Lecture 17 - Life Origins PDF

The following four slides are not covered this year, so disregard. They are on enzyme regulation (by inhibitors and activators). They are shown in the previous lecture (lecture 16), but we did not talk about them in class. Enzyme inhibitors and activators A. Compe...

The following four slides are not covered this year, so disregard. They are on enzyme regulation (by inhibitors and activators). They are shown in the previous lecture (lecture 16), but we did not talk about them in class. Enzyme inhibitors and activators A. Competitive inhibitors – compete with substrate for binding site B. Non-competitive inhibitors – binding somewhere else on the enzyme inactivates the active site C. Non-competitive activators - binding somewhere else activates enzyme. 2 Competitive inhibition (nicer diagram) 3 By Mcy jerry at the English-language Wikipedia, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=7701646 non-competitive inhibition (nicer diagram) 4 By Mcstrother derivative work of Comp_inhib.svg by User:Srhat - Allosteric_comp_inhib_1.svg, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=12101389 Substrate and inhibitor concentrations Substrate can outcompete inhibitor at higher concentrations 5 V. Origins of Life [Chapter 1] A. Chemical origins of life B. Evolution of information flow C. Development of first metabolism D. The tree of life E. Eukaryotes F. Fossils 6 Two biggest questions in biology* How did life start? Is there life elsewhere? *in my humble opinion (imho) Panspermia – ET origins of earth life A meteorite found in the 80’s that contained things that look like microbes, based on shape and size. Originated on Mars. Generally not believed to be life forms. 8 The likely scenario of abiogenesis protocells (a.k.a. protobionts) 9 Early earth – ~4.5 Bya 10 A little later ~4 BYa– the “primordial soup” 11 source different picture from internet of the “primordial soup” 12 ai-generated image for “primordial soup” 13 ai-generated image for “primordial soup” 14 Today’s primordial soup https://www.datacenterknowledge.com/supercomputers/top500-japan-s-fugaku-still-world-s- fastest-supercomputer 15 Early earth’s atmosphere o Hydrogen (H2), carbon dioxide (CO2), ammonia (NH3), methane (CH4), water (H2O) o Very little O2 o No ozone (O3) layer, so strong UV radiation o Lots of lightning, volcanoes, earthquakes, meteors, extreme temperature changes 16 Oparin-Haldane hypothesis: reducing atmosphere o Very little O2 means that atmospheric conditions were reducing (i.e. O2 is not around to be stealing electrons (oxidizing) from everybody)! o Thus, lots of complex, electron rich molecules could form 17 1950’s study simulates early earth The Miller-Urey experiment 18 One week latairrrrr… amino acids and other organic molecules common to life Later, others added in these two. …and all of the main building blocks formed 19 But how did polymers form from these monomers? o There were no enzymes yet. 20 Mineral surface polymerization is a possibility o Clay can act as a catalytic surface for polymer formation. 21 https://doi.org/10.1016/j.jciso.2021.100026 Mineral surface polymerization is a possibility o Tiny pores inside clay acts as a catalytic surface for polymer formation. o Monomers bind to mineral surface o Holding close together increases probability of monomers matching up just right to form bonds. 22 Sound familiar? Enzymes 23 Clays can also catalyze formation of liposomes 24 But why did it take soooooo long then? ~500 million years Dinosaurs go bye-byes ~65 m.y.a. 25 IT TOOK SO LONG BECAUSE CHANGES WERE VERY SLOW OCCURING ON GEOLOGICAL TIME SCALES Change on geological timescales 27 Do this millions of times 28 V. Origins of Life A. Chemical origins of life B. Evolution of information flow C. Development of first metabolism D. The tree of life E. Eukaryotes F. Fossils 29 All known extant earthlings do this 30 The RNA world hypothesis o Life began with RNA o RNA is great candidate because it can store information and catalyze reactions o Can form complex secondary structures 31 source RNAs with enzymatic activity are still in existence o Ribozymes: RNAs that form complex secondary structures that can catalyze simple reactions 32 The RNA world hypothesis Watch it if you did not attend class. Video link. 33 At some point, RNA functions are replaced by DNA and protein o DNA takes over role in information storage very stable two strands protects from mutations o Proteins take over catalytic functions 20 amino acids instead of 4 nucleic acids, so much more versatile 34 Possible scenario for evolution from RNA to modern genetic system 1 RNA stores information and self-replicates RNA can polymerize a few amino 2 acids to form a short peptide with catalytic properties Proteins make DNA from RNA 3 template (“reverse transcription”) 35 The ribosome, the oldest organelle o An enzyme made of proteins + RNA o Catalyzes formation of covalent bonds between amino acids 36 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6298777/