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Lecture 7—Jan 24th 2025 BES 108D Organisms in their environment By Dr. Benazir Alam Copyright © 2025 Pearson Canada, Inc. 27 - 1  2 Topic:1 Prokaryotes: Bacteria...

Lecture 7—Jan 24th 2025 BES 108D Organisms in their environment By Dr. Benazir Alam Copyright © 2025 Pearson Canada, Inc. 27 - 1  2 Topic:1 Prokaryotes: Bacteria and Archaea Chapter: 27…continued Copyright © 2025 Pearson Canada, Inc. 27 - 2  Prokaryotes in Research and Technology Experiments using prokaryotes have led to important advances in DNA technology – E. coli is used in gene cloning (transformation) – Use of DNA polymerase from Pyrococcus furiosus, an archaea that can survive at temperatures upto 100°C, in the polymerase chain reaction (PCR) technique – Through genetic engineering, we can modify bacteria to produce vitamins, antibiotics, hormones, and other products. – Soil bacteria specifically a type of Streptomyces species can produce, Malacidins, a class of antibiotics effective against CMRSA10 a highly virulent strain of methicillin-resistant Staphylococcus aureus (MRSA). In addition, certain Streptomyces species can also produce tetracycline and erythromycin. – CRISPR-Cas9 system for gene knockout Copyright © 2025 Pearson Canada, Inc. 27 - 3  CRISPR-Cas9 system: a prokaryotic 4 antiviral system against viruses The genomes of many prokaryotes contain short DNA repeats, called CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), that it acquired from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence CRISPR play a key role in the antiviral defense system of prokaryotes and provide a form of heritable acquired immunity for prokaryotes. CRISPR: Opening new avenues of q CRISPRs interact with endonuclease (an enzyme research for treating HIV infection. that cuts within a DNA or RNA molecule) proteins known as Cas9 (CRISPR-associated protein 9) that cuts DNA. q Cas9 proteins, acting together with “guide RNA” made from the CRISPR region, can cut any DNA sequence to which they are complimentary. q Scientists have been able to exploit this system to target cells whose DNA they want to alter. Copyright © 2025 Pearson Canada, Inc. 27 - 4  Prokaryotes in Research and Technology: Biodegradable plastic 1. Bacteria synthesize and store a polymer called PHA (polyhydroxyalkanoate), a component of biodegradable plastics. 2. Prokaryotes are the principal agents in bioremediation, use of organisms to remove pollutants from environment such as cleaning up oil spills and precipitating radioactive material (such as uranium) out of groundwater. a. Spraying fertilizer stimulates the growth of native bacteria belonging to the Pseudomonas and Mycobacterium species, that metabolize hydrocarbons (oil) in soil and water, increasing the breakdown process up to fivefold. Copyright © 2025 Pearson Canada, Inc. 27 - 5  Topic: 2 Eukaryotes: Protists Chapter: 28 Copyright © 2025 Pearson Canada, Inc. 27 - 6 Protists Protists are single celled eukaryotes unlike plant, animals and fungi which are multi- cellular. Protists have a nucleus and various membrane bound organelles such as lysosomes, endoplasmic reticulum, golgi apparatus and mitochondria. They also contain some unique organelles not found in other eukaryotes such as contractile vacuole (pump water out of protists) or ocelloid (may help in prey detection) Protists have a well-developed cytoskeleton that extends throughout the cell. It provides structural support that enables them to have asymmetric (irregular) forms, as well as to change shape as they feed, move, or grow. In aquatic environments, photosynthetic protists (such as diatoms, red/green algae) and prokaryotes are the main producers that obtain energy from the sun i.e. they convert carbon dioxide to organic compounds Their populations can explode when limiting nutrients such as nitrogen, phosphorus and iron are added or when fertilizers are washed off by rain to water bodies Some protist symbionts benefit their hosts – Dinoflagellates nourish coral polyps that build reefs – Wood-digesting protists digest cellulose in the gut of termites Copyright © 2025 Pearson Canada, Inc. 27 - 7  Four Supergroups of Eukaryotes (1) (2) (3) (4) Copyright © 2025 Pearson Canada, Inc. 27 - 8 Exploring Protistan Diversity: (1) Excavata Excavata are flagellated protists that have an “excavated” groove, which is a specialized, often asymmetrical indentation or depression along the side of the cell. on one side of the cell body. Excavated groove plays a role in feeding, locomotion or attachment/stabilization to a surface. E.g. Giardia intestinalis, a parasitic organism that belongs to the diplomonad group in Excavata, mostly lives in anaerobic or low oxygen containing conditions, causes giardiasis, an intestinal infection in humans and other animals. Giardia does not contain mitochondria instead, they contain mitosomes, that are a simplified version of mitochondria. Mitosomes cannot use oxygen to help extract energy from carbohydrates and other organic molecules. They derive energy from anaerobic biochemical pathway. Giardia also contains two nuclei. Having two nuclei may contribute to its ability to divide quickly and effectively under the harsh conditions of the host’s intestines. Copyright © 2025 Pearson Canada, Inc. 27 - 9  Think…. Why does it make sense that diplomonads like giardia intestinalis to have mitosomes instead of mitochondria? Copyright © 2025 Pearson Canada, Inc. 27 - 10  Exploring Protistan Diversity: (2) SAR Clade- Diatoms vs foraminifera Diatoms Foraminifera Diatoms are the most abundant single-celled Foraminifera (Forams), are single- photosynthetic protists in aquatic communities celled protists that have a calcareous (made of calcium carbonate) shell Diatoms are a type of algae with a glass-like cell called a "test" wall called frustule that is made up of silicon dioxide. The test wall is calcareous, perforated, The silica in their cell walls makes diatoms with cylindrical pores. incredibly durable and resistant to decomposition and provide effective protection from the crushing Forams take up more magnesium when jaws of predators they are in warmer water than in colder water. Because of its highly porous and mild abrasive nature, diatomaceous earth i.e. fossilized diatom The magnesium content in fossilized cell walls are used for filtering medium or mild forams can be used to estimate abrasive in toothpaste or metal polish changes in ocean temperature over time Copyright © 2025 Pearson Canada, Inc. 27 - 11  Diatoms play an important role in 12 Transportation of atmospheric CO2 to ocean floor: (2) SAR Clade q When plenty of nutrients are available, diatom population blooms and sometimes escape being eaten by predators. q When they die, their dead bodies fall to ocean floor undecomposed and takes centuries to be completely decompose because of the presence of silica in their cell wall, which are incredibly durable and resistant to decomposition. q As a result, the carbon in their bodies remains there for some time, rather than being released immediately as carbon dioxide as the decomposers respire. q The overall effect of these events is that atmospheric carbon dioxide absorbed by diatoms during photosynthesis is transported, or “pumped,” to the ocean floor. q Some scientists advocate fertilizing the ocean to promote diatom blooms and the movement of carbon dioxide from the atmosphere to the ocean Copyright © 2025 Pearson Canada, Inc. 27 - 12 floor.  13 Exploring Protistan Diversity: (2) SAR Clade- Paramecium bursaria Paramecium bursaria is a non-photosynthetic protist that is a member of the species ciliate that lives in marine and brakish waters. Then why is Paramecium bursaria green? It houses hundreds of green algae called zoocholera in their cytoplasm. They live together in a process known as endosymbiosis. Each have mutualistic benefits but can survive without the other – green algae exchange photosynthate with the paramecium – Algae receive various inorganic nutrients in return. Copyright © 2025 Pearson Canada, Inc. 27 - 13  Paramecium moves via coordinated action of Cilia: (2) SAR Clade Paramecium is also known as ciliate because it contains cilia. Cilia are short, hair-like structures that extend from the surface of many eukaryotic cells, including those of protists. They are made up of microtubules and are used for a variety of functions, including movement, feeding, and sensory detection. Copyright © 2025 Pearson Canada, Inc. 27 - 14  Exploring Protistan Diversity: (2) SAR Clade- Plasmodium falciparum The protozoa Plasmodium falciparum belonging to the SAR clade in the Ciliate subgroup is the parasite that causes malaria. It contains a unique subcellular organelle called an apicoplast harbours core metabolic pathways such as fatty acids & heme biosynthesis and essential for parasite’s viability Apicoplast is not present in humans. Because the apicoplast is so critical for the parasite's life cycle and is unique to the parasite, it has been targeted in the development of antimalarial drugs. Inhibiting apicoplast functions could disrupt the parasite's ability to reproduce and survive inside the host. Copyright © 2025 Pearson Canada, Inc. 27 - 15  Exploring Protistan Diversity: (2) SAR Clade- Oomycetes Oomycetes are decomposers Oomycete hyphae radiating that have a filamentous from a decomposing gold fish structure called hyphae. The high surface-to-volume ratio of hyphae enhances the uptake of nutrients from the environment They Include water moulds that grow on dead algae and animals. Copyright © 2025 Pearson Canada, Inc. 27 - 16  Exploring Protistan Diversity: (3) Archaeplastida, Volvox q Volvox is a colonial freshwater multi-cellular green alga that forms spherical colonies with ~50,000 cells q The colony is a hollow ball whose wall is composed of hundreds of biflagellated cells lined up along the circumference of the ball that are embedded in an extracellular gelatinous matrix. The matrix is secreted by q It has two types of differentiated cells: (1) somatic cells of the colony and forms a protective, flagellate somatic cells that are found towards cohesive layer around the the periphery and are responsible for the colony, allowing the cells to locomotion and photosynthesis of the colony and remain in place and (2) germ cells that are present towards the center function together as a single organism and involved in reproduction Copyright © 2025 Pearson Canada, Inc. 27 - 17  Exploring Protistan Diversity: (3) Archaeplastida, Red vs Green algae Red algae Green algae Red algae are red because they contain a Green algae are green because red pigment called phycoerythrin in they contain chlorophyll a and addition to chlorophyll a inside their chlorophyll b inside their chloroplast. Phycoerythrin absorbs blue chloroplasts. Chlorophyll a absorbs and green light and reflects red light, light primarily in the red and blue which is why red algae appear red or parts of the spectrum and reflects purplish. green light, which gives them their characteristic green color. Red algae can thrive in deep water with limited light or those with more turbidity Can thrive in shallow water (murkiness) from suspended particles. Chlorophyll a and b in green algae The ability to capture blue and green are less effective at utilizing the wavelengths in water with limited light to deeper-penetrating blue and green perform photosynthesis allows red algae light. Therefore, green algae to thrive in places where other algae (like typically thrive in shallower waters. green algae) cannot survive due to light limitations. Copyright © 2025 Pearson Canada, Inc. 27 - 18 Life cycle of Red/Green algae: Alternation of Generations Life cycles of red and green algae (and plants) include an alternation of generations, where a diploid (2n) generation called sporophyte (where spores are produced, asexual phase) alternates with a haploid (n) generation called gametophyte (where gametes are produced, sexual phase) The asexual phase allows for rapid reproduction and colonization when conditions are favorable. The spores or seeds produced during the asexual phase can be spread over a wide area, helping the organism to colonize new habitats. In contrast, the sexual phase typically occurs when environmental conditions are more challenging, allowing for the creation of new individuals with genetic variability that may have advantageous traits. A diploid (2n) cell contains two complete sets of chromosomes in its nucleus, whereas haploid cells only contain a single copy. E.g. Most human body cells are diploid, and only the gametes (sperm and egg cells) are haploid. Chromosomes in diploid cells are arranged in homologous pairs. Copyright © 2025 Pearson Canada, Inc. 27 - 19  Alternation of Generations: alternating 20 between the sexual and asexual modes of reproduction depending on environmental conditions Mitosis q The gametophyte generation (bottom) begins with a unicellular spore produced by meiosis. The spore is haploid (n), and all the cells derived from it (by mitosis) are also haploid (n). q this multicellular gametophyte produces gametes — by mitosis. Mitosis Mitosis q Fertilization or Sexual reproduction then produces the diploid (2n) zygote q The zygote undergoes mitosis to produce the Mitosis keeps the number multicellular sporophyte generation that of chromosomes identical contains diploid (2n) number of chromosomes. Meiosis reduces the q Eventually, though, certain cells will undergo number of chromosomes meiosis, forming spores and starting a new by half. gametophyte generation. Copyright © 2025 Pearson Canada, Inc. 27 - 20  Exploring Protistan Diversity: (4) Unikonts, Amoeba This group of eukaryotes includes amoebas that have lobe- or tube-shaped pseudopodia for movement. An amoeba moves by extending a pseudopodium and anchoring its tip; more cytoplasm then streams into the pseudopodium. Copyright © 2025 Pearson Canada, Inc. 27 - 21 Eukaryotic Evolution from prokaryotes: Endosymbiosis Considerable evidence indicates that much protist diversity has its origins in endosymbiosis Endosymbiosis is a relationship between two species in which one organism lives inside the cell or cells of another organism and eventually becomes an organelle (in the case of evolution) – Mitochondria evolved by endosymbiosis of an alpha proteobacterium (gram-negative bacteria) – Plastids/chloroplasts evolved later by endosymbiosis of a photosynthetic cyanobacterium Copyright © 2025 Pearson Canada, Inc. 27 - 22  Endosymbiosis : Eukaryotic Evolution 23 q Roughly 2.2 billion years ago an archaea (a prokaryote) absorbed a bacterium (a prokaryote) through phagocytosis, that eventually became the mitochondria that provide energy to almost all living eukaryotic cells. Both chloroplast q Approximately 1 billion years and mitochondria ago, some of those cells are examples of endosymbiosis. absorbed cyanobacteria that They both have eventually became double membrane, their own chloroplasts, organelles that naked/circular DNA produce energy from and ribosomes sunlight. Copyright © 2025 Pearson Canada, Inc. 27 - 23 What made endosymbiont become dependent on the host 1. It would have been advantageous to the host to maintain the cyanobacterial endosymbiont, as a source of sugar from photosynthesis 2. Horizontal gene transfer from endosymbiont to the host nucleus made it dependent on the host Copyright © 2025 Pearson Canada, Inc. 27 - 24