Lecture 2

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University of Toronto Scarborough
Biological Sciences
Herbert Kronzucker

Lecture 2 September 15 2008 Announcements I gave instructions for the tutorial and most of you are following them well. Use my email for scheduling appointments or just come and see me after class on Wednesdays. Tutorials contain critical information so please attend even though they are not mandatory. Journal Article Critique The journal article critique is an easy assignment. It is only 2 pages and you already know how to use the web of science. If you missed the tutorial Michael will go through it in the 2 tutorial again. Your critique is of 1 article and will be on the ISI web of science. It is the number 1 index system in the world. Remember the article you choose for the critique should have an impact actor larger than 1.0. There could be other articles cited by the author and all of this you can find on the web of science. You want some contradictory views. There is a learning goal and that is how to find science information. You want to hunt down full length articles. One journal does not equal the other. There are different opinions on things like global warming for example. The scientists havent sorted out amongst themselves if it is even real or not. This is an aspect of science. I remember someone who opposed Peter Mitchell. In any day and age of science there will be critical voices of any view and that will be critiqued and you will have to do it intelligently based on reading the primary material. You dont do this by watching TV because that isnt scientific information. Most students do a good job and it is easy to get an A in the assignment. Presentation There is a chance to get good marks with this and the above assignment. LECTURE #2 We started to talk about the limits of life to introduce community ecology. It was Charles Darwin that said nothing in biology makes sense without the concept of evolution and I agree with it. We come back to the timeline of life and the rules/laws that govern the diversity of life forms and development of ecological communities. Everything is connected. Evolutionary framework is given to introduce communities in biology, how diverse they are, what can be expected, etc. There are trenches all through the Atlantic and Pacific oceans and they are 2.1 Km below the surface. In the 70s we understood how diverse the biological communities are that are in these pitch black conditions near the underground smokers. We are 2.1 Km from the surface of the ocean and the pressure the organisms are exposed to is great. For every 10 metres = 1 full atmospheric pressure. 100 Kilopascals are in each atmosphere of pressure. We are all adapted to the atmosphere on earth with slight variations and if you increase the pressure like going deep into the ocean, no human could survive; you would be crushed to death. These tube worms would explode long before they would reach the surface and that is why it is hard for biologists BGYC61H3F.September.15.2008 Lecture 2 1 www.notesolution.com to study these organisms. We cant bring them up and preserve them. Some organisms we have brought them up depressurizing them like we do with divers. Most tube worms wont survive. These are packed with bacteria in their body structures, in the billions/ounce, about 285 billion bacteria for an ounce of tube worm is an average number. It is in the bacteria where the largest amount of chemical activity happens in the underground volcano environment where life is contained. Chemosynthesis happens here, unlike photosynthesis, we use electrons from inorganic sources such as sulphur, hydrogen sulphide, which is important in these underground communities. Sulphur has an oxidation state of -2 so they give 2 electrons to a chemical or biosynthetic process. There are other reduced compounds like iron sulphide that contains it as well. Iron is in oxidation state of +2 so it is ferrous. In essence it can be oxidized and turn into ferric and electron can be fed into biosynthetic reactions. The light reactions split water and grab electrons out of the water molecule in photosynthesis. Whether we make amino acids, sugars, fatty acids, all the building blocks of life as we know it are believed to come about in this way but in the ocean trenches it is different, electrons come from sulphur. Methane can also be used but these are prevalent in the oceanic environment. This is the Pompeii worm which is on record in the Guinness Book. It is an extreme species that can tolerate extreme conditions. They can easily stand 100 degree C without combusting. They live under absence of light and very cold conditions. A 2 4 degree Celsius we can have biochemical activity that doesnt take a back seat to the kind of reactions that our enzymes go through. Between 20 25 degree C is where our enzymes are at their peak. Higher than that the enzyme activity declines and same when it goes lower. The tube worm can do most of these at the high rates. Many of these organisms are good at acclimatizing to a new condition when it changes. Two terms you have to keep separate adaptation (evolutionary term) and acclamation. We are not adapted to perform under these conditions. As humans we are quite bad at acclimatization and we require heating and air conditioning. If you raise or drop temperature too much it is game over. Nobody can survive in Toronto without clothing and shelter. You have heard of a baby in a car in august with the windows up and the baby wont survive. If you did this with the worm it wouldnt even notice anything was wrong. These ranges are of great interest to biologists. You see the dogs in the street in august panting and they cant handle the heat. So ranges of acclimatization are enormous and we are trying to answer the questions of just how high they can go. Perhaps when we understand the limits of life there can be life on Mars or Jupiter. G. Wachtershauser He is a patent lawyer and trained chemist that published some papers. As new information comes out and gain validity I will discuss it. He says in the ocean trenches chemosynthesis is the only game in town. He says that in those environments is where life may have in fact originated. Stanley Miller is the guy who in the 50s tried to recreate the early primordial atmosphere on earth and find out what it would have taken to get biological molecules going. He fed electrical pulses simulating light, he fed in methane and ammonia gas to see if he could find what was in BGYC61H3F.September.15.2008 Lecture 2 2 www.notesolution.comthe atmosphere early in the life of earth. That lead to the assumption that it was above ground that life started. Wachtershauser they say that it isnt very likely. Stanley Miller, methane and ammonia together are actually in the primordial atmosphere in very and were in very short supply. There is no question that he made organic molecules out of these constituents but he used building blocks of those reactions that didnt actually happen in the troposphere at that time. We simulate the Ph (as low at 2.8) that gushes from the smokers and we add the reaction chambers and now we add the gases that come out and noticed he could make acetic acid molecules. Combining carbon with sulphur making thiol (compounds where carbon is connected to the SH group). He made H3C (methyl group) combined with this group making this methyl mercaptan group or methyl thiol. Once that was formed there was a cascade of reactions and these acids form compounds with the SH groups. It forms esters between the compounds and the polarization occurs. Carbon dioxide comes out of the atmosphere and fixes it into organic molecules that can esterifies with other components that form pioneer cells (organisms). There is more to this theory. How they would have been closed in cell structures. There is intelligent thought. He was able to show us it was possible to polymerize carbon after taking it out of the atmosphere and making something similar to what defines life. He couldnt show RNA or DNA formation. The idea that we can have enclosures of biochemical soups in simple cell structures is not new. Simple lipids can aggravate together as cells and if you have an enclose of
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