Microbio Reviewer Lecture 5 PDF

Note: microorganisms are able to swallow up each other. e.g. Amphileptus Lecture 5. Microbial Metabolism Enzymes inside the cell are going to digest the food and the nutrients are Contents going to be reabsorbed. And that basically is the cy...

Note: microorganisms are able to swallow up each other. e.g. Amphileptus Lecture 5. Microbial Metabolism Enzymes inside the cell are going to digest the food and the nutrients are Contents going to be reabsorbed. And that basically is the cycle of life. 1.Microbial nutrients & Nutrient Uptake Histophagy – histophagus organisms such as these single-celled Coleps (eating dying ciliate) attack injured but live animals or other single-celled organisms 2. Energetics, Enzymes, and Redox sucking hunks of tissue rather than consuming whole organisms. When they attack an animal, they enter wounds and ingest tissue often attacking in 3. Catabolism: Fermentation & Respiration groups because their chemical sensing abilities attract many of them from a 4. Biosyntheses (Sugar) distance like microscopic vultures. Metabolism (property of life) is the series of biochemical reactions by which the cell breaks down or biosynthesizes various metabolites. Microorganisms have metabolism to thrive and survive. Anabolism: building up of smaller molecules to larger ones It is the sum of all chemical reactions in an organism, an engine running every living being, the process that keeps e.g. amino acids  protein life ticking over. There are two key aspects to this Catabolism: breaking down of large molecules to smaller ones process: Primary metabolism – breaking nutrient in simplest forms to be used for the production of energy. e.g. protein  amino acids Secondary metabolism – not essential, helping growth, 1. Microbial Nutrients & Nutrient Uptake: Cell Nutrition reproduction and to thrive in challenging environments. Macronutrients: required in large amounts Micronutrients: required in minute amounts Chemical Makeup of a Cell Metabolic pathway – set of interconnected chemical reactions that occur within a cell. The C: needed in the largest amount (50% of a cell’s dry weight) reactants, products, and intermediates of an enzymatic reaction are referred to O & H: combined, 25% of dry weight metabolites. Routes: thru respiration or N: 13% of dry weight P, S, K, Mg, & Se: combined, less than 5% of dry weight fermentation. Essential for all microorganisms: [H, C, N, O, P, S, Se] Essential cations/anions for most microorganisms: [Na, Mg, Cl, K, Ca] Most prokaryotic cells require organic compounds as their source of carbon. Cells can obtain organic carbon by (1) breaking down polymeric substances from environment or (2) direct uptake of monomeric substances or (3) microbes are autotrophs (organisms that can synthesize their own organic compounds from CO2, undergoes photosynthesis).  N: NH3 (amonia) NO3 (nitrate) [used by our cells] N2 (nitrogen gas) [toxic] K, Mg, Ca, Na About 75% of the wet. Weight of C, O, and H, N +(smaller amounts: Phosphorous (PO4-phosphate) & Sulfur (Sulfate, Sulfide) microbial cell is H2O, and the remaining is macromolecules (polymers – monomers): Protein – amino acids dominant. Lipid – fatty acids and glycerols. Polysaccharide (carbohydrates) –monosaccharides. DNA and RNA (nucleic acids) - nucleotid Cofactors – helper molecules of enzymes to carry out ther specific function Growth factors – organic rather metalic (Vita) MO requires several metals in small amount relative to macronutrients. Chief among these metals  Iron (Fe) – plays a role in cellular respiration Trace metals – essential metals that Microbial Nutrients & Nutrient Uptake: Transport of Nutrients are required in very small amounts relative to macronutrients  SIMPLE TRANSPORT reactions are driven by the energy inherent in the proton motive force. (source of energy) SYMPORT: solute and proton are cotransported in one direction If a cell is to grow and divide, it needs to take up macro ANTIPORT: solute and proton are transported in opposite direction and micronutrients from the environment. However, this process is difficult due to the semiermeability of the Sodium-proton cytoplasmic membrane, not all molecules and substances exits E. coli Symport reaction e.g. can enter and exit it. Also, the concentration of the given Proton enters uptake of nutrient in the cytoplasm must often be higher than its disaccharide concentration in the environment. How can microbial sugar cells overcome these fundamental problems? (lactose) & Several Membrane Transport System @Cytoplasmic M Proton  E. coli > Active Transport – requires the expenditure of energy, need energy source for it to happen. Cells accumulate solutes against the concentration gradients. (Prokaryotic cells 3Mech: Simple transport, group translocation, ABC transporter) ST – consists only of transmembrane transport protein GT – employs series of proteins in the transport event ABCT – consists of 3 components: substrate binding protein, transmembrane transporter, ATP hydrolizing protein GROUP TRANSLOCATION All are energy driven to proceed, 1. the transported substance is chemically modified during the transport process; 2. an energy- rich organic compound drives the transport event Differences of Simple transport and group translocation  GT: transported substances is chemically modified during the transport process, while ST doesn’t have that process  GT: required energy is energy rich organic compound, depends on the system, it drives the transport event, while ST’s energy is proton motive force.  Transport the sugars glucose, manose and fructose through group translocation  E.g. there’s a glucose to be transported to E. coli, before it is transported, there’s protein inside the cytoplasm called phosphotransferase system  Phosphorelation – addition of phosphoril group to a molecule (opposite diphosphorelation which is the removal)  Before glucose can be transported, the PS undergoes a series of PR and DR until they reach the protein (Enzyme 2c)  Enzyme 2c (ENZ 2c) makes sure the glucose will undergo phosphorelation, so that it will be chemically modified and as it enters the cytoplasm, it will be in a different form.  PHOSPHOTRANSFERASE SYSTEM: a family of five proteins that work in concert to trasnport any given sugar. ABC TRANSPORT SYSTEM  “ATP- binding cassette” – structural feature of proteins that bind with ATP  Transport system that employ a periplasmic binding protein along with transmembrane and ATP- hydrolyzing components Gram-negative bacteria – contain a region called periplasm (home to proteins that carry out different functions such as transport), it lies between the cytoplasmic membrane and the outer membrane which is part of the gram-negative cell wall. Proteins that enable the transport of substances  Periplasmic Binding Protein (e.g. a substance that needs to be transported entered a cell wall, it will bind with the periplasmic binding protein for it to be transported) 3 Components: Periplasmic binding protein, transmembrane protein, ATP- hydrolyzing protein Transported substance  binds with Periplasmic Binding Protein  enters transmembrane protein  with ATP hydrolyzing protein which is the energy, the transported substance will eventually enter the cytoplasm This can be seen in prokaryotic cells. 2. Energetics, Enzymes, and Redox: Energy Classes of Microbes If a microorganism already has all nutrients needed and are transported already in the cell, the next step is conserve some of the energy released in energy-yielding reactions. Catabolism – breaking down of large molecules into smaller units to produce energy and smaller molecules for other purposes In microorganisms, there energy classes of microbes (they are divided into two classes, depends on their energy source):  Chemicals “chemotrophs” (the process is called chemotrophy) o Divided into two classes, depends on what chemical needed or required:  Organic chemicals “chemoorganotrophs” e.g. E. coli. Most MO in a lab culture are CO.  Inorganic chemicals “chemolithothrophs” e.g. Thiobacillus thioxidans.  Chemical energy  ATP  Light “phototrophs” (the process is called phototrophy) o Phototrophs – contain chlorophylls and other pigments that convert light energy  ATP Energy- yielding reactions are part of metabolism o They don’t require chemicals unlike chemotrophs o Two forms of phototrophy known in bacteria: called catabolism.  Oxygenic photosynthesis – oxygen production 2 major divisions in carbon requirement:  Anoxygenic photosynthesis – no oxygen production  Heterotrophs – carbon is obtained from organic compound  Chemoroganotrophs Regardless of how MO conserves energy, be it from chemical or light, all cells requires large amounts of carbon in one form or another to  Autotrophs – when an MO use CO2 as carbon source  Chemolithotrops make new cell materials. There are 2 major divisios  How exactly is the energy available for chemotrophy and phototrophy conserve by the cell? Bioenergetics – branch of science that deals with energy transformation Basic Principles: Catalysts and Enzymes Two types of chemical reacion: Exorgonic (reaction that release energy) & Endorgonic (reaction that absorbs energy) Catalysts – they have no effect on the energetics or the equilibrium of the reaction, they just affect the rate at which the reaction proceeds, they just increase it. Activation energy is the minimum energy required for a chemical reaction to begin. Catalysts function by lowering the activation energy of a reaction, thereby increasing the reaction rate (green) This specifity is a function of the precise 3D structure of the enzyme. In one enzyme catalyst reaction, enzymes combine with the reactant, reactant called substrate. Active site – binding site of the substrate in the enzyme Substrate  Enzyme’s active site  forming substrate complex  a strain is placed in the bond of substrate  the bond is broken  release of Note: Many enzymes products = 2 products contain small non-protein molecules that participate Once enzyme’s active site is in catalysts, but they are empty, it is ready to begin a not themselves substrates. new catalytic cycle. Enzymes are major catalysts in cells. They are proteins that are highly specific for the reactions they catalyze. Non-protein molecules that are part of enyzme but not of substrate: Cells conserve energy from exorgonic reaction by coupling the reaction to the biosynthesis of  Prostetic groups energy-rich compound such as ATP.  Co-enzymes Oxidation-Reduction Reaction (REDOX) – reactions that release suffiecient energy from ATP. Oxidation – removal of electron from substance. Reduction – addition of an electron to a substance. E.g. Formation of H2O: Oxidation (Hydrogen, electrondonor, gives electron) & Reduction (Oxygen, electron acceptor, accepts electron)  Redox reaction occurs in pairs.  Electrondonor: the substance that is oxidized [removal of electron] e.g. a variety of organic and inorganic compounds  Electron acceptor: the substance that is reduced [addition of electron] Energy released from the REDOX reaction fuels energy requiring cell function. Once this energy is released, this energy must be trapped through the formation of energy-rich compunds e.g. Adenosine triphosphate (ATP) ATP (3 phosphate)– important in all cells. This is the most energy-rich phosphate compound. Cell respiration  ATP (used as fuel by cells) Phosphoenolpyruvate – energy that drive phosphotransferee system during gorup translocation. Acetyl phosphate Acetyl-CoA (Thiester bond – hydrolysis of this bond yield suffiecient free energy to be coupled with the synthesis of an energy-rich phosphate bond) Glucose 6-phosphate (Ester bond) 3. Catabolism: Fermentation & Respiration Fermentation: a form of anaerobic catabolism in which organic compounds both donate & accept electrons. Respiration: a form of aerobic or anaerobic catabolism in which an organic or inorganic electron donor is oxidized with oxygen or some other compound functioning as electron acceptor Major catabolic pathways that result Note: Glycolysis requires glucose (starting point). If the cell got in energy conservation in Glycolysis & Fermentation a nutrient that is not glucose, it needs to be transformed or chemoorganotrophs: Fermentation converted into glucose before it eneters glycolysis. and Respiration. Anaerobic – no oxygen. Aerobic – there is oxygen Very common pathway  Glycolysis Glycolysis – a nearly universal metabolic pathway for catabolism of glucose, which is present in all organisms both micro and macro. Another term: Emden, Meyerhof and Parnas. It is a series of reaction in which glucose is oxidized into pyruvate (end product: pyruvate). Preparatory stage I (preparatory reactions: no REDOX reaction, no energy released, consumption of ATP): converting glucose into intermediate products thru posphorylation When there is pyruvate, if the cell is and isomerization(glucose undergo phosphorylation through 1st enyzme: Hexokinase to anaerobic, can undergo form 1st intermediate product (Glucose 6-P), then undergo Isomerization thru 2nd enzyme: fermentation. Isomerase to produce Fructose 6-P, undergo 2nd phosphofructokinase to produce fructose If the cell is aerobic and others, can 1, 6 biphosphate and so on) REDOX RXNS II = 2 pyruvate  REDOX Balance III undergo Krebs or Citric-acid cycle  Green – enyzmes that are needed. Orange – intermediates (produced during a single-step, not the end product) Alcoholic fermentation  alcohol e.g. wine Homolactic fermentation  lactic Heterolactic fermentation  lactic and ethanol Propionic acid  propionate and acetate Mix acid  variety of acid To ferment, it needs to be anaerobic. That is the reason when fermenting, it needs to be covered or if is in a container it should be sealed with a lid. Fermentative Diversity  Sugars such as glucose & other hexoses (6 carbon) as well as disaccharides & other relatively small sugars are preeminently fermentable.  Since glucose is needed for glycolysis, sugars other than glucose must first be converted to glucose by isomerase enzymes.  Different types of fermentations are classified by either the substrate fermented or the products formed. Benefits of Fermentation  During glycolysis, glucose is consumed, ATP is made, & fermentation products are generated.  For the organism, the crucial product is ATP, fermentation products being merely waste products that must be discarded.  These fermentation products are important to humans, especially in food industry. The Citric Acid Cycle “Krebs Cycle” – alternative to fermentation Krebs Cycle happens when the glucose is ready for respiration, it means that the pyruvate will be oxidized. During respiration, the glucose is first catabolized through glycolysis to produce pyruvate. If the condition is ready for respiration, the pyruvate will be oxidized to carbon dioxide through the citric acid cycle. Pyruvate will be decarboxilated to produce Acetyl CoA (2 carbon)  Acetyl will separate from CoA  Acetyl will combine with Oxaloacetate (4 carbons) through the citrate synthase enzyme = Citrate  Citrate will undergo a series of reactions, conversion and transformation  REDOX reaction  = a-Ketoglutarate (5 carbon)  Succinyl-CoA  CoA = ATP or GTP & Succinyl = Succinate CO2 – toxic gas to the cell At the end of the glycolysis and citric-acid cycle, a total of 38 ATP is produced. The Glyoxylate Cycle 8 ATP produced from glycolysis. 30 ATP produced from citric acid cycle. Glyoxylate Cycle – it helps in regenerating in Oxaloacetate without relying on CAC Common natural products: Citrate, Malate, Fumarate, Succinate, and even glucose are used as electrondonors in energy metabolism employ the citric acid cycle for their catabolism. In contrast, there are organisms that use acetate (2 carbon), which can not be oxidized directly by CAC alone, so it needs Glyoxylate Cycle. CAC – can continue only if Oxaloacetate is continuously regenerated at each turn of the cycle Oxaloacetate – biosynthesis of glucose or amin acid precursor If cell lives in an environment that has no glucose, it needs Oxaloacetate to biosynthesize  If there is no oxygen, the option of microbe is to undergo Anaerobic Respiration Options for Energy Conservation Anaerobic Respiration: electron acceptors other than oxygen support respiration Chemolitotrophs: use inorganic compounds as electron donors Phototrophs: light energy is used instead of a chemical to drive electron flow & generate a proton motive force 4. Biosyntheses If the cells grow on glucose, obtaining glucose is not a problem. However, if Anabolism: process of synthesizing complex molecules from simpler ones they inhabit an environment with no glucose, they need to biosynthesize a glucose. The’re different option that microbes can do, depending on what is available in their environment. Glucose PS can be synthesized through activated forms of glucose, either UDPG or ADPG. Another way is through gluconegenesis, where phosphoenelpyruvate (starting material). Pentose Phosphate Pathway – major pathway of sugar that has 5 carbon  Pentose Phosphate Pathway Pentose Phosphate Pathway: e.g. Dexyribose and Ribose, sugars present in DNA and RNA Summary  Cells are primarily composed of elements H, O, C, N, P, & S.  Nutrients required by a cell in large amounts are called macronutrients while those required in very small amounts, such as trace elements or growth factors, are micronutrients.  Proteins are the most abundant class of macromolecules in the cell.  The active transport of nutrients into the cell is an energy- requiring process driven by ATP (or some other energy-rich compound) or by the proton motive force.  At least three classes of transport systems are known: simple, group translocation, and ABC systems.  Each functions to accumulate solutes against the concentration gradient.  All microorganisms conserve energy from either the oxidation of chemicals or from light.  Chemoorganotrophs use organic chemicals as their electron donors, while chemolithotrophs use inorganic chemicals.  Phototrophic organisms convert light energy into chemical energy (ATP) and include both oxygenic and anoxygenic species.  Enzymes are protein catalysts that increase the rate of bio- chemical reactions by activating the substrates (reactant) that bind to their active site.  Enzymes are highly specific in the reactions they catalyze, and this specificity resides in the three-dimensional structures of the polypeptide(s) that make up the protein(s).  Oxidation–reduction reactions require electron donors and electron acceptors.  The energy released in redox reactions is conserved in compounds that contain energy-rich phosphate or sulfur bonds.  The most common of these compounds is ATP, the prime energy carrier in the cell.  The glycolytic pathway is used to break down glucose to pyruvate and is a widespread mechanism for energy conservation by fermentative anaerobes that employ substrate-level phosphorylation.  The citric acid cycle generates CO2 and electrons for the electron transport chain and is also a source of biosynthetic intermediates.  The glyoxylate cycle is necessary for the catabolism of two-carbon electron donors, such as acetate.  Polysaccharides are important structural components of cells and are biosynthesized from activated forms of their monomers.  Gluconeogenesis is the production of glucose from nonsugar precursors