BIOL 203 - Chapter 05 - Microbial Metabolism PDF

CHAPTER 05 – MICROBIAL METABOLISM CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 1 LEARNING OUTCOMES 5.1 Distinguish among metabolism, anabolism, and catabolism 5.2 Contrast oxidation and reduction reactions 5.3 Compare and contrast the three types of ATP phosphorylation...

CHAPTER 05 – MICROBIAL METABOLISM CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 1 LEARNING OUTCOMES 5.1 Distinguish among metabolism, anabolism, and catabolism 5.2 Contrast oxidation and reduction reactions 5.3 Compare and contrast the three types of ATP phosphorylation 5.4 Make a table listing the six basic types of enzymes and their activities and an example of each 5.5 Describe the components of a holoenzyme, and contrast protein and RNA enzymes 5.6 Define activation energy, enzyme, apoenzyme, cofactor, coenzyme, active site and substrate, and describe their roles in enzyme activity 5.7 Describe how temperature, pH, substrate concentration, and competitive and noncompetitive inhibition affect enzyme activity CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 2 LEARNING OUTCOMES 5.8 In general terms, describe the three stages of aerobic glucose metabolism (glycolysis, the Krebs cycle, and an electron transport chain), including their substrates, products, and net energy production 5.9 Discuss the roles of acetyl-CoA, the Krebs cycle, and electron transport in carbohydrate metabolism 5.10 Contrast electron transport in aerobic and anaerobic respiration 5.11 Identify four classes of carriers in electron transport chains 5.12 Describe the role of chemiosmosis in oxidative phosphorylation of ATP 5.13 Compare and contrast the ED and pentose phosphate pathway with EMP glycolysis in terms of energy production and products CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 3 LEARNING OUTCOMES 5.14 Describe several examples of the vast metabolic diversity in bacteria 5.15 Describe fermentation, and contrast it with respiration 5.16 List three useful end-products of fermentation, and explain how fermentation reactions are used to identify bacteria 5.17 Discuss how biochemical tests for metabolic enzymes and products are used in the identification of bacteria 5.18 Explain how lipids are catabolized for energy and metabolite production 5.19 Explain how proteins are catabolized for energy and metabolite production 5.20 Define photosynthesis CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 4 LEARNING OUTCOMES 5.21 Compare and contrast the basic chemicals and structures involved in photosynthesis in prokaryotes and eukaryotes 5.22 Describe the components and function of the two photosystems PS II and PS I 5.23 Contrast cyclic and noncyclic photophosphorylation 5.24 Contrast the light-dependent and light-independent reactions of photosynthesis 5.25 Describe the reactants and products of the Calvin-Benson cycle 5.26 Define amphibolic reaction 5.27 Describe the biosynthesis of carbohydrates CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 5 LEARNING OUTCOMES 5.28 Describe the biosynthesis of lipids 5.29 Describe the biosynthesis of amino acids 5.30 Describe the biosynthesis of nucleotides 5.31 Describe interrelationships between catabolism and anabolism in terms of ATP and substrates 5.32 Discuss regulation of metabolic activity CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 6 METABOLISM Metabolism: the sum of all catabolic and anabolic pathways: Catabolism: class of reaction where larger molecules are broken down into smaller ones. Exergonic (releases energy). Anabolism: class of reaction where larger molecules are synthesized from smaller ones. Endergonic (requires an input of energy). CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 7 ANABOLIC STEROIDS (ANABOLIC-ANDROGENIC STEROIDS) Testosterone Why are anabolic steroids anabolic? CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 8 PRECURSOR METABOLITES Precursor metabolites: any of 12 molecules typically generated from a catabolic pathway and essential to the synthesis of organic macromolecules in the cell CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 9 OXIDATION-REDUCTION (REDOX) REACTIONS OIL RIG Oxidation Involves Loss Reduction Involves Gain Redox reactions: reactions that involve the transfer of electrons from an electron donor to an electron acceptor. Oxidation: loss of electrons Reduction: gain of electrons Oxidation and reduction reactions happen simultaneously CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 10 REDOX REACTIONS H+ : a hydrogen ion (proton) H : a hydrogen atom Ways to get oxidized Ways to get reduced Lose an electron Gain an electron Lose a hydrogen atom Gain a hydrogen atom Gain an oxygen atom Dehydrogenation: oxidation involving the loss of a hydrogen atom What is being oxidized? Reduced? CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 11  O2 e- e- H+ H+ ELECTRON CARRIERS NAD+ + _______ NADH + H+ What is missing in the blanks? FAD + _______ FADH2 Electrons rarely exist freely in the cytoplasm. Instead, electrons are mobilized in the cell using electron carrier molecules. Usually carry electrons in hydrogen atoms. Nicotinamide Adenine Dinucleotide (NAD+) Flavin Adenine Dinucleotide (FAD) Nicotinamide Adenine Dinucleotide Phosphate (NADP+) CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 12 NADP + AND NADPH H H H NAD+ NADP+ NADPH NADP+ is an electron carrier which is very similar to NAD+, the only difference is the presence of a phosphate group (The “P” in NADP+) NADP+ can accept two electrons and a proton to form NADPH NADPH is often used in anabolic reactions. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 13 ADENOSINE TRIPHOSPHATE (ATP) H2O OR H2O Pyrophosphate mono (AMP) ATP is the main energy currency of the cell. Why is it so suitable? 1. Multifunctional! Can be used for _____ synthesis 2. Water soluble. Can accumulate to high concentrations 3. Different levels of energy donation in one molecule CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 14  ATP Synthase ATP FORMATION Three major methods to form ATP from ADP: 1. Substrate-level phosphorylation: transfer of a phosphate from another phosphorylated organic compound 2. Oxidative phosphorylation: energy from redox reactions of respiration to attach inorganic phosphate (Pi) to ADP 3. Photophosphorylation: light energy is used to phosphorylate ADP with Pi CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 Which picture matches each method? 15 ENZYMES Enzymes are organic catalysts that speed up the rate of reactions Not permanently changed by the reaction that they catalyze Names often end in “-ase” Most are proteins but RNA enzymes called ribozymes also exist Without enzymes, biological reactions would occur very slowly (or not at all!) CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 16 ENZYME TERMINOLOGY Apoenzyme: protein component of an enzyme that requires both a protein and nonprotein portion to function. Cofactor: Nonprotein substance required for apoenzyme to function. Can be an inorganic ion or an organic coenzyme. Coenzyme: Organic molecule (like vitamins) required for apoenzyme to function Holoenzyme: Apoenzyme + cofactor(s). Active. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 17 ENZYME ACTIVITY Enolase dimer Active site of enolase Enzymes bind to substrates – the molecules that enzymes act on Enzymes increase the rate of reaction by reducing the amount of energy needed to trigger a chemical reaction (activation energy) Active site: region of an enzyme that binds and catalyzes the reaction. Typically involves only a few amino acids CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 18 FACTORS AFFECTING RATES OF ENZYMATIC REACTIONS: 1. Temperature 2. pH 3. Enzyme and substrate concentrations 4. Inhibitors CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 19 CONTROL OF ENZYME ACTIVITY Allosteric regulation: The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site Allosteric activators stabilize an active form Allosteric inhibitors stabilize an inactive form CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 20 INHIBITORS Normal binding Competitive inhibition Noncompetitive inhibition Competitive inhibitors: resemble the substrate and can bind reversibly to the enzyme. Competes with the substrate. Noncompetitive inhibitors: binds to a site distinct from the active site that changes the enzymes shape so that it is less effective at catalyzing a reaction. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 21 FEEDBACK INHIBITION Feedback inhibition: the end product of a metabolic pathway acts as an inhibitor of an enzyme within the pathway. Very common method of controlling how much of a product is produced CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 22 REVIEW Open up Kahoot (https://kahoot.it/) Join the game with the game pin: CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 23 CARBOHYDRATE METABOLISM Glucose is catabolized by one of two pathways: 1. Cellular respiration: Involves glycolysis, the Krebs cycle and the NADH electron transport chain (ETC) as major steps 2. Fermentation: Involves glycolysis CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 24 GLYCOLYSIS Glyco = sugar, lysis = splitting Follows the Embden-Meyerhof-Parnas (EMP) pathway Splits the 6-carbon glucose into two 3-carbon sugars (G3P) which are both oxidized to pyruvic acid Occurs in the cytosol Generates 2 ATP and 2 NADH per glucose Which phosphorylation process is used to generate ATP? CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 25 SYNTHESIS OF ACETYL-COA Involves a decarboxylation (removal of a carbon) of pyruvic acid which is lost as CO2 The resulting product is combined with Coenzyme A (CoA) to form acetyl-CoA One NADH is generated for every acetyl-CoA synthesized CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 26 KREBS CYCLE Electron bus Krebs Cycle (also known as the Citric Acid Cycle) outputs the following per acetyl-CoA: 2 CO2 3 NADH Electron bus 1 FADH2 1 GTP (later converted to ATP) Electron bus Do not worry about memorizing each of the individual steps Electron bus CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 27 SUMMARY SO FAR: Each step has been successively oxidizing the carbons from glucose Some energy is stored as 4 ATP NADH 10 NADH produced 2 FADH2 produced How do we harness the stored energy in NADH and FADH2? CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 28 ELECTRON TRANSPORT CHAIN (ETC) Electrons carried by NADH and FADH2 are delivered down the ETC found in the cytoplasmic membrane The ETC pumps protons across a membrane as electrons are passed from one electron carrier to the next to establish a proton gradient The proton gradient is used by ATP synthase to generate ATP CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 29 ELECTRON CARRIERS High potential energy Each successive carrier in the chain has a greater ability to accept electrons Each transfer lowers the potential energy of the electron – some of the energy is used to pump protons In the figure, which carrier has the greatest potential energy? Lowest? Low potential energy CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 30 ELECTRON CARRIER CATEGORIES High potential energy Aerobes: conduct aerobic respiration, using oxygen as the final electron acceptor Anaerobes: conduct anaerobic respiration using inorganic chemicals other than oxygen Examples: SO42-  H2S NO3-  NO2- CO32-  CH4 Low potential energy CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 31 CHEMIOSMOSIS Chemiosmosis: the use of an ion gradient to generate ATP Do protons move from one side of the membrane to the other by passive diffusion? ATP synthase uses the proton gradient to generate ATP Not the only process that uses the proton gradient. Ex: bacterial flagellar movement uses the proton gradient to move, not ATP CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 32 ETC DIVERSITY Cytochrome C Oxidase The specific carriers in the ETC varies between and within bacteria, archaea, and eukaryotes Example: Some bacteria have cytochrome C oxidase while others don’t! CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 33 METABOLIC DIVERSITY Some bacteria use the Entner-Doudoroff (ED) pathway instead of the EMP pathway for ED glycolysis Glucose 6-phosphate enters a new path Products (per glucose): EMP: 2 ATP, 2 pyruvate, 2 NADH ED: 1 ATP, 2 pyruvates, 1 NADH, 1 NADPH CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 34 PENTOSE PHOSPHATE PATHWAY Pentose phosphate pathway: alternative to glycolysis for the breakdown of glucose. ED Major uses: Produce precursors for nucleotide synthesis NADPH production – carries electrons for anabolic reactions CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 35  NAD+ FERMENTATION NADH If the final electron acceptor is not present, electron carriers in the ETC remain stuck in a reduced state ATP can still be generated by glycolysis, but the supply of NAD+ needs to be regenerated Fermentation: partial oxidation of sugar to release energy using an endogenous organic molecule rather than an ETC Less efficient than respiration for energy generation CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 36 FERMENTATION There are several different fermentation products depending on the enzymes and substrates available Can be used to identify microbes CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 37 LIPID CATABOLISM Lipids can also be catabolized for energy Fats are broken down into glycerol and three fatty acids by beta-oxidation: Glycerol is broken down to into a G3P Fatty acids are broken down into acetyl-CoA which enter the Krebs cycle CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 38 PROTEIN CATABOLISM Most cells catabolize proteins as a low priority after glucose and fat Process: 1. Extracellular proteins broken down by proteases first (proteins often too large to take up into the cell) 2. Amino acids are deaminated (removal of amino group) 3. Resulting molecule enters Krebs. NH2 recycled or excreted as waste. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 39 PHOTOSYNTHESIS Bacteriochlorophyll a R is phytyl or geranylgeranyl Chlorophyll a Chlorophyll b Photosynthesis: capture of light energy to drive the synthesis of organic compounds from CO2 and H2O Pigments like chlorophyll a, and bacteriochlorophyll (a - g) capture light energy Chlorophyll is similar to heme (uses Mg2+ instead of Fe2+) Different pigments absorb light best at different wavelengths By A5b - Own work, redraw of http://zhurnal.lib.ru/img/o/oleg_w_m/cdocumentsandsettingsolegmoidokumentybakterialxnyjfotosintezrtf/fotosintez1.jpg, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=11786039 CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 40 THYLAKOIDS Photosynthetic Prokaryotes Photosynthetic Eukaryotes Thylakoids: cellular membranes where photosynthesis takes place In photosynthetic prokaryotes, they are invaginations of the cytoplasmic membrane In photosynthetic eukaryotes, thylakoids are found within chloroplasts CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 41 CHLOROPLASTS - REVIEW Chloroplasts have an inner and outer membrane Have a third membrane which forms flattened sacs called thylakoids Interior: thylakoid space Thylakoids can be stacked into granum The fluid outside of the thylakoids is called the stroma CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 42 PHOTOSYNTHESIS: SUMMARY Stage 1 (Light-dependent reactions): Protons are pumped into the thylakoid space driving the synthesis of ATP. NADP+ is reduced to NADPH. Requires light energy and water. Stage 2 (Light-independent reactions/Calvin Cycle): ATP and NADPH are consumed to drive the manufacture of sugars from CO2. CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 43 LIGHT-DEPENDENT REACTIONS: PHOTOSYSTEMS Exterior of prokaryote or Thylakoid space of chloroplast Cytoplasm of prokaryote or Stroma of chloroplast Pigments are organized in thylakoid membranes as photosystems Two photosystems (PS II and PS I) complete the light-dependent reactions Note their order and location of the H+, ATP, and NADPH relative to the membrane CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 44 NONCYCLIC PHOTOPHOSPHORYLATION Photons excite electrons in PS II which travels down an ETC to pump protons. The electrons from PS II replace the photon-excited electrons in PS I which are used to reduce NADP+ to NADPH. ATP synthase uses proton gradient to generate ATP CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 45 NONCYCLIC PHOTOPHOSPHORYLATION H2S S Oxygenic (oxygen-producing) organisms: Electrons from H2O replace electrons lost from PS II Anoxygenic (not oxygen-producing) organisms: Electrons from inorganic compounds like H2S replaces electrons lost from PS II CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 46 CYCLIC PHOTOPHOSPHORYLATION PS II not used Some organisms only utilize PS I in a process known as cyclic photophosphorylation A photon excites an electron in PS I which travels down an ETC to pump protons. The electron returns back to PS I. ATP synthase uses the proton gradient to generate ATP CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 47 LIGHT-INDEPENDENT REACTIONS Carbon from CO2 is fixed into an organic compound in a series of reactions known as the Calvin-Benson cycle Requires CO2, ATP, NADPH, and existing ribulose 1,5-bisphosphate 3 molecules of CO2 required to produce 1 molecule of glyceraldehyde 3-phosphate CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 48 OVERVIEW OF PHOSPHORYLATION Fill in the blanks CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 49 OTHER ANABOLIC PATHWAYS Glycolysis, Krebs cycle and the pentose phosphate pathway provide the 12 basic precursor metabolites. Some organisms can synthesize all 12, others can’t. Most metabolic pathways are amphibolic reactions: reversible metabolic reactions CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 50 CARBOHYDRATE BIOSYNTHESIS Glyceraldehyde 3-phosphate can be used to synthesize other complex polysaccharides Sugars can be synthesized from other precursors like amino acids and fats in a process known as gluconeogenesis Very endergonic CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 51 LIPID BIOSYNTHESIS Acetyl-CoA is used to synthesize fatty acids Glyceraldehyde 3-phosphate (and DHAP) can be used to glycerol CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 52 AMINO ACID BIOSYNTHESIS Amino acids can be generated from precursors by amination (amino comes from ammonia) or by transamination (amino comes from another amino acid) Essential amino acids: cannot be synthesized and must be obtained from diet/external source CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 53 NUCLEOTIDE BIOSYNTHESIS Adenine nucleotide Glycolysis yields glucose 6-phosphate which can be used to produce the pentose sugar Bases synthesized from glutamine, aspartic acid, ribose 5-phosphate and folic acid Phosphate is derived from ATP CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 54 INTEGRATION & REGULATION OF METABOLIC FUNCTIONS Examples: Synthesis of new transport protein to bring more of a chemical into the cell Use of allosteric regulation to control enzyme activity Methods of regulation are typically one of two types: 1. Control of gene expression: controls the amount and timing of protein (enzyme) production. 2. Control of metabolic expression: controls the activity of the proteins once produced CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 55 INTEGRATION OF CELLULAR METABOLISM ED Be familiar with the major metabolic pathways discussed CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 56 REVIEW Open up Kahoot (https://kahoot.it/) CAPILANO UNIVERSITY - EUGENE CHU - BIOL 203 57