10/26 - 10/30 Class Notes
10/26 - 10/30 Class Notes BIO 1500
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This 6 page Class Notes was uploaded by Diane Notetaker on Sunday November 1, 2015. The Class Notes belongs to BIO 1500 at Wayne State University taught by Daniel M. Kashian in Summer 2015. Since its upload, it has received 29 views. For similar materials see Basic Life Diversity in Biology at Wayne State University.
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Date Created: 11/01/15
BlOlSOO Monday 10262015 Hierarchical organization of life Biosphere 9 Community 9 Population 9 Organism 9 Organs 9 Tissues 9 Call 9 Molecule 9 Atom Murphy s Law If anything can go wrong it will Systems have emergent properties the whole is not necessarily predictable from the sum of the parts specific properties are not predictable just by looking at the components emergent properties when component objects are forced to interact to make a higherlevel aggregate object 0 Ex individual cells function together as one tissue system 0 Ex individuals do not have birthdeath rates but populations groups of individuals do Why is this important Realization that we should be integrating information across various levels of interaction People tend to be reductionist and think each subject is independent from others but this is not so Think globally think multidisciplinarily We must think deeply about how all factors are interacting across a spectrum Ex Starlings tend to outcompete woodpeckers for nest holes at first glance starlings are smaller and don t appear to be able to elbow woodpeckers out of their homes but they do We need to understand a more complex set of knowledge I Environmental background eg when does this happen I Life history eg how often do they reproduce I Mechanism of function eg how does this happen I Genetic basis of traits that allow this to happen What is biodiversity Compilation of all the various kinds of life forms on the planet Where does biodiversity come from There are three ideas out there a creationism all species here today came to be from single creation event and have not changed through time b transformism all species arrived from single creation event the number of species remains constant but change through time c evolution descent with modification from a common ancestor Creationism amp transformism are not testable and will not lead to scientific progress they cannot be supported through experimentation or observation Evolution can be observed through experimentation and observation 0 Darwin proposed experiments that would reject his ideas Darwin presented several instances that would allow for falsification of his theory Ex Darwin purported that all domesticated pigeons came from the wild rock pigeon Ifthis was not true all the various wild pigeons that supposedly gave rise to all the domesticated pigeons were either extinct or undiscovered so go find them Ex complex structures if organisms evolve through selection on small changes we would expect to see intermediate transformational forms between species and we do I What s a mollusk Octopus Snails clams Within mollusks you can see the progression of the eye The structure becomes modified and ability to trap light is improved eventually evolving into complex eye How do we classify organisms Standardized system developed by Linnaeus using binomial nomenclature to describe taxonomic relationships Genus species Linnaeus felt it was his responsibility to catalogue what God put on Earth thus system developed with a anthropogenic perspective system uses Latin bc anything scholarly done so in Latin influence of Catholic Church Individual lt Species lt Genera lt Family lt Order lt Class lt Phylum lt Kingdom King Philip Came Over From Great Spain Genera similar organisms that may not readily interbreed Family groups of Genera with common features Order groups of Families with common features and so on Why a classification system There has to be a single universal way of describing things so we can talk about them Common names change depending on region It is a development of a language We need to be able to describe taxonomic similarities and differences between organisms Species originally described as quottypesquot ignoring variation within populations there was little consensus about what was a species and what wasn t Linneaeus system doesn t necessarily reflect evolutionary history Genera theoretically should be closest relatives but with genetic sequencing this has proven not always the case within Linneaus system How do we organize evolutionary history Phylogenetic trees I Look at shared evolutionary traits Choose a characteristic eg RNA morphology compare amp contrast it and draw a tree The more closely related the taxa the closer they ll appear on the tree I Phylogenic trees will help create nomenclature because will show taxonomic relationships I Organized with tips branches and nodes Tips are most recent represent observed taxa Branches sometimes represent distance eg time to next closest ancestor Nodes are splitting events represent extinct common ancestors How do you interpret a tree Look how each tip connects to its ancestors what is the order of splitting Organization of tree is arbitrary It s how they relate to ancestors not how they re arranged A species will always be more closely related to another species that came after it than one that came before it homology characteristics which are similar due to common descent traits inherited from a common ancestor Ex Mammalian necks many have 7 cervical vertebrae in their necks vertebrae 1 in humans is homologous to vertebrae 1 in giraffes analogy characteristics which are similar due to convergence or parallel evolution they are not inherited from a common ancestor Ex Bats wings vs bees wings have similar function but from different ancestors Ex Bats wings vs birds wings Depends what you compare As wings they re analogous same function but common ancestor did not fly As tetrapod forelimbs they re homologous they shared common ancestor in dinosaurs Bats fly wwebbing between fingers birds fly wwhole arm Are homologies informative when thinking about evolutionary history Yes bc it deals with shared common ancestry Wednesday 10282015 What is that silly creature on slide 1 Blobfish Dichotomous keys can be created by using homologies They are a series of yesno questions that you can use to identify organisms Why are phylogenetic trees important Allow us to answer questions about evolution where do diseases come from when did certain traits evolve Ex 1 Seeds evolved once somewhere between H and I in this group seeds are homologous character because all instances of trait are traced back to one common ancestor Ex 2 Seeds evolved three times this group seeds are NOT homologous because did not come from one common ancestor appeared three separate times Where did SARS come from It appeared and disappeared relatively quickly so we never developed a good way to combat it For this important to understand the source of this disease It came from corona virus that is commonly found in many mammals we probably have all been infected by one at one point in our lives The worst diseases are often the ones that jump host Bird Flu is Bird Flu because it jumped from birds to humans This is our hypothesis that SARS jumped to us from another host Prediction An animal host species will have corona virus similar to SARS How do you test similarity Look at the phylogeny of the DNA sequences of corona viruses in other mammals Results Right side of figure has distinct corona viruses Bottom has difference from first common ancestor Which one is the most similar to human SARS It s the Palm civet It s statistically significant it s almost identical to that of humans We can conclude that Palm civet was original host and jumped to humans Palm civets are quite cute But virus only found in domesticated ones and they are not notable vectors So possibly we could have infected the Palm civets Eventually researchers came to the Chinese Horseshoe Bat According to the phylogeny SARS 1 is different from the other infected bats and is closer in relation to the one found in Humans SARS 4 What is the significant implication of phylogenetic trees Everything comes from a common ancestor Do all living organisms come from the same original ancestor This is a hypothesis We should except to see fundamental similarities among all taxa And we do All organisms use DNA All organisms use the same genetic code of 20 amino acids coding for 64 codons All organisms metabolize with ATP use ribosomes as a mechanism to transcribe proteins all use cellular structure to compartmentalize and concentrate energy It s very unlikely that all organisms developed these systems independently more likely that they came from a common ancestor What are the kingdoms Linneaus recognized Plants and Animals only two kingdoms Eventually it was expanded to five Domains Animals Plants Fungi Protista Monera bacteria and Archaea Prokaryotes Monera Eukaryotes everything else What are the evolutionary relationships of these groups Prokaryotes bacteria and Archaea appeared before Protista Protista Eukaryotes gave rise to Plants Animals and Fungi Ordered according to acquisition of resources Plants are autotrophs photosynthesizers Animals are heterotrophs through digestion Fungi are heterotrophs through absorption Prokaryotes vs E ukaryotes Prokaryotes unicellular except when they form biofilms no nuclear membranes DNA floats around no organelles no cytoskeleton structure of chromosomes wDNA different and thus mitosis does not occur They re difficult to study because lack of fundamental tools At first study of Prokaryotes was only focued on bacteria but with the use DNA sequencing two distinct kinds discovered traditional bacteria and Archaea both considered Prokaryotes The use of the names quotprokaryotesquot and eukaryotes does not reflect evolutionary history Archaea and bacteria should share a more common ancestor and now considered three distinct domains Bacteria Archaea and Eukarya See Table of Key Characteristics of Bacteria Archaea and Eukarya in lecture slides How do bacteria reproduce They do not have DNA structures like Eukarya do they are just single cells They divide through fission just split in two and each is a replica Their chromosome is circular not linear If we can t eat them why should we care about them Prokaryotes are the most abundant group on the planet and provide amazing amounts of diversity Nitrogen fixers that live in nodules on plant roots make atmospheric nitrogen available for plants which in turn provides nutrition for humans The first photosynthesizes were cyanobacteria developed chlorophyll a They decompose They cause diseases intracellular parasites are common They clean our environment Chemoheterotrophs are anaerobic and occupy places without much oxygen including guts of cows producing methane Friday 10302015 Archaea Bacteria Archaea bacteria are more similar to eukaryotes than traditional bacteria Can inhabit extreme environments Methanogens live in guts of cattle swamps and sewage and produce methane anaerobic decomposers that convert C02 and H2 to methane greenhouse gas Extreme halophiles very tolerant to salinity as much as 2535 saline Extreme thermophiles live in hot springs very tolerant to temperatures of 6080 degrees Centigrade This is difficult because enzymes degrade at high temperatures DNA unwinds at 95 degrees Centigrade but these bacteria can survive TAQ is a thermophile and has been vital to the development of our ability to generate large quantities of DNA sequences very rapidly DNA polymerase is isolate then heated and it will replicate in cycles PRC polymerase chain reaction Characteristics of E ukaryotes They are more complex than prokaryotes Cytoskeleton provides support mechanism for the cell allows cell to change shape allows for mitosis allow for chromosomes to be more structures notjust circles like in prokaryotes you can have 2 pairs of 23 chromosomes Flexible cell surface allow infolding to occur changing volume of inside of cell and allowing for membrane bound structure See figure in lecture slides Perhaps at one point in transition from Prokaryotic cell to Eukaryotic membrane infolding encapsulated the DNA to create a nucleus and nuclear envelope and also developed endoplasmic reticulum and other structures which were then allowed to diversify in function Different compartments now doing different things Organelles Did they come from infolding of the membrane Or did they come from symbiosis from bacteria 0 Originated from endosymbiosis between ancestral eukaryote and a bacteria 0 Mitochondria create ATP provide energy for a cell have circular DNA molecules inside like bacteria Hypothesized that a bacteria cell with infolding engulfed an aerobic bacteria and instead of being digested it entered a symbiotic relationship 0 Chloroplasts larger bacteria engulfed smaller photosynthetic bacteria and later evolved to be symbiotic 0 Why Mitochondria first and then Chloroplast Because all plants have mitochondria but not all animals have chloroplasts so a branching event occurred after Mitochondria was developed Chloroplasts and mitochondria have DNA molecules that replicate like bacteria through binary fission not mitosis Ribosomes inside mitochondria and chloroplasts similar to bacterial ribosomes evidenced through DNA sequencing Cyanobacteria DNA and chloroplast DNA are closely related 0 Less likely that organelles were created on their own Once infolding occurs pockets are created It is more difficult for machinery to pass through membranes into pockets to form organelles What is the advantage to cell structures of eukaryotes Energy production in mitochondria metabolism can produce biproducts that are dangerous to DNA and can lead to mutations Compartmentalization protects against mutations and damages to chromosomes Keeps mitochondriachloroplast DNA separate from organism DNA Increased surface area of plasma membrane infolding allows for other metabolic function and greater potential transport through membranes Evolutionary History Archaea were discovered to be more like eukaryotes than prokaryotes therefore prokaryotes was not a useful taxonomic term in that doesn t reflect evolutionary history Is the term Protista reflecting evolutionary history information No for Eukarya to be a valid term all of the Eukarya would have to share a more recent common ancestor with each other than they would with any of the Protista But Eukarya are borne from Protista at multiple times Eukarya is not a group that evolved from a single ancestor they evolved at separate times With new DNA sequencing new information about evolutionary history is available and traditional classifications are being redefined Remember the article from the beginning of the semester Kingdoms is outdated organism should be organized in quotsuper groups Characteristics of Protists Hold the phone Protists aren t even a group But too bad everyone else learns this way so we will too Locomotion Some move through the use of pseudopods cilia or flagella Contain vesicles sacs such as contractile vacuole for elimination of water or food vacuole for digestion Surfaces Some have cell wells some have endoskeletons Reproduction In comparison all bacteria reproduce by fission Some Protists reproduce asexually fission budding spores often through mitosis some reproduce sexually with diploid and haploid forms 0 diploid 2 chromosome sets 1 from each parent haploid half the usual number of chromosome sets Nutrition phototrophs heterotrophs phagotrophs ingest particulate food matter by engulfing it osmotrophs take in food matter across membranes or mixotrophs can go both ways Multicellularity Protists can appear as anything from single cells to colonies to truly multicellular 0 What s so special about being multicellular t fosters specialization different cells can do different things There is a division of labor and thus more complexity and flexibility Animallike Protists Unicellular Heterotrophic usually eating other single cell organisms or dead organic matter that they digest in vacuoles Typically classified by how they move Amoebas Flagellates Sporozoans Ciliates Phyla Amoebas have no cell wall move by using pseudopods extension of plasma engulfs food by flowing around it o Foraminifera make beautiful shelllike skeletons and help to date the fossil record with mineral skeletons are still able to move with pseudopods heterotrophic marine environment complex life cycles with haploid amp diploid phases 0 Radiolarians produce glassy exoskeletons made out of silica Flagellates use flagella to whip and spin through environment some cause disease Giardia Trichomonas Ciliates use hairlike structures called cil to move conjugate copulate with similar mating type Sporozoans they do not move and are parasitic and so move from place to place with help of host 0 Plasmodium causes malaria lives inside red blood cells depends on mosquito for transfer from host to host the red blood cells get infected in the liver Plantlike Protists can be multicellular Photosynthetic each has chlorophyll and other photosynthetic pigments Euglenoids aquatic unicellular move around using flagella and move towards like phototactic can adjust food from surroundings when lite is not available no sexual reproduction Diatoms produce intricate cells made of silica unicellular or in chains contain photosynthetic pigments called carotenoids golden color usually just float around in water but some move with use of two long grooves Dinoflagellates produce lethal toxins Red Tide unicellular or colonial spin around using two flagella Algae Seaweeds microscopic to very large multicellular and marine 0 Green live in fresh water unicellular or multicellular live singularly or in colonies
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