hi everyone welcome back before we begin our next chapter that covers biological macromolecules i want to briefly review a few definitions a solution is a homogeneous mixture that combines a solute and a solvent a solution involves one substance dissolving in another substance which is usually a liquid solutes are the solid part that gets dissolved they become completely surrounded by molecules of another compound called the solvent the solvent is the liquid part that does the dissolving by completely surrounding the molecules of the solute an aqueous solution symbolized by aq is one in which water is the solvent water's versatility as a solvent results from the polarity of its molecules keep in mind that you have a partial positive charge on the hydrogens and a partial negative charge on the oxygen polar or charged solutes dissolve when water molecules surround them forming aqueous solutions table salt is an example of a solute that will go into solution in water again you can see the positive hydrogen ends of water molecules attracted to the negative chloride ion and so water the molecules are able to surround that ion on the other side here you can see that the sodium that has the positive charge the sodium ion is surrounded by the water molecules and it's the partial negative portion of the oxygen that's surrounding that particular ion water is a good solvent for ionic and polar covalent molecules because of its attraction for their charges in general like dissolves like a nonpolar molecule will not dissolve in water oils are carbons and hydrogens with nonpolar covalent bonds this is why oil and water do not mix to form a solution polar and nonpolar are not alike okay with that bit of information [Music] confirmed and gone over we're going to move to our organic portion of the chemistry and talk about carbon hydrogens and our macromolecules so let's begin with our introduction to organic compounds life is carbon based and it's been called a carbon-based phenomena with good reason except for water almost all of the molecules found in organisms contain carbon many molecules that contain carbon bonded to other elements such as hydrogen are called organic compounds other types of molecules are referred to as inorganic carbon has a great importance in biology it's the most versatile atom on earth because of its four valence electrons it will form four covalent bonds we've seen this several times as we practiced with bonding with our electrons and we know that there's four electrons in that outer shell the formation of carbon-carbon bonds was an important event in chemical evolution it represented a crucial step toward the production of organic molecules found in living organisms organic molecules come in almost limitless array of molecular shapes made possible because of different combinations of single and double bonds that can be formed again keep in mind that not all compounds with carbon are organic carbon dioxide which is co2 is inorganic you want to see carbon and hydrogen bonds as a classification or defining reference when you're looking at molecules carbon provides a molecular skeleton and here we're looking at carbon one single carbon atom with its four bonds its ability to bond up to four right four valence electrons the ability to make four bonds and we see carbon sharing an electron with hydrogen hydrogen and carbon sharing so each line is representing a pair of shared electrons here's our structural formula the ball and stick model space filling model all of these are different representations of methane this particular shape that it forms if you were to get some models and build them together is called a tetrahedron when you're looking at compounds that are composed of carbons and hydrogens they're called hydrocarbons hopefully that word makes sense too hydrocarbons hydrogen and carbons carbon with attached hydrogens can form chains of various lengths in molecules that contain more than one carbon atom the shapes can become much more complex for example several carbon and hydrogen atoms can bond to one another to form long hydrocarbon chains as in octane for example pause the recording how many carbon atoms do you think are present in a hydrocarbon chain that's called octane in glucose which is c6h12o6 a ring structure is formed from carbon hydrogen oxygen that are all bonded together octane is one of the primary components in gasoline and sugar glucose is the primary energy storage molecule for organisms so here we've gone from one carbon to two carbons so we've gone from methane to ethane and you can see this would be c2 h6 here we have propane we've added another carbon to our skeleton our length is increasing so we have c3 h8 here are a couple examples with double bonds in the carbon skeleton in the first one here on the left we have butene the image on the right is butane but you can see there's a number in front of the the word so each of these has four carbons you can see each has one two three four five six seven eight and confirm that over here one two three four five six seven eight so we have c4 h8 so what's the difference the one here is because the double bond is between carbon one and two so this is how you would this is nomenclature you don't have to know this for our exam i'm just explaining the pictures and 2-butene is because the double bond starts here at the number two carbon just so that you have some perspective of why they're named named differently okay a carbon skeleton is a chain of carbon atoms we just saw that they can differ in length so they can be straight but they can also be branched here we have butane can be unbranched or isobutane lots of branching you've seen this term iso before and again we still have four carbons one two three four five six seven eight nine 10 hydrogens and we have 10 hydrogens here so you this would still be c4 h10 but they are different right unbranched in branch so this is isobutane our carbon skeleton can also be in a ring so we have cyclohexane and we have a benzene ring you can see the difference is all of these double bonds here in our benzene ring so there's going to be less hydrogens in the benzene ring than there are in our cyclohexane each point here represents where a carbon atom is so each point again is where the carbon is located and then the line on the inside represents the double bond so there's one bond here and one bond here again compounds with the same formula but different structural arrangements are called isomers and that's what we saw here same formula c4 h10 but their shapes are different in general the carbon atoms in an organic molecule furnish a skeleton that gives the molecule its overall shape but the chemical behavior of the compound meaning the types of reactions that it participates in is dictated by groups of hydrogen nitrogen oxygen phosphate and sulfur atoms that are bonded to one of the carbon atoms in a specific way those are the important functional groups that are attached if we look at testosterone and estradiol which we're going to see in the next slide there's very little difference however those functional groups are the key to how reactions occur so here is testosterone and estradiol very little difference we have our four ring structure they both have a oh and a ch3 group in the same location here we have an additional ch3 and testosterone located between these two rings and the oxygen is double bonded on testosterone so let's see what the outcome of that is here we go this testosterone structure is what gives this lion its male traits and the estradiol contributes to the femaleness of the lioness small differences in the chemistry but big differences in how it affects the organism at this point i want you to pause the recording and in your notebooks i want you to draw octane please include the carbons all the hydrogens no abbreviated symbolizing so i want you to draw out the chain for octane so don't draw a space filling model for me um if you need to look it up you can and then i want you to number each of the carbons then i want you to write the formula so pause your recording draw octane include all the carbons include the hydrogens at each carbon label it by number and then write the formula okay so when you come back we're going to be discussing here our functional groups these are important groups in the chemistry of life the critically important hydrogen nitrogen oxygen phosphate and sulfur-containing groups that are found in organic compounds are called functional groups the composition and properties of six prominent functional groups that are commonly have found in organic molecules and recognized by organic chemists are summarized in our table to understand the role that organic compounds play in organisms it's important to analyze how these functional groups behave i do want you to know these functional groups i also want you to know the soft hydro group which consists of a sulfur atom bonded to a hydrogen atom and the soft hydrolyl group is important because they link to one another and this is forms a disulfide bond so we're going to look at each of these and talk about them and again i do want you to know these you are required to know these here we have the hydroxyl group this is the oh group hydroxyl groups are important because they act as weak acids we saw that when we talked about the acids and bases and ph in many cases the protons involved in acid base reactions that occur in cells come from hydroxyl groups on organic compounds because hydroxyl groups are polar molecules containing hydroxyl groups will form hydrogen bonds and they tend to be soluble in water pause the recording and in your notebook write down why is it that you think compounds with hydroxyl groups would be soluble in water think about everything that we have learned in our chemistry unit i'll give you a hint by saying that it should be hydrophilic hydrophilic what does hydrophilic mean i think we've discussed that term but it means water loving hydrophilic water loving so hopefully that will help you with your answer the carbonyl group is our next group this is a c double bond o and then these bonds here mean that it's going to be bonded to something else we have two types we have aldehydes and ketones you still see this functional group here c double bond o c double bond o the difference between the aldehyde and ketone is the c double bond o this carbon that has the double bond with the oxygen and then aldehyde will also have an h bonded to it a hydrogen bonded to it and you're also typically going to see this on the end of your compound and then this would be the rest of the molecule making that fourth bond in the ketone the carbon that is double bonded to the oxygen is found in the middle here so you have a carbon double bonded to an oxygen and then the other two bonds or with another group here we have a ch3 group and another ch3 which we call methyl groups as you can see down here so just to recap carbonyl groups are found in our molecules such as acetyl aldehyde and acetone that those are examples of the aldehyde and ketone and this functional group is the site of reactions that link molecules into larger more complex organic compounds our next group is the carboxyl group the carboxyl group is c double bond o o h the carboxyl family of molecules are carboxylic acids and they act as an acid in solution because they can tend to lose a proton to form the ionized c double bond o with the oxygen that's missing the hydrogen that it dropped off in a solution and now has a negative charge the next group is the amino group amino groups are nh2 you can see the example of the amine that's the family of molecules you can see the n bonded to two hydrogens and in this example it's connected to the carbon with three hydrogens and the amino group functional group or amines they tend to act as a base they tend to attract a proton to form something like nh3 nh3 plus is ammonia and it can be a gas at room temperature it's a gas but when it's dissolved in water it it forms nh4 plus which is also an ionized molecule called an ammonium ion because we're going to have an additional hydrogen which adds another charge to this group so both the amino and carboxyl functional groups are going to tend to attract or release a hydrogen ion or your proton when in solution the amino groups function as bases carboxyl groups act as acids during chemical evolution and in many organisms today the most important types of amino and carboxyl containing molecules are the amino acids amino acids contain both an amino group and a carboxyl group amino acids can be linked together by covalent bonds that form between amino and carboxyl groups in addition both of these functional groups participate in hydrogen bonding the next group is our phosphate group phosphates or organic phosphates are molecules with more than one phosphate linked together to store large amounts of chemical energy the phosphate group itself is op03 carries a two minus charge and that negative two charge comes from two of the oxygen atoms when phosphate groups are transferred from one organic compound to another the change in charge often dramatically will affect the structure of the recipient molecule in addition phosphate groups that are bonded together store chemical energy that can be used in chemical reactions this means that in this example this is atp we have adenosine triphosphate so there are three phosphate groups attached when the bond is broken here but and you take off or cleave off one of these phosphate groups that's how we use energy so we're going to utilize the energy from breaking the bond attach this to another molecule and usually it causes that molecule that it's attaching to to have some kind of reaction it will facilitate some kind of reaction with that molecule whether it changes shape or causes that molecule to signal to another molecule we'll talk about this in great detail in a little bit later in the semester ch3 is a methyl group when you see compounds that have that you would say that it's a methylated compound methylation of dna when ch3 is attached to a da mole dna molecule it can repress a gene for example meaning that it will not allow that gene to be expressed the last group that i wanted you to know we already talked about soft hydro groups they consist of a sulfur atom bonded to a hydrogen atom and they're important because self-hydral groups link to one another forming disulfide bonds and these are important in the structure of proteins but this is quite the interesting slide isn't it i thought it's important to show you the depiction in a period called the haitian period haitian meaning right hell that should remind you of what how what we imagine hell looking like um and so based on our geological evidence from this time this is what we think the earth looked like and at this time when the planet had just been formed it was extremely hot being bombarded by meteors meteorites and we know that at some point the moon crashed into the earth and it broke off and part of that now orbits right orbits our planet uh as far as the chemistry there was no o2 in the atmosphere there was no water um basically the atmosphere consisted probably of carbon dioxide methane ammonia all of these um it seems like just such a harsh environment no life but there is good evidence that during this time the beginnings of life were starting to form and so you know we just got done talking about all those functional groups and organic molecules so you know people always think about that question how in the world could life have formed from this type of environment and this is an image of a experimental setup from what's called the miller yuri experiment and i just want you to watch a short video and just so that you have the perspective of what all of these different functional groups and molecules really mean to life and how we can perceive the idea of life emerging from this type of environment what was the miller yuri experiment it was once believed that if you left food out to rot living creatures like maggots and even rats would simply poof into existence the idea was called spontaneous generation a series of experiments starting in the 1600s disproved this idea and in the 1800s a new scientific law was proposed life only comes from life it's true that rats maggots and even microbes are far too complex to simply poof into existence but in 1859 english naturalist charles darwin put forth the theory of evolution in it he showed that under the right circumstances relatively simple creatures can gradually give rise to more complex creatures given this information serious thinkers began to wonder is it possible that simple life forms actually could come from non-living matter not by poofing into existence but through a natural gradual process similar to what we see in biological evolution darwin himself mentioned this idea when writing to a friend but if and oh what a big if he wrote we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts light heat electricity and so on present that a protein compound was chemically formed ready to undergo still more complex changes in 1924 russian biochemist alexander operon published a book which he titled the origin of life in it he outlined his thoughts on a gradual progression from simple chemistry to living cells he imagined the early ocean as a primordial soup a rich collection of complex molecules produced by natural chemical reactions in this soup further reactions could take place eventually producing living cells at the time darwin's warm little pond and operan's primordial soup were really just speculation they were founded on a good understanding of chemistry and biology but they could not be considered legitimate scientific hypotheses because no one had found a way to test or observe them science after all is the study of observable facts and an ongoing conversation about how those facts can be best linked together chemical reactions like those proposed by darwin and operon are not expected to leave an observable fossil record without either having fossils to examine or a time machine to travel back and observe what happened how could scientists even begin to study the origin of life in the 1950s stanley miller then a graduate student at the university of chicago came up with an idea we could simulate early earth conditions in the lab and then carefully watch what happens if you can't study fish in the sea set up an aquarium working with his professor harold yuri miller designed an apparatus to simulate the ancient water cycle together they put in water to model the ancient ocean it was gently boiled to mimic evaporation along with water vapor for gases of the atmosphere they chose methane hydrogen and ammonia these are simple gases which scientists at the time thought were probably abundant on the ancient earth they added a condenser to cool the atmosphere allowing water molecules to form drops and fall back into their ocean like rain the ancient earth would have had many sources of energy sunlight geothermal heat and even thunderstorms so they added sparks to the atmosphere to simulate lightning the goal of the experiment was not to create life but to simply test the first step in operon's model can simple chemistry naturally give rise to the complex molecules of life after running the experiment for just one week their ocean became brownish black careful analysis revealed that through a series of reactions many complex molecules had been produced among these were amino acids special molecules of life that we once thought could only be built inside the bodies of living creatures this was a pivotal breakthrough in science so significant in fact that it gave rise to an entirely new field of research now known as prebiotic chemistry scientists don't know for sure if the gases used by miller really were the most common gases of the ancient earth because of this many experiments have since been done showing that the molecules of life can form in a wide variety of environments with different starting chemicals and different sources of energy sugars lipids and amino acids have even been found on meteorites this suggests that the molecules of life formed all throughout the ancient solar system and may be forming right now in other regions of our galaxy together these discoveries tell us that operon's primordial soup and darwin's warm little pond could have easily existed in one way or another on our ancient planet so to sum things up what was the miller uri experiment the miller uri experiment was our first attempt at simulating ancient earth conditions in this case the ancient earth's water cycle for the purpose of testing ideas about the origin of life the miller yuri experiment is significant for two main reasons first though it was not a perfect simulation of the early earth it clearly demonstrated for the first time that biomolecules can form under ancient earth-like conditions second the experiment took what was once mere speculation the idea that life may have emerged from chemistry and transformed a portion of that speculation into legitimate testable science many questions remain to be answered about the origin of life but scientists from many nations and many fields of study are now following stanley miller's lead they're finding ways to turn those questions about the origin of life into testable scientific hypotheses simulation experiments cannot tell us exactly how life formed in the past but if enough of them are done they could eventually tell us if it's possible for life to emerge from chemistry i'm john perry and that's the milleriary experiment stated clearly