Chapter 7. "Coenzymes and Vitamins" Reading Assignment
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Revised Glossary for AQA GCSE Biology Student Book
Biology Glossary amino acids small molecules from which proteins are A built abiotic factor physical or non-living conditions amylase a digestive enzyme (carbohydrase) that that affect the distribution of a population in an breaks down starch ecosystem, such as light, temperature, soil pH anaerobic respiration respiration without using absorption the process by which soluble products oxygen of digestion move into the blood from the small intestine antibacterial chemicals chemicals produced by plants as a defence mechanism; the amount abstinence method of contraception whereby the produced will increase if the plant is under attack couple refrains from intercourse, particularly when an egg might be in the oviduct antibiotic e.g. penicillin; medicines that work inside the body to kill bacterial pathogens accommodation ability of the eyes to change focus antibody protein normally present in the body acid rain rain water which is made more acidic by or produced in response to an antigen, which it pollutant gases neutralises, thus producing an immune response active site the place on an enzyme where the antimicrobial resistance (AMR) an increasing substrate molecule binds problem in the twenty-first century whereby active transport in active transport, cells use energy bacteria have evolved to develop resistance against to transport substances through cell membranes antibiotics due to their overuse against a concentration gradient antiretroviral drugs drugs used to treat HIV adaptation features that organisms have to help infections; they -
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. -
NADPH-Dependent A-Oxidation of Unsaturated Fatty Acids With
Proc. Natl. Acad. Sci. USA Vol. 89, pp. 6673-6677, August 1992 Biochemistry NADPH-dependent a-oxidation of unsaturated fatty acids with double bonds extending from odd-numbered carbon atoms (5-enoyl-CoA/A3,A2-enoyl-CoA isomerase/A3',52'4-dienoyl-CoA isomerase/2,4-dienoyl-CoA reductase) TOR E. SMELAND*, MOHAMED NADA*, DEAN CUEBASt, AND HORST SCHULZ* *Department of Chemistry, City College of the City University of New York, New York, NY 10031; and tJoined Departments of Chemistry, Manhattan College/College of Mount Saint Vincent, Riverdale, NY 10471 Communicated by Salih J. Wakil, April 13, 1992 ABSTRACT The mitochondrial metabolism of 5-enoyl- a recent observation of Tserng and Jin (5) who reported that CoAs, which are formed during the (3-oxidation of unsaturated the mitochondrial -oxidation of 5-enoyl-CoAs is dependent fatty acids with double bonds extending from odd-numbered on NADPH. Their analysis of metabolites by gas chroma- carbon atoms, was studied with mitochondrial extracts and tography/mass spectrometry led them to propose that the purified enzymes of (3-oxidation. Metabolites were identified double bond of 5-enoyl-CoAs is reduced by NADPH to yield spectrophotometrically and by high performance liquid chro- the corresponding saturated fatty acyl-CoAs, which are then matography. 5-cis-Octenoyl-CoA, a putative metabolite of further degraded by P-oxidation. linolenic acid, was efficiently dehydrogenated by medium- This report addresses the question of how 5-enoyl-CoAs chain acyl-CoA dehydrogenase (EC 1.3.99.3) to 2-trans-5-cis- are chain-shortened by P-oxidation. We demonstrate that octadienoyl-CoA, which was isomerized to 3,5-octadienoyl- 5-enoyl-CoAs, after dehydrogenation to 2,5-dienoyl-CoAs, CoA either by mitochondrial A3,A2-enoyl-CoA isomerase (EC can be isomerized to 2,4-dienoyl-CoAs, which are reduced by 5.3.3.8) or by peroxisomal trifunctional enzyme. -
Annotation Guidelines for Experimental Procedures
Annotation Guidelines for Experimental Procedures Developed By Mohammed Alliheedi Robert Mercer Version 1 April 14th, 2018 1- Introduction and background information What is rhetorical move? A rhetorical move can be defined as a text fragment that conveys a distinct communicative goal, in other words, a sentence that implies an author’s specific purpose to readers. What are the types of rhetorical moves? There are several types of rhetorical moves. However, we are interested in 4 rhetorical moves that are common in the method section of a scientific article that follows the Introduction Methods Results and Discussion (IMRaD) structure. 1- Description of a method: It is concerned with a sentence(s) that describes experimental events (e.g., “Beads with bound proteins were washed six times (for 10 min under rotation at 4°C) with pulldown buffer and proteins harvested in SDS-sample buffer, separated by SDS-PAGE, and analyzed by autoradiography.” (Ester & Uetz, 2008)). 2- Appeal to authority: It is concerned with a sentence(s) that discusses the use of standard methods, protocols, and procedures. There are two types of this move: - A reference to a well-established “standard” method (e.g., the use of a method like “PCR” or “electrophoresis”). - A reference to a method that was previously described in the literature (e.g., “Protein was determined using fluorescamine assay [41].” (Larsen, Frandesn and Treiman, 2001)). 3- Source of materials: It is concerned with a sentence(s) that lists the source of biological materials that are used in the experiment (e.g., “All microalgal strains used in this study are available at the Elizabeth Aidar Microalgae Culture Collection, Department of Marine Biology, Federal Fluminense University, Brazil.” (Larsen, Frandesn and Treiman, 2001)). -
Nicotinamide Adenine Dinucleotide Is Transported Into Mammalian
RESEARCH ARTICLE Nicotinamide adenine dinucleotide is transported into mammalian mitochondria Antonio Davila1,2†, Ling Liu3†, Karthikeyani Chellappa1, Philip Redpath4, Eiko Nakamaru-Ogiso5, Lauren M Paolella1, Zhigang Zhang6, Marie E Migaud4,7, Joshua D Rabinowitz3, Joseph A Baur1* 1Department of Physiology, Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States; 2PARC, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States; 3Lewis-Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, United States; 4School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom; 5Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States; 6College of Veterinary Medicine, Northeast Agricultural University, Harbin, China; 7Mitchell Cancer Institute, University of South Alabama, Mobile, United States Abstract Mitochondrial NAD levels influence fuel selection, circadian rhythms, and cell survival under stress. It has alternately been argued that NAD in mammalian mitochondria arises from import of cytosolic nicotinamide (NAM), nicotinamide mononucleotide (NMN), or NAD itself. We provide evidence that murine and human mitochondria take up intact NAD. Isolated mitochondria preparations cannot make NAD from NAM, and while NAD is synthesized from NMN, it does not localize to the mitochondrial matrix or effectively support oxidative phosphorylation. Treating cells *For correspondence: with nicotinamide riboside that is isotopically labeled on the nicotinamide and ribose moieties [email protected] results in the appearance of doubly labeled NAD within mitochondria. Analogous experiments with †These authors contributed doubly labeled nicotinic acid riboside (labeling cytosolic NAD without labeling NMN) demonstrate equally to this work that NAD(H) is the imported species. -
Chemistry and Functions of Proteins
TVER STATE MEDICAL UNIVERSITY BIOCHEMISTRY DEPARTMENT CHEMISTRY AND FUNCTIONS OF PROTEINS ILLUSTRATED BIOCHEMISTRY Schemes, formulas, terms and algorithm of preparation The manual for making notes of lectures and preparation for classes Tver, 2018 AMINO ACIDS -amino acids -These are organic acids with at least a minimum of one of its hydrogen atoms in the carbon chains substituted by an amino group.( Show the radical, amino and carboxyl groups) NH2 R | C – H | COOH Proteinogenous and Nonproteinogenous Amino acids - Major proteinogenous (standard) amino acids. (Give the names of each amino acid) R R 1 H – 2 CH3 – 12 HO – CH2 – (CH3)2 CH – 3 CH3 – CH – (CH3)2 CH – CH2 – 4 13 | CH3 – CH2 – CH – OH 5 | CH 3 6 14 HS – CH2 – HOOC – CH2 – 15 CH3 – S – CH2 – CH2 – 7 HOOC – CH2 – CH2 – NH2 | – C – H - | COOH 8 16 NH2 – CO – CH2 – 9 NH2 – CO – CH2 – CH2 – 17 10 NH2 – (CH2)3 – CH2 – 18 NH2 – C – NH – (CH2)3 – CH2 – 11 || NH 19 20 СООН NH -Glycine -Arginine Alanine -Serine -Valine -Threonine Leucine -Cysteine Isoleucine -Methionine Aspartic acid -Phenylalanine Glutamic acid -Tyrosine Asparagine -Tryptophan Glutamine -Histidine Lysine -Proline •Rare proteinogenous (standard) amino acids. ( Derivatives of lysine, proline and tyrosine) NH2 | H2N – CH2 – CH – (CH2)2 – CH | | OH COOH •Nonproteinogenous amino acids. (Name and show them) NH2 NH2 | | H2N – (CH2)3 – CH HS – (CH2)2 – CH | | COOH COOH NH2 | NH2 – C – HN – (CH2)3 – CH || | O COOH Ornithine Homocysteine Citrulline 2 CLASSIFICATION OF PROTEINOGENOUS (STANDARD) AMINO ACIDS Amino acids are classified by: *The structure of the radical (show); - aliphatic amino acids -monoaminodicarboxylic amino acids -amides of amino acids -diaminomonocarboxylic amino acids -hydroxy amino acids -sulfur-containing amino acids -cyclic (aromatic and heterolytic) amino acids *the polarity of the radical (show); -Non-polar (hydrophobic –Ala, Val, Leu, Ile, Trp, Pro.) -Polar (hydrophilic). -
Tricarboxylic Acid (TCA) Cycle Intermediates: Regulators of Immune Responses
life Review Tricarboxylic Acid (TCA) Cycle Intermediates: Regulators of Immune Responses Inseok Choi , Hyewon Son and Jea-Hyun Baek * School of Life Science, Handong Global University, Pohang, Gyeongbuk 37554, Korea; [email protected] (I.C.); [email protected] (H.S.) * Correspondence: [email protected]; Tel.: +82-54-260-1347 Abstract: The tricarboxylic acid cycle (TCA) is a series of chemical reactions used in aerobic organisms to generate energy via the oxidation of acetylcoenzyme A (CoA) derived from carbohydrates, fatty acids and proteins. In the eukaryotic system, the TCA cycle occurs completely in mitochondria, while the intermediates of the TCA cycle are retained inside mitochondria due to their polarity and hydrophilicity. Under cell stress conditions, mitochondria can become disrupted and release their contents, which act as danger signals in the cytosol. Of note, the TCA cycle intermediates may also leak from dysfunctioning mitochondria and regulate cellular processes. Increasing evidence shows that the metabolites of the TCA cycle are substantially involved in the regulation of immune responses. In this review, we aimed to provide a comprehensive systematic overview of the molecular mechanisms of each TCA cycle intermediate that may play key roles in regulating cellular immunity in cell stress and discuss its implication for immune activation and suppression. Keywords: Krebs cycle; tricarboxylic acid cycle; cellular immunity; immunometabolism 1. Introduction The tricarboxylic acid cycle (TCA, also known as the Krebs cycle or the citric acid Citation: Choi, I.; Son, H.; Baek, J.-H. Tricarboxylic Acid (TCA) Cycle cycle) is a series of chemical reactions used in aerobic organisms (pro- and eukaryotes) to Intermediates: Regulators of Immune generate energy via the oxidation of acetyl-coenzyme A (CoA) derived from carbohydrates, Responses. -
Enzymes Main Concepts: •Proteins Are Polymers Made up of Amino Acids
Biology 102 Karen Bledsoe, Instructor Notes http://www.wou.edu/~bledsoek/ Chapter 6, section 4 Topic: Enzymes Main concepts: • Proteins are polymers made up of amino acids. Enzymes are a category of proteins. • Enzymes are catalysts. They speed up the rate of a chemical reaction by reducing the activation energy, which is the energy needed to carry out the reaction. An example of a catalyst: if you put a lit match to a sugar cube, it’s hard to make the sugar catch fire. But if you rub a corner of the sugar cube with ash or charcoal, it catches more easily. The ash or charcoal acts as a catalyst. • Many important chemical reactions in living cells can happen spontaneously, but these reactions happen too rarely and too slowly to sustain life. Enzymes make the reactions happen more quickly and more often. • Some reactions happen too violently to support life. Sugar, when burned, released a lot of energy, but the energy is mostly heat. A rapid reaction like that would overheat our cells. Enzyme-controlled reactions can release energy from sugar in a way that captures most of the energy and loses less of the energy as heat, so that the energy is useful to the cell and does not overheat the cell. • The structure of enzymes allows them to carry out reactions. Each enzyme is shaped to carry out only one specific reaction. This is known as enzyme specificity. Amylase, for example, is an enzyme that breaks down starch into glucose. Amylase only breaks down starch; it does not break down any other molecule, nor does it build starch out of glucose. -
Acetyl Coenzyme a (Sodium Salt) 08/19
FOR RESEARCH ONLY! Acetyl Coenzyme A (sodium salt) 08/19 ALTERNATE NAMES: S-[2-[3-[[4-[[[5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy- hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3- dimethylbutanoyl]amino]propanoylamino]ethyl] ethanethioate, sodium; S-acetate coenzyme A, trisodium salt; Acetyl CoA, trisodium salt; Acetyl-S- CoA, trisodium salt CATALOG #: B2844-1 1 mg B2844-5 5 mg STRUCTURE: MOLECULAR FORMULA: C₂₃H₃₈N₇O₁₇P₃S•3Na MOLECULAR WEIGHT: 878.5 CAS NUMBER: 102029-73-2 APPEARANCE: A crystalline solid PURITY: ≥90% ~10 mg/ml in PBS, pH 7.2 SOLUBILITY: DESCRIPTION: Acetyl-CoA is an essential cofactor and carrier of acyl groups in enzymatic reactions. It is formed either by the oxidative decarboxylation of pyruvate, β-oxidation of fatty acids or oxidative degradation of certain amino acids. It is an intermediate in fatty acid and amino acid metabolism. It is the starting compound for the citric acid cycle. It is a precursor for the neurotransmitter acetylcholine. It is required for acetyltransferases and acyltransferases in the post-translational modification of proteins. STORAGE TEMPERATURE: -20ºC HANDLING: Do not take internally. Wear gloves and mask when handling the product! Avoid contact by all modes of exposure. REFERENCES: 1. Palsson-McDermott, E.M., and O'Neill, L.A. The Warburg effect then and now: From cancer to inflammatory diseases. BioEssays 35(11), 965-973 (2013). 2. Akram, M. Citric acid cycle and role of its intermediates in metabolism. Cell Biochemistry and Biophysics 68(3), 475-478 (2014). 3. Miura, Y. The biological significance of ω-oxidation of fatty acids. -
Coenzymes and Prosthetic Groups Nomenclature
Coenzymes and prosthetic groups Nomenclature • Cofactor: nonprotein component of enzymes • Cofactor - a co-catalyst required for enzyme activity • Coenzyme - a dissociable cofactor, usually organic • Prosthetic group - non-dissociable cofactor • Vitamin - a required micro-nutrient (organism cannot synthesize adequate quantities for normal health - may vary during life-cycle). – water soluble - not stored, generally no problem with overdose – lipid soluble - stored, often toxic with overdose. • Apoenzyme - enzyme lacking cofactor (inactive) • Holoenzyme - enzyme with cofactors (active) Vitamins are precursors of cofactors Why cofactors? Adenine Nucleotide Coenzymes All use the adenine nucleotide group solely for binding to the enzyme! • pyridine dinucleotides (NADH, NADPH) • flavin mono- and dinucleotides (FMN, FADH) • coenzyme A Nucleotide triphosphates • ATP hydrolysis – resonance stabilizes products – reactants cannot be resonance stabilized because of competition with adjacent bridging anhydrides – charge density greater on reactants than products Coenzyme A • Activation of acyl groups for transfer by nucleophilic attack • activation of the alpha- hydrogen of the acyl group for abstraction as a proton • Both these functions are mediated by the reactive -SH group on CoA, which forms thioesters Coenzyme A Nicotinic Acid/Nicotinamide Coenzymes • These coenzymes are two-electron carriers • They transfer hydride anion (H-) to and from substrates • Two important coenzymes in this class: • Nicotinamide adenine dinucleotide (NAD+) • Nicotinamide -
ATP Structure and Function
ATP: Universal Currency of Cellular Energy All living things including plants, animals, birds, insects, humans need energy for the proper functioning of cells, tissues and other organ systems. As we are aware that green plants, obtain their energy from the sunlight, and animals get their energy by feeding on these plants. Energy acts as a source of fuel. We, humans, gain energy from the food we eat, but how are the energy produced and stored in our body. A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery. When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The energy is used to do work by the cell, usually by the released phosphate binding to another molecule, activating it. For example, in the mechanical work of muscle contraction, ATP supplies the energy to move the contractile muscle proteins. Recall the active transport work of the sodium-potassium pump in cell membranes. -
Bioenergetics, ATP & Enzymes
Bioenergetics, ATP & Enzymes Some Important Compounds Involved in Energy Transfer and Metabolism Bioenergetics can be defined as all the energy transfer mechanisms occurring within living organisms. Energy transfer is necessary because energy cannot be created and it cannot be destroyed (1st law of thermodynamics). Organisms can acquire energy from chemicals (chemotrophs) or they can acquire it from light (phototrophs), but they cannot make it. Thermal energy (heat) from the environment can influence the rate of chemical reactions, but is not generally considered an energy source organisms can “capture” and put to specific uses. Metabolism, all the chemical reactions occurring within living organisms, is linked to bioenergetics because catabolic reactions release energy (are exergonic) and anabolic reactions require energy (are endergonic). Various types of high-energy compounds can “donate” the energy required to drive endergonic reactions, but the most commonly used energy source within cells is adenosine triphosphate (ATP), a type of coenzyme. When this molecule is catabolized (broken down), the energy released can be used to drive a wide variety of synthesis reactions. Endergonic reactions required for the synthesis of nucleic acids (DNA and RNA) are exceptions because all the nucleotides incorporated into these molecules are initially high-energy molecules as described below. The nitrogenous base here is adenine, the sugar is the pentose monosaccharide ribose and there are three phosphate groups attached. The sugar and the base form a molecule called a nucleoside, and the number of phosphate groups bound to the nucleoside is variable; thus alternative forms of this molecule occur as adenosine monophosphate (AMP) and adenosine diphosphate (ADP).