University of Guyana Bio 2107: Lecture 3 Microbial Metabolism PDF

UNIVERSITY OF GUYANA FACULTY OF NATURAL SCIENCES DEPARTMENT OF BIOLOGY BIO 2107 THE BIOLOGY OF MICROORGANISMS LECTURE 3 MICROBIAL METABOLISM Dr. Sabrina Dookie 20th September, 2024  Nutritional Requirement...

UNIVERSITY OF GUYANA FACULTY OF NATURAL SCIENCES DEPARTMENT OF BIOLOGY BIO 2107 THE BIOLOGY OF MICROORGANISMS LECTURE 3 MICROBIAL METABOLISM Dr. Sabrina Dookie 20th September, 2024  Nutritional Requirements ESSENTIAL ELEMENTS: Bacterial structure is made up of various components eg. carbohydrates, lipids, proteins, nucleic acids. These compounds are made up of four basic elements: C, H, O, and N. Besides these four elements, phosphorous and sulphur are also required for bacterial growth. MINERALS: 1. Potassium, calcium, magnesium, iron, copper, cobalt, manganese, molybdenum and zinc. 2. These elements are required in trace amounts and are provided by various food sources.  What is microbial metabolism? Metabolism refers to the sum of biochemical reactions required for energy generation and the use of energy to synthesise cellular materials. The energy generation component is referred to as catabolism and the build-up of macromolecules and cell organelles is referred to as anabolism. During catabolism, the energy is changed from one compound to another and finally conserved as high energy bonds of ATP. It is generally energy-releasing or exergonic. ATP is the universal currency for energy. When energy is required for anabolism, it may be sent as high-energy bonds of ATP. It is generally energy-requiring or endergonic. Exergonic reactions provide energy for endergonic reactions!  endergonic exergonic Most biochemical reactions are part of a series of reactions referred to as a metabolic pathway. Pathways can be catabolic or anabolic. Each reaction is catalyzed by its own enzyme. It usually takes multiple reactions to make an end product.  Enzymatic Pathways for Metabolism Almost all biochemical reactions are catalyzed by a specific enzyme: ▪ Proteins that accelerate the rate of a reaction without being changed themselves ▪Lower the activation energy (Ea). ▪The need for enzymes provides a way to control or regulate biochemical reactions. ▪ Reactions won’t occur unless the enzyme that catalyzes the reaction is present & active. ENZYMES LOWER THE ACTIVATION ENERGY! Reactions won’t occur unless the Ea requirement is met. Enzymes physically bind Substrates  Control of Enzyme Activity Biochemical reactions can be controlled by changes in enzyme activity, which can be influenced in several ways: 1) Changes in the amount of enzyme or substrate. 2) Changes in temperature, pH or [salt]. 3) Availability of any necessary cofactors. 4) Effect of inhibitors: more enzyme and/or more substrate = more product! can affect enzyme structure, hence its activity some enzymes don’t work without a non-protein cofactor molecules that bind to enzymes & reduce their activity Factors affecting enzyme activity  Enzyme Denaturation Enzymes are polypeptides that retain their ability to function only when folded properly. Changes in temperature, pH or [salt] can disrupt amino acid “R group” interactions and cause the protein to unfold, i.e. become denatured. Mutations can also lead to misfolded, non- functional enzymes!  Cofactors for Redox Reactions a) Enzymes that catalyze redox reactions typically require a cofactor to “shuttle” electrons from one part of the metabolic pathway to another part. b) There are two main redox cofactors: NAD and FAD. These are (relatively) small organic molecules in which part of the structure can either be reduced (e.g., accept a pair of electrons) or oxidized (e.g., donate a pair of electrons). c) NAD and FAD are present only in small (catalytic) amounts – they cannot serve as the final electron acceptor, but must be regenerated (reoxidized) in order for metabolism to continue. *nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD)  Cofactors can also be a metal ion, vitamin, or other “non-protein” Enzyme is inactive without a cofactor. If the cofactor is organic, it is called a coenzyme (usually a vitamin).  Enzyme Inhibition Inhibitors bind enzymes in 1 of 2 ways: Inhibitors can bind reversibly(can “come Competitive inhibition (binding to the active site) off”) or irreversibly(don’t come off, e.g. Allosteric inhibition (binding elsewhere, changing “poisons”) shape) Adenosine Triphosphate (ATP) Adenosine Triphosphate (ATP)preferred source of useable energy for ALL cells: breaking bond of 3rd phosphate releases ideal amount of energy bond is easily broken (low Ea). This is why organisms convert “food” energy to “ATP” energy. Glycolysis Glycolysis is a catabolic pathway by which sugars such as glucose (and several other “food” sources) are broken down to two 3- carbon molecules of pyruvic acid (or pyruvate): releases energy to yield 2 ATP per glucose also transfers high energy electrons (+ H) to NAD+ to yield 2NADH  Glycolytic Pathways 4 major glycolytic pathways found in different bacteria: This is the pathway of glycolysis most familiar and common to most of the organisms. The pathway is operated by yeast to produce alcohol and lactic acid bacteria to produce lactic acid and several organic acids, gases, fatty acids, and alcohols. The pathway is as follows: Glucose → 2 pyruvate + 2 ATP + 2 NADH2 In aerobic conditions, some bacteria can convert hexoses in the metabolic pathway referred to as the pentose phosphate cycle or the hexose monophosphate pathway (HMP). This type of metabolism is known especially in facultative anaerobic organisms such as E. coli and K. aerogenes. The major purpose of this pathway is generation of reduced NADPH and pentose phosphates for nucleotide synthesis. Glucose 6-phosphate + 2 NADP+ + H2O → ribulose 5-phosphate + 2 NADPH + 2H+ + CO. The Entner-Doudoroff pathway. There are a few bacteria that substitute classic glycolysis with the Entner-Doudoroff pathway. They may lack enzymes essential for glycolysis. The pathway is as follows: The overall reaction is Glucose → 2 ethanol + 2 CO2 + 1 ATP The phosphoketolase pathway is distinguished by the key cleavage enzyme phosphoketolase, which cleaves pentose to glyceroldehyde 3 phosphate and acetyl phosphate. In this reaction, glucose is first metabolized to pyruvate, acetic acid and CO2 by the Pentose phosphate pathway. Pyruvate is then reduced to lactic acid whereas acetic acid is reduced to ethanol and CO2. The overall reaction is, Glucose → 1 lactate + 1 ethanol + 1 CO2 + 1 ATP This pathway is useful in the dairy industry for the preparation of kefir (fermented milk), yoghurt, etc.  Examples of fermentation pathways a) Lactic acid fermentation Found in many bacteria; e.g. Streptococcus sp, Lactobacillus acidophilus b) Mixed acid fermentation e.g. Escherichia coli c) 2,3-Butanediol fermentation e.g. Enterobacter aerogenes Different organisms recycle NAD+ in different ways, resulting in a variety of fermentation end-products. Respiration Chemiosmosis Summary of ATP Production  Photosynthesis Autotrophs can produce organic molecules from CO2, an inorganic carbon source. All heterotrophs require an organic source of carbon. Organic molecules, directly or indirectly, come from autotrophs. The source of energy for autotrophic processes can be: LIGHT: photoautotrophs that carry out photosynthesis. CHEMICAL: chemoautotrophs that use various molecules as a source of high- energy e-. Light-dependent Reactions: Photophosphorylation Light energy is harvested by photosynthetic pigments and transferred to a special reaction centre (photosystem) in chlorophyll molecules (thylakoids). The light energy is used to strip electrons from an electron donor (the electron donor goes from a reduced to an oxidized state). The electrons are shuttled through a series of electron carriers from a high-energy state to a low-energy state. During this process, ATP is formed. In the cyclic pathway of electron transport, electrons are returned to the electron transport chain. In the noncyclic pathway, the electrons are used to reduce NAD (or NADP) to NADH (or NADPH).  Stroma Thylakoid lumen Dark reaction (CO fixation) 2 The dark reaction in which the ATP and NADPH were used as energy and electron sources to fix the CO as carbohydrates. 2 The pathway involved in the dark reaction is the Calvin cycle, by which the CO is fixed as phosphoglyceic acid and leads to the formation of 2 many sugars. The formation of key monomers for anabolic reactions such as hexose phosphate – polysaccharides; pyruvic acid – amino acid and fatty acid; pentose phosphate – DNA and RNA.  Oxygenic photosynthesis a) Found in cyanobacteria (blue-green algae) and eukaryotic chloroplasts. b) Electron donor is H2O: Oxidized to form O2. c) Two photosystems: PSII and PSI. d) Major function is to produce NADPH and ATP for the carbon fixation pathways.  Anoxygenic photosynthesis a) Found in: c) Only one photosystem Green sulphur bacteria (e.g. Chlorobium) In green bacteria, the photosystem is similar to Green nonsulfur bacteria (e.g. PSI. Chloroflexus) In purple bacteria, the photosystem is similar to Purple sulfur bacteria (e.g. Chromatium) PSII. Purple non sulphur bacteria (e.g. Rhodobacter) d) Primary function is ATP production, chiefly via cyclic photophosphorylation. b) Electron donors vary: H2S or So in the green and purple sulfur bacteria H2 or organic compounds in the green and purple nonsulphur bacteria END OF LECTURE 3