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BY2204.Lecture 6 Is this a good definition of life? SF Evolution Life is an amazing piece of chemistry The First Spark of Life But how did we get from small molecules floating in the primordial soup to anything as complex and organised as my niece? What is life? Muller 1966 suggested: 4600mya Earth formed Replication Heredity = LIFE 5000 million years ago 4000mya Life 4000 • Photosynthesis starts Variation BUT this includes prions, and excludes viruses! • Snowball earths The History of Life • Oldest prokaryotes • Multicellularity evolves • Cambrian explosion 3500mya Oldest fossil (?) 2700mya Definitely Prokaryote s • Life started • Earth formed • Eukaryotes appear 3000 3800mya Oldest rock • Oldest rock 2100mya Eukaryotes 543mya Cambrian Explosion 1500mya Multicellularity 2000 1000 Now Snowball Earths until 1500mya 1 The History of Life 4600mya Earth formed 4000mya Life 4000 5000 million years ago 2700mya Photosynthesis starts, producing oxygen 3500mya Oldest prokaryote (?) Read more about these in the “Proof of Life” and “Life’s a gas” articles 1st 2100mya Eukaryotes 2000 1000 Snowball Earths possibly until 650mya Four stages in the start of life: 1) How did the “building blocks” of life appear? Amino Acids to make proteins Sugars to make RNA’s backbone Nucleotides to make the code of RNA Lipids to make cell membranes X (easy!) 2) How did these join together to make polymers? 3) How did replication start? 4) How did the replication mechanism get inside a lipid membrane to form a cell? During the Hadean period these cooled to a thin solid crust, like the skin on cocoa and outgassing occurred. 543mya Cambrian Explosion 1500mya Multicellularity 3/4 of life’s history was single celled! a) b) c) d) Earth formed from an accretion cloud of dust from the big bang, and was made of molten rock. Molten metals sank to the middle leaving silicates on the surface 3000 3800mya Oldest rock Refer to yr notes for differences between prokaryote and eukaryote cells What sort of earth gave rise to life? Now Unstable and kept hot by 1) continued accretion, 2) meteor landings, 3) radioactive decay of rock 4) UV radiation from the sun. Even the seas dried up repeatedly! Stage 1: Origin of Amino Acids, Sugars and Nucleotides Earth had a reducing atmosphere (because no oxygen). This means chemicals were much more reactive than now, but how much more? When scientists thought it was very reactive, Stanley Miller 1953 did a very famous experiment exposing water to that atmosphere, added lightning …… and got all the building blocks of life. Evolution of life thought to be very easy! 2 Then the geologists realised the timing of outgassing was critical to the composition of the atmosphere Early, before the metals went to the core and you get Miller’s very reducing atmosphere. Late, after the core was formed, and the atmosphere was much less reducing so the chemicals less reactive. The geologists believe the outgassing was late. If you re-do Miller’s experiments with this late atmosphere, you get…….. Nothing. So how DO we get the building blocks of life? 2) Extra-terrestrial sources of life Stage 1: Origin of Amino Acids, Sugars and Nucleotides We don’t know, but there are a number of theories. 1) Creation by a supernatural being. e.g. Christians’ creation by God, Aboriginal dreamtime stories, African Bushman’s subterranean origins of life, Iroquois creation story in which a woman from the sky falls to earth and the animals start terrestrial life on the back of a giant turtle. Always remember, these could be true. You can’t prove they are not. Best to look at options open to science too. 3) Warm Shallow Pond Scenario Deep sea vents and estuarine waters can have very reducing conditions Did meteorites bring in the building blocks? Meteorites now often carry hydrocarbons, and amino acids, made in reducing conditions of space Rarely survive transit through the atmosphere now, but thinner atmosphere then. Need a lot to seed the earth, but a lot of meteorites fell then. This is quite a popular theory for the origin of aas and sugars. Bernal 1967 Sea was anyway more reducing than it is now, and in estuaries, clay makes it more so. Organic molecules form: HCN and formaldehyde Sun HCN Amino Acids Formaldehyde UV radiation Sugars sea Clay in estuary The clay concentrates these, and UV makes them react to give sugars and amino acids (no nucleotides though!) 3 Stage 2: Polymerisation Pyrite particles in raindrops in clouds work just like clay in pools, so maybe polymerisation started in clouds Need to get concentrations of the building blocks to allow polymerisation. Clay can again help hold onto chemicals. In boiling mud the amino acids form blobs of all one type of protein, called proteinoid microspheres These float off and cool to make insoluble stable “cells” of protein, but with no cell structure of course. Similar chains stick together Polymerising amino acids Boiling clay Lipid World Or in puddles where the building blocks could build up local concentrations Proteinoid microspheres break off read more about this in “Origin of Life” reference Lipids (fats) in water form themselves into little bubbles called micelles. Interestingly, these have heredity, because when they split the daughter micelles contain the same mixture of lipid molecules as the parent did. The mycelles also stick nucleotides to their outsides so help with the polymerisation process. This is seen as one route to both ploymerisation and getting polymer nucleotides into a cell It’s even been suggested that a very early snowball earth occurred and the remaining liquid water concentrated the building blocks. Stage 3: Replication (So far just chemistry as no replication, so no natural selection, so not life.) The RNA world Once RNA formed, it replicates spontaneously, and catalyses its own replication. So far we can only get this to work for a few base pairs, but the conditions we should be trying it in are unknown. Initially all the replication jobs were done by RNA. Now data storage is done by DNA, and several types of RNA carry the message, make proteins etc. How we swapped to the current system is unknown. 4 Once replication began, life began, and natural selection began. RNA molecules which were better at replication left more copies of themselves…. So stood less chance of going extinct. Faster replicators grabbed the free nucleic acids faster = competition. Mistakes in replication = mutations, ….some of which improved replication speed = adaptation All 3 aspects needed for life are present: replication, heredity (new molecules resemble their parent) and variation (occasional replication errors occur). First branch on the tree of life was between Bacteria, and Archaea Eukarya branched off Archaea later and led to Eukaryotes. The most recent ideas about the origin of life come from reassessing the similarities and differences between these two bacterial lines. It’s Life… but not as we know it! Now replication uses over 30 different proteins to help, and many types of DNA and RNA ALL living things use the SAME system, so the change from RNA world to this one must have been early. Stage 4: Cell formation How the whole system got into a cell, is entirely unknown. The boundary is lipid, but how do nucleotides etc. get inside? What was that first cell like? Mitchell (1972) suggested Chemiosmosis = using energy from food to pump protons through a membrane, then allow them to flow back to release energy in the cell. Earned Mitchell the Nobel Prize for Chemistry in 1978 Read New Scientist article “Cradle of Life” to get the full story. Everyone thought energy from food or light was used to make ATP, then split it to release energy in the cell . But need a lot of energy all at once to make an ATP molecule. But chemiosmosis was ignored initially by scientists looking for the origins of life, even though - proton gradients are common in all types of cell e.g. for active transport across cell membranes. - much smaller amounts of energy needed to pump out one proton than to form ATP so could be a useful steppingstone. 5 Bill Martin 2009 looked at the problem again. He argued: • Features common to Archaea and bacteria are likely to be early. These include DNA, RNA proteins, ribosomes, ATP and a proton gradient powered enzyme for making ATP • Differences between the two lines are likely to have evolved after the split, so weren’t features of the first live cells. These include: DNA replication mechanism Fermentation (= original way to get energy from food so vital to our story.) Cell membranes and cell walls. So what could the ancestor cell be like if it didn’t have a cell membrane, and couldn’t eat? Energy was plentiful – Between the acid sea and the alkaline vent was a proton gradient readymade, allowing chemiosmosis. This would have spontaneously made pyrophosphate, a natural analogue of ATP still found in both archaea and bacteria today. The pyrophosphate could have driven the formation of amino acids, and nucleotides. Temperature gradient between the top and bottom of the pores concentrate nucleotides at one end, increasing their likelihood of ploymerising, forming RNA and proteins. Convection currents would raise and lower the temperature continually, which is what you do to replicate DNA now in the lab. So evolution starts : replicating chemicals breed and compete in the pores. Russell 1990s looking at alkaline hydrothermal vents in the deep seas. Active ones very rare now but would have been more common then. In them, water reacts with certain minerals in the sea floor, to release hydrogen, alkaline fluids and heat. The early ocean was acidic and iron-rich. When upwelling hydrothermal fluids reacted with this seawater they produced carbonate rocks riddled with tiny pores and a “foam” of iron-sulphur bubbles which catalysed further reactions. At some point DNA was also invented Fatty molecules would also be produced and coat the iron-sulphur froth to form cell-like bubbles. Some of the DNA or RNA is likely to have got inside some of them. But they dissolve if they leave the vent as their energy source is still there. To escape the vents and become free-living they needed to make pyrophosphate themselves, which needs the enzyme pyrophosphatase – still found in both bacteria and archaea. They also needed to create their own proton gradient. Allowed them to pump single protons out of the cell when they had a little energy, then let them all flood back to make an ATP energy store. According to the theory this escape from the vents happened twice, which is why archaea and bacteria have different cell membrane and cell wall structures. 6 Once life had become independent, we had the Prokaryotes All the ways of extracting energy from the world were invented by the prokaryotes Heterotrophy (= eating other organisms) Archaea now only survive in extreme environments where nothing else competes with them Bacteria are still common, and use a wide variety of ways of making energy, scattered across their phylogenetic tree. Photo-autotrophy (=energy from the sun) Only one made oxygen cyanobacteria Lithotrophy (=energy from chemical reactions e.g. H2S) Mixotrophy (= energy from any combination of the above) Importance of the Cyanobacteria Cyanobacteria evolved photosynthesis, i.e. splitting water to make oxygen. One group survives today as stromatolites and thrombolites off Western Australia. Fossilized ones exist from 2700mya. Oxygen is very toxic to most other bacteria, so they poisoned almost everything else. It also made an ozone atmosphere. The ozone in the atmosphere protected the land from UV light and so made it habitable to lichens. Summary We still do not know for sure: 1) How the building blocks of life appeared, especially the nucleotides 2) How the replication mechanism got inside the cell membrane 3) How the change to DNA happened 4) When any of this happened, or where. But we’re finally getting some more convincing theories! They helped raise the oxygen levels to today’s levels (eventually – see “Life’s a Gas” article), allowing larger animals onto land. 7 Recommended reading: If you are interested: Freeman and Herron “Evolutionary Analysis” 3rd Edition Chapter 16, Origins of life Skelton “Evolution, a biological and palaeological approach” Chapter 16.1 to 16.4 – Origins of life, life and times of early life forms (prokaryotes). Cambell and Reece “Biology” 6th Edition: Chapter 26 Origins of life. New Scientist 17th Oct 2009 “Cradle of Life” http://www.nick-lane.net/OriginOfLife.pdf - the detail of the alkaline hydrothermal vents theory New Scientist 6 Feb 2010 p36-39 “Life’s a Gas” – current views on how and when the levels of oxygen rose and allowed complex life. NB DO NOT learn the chemical reactions, or even write them out. You don’t need that much detail! New Scientist 11th July 2009 p38-41 “Dawn of the animals”- The latest ideas on why eukaryotes took so long to get going, and evidence of preCambrian life. New Scientist 14 June 2003 p 33-39 “Evolution – Five Big Questions” – views on the origin of life, mechanisms of evolution, speciation, predictability of evolutionary outcomes, and religion’s position. New Scientist 27 Sept 2003 p22-23 “Conference report: Origin of Life” – Some interesting snippets about the evidence for early life. 8