Week 7 PDF - Course Contents

Here is the Course Contents. Why study diversity- application in medicine, agriculture, conservation, etc.; What causes diversity?; Living vs non-living, status of viruses; Origin of life on earth; Spontaneous generation of life- concept and criticism, Evolutionary theories (Natural Selection, neut...

Here is the Course Contents. Why study diversity- application in medicine, agriculture, conservation, etc.; What causes diversity?; Living vs non-living, status of viruses; Origin of life on earth; Spontaneous generation of life- concept and criticism, Evolutionary theories (Natural Selection, neutral theory), Introduction to the Five kingdom classification, Building up organisms- Unicellular, colonies and multicellular organizations, origin of multicellularity, Structural organization and life cycles of different groups of organisms, Eubacteria, archaebacteria, protista (using representative organisms-amoeba, paramecium, plasmodium, euglena, diatoms, etc). Diversity in morphology, cellular organization, ecological adaptations and metabolism; pathogenic and non-pathogenic protists; Introduction to fungi and processes unique to fungi. Introduction to various phyla within fungi, Introduction to Lichens, algae. September 18,23, 25, 2024 Introduction to Unicellular Organisms What is an organism? An organism is any individual living entity that can perform essential life processes such as growth, reproduction, metabolism, and response to stimuli. Organisms can be unicellular (composed of a single cell, like bacteria) or multicellular (composed of multiple cells, like plants and animals). Organisms are classified into various biological groups, including bacteria, fungi, plants, animals, and protists, based on their cellular structure and function. In essence, an organism is the fundamental unit of life.  Five kingdom classification The classification is based on several characteristics, including: cell structure, body organization, mode of nutrition, reproduction, and phylogenetic relationships A Simple Classification Prokaryotic Unicellular Organisms: Bacteria and Archaea Ribosomes are macromolecular machines that perform protein synthesis in all cells. They are made up of ribosomal RNA and ribosomal proteins, and are composed of two subunits: small and large. The ratio of rRNA to ribosomal proteins differs between prokaryotes and eukaryotes Bacteria /Archaea Vs Eukaryotes Ribosomal RNA Introns Almost all known introns in archaea are bulge-helix-bulge (BHB) introns, with the exception of a few group II introns. The BHB motif is a structural feature that forms at the junction of the intron and exon in transfer RNA (tRNA) genes. RNA polymerase (RNAP) in bacteria and archaea have some key similarities and difference Subunits Archaeal RNA polymerase (RNAP) has 11–12 subunits, while bacterial RNAP has four subunits  Bacteria and Archaea Archaea: Use methionine as the start amino acid in protein synthesis. Bacteria: Use formyl methionine as the start amino acid in protein synthesis. A derivative of methionine, with a formyl group added to the amino group. It's used to start protein synthesis in bacteria and organelles, and can be removed after translation  Operons in bacteria and archaea are similar in that they both cluster genes together. An operon is the functional unit of genetic regulation found in prokaryotic cells, such as bacteria. It consists of a cluster of genes that work together as a single unit to give a single messenger RNA (mRNA) molecule, which then encodes multiple proteins. The two most widely studied operons are the lactose (lac) operon and tryptophan (trp) operon in E. coli. promoter of gene in bacteria  Promoter of gene in archaea, bacteria, eukaryotes The B recognition element (BRE) is a DNA sequence in the promoter region of most genes in eukaryotes and Archaea.] It's a cis-regulatory element that's located near the TATA box and consists of seven nucleotides. There are two sets of BREs: BREu Located immediately upstream of the TATA box BREd Located around seven nucleotides downstream of the TATA bo  Cell Wall The cell walls of bacteria and archaea differ in composition, structure, and function: Composition Bacterial cell walls are made of peptidoglycan, a complex of proteins and sugars. Archaeal cell walls are made of polysaccharides, which are polymers of sugar molecules. Structure Archaea have rigid cell walls with diverse structures, including an S layer of glycoproteins attached to the membrane Cell Division in Unicellular Organisms Binary fission in prokaryotes , Mitosis in eukaryotes  Respiration in Unicellular Organisms Unicellular organisms respire through diffusion across their cell membrane and can respire aerobically or anaerobically: Diffusion Unicellular organisms breathe by diffusing oxygen from the air or water into their cells and releasing carbon dioxide back into the environment. Cell membrane The cell membrane acts as a respiratory surface for unicellular organisms, such as amoeba, allowing gases to pass through. No respiratory structures Unicellular organisms lack respiratory structures or breathing apparatuses. Diffusion is a slow, passive transport process, so it's only feasible for small organisms or those with highly-flattened bodies. Larger organisms have evolved specialized respiratory tissues, such as lungs, gills, and respiratory passage mesosomes vs mitochondria Mitochondrial respiration, or OXPHOS, is a process through which electrons are donated by reducing equivalents (e.g. NADH and FADH2) produced from metabolism, and eventually transferred to a final electron acceptor: oxygen  Reproduction in Unicellular Organisms 1. Asexual reproduction (binary fission, budding)  Sexual reproduction (conjugation in bacteria, protists) In bacterial conjugation, a donor cell transfers genetic material to a recipient cell through a pilus, a sex appendage that draws the cells together. The genetic material transferred is often a plasmid, which can give the recipient cell antibiotic resistance, xenobiotic tolerance, or the ability to use new metabolites  Definition of colonies (in the context of microbes) In microbiology, a colony is a group of microorganisms that grow together from a single parent cell on a solid medium like agar. Colonies are important in microbiology because they can help scientists learn about the organisms that produce them Biofilms When colonies form a layer together, it's called a biofilm General appearance of the bacterial colonies grown on agar plates dishes Colonial organisms have several characteristics, including: Physical connection: Colonial organisms are made up of individuals that are physically connected but distinct from each other. Interdependence: The individuals that make up a colonial organism are interdependent and work together as a unit. Size: Colonial organisms can grow to be very large. Lifespan: Colonial organisms can live for very long periods of time. Resilience: The shared connections between individuals make colonial organisms more resistant to disease and predation. Subunits: The subunits of colonial organisms can be either unicellular or multicellular. For example, the alga Volvox is a coenobium, which is a unicellular colonial organism, while the phylum Bryozoa is a multicellular colonial organism. Examples of Colonial Organisms –Volvox, coral colonies, and bacteria. Other examples of colonial organisms include: Mosses Bee hives Ants Termites Wasp colonies Nesting bird colonies Schools of fish  Types of Colonies Different types of colonies: clonal and non-clonal. Non-clonal bacterial colonies are bacterial colonies A clonal colony or genet is a group of genetically identical that are not clonal, which means that they are not individuals, such as plants, fungi, or bacteria, that have grown made up of a single genome that is passed down from in a given location, all originating vegetatively, not sexually, a parent from a single ancestor  Advantages of Colonial Life – Protective, structural, and survival benefits. Longevity Bacterial colonies can be more adaptable and stronger than individual cells. Quorum sensing Bacteria within a colony can communicate with each other to respond to changes in their environment. This process, called quorum sensing, can help the colony survive longer. Quorum sensing is a cell-to-cell communication process that allows bacteria to sense and respond to their population density. It's a way for bacteria to coordinate their behavior and gene expression in response to environmental changes Colonies and Multicellular Organizations  Transition to Multicellularity Hypotheses for Multicellularity Evolution – Colonial theory, symbiotic theory, syncytial theory. The symbiotic theory of multicellular organisms suggests that the first multicellular organisms evolved from the cooperation of different single-celled organisms, each with a specific role Syncytial theory of Multicellular Evolution The syncytial theory of multicellularity, also known as the cellularization theory, proposes that multicellular organisms evolved from a single unicellular organism with multiple nuclei. The theory suggests that the unicellular organism developed internal membrane partitions around each nucleus, creating a multicellular organism. What scenarios could have compelled the selection of multicellular organisms? Three scenarios that may have given rise to multicellularity: i) Resource bartering: In this scenario, different cell types specialize in producing different resources for the survival of the whole multicellular system. ii) Stress protection: Peripheral cells shield internal cells from external chemical or physical stress allowing the whole multicellular system to survive. iii) Division of labor: Different cell types specialize in different tasks allowing the whole multicellular system to navigate and assimilate nutrients. What scenarios could have compelled the selection of multicellular organisms? Scientists have now been able to evolve multicellularity in laboratories from unicellular microbes. One remarkable example of this is multicellular yeast, normally a unicellular organism, evolved in the lab. Yeast cells normally separate after cell division and form individual entities. Mutations in these separation pathways render them stuck to one another after division, enabling them to form multicellular structures. In some specific environmental conditions, these clusters have more fitness compared to their unicellular ancestors, illustrating the incentives of being multicellular. For example, forcing yeast cells to survive on less food gives rise to multicellular structures that can trap nutrients and reduce their leakage away from cells.  Choanoflagellates The choanoflagellates are a group of free- living unicellular and colonial flagellate eukaryotes considered to be the closest living relatives of the animals  De novo origins of multicellularity in response to predation unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia Paramecium tetraurelia is a bacteriophagous organism that eats bacteria, algae, and yeas  Advantages of Multicellularity Specialization Multicellular organisms can differentiate into different cell types that perform specialized functions. This division of labor allows for more efficient use of resources and the production of organs like the brain, heart, and lungs. Increased size Multicellular organisms can be larger than single-celled organisms without the limitations of a decreased surface-to-volume ratio. This allows them to absorb and transport nutrients more effectively, and to escape predators. Ecological dominance Multicellular organisms can occupy different niches than single-celled organisms. Longer lifespans Multicellular organisms can continue living even if some of their cells die. This is due to the increased efficiency of their cells, which is a result of the division of labor  Multicellular organisms have the following characteristics: Cell differentiation Cells in multicellular organisms differentiate and specialize to perform different functions. For example, some cells in the gastrointestinal tract absorb nutrients, while others secrete mucus to help food move through the tract. Tissue formation Cells work together to form tissues, which are organized communities of cells that perform specific functions. The type of cells in a tissue determines its role in the organism. Specialized functions Different cells work together to perform specialized functions that support the organism's homeostasis. For example, the heart pumps blood, the brain processes information, and the stomach digests food. Cell types Cells in multicellular organisms can differ dramatically in structure and function. For example, a mammalian neuron and a lymphocyte have such different structures and functions that it's hard to believe they contain the same genome. Cell division Most cells in adult animals can resume proliferation to replace cells that have died or been injured. However, some cells, like cardiac muscle cells, cannot be replaced if they die. Tissue formation multicellular organisms  Cell Communication in Multicellularity Chemical release Cells can release chemicals that act as signals to other cells. These signals can be benign or noxious, and can be classified based on the distance between the signaling cell and the target cell. Electrical signaling Plants use electrical signaling to send information quickly over long distances. For example, when a plant is wounded, electrical and calcium waves travel along the plant to alert other leaves. Gap junctions These specialized junctions connect the cytoplasms of neighboring cells through water-filled channels. This allows cells to directly communicate with each other without having to overcome the plasma membrane barrier. Exosomes These extracellular vesicles can carry molecules like DNA, proteins, and lipids to other cells. Cytoplasmic bridges These are another way that cells communicate with each other. Direct interactions Adjacent cells can communicate with each other by interacting with the membrane proteins of the other cell. Chemical release Electrical signaling in multicellular organisms  Gap junctions Gap junctions are clusters of intercellular channels facilitating a direct connection between the cytoplasm of two neighbouring cells to mediate intercellular communication. These channels are formed by channel-forming proteins that are densely packed into spatial microdomains of the plasma membrane  extracellular communication exosomes Exosomes are small extracellular vesicles that play a vital role in cell-to-cell communication. They are produced by all cells and carry a variety of substances, including proteins, lipids, nucleic acids, and metabolites. Exosomes can mediate communication over long and short distances, affecting many aspects of cell biology. Extracellular communication by Cytoplasmic bridges Extracellular communication by Direct interactions Structural organization and life cycles of different groups of organisms: Bacterial Growth and Metabolism What is Structural organization in life? Structural organization in life refers to the way that life is built up from cells, tissues, organs, and organ systems, while the life cycle of an organization refers to its stages of development  Bacterial Growth and Metabolism Autotrophs - photo /chemo Heterotrophs Need preformed organic compounds Includes most pathogenic bacteria Fastidious heterotrophs: Organisms that require large amounts of vitamins and other growth-promoting substances to survive. Fastidious bacteria are difficult to grow in laboratories as they require specific nutrients and conditions for their growth Helicobacter pylori A human gastric pathogen that requires complex media containing blood or serum and a low-oxygen atmosphere to grow. Bacteria have cell walls made of: peptidoglycan (polysaccharide linked with chains of amino acids). this may be covered with an outer membrane of lipopolysaccharide (chain of sugar with a lipid attached).  Gram stains: Importance Important in medicine because provides information for treatment of bacterial disease. Bacteria stain either gram positive (purple) or gram negative (pink). Gram positive tend to respond to penicillin and like antibiotics. Gram negative respond to types of antibiotics unrelated to penicillin.  Some bacteria: have a gelatinous layer called a capsule surrounding the cell wall. form thick-walled endospores around chromosomes when they are exposed to harsh conditions (drought, high temperatures) - these types cause botulism Some bacteria have: flagella for locomotion. pili (short, thicker outgrowths that help cell to attach to surfaces) Bacterial Growth Curve 4 phases  Characteristics of the lag phase Adaptation: Bacteria adapt to new environments, such as different media, temperature, pH, or oxygen availability. Synthesis: Bacteria synthesize enzymes, RNA, and other molecules needed for cell division. Size increase: Bacteria increase in size, but do not divide. Duration: The length of the lag phase can vary from 60 minutes to a couple of days, depending on the bacteria and the conditions. Repair: Damaged cells may have a longer lag phase to repair themselves before dividing. Dynamic: The lag phase is a dynamic, organized, adaptive, and evolvable period.  Log (exponential) phase This is when cells divide by binary fission and the doubling of each generation creates the exponential growth for which the phase is named. Metabolic activity during this stage is high but generally limited to the necessary steps required for reproduction When it ends The log phase ends when the bacterial population exhausts essential resources or faces unfavorable conditions. This can be due to depleted nutrients or the accumulation of toxic substances  Characteristics of the log phase Exponential growth The number of cells increases exponentially, with each generation occurring in the same time interval as the previous one. Constant growth rate The cells in the log phase have a constant growth rate and uniform metabolic activity. Viable cells The cell population is considered to be the most viable at this phase. Susceptible to disinfectants Bacteria in the log phase are more susceptible to disinfectants and antibiotics. Nutrient depletion The log phase ends when nutrients are depleted or toxic substances accumulate. Semilogarithmic graph When plotted on a semilogarithmic graph, the growth rate appears linear. Used in research Cells in the log phase are often used in research and industrial applications. Extended by nutrient supplementation The log phase can be extended by adding nutrients to match the increasing growth rate.  Stationary Phase Stable population size The number of bacterial cells remains constant because the rate of cell division equals the rate of cell death. Metabolic activity Cells are still metabolically active, but less so than in other phases. Synthesis of proteins Cells synthesize proteins that help them survive in nutrient-deprived conditions. Increased resistance Bacterial cells in the stationary phase are more resistant to adverse conditions. Changes in gene expression The stationary phase is characterized by increased activity of stationary phase promoters, which drive the expression of genes that help bacteria survive. Spore production Spore-forming bacteria may start producing endospores to survive harsh conditions. Extended by nutrient supplementation The log phase can be extended by adding nutrients to match the increasing growth rate.  Death phase of bacteria: characteristics Cell death rate: The rate of cell death is greater than the rate of cell division. Resource depletion: The culture's resources are used up, such as nutrients. Waste accumulation: Toxic by-products build up in the culture. Cell lysis: As cells die, they lyse and fill the culture with their contents. Survival strategies: Some bacteria may enter a dormant state or form spores to survive harsh conditions. Viable but nonculturable (VBNC) state: Some cells may be thought to be dead but could be revived under certain conditions. Tailing effect: A small population of cells may not be killed off, and they may benefit from the nutrients released by the dead cells Some examples of recombinant proteins produced in bacteria include Factor 8: Used to treat hemophilia A Factor 9: Used to treat hemophilia B DNAase 1: Used to treat cystic fibrosis Insulin: Used to treat type 1 diabetes Interferon-alpha: Used to treat chronic hepatitis C Anti-thrombin-3: Used to prevent blood clots Interleukins: Used to treat various types of cancers Interferon-beta: Used to treat herpes and viral enteritis Human recombinant growth hormone: Used to promote growth  Bacterial Metabolism Help us in identifying bacteria by their end products Help us in knowing how to inhibit bacteria  Energy Generating Process Aerobic respiration: COMPLETE breakdown of glucose to CO2 & H2O Final electron receptor O2 Yield = 38 ATP Fermentation: Yield = 2 ATP Endproducts: Lactic acid/Alcohol Final electron receptor is organic molecule Anaerobic respiration: Yield >2