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Department
Biology
Course
BIO152H5
Professor
Fiona Rawle
Semester
Fall

Description
Readings: - Tree of life 27.1-2 (Vol. 1) - Bacteria and archaea I & II 28.1 -4 - Protists I & II 29.1-4 27.1- Phylogenetic Trees - Phylogeny: the evolutionary history of a group of organisms (usually summarized and depicted in the form of a phylogenetic tree) - A phylogenetic tree shows the ancestor-descendant relationships amongst popn or species, and clarifies who’s related to whom - A branch represents a popn through time - The point where two branches diverge is a node (or fork) and it represents the point in time when an ancestral group split into two or more descendant groups - A tip (or terminal node), the endpoint of a branch represents a group (a species or larger taxon) - Two general strategies for using data to estimate trees: phonetic approach and cladistic approach - Phenetic approach: a method for constructing a phylogenetic tree by computing a statistic that summarizes the overall similarity among popns based on the available data. E.g. researchers might use gene sequences to compute an overall ‘genetic distance’ b/w two popns. - Genetic distance: summarizes the avg % of bases in the DNA sequence that differ b/w the 2 popns - Cladistic approach: a method for constructing a phylogenetic tree that is based on identifying the unique traits of each monophyletic group - The C. Approach is bs based on the realization that relationships among species can be reconstructed by identifying shared, derived characters, or synapomorphies, in the species being studied - Synapomorphy: A shared, derived trait found in two or more taxa that is present in their most recent common ancestor but is missing in more distant ancestors - Synapomorphies allow biologists to recognize monophyletic groups- also called clades or lineages. - The issue is that traits can be similar in two species not because those traits were present in a common ancestor but b/c similar traits evolved independently in two distantly related groups - Homology (“same-source”) occurs when traits are similar due to shared ancestry - Homoplasy (“same-form”) occurs when traits are similar for reasons other than common ancestry. - Convergent evolution occurs when natural selection favours similar solutions to the problems posed by a similar way of making a living. Convergent ev. is a common cause of homoplasy- it results in analogous traits - Parsimony: The logical principle that the most likely explanation of a phenomenon is the most economical or simplest. When applied to comparison of alternative phylogentic trees, it suggests that the one requiring the fewest evolutionary changes is most likely to be correct - Since convergent evolution and other causes of homoplasy should be rare compared with similarity due to shared descent, so the tree that implies the fewest overall ev. changes should be the most accurate - Whales are artiodactyls and share a relatively recent common ancestor with hippos. 27.2 – Fossil Record - Only the fossil record provides direct evidence about what organisms that lived in the past looked like, where they lived, and when they existed. - Fossilization occurs most readily when the remains of an organism are buried in sediments, where the decay is slow. - Fossils are formed in several ways. Different preservation processes give rise to different types of fossils: a) Intact fossil: The pollen was preserved intact because no decompositions occurred b) Compression fossils: Sediments accumulate on the top of the object and compress it into a thin carbon-rich film c) Cast fossil: When the object decomposes after it\s buried. This leaves a hole that filled with dissolved minerals creating a cast. d) Permineralized fossil: when dissolved materials infiltrate the cells graduals and harden into stone - The fossil is a piece of physical evidence from an organism that lived in the past - The fossil record is the total collection of fossils that have been found throughout the world. 28 – Bacteria and Archaea - Virtually all members of B & A are prokaryotic- they lack a membrane bound nucleus. - Organisms in the B & A domains are distinguished by the types of molecules that make up their plasma membranes and cell walls, and by the machinery they use to transcribe DNA and translate msnger RNA into proteins. - Bacteria have a unique compound called peptidoglycan in their cell walls - Archaea have unique phospholipids in their plasma membranes - Also, the structures of the RNA polymerases and ribosomes found in Archaea and Eukarya and distinct from those in bacteria and similar to each other- this is why antibiotics that poison bacterial ribosomes don’t affect ribosomes of A and E. - The oldest fossils of any type are 3.4 billion yr old carbon rich deposits derived from bacteria - Eukaryotes didn’t appear in the fossil record until 1.75 bya. - Only 5000 species of B & A have been formally named but millions exist - Species in a lineage called the Group I marine archaea may be the most successful org on Earth 30 - Biologists estimate a total # of B & A alive today at 5 x 10 - No archaea are known to cause disease in humans but some bacteria cause disease - B that cause disease are said to be pathogenic (literally “disease-producing”) - To establish a link b/w a specific microbe and a specific disease, Koch proposed that four criteria had to be met (these are known as Koch’s postulates) are still used to confirm a causative link b/w new disease and a suspected infectious agent - Koch’s results also became the basis for the germ theory of disease. This theory holds that infectious diseases are caused by bacteria and viruses. (Viruses are acellular particles that parasitize cells) - Pathogenic forms of B come from many lineages in the domain B and that pathogenic B tend to affect tissues at the entry points of the body like wounds/pores in the skin, respiratory, gastrointestinal tracts and the urogenital canal. Some diseases caused by bacteria: - Antibiotics are molecules that kill bacteria - Bioremediation: use of bacteria and archaea to degrade pollutants. It is often based on complementary strategies: • Fertilizing contaminated sites to encourage the growth of existing bacteria and archaea that degrade toxic compounds • “Seeding” or adding, specific species of bacteria and archaea to contaminated sites - Extremophiles: B or A that live in high-salt, high-temp, low-temp of high-pressure habitats (“extreme-lovers”) - Based on the conditions that prevailed in Earth’s history, it seems that extremophiles were the first forms of life - Astrobiologists study extemophles as model organisms for extra-terrestrial life - Certain B and A can live in extreme env and use toxic compounds as food b/c they produce very sophisticated enzymes. The complex chem. That they carry out and their abundance have made them potent forces for global change - Cyanobacteria are a lineage of photosynthetic bacteria – first became numerous 2.7- 2.55 bya - C were the first organisms to perform oxygenic photosynthesis - O. Photo. Depends on the proteins and pigments in photosynthesis II - Fossil and geological record indicates that O2 lvls in the oceans/atm began to increase 2.3-2.1 bya - The evolution of aerobic resp was a crucial event in the history of life. B/c O2 is extremely electronegative. It’s an efficient electron acceptor. Much more nrg is relreased as elec- move through e- transport chains w/ O2 than with other substances as e- acceptors (Cellular resp can produce more nrg with O2 as the final e- acceptor) - First eukaryotes: macroscopic algae - Organisms must have nitrogen to synthesize proteins and nucleic acids. Although N2 is extremely abundant in the atm, most org can’t use it. All eukaryote and many B & A have to obtain N in a form of ammonia (NH3) or nitrate (NO3-)- nitrogen fixation - The only org that are capable of converting N2 to ammonia are bacteria. - In terrestrial env , N- fising bacteria that aren’t cyanob live in close association with plants- often taking up residence in special root structured called nodules - One classical technique for isolating new bacteria and archaea is called enrichment culture. E.C are based on establishing a specified set of growing conditions- temp, lightning, substrates, types of available food, etc. The idea is to sample cells from the env and grow them under extremely specific conditions. Cells that thrive under these conditions will increase in #s enough to be isolated and studied in detail - Direct sequencing is a strategy for documenting the presence of B & A that cannot be grown in culture- it allows biologists to identify and characterize org that have never been seen. - D.s is based on isolating DNA from samples taken directly from the env, purifying and sequencing specific genes, and then analyzing where those DNA sequences are found on the phylogenetic tree of B & A - Researchers thought that Archaea could be conveniently grouped into 4 categories: extreme halophiles, sulphate-reducers, methanogens, and extreme thermophiles - Extreme halophiles (“salt-lover”) live in salt lakes, salt ponds and salty soils. - Sulfate-reducers: species that produce hydrogen sulphide (H2S) as a by-product of cellular resp - Methanogens produce methane (CH4) as a by-product of cell res. - Extreme thermophiles grow best at temps above 80 degress - Based on this, researchers thought that archaea were restricted to extreme env but as a result of direct sequencing studies, these generalizations have been discarded. - Some of the most useful phylogenetic trees for B & A have been based on studies of the RNA molecule found in the ribosomes - Bacteria were the first of the 3 lineages to divert from the common ancestor - A monophyletic group consists of an ancestral popn and all of its descendants. Monophyletic groups can also be called clades or lineages - Morphological diversity among B and A is extensive a) Size varies b) Shape varies: including filaments, spheres, rods, chains, spirals c) Mobility varies; some use flagella to power swimming movements d) Composition of cell walls and plasma membranes - Smallest bacteria: microplasmas with volumes= .03 um 3 - Largest: Thiomargarita namibiensis; v= 200 x 10 6 - Within B, two general types of cell walls exist - When treated with the Gram stain, gram + cells look purple and gram – cells look pink - Cell walls in Gram + bacteria have extensive peptidoglycan - Cell walls in Gram – bacteria have some peptidoglycan and an outer membrane - The most important thing to remember about bacteria and archaea is how diverse they are in the types of compounds they can use as food Metabolic Diversity - Organisms have two fundamental nutritional needs- acquiring chemical nrg in the form of ATP and obtaining molecules with C-C bonds that can be used as building blocks for synthsis of fatty acids, proteins, DNA, etc - Bacteria and Archaea produce ATP in 3 ways: 1. Phototrophs: use light nrg. ATP produced by photophosphorylation 2. Chemoorganotrophs: oxidize organic molecules with high potential nrg, such as sugars. Atp made by cellular resp or via fermentation pathways 3. Chemolithotrophs (rock-feeders) oxidize organic molecules with high potential nrglike NH3 OR CH4. Atp – produced by cell. Resp. - B & A fulfill their 2 nutritional need un two ways: 1. By synthesizing their own from simple starting material such as CO2 or CH4 2. By absorbing ready-to-use org compounds from their env - Autotrophs: Organisms that manufacture their own building block compounds - Heterotrophs: Org that acquire building-blocks from other org - Of the 6 possible ways of producing ATP and obtaining carbon, just 2 are observed in eukaryotes, but B & A do them all. In their metabolism eukaryotes are simpler than B & A - The basic chem. required for photosynthesis, cell. Resp, and fermentation originated in B & A. Then the evolution of variation on each of these processes allowed prokaryotes to diversify into millions of species - Species that use water as a source of electrons for photosynthesis are said to complete oxygenic photosynthesis. In contrast, many phototrophic bacteria use a molecule other that water as the source of electrons (like H2S of Fe2+) and are said to complete anoxygenic photosynthesis and live in habitats with rare O2. - Cell resp. Is based on the electron transport chain - Millions of B & A & E species- including animals and plants are organotrophs; obtain nrg required to make ATP by oxidizing org compounds like sugars, starch, fatty acids. - In cellular resp, a molecule with high potential nrg serves as an original electron donor and is oxidized, while a molecule with low potential nrg serves as a final electron acceptor and becomes reduced - The remarkable metabolic diversity of B & A is important. First, it explains their ecological diversity. B & A are found almost everywhere b/c they exploit an almost endless variety of molecules as electron acceptors and donors. Second, it explains why they play such a key role in cleaning up some types of pollution. Species that use organic solvents or petroleum-based fuels as electron donors/acceptors may be effective agents in bioremediation efforts. Finally metabolic diversity is what makes B & A major players in global changes - Fermentation: any of many metabolic pathways that make ATP by transferring electrons from a reduced compound like glucose to a final electron acceptor other than O2. Allows glycolysis to proceed in the absence of O2. - As a group, B & A can use a wide array of raw materials for cell. resp and fermentation, perform non-oxygenic as well as oxygenic photosynthesis and fix Carbon from several different sources via a variety of pathways As I mentioned, the point about bacteria and archaea are their diversity. So you should be able to recognize/describe this diversity. This means that you should be able to describe some of those characteristics in which the groups are diverse. For example, you should be able to give a concrete example on differences in carbon-fixing pathways that exist in these groups. Bacteria: - Biologists currently recognize at least 16 major lineages, or phyla, within the domain. Some were recognized by distinctive morphological characteristics; others by phylogenetic analyses of gene sequence data. - Some phyla of Bacteria: 1. Firmicutes • Aka “low-GC Gram positives” b/c their cell walls react positively with Gram stain- meaning that they lack a membrane outside of their cell walls and their DNA has low % of GC 2. Spirochaetes • One of the smaller phyla- only 13 genera and 62 species to date 3. Actinobacteria • Aka “high-GC Gram positives” b/c their cell walls react positively with Gram stain- meaning that they lack a membrane outside of their cell walls and their DNA has high % of GC 4. Cyanobacteria • Formerly known as the blue-green algae- even though algae are eukaryotes. Only about 80 species but are among the most abundant org. • Dominate the surface waters in many marine + freshwater env 5. Chlamydiales • May be the smallest of all bacterial lineages. Although they are highly distinct phylogenetically, there are only 4 species in 1 genus 6. Proteobacteroa • Approx. 1200 species of proteobacteria for 5 major subgroups ( alpha, gamma, delta, beta and epsilon) • Named after greek god Proteus , who could assume many shapes, b/c they are so diverse in their morphology and metabolism - Paraphyletic: a group that consist of a common ancestor and some but not all of its descendants - Photosynthetic bacteria are paraphyletic- species that can perform photosynthesis are scattered throughout the phylogenetic tree. Archaea - Bacteria and Archaea are both monophyletic - Currently no parasitic Archaea - Phylogenies based on DNA sequence data have consistently shown that the domain is composed of at least 2 major phyla: Crenarchaeota and Euryarchaeota 1. Crenarchaeota: • Got their name b/c they are considered similar to the oldest Achaeans; cren refers to a source or fount. • 37 species have been names but 1000s are yet to be discovered 2. Euryarchaeota • Members of this phylum live in every possible habitat- some species are adapted to high-salt habitats – almost as basic as ammonia, which others are adapted to acidic conditions. • About 170 species have been identified thus far 29 – PROTISTS - Protists are a paraphyletic grouping that includes all eukaryotes except the green plants, fungi and animals. Biologists study protists to understand how eukaryotes evolved, because they are important in freshwater and marine ecosystems and global warming, and because some species cause debilitating diseases in plants, humans and other organisms - Protists are diverse morphologically. They vary in the types of organelles they contain; they may be unicellular or multicellular and they may have a cell wall or other external covering, or no such covering - Protists vary widely in terms of how they find food. Many species are photosynthetic, while others obtain carbon compounds by ingesting food or parasitizing other organisms - Protists vary widely in terms of how they reproduce. Sexual reproduction evolved in protists, and many protists reproduce both sexually and asexually. - Diatoms are single-celled protists that live inside a glassy case. They may be the most abundant of all eukaryotes found in aquatic environments - The largest and the most complex organisms o the tree of life- algae, plants, fungi and animals- are eukaryotes - Eukaryotes are defined by the presence of the shared derived characteristic called the nuclear envelope - Most E cells are much larger, have many more organelles and are a much more extensive system of structural proteins called the cytoskeleton, than B & A cells. - Multicellularity is rare in bacteria and unknown in A, but has evolved several times in E - Unlike B & A, which reproduce by fission, E can undergo cell division via mitosis and some can also undergo meiosis - Like archaea most E have chromosomes where DNA is complexed with proteins called histones - Protists constitute a paraphylet
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