BIO 2107 Summary PDF

Lecture 1 Modern Era Overview: The Modern Era in microbiology marks a significant advancement in understanding the complexities of microorganisms, particularly through molecular biology. This period emphasizes the study of simpler organisms like bacteria to unravel genetic and biochemical processes that govern life. Molecular Biology: o Focus on understanding the genetic code. o Study of DNA regulation and RNA translation into proteins. o Shift from complex plant and animal cells to simpler bacterial models for research. Genetic Code: o Insights gained into how genes function and are expressed. o Understanding of enzyme mechanisms and gene interactions. Bacterial Research: o Bacteria as ideal tools for studying fundamental biological processes. o Simplified models allow for clearer insights into physiological and biochemical functions. o Contributions to the development of molecular biology as an independent discipline. Historical Context: o By 1900, microbiology had matured into a distinct branch of biology. o Transition from earlier eras (Discovery, Transition, Golden) to a focus on microorganisms as key players in various life processes. Discovery Era Overview: The Discovery Era marks a significant period in the history of microbiology, characterized by the challenge to the Spontaneous Generation Theory and the groundbreaking work of early microscopists. This era laid the foundation for understanding microorganisms through advancements in microscopy and observation. Spontaneous Generation Theory: o Proposed by Aristotle, suggesting living organisms could arise from non-living matter. o Supported for over 2000 years; examples included mice from corn and flies from manure. o Eventually challenged by scientific discoveries in microbiology. Robert Hooke: o Lived from 1635 to 1703; an accomplished microscopist. o Authored Micrographia (1665), the first book dedicated to microscopic observations. o Provided the first known description of microorganisms, including fruiting structures of moulds like Mucor. Antoni van Leeuwenhoek: o Lived from 1632 to 1723; recognized as the "Father of Microbiology." o First to observe and describe microorganisms (termed 'animalcules') in 1676. o Constructed over 250 microscopes with magnification capabilities of 50-300 times. o His precise descriptions of bacteria and protozoa advanced the field of bacteriology and protozoology. Transition Era Overview: The Transition Era marks a significant period in the debate over spontaneous generation (abiogenesis) versus biogenesis. Key figures like Francesco Redi, John Needham, and Lazzaro Spallanzani conducted experiments that challenged or supported the idea of life arising from non-living matter. Francesco Redi: o Conducted experiments in the mid-17th century to disprove abiogenesis. o Used jars with rotting meat; some sealed, others open. o Observed maggots only in open jars where flies could lay eggs, concluding that maggots arise from fly eggs, not spontaneously. John Needham: o Supported abiogenesis theory despite Redi's findings. o Heated chicken broth and corn infusions, then sealed them in flasks. o Claimed organisms appeared spontaneously due to "vital force" in the air, attributing failure to observe microorganisms in Spallanzani’s experiments to destruction of this force by heating. Lazzaro Spallanzani: o Challenged Needham's conclusions regarding abiogenesis. o Showed that nutrient fluids did not contain microorganisms when subjected to prolonged heating in sealed flasks. o Suggested that microorganisms entered Needham’s solutions post-boiling from the air, countering the notion of spontaneous generation. Historical Perspectives of Microbiology Overview: The historical perspectives of microbiology encompass the evolution of the field, highlighting key discoveries and eras that shaped our understanding of microorganisms. This includes the transition from early observations to modern techniques in studying microbial life and its significance in various domains. Course Objectives: o Place the study of microorganisms in a historical context. o Differentiate major groups of microorganisms. o Describe basic biology of microorganisms. o Demonstrate roles of microorganisms in food spoilage and poisoning. o Explain their role in maintaining a healthy environment. o Illustrate the impact of microorganisms on human health. o Write authoritative accounts on specialized aspects of microbiology. Microbiology Definition: o Study of microorganisms, including bacteria, viruses, fungi, and protozoa, focusing on their biology, ecology, and interactions with humans and the environment. Microbial Diversity: o Exploration of the vast variety of microorganisms, their classifications, and ecological roles. Microbial Communities: o Examination of how different microorganisms interact within communities and ecosystems, influencing health and environmental processes. Historical Eras of Microbiology: o Discovery Era: Early observations and identification of microorganisms. o Transition Era: Development of techniques for studying microbes and understanding their roles. o Golden Era: Major advancements in microbiology, including germ theory and antibiotic discovery. o Modern Era: Current research trends, technologies, and applications in microbiology, including genetic engineering and biotechnology. Golden Era Overview: The Golden Era of microbiology, spanning the late 19th century, marked significant advancements in understanding infectious diseases and the role of microorganisms. Key figures like Louis Pasteur and Robert Koch laid the groundwork for germ theory, pure culture techniques, immunization, and antibiotic discovery. Louis Pasteur: o Demonstrated that fermentation is caused by microbial activity. o Introduced terms 'aerobic' and 'anaerobic' to describe life forms based on oxygen presence. o Invented pasteurization to kill harmful microbes in food and beverages. Germ Theory of Disease: o Concept that microorganisms can cause disease. o Early contributions from Benedict Prevost (fungal disease in wheat) and C.J. Davaine (bacterial agents in anthrax). o Joseph Lister applied this theory in surgery, using phenol to prevent infections. Robert Koch: o Confirmed germ theory through his work with Bacillus anthracis and anthrax. o Developed Koch’s Postulates, a systematic method for identifying disease-causing organisms. o His methods established the foundation for modern scientific research. Pure Culture Techniques: o Around 1870, the importance of isolating microorganisms in pure cultures was recognized. o Joseph Lister first obtained pure cultures using serial dilutions in liquid media. Immunization: o Pioneered by various researchers during this era, leading to the development of vaccines against infectious diseases. Antibiotics Discovery: o Alexander Fleming discovered penicillin in 1928 after observing antibacterial properties of Penicillium notatum mold. o This discovery led to the development of many antibiotics used today. Lecture 2 Microbial Biodiversity Overview: Microbial biodiversity refers to the variability among microorganisms, encompassing their evolution, morphology, metabolism, and ecological roles. This diversity has developed over nearly 4 billion years, allowing microbes to adapt to a wide range of environments on Earth. Definition: o Variability among microorganisms. o Encompasses differences in structure, function, and ecology. Evolution: o Result of nearly 4 billion years of evolutionary processes. o Microbes exhibit greater evolutionary diversity than macroscopic organisms. o Evolutionary diversity is often represented through genealogical trees based on genetic sequences. Morphological Diversity: o Variation in cell size and shape (morphology). o Differences in cellular structures across various microbial groups. Structural Diversity: o Differences in cellular organization and architecture. o Includes variations in cell walls, membranes, and organelles. Metabolic Diversity: o Enormous metabolic versatility allows prokaryotes to thrive in diverse habitats. o Microbes can utilize various energy sources and perform different biochemical processes. Ecological Diversity: o Microbes inhabit a vast range of environments, from extreme conditions (e.g., high salinity, temperature extremes) to more common habitats. o Examples include freshwater, marine environments, and extreme pH levels. Behavioral Diversity: o Variation in motility and interaction with other organisms. o Includes behaviors related to nutrient acquisition, communication, and symbiosis. Evolutionary Diversity: o Genetic diversity underlies all aspects of microbial diversity. o Expressed quantitatively through phylogenetic trees that illustrate relationships based on genetic data. Phylogenetic Analysis Overview: Phylogenetic analysis is the study of evolutionary relationships among biological entities, often using genetic data. It involves constructing phylogenetic trees to visualize these relationships and understand the history of species' evolution based on shared ancestry. Phylogenetic Trees: o Graphic representation of evolutionary relationships. o Composed of nodes (divergence points) and branches (evolutionary pathways). o Tips represent current species; branch lengths indicate the number of changes over time. o Closer related species share more recent common ancestors. Tree Construction: o Utilizes character-state methods, also known as cladistics. o Involves analyzing nucleotide changes at specific positions in sequences. o Computer-based analyses generate phylogenetic trees or cladograms. Character-State Methods: o Focus on phylogenetically informative characters from aligned sequences. o 16S ribosomal RNA (16S rRNA) is commonly used for microbial phylogenetic studies due to its conserved and variable regions. Cladistics: o A method that groups organisms based on shared derived characteristics. o Parsimony is a widely used approach, assuming evolution occurs with the fewest changes. DNA Sequence Analysis: o Provides insights into evolutionary lineages beyond traditional kingdom classifications. o Reveals three primary domains of life: Bacteria, Archaea (both prokaryotic), and Eukarya (eukaryotic organisms including plants, animals, fungi, and protists). Microbial Diversity Aspects Overview: Microbial diversity encompasses the variability among microorganisms, reflecting their differences in morphology, structure, metabolism, ecology, behavior, and evolution. This diversity is a result of nearly 4 billion years of evolutionary processes, highlighting the vast range of life forms at the microbial level. Morphological Diversity: o Variations in cell shape and size among different microorganisms. o Includes structures such as cocci, bacilli, spirilla, and filamentous forms. Structural Diversity: o Differences in cellular organization and architecture. o Variation in cell wall composition, membrane structures, and organelles. Metabolic Diversity: o Range of metabolic pathways utilized by microorganisms. o Includes autotrophic (carbon fixation) and heterotrophic (organic matter utilization) strategies. o Ability to thrive in diverse environments through various energy sources (e.g., light, chemicals). Ecological Diversity: o Different roles microorganisms play in ecosystems (e.g., decomposers, pathogens, symbionts). o Adaptation to extreme environments (extremophiles) like hot springs, deep-sea vents, and acidic lakes. Behavioral Diversity: o Variability in movement and response to environmental stimuli. o Includes motility mechanisms (flagella, cilia) and behaviors like biofilm formation and quorum sensing. Evolutionary Diversity: o Genetic diversity underlying all other aspects of microbial diversity. o Expressed through phylogenetic trees that illustrate the evolutionary relationships based on genetic sequences. o Highlights that microbes are more evolutionarily diverse than macroscopic organisms, contributing to overall biological diversity. Major Groups of Microorganisms Overview: Microorganisms are diverse entities that include bacteria, archaea, protists, fungi, and viruses. Each group has distinct characteristics, structures, and modes of life, contributing to the complexity of microbial diversity in various environments. Bacteria: o Prokaryotic microorganisms. o Typically unicellular with a wide range of shapes (spherical, rod-like, spiral). o Reproduce asexually through binary fission. o Can be found in various environments, including extreme conditions. Archaea: o Prokaryotic organisms similar to bacteria but genetically distinct. o Often found in extreme environments (e.g., hot springs, salt lakes). o Possess unique membrane lipids and metabolic pathways. o Some are methanogens, halophiles, or thermophiles. Protists: o Eukaryotic microorganisms, mostly unicellular. o Size ranges from 1 μm to 2,000 μm. o Include protozoa (animal-like) and algae (plant-like). o Protozoa can move using cilia, flagella, or pseudopodia; some perform photosynthesis. Fungi: o Eukaryotic organisms with rigid cell walls. o Can be unicellular (yeasts) or multicellular (molds). o Absorb nutrients from the environment rather than ingesting food. o Molds form hyphae and mycelium; yeasts ferment carbohydrates. Viruses: o Not considered living organisms; obligate parasites. o Lack cellular structure (no cytoplasm, membranes, or ribosomes). o Replicate only within host cells by hijacking their metabolic machinery. o Composed of DNA or RNA genomes, which can be single- or double-stranded. o Infect a wide variety of hosts, including bacteria (bacteriophages). Lecture 3 Fermentation Pathways Overview: Fermentation pathways are metabolic processes that convert sugars into acids, gases, or alcohol in the absence of oxygen. These pathways allow organisms to regenerate NAD+ from NADH, enabling glycolysis to continue and produce ATP under anaerobic conditions. Lactic Acid Fermentation: o Commonly found in bacteria such as Streptococcus and Lactobacillus acidophilus. o Converts glucose to lactic acid, producing 2 ATP and regenerating NAD+. o Used in the production of yogurt and cheese. Alcohol Fermentation: o Carried out by yeasts like Saccharomyces cerevisiae. o Converts glucose to ethanol and carbon dioxide, producing 2 ATP and regenerating NAD+. o Utilized in brewing beer and winemaking. Mixed Acid Fermentation: o Example organism: Escherichia coli. o Produces a mixture of products including acetic acid, formic acid, ethanol, and hydrogen gas. o Important in food spoilage and some industrial applications. 2,3-Butanediol Fermentation: o Example organism: Enterobacter aerogenes. o Converts pyruvate to 2,3-butanediol and other products. o Relevant in certain fermentation processes for flavoring and fuel. Photosynthesis Overview: Photosynthesis is the process by which autotrophs convert light energy into chemical energy, producing organic molecules from carbon dioxide (CO2) and water. It consists of light-dependent reactions that generate ATP and NADPH, followed by the Calvin cycle where CO2 is fixed into carbohydrates. Light Reactions: o Occur in thylakoid membranes. o Light energy excites electrons in chlorophyll, stripping them from water (H2O). o Electrons move through an electron transport chain, generating ATP via chemiosmosis. o Noncyclic photophosphorylation produces NADPH; cyclic pathway returns electrons to the chain. Calvin Cycle: o Also known as the dark reaction or Calvin-Benson cycle. o Utilizes ATP and NADPH from light reactions to fix CO2 into carbohydrates. o Converts CO2 into phosphoglyceric acid, leading to sugar formation (e.g., glucose). o Produces key monomers for anabolic processes like amino acids and nucleotides. Oxygenic Photosynthesis: o Involves the use of water as an electron donor. o Produces oxygen (O2) as a byproduct. o Common in plants, algae, and cyanobacteria. Anoxygenic Photosynthesis: o Does not produce oxygen; uses other electron donors (e.g., hydrogen sulfide). o Found in certain bacteria (e.g., purple and green sulfur bacteria). o Utilizes different pathways and pigments compared to oxygenic photosynthesis. ATP Production Overview: ATP production is the process by which cells convert energy from food sources into adenosine triphosphate (ATP), the primary energy currency of the cell. This occurs through glycolysis followed by either fermentation or respiration, with respiration yielding significantly more ATP than fermentation. Adenosine Triphosphate (ATP): o Main energy carrier in cells. o Produced during cellular metabolism. Glycolysis: o Initial step in both fermentation and respiration. o Converts glucose to pyruvate, producing a net gain of 2 ATP and 2 NADH. o Occurs in the cytoplasm. Fermentation: o Anaerobic process following glycolysis. o Low ATP yield (2 ATP per glucose). o Recycles NAD+ to allow glycolysis to continue. ▪ Types: ▪ Lactic Acid Fermentation: Pyruvate is reduced to lactic acid. ▪ Alcohol Fermentation: Pyruvate is converted to ethanol and CO2. Respiration: o Aerobic process that follows glycolysis. o High ATP yield (up to 38 ATP per glucose). o Involves two main stages: ▪ Krebs Cycle (Citric Acid Cycle): ▪ Breaks down pyruvate into CO2. ▪ Produces NADH and FADH2 for electron transport chain. ▪ Electron Transport Chain (ETC): ▪ Uses electrons from NADH and FADH2 to create a proton gradient. ▪ Drives ATP synthesis via chemiosmosis. Chemiosmosis: o Process where the H+ gradient generated by the ETC is used to produce ATP. o ATP synthase enzyme facilitates the conversion of ADP to ATP. Flow of Electrons: o Glycolysis → Krebs Cycle → Electron Transport Chain → ATP Production. o Total potential ATP yield from one glucose molecule can reach up to 38 ATP under optimal conditions. Microbial Metabolism Overview: Microbial metabolism encompasses the biochemical reactions that enable microorganisms to generate energy and synthesize cellular materials. It includes catabolic processes that release energy and anabolic processes that utilize energy, primarily through ATP as the energy currency. Nutritional Requirements: o Essential Elements: ▪ Bacterial structures consist of carbohydrates, lipids, proteins, and nucleic acids. ▪ Key elements include Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Phosphorus (P), and Sulfur (S). o Minerals: ▪ Required in trace amounts for growth: Potassium, Calcium, Magnesium, Iron, Copper, Cobalt, Manganese, Molybdenum, Zinc. Metabolism Definition: o The sum of all biochemical reactions for energy generation and cellular material synthesis. o Divided into two main components: Catabolism (energy-releasing) and Anabolism (energy-consuming). Catabolism: o Energy is released from the breakdown of compounds, ultimately conserved as high-energy bonds in ATP. o Generally exergonic reactions that provide energy for endergonic reactions. Anabolism: o Utilizes energy (from ATP) to build macromolecules and cell organelles. o Typically endergonic reactions requiring energy input. Metabolic Pathways: o Series of interconnected biochemical reactions. o Can be either catabolic or anabolic. o Each reaction is catalyzed by specific enzymes. o Multiple reactions are often needed to produce an end product. Enzymatic Pathways: o Enzymes are proteins that accelerate reactions without being consumed. o They lower activation energy (Ea) required for reactions. o Control and regulation of metabolic reactions depend on enzyme presence and activity. Energy Sources Overview: Energy sources are classified based on how organisms obtain energy and carbon for growth. Autotrophs produce their own organic molecules, while heterotrophs rely on organic compounds from other organisms. Various types of organisms utilize different methods to harness energy, including light and chemical processes. Autotrophs: o Produce organic molecules from inorganic carbon (CO2). o Types: ▪ Photoautotrophs: Use light for energy (e.g., plants, algae). ▪ Chemoautotrophs: Use chemical reactions involving inorganic substances for energy. Heterotrophs: o Require organic sources of carbon for growth. o Obtain organic molecules directly or indirectly from autotrophs. Chemotrophs: o Organisms that obtain energy by oxidizing chemical compounds. o Can be further divided into: ▪ Chemoheterotrophs: Use organic compounds as both energy and carbon sources (e.g., animals, most fungi). ▪ Chemoautotrophs: Use inorganic compounds for energy but fix CO2 for carbon (e.g., certain bacteria). Phototrophs: o Organisms that capture light energy to synthesize organic compounds. o Include: ▪ Photoautotrophs: Perform oxygenic photosynthesis using water (e.g., plants, cyanobacteria). ▪ Photoheterotrophs: Use light for energy but require organic compounds for carbon (e.g., some purple nonsulfur bacteria). Metabolism: o Sum of biochemical reactions for energy generation and cellular material synthesis. o Divided into: ▪ Catabolism: Energy-releasing processes that convert complex molecules into simpler ones, producing ATP. ▪ Anabolism: Energy-consuming processes that build macromolecules and cell structures using ATP. Photosynthesis: o Involves light reactions that energize electrons from water, leading to ATP and NADPH production. o Dark reactions use ATP and NADPH to synthesize sugars. Respiration: o Aerobic Respiration: Uses molecular oxygen as the final electron acceptor; produces up to 38 ATP per glucose molecule. o Anaerobic Respiration: Uses inorganic substances (not O2) as electron acceptors; produces variable ATP. o Fermentation: An anaerobic process that uses an organic molecule as the final electron acceptor; generates fewer than 38 ATP. Lecture 4 Prevention of Foodborne Illness Overview: Preventing foodborne illness involves implementing safe food handling practices, proper cooking and storage techniques, and maintaining hygiene to reduce the risk of contamination. Awareness of potential hazards and adherence to guidelines can significantly lower the incidence of food poisoning. Sanitation Practices: o Keep workspaces clean and sanitized. o Wash hands thoroughly and regularly. o Avoid coughing or sneezing over food. o Wash fruits and vegetables before consumption. Food Handling Guidelines: o Always follow ‘use by’ dates on food products. o Separate raw and cooked foods to prevent cross-contamination. o Do not prepare food too far in advance. o Ensure infected food handlers do not handle food. Cooking Temperatures: o Thoroughly cook food, especially meat (e.g., ground beef should reach >70°C). o Use a food thermometer to ensure proper cooking temperatures are achieved. Storage Recommendations: o Store food correctly: keep cold foods cold and hot foods hot; never leave food at ambient temperature. o Maintain proper cooling and reheating methods. o Follow guidelines for thawing food safely. o Implement food preservation methods to slow microbial growth, such as altering temperature, acidity, or moisture levels. Food Spoilage Overview: Food spoilage refers to any change in the appearance, smell, or taste of food that renders it unacceptable for consumption. This can result from microbial growth or other factors and is categorized based on the perishability of the food items. Definition: o Change in food characteristics (appearance, smell, taste) making it unacceptable to consumers. Categories of Food: o Perishable Foods: Fresh items like meats, fruits, and vegetables; high moisture content leads to rapid spoilage. o Semi-perishable Foods: Items such as potatoes, some apples, and nuts; moderate moisture levels allow for longer storage than perishable foods. o Non-perishable Foods: Low moisture items like sugar and flour; can be stored for long periods without spoilage. Microbial Growth: o Spoilage caused by specific microorganisms depending on the food type. o Microorganisms often psychrotolerant, growing best above 20°C but also at refrigeration temperatures (3–5°C). o Time for significant microbial population growth depends on initial inoculum size and growth rate during exponential phase. Chemical Properties: o Influenced by moisture level, nutrient content, and acidity/alkalinity of foods. o Each food type has a unique susceptibility to specific groups of microorganisms. Storage Conditions: o Perishable and semi-perishable foods require conditions that inhibit microbial growth to prolong shelf life. o Preservation methods include altering temperature, acidity, moisture, or using radiation/chemicals to prevent spoilage. Fermentation Overview: Fermentation is a metabolic process that converts sugars to acids, gases, or alcohol using microorganisms. It plays a crucial role in preserving food and beverages by producing preservative chemicals that inhibit spoilage organisms and pathogens. Microorganisms in Fermentation: o Major bacteria involved include: ▪ Lactic acid bacteria (e.g., Lactococcus, Lactobacillus) ▪ Acetic acid bacteria (e.g., Acetobacter) ▪ Propionic acid bacteria (e.g., Propionibacterium) o Yeast species such as Saccharomyces cerevisiae are essential for alcoholic fermentation. Preservative Chemicals: o Organic acids (lactic, acetic, propionic) and ethanol produced during fermentation act as preservatives. o High levels of these compounds prevent the growth of spoilage organisms and pathogens. Common Fermented Foods: o Dairy Products: ▪ Cheeses (Lactococcus, Lactobacillus) ▪ Yogurt (Streptococcus thermophilus) ▪ Buttermilk and sour cream (Lactococcus) o Alcoholic Beverages: ▪ Beer and wine (Saccharomyces cerevisiae) ▪ Sourdough bread (Lactobacillus) o Meat Products: ▪ Dry sausages (pepperoni, salami) o Vegetables: ▪ Sauerkraut (Lactic acid) ▪ Pickles (Lactic acid) o Vinegar: ▪ Produced from acetic acid bacteria. Yeast and Bacteria Roles: o Yeasts like Saccharomyces cerevisiae are primarily responsible for alcohol production in beverages and baking. o Lactic acid bacteria are key in dairy fermentation and vegetable preservation, contributing to flavor and texture. Foodborne Diseases Overview: Foodborne diseases are illnesses resulting from the improper handling and preparation of food, leading to infections or intoxications. They can be classified into two main types: food poisoning (due to pre-formed toxins) and food infection (due to viable pathogens causing disease in the host). Food Poisoning: o Caused by ingestion of foods containing pre-formed microbial toxins. o Microorganisms do not need to grow in the host; the toxin's activity causes illness. o Common pathogens include Staphylococcus aureus, Bacillus cereus, and Clostridium botulinum. Food Infection: o Results from ingesting food with sufficient viable pathogens that colonize and grow in the host. o Two types: ▪ Invasive Type: Pathogens invade the intestinal tract (e.g., Shigella, E. coli). ▪ Enterotoxigenic Type: Pathogens produce enterotoxins in the intestinal tract (e.g., Vibrio cholerae). Common Pathogens: o Bacteria: Salmonella spp., Campylobacter jejuni, Escherichia coli O157:H7, Listeria monocytogenes. o Viruses: Norovirus (most common), Hepatitis A, Rotavirus. o Protists: Giardia intestinalis, Cryptosporidium parvum. Symptoms and Treatment: o Symptoms vary but often include diarrhea, nausea, vomiting, and abdominal pain. o Recovery is usually spontaneous for viral infections like norovirus within 24–48 hours. o Treatment may involve hydration and supportive care; antibiotics may be necessary for bacterial infections. Prevention Strategies: o Proper food handling and cooking techniques. o Avoid cross-contamination between raw and cooked foods. o Regular handwashing and maintaining proper food storage temperatures. o Awareness of high-risk foods, such as undercooked meats and unwashed produce. Food Preservation Techniques Overview: Food preservation techniques are methods used to slow or stop the growth of microorganisms that spoil food or cause foodborne diseases. These techniques include altering temperature, acidity, moisture levels, and using chemical treatments, radiation, or aseptic packaging to extend shelf life and maintain food safety. Temperature Control: o Methods: Canning, refrigeration, pasteurization o Purpose: Slows microbial growth by lowering temperatures or creating high heat environments. Acidity Adjustment: o Process: Fermentation and pickling increase acidity. o Effect: High acidity inhibits the growth of spoilage organisms and pathogens. Moisture Reduction: o Techniques: Desiccation (freeze drying), osmotic pressure (adding salt/sugar). o Goal: Reduces water activity in food, making it less hospitable for microbes. Chemical Treatments: o Examples: Addition of antimicrobial chemicals like nitrites and sulfites. o Application: Used in products like dried fruits, sausages, and wine to prevent spoilage. Radiation: o Uses: Kills insects, reduces sprouting, and decreases specific bacterial pathogens. o Method: Gamma rays or electron beams applied to food products. Aseptic Packaging: o Definition: Packaging process that maintains sterility of food products. o Benefit: Extends shelf life without refrigeration by preventing contamination. Fermentation: o Role: Utilizes metabolic activities of microorganisms to produce preservative chemicals. o Key Microorganisms: Lactic acid bacteria, acetic acid bacteria, and yeast (e.g., Saccharomyces cerevisiae). Food Spoilage: o Definition: Changes in appearance, smell, or taste that make food unacceptable. o Categories: ▪ Perishable foods: Fresh meats, fruits, vegetables (high moisture). ▪ Semi-perishable foods: Potatoes, some apples, nuts (moderate moisture). ▪ Non-perishable foods: Sugar, flour (low moisture, long shelf life). Microbial Pathogens Overview: Microbial pathogens are microorganisms that cause disease in hosts. They include bacteria, viruses, protists, and prions, each with distinct characteristics and transmission routes, playing significant roles in foodborne illnesses and other infections. Bacteria: o Major foodborne pathogens include: ▪ Bacillus cereus: Associated with rice, starchy foods, high-sugar foods. ▪ Campylobacter jejuni: Found in poultry and dairy. ▪ Clostridium botulinum: Causes botulism; linked to improperly canned foods. ▪ Escherichia coli (e.g., O157:H7): Linked to undercooked meat and raw vegetables. ▪ Listeria monocytogenes: Found in deli meats and dairy products. ▪ Salmonella spp.: Common in poultry, meat, eggs, and dairy. ▪ Staphylococcus aureus: Associated with meats and desserts. ▪ Yersinia enterocolitica: Found in pork and milk. Viruses: o Notable foodborne viruses include: ▪ Norovirus: Transmitted through contaminated shellfish and various foods. ▪ Hepatitis A virus: Spread via shellfish and some raw foods. Protists: o Key pathogenic protists include: ▪ Giardia intestinalis: Spread through contaminated water used for washing crops. ▪ Cryptosporidium parvum: Similar transmission route as Giardia. ▪ Cyclospora cayetanensis: Often associated with fresh produce like cilantro. ▪ Toxoplasma gondii: Primarily spread through cat feces and undercooked meat. Prions: o Non-cellular infectious agents causing neurodegenerative diseases. o Example: Variant Creutzfeldt–Jakob disease (vCJD) linked to BSE-infected beef consumption. o Symptoms include depression, motor coordination loss, and dementia. Transmission Routes: o Contaminated food and water sources are primary transmission routes for many microbial pathogens. o Fresh produce, undercooked meats, and shellfish are common vehicles for infection. Lecture 5 Microbial Genetics Overview: Microbial genetics is the study of the genetic material and processes in microorganisms, particularly bacteria. It encompasses the structures involved in genetic information flow, including DNA replication, transcription, translation, and the role of plasmids in gene expression. Genetic Structures: o Chromosomes: Double helix structure twisted counterclockwise; contains essential genetic information. o Plasmids: Autonomous circular DNA molecules located in the cytoplasm; can carry genes for specific traits. Central Dogma Theory: o Describes the flow of genetic information: DNA → RNA → Protein. o Major processes include replication, transcription, and translation. Molecular Processes: o DNA Replication: The process by which DNA makes a copy of itself before cell division. o Transcription: Conversion of DNA into RNA by RNA polymerase, producing mRNA, rRNA, and tRNA. o Translation: Process where mRNA directs protein synthesis with the help of tRNA. o Reverse Transcription: Copying RNA back into DNA using reverse transcriptase, expanding the central dogma (e.g., retroviruses). DNA Replication in Bacteria Overview: DNA replication in bacteria is a semi-conservative process where the bacterial chromosome and plasmids are duplicated. This involves unwinding the double helix, synthesizing new strands using templates, and ensuring accurate duplication for cell division. Chromosomes: o Bacteria typically contain one circular chromosome. o Chromosomes consist of double-stranded DNA twisted into a helical structure. Plasmids: o Many bacteria also contain plasmids, which are small, autonomous circular DNA molecules. o Plasmids can carry genes that confer specific traits to the host cell. Replication Fork: o DNA replication begins at the origin of replication. o The double helix is unwound by helicase, forming two replication forks. Enzymes Involved: o Helicase: Unwinds the DNA double helix. o Single-Strand Binding (SSB) Proteins: Stabilize unwound DNA. o DNA Topoisomerases: Prevent supercoiling ahead of the replication fork. o Primase: Synthesizes RNA primers to initiate strand synthesis. o DNA Polymerase III (DNAP III): Synthesizes new DNA strands in the 5′ to 3′ direction. o DNA Polymerase I (DNAP I): Replaces RNA primers with DNA nucleotides. o DNA Ligase: Seals gaps between Okazaki fragments on the lagging strand. Leading and Lagging Strands: o Leading Strand: Synthesized continuously in the 5′ to 3′ direction. o Lagging Strand: Synthesized discontinuously, forming short segments known as Okazaki fragments. Okazaki Fragments: o Short DNA segments formed on the lagging strand during replication. o Later joined together by DNA ligase to create a continuous strand. Transcription and Translation Overview: Transcription is the process of synthesizing RNA from a DNA template, primarily involving RNA polymerase. Translation follows, where messenger RNA (mRNA) directs protein synthesis with the help of transfer RNA (tRNA) at ribosomes, resulting in protein formation. RNA Polymerase: o Enzyme responsible for synthesizing RNA from a DNA template. o Binds to promoter sites on DNA to initiate transcription. mRNA (Messenger RNA): o Carries genetic information from DNA to ribosomes for protein synthesis. o Synthesized during transcription as a complementary strand to the DNA template. tRNA (Transfer RNA): o Transfers specific amino acids to the ribosome based on the codon sequence of mRNA. o Plays a crucial role in translating the mRNA sequence into a polypeptide chain. Ribosomes: o Cellular structures where translation occurs. o Composed of rRNA and proteins; facilitate the assembly of amino acids into proteins. Protein Synthesis: o Involves two main processes: transcription and translation. o Occurs in three stages: 1. Initiation: Assembly of ribosomal subunits, mRNA, and tRNA. 2. Elongation: Sequential addition of amino acids to form a polypeptide chain. 3. Termination: Completion of protein synthesis when a stop codon is reached. Simultaneous Processes in Prokaryotes: o In prokaryotic cells, transcription and translation occur simultaneously in the cytoplasm. o This allows for rapid responses to environmental changes by quickly producing proteins. Genetic Variability in Bacteria Overview: Genetic variability in bacteria arises from mutations and genetic recombination processes, leading to changes in bacterial DNA. These variations can result in new traits, which may be beneficial or detrimental, influencing bacterial evolution and adaptation. Mutations: o Heritable changes in the nucleotide sequence of a gene. o Can be detrimental or beneficial. o Types of Mutants: ▪ Auxotrophs: Require additional nutrients due to mutations. ▪ Prototrophs: Wild-type strains that do not have such requirements. Types of Mutations: o Point mutations (single nucleotide changes). o Insertions and deletions (frameshift mutations). o Large-scale mutations (chromosomal rearrangements). Mutagens: o Agents that increase mutation rates (e.g., chemicals, radiation). Genetic Recombination: o Transfer of DNA between organisms. o Can occur through various mechanisms: homologous (identical) or heterologous (non-identical). o Results in merozygotes (partially diploid cells). Transformation: o Uptake of naked DNA by competent recipient bacteria. o Occurs naturally in certain species (e.g., Bacillus, Haemophilus). o In Gram-positive bacteria, single-stranded DNA is taken up; in Gram-negative, double-stranded DNA is transformed. Transduction: o Transfer of bacterial DNA via bacteriophages (viruses that infect bacteria). o Can lead to genetic variation among bacterial populations. Conjugation: o Direct transfer of DNA between two bacteria through physical contact (sex pilus). o Often involves plasmids carrying antibiotic resistance genes. Factors Affecting Transformation: o Size and state of DNA. o Sensitivity to nucleases. o Competence of the recipient bacteria. o Induced competence through chemical manipulation in laboratory settings. Lecture 6 Microbial Habitats Overview: Microbial habitats are diverse environments where microorganisms thrive, including terrestrial and aquatic ecosystems. These habitats support complex interactions among microbial communities and their abiotic surroundings, influencing nutrient cycles and ecosystem dynamics. Terrestrial Habitats: o Only 1% of soil microbes have been identified. o Essential for soil formation and ecosystem functioning. o Bacteria and fungi feed on organic matter (plants and animals). o Sensitive to environmental factors: CO2 levels, O2 levels, pH, temperature, moisture. Aquatic Habitats: o Microbes inhabit both saltwater and freshwater environments. o Includes microscopic plants, animals, bacteria, fungi, and viruses. o Adapted to specific conditions in various water bodies (oceans, lakes, rivers). Microbial Symbiosis: o Microorganisms can live in extreme environments and within other organisms' cells. o Interactions between species can influence habitat conditions through metabolic activities. o Microenvironments exist within larger habitats, with rapidly changing conditions. Microbial Ecosystems: o Ecosystems consist of dynamic interactions among plant, animal, and microbial communities. o Microorganisms are ubiquitous, found in extreme conditions (boiling springs, acidic environments, etc.). o Metabolic diversity drives nutrient cycling and influences the overall ecosystem health. o Rates of microbial activity depend on available nutrients and growth conditions, impacting both microbes and macroorganisms. Microbial Biofilms Overview: Microbial biofilms are structured communities of microorganisms attached to surfaces, encased in a self-produced matrix. They enhance microbial survival by providing protection against physical forces, immune responses, and antibiotics while facilitating nutrient acquisition and intercellular communication. Biofilm Formation: o Bacterial cells grow on surfaces, forming biofilms through attachment and excretion of adhesive matrices. o Biofilms can consist of single or multiple species, creating diverse microbial communities. o Nutrient-rich surfaces promote biofilm development, allowing bacteria to thrive in favorable niches. Biofilm Function: o Traps nutrients for growth and prevents detachment from dynamic surfaces (e.g., flowing systems). o Facilitates cell-to-cell communication and genetic exchange among bacteria. o Increases overall chances of survival in various environments. Microbial Self-Defense: o Biofilms resist phagocytosis by protozoa and immune cells. o Provide a barrier against toxic substances, including antibiotics. o Enhance resilience against physical disturbances that could dislodge cells. Microbial Ecosystems Overview: Microbial ecosystems are dynamic communities of microorganisms interacting with their environment, playing crucial roles in nutrient cycling and ecosystem functioning. They exhibit vast metabolic diversity and can thrive in various habitats, including extreme environments. Ecosystem Dynamics: o Complex interactions among plant, animal, and microbial communities. o Rates of microbial activities influenced by nutrient availability and growth conditions. o Microbial activities can significantly impact both microorganisms and macroorganisms within the ecosystem. Microbial Habitats: o Microorganisms inhabit diverse environments, from soil and water to extreme conditions (e.g., hot springs, acidic lakes). o Ecosystems may contain multiple habitats suited for specific populations. o Some ecosystems are predominantly or entirely microbial. Microbial Metabolic Diversity: o Microbes exhibit a wide range of metabolic capabilities, essential for nutrient cycling. o Interactions between species can influence habitat conditions; one species' by- product can serve as another's resource. o Microenvironments exist within larger habitats, each with unique physicochemical conditions. Nutrient Cycling: o Microorganisms play a key role in breaking down organic matter and recycling nutrients. o Nutrient availability is often intermittent, leading to feast-or-famine scenarios for microbes. o Growth rates are typically lower in natural settings compared to laboratory conditions due to suboptimal physicochemical factors. Microbial Diversity Overview: Microbial diversity refers to the variety of microorganisms present in different habitats, encompassing species richness and abundance. It plays a crucial role in ecosystem functioning and nutrient cycling, influenced by environmental conditions and available nutrients. Species Richness: o Total number of different species present in a habitat. o Can be assessed through cell identification and molecular techniques (e.g., ribosomal RNA genes). o High species richness is common in nutrient-rich environments like organic soils. Species Abundance: o Proportion of each species within a community. o Varies significantly across different habitats; some may have low species richness but high abundance of certain species due to environmental constraints. Microbial Populations: o Defined as groups of microorganisms of the same species residing together at the same time. o May originate from a single cell, forming a distinct population. Microbial Communities: o Comprise multiple populations of one or more species living in association. o Interactions among different microbial populations can influence community dynamics and functions. Microbial Ecosystems and Habitats: o Ecosystems are dynamic complexes of various communities interacting with their abiotic surroundings. o Microorganisms inhabit diverse environments, including extreme conditions (e.g., hot springs, acidic lakes). o The types of microbial activities depend on species presence, population sizes, and physiological states. The Microbial Environment: o Microorganisms thrive not only in soil and water but also in extreme environments and within other organisms. o Physicochemical conditions of habitats are shaped by microbial metabolic activities. o Microenvironments exist within larger habitats, often exhibiting rapid changes in conditions. Environmental Microbiology Overview: Environmental microbiology is the study of microbial interactions, processes, and communities in various environments. It encompasses the structure and activities of microbial populations, their interactions with each other and macroorganisms, and their roles in biogeochemical cycles. Microbial Interactions: o Study of how microorganisms interact with one another and with larger organisms. o Includes symbiotic relationships, competition, and predation among microbes. Microbial Communities: o Examination of the structure and dynamics of microbial populations within ecosystems. o Focus on community genetics and evolutionary processes. Population Biology: o Analysis of population dynamics, growth patterns, and ecological roles of microorganisms. o Investigates factors affecting microbial population sizes and distributions. Element Cycles: o Exploration of biogeochemical cycles (e.g., carbon, nitrogen, sulfur) mediated by microbial activity. o Understanding how microbes contribute to nutrient cycling and ecosystem functioning. Extreme Environments: o Study of microbial life in extreme conditions such as high temperatures, acidity, salinity, and pressure. o Investigation of extremophiles and their adaptations to harsh habitats. Microbial Ecosystems and Habitats: o Definition of ecosystems as dynamic complexes of living organisms and their abiotic surroundings. o Recognition of diverse habitats where microorganisms thrive, including soil, water, and extreme environments. Microenvironments: o Concept of microenvironments that provide localized conditions for microbial activity. o Importance of physicochemical conditions influenced by microbial metabolism. Metabolic Diversity: o Overview of the vast metabolic capabilities of microorganisms. o Role of microbes as primary catalysts in nutrient cycles and their impact on ecosystem health. Extremophiles Overview: Extremophiles are microorganisms that thrive in extreme environments, exhibiting unique adaptations to survive conditions such as high temperatures, pressures, acidity, and salinity. They encompass members from all three domains of life: bacteria, archaea, and eukarya. Extreme Environments: o Found in diverse habitats including: ▪ Depths of Earth's crust (up to 6.7 km) ▪ Ocean depths (over 10 km deep, pressures up to 110 MPa) ▪ Extreme pH levels (from 0 to 12.8) ▪ Hydrothermal vents (temperatures up to 122 °C) ▪ Frozen seawater (down to −20 °C) Adaptations: o Developed specialized mechanisms to tolerate harsh conditions. o Examples include heat-shock proteins for high temperatures and unique membrane structures for pressure resistance. o Metabolic pathways adapted to utilize available resources in extreme conditions. Types of Extremophiles: o Thermophiles: Thrive at high temperatures. o Psychrophiles: Prefer cold environments. o Halophiles: Adapted to high salt concentrations. o Acidophiles: Survive in acidic conditions. o Alkaliphiles: Live in alkaline environments. o Barophiles: Tolerate high pressure. Microbial Habitats: o Microbes inhabit a variety of ecosystems beyond soil and water, including within other organisms. o Each microbial community's habitat is influenced by physicochemical conditions shaped by metabolic activities. o Microenvironments can vary significantly even within the same habitat. Microbial Ecosystems: o Microorganisms play crucial roles in nutrient cycles and ecosystem functioning. o Their activities depend on species diversity, population sizes, and environmental conditions. o Interactions between microbes and macroorganisms can influence ecological dynamics. Microbial Interactions Overview: Microbial interactions encompass various relationships between microorganisms, which can be positive or negative. These interactions include competition for resources, cooperation in metabolic processes, and different forms of symbiosis, each influencing microbial community dynamics and ecosystem functioning. Competition: o Negative interaction where two microbial populations compete for the same resources (e.g., nutrients, space). o Results in reduced growth rates and survival for both populations. o Inhibits coexistence in the same ecological niche; one population typically outcompetes the other. Cooperation: o Positive interaction where microbes work together to achieve outcomes neither can accomplish alone. o Includes processes like syntrophy, important for nutrient cycling in anoxic environments. o Metabolic cooperation observed in complementary metabolisms (e.g., nitrifying bacteria and archaea). Symbiosis: o Prolonged and intimate relationships between organisms, either among microorganisms or between microorganisms and macroorganisms. o Divided into: ▪ Positive interactions: Mutualism and commensalism. ▪ Negative interactions: Parasitism and amensalism. Predation: o A negative interaction where one microorganism preys on another, impacting population dynamics and community structure. Amensalism: o Negative interaction where one microbial population produces inhibitory substances affecting another population. o The inhibiting population remains unaffected while the inhibited population suffers, often referred to as antibiosis. Lecture 7 Human Impact on Biogeochemical Cycles Overview: Human activities significantly disrupt biogeochemical cycles, including the carbon and nitrogen cycles. These disruptions lead to global warming, altered nutrient cycling, and increased pollution, which collectively impact ecosystems and biodiversity. Carbon Cycle Disruption: o Increased carbon dioxide levels contribute to global warming through the greenhouse effect. o Radiative forcing measures the energy imbalance caused by added greenhouse gases. o Rise in chlorofluorocarbons (CFCs) exacerbates atmospheric changes. Global Warming Effects: o Enhanced greenhouse gas emissions lead to climate change. o Altered weather patterns affect ecosystems and species distributions. o Increased frequency of extreme weather events impacts biodiversity and human systems. Nutrient Cycling Alteration: o Excessive use of nitrogen-based fertilizers increases biologically available nitrogen. o Nutrient imbalances can harm forest health and reduce biodiversity. o In agricultural areas, unused nitrogen leaches into water bodies, affecting drinking water quality. Pollution Effects: o Increased nitrogen in aquatic systems leads to anoxia or hypoxia, harming marine life. o Changes in food-web structure and habitat degradation result from nutrient overload. o Harmful algal blooms occur due to excess nitrogen, posing risks to aquatic ecosystems. Chemical Pollution Overview: Chemical pollution refers to the introduction of harmful industrial and agricultural chemicals into the environment, particularly water bodies. These pollutants can lead to significant ecological issues such as eutrophication, algal blooms, and contamination of groundwater. Industrial Chemicals: o Sources include manufacturing processes and waste disposal. o Common pollutants include heavy metals (e.g., mercury) and persistent organic pollutants. o Can leach into water systems, causing long-term environmental damage. Eutrophication: o Caused by an overabundance of nutrients (nitrogen and phosphorus) in aquatic ecosystems. o Often results from runoff containing fertilizers and detergents with phosphates. o Leads to oxygen depletion in water bodies, harming aquatic life. Algal Blooms: o Dense growths of algae triggered by nutrient overload. o Can produce toxins harmful to marine life and humans. o Result in decreased water quality and disruption of aquatic ecosystems. Nutrient Overload: o Excessive nutrients from agricultural runoff and wastewater contribute to chemical pollution. o Alters natural nutrient cycling, leading to imbalances in ecosystems. o Increases biological oxygen demand (BOD), affecting fish and other aquatic organisms. Phosphorus Cycle Overview: The phosphorus cycle describes the movement of phosphorus through the lithosphere, hydrosphere, and biosphere. It involves processes such as mineralization, solubilization, and plant absorption, which are crucial for making phosphorus available to living organisms. Phosphate Availability: o Phosphorus is essential for life, found in both organic (e.g., nucleic acids) and inorganic forms. o Plants primarily absorb phosphorus as soluble orthophosphate ions. o Mycorrhizae enhance phosphorus uptake by plants. Mineralization: o Conversion of organic phosphorus into insoluble inorganic phosphates. o Soil microorganisms produce enzymes (phosphatases) that break down organic phosphorus compounds. o This process releases inorganic phosphate, making it available for plant use. Solubilization: o Transformation of insoluble inorganic phosphates into soluble forms. o Microorganisms produce organic and inorganic acids that facilitate this conversion. o Key soil fungi (e.g., Aspergillus, Penicillium) and bacteria (e.g., Bacillus, Pseudomonas) play significant roles in solubilization. Plant Absorption: o Plants absorb phosphorus mainly in its soluble form. o Phosphorus is critical for various biological functions, including energy transfer and genetic material formation. o Erosion, sedimentation, and fertilizer application influence phosphorus availability in soils. Pesticide Cycle Overview: The pesticide cycle describes the various processes that pesticides undergo in the environment after application. It includes phases such as adsorption, volatilization, run-off, and degradation, which influence the behavior and impact of pesticides on ecosystems and human health. Key Phases: o Adsorption: ▪ Binding of pesticides to soil particles. ▪ Influenced by pesticide type, soil type, moisture, and pH. o Volatilization: ▪ Conversion of solids or liquids into gas, allowing movement away from the application site. ▪ Increased by spraying or hot, dry weather. o Run-off: ▪ Movement of pesticides in water over a slope. ▪ Can pollute waterways and contaminate groundwater, harming aquatic life and animals. o Leaching: ▪ Movement of pesticides through soil with water. ▪ Potentially contaminates groundwater. o Absorption: ▪ Uptake of pesticides by plants or microorganisms. ▪ Residues may be broken down within organisms and released back into the environment upon death. o Degradation: ▪ Breakdown of pesticides through: ▪ Microbial action (e.g., fungi and bacteria). ▪ Chemical reactions in soil. ▪ Photolysis (breakdown via sunlight). ▪ Hydrolysis (water-induced breakdown of large molecules). Environmental Microbiology Overview: Environmental microbiology studies the role of microorganisms in natural environments, focusing on their contributions to nutrient cycling and biogeochemical processes. It emphasizes how microbial activities are crucial for maintaining ecosystem health and sustainability. Role of Microbes: o Dominant players in nutrient cycling compared to macroorganisms. o Essential for maintaining nutrient balance and waste management in ecosystems. o Contribute to the preservation of the natural environment through biogeochemical cycles. Nutrient Cycling: o Key nutrients cycled include nitrogen, carbon, sulfur, and phosphorus. o Microbial activities drive these cycles, impacting plant agriculture and ecosystem health. Biogeochemical Cycles: o Nitrogen Cycle: ▪ Processes include nitrification, denitrification, nitrogen fixation, ammonification, and anammox. ▪ Key microbes involved: Nitrosomonas, Nitrospira, Azotobacter, Rhizobium, Clostridium, and others. o Carbon Cycle: Involves decomposition and respiration by microbes that recycle carbon back into the ecosystem. o Sulfur and Phosphorus Cycles: Microbes facilitate the transformation and availability of these essential nutrients. Microbial Activities: o Microbes play a critical role in degrading pollutants, including pesticides. o Degradation processes involve: ▪ Microbial action (fungi and bacteria) ▪ Chemical reactions in soil ▪ Photolysis (sunlight-induced breakdown) ▪ Hydrolysis (water-assisted breakdown) Mercury Cycling Overview: Mercury cycling refers to the biogeochemical processes that govern the transformation, transport, and accumulation of mercury in the environment. Due to its toxicity and ability to bioaccumulate, understanding mercury cycling is crucial for assessing environmental health and risks associated with mercury exposure. Mercury Transformation: o Major atmospheric form: Elemental mercury (Hg0), which is volatile. o Oxidation process: Hg0 is photochemically oxidized to mercuric ion (Hg2+). o Entry into aquatic environments primarily as Hg2+. Methylmercury Production: o Anaerobic microbial activity converts Hg2+ to methylmercury (CH3Hg+). o Methylmercury can further be transformed into dimethylmercury ((CH3)2Hg). o Both forms are highly toxic and readily absorbed by living organisms. Toxicity: o Methylmercury and dimethylmercury are potent neurotoxins, causing cell lysis in the central nervous system (CNS). o Bioaccumulation in food chains leads to increased toxicity in higher trophic levels. Microbial Resistance: o Certain gram-positive and gram-negative bacteria possess mechanisms to detoxify mercury. o Enzymes involved: ▪ Organomercury lyase degrades CH3Hg+ to less toxic Hg2+ and methane (CH4). ▪ Mercuric reductase reduces Hg2+ to volatile Hg0, enhancing mobility. o These microbial processes play a critical role in mitigating mercury toxicity in contaminated environments. Nitrogen Cycle Overview: The nitrogen cycle is a biogeochemical process that transforms nitrogen in various forms, essential for life. It involves several key processes including nitrogen fixation, nitrification, denitrification, ammonification, and nitrogen assimilation, which recycle nitrogen through the ecosystem. Nitrogen Fixation: o Conversion of atmospheric nitrogen (N2) into ammonia (NH3) by specific bacteria and archaea. o Essential for replenishing fixed nitrogen in ecosystems. o Key organisms include Azotobacter, Rhizobium, and cyanobacteria. Nitrification: o Process of converting ammonium (NH4+) to nitrate (NO3-) via nitrite (NO2-). o Involves two steps: 1. Ammonium oxidation to nitrite (e.g., Nitrosomonas). 2. Nitrite oxidation to nitrate (e.g., Nitrobacter). o Important for making nitrogen available to plants. Denitrification: o Reduction of nitrate (NO3-) back to nitrogen gas (N2), completing the nitrogen cycle. o Carried out by anaerobic bacteria such as Pseudomonas denitrificans. o Helps maintain soil fertility and reduce excess nitrates in water bodies. Ammonification: o Decomposition of organic nitrogen from dead organisms or waste into ammonium (NH4+). o Performed by bacteria and fungi during the breakdown of organic matter. o Releases NH4+ which can be reused by plants. Nitrogen Assimilation: o Uptake of nitrate or ammonium by plants through root hairs. o Nitrate is reduced to nitrite and then to ammonium for incorporation into amino acids and nucleic acids. o Critical for plant growth and development. Sulfur Cycle Overview: The sulfur cycle is a biogeochemical process that describes the movement of sulfur through the environment, including its transformation and microbial processes. It plays a crucial role in maintaining ecosystem health as sulfur is essential for all living organisms, particularly in amino acids and proteins. Sulfur Transformation: o Involves various oxidation states of sulfur: -2 (sulfide), 0 (elemental sulfur), +6 (sulfate). o Sulfur exists primarily in sediments and rocks as sulfate minerals (e.g., gypsum) and sulfide minerals (e.g., pyrite). Microbial Processes: o Microorganisms mediate the transformation of sulfur compounds. o Key groups include: ▪ Sulfide/Sulfur Oxidation: ▪ H₂S → Sº → SO₄²⁻ ▪ Organisms: Thiobacillus, Beggiatoa, purple and green phototrophic bacteria. ▪ Sulfate Reduction (Anaerobic): ▪ SO₄²⁻ → H₂S ▪ Organisms: Desulfovibrio, Desulfobacter, Archaeoglobus. ▪ Sulfur Reduction (Anaerobic): ▪ Sº → H₂S ▪ Organisms: Desulfuromonas, hyperthermophilic Archaea. Sulfate Reduction: o Sulfate is reduced to hydrogen sulfide (H₂S) by sulfate-reducing microorganisms under anaerobic conditions. o Bacteria involved include Bacillus, Pseudomonas, and Desulfovibrio. o Process involves ATP-dependent reduction of sulfate to sulfite, followed by sulfite to H₂S. Elemental Sulfur: o Produced from the oxidation of hydrogen sulfide (H₂S) by photosynthetic sulfur bacteria. o Important for the cycling of sulfur back into the environment. Organic Sulfur Compounds: o Volatile compounds like dimethyl sulfide and methanethiol can enter the atmosphere, influencing the global sulfur cycle. Human Impact: o Significant amounts of sulfur dioxide (SO₂) are released into the atmosphere from human activities, especially fossil fuel combustion, affecting the sulfur cycle. Lecture 8 Adaptive Immunity Overview: Adaptive immunity is the acquired ability of the immune system to recognize and eliminate specific pathogens. It involves lymphocytes, which provide a targeted response and develop memory for faster reactions upon re-exposure to the same antigen. Principles of Adaptive Immunity: o Involves phagocytes that process antigens and present them to lymphocytes. o Takes several days to develop, with increasing strength as more antigen-reactive lymphocytes are produced. o Highly specific responses directed at unique pathogen surface molecules (antigens). Antigen Recognition: o Antigens are unique molecules on pathogen surfaces that trigger adaptive immune responses. o Specificity allows the immune system to target particular strains or types of pathogens effectively. Lymphocyte Activation: o Lymphocytes (B cells and T cells) are primary effector cells in adaptive immunity. o Activation occurs after exposure to specific antigens, leading to proliferation and differentiation into effector and memory cells. Immune Memory: o The ability to quickly produce specific immune cells or antibodies upon subsequent exposures to previously encountered antigens. o Memory B and T cells facilitate rapid and robust responses during reinfection. Antimicrobial Proteins Overview: Antimicrobial proteins enhance the innate immune defense by directly attacking microorganisms or inhibiting their reproduction. Key components include interferons, complement proteins, and the fever response, which collectively contribute to the body's ability to combat infections. Interferons: o Family of immune-modulating proteins released in response to viral infections. o Viral-infected cells secrete interferons (e.g., IFN alpha and beta) to alert neighboring cells. o Neighboring cells produce proteins that block viral replication and degrade viral RNA. o Mechanism involves: 1. Virus enters a cell, triggering interferon production. 2. Interferons are released and bind to nearby cells. 3. Neighboring cells activate genes for antiviral proteins, preventing further viral replication. Complement System: o A group of proteins that enhances the immune response. o Functions include: ▪ Promoting cell lysis (breaking down cell membranes). ▪ Enhancing phagocytosis (engulfing pathogens). ▪ Triggering inflammation to recruit immune cells to sites of infection. Fever Response: o An abnormally high body temperature as a systemic response to infection. o Induced by pyrogens secreted by leukocytes and macrophages when exposed to foreign substances. o Benefits of moderate fever: ▪ Sequesters iron and zinc from the bloodstream, limiting availability to microorganisms. ▪ Increases metabolic rate, facilitating faster tissue repair. ▪ Prevents microbial proliferation by making essential nutrients less accessible. Immunity and Immune Response Overview: Immunity is the ability of an organism to resist infection, employing a two- pronged defense system: innate immunity, which provides immediate but non-specific responses, and adaptive immunity, which develops over time for specific pathogens and includes memory for future encounters. Innate Immunity: o Built-in capacity to target common pathogens regardless of identity. o Rapid response within hours of exposure. o Primarily involves phagocytes (e.g., neutrophils, macrophages) that ingest and destroy pathogens. o Does not require previous exposure to activate. o Recognizes structural features of pathogens through universal receptors. Adaptive Immunity: o Triggered by exposure to specific pathogens. o Involves lymphocytes (B and T cells) as primary effector cells. o Takes several days to develop; strength increases with more antigen-reactive lymphocytes. o Highly specific targeting of particular pathogens. o Results in immune memory, allowing rapid response upon re-exposure. Pathogen Recognition: o Phagocytes process antigens and present them to lymphocytes. o Essential for initiating the adaptive immune response. Phagocytes: o Key players in innate immunity. o Ingest, kill, and digest microbial pathogens. o Activate genes leading to pathogen destruction upon recognizing pathogens. Lymphocytes: o Central to adaptive immunity. o B lymphocytes produce antibodies; T lymphocytes can directly kill infected cells. o Memory cells formed after initial exposure enhance future immune responses. Phagocytosis Mechanism Overview: Phagocytosis is a vital immune response where phagocytes engulf and destroy pathogens. This process involves adherence to the pathogen, its engulfment into a vesicle, and subsequent destruction through enzymatic action and reactive substances. Adherence: o Phagocyte must adhere to the particle for effective phagocytosis. o Some microorganisms evade adherence using capsules. o Opsonization enhances adherence by marking pathogens with complement proteins or antibodies. Engulfment: o Cytoplasmic extensions of the phagocyte bind to and engulf particles, forming a vesicle called a phagosome. o The phagosome then fuses with a lysosome to form a phagolysosome. Pathogen Destruction: o Pathogens are killed by acidification and digestion via lysosomal enzymes within the phagolysosome. o Helper T cells can enhance pathogen destruction by: ▪ Triggering enzyme release through direct contact with phagocytes. ▪ Inducing a respiratory burst that produces cell-killing free radicals and oxidizing chemicals (e.g., hydrogen peroxide). ▪ Increasing pH and osmolarity in the phagolysosome. ▪ Utilizing defensins, which are antimicrobial peptides that disrupt pathogen membranes. Role of Helper T Cells: o Facilitate enhanced killing of pathogens resistant to lysosomal enzymes. o Promote the activation of phagocytes and their responses against infections. Innate Immunity Principles: o Innate immunity relies heavily on phagocytes, which ingest and digest microbial pathogens. o Responses occur rapidly, typically within hours of pathogen exposure. o Phagocytes recognize common structural features of pathogens, activating genes that lead to pathogen destruction. Cells and Organs of the Immune System Overview: The immune system comprises various cells and organs that work together to defend the body against pathogens. Key components include blood, lymphatic systems, and specialized organs like bone marrow and thymus, which produce and mature immune cells. Blood Components: o Composed of cellular (erythrocytes, leukocytes) and noncellular components (plasma). o Erythrocytes: Carry oxygen; most numerous blood cells. o Leukocytes: White blood cells involved in immune response, including phagocytes and lymphocytes. o Plasma: Liquid component containing proteins and solutes; serum is the fluid remaining after clotting. Leukocyte Types: o Derived from hematopoietic stem cells in bone marrow. o Types of Lymphocytes: ▪ B cells: Originate and mature in bone marrow; precursors to antibody- producing plasma cells. ▪ T cells: Mature in the thymus; involved in cell-mediated immunity. ▪ Natural Killer (NK) cells: Part of innate immunity. o Other leukocytes include monocytes, granulocytes, macrophages, neutrophils, and mast cells. Lymphatic System: o Comprises vessels and nodes that transport lymph, a fluid containing immune cells. o Major components include lymph nodes, spleen, and mucosa-associated lymphoid tissue (MALT). o Plays a crucial role in filtering pathogens and facilitating immune responses. Bone Marrow: o Primary site for hematopoiesis (blood cell formation). o Produces all types of blood cells, including leukocytes. Thymus: o Site of T cell maturation. o Essential for developing adaptive immune responses. Immune Response Mechanisms: o Innate Immunity: Immediate defense through phagocytosis and inflammatory responses. o Adaptive Immunity: Specific responses involving antibodies produced by B cells and cell-mediated responses by T cells. Inflammatory Response Overview: The inflammatory response is a complex biological process triggered by tissue injury or infection, characterized by the release of chemical mediators that lead to vasodilation, increased vascular permeability, and recruitment of immune cells. This response aims to eliminate pathogens, clear debris, and initiate healing. Chemical Mediators: o Types: Kinins, prostaglandins (PGs), complement system. o Functions: ▪ Dilate local arterioles causing hyperemia (increased blood flow). ▪ Increase capillary permeability, making them leaky. ▪ Attract leukocytes to the inflamed area. ▪ Contribute to redness and heat in the affected region. Vasodilation: o Increased blood flow leads to redness and warmth. o Enhanced permeability allows fluid and proteins to leak into tissues, causing swelling (edema). o Swelling can compress nerve endings, resulting in pain. Phagocyte Mobilization: o Steps: 1. Leukocytosis: Release of neutrophils from bone marrow due to factors from injured cells. 2. Margination: Neutrophils adhere to capillary walls via cell adhesion molecules (CAMs). 3. Diapedesis: Neutrophils flatten and exit capillaries. 4. Chemotaxis: Inflammatory chemicals guide neutrophils to the site of inflammation. Signs of Inflammation: o Redness, heat, swelling, and pain are classic indicators. o Local temperature increase enhances metabolic activity and may impair function temporarily. o Formation of exudate (fluid rich in proteins) aids in healing and isolates the injury. Role of Toll-like Receptors (TLRs): o Found on macrophages and epithelial cells, TLRs recognize specific microbes. o Activation triggers cytokine release, promoting further inflammation and immune response. Healing Process: o Phagocytosis of pathogens and dead cells occurs through neutrophils initially and macrophages later. o Clotting proteins form a fibrin mesh, providing a scaffold for tissue repair and isolating the damaged area to prevent spread of infection. Lecture 9 Antigens Overview: Antigens are substances that can provoke an immune response by mobilizing adaptive defenses. They are typically large, complex molecules not normally found in the body ('non-self') and serve as targets for adaptive immune responses. Complete Antigens: o Immunogenicity: Ability to stimulate proliferation of specific lymphocytes. o Reactivity: Ability to react with activated lymphocytes and antibodies. o Examples: Foreign proteins, polysaccharides, lipids, nucleic acids. Haptens: o Small molecules that are not immunogenic on their own but can become immunogenic when attached to a larger carrier molecule (e.g., proteins). Antigenic Determinants: o Specific parts of an antigen that are recognized by antibodies or lymphocyte receptors. o Mobilize different lymphocyte populations and form various antibodies. o Most antigens have multiple antigenic determinants (epitopes) that enhance immune response. Self-Antigens: o Molecules produced by the body that are usually tolerated by the immune system. o Important in distinguishing between self and non-self to prevent autoimmune reactions. Cytokines Overview: Cytokines are chemical messengers produced by immune cells that mediate cell development, differentiation, and responses within the immune system. They play a crucial role in regulating both innate and adaptive immune responses, including interleukins and interferons. Chemical Messengers: o Serve as signaling molecules in the immune system. o Facilitate communication between cells to coordinate immune responses. Interleukins: o A subset of cytokines, such as Interleukin 1 (IL-1) and Interleukin 2 (IL-2). o IL-1 is released by macrophages and co-stimulates T cells to release IL-2 and synthesize more IL-2 receptors. o IL-2 acts as a key growth factor for T cells, promoting their rapid division. Immune Response Regulation: o Cytokines amplify and regulate both innate and adaptive immune responses. o Examples include: ▪ Tumor necrosis factor (TNF): Acts as a cell toxin. ▪ Gamma interferon: Enhances the killing power of macrophages. Role in Lymphocyte Function: o B lymphocytes: Involved in humoral response and antibody secretion. o T lymphocytes: Involved in cellular immunity, targeting intracellular pathogens and cancer cells. o Cellular immunity can act directly by killing infected cells or indirectly by enhancing inflammatory responses and activating other immune cells. Cellular Immunity Overview: Cellular immunity is a crucial component of the adaptive immune response, primarily involving T lymphocytes and their subsets. It plays a vital role in defending against intracellular pathogens, such as viruses and some bacteria, by directly attacking infected cells or coordinating other immune responses. T Lymphocytes: o Key players in cellular immunity. o Develop in the thymus and differentiate into various subtypes. o Recognize antigens presented by Major Histocompatibility Complex (MHC) molecules on infected or abnormal cells. Cytotoxic T Cells (CD8+ T Cells): o Directly kill infected or cancerous cells. o Recognize antigens presented by MHC class I molecules. o Release perforin and granzymes to induce apoptosis in target cells. Helper T Cells (CD4+ T Cells): o Assist other immune cells by releasing cytokines. o Activate B cells for antibody production and enhance the activity of cytotoxic T cells and macrophages. o Recognize antigens presented by MHC class II molecules. Natural Killer Cells: o Part of the innate immune system but play a role in cellular immunity. o Target and destroy virus-infected cells and tumor cells without prior sensitization. o Recognize stressed cells in the absence of antibodies and MHC, allowing for rapid responses. Humoral Immunity Overview: Humoral immunity is a component of the adaptive immune system that involves the production of antibodies by B lymphocytes. It plays a crucial role in defending against extracellular pathogens and toxins through the recognition and neutralization of antigens. Antibodies: o Proteins produced by B cells. o Bind specifically to antigens, marking them for destruction or neutralization. o Types include IgG, IgA, IgM, IgE, and IgD, each with distinct functions. B Lymphocytes: o White blood cells responsible for producing antibodies. o Differentiate into plasma cells upon activation, which secrete large amounts of antibodies. o Memory B cells are formed after an infection, providing long-term immunity. Antigen-Antibody Complex: o Formed when antibodies bind to specific antigens. o Triggers various immune responses, including opsonization, neutralization, and complement activation. o Enhances phagocytosis and clearance of pathogens. Active and Passive Immunity: o Active Immunity: ▪ Developed through exposure to antigens (natural infection) or vaccination. ▪ Results in long-lasting immunity due to memory cell formation. o Passive Immunity: ▪ Acquired through the transfer of antibodies from another individual (e.g., maternal antibodies). ▪ Provides immediate but temporary protection as no memory cells are generated. Lymphocyte Development Overview: Lymphocyte development is a critical process in the immune system, involving the origin, maturation, activation, and self-tolerance of lymphocytes. This ensures that B and T cells can effectively respond to pathogens while avoiding attacks on the body's own tissues. Origin: o All lymphocyte precursors originate in red bone marrow. o Both B and T lymphocyte precursors are produced here. Maturation: o B cells mature in the bone marrow; T cells migrate to the thymus for maturation. o During maturation, lymphocytes develop immunocompetence (ability to recognize specific antigens) and self-tolerance (unresponsiveness to own antigens). o Mature lymphocytes display unique antigen receptors, binding only to one specific antigen. Seeding Secondary Lymphoid Organs and Circulation: o Immunocompetent but naive lymphocytes leave the thymus and bone marrow. o They seed secondary lymphoid organs (e.g., lymph nodes, spleen) and circulate through blood and lymph. Antigen Encounter and Activation: o Lymphocytes become activated when their antigen receptors bind to specific antigens. Proliferation and Differentiation: o Activated lymphocytes proliferate (multiply) and differentiate into effector cells (e.g., plasma cells, cytotoxic T cells) and memory cells. o Memory cells and effector T cells continuously circulate in blood and lymph, maintaining readiness against future infections. Key Points: B Lymphocytes: o Type of immune response: Humoral immunity o Function: Antibody secretion targeting extracellular pathogens o Site of origin: Red bone marrow o Site of maturation: Red bone marrow o Effector cells: Plasma cells o Memory cell formation: Yes T Lymphocytes: o Type of immune response: Cellular immunity o Function: Target intracellular pathogens and cancer cells o Site of origin: Red bone marrow o Site of maturation: Thymus o Effector cells: Cytotoxic T cells, Helper T cells, Regulatory T cells o Memory cell formation: Yes Lecture 10 Infections and Diseases Overview: Infections and diseases are caused by pathogenic microorganisms, including bacteria, viruses, fungi, and prions. These agents can invade the body, multiply, and disrupt normal physiological functions, leading to a range of health issues. Bacterial Infections: o Caused by harmful bacteria. o Examples include strep throat, tuberculosis, and urinary tract infections. o Treatment typically involves antibiotics. Viral Infections: o Caused by viruses that replicate inside host cells. o Examples include influenza, HIV/AIDS, and COVID-19. o Treatment may involve antiviral medications and vaccines. Fungal Infections: o Caused by fungi, which can be opportunistic pathogens. o Examples include athlete's foot, candidiasis, and aspergillosis. o Treatment often includes antifungal medications. Prion Diseases: o Caused by misfolded proteins (prions) that induce abnormal folding in other proteins. o Examples include Creutzfeldt-Jakob disease and mad cow disease. o No effective treatment; prevention is key. Medically Important Microorganisms Overview: Medically important microorganisms include various pathogens that can cause diseases in humans. They are classified into four main categories: bacteria, viruses, fungi, and prions, each with distinct characteristics and implications for health and disease management. Bacteria: o Single-celled organisms that can be pathogenic or beneficial. o Examples of pathogenic bacteria include Streptococcus, Staphylococcus, and Escherichia coli. o Can reproduce rapidly and may develop antibiotic resistance. Viruses: o Acellular entities that require a host cell to replicate. o Examples include influenza virus, HIV, and SARS-CoV-2. o Cause a wide range of diseases, from mild colds to severe illnesses. Fungi: o Eukaryotic organisms that can be unicellular (yeasts) or multicellular (molds). o Pathogenic fungi include Candida species and Aspergillus. o Can cause infections, particularly in immunocompromised individuals. Prions: o Infectious proteins that cause neurodegenerative diseases. o Not living organisms; they induce abnormal folding of normal proteins. o Associated with diseases such as Creutzfeldt-Jakob disease and mad cow disease. Normal Flora Locations Overview: Normal flora, or microbiota, refers to the diverse community of microorganisms that reside in various parts of the human body. These organisms play a crucial role in maintaining health by preventing pathogen colonization and contributing to immune function. Skin: o Hosts a variety of bacteria, fungi, and yeasts. o Common genera include Staphylococcus, Corynebacterium, and Malassezia. o Functions include barrier protection and mo

BIO 2107 Summary PDF

Document Details

Tags

Related

Summary

Full Transcript

Upgrade to continue