Metabolic pathways in Micro organisms.pptx

Microbial metabolism

1. Title: Utilization of Oxygen by Microbes Submitted To: Dr. Javed Iqbal Dasti PRESENTED BY: GROUP #5

2. Microbial Metabolism Definition: “Metabolism refers to the sum of all chemical reactions that occur within a living organism to maintain life. These reactions are involved in the processes of breaking down nutrients to produce energy and constructing cellular components.” Catabolism Anabolism Catabolism breaks down complex molecules for energy release. Catabolism releases energy (exergonic) . Example Glycolysis breaks down glucose into pyruvate, releasing energy. Anabolism builds complex molecules, requiring energy input. Anabolism requires energy (endergonic). Example Bacteria synthesize peptidoglycan for cell walls, requiring energy input.

3. Importance of Metabolism in Microorganisms Energy Production: Microorganisms rely on metabolism to generate energy (ATP) needed for growth, reproduction, and survival. Nutrient Cycling: Metabolic activities of microorganisms play a crucial role in nutrient cycling in ecosystems (e.g., nitrogen fixation, carbon cycling). Adaptation and Survival: Metabolic flexibility allows microorganisms to adapt to various environmental conditions and utilize different substrates for energy. Biotechnological Applications: Understanding microbial metabolism is essential for applications in biotechnology, such as fermentation, bioremediation, and the production of antibiotics.

4. Role of Oxygen in Metabolic Processes Aerobic Respiration: Oxygen acts as the final electron acceptor in the electron transport chain, enabling the production of a large amount of ATP through oxidative phosphorylation. Typical in aerobic microorganisms (e.g., many bacteria, fungi). Anaerobic Respiration: Some microorganisms use alternative electron acceptors (e.g., nitrate, sulfate) in the absence of oxygen to generate energy. Fermentation: In the absence of oxygen, some microorganisms rely on fermentation to produce ATP, resulting in by-products like ethanol or lactic acid. Common in anaerobic conditions or facultative anaerobes.

5. Diagram contrasting aerobic respiration, anaerobic respiration, and fermentation

6. Classification of Microorganisms Based on Oxygen Requirement

7. Why Classify Microorganisms by Oxygen Requirement? Microorganisms are classified based on their oxygen requirements. Microorganisms have varying needs and tolerances for oxygen. Oxygen requirements influence where and how these organisms live and thrive. This classification helps understand their ecological niches and metabolic strategies.

8. Obligate Aerobes Definition: Require oxygen for survival and growth. Oxygen is the final electron acceptor in their metabolic pathways. Characteristics: Grow at the top of a culture medium where oxygen concentration is highest. Possess enzymes like superoxide dismutase and catalase to detoxify reactive oxygen species (ROS). Example: Mycobacterium tuberculosis

9. Obligate Anaerobes Definition: Cannot survive in the presence of oxygen. Use other molecules as electron acceptors in metabolic processes. Characteristics: Lack enzymes to neutralize ROS. Grow at the bottom of a culture medium where oxygen concentration is lowest. Example: Clostridium botulinum Laboratory Test: GasPak Jar: Creates an anaerobic environment for the growth of obligate anaerobes. Thioglycollate Broth Test: Obligate anaerobes will grow at the bottom of the broth where oxygen concentration is lowest.

10. Facultative Anaerobes Definition: Can grow with or without oxygen. Prefer oxygen for aerobic respiration but can switch to anaerobic methods like fermentation when oxygen is absent. Characteristics: Versatile metabolic pathways. Grow throughout the culture medium but denser at the top. Example: Escherichia coli Laboratory Test: Thioglycollate Broth Test: Aerotolerant anaerobes will grow uniformly throughout the broth. Catalase Test: Detects the presence of catalase enzyme, which breaks down hydrogen peroxide into water and oxygen.

11. Aerotolerant Anaerobes Definition: Do not require oxygen but can tolerate its presence. Exclusively use anaerobic metabolism (e.g., fermentation). Characteristics: Possess some enzymes to deal with ROS but do not use oxygen for energy production. Grow uniformly throughout the culture medium. Example: Lactobacillus species Laboratory Test: Thioglycollate Broth Test: Aerotolerant anaerobes will grow uniformly throughout the broth. Oxidase Test: Typically negative as aerotolerant anaerobes do not use oxygen in their electron transport chain.

12. Microaerophiles Definition: Require oxygen for growth but at lower concentrations than atmospheric levels. High concentrations of oxygen are toxic to them. Characteristics: Grow in a specific layer of culture medium where oxygen concentration is optimal (usually just below the surface). Have limited capability to detoxify ROS. Example: Helicobacter pylori Laboratory Test: Candle Jar Method: Creates a microaerophilic environment suitable for the growth of microaerophiles. Thioglycollate Broth Test: Microaerophiles will grow in a specific zone just below the surface of the broth where oxygen concentration is lower than atmospheric levels.

13. Aerobic metabolism: It is a type of cellular respiration that requires oxygen to generate energy from organic molecules. It is the most efficient way for cells to produce ATP, the energy currency of the cell. In aerobic metabolism, oxygen serves as the final electron acceptor in the ETC. Use of Oxygen as final electron acceptor: Electron Transport Chain(ETC): During aerobic respiration, electrons are transferred through a series of protein complexes (Complexes I-IV) in the mitochondrial inner membrane. Protein Gradient: The transfer of electrons through these complexes is coupled with the pumping of protons (H⁺ ions) from the mitochondrial matrix to the intermembrane space, creating an electrochemical gradient (proton motive force). 13

14. More info ATP Synthesis: Protons flow back into the mitochondrial matrix through ATP synthase, a process that drives the synthesis of ATP from ADP and inorganic phosphate (Pi). Reduction of oxygen: At Complex IV (cytochrome c oxidase), electrons combine with molecular oxygen (O₂) and protons to form water (H₂O). This reaction is crucial as it removes low-energy electrons from the ETC, allowing the continuous flow of electrons and sustaining the production of ATP. 14

15. Obligate aerobes: 15 Obligate aerobes are organisms that require oxygen for their survival and growth. These organisms depend on aerobic metabolism to produce ATP, as they rely exclusively on oxygen as the final electron acceptor in the electron transport chain. Without oxygen, obligate aerobes cannot generate sufficient energy to sustain their cellular functions and will eventually die. Applications of obligate aerobes: Medical Microbiology: Identifying obligate aerobes helps diagnose infections and determine appropriate treatments. For example, the bacterium Mycobacterium tuberculosis, an obligate aerobe, causes tuberculosis and requires oxygen for its growth in the lungs.

16. More info: Biotechnology: Obligate aerobes are used in industrial processes that require aerobic conditions. For instance, Acetobacter aceti is an obligate aerobe used in the production of vinegar, where it oxidizes ethanol to acetic acid. Environmental Science: Obligate aerobes play a crucial role in biodegradation and bioremediation. These organisms can degrade pollutants in aerobic environments, such as soil and water, aiding in the cleanup of contaminated sites. Food Industry: The preservation and spoilage of food can be influenced by obligate aerobes. Understanding which microbes require oxygen can help in developing packaging methods that limit oxygen exposure, thus extending the shelf life of food products. 16

17. Obligate Anaerobes Obligate anaerobes are microorganisms that require an oxygen-free environment to grow and survive. They are unable to tolerate oxygen and are typically killed or inhibited by its presence. These microorganisms have evolved to thrive in environments where oxygen is absent or present in very low concentrations, such as: 1. Deep-sea vents 2. Soil and sediment 3. Human gut and other animal intestines 4. Fermenting food and beverages 5. Industrial processes like biogas production.

18. Examples Examples obligate anaerobes include: 1. Clostridium (e.g., C. difficile, C. perfringens) 2. Bacteroides (e.g., B. fragilis) 3. Fusobacterium (e.g., F. nucleatum) 4. Peptostreptococcus 5. Methanobrevibacter (methane-producing archaea)

19. Characteristics Obligate anaerobes have unique physiological and biochemical adaptations to survive in oxygen-free environments, such as: 1. Absence of catalase and superoxide dismutase (enzymes that protect against oxygen toxicity) 2. Specialized electron transport chains and energy metabolism 3. Ability to produce antioxidants and reduce oxygen toxicity 4. Tolerance to high concentrations of carbon dioxide and hydrogen.

20. Medical Applications - Infections : Obligate anaerobes are a major component of the normal microflora on mucous membranes and can cause disease when mucosal barriers break down ¹. - Antibiotics : Research into anaerobic bacteria has led to the development of antibiotics ². - Vaccine Development : Anaerobic bacteria have been used to develop vaccines ².

21. Environmental Applications - Biodegradation : Anaerobic microorganisms play a crucial role in biodegrading organic pollutants ². - Wastewater Treatment : Anaerobic microorganisms are used in wastewater treatment to break down organic matter ². - Soil Remediation : Anaerobic microorganisms have the potential to clean pollutants from soil ².

22. Anaerobic metabolism Anaerobic metabolism , which can be defined as ATP production without oxygen (or in the absence of oxygen). Anaerobic metabolism in microbes refers to the process by which certain microorganisms can generate energy without the presence of oxygen. Instead of using oxygen as a final electron acceptor in their metabolic pathways, these microbes utilize alternative molecules, such as nitrate, sulfate, or carbon dioxide Importance: Anaerobic metabolism is particularly important in short-duration, high-intensity exercise. With extreme exertion, most of the adenosine triphosphate (ATP) for contraction is generated from a net breakdown of creatine phosphate and an acceleration of the conversion of glycogen or glucose to lactate. The anaerobic metabolism used by anaerobic bacteria not only produced energy but also produced nutrients required by bacteria ANAEROBIC METABOLISM

23. ANAEROBIC RESPIRATION Anaerobic metabolism enables the breakdown of complex organic compounds that cannot be metabolized through aerobic respiration. This process helps in the recycling of organic matter and the release of nutrients back into the ecosystem. Anaerobic metabolism contributes to the production of various useful compounds, including methane gas and certain types of organic acids. A naerobic respiration: Metabolic reactions and processes that take place in the cells of organisms that use electron acceptors other than oxygen Types of Anaerobic Respiration Lactic Acid Fermentation. Alcohol Fermentation.

24. Uses of alternative electron acceptors

25. WHAT IS FERMENTATION? Fermentation  is a  metabolic process that produces chemical changes in organic  substances  through the action of  enzymes . In  biochemistry , it is broadly defined as the extraction of energy from  carbohydrates  in the absence of  oxygen . Process of fermentation Fermentation is an anaerobic biochemical process. In fermentation, the first process is the same as cellular respiration, which is the formation of pyruvic acid by glycolysis where net 2 ATP molecules are synthesized. In the next step, pyruvate is reduced to lactic acid, ethanol or other products. Types Lactic Acid Fermentation . Lactic acid is formed from pyruvate produced in glycolysis. Alcohol Fermentation . This is used in the industrial production of wine, beer, biofuel, etc. This Photo by Unknown Author is licensed under CC BY-SA-NC

26. Lactic acid fermentation Lactic acid fermentation is a metabolic process by which glucose or other six-carbon sugars (also, disaccharides of six-carbon sugars, e.g. sucrose or lactose) are converted into cellular energy and the metabolite lactate, which is lactic acid in solution

27. Alcoholic fermentation Alcoholic  fermentation , also called ethanol fermentation, is the  anaerobic respiration  pathway in yeasts where sugars are used as a substrate to form ethanol and carbon dioxide.

28. Facultative Anaerobes Characteristics: Metabolic Flexibility: Can grow in both the presence and absence of oxygen. Aerobic Conditions: Preferentially use oxygen for respiration when available, resulting in higher ATP yield. Anaerobic Conditions: Switch to anaerobic respiration or fermentation when oxygen is scarce.

29. Facultative Anaerobes Examples of Facultative Anaerobes: Escherichia coli (E. coli): Commonly found in the intestines of warm-blooded organisms; widely studied model organism. Saccharomyces cerevisiae: A type of yeast used in baking and brewing; can ferment sugars to produce alcohol and CO2 in anaerobic conditions. Staphylococcus aureus: A bacterium that can cause skin infections and other illnesses; can survive in various environments.

30. Facultative Anaerobes Applications: Industrial Fermentation: Utilized in the production of alcoholic beverages, bread, and biofuels due to their ability to perform fermentation. Biotechnology: Employed in genetic engineering and recombinant protein production, as their ability to grow in different conditions facilitates laboratory cultivation. Medical Relevance: Some facultative anaerobes are pathogenic; understanding their metabolism aids in developing treatments for infections. Environmental Impact: Play a role in bioremediation, helping to break down pollutants in both aerobic and anaerobic environments.

31. Facultative Anaerobes in Various Environments Versatility in Diverse Environments: Soil and Water: Adaptable to fluctuating oxygen levels, contributing to nutrient cycling. Human Body: Can colonize different niches, such as the gut, skin, and mucous membranes. Extreme Environments: Some species can withstand harsh conditions, making them useful in biotechnological applications. Case Study: E. coli in the Human Gut Function: Helps in digestion and synthesizes vitamins. Pathogenic Strains: Some strains cause diseases like food poisoning and urinary tract infections.

32. Aerotolerant Anaerobes Microorganisms capable of surviving in the presence of oxygen but do not utilize it for growth. Unique characteristics make them valuable in various industries. Challenges: Contamination risk due to aerobic organisms. Optimization of fermentation conditions. Future Directions: Genetic engineering for improved strains. Enhanced fermentation technology

33. Aerotolerant to Oxygen Indifferences to Oxygen: Tolerate the presence of oxygen. Lack the enzymes needed for aerobic respiration. Utilize alternative metabolic pathways for energy production. Examples: Lactic acid bacteria (e.g., Lactobacillus, Streptococcus). Certain species of Clostridium. Some yeast species.

34. Fermentative Industries Applications in Food Fermentation: Production of yogurt, cheese, pickles, and sauerkraut. Preservation and flavor enhancement. Applications in Biotechnology Bioprocessing: Production of organic acids, alcohols, and enzymes. Used in biofuel production Applications in Pharmaceutical Industry Antibiotic Production: Certain strains of aerotolerant anaerobes are used in antibiotic production. Streptomycin, tetracycline, etc

35. MICROAEROPHILES Characteristics of Microaerophiles:- Oxygen Requirement : Require oxygen for growth but at lower concentrations than atmospheric levels.  Oxygen level is significantly reduced compared to the 21% found in normal air. Cannot grow in anaerobic (oxygen-free) conditions. Growth Conditions : Optimal growth occurs at oxygen levels between 1% and 10%. Often found in specific niches where oxygen is limited, such as the gastrointestinal tract, deep soil layers, or sediments. Metabolic Adaptations : Possess enzymes like superoxide dismutase and catalase to manage reactive oxygen species, but at levels suited to their low-oxygen environment.

36. MICROAEROPHILES Examples:-  Helicobacter pylori : colonizes the human stomach lining Campylobacter jejuni : thrives in the gastrointestinal tract of birds and mammals. Borrelia burgdorferi : transmitted by ticks and surviving in low-oxygen environments within hosts.

37. Ecological and Medical Importance Pathogenicity: ​ Many microaerophiles are significant human pathogens. ​ Eg :- peptic ulcers, stomach cancer, Lyme disease ​ Ecological Roles: ​ Play roles in nitrogen cycling, carbon cycling, and other environmental processes in low-oxygen habitats. ​

38. MICROAEROPHILES ​ Culturing  methods . ​ Candle jars:  Candle jars are containers into which a lit candle is introduced before sealing the container's airtight lid. The candle's flame burns until extinguished by oxygen deprivation, creating a carbon dioxide-rich, oxygen-poor atmosphere. ​ Gas-Pak Jars : ​  Used to create a microaerophilic environment for culturing these organisms. ​ Controlled Atmosphere Incubators : ​  More sophisticated equipment that allows precise control of oxygen and carbon dioxide levels to mimic natural habitats. ​

39. Introduction to Metabolic Pathways Definition: Metabolic pathways are a series of chemical reactions in a cell, facilitated by enzymes, to sustain life. Types: Catabolic (break down molecules) Anabolic (build up molecules) Importance: Energy production synthesis of biomolecules waste management.

40. Enzymes in Metabolic Pathways Role of enzymes: Catalysts that speed up chemical reactions without being consumed. Specificity: Each enzyme is specific to a particular substrate. Examples: Hexokinase in glycolysis, (catalyzes the phosphorylation of glucose) DNA polymerase in DNA replication.

41. Mechanisms to Detoxify Reactive Oxygen Species (ROS) There are following mechanism to detoxify Reactive Oxygen Species (ROS): Enzymatic Antioxidant Defense Systems Non-Enzymatic Antioxidant Defense Systems Repair Systems

42. 1.Key Enzymes:(Catalases) Function: Catalase catalyzes the decomposition of hydrogen peroxide (H₂O₂) into water (H₂O) and oxygen (O₂). Reaction: 2H₂O₂ → 2H₂O + O₂ Location: Found in peroxisomes in nearly all aerobic cells. Mechanism: Catalase contains a heme group that facilitates the breakdown of H₂O₂. It operates at high efficiency, preventing the accumulation of H₂O₂ which can be harmful.

43. Key Enzymes: Peroxidase and Superoxide Dismutase (SOD) Function: Peroxidases reduce peroxides, such as hydrogen peroxide, using various electron donors. Reaction: H₂O₂ + AH₂ → 2H₂O + A (where AH₂ is a generic electron donor, such as glutathione). Types: Includes enzymes like glutathione peroxidase, which uses glutathione as a substrate to neutralize peroxides. Mechanism: These enzymes contain a heme group or a selenocysteine residue that helps in the reduction of H₂O₂ to water, thereby neutralizing it. Function: SOD catalyzes the dismutation of superoxide radicals (O₂⁻) into oxygen (O₂) and hydrogen peroxide (H₂O₂). Reaction: 2O₂⁻ + 2H⁺ → O₂ + H₂O₂ Types: Cu/Zn-SOD (found in the cytoplasm), Mn-SOD (found in mitochondria), and Fe-SOD (found in prokaryotes). Mechanism: SOD alternates between reduced and oxidized states to facilitate the conversion of superoxide radicals into less reactive species.

44. 2. Non-Enzymatic Antioxidant Defense Systems I. Glutathione: Function: Glutathione (GSH) is a tripeptide that acts as a reducing agent and a substrate for glutathione peroxidase. Mechanism: It directly reacts with ROS or serves as a cofactor for enzymes that reduce ROS. GSH is oxidized to glutathione disulfide (GSSG) in the process, which can be regenerated back to GSH by glutathione reductase. II. Vitamin C (Ascorbic Acid): Function: Vitamin C is a water-soluble antioxidant that can donate electrons to neutralize ROS. Mechanism: It directly scavenges reactive species such as superoxide, hydroxyl radicals, and singlet oxygen. It can also regenerate other antioxidants, like vitamin E, from their oxidized forms.

45. Non-Enzymatic Antioxidant Defense Systems III. Vitamin E (α-Tocopherol): Function: Vitamin E is a lipid-soluble antioxidant that protects cell membranes from lipid peroxidation. Mechanism: It reacts with lipid radicals produced in the lipid peroxidation chain reaction, thereby terminating the reaction and preventing further damage to cell membranes. IV. Carotenoids : Function: Carotenoids, such as beta-carotene, are pigments with antioxidant properties. Mechanism: They quench singlet oxygen and scavenge free radicals, protecting cells from oxidative damage.

46. 3.Repair System I. DNA Repair Enzymes: Function: These enzymes detect and repair damaged DNA caused by ROS. Mechanism: Includes base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). They recognize damaged DNA bases, remove them, and fill in the correct bases using the undamaged strand as a template. II. Proteases: Function: Proteases degrade oxidatively damaged proteins. Mechanism: Specific proteases recognize and selectively degrade damaged proteins, preventing the accumulation of dysfunctional proteins that can disrupt cellular functions.

47. Ecological and Environmental Impact Microorganisms decompose organic matter. Influence oxygen levels in various habitats (e.g., soil, water bodies). D etoxification of pollutants.

48. Industrial Application: Biotechonolgy : Genetic engeneering Protein production Pharmaceuticals Antibiotics Probiotics Food and beverage industry Fermentation Food preservation

49. Environmental applications Bioremediation Waste treatment Agriculture applications Biofertilizers Biopesticides

50. Medical Applications: Pathogen Identification Importance of rapid and accurate pathogen identification in disease control use of PCR, DNA sequencing, and biosensors Examples: Identification of bacteria, viruses, and fungi in clinical samples Faster diagnosis leading to timely treatment Im proved patient outcomes Industrial Applications: Biofuel Production Need for renewable energy sources Conversion of biomass into biofuels using microorganisms Examples: Ethanol production from corn, biodiesel from algae Reduces dependence on fossil fuels Lower carbon footprint

51. Waste Treatment Why we need it? Protects air, water, and soil quality. Reduces the risk of disease transmission from untreated waste. Ensures clean and safe drinking water supplies. Encourages recycling and reuse, reducing the extraction of raw materials. How it works? Waste is collected from households, industries, and businesses and transported through specialized vehicles. Separation of waste into categories: recyclable, non-recyclable, hazardous, and organic. Decomposition of organic waste (food scraps, yard waste) into nutrient-rich compost.

52. Burning of non-recyclable waste at high temperatures called incineration. Reduces waste volume and generates energy, though it must be managed to control emissions. Disposal of waste in designated landfill sites. Advanced Treatment Technologies Biological treatment (e.g., anaerobic digestion) for wastewater Chemical treatment (e.g., neutralization, precipitation) for industrial waste. Thermal treatment (e.g., pyrolysis, gasification) for converting waste into energy.

53. ADVANCEMENTS Systems Biology Approaches: Integration of omics technologies (genomics, transcriptomics, proteomics, metabolomics) has provided a holistic view of metabolic pathways and their regulation. 2. Metabolic Flux Analysis: Techniques like stable isotope labeling coupled with mass spectrometry have enabled researchers to measure metabolic fluxes in cells and tissues.

54. 3. Microbiome Influence: Understanding the role of the gut microbiome in metabolism has emerged as a significant area of research. The gut microbiota can metabolize nutrients and produce metabolites that influence host metabolism and overall health. Advances in metagenomics and metabolomics have facilitated the study of these interactions. 4. Metabolic Diseases: Progress in genetics and molecular biology has deepened our understanding of metabolic diseases such as diabetes, obesity, and metabolic syndrome. Genome-wide association studies (GWAS) have identified genetic variants associated with these conditions, shedding light on their underlying mechanisms. 5. Mitochondrial Function: Mitochondria play a central role in cellular metabolism, and advancements in imaging and molecular biology have allowed researchers to study mitochondrial dynamics, function, and their role in various metabolic pathways.

55. 6. Metabolic Regulation: Elucidating the regulatory mechanisms governing metabolic pathways is crucial for understanding how cells adapt to different physiological and environmental conditions. Signaling pathways, transcriptional regulation, and post-translational modifications are all areas of intense study in this regard. 7. Therapeutic Interventions: Targeted therapies, such as drugs that modulate specific metabolic pathways or hormone signaling, are being explored for conditions like diabetes and cancer. 8. Nutritional Metabolism: Advances in nutritional science have refined our understanding of how dietary components are metabolized and their impact on health. This includes research on macronutrient metabolism, micronutrient requirements, and the role of dietary patterns in disease prevention.

56. CONCLUSION Diversity of Metabolic Pathways: Gut Microbiota: Environmental Metabolism: Biotechnological Applications: Synthetic Biology: Microbial Communities: Metabolic Modeling and Systems Biology: Emerging Technologies: