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MIDTERM NOTES.docx

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Department
Biology
Course
Biology 1001A
Professor
Tom Haffie
Semester
Fall

Description
MIDTERM NOTES Evolution in action: Human immunodeficiency Virus  HIV pandemic 1981 (AIDS) o Pandemic: outbreak all over the world  Sub-Saharan Africa is hit hard o No access to clean watereasily transmitted o Standard of living is a lot lower o Lack of medication o Lack of education/awareness o More animal interaction  HIV=zoonosis (affects non human animals and humans)  Still no cure after 32 years, why? o Higher mutation rate than for any other virus genetic variation in the virus itself o HIV associated with “gay” transmissions  Viruses are different from bacteria  they are not living  RETROVIRUSES- disobey central dogma of molecular biology o DNA (replication)  RNA (Transcription)  protein (Translation)  Reverse transcription (no proof reading enzymes for virus)  Genetically variable viruses, mutations occur here  Anti-viral drugs have serious side effects- attacks your own cells as well as virus cells  HIV lifecycle: hijack immune cells: o Virion (viral particle) enters host cell o Reverse transcription: injects into host cell  viral DNA o Integrase splices viral DNA into host DNA o Transcription, translation, new virions assemble and enter circulation o Immune system collapses  Anti-retroviral therapies (ARTs) o To minimize side effects, attack steps unique to the virus o Target reverse transcription step  reverse transcriptase (RT) o The drug AZT mimics thymidine („fools‟ RT) = jams progression of nucleotides and blocks reverse transcription. An INHIBITORY DRUG o AZT eventually stopped working, what happened?  The virus is evolving resistance to AZT even before a patient is treated with AZT  Evolution of AZT resistance o Mutation  variation in AZT resistance is passed on from parent to offspring o Not all virions reproduce o When AZT is PRESENT, AZT RESISTENCE forms and more likely to reproduce than others (AZT susceptible) o Viral population changes over time in response to selection pressure  Evolution by Natural Selection  Resistance to one drug is inevitable; resistance to many drugs is less likely  Drugs need to be used together, not in isolation to prevent further resistance; “Drug cocktail”  Human CCR5 32 allele  HIV resistance o Expressed on surface of white blood immune cells, which HIV uses as a host o Mutation of cell are more likely to be immune to HIV (have one or two copies of 32 mutation) o Why is this mutation more common in North Europe?  Allele is increasing in certain places because it‟s better to have natural selection?  Chance and history? Mutation may have spread during middle ages and through colonization  Evolutionary response to past outbreaks of infectious diseases ie. Bubonic plague  allele may have been favoured in resistance to other diseases hit in NE  Summary: Evolution in Action o Evolution can be very fast o Even non-living things can evolve o HIV evolution involves themes such as:  Mutation and variation  Natural selection  Evolutionary history  Humans as a evolutionary force and as products of evolution ORIGIN OF LIFE What is life? Characteristics: -order -harness and utilize energy -reproduce -respond to stimuli -exhibit homeostasis -growth and development -evolve -ORDER, REPRODUCE, EVOLVE = VIRUSES (are a form of life) -3 domains of life: bacteria, archaea, eukaryotes (LUCA: last universal common ancestor)  Does not mean LUCA was the first organism on earth but everything has descended from LUCA  Most likely explanation for similarities between all branches (all forms of life share fundamental biochemistry) o Genetic system based on DNA o DNA to RNA to protein transfer of info o Common system of protein assembly (ribosomes) o ATP o Glucose and glycolysis o Phospholipid bilayer (lipids) -What came before LUCA? Died out, no biological traces -Characteristic used to build the tree: DNA, ONE GENE -Prokaryotes don‟t exist  Suggests that everything in that group is evolutionary related  Each group has a distinct domain  Pro means before ie. Before nucleus, no evidence to suggest that a nucleus is a derived structure that developed after LUCA -Reductive Evolution: “Streamlining”  Getting rid of “stuff” to replicate faster  Fewer complex structures  Can grow faster=evolve faster  Extremophiles -Life developed early: mostly speculation  Stromatolites: Australia 3.5 billion years ago  Cyanobacteria: still today, complex -Stages of prebiotic Evolution:  What do you need for life?  Abiotic synthesis, Heritable information, cells, metabolism (respiration and photosynthesis) -Geophysical stage: what was the composition of the earth and the atmosphere -Chemical stage: how could the building blocks of life be synthesized  Miller-Urey experiment: Gases light a spark and amino acids, nucleic acids, urea came out  Proved? ABIOTIC SYNTHESIS IS PLOSABLE but left with unanswered questions o No development of polymers o Chirality: “handedness”  2 enantomers (optical isomers) mirror images  left and right hand, amino acids  D-alanine  L-alanine  Position of bonding is different, same chemical and physical properties  Ie. Thalidomide: used as a drug to help morning sickness in 50s 60s. A teratogen causes birth defects. In cells the drug is rapidly converted to chiral form, which is teratogen and detrimental o Life is homochiral: only use one form in life: essential to the evolution of life o All life: L amino aids, D sugars o Miller-Urey…RACEMIC: get 50% of one chiral form and 50% of the other regardless of the product you got o Before LUCA, life had to decide which chiral unit to use -Biological stage: How did the building blocks organize into living cells? (not as well understood)  Heritable information, cells, metabolism  Central dogma  RNA: the molecule that can do it all  RNA world: information, structure & function (catalyst)  “genes” on DNA  mRNA through transcription, then to protein  tRNA, rRNA  genes that code for  rRNA gene founded all organisms on planet: tree of life is built on this  RNA is single stranded and can fold back on itself to make 3 dimensional structures: proteins  Some RNAs are catalytic (when they form proteins) RIBOZYMES are biological catalysts but NOT proteins  Ribosome is a ribozyme: peptidyl transferase activity  Evolution of information transfer o Replication is never perfect when you replicate RNA o We think this lead to the development of protein o Proteins: structure and catalysis o Diversity o Ribonucleoprotein: a functional unit that has RNA and protein suggests an ancient structure that evolved, RNA and protein coming together to make a functional system ie. Ribosome has BOTH o DNA hold genetic information  Thymine replaces uracil  C to U mutation common Stability: DNA versus RNA -RNA is much less stable cause of hydroxyl group easily breaking down BIODIVERSITY -BIOLOGY: THE STUDY OF LIFE -New species are discovered each year -18 000 species discovered in just the last year  Chondrocladia lyra: under the see late 2012  Zospeum tholossum: transparent snail lives in caves  Semachrysa Jade: insect discovered by a tourist  Paedophryne amanuensis: smallest vertebrae animal, frog  Bassaricyon neblina: raccoon like animal  Cercopithecus lomamiensis: new monkey lives in Congo rainforest -1.2 million species of eukaryote that have been discovered/described, but 90% have not yet been discovered (share the planet with 7-10 million species) -Universal common descent and origin of species -Every living thing on earth is related by a single common ancestor who is now extinct (LUCA)  Similarities due to single common ancestors  Genetic code is almost always the same  Homologies: inherited traits from common ancestor -Many MRCAs one for each grouping -The Ancestor’s Tale- Richard Dawkins  Reverse tour of evolutionary history  Start present day and climb down tree  8.7 million other species doing the same thing  Branching points on tree of life  rendezvous points  At each point, meet other species  Rendezvous zero? MRCA of all humans -Most recent since humans last shared an common ancestor? 3000 years Rendezvous 1: Chimps & bonobos: -Closest related other species -5 to 6 million years ago -What would this common ancestor have been more like? Us or them? -Probably not exactly like either, the lineage has morphed over time -If we are descended from chimps, why are there still chimps around? We are not descended from them, we share a common ancestor, like cousins and grandparents Rendezvous 2: Gorillas: -7 million years ago -Mountain gorillas, only 700 left -Gave rise to modern day gorillas -Are African great apes (most evolutionary history happened in Africa) Rendezvous 3: Orang Utans -14 million years -In rainforest in Southeast Asia -Much more solitary not in big social packs -Very arboreal -MRCA of all great apes -Most common ancestor occurred farther back in time with humans Rendezvous 4: Gibbons: -18 million years -Restricted to Southeast Asia -Highly athletic (swing from tree branch to tree branch up to 10 meters) -Socially monogamist: mate for life -MRCA of all apes Rendezvous 5 and 6: Old world and new world monkeys: -25 million years ago -100 species of old world monkey ie. Baboons -Spent most of evolutionary history in Africa and Asia -40 million years ago new world monkeys evolve in South America Rendezvous 7: Tarsiers Rendezvous 8: Lemurs and Lorises -Active at night -60 million years ago -Lorises: most recent common ancestor of ALL primates END-CRETACEOUS MASS EXTINCTION, 65 MILLION YEARS AGO -Meteor hit earth and caused species on earth to go extinct Rendezvous 10: Rodents & Rabbits -2000 rodent species -40% mammal species are rodents, some kind of mouse Rendezvous 11: Laurasiatheres -Bats, Whales, insects, carnivores -85 million years ago Rendezvous 14: Marsupials Rendezvous 15: Monotremes -Moles  environments lead to claws for digging -180 million years ago with egg laying mammals -MRCA of all mammals Rendezvous 16: Reptiles -300 million years ago -snakes and birds, lizards and birds, are more closely related than to turtles Rendezvous 17: Amphibians -over 300 million years ago -MRCA of all tetrapods 340 mya Rendezvous 18- 22: Lungfish; coelacanths;sharks; jawless fish - These „fish‟ are no more closely related to each other that they are to us - MRCA of all vertabrates 530 mya Rendezvous 26: Protostomes -1 million described species -“To a first approx, all animals are insects” Rendezvous 34. 35, 36 ,: fungi, Amoebozoans, plants -Humans more closely related to fungi than the others -Multi cellularity ahs evolved more than once Rendezvous 38: Archea -Whole new domain of life -Extreme environments (heat, cold) -More closely related to us than bacteria Rendezvous 39: Bacteria Summary: diversity of life -All life on earth is related through common decent -We can trace our ancestry back to LUCA in just 39 steps -Some similarities reflect shared ancestry; other similarities reflect convergence -If evolution were to be rerun, would the outcomes be the same? WHY EVOLUTION IS TRUE -Dover trial in Pennsylvania evolution by natural selection to be learned in schools -Humans evolved from earlier species of animals  Idea not accepted by all- evolutionary process of humans  Belief in a god that created life forms? No god(s)? Different beliefs.  Acceptance of human evolution (USA, 1982-2012) most believed that god created humans in present form within last 10,000 years  Teach the controversy? What should be taught in science classrooms? Different view: religious, political, geographical, Darwin‟s theory, creationism  Two sides to every story? Should be presenting both and both have equal times? -Evolution as a fact and a theory  What do scientists mean by a “theory”?  What do we mean by “true”?  What IS the theory of evolution  What empirical evidence supports this theory -Evolution is only a theory…  “An assumption based on limited knowledge…a estimate”  “A coherent set of testable hypothesis that attempt to explain facts about the natural world”  ADJUST THEORY TO FIT DATA, NOT OTHER WAY AROUND  ie. Atomic theory of matter, germ theory of infectious disease, gravitational theory -What do scientists mean when we say that something is “true”?  “An assertion for which there is so much evidence that it would be perverse to deny it” –SJ Gould  Test a theory by attempting to alter it- trying to prove theory false  Theories graduate to “fact-hood” after repeated testing fails to falsify them -Unfalsifiable assertions are no scientific (if theory is wrong, outcomes of test will show us- idea has to be falsifiable)  Russell‟s teapot: there is a teapot out there, prove to me it doesn‟t exist. This assertion that there is a teapot orbiting the sun but too small to see, is not a falsifiable statement-cannot be disproven and are not scientific statements  Testing, debating and refining theories= the scientific process: scientific debate is a discipline that is still healthy for the topic, leads to new discoveries- change revise theories to account for data -What is the theory of evolution?  Highly synthetic theory- supported by many lines of thought 1. Evolution happens. Allele frequencies in a population change from one generation to the next 2. Most evolution is gradual 3. Lineages diverge (speciate) into multiple daughter lineages 4. All life is related through common ancestry 5. Much evolutionary change (but not all) results from natural selection 6. Evolution occurs in populations, not in individuals o Difference between Darwin and Lamarck: Darwinian evolution start with population that is variable, Lamarck don‟t need to change genoty
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