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UT AST 309L - Lecture Notes

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We want to understand how something like the sequence of events shown below could haveoccurred. To do this we need to know what the Earth was like very early in its life.This is the genetic code used by nearly every organism on Earth today. The “code” refers to themanner in which codons are assigned. (Note: there are a few exceptions.) However the overalluniversality of this code, and especially the similar genes (sequences of codons that specify afunction) found from bacteria to fruit flied to humans suggests that there was a common ancestor.Prokayotic vs. Eukaryotic cells. Notice nuclear membrane, organelles (e.g. mitochondria),cytoskeleton (not shown--next slide). Clearly the jump to eukaryotes was a large increasein complexity, and it only occurred relatively recently (compared to the origin of life).Eukaryotic cells all have a cytoskeleton, an amazing network of filaments (mostly made of actinand tubulin proteins) that participate in a large number of cellular activities such as cell supportand nutrient transport. The network deforms, flows, and reforms continuously. Recentlydiscovered that bacteria actually make similar proteins, so there is continuity betweenprokaryotes and eukaryotes.Human airway actin networkGiant cell cytoskeleton (microtubules)A typical actin networkThree domains of life, all with similar basic biochemistry and genetic codeWe are interested in the first billion years (Gyr) or so of Earth’s history.This encompasses the “Hadean” and “Archaean” eras.Overview of the various processes that were probably occurring on the very young Earth.How could life arise in such a tumultuous environment?Zircon crystals from 4.4 Gyr ago--Earth may have already had continents,oceans, instead of covered by a magma ocean as previously thought.When did the first life arise? Direct evidence: until recently the “microfossil” imprints found in3.5 Gyr rocks were considered strong evidence not only for early life, but even forphotosynthesis (Schopf 1993). Reanalysis (Brasier et al. 1999) strongly questions thatinterpretation. See picture, where inset is the part shown by Schopf.Biological organisms selectively use C12 over C13 and so have a 5 to 50% deficitof C13 relative to C12. This deficit is denoted δ 13CO.An indirect indicator of biological activity: the “delta C-13” index. Most living organismsuse C-12 more than C-13, so they show a deficit of C-13 by 10 to 40%. Illustration showsaverage value and spread for (blue) inorganic carbonate minerals and (red) keratin pigmentfrom biological fossils as a function of time in the past. Note the recent results for the3.8 Gyr-old Isua rocks!The Miller-UreyexperimentEnergy sources: plenty available. That is not a problem for Miller-Urey-typeexperiments (although different energy sources do give somewhat different results.The problem is that the experiments only give large yields of interesting organics (aminoacids, nucleic acids, sugars) if the gas is H-rich (highly reducing). What was the source ofthe early Earth’s atmosphere? Outgassing from the crust due to volcanoes (top two) orplanetesimal impact (lower left), or comet vaporization (lower right)?Interesting pre-biological molecules are found in meteorites as well as in Miller-Urey-type experiments (and in comets too!)Another potential source of prebiological organics (and methane!):deep-sea hydrothermal ventsDeep hydrothermal vents are hot and have produced a variety of strange life forms (e.g.“tubeworms” lower right), many of which do not rely on oxygen, and some of which produce methaneand other reducing (H-rich) gases (see “black smoker” top left)My favorite hydrothermal vent organismMost likely evolution of the Earth’s atmosphere. Note that oxygen could onlyrise after photosynthesis AND after the crust was saturated with oxygen.Review--we are trying to understand how life got from the formation ofprebiological organic molecules (left) to modern cells with a DNA genome (right).So far we have discussed (1) below, but what is evidence for RNA-first, how didRNA evolve, and what preceded it?Some major experimental results leading to the “RNA world”:Spiegelmann (1960s): Qβ virus (long RNA) + enzyme (“replicase”) + free nucleotides  serialtransfer  short RNAs. This was direct demonstration of evolution at molecular level.Eigen (1970s): enzyme + free nucleotides + salts (but no Qβ RNA)  short RNA random replicator.Eigen called thee “quasi-species.” But could not grow longer than about 100 nucleotidesbecause of “error catastrophe” associated with mutations.Cech et al.(1980s): self-catalytic RNA = “ribozymes”, RNA that can act as its own enzyme. Thissuggested likelihood of an “RNA world,” discussed in your textbook.1994: Joyce et al. made synthetic RNA that can copy part of itself (given right proteins)1997: Two studies claim experimental evidence for enzymes that convert between RNA and DNA2001: Johnston et al. discover an RNA that can catalyze its own polymerization needed for RNAreplication without (protein enzymes). Major support for RNA world idea.Problems: [1.and 2. are discussed in more detail in class notes]1. How does 1st RNA form by chance encounter between ~ 100 nucleotides?2. Water opposes polymerization reaction.3. Error rate (due to mutations, copying errors) too large to allow growth to longer RNAs withoutan enzyme, but RNA enzymes are long  “error catastrophe”These are discussed in more detail in the class notes; there is also discussion of pre-RNAcandidates but you don’t have to know details about that for the exam, only that there areseveral proposed pre-RNA candidates (next slide).Since it is difficult to form RNA, there may have been earlier forms thatdeveloped into RNA. Some suggestions are shown below (see notes for discussion)Proteins first?Sydney Fox (1960s-1970s): heated (dry) amino acids (maybe deserts, volcano rims), got“proteinoids.”When he dissolved these in warm water and then cooled, got “proteinoid microspheres”Pro: ϑ Sizes and appearance like single-celled organisms (see photo in your textbook) ϑ Can catalyze chemical reactions ϑ Surfaces “like cell membranes” ϑ Can produce electrical responses “like nerve cells” ϑ Sensitive to light ϑ Can “proliferate” (fission and form buds) and evolve by natural selection (really?)Con: ϑ Many microscopic inorganic particles have these traits (like dust grains in the room) ϑ They don’t grow,


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UT AST 309L - Lecture Notes

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