Terpenoids and Their Biosynthesis in Cyanobacteria
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Enzyme Activity and Assays Introductory Article
Enzyme Activity and Assays Introductory article Robert K Scopes, La Trobe University, Bundoora, Victoria, Australia Article Contents . Factors that Affect Enzymatic Analysis Enzyme activity refers to the general catalytic properties of an enzyme, and enzyme assays . Initial Rates and Steady State Turnover are standardized procedures for measuring the amounts of specific enzymes in a sample. Measurement of Enzyme Activity . Measurement of Protein Concentration Factors that Affect Enzymatic Analysis . Methods for Purifying Enzymes . Summary Enzyme activity is measured in vitro under conditions that often do not closely resemble those in vivo. The objective of measuring enzyme activity is normally to determine the exactly what the concentration is (some preparations of amount of enzyme present under defined conditions, so unusual substrates may be impure, or the exact amount that activity can be compared between one sample and present may not be known). This is because the rate another, and between one laboratory and another. The measured varies with substrate concentration more rapidly conditions chosen are usually at the optimum pH, as the substrate concentration decreases, as can be seen in ‘saturating’ substrate concentrations, and at a temperature Figure 1. In most cases an enzyme assay has already been that is convenient to control. In many cases the activity is established, and the substrate concentration, buffers and measured in the opposite direction to that of the enzyme’s other parameters used previously should be used again. natural function. Nevertheless, with a complete study of There are many enzymes which do not obey the simple the parameters that affect enzyme activity it should be Michaelis–Menten formula. -
Opportunities for Catalysis in the 21St Century
Opportunities for Catalysis in The 21st Century A Report from the Basic Energy Sciences Advisory Committee BASIC ENERGY SCIENCES ADVISORY COMMITTEE SUBPANEL WORKSHOP REPORT Opportunities for Catalysis in the 21st Century May 14-16, 2002 Workshop Chair Professor J. M. White University of Texas Writing Group Chair Professor John Bercaw California Institute of Technology This page is intentionally left blank. Contents Executive Summary........................................................................................... v A Grand Challenge....................................................................................................... v The Present Opportunity .............................................................................................. v The Importance of Catalysis Science to DOE.............................................................. vi A Recommendation for Increased Federal Investment in Catalysis Research............. vi I. Introduction................................................................................................ 1 A. Background, Structure, and Organization of the Workshop .................................. 1 B. Recent Advances in Experimental and Theoretical Methods ................................ 1 C. The Grand Challenge ............................................................................................. 2 D. Enabling Approaches for Progress in Catalysis ..................................................... 3 E. Consensus Observations and Recommendations.................................................. -
Chemical Intra-Mediterranean Variation and Insecticidal Activity of Crithmum Maritimum
Chemical Intra-Mediterranean Variation and Insecticidal Activity of Crithmum maritimum Maria Tsoukatou3, Christina Tsitsimpikoub, Constantinos Vagias 3 and Vassilios Roussis3’* a School of Pharmacy, Department of Pharmacognosy, University of Athens, Panepistimioupolis Zografou, Athens 15771, Greece. Fax: ++3017274592. E-mail: [email protected] b Doping Control Laboratory of Athens, Olympic Athletic Centre of Athens “Spiros Louis”, Kifissias 37, 15123, Maroussi, Greece * Author of correspondence and reprint requests Z. Naturforsch. 56c, 211-215 (2001); received October 27/December 7, 2000 Crithmum maritimum, Terpenes, Dillapiole, Ant Repellency The chemical composition of the volatile metabolites of Crithmum maritimum harvested from several geographic localities along the Mediterranean coasts was studied by GC and GC-MSD. The major oil constituents were found to be dillapiole, y-terpinene, sabinene, limo- nene and ß-phellandrene. The Western populations were richer in dillapiole, whereas the Southern collections were characterized by increased amounts of thymol methyl ether and y-terpinene. The Italian chemical profiles differentiated by the significant contributions of carvacrol methyl ether and isoterpinolene. The essential oils were also investigated for their insecticidal activity and their repellency against Pheidole pallidula (Nylander) ants and found to possess significant activity. Introduction Among a large set of the initially investigated Crithmum maritimum is a halophyte and chas- plants, C. maritimum, exhibited one of the highest mophyte apiaceous plant, which grows on all the antifeedant and insecticidal activities against the world’s coastlines but is particularly abundant in Pheidole pallidula ants. Other members of the the Mediterranean countries (Coiffard et al., family Apiaceae (Umbelliferae) have been re 1993). It is also referred to as rock sapphire and cently shown to exhibit antifeedant and neuro- ac was well known to sailors since ancient years for tivity against the field slug D. -
Recitation Section 4 Answer Key Biochemistry—Energy and Glycolysis
MIT Department of Biology 7.014 Introductory Biology, Spring 2005 Recitation Section 4 Answer Key February 14-15, 2005 Biochemistry—Energy and Glycolysis A. Why do we care In lecture we discussed the three properties of a living organism: metabolism, regulated growth, and replication. Today we will focus on metabolism and biosynthesis. 1. It was said in lecture that chemical reactions are the basis of life. Why do we say that? Being alive implies being able to change your state in response to a change in internal or environmental conditions. We discussed previously that any change in the observable characteristics of a cell begins as and is propagated by molecular interactions. Molecular interactions propagate the signal by changing the state of molecules, i.e. by reactions. 2. Why is metabolism required for life? A cell is subject to all laws of chemistry and physics, including the first and second law of thermodynamics. Changing the state of molecules dissipates energy along the way, so getting or making new energy is essential to life. The energy is then used for many purposes, including making the building blocks and precursors and then using them to build macromolecules that make up cells—biosynthesis. 3. Can an entity that performs no chemical reactions be considered “alive?” In general, no. But there are special cases of the cells that do not perform reactions right at the moment, but have the potential to perform reactions if they encounter particular conditions. Some examples of such cells are spores in nature or frozen permanents in laboratory. If they experience certain conditions, such as availability of food for spores, or defrosting and food source for frozen permanents, these cells will again perform metabolism. -
2.4 the Breakdown Chemical Reactions Bonds Break and Form During Chemical Reactions
DO NOT EDIT--Changes must be made through “File info” CorrectionKey=B 2.4 Chemical Reactions KEY CONCEPT VOCABULARY Life depends on chemical reactions. chemical reaction MAIN IDEAS reactant Bonds break and form during chemical reactions. product Chemical reactions release or absorb energy. bond energy equilibrium activation energy Connect to Your World exothermic When you hear the term chemical reaction, what comes to mind? Maybe you think endothermic of liquids bubbling in beakers. You probably do not think of the air in your breath, but most of the carbon dioxide and water vapor that you breathe out are made by chemical reactions in your cells. MAIN IDEA Bonds break and form during chemical reactions. Plant cells make cellulose by linking simple sugars together. Plant and animal cells break down sugars to get usable energy. And all cells build protein mol- ecules by bonding amino acids together. These are just a few of the chemical reactions in living things. Chemical reactions change substances into different substances by breaking and forming chemical bonds. Although the matter changes form, both matter and energy are conserved in a chemical reaction. Reactants, Products, and Bond Energy Your cells need the oxygen molecules that you breathe in. Oxygen (O2) plays a part in a series of chemical reactions that provides usable energy for your cells. These reactions, which are described in detail in the chapter Cells and Energy, break down the simple sugar glucose (C6H12O6). The process uses oxygen and glucose and results in carbon dioxide (CO2), water (H2O), and usable energy. Oxygen and glucose are the reactants. -
Enzyme Kinetics in This Exercise We Will Look at the Catalytic Behavior of Enzymes
1 Enzyme Kinetics In this exercise we will look at the catalytic behavior of enzymes. You will use Excel to answer the questions in the exercise section. At the end of this session, you must hand in answers to all the questions, along with print outs of any plots you created. Background Enzymes are the catalysts of biological systems and are extremely efficient and specific as catalysts. In fact, typically, an enzyme accelerates the rate of a reaction by factors of at least a million compared to the rate of the same reaction in the absence of the enzyme. Most biological reactions do not occur at perceptible rates in the absence of enzymes. One of the simplest biological reactions catalyzed by an enzyme is the hydration of CO2. The catalyst in this reaction is carbonic anhydrase. This reaction is part of the respiration cycle which expels CO2 from the body. Carbonic anhydrase is a highly efficient enzyme – each enzyme molecule 5 can catalyze the hydration of 10 CO2 molecules per second. Enzymes are highly specific. Typically a particular enzyme catalyzes only a single chemical reaction or a set of closely related chemical reactions. As is true of any catalyst, enzymes do not alter the equilibrium point of the reaction. This means that the enzyme accelerates the forward and reverse reaction by precisely the same factor. For example, consider the interconversion of A and B. A ↔ B (1) -4 -1 Suppose that in the absence of the enzyme the forward rate constant (kf) is 10 s and the -6 -1 reverse rate constant (kr) is 10 s . -
Enzyme Catalysis: Structural Basis and Energetics of Catalysis
PHRM 836 September 8, 2015 Enzyme Catalysis: structural basis and energetics of catalysis Devlin, section 10.3 to 10.5 1. Enzyme binding of substrates and other ligands (binding sites, structural mobility) 2. Energe(cs along reac(on coordinate 3. Cofactors 4. Effect of pH on enzyme catalysis Enzyme catalysis: Review Devlin sections 10.6 and 10.7 • Defini(ons of catalysis, transi(on state, ac(vaon energy • Michaelis-Menten equaon – Kine(c parameters in enzyme kine(cs (kcat, kcat/KM, Vmax, etc) – Lineweaver-Burk plot • Transi(on-state stabilizaon • Meaning of proximity, orientaon, strain, and electrostac stabilizaon in enzyme catalysis • General acid/base catalysis • Covalent catalysis 2015, September 8 PHRM 836 - Devlin Ch 10 2 Structure determines enzymatic catalysis as illustrated by this mechanism for ____ 2015, September 8 PHRM 836 - Devlin Ch 10 www.studyblue.com 3 Substrate binding by enzymes • Highly complementary interac(ons between substrate and enzyme – Hydrophobic to hydrophobic – Hydrogen bonding – Favorable Coulombic interac(ons • Substrate binding typically involves some degree of conformaonal change in the enzyme – Enzymes need to be flexible for substrate binding and catalysis. – Provides op(mal recogni(on of substrates – Brings cataly(cally important residues to the right posi(on. 2015, September 8 PHRM 836 - Devlin Ch 10 4 Substrate binding by enzymes • Highly complementary interac(ons between substrate and enzyme – Hydrophobic to hydrophobic – Hydrogen bonding – Favorable Coulombic interac(ons • Substrate binding typically involves some degree of conformaonal change in the enzyme – Enzymes need to be flexible for substrate binding and catalysis. – Provides op(mal recogni(on of substrates – Brings cataly(cally important residues to the right posi(on. -
PDF (Chapter 5
~---=---5 __ Heterogeneous Catalysis 5.1 I Introduction Catalysis is a term coined by Baron J. J. Berzelius in 1835 to describe the property of substances that facilitate chemical reactions without being consumed in them. A broad definition of catalysis also allows for materials that slow the rate of a reac tion. Whereas catalysts can greatly affect the rate of a reaction, the equilibrium com position of reactants and products is still determined solely by thermodynamics. Heterogeneous catalysts are distinguished from homogeneous catalysts by the dif ferent phases present during reaction. Homogeneous catalysts are present in the same phase as reactants and products, usually liquid, while heterogeneous catalysts are present in a different phase, usually solid. The main advantage of using a hetero geneous catalyst is the relative ease of catalyst separation from the product stream that aids in the creation of continuous chemical processes. Additionally, heteroge neous catalysts are typically more tolerant ofextreme operating conditions than their homogeneous analogues. A heterogeneous catalytic reaction involves adsorption of reactants from a fluid phase onto a solid surface, surface reaction of adsorbed species, and desorption of products into the fluid phase. Clearly, the presence of a catalyst provides an alter native sequence of elementary steps to accomplish the desired chemical reaction from that in its absence. If the energy barriers of the catalytic path are much lower than the barrier(s) of the noncatalytic path, significant enhancements in the reaction rate can be realized by use of a catalyst. This concept has already been introduced in the previous chapter with regard to the CI catalyzed decomposition of ozone (Figure 4.1.2) and enzyme-catalyzed conversion of substrate (Figure 4.2.4). -
Lactate in the Brain: from Metabolic End-Product to Signalling Molecule
REVIEWS Lactate in the brain: from metabolic end-product to signalling molecule Pierre J. Magistretti1,2,3* and Igor Allaman2 Abstract | Lactate in the brain has long been associated with ischaemia; however, more recent evidence shows that it can be found there under physiological conditions. In the brain, lactate is formed predominantly in astrocytes from glucose or glycogen in response to neuronal activity signals. Thus, neurons and astrocytes show tight metabolic coupling. Lactate is transferred from astrocytes to neurons to match the neuronal energetic needs, and to provide signals that modulate neuronal functions, including excitability, plasticity and memory consolidation. In addition, lactate affects several homeostatic functions. Overall, lactate ensures adequate energy supply, modulates neuronal excitability levels and regulates adaptive functions in order to set the ‘homeostatic tone’ of the nervous system. Pyruvate dehydrogenase When studied at the organ level, brain energy meta Notably, under physiological conditions, the (PDH). The first component bolism can be considered as being almost fully oxida lactate:pyruvate concentration ratio is at least 10:1 enzyme of the pyruvate tive: elegant studies pioneered in the 1940s and 1950s (REF. 11). Thus, when considering the intercellular trans dehydrogenase complex; by Schmitt and Kety1 and later by Sokoloff 2 showed fer of a glycolytic substrate, lactate is the predominant it converts pyruvate into acetyl-CoA, which enters the that glucose is the obligatory physiological energy substrate in the brain. This ratio can also massively tricarboxylic acid (TCA) cycle substrate of the brain and is metabolized to CO2 and increase under hypoxia, as decreases in the partial for cellular respiration. -
Synthetic Biology Applications Inventory
INVENTORY OF SYNTHETIC BIOLOGY PRODUCTS – EXISTING AND POSSIBLE (Draft – July 27, 2012) Why This Inventory? For good or ill, new technologies are often defined by a few iconic examples that capture the public imagination. Early on, nanotechnology was defined by its application to stain-resistant clothing and sunscreens, convenient improvements but hardly transformational. Of course, the real revolution was occurring in the background, which involved a newfound ability to see, simulate, and manipulate matter at an atomic scale. Slowly, it became apparent that nanoscale science and engineering were having pervasive impacts across multiple economic sectors and products, as well as up and down value chains, and creating significant potential for improvements in costs and efficiency. So far, synthetic biology has been associated with a few limited applications, but this initial inventory provides a glimpse of its impact on multiple sectors ranging from energy to pharmaceuticals, chemicals, and food. The real power of synthetic biology may be creating a field of knowledge critical to the design of new technologies and manufacturing processes in general. This exploratory inventory is an attempt to look over the horizon of this emerging science. As such, it is a “work in progress” and we hope others will help us as we update and expand the inventory. Research on specific applications or near-commercial activities does not guarantee eventual market entry and economic impact, but the breadth of commercial and upstream activity is important to track as the science advances. Methodology This inventory of the applications of synthetic biology was compiled from a) a Lexis-Nexis search of US newspapers and newswires on the terms “’synthetic biology’ and applications” for the years 2008-2011; b) a Web of Science search on the term “synthetic biology” for 2008-2011; c) a visual search of project descriptions and websites entered into the 2010 and 2011 iGEM competition, as provided on the iGEM website1; and d) a web search for specific companies and synthetic biology via Google. -
Heterogeneous Catalyst Deactivation and Regeneration: a Review
Catalysts 2015, 5, 145-269; doi:10.3390/catal5010145 OPEN ACCESS catalysts ISSN 2073-4344 www.mdpi.com/journal/catalysts Review Heterogeneous Catalyst Deactivation and Regeneration: A Review Morris D. Argyle and Calvin H. Bartholomew * Chemical Engineering Department, Brigham Young University, Provo, UT 84602, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel: +1-801-422-4162, Fax: +1-801-422-0151. Academic Editor: Keith Hohn Received: 30 December 2013 / Accepted: 12 September 2014 / Published: 26 February 2015 Abstract: Deactivation of heterogeneous catalysts is a ubiquitous problem that causes loss of catalytic rate with time. This review on deactivation and regeneration of heterogeneous catalysts classifies deactivation by type (chemical, thermal, and mechanical) and by mechanism (poisoning, fouling, thermal degradation, vapor formation, vapor-solid and solid-solid reactions, and attrition/crushing). The key features and considerations for each of these deactivation types is reviewed in detail with reference to the latest literature reports in these areas. Two case studies on the deactivation mechanisms of catalysts used for cobalt Fischer-Tropsch and selective catalytic reduction are considered to provide additional depth in the topics of sintering, coking, poisoning, and fouling. Regeneration considerations and options are also briefly discussed for each deactivation mechanism. Keywords: heterogeneous catalysis; deactivation; regeneration 1. Introduction Catalyst deactivation, the loss over time of catalytic activity and/or selectivity, is a problem of great and continuing concern in the practice of industrial catalytic processes. Costs to industry for catalyst replacement and process shutdown total billions of dollars per year. Time scales for catalyst deactivation vary considerably; for example, in the case of cracking catalysts, catalyst mortality may be on the order of seconds, while in ammonia synthesis the iron catalyst may last for 5–10 years. -
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Arch Microbiol (2014) 196:853–861 DOI 10.1007/s00203-014-1024-9 ORIGINAL PAPER Carbon partitioning to the terpenoid biosynthetic pathway enables heterologous β-phellandrene production in Escherichia coli cultures Cinzia Formighieri · Anastasios Melis Received: 27 June 2014 / Revised: 24 July 2014 / Accepted: 1 August 2014 / Published online: 13 August 2014 © Springer-Verlag Berlin Heidelberg 2014 Abstract Escherichia coli was used as a microbial sys- Keywords β-Phellandrene · Isoprenoid biosynthetic tem for the heterologous synthesis of β-phellandrene, a pathway · Metabolic engineering · Monoterpene monoterpene of plant origin with several potential com- biosynthesis mercial applications. Expression of Lavandula angusti- folia β-phellandrene synthase (PHLS), alone or in com- Abbreviations bination with Picea abies geranyl-diphosphate synthase DCW Dry cell weight in E. coli, resulted in no β-phellandrene accumulation, DMAPP Dimethylallyl-diphosphate in sharp contrast to observations with PHLS-transformed GPPS Geranyl-diphosphate synthase cyanobacteria. Lack of β-phellandrene biosynthesis in E. IPP Isopentenyl-diphosphate coli was attributed to the limited endogenous carbon par- IPTG Isopropyl β-D-1-thiogalactopyranoside titioning through the native 2-C-methylerythritol-4-phos- MEP 2-C-methyl-erythritol-4-phosphate phate (MEP) pathway. Heterologous co-expression of the MVA Mevalonic acid mevalonic acid pathway, enhancing cellular carbon parti- OD Optical density tioning and flux toward the universal isoprenoid precur- β-PHL β-Phellandrene sors, isopentenyl-diphosphate and dimethylallyl-diphos- PHLS β-Phellandrene synthase phate, was required to confer β-phellandrene production. TIR Translation initiation region Differences in endogenous carbon flux toward the synthe- sis of isoprenoids between photosynthetic (Synechocystis) and non-photosynthetic bacteria (E.