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Chapter 5 Microbial Metabolism © 2013 Pearson Education, Inc. Copyright © 2013 Pearson Education, Inc. Lectures prepared by Christine L. Case Lectures prepared by Christine L. Case © 2013 Pearson Education, Inc. Catabolic and Anabolic Reactions Metabolism: the sum of the chemical reactions in an organism Catabolism: provides energy and building blocks for anabolism Anabolism: uses energy and building blocks to build large molecules © 2013 Pearson Education, Inc. Catabolic reaction: Larger molecule + ADP+ Pi→ ATP + smaller molecule Anabolic reaction: smaller molecule +ATP → ADP + Pi + larger molecule © 2013 Pearson Education, Inc. Figure 5.1 The role of ATP in coupling anabolic and catabolic reactions. © 2013 Pearson Education, Inc. © 2013 Pearson Education, Inc. Catabolic and Anabolic Reactions A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a cell Metabolic pathways are determined by enzymes Enzymes are encoded by genes ANIMATION Metabolism: Overview © 2013 Pearson Education, Inc. Collision Theory The collision theory states that chemical reactions can occur when atoms, ions, and molecules collide Activation energy is needed to disrupt electronic configurations Reaction rate is the frequency of collisions with enough energy to bring about a reaction Reaction rate can be increased by enzymes or by increasing temperature or pressure © 2013 Pearson Education, Inc. Figure 5.2 Energy requirements of a chemical reaction. Reaction without enzyme Reaction with enzyme Reactant Activation energy without enzyme Activation energy with enzyme Initial energy level Final energy level Products © 2013 Pearson Education, Inc. Enzyme Components Biological catalysts Specific for a chemical reaction; not used up in that reaction Protein in nature with specific 3 D configuration for finding its specific substrate (specificity) One compound may be the substrate for different enzymes. The fate of this compound is depended on the enzyme used. Eg. At least 4 different enzymes can react Glu-6-p Apoenzyme: protein Cofactor: nonprotein component Coenzyme: organic cofactor Holoenzyme: apoenzyme plus cofactor Active site: the region in enzyme that interacts with subatrate © 2013 Pearson Education, Inc. Figure 5.3 Components of a holoenzyme. Coenzyme Apoenzyme (protein portion), inactive © 2013 Pearson Education, Inc. Cofactor (nonprotein portion), activator Substrate Holoenzyme (whole enzyme), active Important Coenzymes NAD+: nicotinamide adenine dinucleotide→NADH NADP+: nicotinamide adenine dinucleotide phosphate →NADPH FAD: flavin adenine dinucleotide → FADH2 Coenzyme A (CoA) © 2013 Pearson Education, Inc. Enzyme Specificity and Efficiency The turnover number is generally 1 to 10,000 molecules per second Eg. DNA polymerase I with turnover number 15, lactate dehydrogensae with turnover number 1000 Enzymes in cell may be in active form or inactive form ANIMATION Enzymes: Overview ANIMATION Enzymes: Steps in a Reaction © 2013 Pearson Education, Inc. Figure 5.4a The mechanism of enzymatic action. Active site Substrate Enzyme © 2013 Pearson Education, Inc. Enzyme–substrate complex Products Figure 5.4b The mechanism of enzymatic action. Substrate Enzyme Substrate © 2013 Pearson Education, Inc. Enzyme Classification Oxidoreductase: oxidation-reduction reactions Transferase: transfer functional groups Hydrolase: hydrolysis Lyase: removal of atoms without hydrolysis Isomerase: rearrangement of atoms Ligase: joining of molecules; uses ATP © 2013 Pearson Education, Inc. Factors Influencing Enzyme Activity Temperature pH Substrate concentration Inhibitors © 2013 Pearson Education, Inc. Factors Influencing Enzyme Activity Temperature and pH denature proteins © 2013 Pearson Education, Inc. Figure 5.6 Figure 5.5a Factors that influence enzymatic activity, plotted for a hypothetical enzyme. (a) Temperature. The enzymatic activity (rate of reaction catalyzed by the enzyme) increases with increasing temperature until the enzyme, a protein, is denatured by heat and inactivated. At this point, the reaction rate falls steeply. © 2013 Pearson Education, Inc. Figure 5.5b Factors that influence enzymatic activity, plotted for a hypothetical enzyme. (b) pH. The enzyme illustrated is most active at about pH 5.0. optimal pH 5.0 Extreme pH causes enzyme denaturation because H+ or OHcompete with hydrogen and ionic bonds in enzymes © 2013 Pearson Education, Inc. Figure 5.5c Factors that influence enzymatic activity, plotted for a hypothetical enzyme. (c) Substrate concentration. With increasing concentration of substrate molecules, the rate of reaction increases until the active sites on all the enzyme molecules are filled, at which point the maximum rate of reaction is reached. © 2013 Pearson Education, Inc. Enzyme Inhibitors: Competitive Inhibition © 2013 Pearson Education, Inc. Figure 5.7a–b Enzyme Inhibitors: Competitive Inhibition © 2013 Pearson Education, Inc. Enzyme Inhibitors: Noncompetitive Inhibition ANIMATION Non-competitive Inhibition © 2013 Pearson Education, Inc. Figure 5.7a, c Enzyme Inhibitors: Feedback Inhibition © 2013 Pearson Education, Inc. Figure 5.8 Ribozymes RNA that cuts and splices RNA Function as catalyst Have active site to bind substrate Not used up in reaction Acts on strands of RNA by removing sections and splicing together the remaining pieces © 2013 Pearson Education, Inc. Oxidation-Reduction Reactions Oxidation: Removal of electrons Reduction: Gain of electrons Redox reaction: An oxidation reaction paired with a reduction reaction © 2013 Pearson Education, Inc. Oxidation-Reduction Reactions In biological systems, the electrons are often associated with hydrogen atoms. Biological oxidations are often dehydrogenations. ANIMATION Oxidation-Reduction Reactions © 2013 Pearson Education, Inc. The Generation of ATP ATP is generated by the phosphorylation of ADP © 2013 Pearson Education, Inc. Three ways for generation of ATP 1. Substrate-level phosphorylation 2. Oxidative phosphorylation 3. Photophosphorylation © 2013 Pearson Education, Inc. Substrate-Level Phosphorylation Energy from the transfer of a high-energy PO4– to ADP generates ATP © 2013 Pearson Education, Inc. The Generation of ATP Oxidative phosphorylation Energy released from the transfer of electrons (oxidation) of one compound to another (reduction) is used to generate ATP by chemiosmosis. Electron transport chain (ETC): the sequence of electron carriers used in oxidative phosphorylation. Prokaryote: ETC present in plasma membrane Eukaryote: ETC present in inner membrane of mitochondria © 2013 Pearson Education, Inc. © 2013 Pearson Education, Inc. Figure 5.14 An electron transport chain (system). Energy © 2013 Pearson Education, Inc. The Generation of ATP Photophosphorylation Light causes chlorophyll to give up electrons. Energy released from the transfer of electrons (oxidation) of chlorophyll through a system of carrier molecules is used to generate ATP. Convert light energy to chemical energy (ATP) © 2013 Pearson Education, Inc. © 2013 Pearson Education, Inc. Figure 5.25 Photophosphorylation. Electron transport chain Light Excited electrons Energy for production of ATP Electron carrier In Photosystem I (a) Cyclic photophosphorylation Light Excited electrons Electron transport chain In Photosystem I Light Excited electrons In Photosystem II (b) Noncyclic photophosphorylation © 2013 Pearson Education, Inc. Energy for production of ATP Metabolic Pathways of Energy Production © 2013 Pearson Education, Inc. Carbohydrate Catabolism The breakdown of carbohydrates to release energy Glycolysis Krebs cycle Electron transport chain © 2013 Pearson Education, Inc. Figure 5.11 An Overview of Respiration and Fermentation. respiration fermentation Glycolysis produces ATP and reduces NAD+ to NADH while oxidizing glucose to pyruvic acid. In respiration, the pyruvic acid is converted to the first reactant in the Krebs cycle, acetyl CoA. The Krebs cycle produces some ATP by substratelevel phosphorylation, reduces the electron carriers NAD+ and FAD, and gives off CO2. Carriers from both glycolysis and the Krebs cycle donate electrons to the electron transport chain. In the electron transport chain, the energy of the electrons is used to produce a great deal of ATP by oxidative phosphorylation. 1 Glycolysis Glucose NADH ATP Pyruvic acid 2 Pyruvic acid Acetyl CoA (or derivative) NADH FADH2 Kreb’s cycle NADH & FADH2 Formation of fermentation end-products CO2 ATP 3 Electrons ATP Electron transport chain and chemiosmosis © 2013 Pearson Education, Inc. NADH In fermentation, the pyruvic acid and the electrons carried by NADH from glycolysis are incorporated into fermentation endproducts. O2 H2O brewer’s yeast Glycolysis The oxidation of glucose to pyruvic acid produces ATP and NADH © 2013 Pearson Education, Inc. Figure 5.11 Preparatory Stage of Glycolysis 2 ATP are used Glucose is split to form 2 glucose-3-phosphate © 2013 Pearson Education, Inc. Figure 5.12, steps 1–5 Figure 5.12 An outline of the reactions of glycolysis (Embden-Meyerhof pathway). 1 Glucose enters the cell and is phosphorylated. A molecule of ATP is invested. The product is glucose 6-phosphate. Glucose 6-phosphate 2 2 Glucose 6-phosphate is rearranged to form fructose 6-phosphate. Fructose 6-phosphate 3 The P from another ATP is used to produce fructose 1,6diphosphate, still a six-carbon compound. (Note the total investment of two ATP molecules up to this point.) Fructose 1,6-diphosphate 4 An enzyme cleaves (splits) the sugar into two three-carbon molecules: dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GP). Glyceraldehyde 3-phosphate (GP) 2-phosphoglyceric acid DHAP is readily converted to GP (the reverse action may also occur). 6 The next enzyme converts each GP to another three-carbon compound, 1,3-diphosphoglyceric acid. Because each DHAP molecule can be converted to GP and each GP to 1,3-diphosphoglyceric acid, the result is two molecules of 1,3-diphosphoglyceric acid for each initial molecule of glucose. GP is oxidized by the transfer of two hydrogen atoms to NAD + to form NADH. The enzyme couples this reaction with the creation of a highenergy bond between the sugar and a P . The three-carbon sugar now has two P groups. 1,3-diphosphoglyceric acid 3-phosphoglyceric acid 5 7 The high-energy P is moved to ADP, forming ATP, the first ATP production of glycolysis. (Since the sugar splitting in step 4, all products are doubled. Therefore, this step actually repays the earlier investment of two ATP molecules.) 8 An enzyme relocates the remaining P of 3-phosphoglyceric acid to form 2-phosphoglyceric acid in preparation for the next step. Phosphoenolpyruvic acid (PEP) © 2013 Pearson Education, Inc. 9 By the loss of a water molecule, 2-phosphoglyceric acid is converted to phosphoenolpyruvic acid (PEP). In the process, the phosphate bond is upgraded to a high-energy bond. 10 This high-energy P is transferred from PEP to ADP, forming ATP. For each initial glucose molecule, the result of this step is two molecules of ATP and two molecules of a three-carbon compound called pyruvic acid. Energy-Conserving Stage of Glycolysis 2 glucose-3-phosphate oxidized to 2 pyruvic acid 4 ATP produced 2 NADH produced © 2013 Pearson Education, Inc. Figure 5.12, steps 6–10 Glycolysis Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+ 2 pyruvic acid + 4 ATP + 2 NADH + 2H+ ANIMATION Glycolysis: Overview ANIMATION Glycolysis: Steps © 2013 Pearson Education, Inc. Alternatives to Glycolysis Pentose phosphate pathway Uses & produces pentoses and NADPH Pentoses used in synthesis of nucleic acids 1 glucose produces 1 only ATP Operates with glycolysis Entner-Doudoroff pathway 1 glucose produces 2 NADPH and 1 ATP Does not involve glycolysis Pseudomonas, Rhizobium, Agrobacterium © 2013 Pearson Education, Inc. Intermediate Step Pyruvic acid (from glycolysis) is oxidized and decarboyxlated © 2013 Pearson Education, Inc. Figure 5.13 The Krebs Cycle Also called tricarboxylic acid (TCA) cycle or citric acid cycle Oxidation of acetyl CoA produces NADH and FADH2 ANIMATION Krebs Cycle: Overview ANIMATION Krebs Cycle: Steps © 2013 Pearson Education, Inc. Figure 5.13 The Krebs cycle. 1 A turn of the cycle begins as enzymes strip off the CoA portion from acetyl CoA and combine the remaining twocarbon acetyl group with oxaloacetic acid. Adding the acetyl group produces the sixcarbon molecule citric acid. – 8 Enzymes rearrange chemical bonds, producing three different molecules before regenerating oxaloacetic acid. In step 6, an oxidation produces FADH2. In step 8, a final oxidation generates NADH and converts malic acid to oxaloacetic acid, which is ready to enter another round of the Krebs cycle. 6 5 ATP is produced by substratelevel phosphorylation. CoA is removed from succinyl CoA, leaving succinic acid. © 2013 Pearson Education, Inc. 2 – 4 Oxidations generate NADH. Step 2 is a rearrangement. Steps 3 and 4 combine oxidations and decarboxylations to dispose of two carbon atoms that came from oxaloacetic acid. The carbons are released as CO2, and the oxidations generate NADH from NAD+. During the second oxidation (step 4), CoA is added into the cycle, forming the compound succinyl CoA. Cellular Respiration An ATP-generating process in which molecules are oxidized and the final electron acceptor is an inorganic molecule. ATP is generated by oxidative phosphorylation 2 types of respiration: aerobic respiration: use O2 as final e acceptor anaerobic respiration: use inorganic molecule other than O2 © 2013 Pearson Education, Inc. The Electron Transport Chain A series of carrier molecules that are, in turn, oxidized and reduced as electrons are passed down the chain 3 classes of e carriers: (1)flavoproteins: proteins with flavin (FMN) (2)Cytochromes: proteins with iron, cyt b, cyt c1, cyt c, cyt a, cyt a3 (3)Coenzyme Q: nonprotein carrier Energy released can be used to produce ATP by chemiosmosis ANIMATION Electron Transport Chain: Overview © 2013 Pearson Education, Inc. Figure 5.11 An Overview of Respiration and Fermentation. respiration fermentation Glycolysis produces ATP and reduces NAD+ to NADH while oxidizing glucose to pyruvic acid. In respiration, the pyruvic acid is converted to the first reactant in the Krebs cycle, acetyl CoA. The Krebs cycle produces some ATP by substratelevel phosphorylation, reduces the electron carriers NAD+ and FAD, and gives off CO2. Carriers from both glycolysis and the Krebs cycle donate electrons to the electron transport chain. In the electron transport chain, the energy of the electrons is used to produce a great deal of ATP by oxidative phosphorylation. 1 Glycolysis Glucose NADH ATP Pyruvic acid 2 Pyruvic acid Acetyl CoA (or derivative) NADH FADH2 Kreb’s cycle NADH & FADH2 Formation of fermentation end-products CO2 ATP 3 Electrons ATP Electron transport chain and chemiosmosis © 2013 Pearson Education, Inc. NADH In fermentation, the pyruvic acid and the electrons carried by NADH from glycolysis are incorporated into fermentation endproducts. O2 H2O brewer’s yeast Figure 5.16 Electron transport and the chemiosmotic generation of ATP. Cell Periplasmic Plasma Outer wall space membrane membrane Inner membrane Intermembrane space Mitochondrial matrix Cytoplasm Bacterium Mitochondrion Periplasmic space of prokaryote or intermembrane space of eukaryote Prokaryotic plasma membrane or eukaryotic inner mitochondrial membrane Cytoplasm of prokaryote or mitochondrial matrix of eukaryote © 2013 Pearson Education, Inc. Chemiosmosis As e from NADH pass down e transfer chain, some of carriers actively transport protons across the membrane (proton pump) A proton gradient is established. Outside membrane becomes more positive compared with the other side. The resulting electrochemical gradient called proton motive force. Protons across the membrane only through protein channels that contain ATP synthase. When this flow occurs, energy is released and used to synthesize ATP © 2013 Pearson Education, Inc. Figure 5.15 Chemiosmosis. High H+ concentration Membrane Low H+ concentration © 2013 Pearson Education, Inc. Figure 5.14 An electron transport chain (system). Energy © 2013 Pearson Education, Inc. A Summary of Respiration Aerobic respiration: the final electron acceptor in the electron transport chain is molecular oxygen (O2) Anaerobic respiration: the final electron acceptor in the electron transport chain is NOT O2 Yields less energy than aerobic respiration because only part of the Krebs cycle operates under anaerobic conditions © 2013 Pearson Education, Inc. Anaerobic Respiration Electron Acceptor Products NO3– NO2–, N2 + H2O SO4– H2S + H2O CO32 – CH4 + H2O © 2013 Pearson Education, Inc. Carbohydrate Catabolism Pathway Eukaryote Prokaryote Glycolysis Cytoplasm Cytoplasm Intermediate step Cytoplasm Cytoplasm Krebs cycle Mitochondrial matrix Cytoplasm ETC Mitochondrial inner membrane Plasma membrane © 2013 Pearson Education, Inc. Carbohydrate Catabolism Energy produced from complete oxidation of one glucose using aerobic respiration ATP Produced NADH Produced FADH2 Produced Glycolysis 2 2 0 Intermediate step 0 2 0 Krebs cycle 2 6 2 Total 4 10 2 Pathway © 2013 Pearson Education, Inc. Carbohydrate Catabolism ATP produced from complete oxidation of one glucose using aerobic respiration Pathway By Substrate-Level Phosphorylation By Oxidative Phosphorylation From NADH From FADH Glycolysis 2 6 0 Intermediate step 0 6 0 Krebs cycle 2 18 4 Total 4 30 4 © 2013 Pearson Education, Inc. Carbohydrate Catabolism 36 ATPs are produced in eukaryotes Pathway By Substrate-Level Phosphorylation By Oxidative Phosphorylation From NADH From FADH Glycolysis 2 6 0 Intermediate step 0 6 0 Krebs cycle 2 18 4 Total 4 30 4 © 2013 Pearson Education, Inc. Fermentation Any spoilage of food by microorganisms (general use) Any process that produces alcoholic beverages or acidic dairy products (general use) Any large-scale microbial process occurring with or without air (common definition used in industry) © 2013 Pearson Education, Inc. Fermentation Scientific definition: Releases energy from oxidation of organic molecules Does not require oxygen Does not use the Krebs cycle or ETC Uses an organic molecule as the final electron acceptor Produces small amount of ATP Regenerate NAD+ and NADP+ © 2013 Pearson Education, Inc. An Overview of Fermentation ANIMATION Fermentation © 2013 Pearson Education, Inc. Figure 5.18a End-Products of Fermentation © 2013 Pearson Education, Inc. Figure 5.18b Fermentation Alcohol fermentation: Produces ethanol + CO2 Lactic acid fermentation: Produces lactic acid Homolactic fermentation: Produces lactic acid only Heterolactic fermentation: Produces lactic acid and other compounds © 2013 Pearson Education, Inc. Types of Fermentation © 2013 Pearson Education, Inc. Figure 5.19 Figure 5.23 A fermentation test. © 2013 Pearson Education, Inc. Table 5.4 Some Industrial Uses for Different Types of Fermentations* © 2013 Pearson Education, Inc. Lipid Catabolism © 2013 Pearson Education, Inc. Figure 5.20 Catabolism of Organic Food Molecules © 2013 Pearson Education, Inc. Figure 5.21 Protein Catabolism Protein Extracellular proteases Deamination, decarboxylation, dehydrogenation, desulfurization © 2013 Pearson Education, Inc. Amino acids Organic acid Krebs cycle Figure 5.22 Detecting amino acid catabolizing enzymes in the lab. © 2013 Pearson Education, Inc. Figure 5.24 Use of peptone iron agar to detect the production of H2S. © 2013 Pearson Education, Inc. Protein Catabolism Urea © 2013 Pearson Education, Inc. Urease NH3 + CO2 Clinical Focus: Human Tuberculosis – Dallas, Texas Figure B The urease test. © 2013 Pearson Education, Inc. Clinical Focus: Human Tuberculosis – Dallas, Texas Biochemical Tests Used to identify bacteria Figure A An identification scheme for selected species of slow-growing mycobacteria. © 2013 Pearson Education, Inc. Figure 4.15 Chromatophores. Chromatophores © 2013 Pearson Education, Inc. Photosynthesis Photo: conversion of light energy into chemical energy (ATP) Light-dependent (light) reactions Synthesis: Carbon fixation: fixing carbon into organic molecules Light-independent (dark) reaction: Calvin-Benson cycle ANIMATION Photosynthesis: Overview © 2013 Pearson Education, Inc. Photosynthesis Oxygenic: Anoxygenic: ANIMATION: Photosynthesis: Comparing Prokaryotes and Eukaryotes © 2013 Pearson Education, Inc. Cyclic Photophosphorylation ANIMATION Photosynthesis: Light Reaction: Cyclic Photophosphorylation © 2013 Pearson Education, Inc. Figure 5.25a Figure 5.25b Photophosphorylation. Electron transport chain Energy for Light production Excited of ATP electrons In Photosystem I Light Excited electrons In Photosystem II H+ + H+ 1 2 (b) Noncyclic photophosphorylation © 2013 Pearson Education, Inc. © 2013 Pearson Education, Inc. Calvin-Benson Cycle ANIMATION Photosynthesis: Light Independent Reaction © 2013 Pearson Education, Inc. Figure 5.26 A simplified version of the Calvin-Benson cycle. Input Ribulose diphosphate 3-phosphoglyceric acid 1,3-diphosphoglyceric acid Calvin-Benson cycle Glyceraldehyde 3-phosphate Glyceraldehyde 3-phosphate Output Glyceraldehyde 3-phosphate Glyceraldehyde 3-phosphate © 2013 Pearson Education, Inc. Photosynthesis Compared © 2013 Pearson Education, Inc. Table 5.6 Chemotrophs Use energy from chemicals Chemoheterotroph Glucose NAD+ ETC Pyruvic acid NADH Energy is used in anabolism © 2013 Pearson Education, Inc. ADP + P ATP Chemotrophs Use energy from chemicals Chemoautotroph, Thiobacillus ferrooxidans 2Fe2+ NAD+ ETC 2Fe3+ NADH ADP + P ATP 2 H+ Energy is used in the Calvin-Benson cycle to fix CO2 © 2013 Pearson Education, Inc. Phototrophs Use light energy Chlorophyll ETC Chlorophyll oxidized ADP + P ATP Photoautotrophs use energy in the Calvin-Benson cycle to fix CO2 Photoheterotrophs use energy © 2013 Pearson Education, Inc. Figure 5.27 Requirements of ATP production. © 2013 Pearson Education, Inc. Figure 5.28 A nutritional classification of organisms. Light Chemical Organic compounds O2 Not O2 Organic Inorganic compound compound © 2013 Pearson Education, Inc. CO2 CO2 Organic compounds Yes No Metabolic Diversity among Organisms Nutritional Type Photoautotroph Energy Source Light Carbon Source CO2 Example Oxygenic: Cyanobacteria, plants Anoxygenic: Green bacteria, purple bacteria Photoheterotroph Light Organic compounds Green bacteria, purple nonsulfur bacteria Chemoautotroph Chemical CO2 Iron-oxidizing bacteria Chemoheterotroph Chemical Organic compounds Fermentative bacteria © 2013 Pearson Education, Inc. Animals, protozoa, fungi, bacteria Figure 5.29 The biosynthesis of polysaccharides. Glycogen (in bacteria) Glycogen (in animals) Peptidoglycan (in bacteria) © 2013 Pearson Education, Inc. Figure 5.30 The biosynthesis of simple lipids. Krebs cycle © 2013 Pearson Education, Inc. Figure 5.31a The biosynthesis of amino acids. Krebs cycle Amination or transamination Amino acid biosynthesis © 2013 Pearson Education, Inc. Figure 5.31b The biosynthesis of amino acids. Transamination Glutamic acid Oxaloacetic acid Process of transamination © 2013 Pearson Education, Inc. α-Ketoglutaric acid Aspartic acid Figure 5.32 The biosynthesis of purine and pyrimidine nucleotides. Krebs cycle © 2013 Pearson Education, Inc. The Integration of Metabolism Amphibolic pathways: metabolic pathways that have both catabolic and anabolic functions © 2013 Pearson Education, Inc. Amphibolic Pathways © 2013 Pearson Education, Inc. Figure 5.33 Amphibolic Pathways © 2013 Pearson Education, Inc. Figure 5.33