okay so we are going to go over a couple of things here this is the first part of chemistry I'm not going to go through the whole the whole chapter I'm just going to go through the basic structure and then I'm going to talk about bonds and the bonding especially well not especially any of them they're all they're all very important but we're going to be talking a lot about ions in this class and we're also going to be talking about polarity which involves hydrogen bonds so we'll we'll take some time with that alright so in case you weren't paying attention in grade school or junior high or wherever it is you learn this stuff the basic structure of an atom includes this middle part here which is the nucleus and that has the protons and the neutrons okay so protons and neutrons make up the nucleus around that are electrons and that's what these guys here are so if you have protons in here the protons protons have a plus consider it a plus one charge and then there are neutrons so if we're making up the nucleus so neutrons neutrons have a zero charge and then around the whole thing are these electrons and they're very small but electrons have a minus one charge okay why is that important because if you look at this little atom that I just drew okay there's my little electron you can see that there's one proton with a plus one charge there's one electron with a minus one charge so what's the overall charge of this atom it's going to be zero because there's one positive charge one neg and positive charge one negative charge through the overall charge is zero if you look at this one and you say okay well there are two protons so that means it's plus two in the middle and there are two electrons I will say what's the overall charge of this you're going to say yeah it's also zero okay so that's gonna come in come into play later on when we start talking about what happens when the number of electrons and protons and neutrons and stuff differs okay all right so what we're talking about here right now are the elements okay so there are a number of elements and since we're focused on physiology we're kind of concerned about these guys right here because these are the elements this is the periodic table so you can see carbon carbon sits right over here oxygen oxygen nitrogen hydrogen these are all what they're calling here the big four okay carbon oxygen hydrogen nitrogen 96% of what you what makes you you is composed of carbon oxygen hydrogen nitrogen and then we have a bunch that are major elements okay so these are really important and you may as well get used to seeing stuff like this because this is calcium and we typically see calcium ions because they're dissolved in water okay and then we see phosphorus there's a lot of phosphorus potassium is another really important one sodium is gonna be we're gonna see a lot of that we're going to see some chloride we may from time to sign to see magnesium it's a 2 plus these are all ions and we'll talk about what that means here in a minute and then you have the trace elements these things are things that you that you need and that are found in there but but they're they're needed in very very small quantities okay now the atomic number is listed here okay so I'm gonna make a pretty important point here that a lot of people kind of miss so the atomic number for titanium is 22 that means that titanium has 22 protons remember when we saw this and this one had two protons this one only had one well if we look at the periodic table one is hydrogen so that means if it has one proton its hydrogen doesn't matter how many electrons doesn't matter how many neutrons if it has one proton it is hydrogen therefore we that that gives the ID the identification that identifies it the other one had two protons and two neutrons but specifically the important thing was that it had two protons if it has two protons its helium the number of lithium has three so the number of electrons may vary but if it has three protons it's a lithium okay so so that's that's a pretty important point atomic mass that just when you weigh them all together that's something that you get into more in chemistry we're not going to be we're not too concerned with atomic mass at this point not really all right so now we just mentioned that what if you have let's say we have one two three four five six seven eight let's say we have eight protons inside now if we if we cheat we go back here and we look and we say okay if it has eight protons that makes it an oxygen okay so we know that but let's say also that it has and I'm not making a real realistic element here but let's say it has a bunch of neutrons on the inside okay let's say I add a few I can add a few and then I have a different isotope I could take a few away that gives me different isotopes of oxygen it's still oxygen but if you change the number I know you've heard the word isotope before if you change the number of neutrons you're just making a different isotope there I just made a different I made another one different isotope of oxygen okay now usually there are only a few isotopes of oxygen that's why this isn't very realistic but the concept is that if you change the number of neutrons you have a different isotope still of in this case oxygen so I'm changing then changing the the isotope okay well because because neutrons have mass they have about the same mass as a proton it changes the mass of the the of the atom but again we're not too concerned about that right now the thing that's interesting about isotopes is that in medicine isotopes or a lot of times use so for instance I don't want to draw it's been too much time drawing on this but if you have something like iodine that sits right down here there's iodine it has 53 protons okay I'm gonna I'm making a point here and it's and it's important because it's part of your homework now let's pretend there are 53 protons now iodine has a number of different isotopes okay and you can vary that number of isotopes and you can make it let's say really really heavy well what happens if you add a whole lot of neutrons this eventually can become unstable because that nucleus is just getting really big and it's almost I almost think of it as like kind of like jello it's like wobbly but really what tends to happen is that it will start to throw off neutrons they'll just it'll it'll start to decay and those neutrons will just fly off some things that are radioactive you hear about radioactive elements that's because their nucleus is unstable and they tend to lose these neutrons at a high rate and they might come off with different amounts of energy okay so and that's what this is you have alpha which isn't as bad beta and gamma gamma emissions are are very highly energetic and these things may be so energetic that a radioactive isotope that's a high-energy radioactive isotope that emits gamma emission sounds very fancy doesn't it but all that means is it's decaying it's losing some of these neutrons and in the process it's releasing high-energy photons which is you can hit your DNA and that's what this is this is DNA and it's this DNA is a molecule and it might knock out one of those bases in there just and it can break it and it can cause a mutation and if you mutate a cell in just the right way the Sun can do this lots of things can do this if you mutate this DNA and such in just the right way it can one it can kill the cell because the cell is not going to be able to function anymore if you hid it somewhere that's really important or if you mutate certain genes it can actually become cancerous okay so that's why radiation can cause cancer that's why the Sun because the Sun is is constantly beating down and and it's sending out radiation of its own and it can also damage this DNA can damage cells it can damage proteins themselves it's it's not discriminatory it doesn't say oh that's DNA we can only damage the DNA damages whatever whatever gets in its way these high-energy beams do okay so what we do and medical uses as tracers now is we can monitor we can measure this energy so is this energy is coming out we have sensors that can measure that energy and you can actually see the energy coming off you can you can graph it and you can see the energy and so another thing and that's how you can use it as a tracer another thing you give somebody something a radioactive isotope and then you can monitor where it is because you can see that energy coming on for the reason I used iodine as an example this is because iodine tends to accumulate in the thyroid gland okay and we're gonna get into why that's important later what iodine is doing there but right now we can just say it accumulates in the thyroid gland what's that we don't know yet but when it when it does if you give a radioactive isotope of iodine then it's very unstable and it will throw off these neutrons and it'll therefore release lots of energy and if you have thyroid cancer and you have a tumor growing there that's a tumor then this energy as these things are flying off and that energy is being released it's beating up on this cancer that's the idea is it beating up on everything else in the area yes yes it can it can cause other damage which is why you don't want to do it for too long but accumulating that radioactive iodine right in that one area will whittle away at that tumor and you can shrink a tumor just by giving that radioactive isotope so there are lots of uses for isotopes and again the only difference is that it has a different number of neutrons okay which in some cases makes it unstable because it releases high-energy gamma emissions or it can be or it can just release lower energy emissions that are that are that are less harmful okay and then we can use those as tracers all right the last thing of these are ions okay so we've already talked about protons and how protons are ID that identifies it and neutrons form isotopes so what happens if you change the number of electrons well remember if you have say we have three protons and we have we're not going to draw any neutrons on this for now and we have three electrons well that's neutral but what happens if we get rid of one of these okay so what happens if that electron decides to leave well it's no longer neutral now you have three positive charges and only two negative charges which means that you're going to be plus one if we look at the ID of this this is lithium and because it has a charge it's going to be lithium plus which makes it the lithium Aion okay so now this is going to be a it's pronounced cation because we want to focus on this word ion it's not patient this is not an Yin this is an ion so in the case of chloride what it does is it tends to it doesn't have four it doesn't only have three but it takes on an extra electron and when you have more electrons than you have protons and it tends to be negatively charged okay so so chloride tends to form an anion okay which is a negative charge okay and I'll show I'll show other pictures of this in a minute okay so some of the ions that we're really going to see and every time pretty much we talk about sodium we're talking about this we're talking about the sodium cation potassium cation okay so these are all ions calcium ion calcium is very very important usually when I ask people what their bones or what calcium is good for they say bones but really your body uses your cells use calcium all the time muscle cells use calcium neurons use calcium calcium is a very very important signaling molecule in fact your body will sacrifice its bones to to get calcium into the blood when you're when your blood calcium levels get low we'll also see chloride phosphate we're going to be talking about ATP which is adenosine triphosphate hydrogen we usually think of hydrogen as free hydrogen it's also bound to a lot of things it's found just about everything that has carbon and which is just about everything and we usually think of this in terms of acids so something with a lot of hydrogen tends to be acidic okay that means it has a low backwards pH okay something that's basic would have a high pH okay so acidic means low pH we'll discuss that later on - all right so summary electrons change the number of electrons you get anion if you change the number of protons that's the identification you have a different element if you add a proton to it it's a different element it's not what it was and if you change the number of neutrons you have an isotope ok so hydrogen hydrogen mm-hmm if you if you take away that electron that's what this is showing if you take away that electron so the electrons gone there it was here and now it's gone then you have a hydrogen ion okay if you add a neutron you have you still have hydrogen because it still just has one proton but now you have a neutron here which means that you have something called deuterium which is a hydrogen isotope okay so keep those straight all right okay so now we're gonna start talking about bonding now this says right here four primary roles of electrons now the thing about electrons we have I'm not going to change colors here if we have you know if you will say we have 1 2 3 4 5 6 protons here and then we have out here 1 2 3 4 5 here we'll draw like this 3 4 5 6 ok so these are the electrons on the outside who do you think if you look at this I can make these bigger I like to make my electrons small because they're technically much much smaller than the neutrons and protons but if this is your atom and this is what's called an outer shell where do you think a reaction is going to take place do you think the reaction is gonna take place in here no this is down here it's down in here and it's protected these guys that first shell is already full it can only fit two because it's very small but the outside these guys are the social ones they're the ones that are out there interacting with the electrons of other atoms okay so these guys can interact and they do and that's what creates bonds okay creates bonds forms ions because like I said if these guys leave or it takes on more than then you have you have that that ion takes on or loses high-energy electron electron carriers are a number of atoms that have that have extra electrons in them okay and those are those are important we'll talk about that when we talk about metabolism we'll talk about electron carriers NADH and ATP H things like that and then free radicals now every now and then I'll say something about that it's not it's not incredibly important because we're not really going to mention at this one time but a lot of times in normal reactions what happens is a molecule we can say you know we'll say this is a molecule will have an extra electron just sitting out there and exposed that electron is going to react with the next thing that it sees this is called a free radical and we create these all the time with little electrons sitting outside just waiting to react okay and it will it will react with whatever it whatever it comes into contact with next and those are called free radicals if it's a collagen it will damage the collagen protein whatever and so we have the system in place called antioxidants that will absorb that and so when this guy is ready to start causing trouble instead if you have antioxidants in your system the antioxidants are designed to react with that and it will remove that electron and then this thing will be harmless and that electron won't do any harm to anything else okay so that's why we take antioxidants it's a antioxidants are very important and very real okay but again it's the electrons the electrons sitting out here the electrons are the ones that are interacting for whether it's good or bad usually it's usually it's good okay so but they're also the ones that form bonds okay so they're the ones that are actually interacting with the next-door neighbors here to form these bonds now bonds capture energy so we have a couple of things here I just said bonds linked atoms or that electrons form the bonds and that and the bonds then link those atoms together but it takes energy there's there's energy contained in this bond and what I've drawn here this is glucose okay glucose is a sugar this is fat also we could call that a lipid more specifically it's a triglyceride tri meaning three it has three tails one two three okay we know that glucose is energy okay we know if you've ever if you've ever roasted a marshmallow marshmallow is uh is sugar and pretty much just mostly sugar and we know that if we light a marshmallow on fire that it will burn all by itself we could put it in there for a brief period of time light it on fire and then we could just hold it up and it will just burn like a torch okay that means that marshmallow had energy inside it that it's now releasing okay what it's doing is these bonds are breaking and when it breaks it releases energy okay so as those bonds break energy is released and usually well not usually but when we're burning marshmallows or sugar we see that as fire okay that's supposed to be fire okay so that's where the burning comes from that's where the energy is the energy is actually contained in this bond okay so fats are the same thing if you burn if you you can burn fat and it will release in and it will - it will also burn releases carbon dioxide and water that's that's the reaction that ultimately that ultimately comes from it and so we know that they're that they're containing that they contain that energy and that when we eat sugar to get energy of course we don't set it on fire inside our bodies we break these bonds enzymatically we use enzymes that will carefully take this apart and then it will release some of that energy and we use that energy to make something called ATP which we'll talk about when we talk about metabolism okay so I might mention this again when we when we discuss that okay so these linking of atoms we're going to talk about covalent bonds we're going to talk about ionic bonds and we're going to talk about hydrogen bonds we're also going to come back and we're going to talk about polar so if we have something like water water uses a it's kind of a spoiler here covalent bond and I will say specifically that it is a polar this might not mean anything to you yet but it's a polar covalent bond fats also are covalent bonds but they are nonpolar covalent bonds again this may not mean anything to you but but once we figure out what polar and nonpolar means you'll think okay that makes sense I hope all right ionic bonds those are things that well if we have sodium and we have chloride we put them together opposites attract right opposite charges attract then we have a salt sodium chloride okay so let's let's talk a little bit let's talk a little bit about those okay so first of all I on ik bonds atoms gain or lose electrons remember we had a nucleus in here and we had electrons on the outside of it okay so if we lose electrons or if we gain extra electrons we create an Aion okay opposite charges attract again we saw that we had sodium which is positively charged chloride which is negatively charged they're attracted to each other and you end up with a salt sodium chloride covalent bonds share electrons so we'll we'll see I have some pictures down here that'll make this a lot easier and we'll see that so first of all let's talk about the the ionic bonds here's a sodium now there's a special property it's called the octet rule or the rule of eight which says that for anything larger than a helium so hydrogens and helium's they only they only get two but in the outer shell out here it can hold a total of eight okay so one so it could technically have eight electrons out here and then it moves up to the next shell so two to go back to this I said hydrogen is really small it only gets two so the very inner shell only gets two but once that's full it starts to fill the next shell and you see one two three four five six seven eight okay so this shell is full so now it's ready to start the next shell if you look at sodium this is what this is how sodium is made it's got one little electron sitting out there in this outer shell all by itself so sodium says you know I'd really like to have a full outer shell what are my chances of recruiting in seven more electrons mmm not so good what are my chances of just booting this one out pretty good so that's what it tends to do it tends to boot that out okay so that tends to leave it's very easily it's not that sodium tells it to leave it's that it's very easily drawn off by water anything will will pull that electron off of there okay so in this case it's showing that it's moving over here to chloride okay so here's chloride and it's got this shell is full it has eight in it so it started building another one and it got all the way up to seven okay so it has seven in its outer shell and it thinks oh I'd really like to have eight okay it wants to have eight but so we can either dump all of these well that's not that's not gonna make any sense because that would give it a really really high charge if it loses all those electrons what's much easier is it for just just for it to grab one more electron and now it's happy it has the full eight so it added its eight electron so chloride tends to take them on now if we do the math and we remember those really simple things and that is that an electron is negatively charged well when this one loses a negative charge what's that going to do it's not losing any proton to cells the same number of protons if it loses one elective charge that's going to make it a charge of plus one this one takes on an electric it takes on an electron with its negative charge without changing the number of protons it's going to make it minus one okay so you end up with CL minus and then na plus okay na is the the symbol for sodium okay so that's what this is showing it's showing after that transition that the chloride actually and that's I guess a pretty important point it actually took on an extra electron okay so it owns it now this electron is now part of chlorine sodium gave its up okay so it's electron is gone they both have full outer shells everybody's happy except they have this little charge issue well now they're kind of attracted to each other okay now did sodium actually give chloride that electron and probably not it doesn't really matter anything can pull the electron off of sodium and chloride will take its electron from anywhere but it helps to make sense out of how how an ionic bond forms by thinking okay well sodium gave up an electron I gained an electron now they're oppositely charged by one and so we end up with sodium chloride okay and that's going to form this salt crystal that we that we see here okay so and they all they all stick together just just just like that form the little salt cube all right covalent bonds they actually share a pair of electrons so here's hydrogen remember I said hydrogen wants to have its it's the teeny tiny one if we go back to the periodic table it's the very first one listed it has one little proton but it also just like everybody else wants to have a full shell the trouble is it's shell can only get two okay so it only gets two in its outer shell it's the only one hide your hydrogen and helium they only get two in their outer shell but it still wants to have a full shell and the full shell for it means two now for every other element a full shell means eight so here's oxygen and oxygen has one two three four five six little pink ones here it has six in its outer shell and it's thinking hmm I would really like to have eight so here's hydrogen that comes by saying okay I tell you what I'm not going to give you my electron like chloride did but I would because I want one two and you want one we both want an extra electron let's just share I'll I'll borrow yours for a little while you can borrow mine for a little while I can pretend I have two and you can pretend you have an extra well chloride well oxygen is actually missing two in its outer shell so it's going to react with two hydrogen that's why h2o is h2o okay because oxygen is actually missing two and its outer shell so we can react with two of these hydrogen's okay and it seems very very fair right they're sharing electrons oxygen says you know yes oxygen hey how many how many electrons you have in your outer shell so yeah I got eight yes hydrogen yeah I got two but there's a problem do you really think it's fair if you tell a big kid to share with a little kid you really think that big kid is the little kid and the big kid are gonna get the toy or whatever they're sharing for the same amount of time no oxygen is a bully oxygen is more electronegative and so it actually if I were to ask you where do you think those electrons are most of the time and you said well oxygen looks you know a little shady so I think he's probably keeping it most of the time you would be right oxygen keeps those electrons way more than hydrogen hydrogen doesn't get a good deal out of this and so what tends to happen is that this side becomes negative remember electrons are negatively charged so if oxygen is holding on to that electron more then and the electron is negatively charged then this side of the molecule tends to be negative and this side because it's missing these electrons tends to be a little bit positive okay remember earlier when I started talking about polarity okay it's like poles of a magnet okay you have the positive pole just down here on this side and you have the negative pole which is up here on this side okay now if we were to count so we have 10 electrons right here if you look at if you were to count protons you would have 1 and then oxygen has 8 and then this one has 1 that's 10 protons so what we have is 10 protons and 10 electrons are you following me I hope so so if this has because this one has eight protons and each of these has one proton and if you look at the periodic table you'll see that that's true it's going to be number eight on the electron periodic table so that's ten and we have one two three four five six seven eight nine ten electrons so we have it is neutral but we just said that it's kind of has a positive charge and a negative charge but that's polarity okay so keep those straight make sure you make sure you understand those things that because that's what I'm saying here is here's this water it's a polar molecule because it's a little bit negative it's always going to be negative on the oxygen side because the oxygen is the electron hog it's the bully and the poor little hydrogen over here doesn't have the electrons but it's proton isn't going anywhere so it's partially positively charged okay but overall it still has 10 electrons 10 protons it is neutral okay so this is the trick question that sometimes pops up when I say is water a charged molecule no it's not a charged molecule it's polar and I think now would be as good a time as any what does polar mean the best definition I've seen polar because we're gonna see the word polar again is an unequal distribution of charge okay so this definition works for a lot of things polar means it has an unequal distribution of charge okay so in this case overall neutral but it's polar all right now if we think about let's see we'll just draw one of these out there's a water there's a water okay so do these guys what about the interaction these guys might have with each other okay if this is neutral and this is neutral well opposites attract they're not really opposites so they get are they going to be attracted to each other if you're thinking and you're following me you might say wait a minute if you if this is a little bit negative here and that's a little bit positive on this side then maybe just maybe when two water molecules come together that negative charge might actually be attracted to that positive charge and that's exactly what we see and this not to be true dramatic but this is why we're doing things like looking for water on Mars okay this is why we say water is essential to life it's because we have this little interaction that takes place here between the partially positive height hydrogen and the partially negative oxygen of a water molecule and that is called a hydrogen bond okay is it really a bond yeah I mean it it is I mean in the case of water water's moving all over the place so it's it's a very very very temporary bond so this guy might be rushing past in it and it might you know hang out a little bit longer than it normally would and then it's gonna see another oxygen down here and so that hydrogen will then interact with that one and they're moving all over the place all the time but but they do have this interaction and that's what a hydrogen bond is now this is very important so I hope you're understanding this because this is again where the trick question comes in what is actually holding this hydrogen to that oxygen remember they're sharing electrons and what do we call that covalent so what's actually so this is this is the take-home message here what is actually holding the water molecule together covalent bonds what is causing an interaction between two water molecules hydrogen bonds okay so we have hydrogen bond two covalent bonds working at the same time and you need to keep them straight you need to say oh yeah it's being held together by a covalent bond but two water molecules do associate with each other through this thing called a hydrogen bond okay and that's what we see in this picture so we see all of these guys and they're all moving around it's it's hard to show in a picture but they're all moving all over the place but if you were to take a snapshot if you were to take a picture if there was a way to do that at any one time you would see that they would be lined up just like this you would see the hydrogen's as close as they can get to the oxygens okay these are all hydrogen bonds okay all of these are all these little interactions here hydrogen bonds okay so what does that mean for us well let's say you have a bunch of water molecules in a pan or a beaker make this bigger and a pan or a beaker then what you would see is that they would be hydrogen bonding with each other they're gonna be hydrogen bonding with each other and so if I were to try to heat this they have a high heat capacity they can hold on to a lot of energy why because they have hydrogen bonds so you're heating this up and you're heating it and they're and that's what heat is when you heat a liquid it's very anything it's molecules are just moving faster and faster and faster and faster until eventually one of them flies off well if these guys like each other so much water is very self loving so it loves other other water molecules and so you're heating it but it doesn't they don't really want to leave each other and so they're kind of holding on to each other almost like a magnet and so it takes a lot of energy to get that to fly off in fact the fact that water is a liquid at room temperature is one of the most interesting properties of it we're used to it because of course it's water it's liquid at room temperature it's water but it's actually kind of unusual and it's only because it forms these hydrogen bonds that that even takes place and so that's one of the reasons it's really really important for for life if we look at something like methane methane and then you put another methane molecule right next to it they don't care about each other why would they I mean even if there was an sharing of a unequal sharing of electrons there's not gonna be any weird distribution of charge because it's it's symmetric it's they're all there all around there and so there is no there is no link between this one and this one so if you were to heat this up if you were to have this in a beaker or whatever it's a very bad beaker and you were to heat it up it wouldn't take anything at all they're like okay whatever you know they start moving around they just fly off okay so that means that methane is a gas at room temperature okay so methane we think of methane is being a gas and that's because it has no association with itself water is different and that's very important another thing especially if you're if you like you know water spiders or something like that if we take some of this water now let me draw it this way if we take some of this our water that we had earlier and we pour it out it's supposed to be a drop and we pour it and we cause a water droplet this drop this is supposed to be a water droplet here okay that's a water drop okay it's a lot bigger than what I drew here but you get the idea it forms a bead okay so when water tends to drip on the floor or something like that it forms a bead why does it form a bead that's kind of odd I mean we're used to it of course but it's still kind of weird what's going on in there well all the water molecules are trying to be as close as they can to other water molecules so if this water molecule wants to slip away it's not going to it's gonna try to stay up here and it's gonna try to get as small as it can it's going to try to associate with all of these guys all the time and so it forms these little beads okay and that's surface tension okay and surface tension is important for a lot of reasons and one of those I mean how does this relate back to physiology it relates in a very important way so it's something that you hopefully understand at least this concept of water tension you need to understand hydrogen bonding and polarity because what happens with the premature infant when you have a premature infant it one of the things that you usually see is these babies come out and the doctor says oh that's perfectly healthy but it's on a respirator or a ventilator and it's got something that's like helping it breathe and you're thinking well gosh what's what's wrong doc you know he's just too much surface tension within the lungs okay so what does that mean well I'm going to go into a lot of detail but what happens is that the water that's inside the alveoli of the lungs tends to stick to itself and so what it does is it snaps these alveoli shut and so your alveoli which are the parts where you have gas exchange in the lungs can't do anything the water is just sticking to itself it's attracted to the other water and it just shuts up fills with water and pulls that thing closed okay but after a while usually late in development that surface tension is relieved by something called a surfactant and the baby after a certain stage of development will start to form surfactant those will open up everything's fine and and and it and it can be it can go on its way just fine okay so so this idea of polarity water surface surface tension the polarity of water is really really important for everything we're going to be doing okay so I'm going to hopefully get the next section up here in a minute so good luck