chapter three was the story of water and chapter four is the story of carbon carbon is an amazingly versatile element even without ending any other elements carbon has multiple different forms just carbon including coal graphite and diamonds and more recently organic chemists have even been able to synthesize molecules like these buckyballs at the bottom down here while coal is derived from living molecules graphite and diamonds are not organic chemistry which is the chemistry of a single element carbon is a subject that is quite challenging and difficult to ask how many different molecules can be made with carbon is akin to asking how many different things can you make with lego blocks in this chapter we'll dip a toe into the very deep water that is organic chemistry here again are our learning objectives for this chapter to begin our lesson on carbon chemistry i'm going to discuss two conflicting ideas about the molecules of life one idea is called vitalism and vitalism is the idea that living molecules can only have a living source we cannot generate living molecules synthetically nor can we generate life synthetically mechanism by contrast is the idea that all atoms of all elements can cycle between living and non-living and that there is no life force that living molecules possess that non-living molecules lack living molecules are indeed complex among the many science fiction marvels in futuristic space travel shows such as star trek the next generation are food replicators while not as buzz worthy as travel at warp speed or teleportation or phaser weapons the food replicator is still only the fevered dream of a madman at this point as a biologist the idea that we could have a machine that takes simple chemicals and instantly reworks them into a cup of tea with all of its complex tannins and essence of bergamot is still a marvel in the 19th century the german chemist friedrich voller first synthesized a molecule found in living organisms from non-living starting materials that simple molecule was urea which is a component of urine and more marketably a type of fertilizer the urea he produced had the same physical properties as urea isolated from urine the question about where the molecules of life come from was later considered by stanley miller about a hundred years later in his experiment miller wanted to simulate the atmosphere of the early earth before life altered the composition to the current condition in his closed system he included water vapor methane ammonia and hydrogen gas he attached electrodes and a bunsen burner as sources of energy he recirculated the mix through the system and sampled the resulting products he found that the simple molecules of life such as amino acids and hydrocarbons had formed he didn't get any living things creepy crawling out of the reaction chamber however so the idea that life on earth began from very simple molecules that through the input of energy and time developed into life is one hypothesis there is another and there are others since miller's time in the 1950s our knowledge of the universe beyond the biosphere has increased exponentially among the building blocks for life are simple sugars and nitrogenous bases that we'll discuss more in chapter five in this article published just in 2019 a group of japanese scientists analyzed a couple of meteorites and found that they contain some of these compounds one hypothesis is that the meteorites were contaminated with early sugars when they made landfall kind of like dropping a piece of toast and finding dirt on it that wasn't there when you buttered it an alternative and more interesting hypothesis is that the sugars in the meteorite came from space kind of like the dirt was already on the toast before you dropped it for whatever reason how to test these hypotheses think back to chapter 2 when i mentioned isotopes remember when i said that 12.011 was the average mass of a carbon atom in a sample well that's true but only for early earthly carbon samples in fact we can compare the ratios of different carbon isotopes to determine when a sample was formed or in this case where it was formed starting with known and earthly known earthly and extraterrestrial samples furukawa and colleagues found that the sugars in the meteorite appear to have been formed in space based on the abundance of carbon 13. does this prove the existence of extraterrestrial life no what's been found in meteorites to date have only been fairly simple molecules components of life on earth but no cells no dna nothing to indicate that the parts were once a more complex hole but it does raise some interesting questions so what makes carbon such a useful building block it has to do with its place on the periodic table an element's properties are determined by the electron configuration which is influenced by the number of protons in the nucleus if we compare the four most abundant elements in living tissue we see that they each have a different valency or number of covalent bonds that they can form hydrogen although currently the most abundant element in the universe can only bond to one other atom oxygen is very electronegative which makes it reactive but with a valency of two it doesn't lend itself to making large molecules on its own nitrogen has a valency of three and most of the planet's nitrogen budget is tied up in nitrogen gas which has two nitrogen atoms triple bonded to each other that's really tough to break carbon with a valence of four is the most versatile just by being able to bond to more atoms if we look at the simplest carbon molecules containing only carbon and hydrogen we can see that variability starts early on in this table we see three different simple hydrocarbons methane ethane and ethylene the molecular formula tells us how many atoms of each element are present in a molecule that's over here on the left the structural formula shows us the arrangement of the covalent bonds in two dimensions but when you look at the different three-dimensional molecules the ball and stick and the space filling models our eyes are opened to the differences in these molecules adding a second carbon makes a big difference in the three dimensional shape and swapping two hydrogens for a double covalent bond gives a planar or flat molecule why this tetrahedral arrangement of single covalent bonds orbital shells can only hold two electrons in each however the first few orbitals can swap electrons around and the spherical s orbitals combine with the dumbbell shaped p orbitals to form this tetrahedral shape in a process called sp3 hybridization when double bonds form as in carbon dioxide the orbitals change shape to become rigid and planar again we'll see how carbon dioxide is special at the end of unit 2. methane ethane and ethylene are just the beginning as we start adding carbon atoms and filling in the valence shells of carbon atoms with hydrogens we see the options increase again just carbon and hydrogen we can add carbons to a chain making ethane propane butane pentane with two three four and five carbons in a chain once we have a longer carbon chain we can add branches and move the branches around or we can add in double bonds if we moved this double bond over here from between the second and third to the third and fourth carbons notice we just end up getting back to the first molecule over here just flipped around and one other trick with just carbon and hydrogen once we get up to a six carbon chain we can produce rings and not just one kind of ring cyclohexane and benzene behave very differently something else we can see in this image is a shorthand that is used in chemistry if there is only carbon and hydrogen in a molecule you only need to draw lines to indicate where the carbon atoms are and assume that hydrogens fill in the rest of the four covalent bonds a double line means a double bond so you can see this hexagon here represents cyclohexane this hexagon over here with the alternating double bonds represents benzene these molecules with only carbon and hydrogen are called hydrocarbons hydrogen and carbon are very close in their electronegativity so these covalent bonds are nonpolar with very equal sharing in living tissue hydrocarbons are found mostly in fats in other lipids these nonpolar bonds store a lot of potential energy which is one of the functions of lipids as we'll find in chapter 5. in our cells we use the nonpolar hydrophobic nature of these compounds to act as partitions between cell parts called membranes as well as storing energy in those tasty fatty bonds hydrocarbons are an important part of our economy octane is a hydrocarbon with eight carbon atoms and you've probably heard of it if you've ever put gas in a car here's a space filling molec model and a line drawing of octane just to show that there are different ways to represent the molecule because of the versatility of carbon branching double bonds etc the same molecular formula can produce different structures with different properties these different arrangements of the same complement of atoms are called isomers don't confuse them with isotopes iso is a prefix that suggests something is the same about them not only can we arrange the same atoms in different ways there are different ways of those different ways three of them for our purposes structural isomers cis-trans-isomers formerly called geometric isomers and enantiomers structural isomers are compounds that have the same molecular formula but a different arrangement of the covalent bonds as you can see in these two molecules both have five carbons and 12 hydrogens go ahead and count if you don't believe me but they have a different arrangement of covalent bonds on the left pentane a linear molecule and on the right 2-methylbutane which is a branched molecule cis-trans-isomers are found where there is a double bond in these two molecules the molecules in blue labeled x represent something other than hydrogen but not some element x per se on the left the two substitutions as they are called are on the same side of the double bond cis is on the same side in the trans-isomer the substitutions the x's are on opposite sides of the double bond trans is a word root that means a cross if you take a transatlantic voyage you are crossing that ocean if something is transparent you can see through or across it i also have a little dance to show you the sis trans dance