1- INTRODUCTION TO METABOLISM.pdf

INTRODUCTION TO METABOLISM Dr. Asmaa Abu Obaid METABOLISM IS THE SUM OF CELLULAR REACTIONS The large biological molecules  Metabolism-the entire network of chemical reactions carried out by living cells Metabolites-small molecule intermediates in the degradation and synthesis of...

INTRODUCTION TO METABOLISM Dr. Asmaa Abu Obaid METABOLISM IS THE SUM OF CELLULAR REACTIONS The large biological molecules  Metabolism-the entire network of chemical reactions carried out by living cells Metabolites-small molecule intermediates in the degradation and synthesis of polymers Catabolic reactions- degrade molecules to create smaller molecules and energy Anabolic reactions- synthesize molecules for cell maintenance, growth and reproduction There is a third class of reactions called amphibolic reactions. They are involved in both anabolic and catabolic pathways  More than 10 million species may be living on Earth and several hundred million species may have come and gone throughout the course of evolution. Multicellular organisms have a striking specialization of cell types or tissues. Despite this extraordinary diversity of species and cell types the biochemistry of living cells is surprisingly similar not only in the chemical composition and structure of cellular components but also in the metabolic routes by which the components are modified. These universal pathways are the key to understanding metabolism. Once you’ve learned about the fundamental conserved pathways you can appreciate the additional pathways that have evolved in some species. THERE ARE FIVE COMMON THEMES IN METABOLISM 1. Organisms or cells maintain specific internal concentrations of inorganic ions, metabolites and enzymes 2. Organisms extract energy from external sources to drive energy- consuming reactions 3. Organisms grow and reproduce according to instructions encoded in the genetic material 4. Organisms respond to environmental influences 5. Cells are not static, and cell components are continually synthesized and degraded (i.e. undergo turnover) METABOLIC PATHWAYS The vast majority of metabolic reactions are catalyzed by enzymes so a complete description of metabolism includes not only the reactants, intermediates, and products of cellular reactions but also the characteristics of the relevant enzymes METABOLIC PATHWAYS ARE SEQUENCES OF REACTIONS Metabolism includes all enzyme reactions Metabolism can be subdivided into branches The metabolism of the four major groups of biomolecules will be considered: Carbohydrates Lipids Amino Acids Nucleotides  FORMS OF METABOLIC PATHWAYS a.The biosynthesis of serine is an example of a linear metabolic pathway. The product of each step is the substrate for the next step b. The sequence of reactions in a cyclic pathway forms a closed loop. In the citric acid cycle, an acetyl group is metabolized via reactions that regenerate the intermediates of the cycle. c. In fatty acid biosynthesis, a spiral pathway, the same set of enzymes catalyzes a progressive lengthening of the acyl chain. B. METABOLISM PROCEEDS BY DISCRETE STEPS Multiple-step pathways permit control of energy input and output. Energy flow is mediated by energy donors and acceptors that carry discrete quanta of energy. Catabolic multi-step pathways provide energy in smaller stepwise amounts Each enzyme in a multi-step pathway usually catalyzes only one single step in the pathway Control points occur in multistep pathways  Single-step vs multi- step pathways A multistep enzyme pathway releases energy in smaller amounts that can be used by the cell C. METABOLIC PATHWAYS ARE REGULATED Metabolism is highly regulated to permit organisms to respond to changing conditions Most pathways are reversible Flux- flow of material through a metabolic pathway which depends upon: (1) Supply of substrates(2) Removal of products (3) Pathway enzyme activities THERE ARE TWO COMMON PATTERNS OF METABOLIC REGULATION 1. Feedback inhibition: occurs when a product (usually the end product) of a pathway controls the rate of its own synthesis through inhibition of an early step, usually the first committed step 2. feed-forward activation: occurs when a metabolite produced early in a pathway activates an enzyme that catalyzes a reaction further down the pathway.  THE ACTIVITY OF INTERCONVERTIBLE ENZYMES Interconvertible enzyme activity can be rapidly and reversibly altered by covalent modification Protein kinases phosphorylate enzymes (+ ATP) Protein phosphatases remove phosphoryl groups The initial signal may be amplified by the “cascade” nature of this signaling Individual enzymes differ in whether their response to phosphorylation is activation or deactivation MAJOR PATHWAYS IN CELLS Metabolic fuels Three major nutrients consumed by mammals: (1) Carbohydrates-provide energy(2) Proteins-provide amino acids for protein synthesis and some energy(3) Fats- triacylglycerols provide energy and also lipids for membrane synthesis WE WILL EXAMINE METABOLISM IN THE NEXT FEW CHAPTERS. glycolysis, a ubiquitous pathway for glucose catabolism Then following chapters describe the synthesis of glucose, or gluconeogenesis Then citric acid cycle facilitates complete oxidation of the acetate carbons of acetyl CoA to carbon dioxide Then come chapters examine the anabolism and catabolism of lipids, amino acids, and nucleotides. COMPARTMENTATION AND INTERORGANMETABOLISM Compartmentation of metabolic processes permits: -separate pools of metabolites within a cell -simultaneous operation of opposing metabolic paths -high local concentrations of metabolites -coordinated regulation of enzymes Example: fatty acid synthesis enzymes (cytosol), fatty acid breakdown enzymes (mitochondria) THE FREE ENERGY OF ATP HYDROLYSIS ATP is a donor of several metabolic groups, usually a phosphoryl group, leaving ADP, or an AMP group. ATP and the other nucleoside triphosphates (UTP, GTP, and CTP) are often referred to as energy-rich compounds Several factors contribute to the large amount of energy released during hydrolysis of the phosphoanhydride linkages of ATP:  1. Electrostatic repulsion. Electrostatic repulsion among the negatively charged oxygen atoms of the phosphoanhydride groups of ATP is less after hydrolysis 2. Solvation effects. The products of hydrolysis, ADP and inorganic phosphate, or AMP and inorganic pyrophosphate, are better solvated than ATP itself 3. Resonance stabilization. The products of hydrolysis are more stable than ATP  THE METABOLIC ROLES OF ATP The energy produced by one biological reaction or process, such as the synthesis of in Reaction 10.15, is often coupled to a second reaction, such as the hydrolysis of ATP. The first reaction would not otherwise occur spontaneously. Energy flow in metabolism depends on many coupled reactions involving ATP. In many cases, the coupled reactions are linked by a shared intermediate such as a phosphorylated derivative of reactant X. The activated compound , can be either a metabolite or the side chain of an amino acid residue in the active site of an enzyme. The intermediate then reacts with a second substrate to complete the reaction. PHOSPHORYL GROUP TRANSFER The ability of a phosphorylated compound to transfer its phosphoryl group(s) is termed its phosphoryl group transfer potential Some compounds, such as phosphoesters, are poor phosphoryl group donors. They have a group transfer potential less than that of ATP. Thus, the group transfer potential is a measure of the free energy required for formation of the phosphorylated compound. PRODUCTION OF ATP BY PHOSPHORYL GROUP TRANSFER Often, one kinase catalyzes transfer of a phosphoryl group from an excellent donor to ADP to form ATP, which then acts as a donor for a different kinase reaction. Phosphoenolpyruvate and 1,3-bisphosphoglycerate are two examples of common metabolites that have higher energy than ATP even under conditions found inside the cell Some of these compounds are intermediates in catabolic pathways; others are energy storage compounds In cells, this metabolically irreversible reaction is an important source of ATP. PHOSPHAGENS Phosphagens, including phosphocreatine and phosphoarginine, are “high energy” phosphate storage molecules found in animal muscle cells. and have higher group transfer potentials than ATP. In resting muscle, the concentration of phosphocreatine is about five fold higher than that of ATP. When ATP levels fall, creatine kinase catalyzes rapid replenishment of ATP through transfer of the activated phosphoryl group from phosphocreatine to ADP.  ATP Because ATP has an intermediate phosphoryl group transfer potential, it is thermodynamically suited as a carrier of phosphoryl groups Not surprisingly, ATP mediates most chemical energy transfers in all organisms  THIOESTERS HAVE HIGH FREE ENERGIES OF HYDROLYSIS Thioesters are another class of “high energy” compounds forming part of the currency of metabolism. Acetyl CoA is one example. It occupies a central position in metabolism The high energy of thioester reactions can be used in generating ATP equivalents The high energy of hydrolysis of a CoA thioester is used in the fifth step of the citric acid cycle, when the thioester succinyl CoA reacts with GDP (or sometimes ADP) and Pi to form GTP (or ATP).  EXPERIMENTAL METHODS FOR STUDYINGMETABOLISM Reaction conditions used with isolated reactants in the test tube (in vitro) are often very different from the reaction conditions in the intact cell (in vivo). A classical approach to unraveling metabolic pathways is to add a substrate to preparations of tissues, cells, or subcellular fractions and then follow the emergence of intermediates and end products. The fate of a substrate is easier to trace when the substrate has been specifically labeled. Valuable information can be acquired by studying mutations in single genes associated with the production of inactive or defective individual enzyme forms. The investigation of mutant organisms has helped identify enzymes and intermediates of numerous metabolic pathways. In humans, enzyme defects are manifested in metabolic diseases. Hundreds of single-gene diseases are known.  Biochemists have characterized entire pathways by producing a series of mutants, isolating them, and examining their nutritional requirements and accumulated metabolites. More recently, site-directed mutagenesis has proved valuable in defining the roles of enzymes. Bacterial and yeast systems have been the most widely used for introducing mutations because large numbers of these organisms can be grown in a short period of time. It is possible to produce animal models—particularly insects and nematodes—in which certain genes are not expressed. It is also possible to delete certain genes in vertebrates. “Gene knockout” mice, for instance, provide an experimental system for investigating the complexities of mammalian metabolism. In a similar fashion, investigating the actions of metabolic inhibitors has helped identify individual steps in metabolic pathways. The use of inhibitory drugs not only helps in the study of metabolism but also determines the mechanism of action of the drug, often leading to improved drug variations.