then converted by fructose 1,6- bisphosphatase to form fructose -6-phosphate. This will bypass the step of PFK reaction (see step 3 of glycolysis). Then fructose-6-phosphate is isomerized to glucose-6-phosphate by the freely reversible reaction catalyzed by hexose phosphate isomerase (step2 in glycolysis). -
Lipid Metabolism - 1
Lipid metabolism - 1. Catabolism of triacylglycerols, oxidation of fatty acids and glycerol. Ketogenesis. ASSOC. PROF. BILETS M.V. Lecture plan Catabolism of triacylglycerols in adipocytes of adipose tissue. Biosynthesis of triacylglycerols. Oxidation of glycerol: enzyme reactions, bioenergetics. Lipoproteins. Hyperlipoproteinemias. Oxidation of glycerol: enzyme reactions, bioenergetics. Oxidation of fatty acids (β-oxidation). Ketone bodies. Biosynthesis of fatty acids. Lipids are organic compounds, are nonpolar molecules, which are soluble only in nonpolar solvents and insoluble in water. Types of Lipids: Simple Lipids Esters of fatty acids with various alcohols. Fats: Esters of fatty acids with glycerol. Oils are fats in the liquid state Steroids (cholesterol) Complex Lipids Esters of fatty acids containing groups in addition to alcohol and a fatty acid. Phospholipids: These are lipids containing, in addition to fatty acids and alcohol, a phosphoric acid residue. They frequently have nitrogen-containing bases and other substituents, eg, in glycerophospholipids the alcohol is glycerol and in sphingophospholipids the alcohol is sphingosine. Glycolipids (glycosphingolipids): Lipids containing a fatty acid, sphingosine, and carbohydrate. Structure of triacylglycerol https://www.researchgate.net/figure/Triacylglycerol-TAG-structure-showing-glycerol-with- three-fatty-acids_fig1_316787887 Lipolysis is the metabolic pathway through which lipid triacylglycerols are hydrolyzed into a glycerol and three fatty acids. Occurs in adipocytes. Lipolysis -
The Postabsorptive State
Chapter 26 Lecture Outline See separate PowerPoint slides for all figures and tables pre- inserted into PowerPoint without notes. Copyright © McGraw-Hill Education. Permission required for reproduction or display. 1 Introduction • Nutrition is the starting point and the basis for all human form and function – The source of fuel that provides energy for all biological work – The source of raw materials for replacement of worn- out biomolecules and cells • Metabolism is the chemical change that lies at the foundation of form and function 26-2 Nutrition • Expected Learning Outcomes – Describe some factors that regulate hunger and satiety. – Define nutrient and list the six major categories of nutrients. – State the function of each class of macronutrients, the approximate amounts required in the diet, and some major dietary sources of each. – Name the blood lipoproteins, state their functions, and describe how they differ from each other. – Name the major vitamins and minerals required by the body and the general functions they serve. 26-3 Body Weight and Energy Balance • Weight—determined by the body’s energy balance – If energy intake and output are equal, body weight is stable – Gain weight if intake exceeds output – Lose weight if output exceeds intake – Weight seems to have a stable, homeostatic set point • Varies from person to person • Combination of heredity and environmental influences – 30% to 50% of variation in human weight is hereditary – Environmental factors such as eating and exercise habits account for the rest of the variation -
Branched Chain Amino Acid Catabolism Fuels Adipocyte Differentiation and Lipogenesis
CORE Metadata, citation and similar papers at core.ac.uk Provided by eScholarship - University of California UCLA UCLA Previously Published Works Title Branched-chain amino acid catabolism fuels adipocyte differentiation and lipogenesis. Permalink https://escholarship.org/uc/item/6zd459ds Journal Nature chemical biology, 12(1) ISSN 1552-4450 Authors Green, Courtney R Wallace, Martina Divakaruni, Ajit S et al. Publication Date 2016 DOI 10.1038/nchembio.1961 Peer reviewed eScholarship.org Powered by the California Digital Library University of California HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Chem Manuscript Author Biol. Author Manuscript Author manuscript; available in PMC 2016 May 18. Published in final edited form as: Nat Chem Biol. 2016 January ; 12(1): 15–21. doi:10.1038/nchembio.1961. Branched chain amino acid catabolism fuels adipocyte differentiation and lipogenesis Courtney R. Greena, Martina Wallacea, Ajit S. Divakarunib, Susan A. Phillipsc,d, Anne N. Murphyb, Theodore P. Ciaraldic,d, and Christian M. Metallo*,a,e aDepartment of Bioengineering, University of California–San Diego, La Jolla, CA 92093 bDepartment of Pharmacology, University of California–San Diego, La Jolla, CA 92093 cVeterans Affairs San Diego Healthcare System, San Diego, CA; Department of Medicine, University of California, San Diego, La Jolla, CA dMedicine, University of California, San Diego, La Jolla, CA eInstitute of Engineering in Medicine, University of California, San Diego, La Jolla, CA Abstract Adipose tissue plays important roles in regulating carbohydrate and lipid homeostasis, though less is known about the regulation of amino acid metabolism in adipocytes. Here we applied isotope tracing to pre–adipocytes and differentiated adipocytes to quantify the contributions of different substrates to tricarboxylic acid metabolism and lipogenesis. -
Supercomplexes of Prokaryotic Aerobic Respiratory Chains Escherichia Coli and Bacillus Subtilis Supramolecular Assemblies Pedro M.F
Supercomplexes of Prokaryotic Aerobic Respiratory Chains Escherichia coli and Bacillus subtilis supramolecular assemblies Pedro M.F. Sousa Dissertation presented to obtain the Ph.D degree in Biochemistry Instituto de Tecnologia Química e Biológica | Universidade Nova de Lisboa Instituto de Investigação Científica Tropical Oeiras, December, 2013 Supercomplexes of Prokaryotic Aerobic Respiratory Chains Escherichia coli and Bacillus subtilis supramolecular assemblies Pedro M.F. Sousa Dissertation presented to obtain the Ph.D degree in Biochemistry Instituto de Tecnologia Química e Biológica | Universidade Nova de Lisboa Instituto de Investigação Científica Tropical Supervisor: Ana M.P. Melo Co-supervisor: Miguel Teixeira Oeiras, December, 2013 From left to right: Prof. Miguel Teixeira, Dr. Lígia Saraiva, Prof. Carlos Romão, Prof. Thorsten Friedrich, Pedro Sousa, Dr. Margarida Duarte, Prof. João Arrabaça, Dr. Ana Melo. Instituto de Investigação Científica Tropical (IICT) Rua da Junqueira Nº86, 1º 1300-344 Lisboa Portugal Tel. (+351) 213 616 340 Instituto de Tecnologia Química e Biológica (ITQB) Av. da República Estação Agronómica Nacional 2780-157 Oeiras Portugal Tel. (+351) 214 469 323 The molecular cup is now empty. The time has come to replace the purely reductionist “eyes-down” molecular perspective with a new and genuinely holistic “eyes-up” view of the living world, one whose primary focus is on evolution, emergence, and biology’s innate complexity. Carl R.Woese (1928 – 2012) in “A new biology for a new century” Microbiology and Molecular Biology Reviews 68(2), 173 – 186 (2004) Acknowledgements The work summarized in this thesis is the product of several collaborations established during my research grant. It is with great appreciation that I would like to acknowledge the following groups and people: Ana Melo, my supervisor, for her endless support on my work. -
Biol 219 Lec 7 Fall 2016 Dr. Scott 1
Biol 219 Lec 7 Fall 2016 Dr. Scott Cellular Respiration: Harvesting Energy to form ATP Cellular Respiration and Metabolism Glucose Oxidation: The Central Metabolic Pathway Introducing “The Players” ATP glucose + 6 O2 → 6 CO2 + 6 H2O + energy heat Glucose primary substrate for cellular respiration ATP the “energy currency” molecule Pyruvate end product of glycolysis; branch point between 1. Glycolysis aerobic and anaerobic metabolism Lactate end product of anaerobic metabolism Acetyl CoA the 2-carbon shuttle; a key intermediate in aerobic metabolism 2. Citric Acid NAD+ oxidized coenzyme (also FAD) (Krebs) Cycle NADH reduced coenzyme (also FADH2): carrier of 2 high-energy electrons O2 the final electron acceptor in aerobic metabolism 3. Electron CO2 end product of aerobic metabolism Transport H2O other end product of aerobic metabolism Chain 1 Biol 219 Lec 7 Fall 2016 Dr. Scott Glycolysis Summary of Glycolysis 1. Energy investment steps: input 2 ATP Glucose + 2 ADP + 2 NAD+ 2 Pyruvate + 2 ATP + 2 NADH 2. Cleavage step: 6C → 2 x 3C (Aerobic - requires O2) 3. Energy capture steps: Net yield = 2 ATP an d 2 NADH (4 high-energy e-) X 2 Anaerobic Metabolism: Aerobic Metabolism: The Lactic Acid Pathway Transition from Glycolysis to the Citric Acid Cycle • Pyruvate enters the matrix of • Pyruvate is converted to Lactate the mitochondria + • NADH is converted back to NAD • Pyruvate is broken down into which is needed for glycolysis a 2-carbon unit of Acetyl CoA • Net yield is 2 ATP • Yields 1 NADH and 1 CO2 is produced • Acetyl CoA transfers the 2C unit into the Citric Acid Cycle 2 Biol 219 Lec 7 Fall 2016 Dr. -
Ch 24 Metabolism and Nutrition 24-1 Metabolism Metabolism Refers to All Chemical Reactions in an Organism
Ch 24 Metabolism and Nutrition 24-1 Metabolism Metabolism refers to all chemical reactions in an organism Cellular Metabolism . Includes all chemical reactions within cells . Provides energy to maintain homeostasis and perform essential functions Cells break down organic molecules to obtain energy . Used to generate ATP . Most energy production takes place in mitochondria Metabolism Metabolic turnover . Periodic replacement of cell’s organic components Growth and cell division Special processes, such as secretion, contraction, and the propagation of action potentials Organic Nutrients Nutrients- carbohydrates, proteins, fats, water, vitamins, minerals Are building blocks cell need for: Homeostasis – include: . Energy . Growth, maintenance, and repair Catabolism (digestion, repair, maintenance) . Is the breakdown of organic substrates . Releases energy used to synthesize high-energy compounds (e.g., ATP) Anabolism (growth, maintenance) . Is the synthesis of new organic molecules Organic Nutrients Functions (all these functions need ATP for energy) . Perform structural maintenance and repairs . Support growth . Produce secretions . Store nutrient reserves Glycogen - Most abundant storage carbohydrate . A branched chain of glucose molecules Triglycerides- Most abundant storage lipids . Primarily of fatty acids Proteins - Most abundant organic components in body . Perform many vital cellular functions Cellular Energy Acetyl CoA- 2 (C) 24-2 Carbohydrate Metabolism Generates ATP and other high-energy compounds by breaking down (catabolism) carbohydrates: glucose + oxygen carbon dioxide + water Glucose Breakdown . Occurs in small steps . Glycolysis . Breaks down glucose in cytosol into smaller molecules used by mitochondria . Does not require oxygen: anaerobic reaction Aerobic Reactions . Also called aerobic metabolism or cellular respiration . Occur in mitochondria, consume oxygen, and produce ATP Carbohydrate Metabolism Glycolysis . Breaks 6-carbon glucose .