BIOL 112 1st Edition Exam 1 Study Guide Lectures 11 21 Lecture 11 September 20 What is phylogeny o A hypothesis about the evolutionary between a group of organisms o The analytical approach used to determine phylogenetic relationships systematics o A phylogenetic tree graphical representation of the hypothesis o Relationship is down based on shared characteristics o Phylogeny uses the same approach as taxonomy comparison of similar characteristics Systematics o What characteristics can we compare Traditional pre genome era 1990 Morphology Comparative embryology Biochemistry ex Isoenzyme properties mobility isoelectric points Molecular era post 1990 Big technological advances made it possible to o Sequence entire genomes o Identify open reading flaws in sequence using special computer algorithms that 1 D start codon ATG introns exons stop codon Computer programs that can predict the way a protein folds function Computer programs that can pull out the homologous genes for a group of organisms Can build trees by comparing the degree of sequence similarity between homologs Molecular data new phylogenetic trees o Ex Animals and fungi more closely related to each other than fungi to plants o But more significantly we can draw organisms with no morphological similarities ex Humans and bacteria Lecture 12 September 23 Lecture cancelled Lecture 13 September 25 Homologous sequences o Orthologs Tend to have high sequence identity May may not have same function Ex Sequence from species A Compare to genome data base for all genome 8 identities approximate to 80 identities 11 total population o High so high the two genes are probably homologs Use different types of genes for comparing different organisms o For organism likely to be distantly related ex Human vs bacteria use slow evolving sequences o Slow evolving means doesn t change over time Don t change because changes likely to be detrimental o For organisms that are closely related use fast evolving sequences o Slow evolving sequences will show no difference between closely related organisms o Fast evolving sequences will be different between e g Races or strains within a species Evolve changes rapidly because not essential for function Ex Comparison of human ethnic groups compare hyper variable region of mitochondrial genome Beware of misinterpreting analogy as homology o Distinguish between the two by looking for many points of characteristic initially compared Molecular homology vs analogy o If homologous sequence identity high 50 o If analogous low sequence identity about 25 Lecture 14 September 27 Percent conservation aka percent identity o Highly conserved high identity o Low conservation low identity o Highly conserved sequences functionally important sequences o Not altered much over time because changes disrupt function Genomes tell evolutionary history o 1 Origin of mitochondria chloroplast both originate from Endosymbiotic event Evidence Mitochondria have their own genome resemble a prokaryote genus i e circular DNA With highest sequence homology to extent alpha proteobacteria o 2 Chloroplast Similar processes Mitochondrial containing cell engulfed a cyanobacteria ancestor Cyanobacteria photosynthetic bacteria Evidence Chloroplast has its own genome bacterial like circular DNA sequence homology greatest with cyanobacteria Chloroplasts are also membrane enclosed o Also both mitochondria and chloroplasts divide with oclis by a process that resembles prokaryotic division i e binary fission o For both mitochondria and chloroplasts Organelles are co dependent on cell cell nucleus Some are replaced by nuclear gene Origin nucleus golgi ER o Process by which genetic material is transferred between organism horizontal transfer See Fig 26 22 Paralogs orthologs o Both homologous genes Come from a common ancestor High sequence identity o Ortholog ortho straight o Paralog para beside Duplication of an ortholog within a species Example of this Olfactory receptor genes Hox genes only in animals o Encodes transcription factors that conduct animal development Transcription factors DNA binding protiens bind specific sequence in gene promoters control region help recruit RNA polymerase to gene for transcription o Hox gene make a particular class of TF homeodom Lecture 15 October 2 Hox genes o Very important for animal evolution o Hox genes regulate development master regulators control expression of many target genes o Therefore change in hox gene sequence can dramatically impact animal form o Ex Fly hox genes In a specific region control development of all structure in that region o Hox genes are organized in clusters of a gene Gene rated by gene duplication paralogs o Also see Fig 25 23 Earth is approximately 4 6 billion years old o No life before 3 billion years ago o Planet bombarded with ice rock from out of space o Earth hypothesis Haldene and Oparin How building formed initially o 1950s Miller and Urey tested experimentally in lab Amino acids bases not nucleotides Almost right o 2008 based on atmospheric conditions around thermal vents cracks in the ocean Amino acids etc more abundant Close to actual conditions in early Earth Lecture 16 October 4 Life accurate replication and metabolism Lipid membranes o Lipids have a tendency to form vesicles in aqueous solutions o Lipid vesicle selective barriers concentrates compounds inside increase probability of interaction provided a controlled environment o Clay from volcanic acts as a catalyst for RNA uptake into lipid vesicle Fig 25 3 o RNA probably the first genetic material because of intrinsic properties Can self assemble Can fold into 3D structures that can self cleave o Later smitten to DNA because DNA is more stable Proto cell prokaryote What did LUCA look like o Had characteristics common to bacteria and archaea o Bacteria and archaea DNA genome Nonnuclear envelope Electron transport ATP or ATP analogs Proteins Same genetic code Both present in LUCA o Bacteria and archaea differ rDNA gene sequences Cell wall composition Evidence of first prokaryote o Fossil evidence prokaryote stromalites Stromalites fossilized prokaryotes Date to 3 5 billion years ago o Early prokaryote cyanobacteria Produce O2 to increase atmospheric O2 Increase O2 rust formation in rocks Date to 2 75 billion years ago Bacterial cell organization o 1 5 u diameter c f eukaryotic cell 10 100 u diameter o Common shapes Cocci sphere Baccili ros Spiral helical o Cell wall surrounds plasma membrane Cell wall protection but
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