Bio 201 F11 Lect 10 (True)r

Bio 201 F11 Lect 10 (True)r - Biology in the News [see...

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Unformatted text preview: Biology in the News [see folder on BB] •  •  •  •  •  •  •  •  •  the compe77ve strategy that woody vines use to complete with other plants is to grow quickly and outshade their compe7tors, such as trees kudzu (Pueraria lobata) is an invasive species in the US and elsewhere that rapidly climbs trees and other structures to complete for sunlight in the tropics, lianas (many different species in different phylogene7c groups of plants), are even more effec7ve than kudzu at this strategy their roots also strongly compete for water and minerals below ground in tropical forests, over a quarter of woody species have this growth form lianas are increasing in abundance in recent decades, at the cost of trees and other forest plants e.g. tree crown infesta7ons of lianas increased from 32% in 1967‐1968 to 75% in 2007 in Barro Colorado Island, Panama some liana species are also invasive in non‐tropical areas of North America if these increases con7nue, biologists may eventually worry about preserving many tree species in the tropics hUp://www.nsf.gov/news/news_summ.jsp? cntn_id=119057&WT.mc_id=USNSF_51&WT.mc_ev= click st mid term exam 1 •  •  •  •  •  •  •  •  Wed. September 28th in class covers material through Friday 9/23 lecture (first 10 lectures) prac7ce ques7ons will be posted; review sessions listed on next slide Be on 7me –  >10 min late will not be allowed into room Bring only your ID and pencils –  All other materials have to be lee on periphery of the room 35 mul7ple choice ques7ons + 3 bonus bio news ques7ons lowest of the three mid terms is dropped, avg. of other 2 = 60% of your grade Only documented medical/family/accident excuses accepted •  we need to be NOTIFIED before end of the day on the day of the exam Exam 1 Review Sessions •  •  •  •  •  •  •  held in Life Sciences 026 Friday 9/23 ‐ 3:00 ‐ 4:00 ‐ Alvin Ho Monday 9/26 ‐ 2:00 ‐ 3:00 ‐ Safa Abdelhakim Monday 9/26 ‐ 4:00 ‐ 5:00 ‐ Harrison Dai Tuesday 9/27 ‐ 8:30 AM ‐ 9:30 AM ‐ Redwan Ahmed Tuesday 9/27 ‐ 10:30 ‐ 11:30 AM ‐ Dana Opulente Tuesday 9/27 ‐ 2:00 ‐ 3:00 ‐ Dana Opulente •  BRING YOUR QUESTIONS; TA’s do not make presenta7ons more on phylogene7c trees •  one major set of tree‐building methods is based on the concept of parsimony – the hypothesis that involves the fewest evolu7onary events is thought to be the most likely –  parsimony is essen7ally the concept of Occam’s razor – given compe7ng hypotheses to explain a phenomenon, the hypothesis involving the fewest assump7ons is considered the most likely an example of the use of parsimony hUp://www.geology.wisc.edu/~museum/ hughes/images/parsimony.jpg but parsimony is not always a good assump7on •  homoplasies defy parsimony –  complex traits can evolve independently more than ones •  example from previous lecture: 4 chambered hearts in birds and mammals mammalian heart hUp:// science.kenn esaw.edu/ ~jdirnber/ Bio2108/ Lecture/ LecPhysio/ 42_06Mamm alHeart_L.jpg 12 hUp://www.paulnoll.com/Oregon/Birds/Avian‐Circulatory.jpg there are many other examples Reading phylogeneCc trees Reading phylogeneCc trees The goal of phylogene7c systema7cs is to designate taxonomic groups at all levels as the monophyle7c groups in the tree of life PARAPHYLETIC GROUP ‐ contains an ancestor and only some, not all of its descendants POLYPHYLETIC GROUP ‐ does not contain the common ancestor MONOPHYLETIC GROUP ‐ contains a common ancestor and all of its descendants Is this a monophyleCc group? Bryophytes Ferns Fungi Insecta Amphibia Aves Mammalia clades •  a clade is a group of organisms (taxa) that is hypothesized to be descended from a common ancestor –  i.e. a monophyle7c group hUp://www.ib.usp.br/evolibrary/ images/evo/clade‐not‐a‐clade.gif Which (if any) of these trees are idenCcal? Amphibia Aves Mammalia A B Amphibia Amphibia C Mammalia Aves Amphibia D Aves Aves Mammalia Mammalia a phylogene7c tree is a hypothesis a ‘phylogeneCc hypothesis’ •  it is always open to revision if new data or methods of analysis become available A B C D also: avoid this common mistake: •  in the tree on the lee, B is not more closely related to A than C and D are •  B, C, and D are equally closely related to A Using phylogene7c trees The EvoluConary History of HIV History of life on Earth as a calendar 4 billion years ago: Earth started to cool, crust started to solidify (but s7ll many volcanoes). Atmosphere: Very liUle oxygen No ozone layer, lots of UV radia7on Life arose ‐ how? water: the sine qua non of life as we know it molecules are less closely packed in ice than in water ⇒ ice is less dense than water ⇒ ice floats what would happen to ponds and lakes if ice sank instead of floated? water: the sine qua non of life as we know it •  ice is very stable –  takes a lot of energy to break H bonds and melt it –  leads to stability in the temperature of oceans •  ice is also a good insulator –  most lakes and ponds do not go below 0˚C in the winter hUp://www.travelblog.org/Photos/1734388 hUp://commons.wikimedia.org/wiki/ File:Frozen_Lake_Michigan.jpg water: the sine qua non of life as we know it •  the most abundant molecule in most living organisms •  the most effec7ve solvent of polar molecules •  the inside of a cell is an aqueous environment –  most of cri7cal biochemical reac7ons in life occur in aqueous solu7on hUp://brooke‐gra7tude.blogspot.com/2008_08_24_archive.html There is water on Mars •  But experiments by landers have not found evidence of living organisms –  Two Viking landers in 1976 •  Na+, Mg2+, K+, Cl‐ were found in soil •  mixed soil with sugars and other nutrients and tried to detect CO2 –  Phoenix and others in 2008 •  found ice under the surface •  Search con7nues there for life or signs of ex7nct life hUp://www.daviddarling.info/images/Mars_panorama.jpg Life arose at least once on Earth hUp://www.wha7schemistry.unina.it/merlinog4.jpg •  What is life? p 40: Box 3.1 – ReplicaCon •  Transmission of informaCon – Catalysis •  TransformaCon of energy and conversion to structure hUp://www.mdc‐berlin.de/en/research/ research_teams/intracellular_proteolysis/ Research/UPS.png The macromolecular basis of life on earth •  •  •  •  •  nucleic acids (informa7on), proteins (structure and cataly7c func7on) lipids (energy source, membrane structure) carbohydrates (structure and energy) Where did the first of these macromolecules come from: –  Prevailing theory: CHEMICAL EVOLUTION MUST HAVE PRECEDED BIOLOGICAL EVOLUTION –  Monomers ‐> polymers (macromolecules) nucleic acids Complementary paring between bases on anCparallel strands (and within molecules, for RNA) is enabled by •  hydrogen bonding sites on each base •  sugar–phosphate backbone geometry –  brings complementary bases near each other •  each base pair consists of a larger purine paired with a smaller pyrimidine –  stability and structural uniformity •  tremendous medium for storing informa7on and retrieving it The quesCon: “how did life arise” is a compound quesCon: (1) how did the macromolecules arise (nucleic acids, proteins, lipids, carbohydrates)? (2) how did cells arise? Hypothesis: organic monomers can be synthesized abioCcally DemonstraCon: organic monomers can be synthesized abioCcally Stanley Miller and Harold Urey Miler’s later experments at very low temperature with no sparks and taking 25 years also found forma7on of amino acids and nucleo7des Amino acids, purines and pyrimidines were formed Miller’s and Urey’s and subsequent work form the basis of “Primordial Soup Theory” later experiments found that many sugars, vitamin B12 (pantothenic acid), nico7namide (NAD, essen7al to metabolism), lac7c acid, and faUy acids can also be formed in these condi7ons views of primordial atmosphere have also changed since the original Miller‐ Urey work: CO2, N2, H2S, SO2 may also have been abundant in the atmosphere due to volcanic erup7ons hUp://www.dailygalaxy.com/photos/uncategorized/ 2008/05/01/early_earth_2.jpeg Primodial soup theory + RNA world is the most widely held theory of abiogenesis •  but many other theories exist in the complex and growing field hUp://www.cartoonstock.com/directory/o/origin_of_life.asp where did the first complex macromolecules come from? •  a few of the many alterna7ve theories (these are not necessarily mutually exclusive): –  clay theory: silica crystals in solu7on – ‘parent’ molecules seed the produc7on of ‘daughter’ molecules which ‘inherit’ imperfec7ons –  lipid‐world – before phospholipids were common, other types of lipids could form vesicles, that could bud off and store informa7on in their chemical composi7on –  exogenesis (see cartoon in previous slide; sort of) •  meteors may have supplied the first complex polymers, either formed in space or on other planets, moons, etc. hUp://www.e‐ nox.net/images/ illustra7ons/ exogenesis_full.jpg evidence for exogenesis? The 1969 Murchison, Australia meteor contained purines, pyrimidines, sugars, and many different amino acids (care was taken in handling it, but the possibility of terrestrial contamina7on has not been en7rely ruled out) 1984 ALH 84001 meteor found in Antarc7ca, from Mars, 4.5 billion years old, ejected from Mars 16 mya, landed on Earth 13,000 ya contained water and polycyclic aroma7c hydrocarbons and magne7te (iron oxide mineral produced by living organisms) hUp://www.lpi.usra.edu/lpi/meteorites/Themeteorite.gif hUp://www.truthaboutcoaltar.com/aboutcoaltar.html did ALH 84001 actually contain living organisms? •  the magne7te in the meteor would have aligned itself with the Earth’s magne7c field during its descent, possibly protec7ng the interior from being higher than about 40˚C according to es7mates •  microorganisms could have survived inside it •  this would provide evidence for an even more extreme theory of the origin of life on Earth: panspermia hUp://en.wikipedia.org/wiki/File:Panspermie.svg no maUer how things got started •  nucleic acid based cellular life became dominant –  current evidence suggests a single origin •  polymerases •  ribosome •  cellular structures hUp://cellnews‐blog.blogspot.com/2010/05/ar7ficial‐life‐first‐self‐ replica7ng.html RNA, the replicator We know that RNA polymers can also have catalyCc proper7es like protein enzymes “Ribozymes” An RNA world? Machinery for making polypep7dies ribosomes May have evolved during the “RNA world” leading to the macromolecular components we know today How did nucleic acid based replica7on come to ‘take over’? •  maybe they were the only polymer that could replicate itself? •  maybe there were other systems but they were not as efficient? (see earlier slide) hUp://www.chrismadden.co.uk/wordpress/wp‐content/uploads/ 2008/08/gene‐dna‐climb.gif ...
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This note was uploaded on 12/16/2011 for the course BIO 201 taught by Professor True during the Fall '08 term at SUNY Stony Brook.

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