Organismal Biology Lecture 1 PDF

BIO 211 Organismal Biology  BIO 211 Lecture 1 Diversity of Life (Part A) Yashraj Chavhan Assistant Professor Syllabus What is life? What qualifies as a living thing? Some key characteristics of living organisms Organization (high order...

BIO 211 Organismal Biology  BIO 211 Lecture 1 Diversity of Life (Part A) Yashraj Chavhan Assistant Professor Syllabus What is life? What qualifies as a living thing? Some key characteristics of living organisms Organization (high order states): organisms are made up of highly organized units called cells. Homeostasis: Cells are bounded chambers that interact with their external environment and transform energy to maintain a regulated balance of chemicals within them. Reproduction: Organisms can make structurally distinct copies that resemble them by making use of an instructional (genetic) code. Evolution: Organisms inevitably generate variation (due to replication errors), and the The smallest free-living organism on Earth Pelagibacter ubique This bacterium is one of the most common organisms found in the ocean. The combined weight of all P. ubique bacteria outweighs all the fish in the ocean. A single P. ubique cell has a volume ranging from 0.019 to 0.039 µm3. Steindler et al. 2011 PLoS One A typical blue whale is as big as And the blue whale may not even be the largest organism on the Earth! Two of the largest organisms on Earth Armillaria solidipes (a parasitic fungus) A single fungal individual can be composed of a huge network of hyphae that spans ~10 km2. This individual is likely ~ 2400 years old. It primarily grows underground. Armillaria solidipes on a tree Two of the largest organisms on Earth Posidonia australis (an aquatic plant) A single individual spans ~180 km2 © University of Western Australia / Rachel Austin  Number of individuals Image credit: Mark Belan Source: Bar-On et al. 2018 PNAS Life on Earth is extremely diverse Size Abundance Habitat Nutritional requirements and preferences Life span Mobility Variability But all life on Earth shares some key features There is a unity of organization in the highly diverse living world. Examples: 1. The genetic material: DNA All things that can be unquestionably categorized as “living” organisms have the same kind of biomolecule (deoxyribonucleic acid (DNA)) as their genetic material. 2. Fundamental information processing: All living things transcribe DNA into RNA (ribonucleic acid), the RNA then gets translated into proteins. Proteins are the primary functional building blocks of all living cells. 3. Energy currency: ATP All living organisms use adenosine triphosphate ATP as the energy currency of their cells. 4. The Genetic Code Although the genetic code is not universal, an overwhelming majority of organisms on the planet uses the exact same genetic code (which contains information about how RNA sequences are translated into protein sequences. Moreover, while some alternative https://open.lib.umn.edu/evolutionbiology/chapter/5-8- genetic codes are found in very-very We will try to understanding life’s diversity through its history on planet Earth  The origin of life The Earth is ~4.5 billion years old. The oldest known fossils (the earliest signs of life) are ~3.7 billion years old. The current theories state that life could have originated in two1.different places: Geothermal pools on land 2. Hydrothermal vents in oceanic depths Credit: Jeff Vanuga/Nature Picture Library Source: https://oceangeneration.org/are-hydrothermal-vents-the-origin-of-life-on- earth/ Source: https://oceangeneration.org/are-hydrothermal-vents-the-origin-of-life-on- A prebiotic soup, an RNA world, or something else? We do not exactly know how life originated. Although there are many promising clues, the origin of cascaded catalytic reactions remains challenging. RNA molecules can act as both enzymes and replicators (they can make copies of themselves). But it is difficult to explain how RNA could catalyze some of the reactions essential to cellular metabolism. The Last Universal Common Ancestor All life on the Earth shares a common ancestor (referred to as the Last Universal Common Ancestor or LUCA). LUCA likely lived ~4.2 billion years ago and had a genome (the sum-total of the genetic material) with at least 2.5 million base pairs od DNA. LUCA was unicellular and prokaryotic (it did not have a nucleus). LUCA was anaerobic (its Source: Moody et al. 2024 Natur  The three-domain system Prokaryotes Eukaryotes (cells without a nucleus) (cells with a nucleus*) F Image credit: Chiswick Chap (Last Universal Common Ancestor) LUCA would not have been alone on the Earth ~4.2 billion years ago (Last eukaryotic common ancestor) (Last bacterial common ancestor) (Last archaeal common ancestor) Source: Moody et al. 2024 Nature Prokaryotic diversity: Bacteria and Archaea  Prokaryotes were the first organisms to inhabit the Earth. https://www.mun.ca/biology/scarr/Prokaryota_&_Eukaryota.ht Prokaryotes existed for billions of years before plants and animals appeared. The first prokaryotes could withstand high Image source: temperatures while thriving in presence of very little or no oxygen. ml Prokaryotes constitute ~14% of all biomass on the Earth. The prokaryotic cell  The Metabolic Diversity of Image source: https://bpb-us-w2.wpmucdn.com/sites.gatech.edu/dist/6/1810/files/2018/12/metabolic- Prokaryotes Prokaryotes can live in a vast diversity of environments. This is because prokaryotes can use multiple diverse energy and carbon sources for their metabolism: Energy from chemical oxidation (organism uses chemical reactions as the energy source to catalyze biochemical reactions)  Image source: https://bpb-us-w2.wpmucdn.com/sites.gatech.edu/dist/6/1810/files/2018/12/metabolic- It is important to note that not every bacterial or archaeal cell has the capacity to have all these four modes of metabolism. Energy from chemical oxidation (organism uses chemical reactions as the energy source to catalyze biochemical reactions) Some prokaryotes specialize in chemoautotrophy (e.g., Sulfolobus) while others specialize in photoautotrophy (e.g., cyanobacteria). But Sulfolobus is not a photoautotroph, and Cyanobacteria are capable of photosynthesis Cyanobacteria have photosynthetic pigments (e.g., phycobilins in many species, chlorophyll b in some others) which they use to convert photonic energy (from sunlight) into chemical energy. Cyanobacteria were also the first multicellular living organisms. Credit: Epipelagic @ Wikimedia Commons Credit: Epipelagic @ Wikimedia Commons Since such photosynthesis releases oxygen, cyanobacteria are considered to be an important cause of the rise on atmospheric oxygen concentrations. Such rise in atmospheric oxygen led to the upsurge of more efficient (aerobic) respiration, which allowed the evolution of larger and more Our planet’s primary productivity has mostly been cyanobacterial Although land plants drive most of the primary carbon fixation (conversion of inorganic carbon (CO2) to organic forms) at present, most of the carbon fixation over the course of our planet’s history has been done by cyanobacteria. Crockford et al. 2023 Curr. Biol. Many archaea live in extreme environments Organisms living in extreme environments are called extremophiles. For example, some archaea prefer to live in environments with salt concentrations of 10% w/v (~3-fold that of the oceanic salinity): Credit: Crion @ Wikimedia Commons Credit: Grombo~commonswiki @ Wikimedia Commons Many archaea live in extreme environments Some other archaea (e.g., Sulfolobus) prefer to live in hot springs where the pH is 2–3 and the temperatures are 75–80 °C. This makes them acidophiles and thermophiles, respectively. Credit: Lascorz @ Wikimedia Commons Credit: Ser Amantio di Nicolaoi @ Wikimedia Commons Many archaea live in extreme environments Some other archaea (e.g., Methanogenium frigidum) live in the Antarctic sea ice. This makes them psychrophiles. Credit: Maasstev @ Microbewiki Prokaryotes are key to biogeochemical cycling Prokaryotes are critical players in the biogeochemical cycling of nitrogen, carbon and phosphorus. Their role in the nitrogen cycle is particularly critical for the survival of other living organisms (i.e., eukaryotes). Nitrogen is the building block of amino acids and nucleotides; therefore, it is an essential component of all organisms. Although N2 is the most abundant gas in the atmosphere, it cannot be used by eukaryotes in its  Prokaryotes fix the atmospheric N2 into reduced forms (e.g., NH3). Examples of N2 fixing prokaryotes: soil bacteria, cyanobacteria, Frank ia spp., etc. Modified from “Nitrogen cycle” by Johann Dréo (CC BY-SA 3.0) Prokaryotes are important agents for bioremediation Pic source: https://organismalbio.biosci.gatech.edu/biodiversity/prokaryotes-bacteria- Bioremediation refers to processes that use a biological system to remove environmental pollutants. Microbes have been used in the bioremediation of pesticides, fertilizers, toxic metals, etc. Interestingly, bacteria have been used effectively to clean oil spills in the ocean. Many bacteria are pathogenic Many (but not all, not even most) bacteria cause diseases in humans, animal, and/or plants. Many pathogenic bacteria form biofilms, which are ecological communities of microbes that are held together by an extracellular matrix that is secreted by the constituent microbes. Biofilms are difficultSchematic to treat with antimicrobial agents such as antibiotics. Source: Magdalena Kegel @ cysticfibrosisnewstoday  Surprisingly, archaea are not known to cause many diseases in either animals or plants. it is possible that archaea-caused diseases are real but just remain undiscovered or understudies. Another possible explanation might be that many archaea live in extreme environments where a larger host species may not be found.