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Perspectives of Biology 113 Notes

by: charlotteee

Perspectives of Biology 113 Notes

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Second semester of a two-course introductory sequence for students with a strong background and interest in science. Topics include: evolution, organismal diversity, ecology, and functional biology...
Perspectives in Biology 113
Class Notes
Perspectives of Biology 113, Biology 113, Bio113
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This 6 page Class Notes was uploaded by charlotteee on Wednesday June 1, 2016. The Class Notes belongs to at University of Rochester taught by Bickel in Spring 2016. Since its upload, it has received 10 views. For similar materials see Perspectives in Biology 113 in Biology at University of Rochester.


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Date Created: 06/01/16
Conjugation : exchange of bacterial genes, direct transfer of DNA form one bacterial cell to another Transduction: phage-mediated transfer (phage = bacterial virus) Transformation: uptake of naked DNA from the environment. **Recombination rate is the highest the more similar the sequences are between two different individuals. The more the sequences diverge, the lower the recombination rate is. More likely to have recombination with other individuals with similar genomes because more coherent and more similarities. ***Lower recombination means less genetic coherence allowing divergence to separate species. Recombination makes their genome more similar to each other. Two groups that are separate and then come together and then their divergence will become closer and closer together and Recombination rate much more higher. Different groups will have recombination to make them more alike. More sequence divergence will make it more different. Bifurcating Tree A rooted bifurcating tree has exactly two descendants arising from each interior node (that is, it forms a binary tree), and an unrooted bifurcating tree takes the form of an unrooted binary tree, a free tree with exactly three neighbors at each internal node Lateral Gene Transfer: important for bacterial species because antibiotic resistance can spread between unrelated bacteria because can pick up genes from other species. (horizontal gene transfer), transmission of DNA (deoxyribonucleic acid) between different genomes. Horizontal gene transfer is known to occur between different species, such as between prokaryotes (organisms whose cells lack a defined nucleus) and eukaryotes (organisms whose cells contain a defined nucleus), and between the three DNA- containing organelles of eukaryotes—the nucleus, the mitochondrion, and the chloroplast. Acquisition of DNA through horizontal gene transfer is distinguished from the transmission of genetic material from parents to offspring during reproduction, which is known as vertical gene transfer. Not coming from the parent but completely separate lineage. Gene content can vary immensely: each circle represents a bacteria species (certain strains). How many genes are shared between all three strains of bacteria, and how many genes that aren’t found in any of the other two strains. **Bacterial genomes seem to have a relatively uniform G-C content: Red is greater than average and blue is less than average. G-C content is higher in some because it comes in different bacteria that has a different average of G-C content (region has not evolved yet) show signs of horizontal transfer Genomic Islands: regions that have evidence of horizontal transfer; extended region that has multiple genes and has evidence of horizontal transfer and shared functions. Pathogenicity Islands: genomic regions carrying genes contributing to virulence. group of genes that make a bacteria to be pathogenic; transferred to other strains. Genomic islands seem to resist heavy metals, nitrogen fixation making nitrogen usable in organic forms, antibiotic resistance from genomic islands. A genomic island (GI) is part of a genome that has evidence of horizontal origins. The term is usually used in microbiology, especially with regard to bacteria. A GI can code for many functions, can be involved in symbiosis or pathogenesis, and may help an organism's adaptation. Many sub-classes of GIs exist that are based on the function that they confer. Pathogenicity Islands: seem to always have a lower G-C content. The boxes are pathogenicity islands with genes for attachment to host cell (transfer of these new genes give them more advantages and adaptation; able to evolve by lateral gene transfer), invasion of host cell, toxin production and secretion systems Endosymbionts: any organism that lives within the body or cells of another organism Symbiosis: close and often long-term interaction between two or more different biological species Symbiont: an organism living in symbiosis Endosymbiosis: symbiosis in which one of the partners lives intracellularly within the other Endosymbiont: any organism that lives within the body or cells of another organism Most likely to last longer if there are positive effects for both species What does the aphid get from their symbiont: bacteria can produce all these essential amino acids because they only eat glucose What does the bacteria get from the aphid: safe place to live; get energy and food source right from the aphid/organism The primary benefit of the Buchnera bacteria is that they make the tryptophan amino acid for the aphid and the secondary benefit is that it give the aphid Hamiltonella defensa which gives the aphid resistance to wasps Primary Obligate symbiont: something you cannot live without; you’ll see more congruent development so when host develops, the symbiont will develop in the same way; provides necessary service, congruent with the host group in terms of phylogenetic because indicates long term association Secondary Facultative symbiont: context-dependent, long term association; one that they can live without; not required, phylogeny is not congruent so frequent lateral transfer from the host lineage to another Microbial Endosymbionts: intracellular, maternally transmitted through the egg/embryo, widespread occurrence recently discovered; you’ll see more horizontal transfer Wolbachia: broadly distributed among arthropods and nematodes (because both are ecdyzoans) as reproductive parasites. For some nematodes, they are obligate symbionts Cytoplasmic incompatibility when male has Wolbachia the bacteria will kill the eggs; so kill males or feminizing to spread Wolbachia (reproductive parasite manipulating in order to be transferred) Endosymbiosis and the chimeric nature of eukaryotes (Chimera = fusion of distantly related organsims): fusion of two distantly related organisms.  Wolbachia modifies host reproduction in several ways in order to enhance its own spread. One such modification results in the induction of parthenogenesis, where males, which are unable to transmit Wolbachia, are not produced. Male killing: infected males die during [9]val development, which increase the rate of born, infected, females.  Feminization: infected males develop as females or infertile pseudo- females.  Parthenogenesis: reproduction of infected females without males. Some scientists have suggested that parthenogenesis may always be [10] attributable to the effects of Wolbachia. An exampl[11] a parthenogenic species is the Trichogramma wasp, which has evolved to procreate without males with the help of Wolbachia. Males are rare in this tiny species of insect, possibly because many have been killed by that very same strain of Wolbachia. [12]  Cytoplasmic incompatibility: the inability of Wolbachia-infected males to successfully reproduce with uninfected females or females infected with another Wolbachia strain. In the mechanism of cytoplasmic incompatibility, Wolbachia interferes with the parental chromosomes during the first mitotic divisions to the extent that they can no longer divide in sync. [ Mitochondrion and chloroplast evidence for bacterial origin: arise only from preexisting mitochondria or chloroplast or plasmids; have two or more plasma membranes engulfed by other organism, have their own genome (single circular molecule, no histones associated with the DNA), have their own protein synthesizing machinery (such as antibiotics block protein synthesis, first amino acid transcript is fMet and not Met), Antibiotics block protein synthesis and the Inhibitors of eukaryotic protein synthesis don’t work **Mitochondrion and Chloroplasts are related to bacteria Primary Endosymbiosis: Primary endosymbiosis is the process in which a eukaryote engulfs another living prokaryote. An organism may then use that organism to its advantage. If a eukaryotic cell engulfs a photosynthetic alga cell, the larger organism can then use the products of the alga and become an autotrophic organism. But if the larger cell dies the smaller cell may not die and may leave the remains of the old cell to survive. Or if the smaller cell dies then the larger organism can stay alive. Scientists believe that this process has only happened a few times in history and is what leads to the creation and evolution of mitochondria and chloroplasts. An instance of this process would be when a cell long ago engulfed a photosynthetic Cyanobacterium. This bacterium would then become a plastid inside the cell and begin to share genetic material. A plastid is a major organelle found within plant and alga cells that contain and manufacture important chemicals. Over time this plastid evolved and became the current chloroplast. Secondary Endosymbiosis: Secondary endosymbiosis is when a eukaryote cell engulfs another eukaryote cell that has undergone primary endosymbiosis. This process has happened very often through time and has lead to the great genetic diversity we find on earth. The main difference between primary and secondary endosymbiosis that after the cell is engulfed it becomes dependent on the larger cell. It cannot leave and return to its original state. As you can see in the picture below there is a fairly large difference between primary and secondary endosymbiosis. After the initial endosymbiosis, the original hybrid cell reproduced and one of the new offspring was engulfed by another non-photosynthetic organism, allowing that new cell to be photosynthetic. This is all possible because of a double membrane that was made by the first layer of the endosymbiosis in primary endosymbiosis, and the membrane of the cell that was engulfed in secondary endosymbiosis forms the second layer. This is the reason that mitochondria and chloroplasts have a double phospholipid bi-layer. Human Gut Microbiome: differences among different people, differences along gut, incredible diversity of bacterial types; beneficial for synthesizing essential amino acids and vitamins; help digest things like plant polysaccharides such as Methanogenesis: removes products of fermentation (CO2 + 4 H2 → CH4 + 2 H2O), improving energy extraction from polysaccharide digestion Archaea are the functional members of the gut community: Archaeans include inhabitants of some of the most extreme environments on the planet. Some live near rift vents in the deep sea at temperatures well over 100 degrees Centigrade. Others live in hot springs (such as the ones pictured above), or in extremely alkaline or acid waters. They have been found thriving inside the digestive tracts of cows, termites, and marine life where they produce methane. They live in the anoxic muds of marshes and at the bottom of the ocean, and even thrive in petroleum deposits deep underground. Some archaeans can survive the desiccating effects of extremely saline waters. Archaeans may be the only organisms that can live in extreme habitats such as thermal vents or hypersaline water. They may be extremely abundant in environments that are hostile to all other life forms. However, archaeans are not restricted to extreme environments; new research is showing that archaeans are also quite abundant in the plankton of the open sea **Bacteria provide helpful metabolic pathways for organisms Animal Diversity Monophyletic group: eukaryotic, heterotrophic (carbon from outside sources), lack cell walls, multicellular, motile at some life stage (can move around) muscle and nervous tissues at most, life cycle with diploid phase is dominant (sexual reproduction and no haploid multicellular stage) **Animals can respond to electrical stimuli except Sponges Sponges are a very early branch of animals Animals are made up of a large amount of collagen (the main protein of connective tissue and makes up 25 to 35% of the whole body protein content of mammals); unique animal tissues, nerve and muscles Cambrian Explosion: The Cambrian Explosion relates to an abrupt appearance of a wide range of organisms, mainly invertebrates, with hard (fossilizable) parts in Cambrian strata which mainstream scientists date from about 540 million years ago. They were complex, well-developed organisms with many types of differentiated cells, and it is widely conceded that evolution of these organisms from unicellular precursors within such a short period of time is highly doubtful. Look at rocks from Cambrian Explosion and see a lot of animals after this period Sessile: Once formed, sponges cannot move around.  They are sessile, meaning  that they generally stay in one place. Origin of Animals (Metazoa): the closest outgroup is the Choanoflagellates (solitary organism or colonial organisms) freshwater or marine, pelagic (relating to open water) or benthic (sediment) Cadherins: molecular Velcro for holding adjoining cells together; any of a family of cell adhesion molecules that facilitate cell to cell adhesion in a homophilic manner and only when calcium ions are bound to it. Different organisms have different numbers of cadherins; seems like animals have more cadherins than plants and yeast and algae (Multicellular organisms need a way to hold cells together in like cell-tissues.) Group # Cadherin genes Plant 0 Slime mold 0 Yeast 0 Choanoflagellate 23 Cnidarian 46 Drosophila 17 Ascidian 32 Mouse 127


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