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Today’s Plan: 3/22/10 Bellwork: Announcements/Housekeeping (5 mins) Endosymbiant Article and questions (20 mins) Classification Activities (30 mins) Notes on Classification (25 mins) Pack/Wrap-up (last few mins of class) Today’s Plan: 3/23/10 Bellwork: Graphic for Classification lab (15 mins) Bacteria essential questions/activities (45 mins) Finish Bacteria Notes (the rest of class) Today’s Plan: 3/24/10 Bellwork: Finish Prokaryote Notes (15 mins) Prokaryote and Protist Activities (45 mins) Protist notes (the rest of class) Classification Recall that in Biology, you learned the 7-step hierarchical classification scheme: KPCOFGS Some scientists have proposed a less-hierarchical, more descriptive PhyloCode for classification, which would include more info about evolutionary history, but this is still controversial Modern scientists have added a step to the front of this scheme: Domain. 3 domains Archea: contains only the archaebacteria Bacteria: contains only the eubacteria Eukarya: contains the other 4 kingdoms; Protista, Fungi, Plantae, and Animalia (all are eukaryotic) Also recall that this is simply a modernization of Linnaeus’ scheme. We still use his Binomial Nomenclature for scientific names Remember that this is correctly written as Genus species or G. species, and that scientific names are in Latin If you’re handwriting a scientific name, you underline it in stead of using italics Phylogeny vs. Cladistics Phylogeny is the study of an organism’s evolutionary history This is traced on phylogenetic trees, which are based on all known data for classification and branch according to the hierarchical system of classification Branch points aren’t always accurate with respect to time, but you can get a sequence from the tree It’s sometimes difficult to tell the evolutionary relationships between certain taxa (like families) on phylogenetic trees We can’t necessarily infer that an organism directly evolved from the taxon next to it on the tree Cladistics is a slightly different approach that uses common ancestry as the primary criterion for classifying organisms. This is used to construct Cladograms, graphic representations of the relationships between Clades (a group containing the ancestral species and all of its descendants) Cladograms are constructed using Derived Characters, which are new characteristics that appear with each branch on a cladogram. If all organisms have a trait, and that trait is used to determine common ancestry, it’s called the shared ancestral character If all organisms have a trait, and the trait is not used as the primary trait for determining common ancestry, it’s called a shared derived character Figure 27-1 Distinguishing between Homology and Analogy Homology=traits that are similar due to shared ancestry Analogy=traits that are similar due to convergent evolution (also called homoplasies) In general, to distinguish between these, Molecular data, as well as complete anatomical/physiological data is necessary Figure 27-2 The difficult nature of classification As you’ve done your lab work, you’ve no doubt noticed that there’s a certain arbitrary nature to this work, and that the graphics used are often unable to depict something important about an organism’s lineage We should always remember that all phylogenetic trees are hypothetical! Scientists use several things to try to be as accurate as possible (achieve maximum parsimony) Some phylogenetic trees use proportional branch lengths to demonstrate the degree of genetic change since divergance Scientists try to use the simplest explanation consistent with the facts (Occam’s razor) Some scientists use the principle of maximum likelihood-given certain rules about how DNA changes over time, a tree can be constructed that reflects the most likely sequence of genetic change Figure 28-11 Bacteria According to morphological similarities, prokaryotes should be closely related Archaea Eukarya Prokaryotes Mostly single-cellular, but sometimes form colonies Have cell walls that contain peptidoglycan (hybrid sugar-protein molecules) as opposed to chitin or cellulose of eukaryotic cells React to Gram staining differently Gram positive have simpler cell walls and retain the stain Gram negative have less peptidoglycan in their cells walls, are more complex and retain less stain This is important b/c it has treatment implications for patients with bacterial infections, since gram negative bacteria tend to be more resistant to the body’s defenses and to antibiotics Figure 28-14a Gram-positive cells retain Gram stain more than Gram-negative cells do. Gram-positive cells Gram-negative cells Figure 28-14b Cell walls in Gram-positive bacteria have extensive peptidoglycan. Gram-positive cell wall Polysaccharides Cell wall Plasma membrane Peptidoglycan Protein Figure 28-14c Cell walls in Gram-negative bacteria have some peptidoglycan and an outer membrane. Gram-negative cell wall Polysaccharides Cell wall Outer membrane Peptidoglycan Plasma membrane Protein Prokaryotes, cont. Many have a capsule, which is sticky (made of polysaccharides or proteins) and allows the bacteria to stick to a substrate or to other bacteria to form a colony Some have fimbriae, which are long, hair-like projections that allow them to fasten to the mucous membranes of their hosts Many also have sex pili for conjugation (passing pieces of DNA back and forth for sexual reproduction) About ½ have flagella to help them move directionally (the flagellum isn’t as thick as a eukaryotic flagellum and is not covered by an extension of the plasma membrane) Come in 3 main shapes, bacillus, coccus, and spiral Figure 28-10 Escherichia coli, strain K-12 Growth in liquid medium Growth on solid medium Reproduction and Adaptation Recall that prokaryotes have a single chromosome but also may contain small plasmids that occurs in the nucleoid region of the cell Prokaryotes can reproduce asexually by binary fission (see the cell division notes) or can reproduce sexually using conjugation and binary fission Under ideal conditions, bacteria can divide every 20 minutes (in reality, they divide every 12-24 hours) Certain bacteria can produce an endospore when conditions are lacking The bacteria produces a copy of its chromosome (internally), and surrounds it with a tough wall. The rest of the cell dehydrates and dies When conditions are better, the endospore resumes its metabolism Endospores can be hard to kill (can survive heat up to 121 C The success of Prokaryotes Rapid reproduction, genetic recombination, and mutation provides diversity Prokaryotes are therefore highly evolved Genetic recombination happens b/c of Transformation-this can happen spontaneously in nature if bacteria come into contact with other strains that have died Transduction-bacteriophages carry genes from one host to the other. This is accidental as it provides no advantage for the virus Conjugation-through the sex pilus b/c of the F factor (25 genes) that are required for production of the sex pilus (can be on a plasmid or in the chromosome) R plasmids (resistance to antibiotics) can be transferred by conjugation too Prokaryote Metabolism Like Eukaryotes, some Prokaryotes are autotrophic, while others are heterotrophic There are 4 main Nutritional Modes: Autotrophs Photoautotrophs-Do photosynthesis Chemoautotrophs-Do chemosynthesis using Hydrogen sulfide in stead of light Heterotrophs Photoheterotrophs-Can harness light energy but need to get Carbon in an organic form Chemoheterotrophs-Must consume organic molecules to get energy and carbon More Metabolism Role of oxygen Some are obligate aerobes, some are obligate anaerobes Anaerobes can do fermentation, while others just do anaerobic respiration in which nitrates or sulfates act as electron acceptors in stead of Oxygen Facultative anaerobes can use oxygen if present, but can also carry out anaerobic respiration in the absence of oxygen Metabolic cooperation Bacteria in colonies can become specialized to carry out just 1 metabolic function (ex: just nitrogen fixation, or photosynthesis) Such bacteria form Biofilms with channels that allow nutrient transport. The cells in a biofilm chemically signal one another Figure 28-00 Ecological Importance of Prokaryotes Nitrogen fixation-Eukaryotes can only accept Nitrogen in certain forms, prokaryotes can accept it in virtually any form, which allows them to pull atmospheric nitrogen and convert it to ammonia and other nitrogen-containing compounds Root nodules of plants contain bacteria that release usable nitrogen to plants Figure 28-16 N2 in atmosphere Fixation by bacteria and archaea Denitrification by bacteria and archaea Organic compounds with amino (–NH2) groups Uptake from soil Decomposition by bacteria, archaea, fungi Decomposition Uptake from soil NO3– (nitrate) Plants Uptake from soil Nitrification by bacteria NH3 (ammonia) Decomposition NO2– (nitrite) Nitrification by bacteria Figure 28-6 Root nodules Other Interactions of bacteria Mutualistic relationships Gut bacteria that help you digest food Root nodule bacteria Decomposing bacteria in the soil Commensal relationships Bacteria that live on your skin’s surface Parasitic relationships Disease-causing bacteria produce poisons that cause illness Exotoxins-proteins secreted by bacteria (Ex: Cholera, botulinum) Endotoxins-lipopolysaccharide components of gramnegative bacteria which are only released when the bacteria die (Ex: Salmonella, typhoid fever) Figure 28-2-Table 28-2 Non-symbiotic uses of Prokaryotes Food Production Biomedical Research Biormediation-using bacteria to remove pollutants from soil, air, or water But we’re still dealing with 2 Domains, right? Archaea Known as the extremophiles 3 main types: Extreme halophiles-”love salt” like in the Great Salt Lake or the Dead Sea. Their cell walls are adapted to such conditions Extreme thermophiles-”love heat” like in volcanic springs. Their DNA and proteins are adapted so that they don’t denature in high heat Methanogens-Anaerobic bacteria that relase methane as their waste product. Found in marshes or under ice in Greenland Bacteria These are the bacteria that you’re most familiar with and are also extraordinarily diverse Figure 28-12 Bacteria Archaea Eukarya Bacteria Archaea Proteobacteria Crenarchaeota Euryarchaeota Figure 28-1-Table 28-1 Figure 28-13 Small Size varies The sizes of bacteria and archaea vary. Mycoplasma cells (left) are about 0.5 µm in diameter, while Thiomargarita namibiensis cells (right) are about 150 µm in diameter. Shape varies The shapes of bacteria and archaea vary from rods such as Bacillus anthracis (left) and spheres to filaments or spirals such as Rhodospirillum. In some species, such as Streptococcus faecalis (right), cells attach to one another and form chains. Mobility varies A wide variety of bacteria and archaea use flagella (left) to power swimming movements. These cyanobacterial cells (right) move by gliding across a substrate. Large Compare relative sizes