Microprara Finals PDF

MICROBIAL METABOLISM CONTENTS 1. Microbial Nutrients and Nutrient Uptake 4. Biosyntheses 2. Energetics, Enzymes, and Redox 3. Catabolism: Fermentation and Respiration INTRODUCTION 2 Key Aspects of Process 1. Primary Metabolism 2. Se...

MICROBIAL METABOLISM CONTENTS 1. Microbial Nutrients and Nutrient Uptake 4. Biosyntheses 2. Energetics, Enzymes, and Redox 3. Catabolism: Fermentation and Respiration INTRODUCTION 2 Key Aspects of Process 1. Primary Metabolism 2. Secondary Metabolism - Vital for microbe’s survival - Grow, reproduce, survive - Breaks down nutrients into simplest forms Metabolism - Series of biochemical reactions by which the cell breaks down or biosynthesizes various metabolites. 2 Types of Metabolism 1. Anabolism 2. Catabolism - Building up of smaller molecules to - Breaking down of large molecules to bigger ones smaller ones Example: Amino acids to protein Example: Protein will become amino acids Microbial Nutrients and Nutrient Uptake: Cell Nutrition 2 Types of Nutrients 1. Macronutrients 2. Micronutrients - Required in large amounts - Required in minute amounts Chemicals in Predominant in Living Systems Dry Weight - C (Carbon) - Needed in the largest amount (50% of a cell’s dry weight) - O (Oxygen) & H (Hydrogen) - When combined, 2% of a cell’s dry weight - N (Nitrogen) - 13% of a cell’s dry weight - P (Phosphorus), S (Sulfur), K (Potassium), Mg (Magnesium), & Se (Selenium) - When combined, less than 5% of a cell’s dry weight Wet Weight - 75% of the wet weight is water (H 2O) and the rest is primary macromolecules Macromolecular Composition of a Cell - Protein - Amino acids - Lipid - Glycerol/fatty acids and can be found in cytoplasmic membrane - Polysaccharide & Lipopolysaccharide - Monosaccharide/Simple sugar - DNA & RNA - Nucleic acid/Nucleotide - Monomers are the building blocks of polymers (amino acids is to protein) Autotrophs - Organisms that can synthesize their own organic compounds from CO 2 Trace Metals - Essential metals that are required in small amounts - Functions as cofactors/helper molecules of enzymes Growth Factors - Organic rather than metallic - Include vitamins, amino acids, etc. - Functions as cofactors/help molecules of enzymes Microbial Nutrients and Nutrient Uptake: Transport of Nutrients Transport of Nutrients - An issue of transportation of nutrients is permeability of the cytoplasmic membrane and concentration of given nutrient inside the cytoplasm must be higher than outside. Active Transport - Requires the expenditure of energy - Process by which cells accumulate solutes against the concentration gradient 3 Basic Mechanism of Active Transport in Prokaryotic Cells 1. Simple Transport 3. ABC Transport 2. Group Translocation 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 o Example: Uptake of disaccharide sugar (lactose) - Antiport - Solute and proton are transported in opposite direction o Example: Sodium-proton antiporter - Only thing needed is transmembrane protein Proton - Also called the hydrogen ion Group Translocation - The transported substance is chemically modified during the transport process - Energy-rich organic compound drives the transport event - Phosphotransferase system - A family of five proteins that work in concert to transport any given sugar Phosphorylation - Addition of phosphoryl group to a molecule Dephosphorylation - Removal of phosphoryl group from a molecule ABC (ATP Binding Cassette) Transport System - Transport system that employs a periplasmic binding protein along with transmembrane and ATP-hydrolyzing components Energetics, Enzymes, and Redox Energy - Yielding reactions are part of metabolism called catabolism Energy Classes of Microbes Chemotrophs - Energy source is chemical 2 Types of Chemotrophs 1. Chemoorgenotrophs 2. Chemolithotrophs - Can live off of organic chemicals - Organisms using inorganic chemicals Example: E-coli Example: Thiobacillus thiooxidans Phototrophs - Energy is light - Contains chlorophyll 2 Types of Phototrophs 1. Oxygenic photosynthesis 2. Anoxygenic photosynthesis Heterotrophs vs Autotrophs - Carbon is obtained from organic compound (heterotrophs) - Microorganism uses CO2 as carbon source (autotrophs) Catalysis and Enzymes Activation Energy - Minimum energy required for a chemical reaction to begin 2 Types of Chemical Reactions 1. Exergonic 2. Endergonic - Releases energy - Absorbs energy Catalysts - Lowering the activation energy of a reaction thereby increasing the reaction rate - Enzymes are major catalysts in cells Non-protein Molecules - Prosthetic Groups - Coenzymes Electron Donors and Acceptors Oxidation-Reduction Reaction (Redox) - Occurs in pairs - Addition of electron to a substance - Removal of electron from a substance (reduction) (oxidation) Electron Donor - Substance that is oxidized Electron Acceptor - Substance that is reduced Energy-Rich Compounds - Energy released from the redox reaction fuels energy requiring cell function - Example: ATP (Adenosine Triphosphate - Most energy-rich phosphate compound), Acetyl-CoA, Acetyl Phosphate, Glucose 6-Phosphate, Phosphoenolpyruvate Fermentation and Respiration Fermentation - Form of anaerobic catabolism in which organic compounds both donate and accept electrons Respiration - 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 Glycolysis - Embden-Meyerhof-Parnas pathway - Always start with glucose - End product is pyruvate Glycolysis Stages Stage 1 (Preparatory Stage) - No redox reaction and releasing of energy - Only prepares glucose Steps in Stage 1 1. Phosphorylation through hexokinase (produces Glucose 6P) 2. Glucose 6P undergoes isomerization through isomers (produces fructose 6P) 3. Fructose 6P undergoes second phosphorylation through phosphofructokinase (produces fructose 1,6 biphosphate) 4. Aldolase splits fructose 1,6 biphosphate into two molecules with 3 carbon (glyceraldehyde 3- phosphate, dihydroxyacetone phosphate) 5. Triosephosphate isomerase converts dihydroxyacetone phosphate to glyceraldehyde 3- phosphate Stage 2 - Redox reactions Steps in Stage 2 6. First redox reaction where glyceraldehyde 3-phosphate is oxidized through glyceraldehyde 3- phosphate dehydrogenase (1,3 bisphosphoglycerate) 7. Phosphoglycerokinase convert 1,3 bisphosphoglycerate to 3P Glycerate 8. Phophoglyceromutase converts 3P glycerate into 2P glycerate 9. Enolase converts 2P glycerate into phosphoenolpyruvate 10. Pyruvate kinase converts phosphoenolpyruvate into pyruvate (end product is 2 pyruvate) Stage 3 - Redox balance - Either produce lactate or pyruvate decarboxylase and alcohol dehydrogenase - Green - Enzymes - Orange - Intermediates Fermentative Diversity - Sugars such as glucose and other hexoses as well as disaccharides and other relatively small sugars are preeminently fermentable Benefits of Fermentation - Organisms’ waste product from fermentation are important to humans since what’s important to these organisms is the ATP - Wine, bread, cheese, etc. Citric Acid Cycle - Alternative to fermentation - Happens when glucose is ready for respiration - Pyruvate will be oxidized Glyoxylate Cycle Options for Energy Conservation 1. Anaerobic Respiration 3. Phototrophs - Electron acceptors other than oxygen - Light energy is used instead of a support respiration chemical to drive electron flow and 2. Chemolithotrophs generate a proton motive force - Inorganic compounds as electron donors Biosynthesis Anabolism - Process of synthesizing complex molecules from simpler ones Pentose Phosphate Pathway MICROBIAL INTERACTION IN NATURE CONTENTS 1. Microbial Interactions at a Glance 3. Microbe: Host Interactions 2. Microbial Community Interactions 4. Human: Microbial Interactions Symbiosis - A long-term biological interaction between two or more organisms of the same or different species Fungal Interactions Morphology - Production of morphology-modulating compounds Survival - Production of antifungal compounds - Protection from antibiotics/antimycotics mycoparasitism Growth - Bacterial growth promoting factors - Co-aggression - Change in nutrient availability - Competitive inhibition Virulence - Production of virulence factors - Bacterial precursors for fungal secondary metabolites Fungi-Bacteria Interaction Endofungal Bacteria - Bacteria symbionts of fungi residing within the fungal mycelium - Example: Burkholderia - Produces the rice-killing toxin, rhizoxin and enables the fungus to produces infecting spores Fungi-Fungi Interaction Mycoparasitism - One fungus becomes parasite towards other fungus - Example: Mycoparasitic fungus establishes itself as a parasite on another fungus - Trichoderma species are applied in the biological control of fungal plant diseases Archaeal Interactions 1. Archeaon-Archeaon 3. Archaea-Unicellular Eukaryote 2. Archaea-Bacteria 4. Archaea-Metazoa Archaea-Archaea Interaction - Symbiont Nanoarchaeum Equittans directly attaches to the specialized outer membrane of Ignicoccus Hospitalis and obligatorily depends on the Ignicoccus host. Archaea-Bacteria Interaction - Methanobacillus Omelianskii comprises a methanogenic archaeon and a gram-negative bacterium, which in syntropy, converts ethanol to acetate and methane. Bacterial Interactions Virus-Bacteria Interaction - Bacteriophages or phages are viruses that infect bacteria Bacteria-Bacteria Interaction - Quorum Sensing - Cell-to-cell communication system used by many bacteria to coordinate colony-wide functions such as: bioluminescence, virulence, conjugation, and biofilm formation. - Release of AI (Autoinducer) Biofilm - Aggregate of microorganisms in which cells are embedded in a self-produced matrix of extracellular polymeric substance (EPS) Lynn Margulis - First to recognize the importance of bacteria in the evolution of higher organisms Endosymbiotic Theory - Origin of mitochondria and chloroplast Holobiont/Metaorganism Theory - A host organism and microorganisms that live in or on it are a single ecological unit - Describes the relationship between a host and its associated microorganism - Impacts: immune system, pathogen protection, development, organ morphogenesis, metabolism, reproduction, aging, behavior, colonization resistance, and speciation Impacts 1. Health and Fitness - Host appears to be fundamentally multiorganismal, where any disturbance within the complex partnership can have drastic consequences for the member’s health 2. Gut microbiome was shown to shape the tissues, cells, and molecular profile of mammalian gastrointestinal immune system during development - Can gut microbiota really affect psychology? Ruminant Gut Microbiome - Digestion happens in rumen (home for billions of bacteria) - Produces CH4 Zooxanthellae-Corals - Microalgae - Host provides shelter while - Located In polyps zooxanthellae provide nutrients - Colors comes from zooxanthellae Coral Bleaching - Occurs when there is a change in temperature, runoff and pollution, overexposure to sunlight, and extreme low tides - Acidic environment will stress a coral that makes the algae leave - Bleached coral appears white since its colors comes from the algae Anglerfish-Bioluminescent Bacteria - Eska has chambers for Vibro sp. that exudes luminescence - Host gives shelter and nutrients while bacteria provides light Legumes-Rhizobium - Nitrogen-fixing microbes in legumes - Bacteria supplies nitrogen to plant host while it supplies carbon bacteria Human Host Interactions Infection - Used to imply the growth of microorganism on or in the host Disease - Reserved for actual tissue damage or injury that impairs in the host function Pathogen - An organism or agent that causes disease in a host Microbial Adherence - Enhanced ability of a microorganism to attach to a cell surface - Fimbriae/capsule/slime layer for attachment to surface while flagellum for mobility Invasion - The ability of the pathogen to enter into hos cells or tissues, spread, and cause diseases - Some pathogens enter bloodstreams Colonization - Growth of microorganism after it has gained access to host tissues; typically begins at sites in the mucous membranes Pathogenicity, Virulence, and Attenuation Pathogenicity - Overall ability of the pathogen to cause disease Virulence - Measure of pathogenicity (lethal dose) Virulence Factors - Toxic or destructive produced by the pathogen that directly or indirectly enhance invasiveness and host damage by facilitating and promoting infection Attenuation - Decrease or loss of virulence of a pathogen Toxins Toxicity - The ability of an organism to cause disease by means of a toxin that inhibits host cell functions or kills host cells 2 Types of Toxins 1. Exotoxins 2. Endotoxins - Toxic proteins released from the - Toxic lipopolysaccharides found in the pathogen as it grows cell wall of most gram-negative bacteria cell wall Fundamentals of Host Defense Immunity - Ability of an organism to resists infection 2 Types of Immunity 1. Innate Immunity - Noninducible (does not need prior exposure) - Heavily dependent on phagocytes 2. Adaptive Immunity - Acquired ability to recognize and destroy a specific pathogen or its products - Specificity due to direct attack towards antigens - Phagocytes ingest and process antigen molecules and present them to immune cells called lymphocytes - Presented antigens bind specific receptors on the surface of the lymphocyte, triggering genes of antigen-specific proteins called antibodies (immunoglobulins) Immune memory - The ability to quickly produce specific immune cells or antibodies after subsequent exposure to previously encountered antigen Natural Host Resistance - Several resistance factors common to vertebrate hosts inhibit infection by most pathogens in a nonspecific way Other Innate Host Defenses Inflammation - A nonspecific reaction to noxious stimuli such as toxins and pathogens - Cytokines and Chemokines - Will produce high concentration of phagocytes Fever - Caused by certain cytokines Cytokines - Stimulate hypothalamus to produce prostaglandins Natural Killer Cells (NK Cells) - Cytotoxic lyphocytes that are distinct from T and B cells - Seeks out and destroys compromised cells, such as cells infected by intracellular pathogens or cancer cells Interferons (IFN-a and IFN-6) - Small proteins in the cytokine family that prevent viral replication by stimulating production of antiviral proteins in uninfected cells