in Chapter two we got a really nice introduction and basic foundation for chemistry or able now to move on to chapter four that focuses on essentially organic chemistry or chemistry and involving those compounds that are carbon-based so we know that living organisms consists mostly of carbon-based compounds and those there's a really good reason for this carbon as you'll recall has a valence of four has a bonding capacity of four the meaning it can form up to four covalent bonds with other molecular components or atoms much like the model I'm holding here or the image that's shown in the bottom right hand corner of this slide because carbon can form those four bonds it's really useful for building very complex and varied molecules these molecules include proteins includes DNA carbohydrates and even lipids which are all biologically relevant molecules I'll spend some time discussing those in a later chapter now again by definition organic chemistry is the study of compounds that contain carbon organic compounds can be really small we're going to talk about some of the simplest organic molecules in the next few slides but it can also include those molecules that are huge and carbon-based like your proteins in your DNA now most organic compounds not only do they just contain carbon but they also contain hydrogen atoms and so it is a little bit of a discussion within the scientific community whether organic chemistry is limited just to those molecules that have carbons and hydrogen's or if we'll just include any carbon-based molecules irregardless of whether they have hydrogen's along with the carbons now back in the day back when we had we didn't have a lot of information about how life on our planet perhaps started we definitely as a scientific community subscribe to this idea of vitalism or a belief in a life force that's outside of any jurisdiction of physical and chemical laws on our planet pretty much what that means is we couldn't explain life we didn't we didn't have an answer for why living things were alive and so we just consider it to be kind of magical and yes while life is very magical we have now shifted away from this idea of vile ism when we have some better ideas simply because of maybe even some accidental experiments that were performed particularly by chemists but before we move to that right when we did subscribe to this idea of vitalism it was really thought that organic compounds these carbon-based compounds that were found in living organisms could only be produced by living organisms because that they contain whatever that magic that it was that allowed for those carbon-based compounds to be produced and so the first sort of data to help us reject this idea of vitalism came from actually some chemists particularly one chemist a german chemist who was trying to make an inorganic salt at the bench in his lab and ended up in an abiotic system producing urea which is one of the components and urine that living organisms can produce another scientist that contributed his work to helping disprove the idea of vitalism was a man by the name of Stanley Miller and his experiments are pretty famous what he tried to do was replicate the environment on our planet before life existed to see if he could produce any organic based molecules without life and just to get a better idea of how maybe life did start on our planet so on the right hand side you see the contraption that he put together for his experiments to simulate the environment found on our planet before life existed so down here you've got the sea so he's got a round bottom flask filled with water he heats that water to allow some of that water to become water vapor and he sends that water vapor up here to the quote-unquote atmosphere now he probably didn't get the composition of the atmosphere quite right but he did make a point with his experiment so what he put into the atmosphere were some methane ch4 we have some ammonia nh3 some hydrogen gas obviously the water vapor in there as well and then he had put some electrodes in there to introduce a spark now those spark slightly came from maybe storms on the planet producing lightning this could also be static electricity between some of the ash clouds that were the result of volcanic activity on the planet regardless those by the those sparks produced the necessary push-to-start chemical reactions in the atmosphere allowing the atoms and the molecules up there to become rearranged to form new molecules aka chemical reactions and so Stanley Miller allowed his atmosphere to sort of exist for a little while to go through those chemical reactions initiated by the sparks from the electrodes and then he would allow the water to to condense and as it condensed it would fall back through and be sent back to the ocean but not before he would collect a sample for analysis to see what kinds of molecules were produced in the atmosphere after those chemical reactions and then were dragged down by the water as it condensed and what he found was that he could actually produce an abiotic system in his atmosphere some amino acids that are important for living organisms on the planet I'm so Stanley Miller and the German scientists they were these pioneers of organic chemistry that helped to shift our view from vitalism to something called mechanism mechanism is the opposite so it's the view that physical and chemical laws still govern all natural natural phenomena on our planet so it's a little bit of history let's go ahead now and before we build these carbon-based or organic molecules let's review carbon for a minute so if you'll recall from chapter 2 electron configuration is going to determine the kinds and the number of bonds an atom will form with other atoms so if we again review carbon really quickly all right carbon is our sixth element so that means that carbon has an atomic number of six it's got six protons six electrons so if we draw the atomic nucleus we're going to start filling electron shells with those six electrons we've got two electrons that go in the first shell that one remember is full so we need a second shell we have four electrons remaining one two three and four and there are your six electrons for four carbon now the valence shell for carbon here only has four electrons it has a capacity of eight so I would like to get eight more I'm sorry you would like to get four more and so carbon is very happy to share four more electrons with other atoms to fill that valence shell and so therefore it has a valence or bonding capacity of four requiring those extra four electrons and so this allows for really complex very large molecules to be built using carbon now as we start looking at carbon-based molecules they have specific shapes this is all a result of the way that those electron orbitals sort of interact with each other but if we take a look at pretty simple organic molecules involving maybe just one carbon at a time all right so we've got my model again it's got the one black carbon in the middle and four covalent bonds with other atoms or molecular components there and you can see it has a very specific shape it's a tetrahedron and we can see this also in the first example on the next slide so you've got your methane there this is the simplest organic molecule it's got one carbon in the middle and then it's surrounded by four hydrogens to satisfy that need for those valence electrons for that center carbon and again you can see it's got that tetrahedral shape now the tetrahedral shape is a theme that has continued when you start building even larger organic molecules the second example here ethane instead of having one carbon has two carbons that share a single covalent bond in between them and you can see that there are two tetrahedrons one on either side one on one for each of the carbons and they're flipped on their sides as those two carbons are bonded to each other and that looks perhaps something like this an interesting thing about when you have two carbons here in black that share that single covalent bond there's a certain amount of spin to the molecule so I can rotate one of the carbons and all the other things that are attached to that carbon are on like that now we can get even more complicated if we go back a slide you don't necessarily have to have carbons sharing just a single covalent bond carbons can also share a double covalent bond so if I take for example this molecule and allow these two carbons to share a double covalent bond I'm going to have something that looks like this so you've got your double covalent bond between those two carbons and now you don't need as many atoms bonded to the carbons because the carbons satisfy their valence need with two electrons alright sorry with yes with sharing two pairs of electrons right for a double bond and so very similar to the model that I'm holding we've got here a scene so a scene is essentially the same thing as ethane except is that single bond between the carbons now you share that double bond what's unique about the molecules that share that double bond between the carbons the extra components these four components are attached to the carbons they're all in the same plane so you no longer have that tetrahedral shape when you have a double bond in the middle instead it's more of a polar molecule in that particular spot where that double bond exists the other thing to note is that there is no rotation having that double bond there prevents me from turning one of the carbons in respect to the other so this means that it really matters what's on all four of these corners of the molecule because you can't rotate it this will be something that will come into play one more time when we start talking about isomers in later slides so hold on to that thought okay so we know that the electron configuration of carbon gives it covalent compatibility with many different elements but carbon has its favorites it really likes to form those covalent bonds with hydrogen's oxygens and nitrogen's and this makes a lot of sense that these are gonna be the most frequent binding partners for carbon based on their electron distribution and therefore it also makes sense that our body is an organic or let's say living organisms are made primarily of those four elements as we discussed earlier in Chapter two right our bodies are mostly 96% made out of hydrogen oxygen nitrogen and carbon simply because we're made out of carbon-based molecules and nitrogen oxygen hydrogen are the favorite binding partners for carbon ok so carbon right is the basic atom that's used to build these biologically relevant molecules and sometimes it bonds to hydrogen directly and sometimes it doesn't on this leg we're giving you two examples of still molecules that are still highly relevant to living organisms but that they don't necessarily have hydrogens directly attached to the carbons so the top molecule is carbon dioxide co2 it doesn't have any carbons to begin with it's just a sorry it doesn't have any hydrogen's to begin with it does have a carbon in the middle double bonded to each of two oxygen atoms and this molecule even though it doesn't have any hydrogens still very relevant to living organisms this is what we exhale as one of the byproducts of cellular respiration and it's also maybe even more importantly the material that photosynthetic organisms use as their source of carbon to build organic molecules that we as consumers on the planet depend on for food and then the bottom molecule is urea urea again it's carbon-based and it does have hydrogen's it's just that the hydrogen's are not directly bound to the carbon itself right instead the hydrogens are bound to the nitrogen and but this is still an organic molecule still a component of gearing produced by some animals and again biologically relevant