#Week 2 • Bioenergetics • PHOTOSYNTHESIS: PRIMARY PRODUCTION AND OXYGEN • NUTRITION: BASIC CONCEPTS AND FEEDING IN INVERTEBRATES • Lab - Environment (Field trip) -what challenges do organisms have in this environment / EXTRACTION OF PHOTOSYNTHETIC PIGMENTS USING THIN LAYER CHROMATOGRAPHY --- Ch 5 Ch44 882-885 Ch10 --- #4. BIOENERGETICS Note: Based on the syllabus BIO200, the students should have knowledge on principles of glucose biochemistry, respiration/ATP synthase, glycolysis, Krebs cycle and fermentation/anaerobic respiration. Student can be referred to online lectures to refresh concepts (see links of interest). - What is bioenergetics and why we study it? - What are cells doing with energy harvested from the environment? - Homeostasis (keep intracellular conditions stable -revise important concepts from previous week-) - Growing and producing: creation of new cells/cell constituents (requires synthesis of specific biomolecules) - Transporting material against concentration gradients (active transport) - Moving (motility) - Overview: Sources of energy in aquatic environments: - Sunlight is the ultimate energy source for life in the sea, and this is true even in deep water ecosystems (e.g. marine snow, whale falls, etc). Phototrophs are the base of the food chain. - Exception in hydrothermal vents and cold seeps/brine pools. Chemotrophs are the base of the food chain. These use hydrogen sulfide and methane as energy source to produce carbohydrates. - However, although it is often said that these communities exist independently of the sun, some of the organisms are actually dependent upon oxygen produced by photosynthetic organisms.- - Review basic concepts in bioenergetics (students should be familiar with these concepts after BIO200): - Redox reactions (“OIL RIG”) Ch 8 - Carbohydrates and energy storage Ch 5, pp 80-81 - ATP as universal energy current Ch 8, pp 143-144 - NAD/NADH and FAD/FADH2 as reducing equivalent Ch8 pp 142 - Metabolic diversity in eukaryotes vs. bacteria and archaea. All metabolisms can be arranged according to these three principles (Ch 29, pp 538-541): - How the organism obtains energy for living and growing (Source of energy): Phototrophs (ATP is produced by photophosphorilation-this will be explained in detail in the next class-) and chemotrophs (ATP is produced by cellular respiration or fermentation). - How the organism obtains reducing equivalents (source of electron donor): Organotrophs (oxidize organic molecules with high potential energy -sugar, starch or fatty acids- for ATP synthesis) and lithotrophs (oxidize inorganic molecules with high potential energy -eg., NH3, CH4, H2S- for ATP synthesis). - How the organism obtains carbon for synthesizing cell mass (source of C-C bonds): Autotrophs (synthesize its own compounds from CO2 and more rarely CH4, CH3OH, and CO) or heterotrophs (cannot fix C, and use organic C to growth). - Compared with eukaryotes (most of eukaryotes are photolithoautotrophs -green plants and algae-, or chemoorganoheterotrophs -metazoan and fungi-), the metabolic capabilities of bacteria and archaea are remarkably complex and diverse. Bacteria and archaea have evolved dozens of variation on the basic processes of respiration and photosynthesis (Chapters 9 and 10). - Producing ATP through cellular respiration: variation in electron donor and acceptor. Ch 29, pp 538-540. Introduce role in bioremediation (Ch 29, pp 533) E.g., some bacteria and archaea use hydrocarbons in cellular respiration. - Producing ATP via fermentation: Variation in substrate. Ch 29, pp 540-541. - Producing ATP via photosynthesis: variation in electron sources and pigments (this will introduce and put into perspective the next class and the lab work this week). Ch 29, pp 541 Links of interest: Lectures by Dr. Jennifer Doudna from UC Berkeley For this class, see lectures 9, 10 and 11. https://www.youtube.com/watch?v=DRiokVd-ID8&list=PLjyM1bt_7m8utrHfsvJnho2P5ECw2Zj3A Lectures by Khanacademy, 20-min lectures total on bioenergetics (9 lectures total) https://www.khanacademy.org/science/biology/cellular-molecular-biology/cellular-respiration/v/electron-transport-chain NOAA on marine snow http://oceanservice.noaa.gov/facts/marinesnow.html   #5. PHOTOSYNTHESIS: PRIMARY PRODUCTION AND OXYGEN - Overview: Different types of Photosynthesis. Variation is electron sources and pigments (this can be used to revise concepts from the previous class, and contextualize phototrophic organisms). Ch 29 pp541 Phototrophs in aquatic environments: - Rhodopsin-based retinalophototrophy. Use bacteriorhodopsin and archaerhodopsin. Haleobacteria in water saturated or nearly saturated with salt. - Photosynthesis by absorbing getothermal radiation. Photosynthetic green sulfur bacteria at a deep-sea hydrothermal vent. See links of interest. - Chlorophyll-based chlorophototrophy. Two types: - Anoxygenic. Many phototrophic bacteria use a molecule other than water as the source of electrons (e.g., H2S or Fe2+). Instead of producing oxygen they produce S or the ferric ion Fe3+. Anoxygenic photosynthesis: green sulfur bacteria, green and red filamentous anoxygenic phototrophs (FAPs), phototrophic purple bacteria, phototrophic acidobacteria, and phototrophic heliobacteria. Use of bacteriochlorophylls. - Oxygenic. When organism “split” water molecules apart to obtain electrons, they generate oxygen as a by-product. Species that use H2O as a source of electrons (electron donor) for photosynthesis are said to complete oxygenic photosynthesis: plants, algae and cyanobacteria. Use mainly chlorophyll, and other pigments (phycocyanin, carotenes, xanthophylls –green algae-, phycoerythrin –red algae-, and fucoxanthin –brown algae and diatoms-). - Importance of the oxygenic (“oxygen-producing”) photosynthesis (plants, algae and cyanobacteria): fix C and produce O2. Basics: - Photosynthesis occurs in chloroplasts: Description of chloroplasts components (thylakoids, grana, lumen, stroma, etc). Ch 10 pp178 - How do pigments capture light energy? Part of this can be covered in lab activity (extraction of pigments, and introduction to pigments -not only in chlorophylls but also in algal pigments, e.g., phycocyanin, ficoerythrin, fucoxantin, etc-) Ch 10 pp 179-183 - Photosynthesis consists of two linked sets of reactions. - Light-dependent reaction: Produce oxygen, ATP and NADPH from H2O -Photosystem II (P680) and I (P700), and how they both interact: The Z scheme. Ch 10 184-189. - Light-independent reaction: Produce sugar from CO2 -The Calvin cycle (C3 pathway) Ch 10 190-194. -Importance of rubisco - Photosynthesis in aquatic ecosystems. Use this last part of the section to correlate concepts shown in this lecture with concepts that students have (or should have) learnt from Marine Biology 250. Links of interest: Quick and easy video on photosynthesis by Bozeman Science: https://www.youtube.com/watch?v=g78utcLQrJ4 Lectures on photosynthesis by Dr. Jennifer Doudna from UC Berkeley: Photosynthesis I https://www.youtube.com/watch?v=gokwqaS0bGM Photosynthesis II https://www.youtube.com/watch?v=Tw0eGx1_jGU Moonlight photosynthesis? http://www.thenakedscientists.com/HTML/questions/question/1769/ An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent http://www.pnas.org/content/102/26/9306.full Algae phytoplankton and chlorophyll: http://www.fondriest.com/environmental-measurements/parameters/water-quality/algae-phytoplankton-chlorophyll/#algae14 Photosynthesis in the open ocean: http://www.sciencemag.org/content/326/5955/945.full   #6. NUTRITION: BASIC CONCEPTS AND FEEDING IN INVERTEBRATES - Review key concepts from previous lectures: - Sunlight is the ultimate energy source for life in the sea - Phototrophs are the base of the food chain; they use sun’s energy to fix inorganic carbon into reduced organic material (previous lecture). - Modes of nutrition autotrophy vs, heterotrophy - Overview: - Animals (i.e., heterotrophs) need to incorporate nutrients from the external environment. - Animals get chemical energy from carbon containing “building blocks” (carbohydrates, proteins and fat), which have high potential energy. These compounds are used to synthesize ATP and key macromolecules. Remind catabolic pathways. Figure 9.3 in Ch 9, pp 157. - In addition to obtaining chemical energy and the “building blocks” from carbohydrates and other compounds in food, animal require other essential nutrients (essential amino acids, vitamins, minerals, electrolytes). Ch 44, pp883-884. - Basic concepts: - Modes of feeding attending to two different criteria: - What animal eat: Diversification of ecological roles. Ch 33, pp 647-648 - Detritivores - Herbivores - Carnivores - Omnivores - How animal feed: Four general strategies. Ch 33 648-649 - Suspension feeders - Deposit feeders - Fluid feeders - Mass feeders - The digestive system: General steps: - Ingestion: Food is taken - Digestion: Food is broken down into smaller pieces/molecules - Absorption: Nutrients molecules are absorbed into body cells - Elimination: Undigested material exits the body - Types of digestion - Intracellular. - In the animal kingdom, only sponges (filter feeders) do this exclusively - Lack of digestive tract (do not confuse digestive tract and central cavity/atrium) - Cells engulf food via phagocytosis or pinocytosis, forming food vacuole - Lysosomes fuse with food vacuoles; hydrolytic enzymes break down food. - Extracellular - All animals (except sponges) perform this mode of digestion. - Digestion begins in a compartment continuous with the outside of the animal’s body (gastrovascular cavity or digestive tract) - Enzymes are secreted to break food into smaller molecules - What is the advantage of extracellular digestion? Animal can take in a lot of food at once and slowly digest it - Animals are the only multicellular heterotrophs on the tree of life that usually ingest their food first, before they digest it. As a result digestion in animals typically occurs within the space, or lumen of the digestive tract rather than in the open space. Ch 33 pp 637. Ch 44, pp 886-887. Types of digestive tracts: - Incomplete digestive tracts: Gastrovascular cavity (aka coelenteron, bind sac, or blind gut). Ch 33, pp 652-654 - Cnidarians, ctenophores, flatworms - Gastrovascular cavity = digestive sac with a single opening for both input and output - Gastrovascular cavity serves as stomach and intestine - Different strategies to catch the prey (sticky tentacles –ctenophora-, cnidocytes –cnidaria-, etc) - Digestive enzymes are secreted to allow for extracellular digestion - Nutritive muscular cells then engulf food particles - Indigestible material leaves through mouth (no anus) - Complete digestive tracts - Nematodes, annelids, mollusks, arthropods, echinoderms and chordates - Two openings: one for input and the other for output - Complete digestive tract = digestive tube running throughout body (alimentary canal) - Organisms with a complete digestive tract have both a mouth and an anus - Why would having a separate entry and exit point be beneficial? Digestion can be broken down into steps, and there can be specialization of digestive tissues for these steps - For information on feeding: - Feeding in non-bilaterian: the most ancient of all major animal lineages. See sponges, ctenophores and cnidarians, Ch 33, pp 652-654 - Feeding in protostome animals (arthropod, mollusk and annelid), Ch 34, pp 660-669, pp 674-678. - Feeding in deuterostome animals (echinoderms, invertebrate chordates) Ch 35, pp 683-687. Links of interest: Slides and basic information on different digestive systems-Good for images http://digestivemack.weebly.com/index.html# No all sponges are suspension feeders: “Killer sponges” http://www.mbari.org/news/news_releases/2014/killersponges/killersponges-release.html The exception: Extracellular digestion in killer sponges http://faculty.uml.edu/rhochberg/hochberglab/Courses/InvertZool/Carnivorous%20Asbestopluma.pdf   #LAB WORK 2: EXTRACTION OF PHOTOSYNTHETIC PIGMENTS USING THIN LAYER CHROMATOGRAPHY Content: Introduction/revise basic concepts on phycology (Not sure how familiar students are with algae/phytoplankton) Photosynthetic pigments and absorption spectra with emphasis not only in chlorophylls but also in algal pigments Extraction of photosynthetic pigments using thin layer chromatography -We can compare terrestrial plants vs. algae and discuss presence of specific pigments. Pigment extraction (there are many protocols). This is one of them: http://wordpress.clarku.edu/debrobertson/laboratory-protocols/algal-pigments/ What can we tell about the organism based on the pigments that it contains? Seegrass in the Salish sea http://www.beachwatchers.wsu.edu/ezidweb/seaweeds/