hello out there today we're going to be talking about a part of chapter two so this is section 2.1 the chemical context of life and i know you're all out there looking at me going mrs kilhaney did you forget that this was ap bio not ap chem well chemistry is fundamental to biological life so let's take a look at an example so these are ants of course and what you might not know about ants is that they actually release a compound called formic acid and the formic acid that you see here is used actually to start to fight other organisms so these ants are protecting their home right now they're actually fighting off predators that are attempting to destroy their home you'll see this formic word by the way is actually related to chemicals that you probably have heard of before formaldehyde or maybe even formalin and both of those act as preservatives in biological systems as well so that's another connection to this word you may not have seen before so in order to understand the composition of a lot of these different biological chemicals we need to understand chemistry we need to understand the basics of biochemistry so a lot of this is going to be review and that's okay this should help you remember some of what you've learned in chemistry in prior years so the first thing we can think about is that all organisms are composed of matter and hopefully you remember that matter is anything that takes up space and has mass so matter is anything that takes up space and has mass and you probably remember before that matter does come in different forms so we've talked about solid matter liquid matter gaseous matter plasma as another example all of these are things that take up space and that have mass and as you're talking about chemistry these different types of matter are all made of what are called elements and the elements are substances that cannot be broken down to other substances via chemical reactions in biology we're going to be concerned with some very specific elements and they are the elements that i actually call the schnapps elements c h n o p and s so carbon hydrogen nitrogen oxygen phosphorus and sulfur quick way to remember that is schnapps these are actually the six most common elements in living systems in order so a great way to remember each one of those and again that stood for carbon hydrogen nitrogen oxygen phosphorus and sulfur we can then take those schnapps elements and we can take other elements and begin to make something called compounds so a compound is a substance that consists of two or more elements and this is found in a fixed ratio some great examples might be for example water h2o this two i hope you will remember from chemistry means that there are two hydrogen hydrogen atoms which we'll talk about in a second for every one oxygen atom o if there's no number next to this this implies that this is a one some other compounds that are going to be common to you will be glucose c6h12o6 this is glucose we might talk about things oh say for example like oxygen gas right we might talk about carbon dioxide all of these are compounds and what we can do is take those elements to form different kinds of compounds so when you are looking at a compound you'll notice that the compound itself in this case sodium chloride or table salt which is nacl this is not a capital i this is an l so chlorine is cl you'll see i'll often write it this way to remind you that that is lowercase l so when i take sodium sodium is a metal that is reactive with water chlorine is a pale green gas and i combine them together into the compound sodium chloride which is crystalline it's safe to eat this is table salt you'll notice that the compound has different characteristics than of the two elements that make it up so the properties we call these properties of compounds are not the same as the elements that make them up in biology we'll be concerned with not all uh the main elements on the periodic table right so of those elements on the periodic table 92 are naturally occurring but only about 20 to 25 of those are necessary for life and we call those the essential elements pause the video for a second which ones did i say were the most common in living matter i hope you said those were the schnapps elements carbon hydrogen nitrogen oxygen phosphorus and sulfur those six elements make up 96 of living matter so most living matter is made of these particular elements that have then been combined into compounds or large molecules so we're going to see a lot of each of these this semester expect those six elements to follow you around in this first half of the year all right effort so most of the remaining four percent that's left is going to consist of calcium and potassium all right so phosphorus and sulfur actually are not quite as common as the other two right we mentioned these before so chn and o make up 96 percent the phosphorus and sulfur are down here there's not quite as much of either of those but i wanted you to try to make that connection between what we said before about schnapps elements and these now all right other elements that are required in living systems are your trace elements you really don't need a whole lot some great examples of trace elements we're going to see on this next chart so great examples of trace elements might be things like magnesium chlorine for example both of these are trace elements so you can see here here at the top i have my living body mass in the human body most of it is made of carbon hydrogen nitrogen and oxygen as we're moving down here are phosphorus and sulfur we see calcium and we see potassium as well other trace elements might include boron chromium cobalt copper iodine in particular we're going to talk about some applications of iodine later this school year so these are elements that can be found in the human body moving forward so talking about the structure of atoms that's atom not atom as in the person all right so elements consist of atoms and these atoms are very specific each element has its own unique type of atom so what is an atom atoms are the smallest unit of matter and these atoms still contain the properties of the element so when we're talking about each one of those elements say like sodium for example right the hunk of sodium and this excuse me the hunk of sodium metal and a sodium atom are still going to have the same properties well why is that this is all the case because of the unique composition of each atom so hopefully you'll remember from chemistry that atoms are composed of things called subatomic particles and there are three main some pardon me subatomic particles all right one of them is protons i'm going to continue to be abbreviating this p plus or you may also see me do this protons which have a positive charge neutrons i'm going to abbreviate neutrons n0 or 0 they have no charge whatsoever and then finally we're going to have electrons i'll be abbreviating electron e minus and you should remember that electrons have a negative charge so i have three main subatomic particles one are protons protons have a positive charge think proton p positive next one neutron neutrons have no charge or they are neutral it's a great way to remember it and then lastly i have electrons and electrons have a negative charge so the different numbers of protons neutrons and electrons found within an atom are what are getting excuse me are what are going to give each of those atoms their properties the way that they act so neutrons and protons will sit in the center of the atom and they're going to form something called the atomic nucleus where the electrons are going to form a cloud around that nucleus so i'll have protons and neutrons in the middle whereas the electrons are going to be in a cloud on the outside neutrons and protons are larger and they're massive to each other is almost identical we are going to measure that mass in something called the dalton so daltons or d a so we're talking about mass of protons or neutrons we're measuring those in daltons electrons on the other hand are much much smaller in mass so when we start talking about the mass of an atom we are mostly going to be talking about the mass of the protons and the neutrons because electrons are so so much smaller so let's look at what this actually looks like so here is my atomic nucleus here in the center and then out on the outside i'm going to have a cloud and somewhere in that cloud of negative charge i will find two electrons so let's quickly count how many of each particle are in the atom that you see here i have one positive two positives two positives two positive charges are two protons i have two that have no charge here in the center so two with no charge means i have two neutrons and then what we're going to actually see in your textbook will be a representation that looks more like this that'll show the electron cloud in a different form just so it makes it easier for them to follow so i have two negatives here meaning that in this atom i have two electrons so in the atom that you see here i have two protons two neutrons and two electrons you may also see that in this particular atom the charge of the atom is balanced is this always the case no but we'll talk more about those exceptions later and when i say the charge is balanced i mean that for every positive these two positives here these two protons i have the same number of negatives i have the same number of electrons that's going to keep my charge balanced moving forward another way that we are going to differentiate atoms in particular is to look at their atomic number and to look at their atomic mass so every element is defined by its atomic number which is the number of protons in the nucleus and every single element has a different number of protons if you change the diff pardon me if you change the number of protons if you change the atomic number you are changing the element that you are working with so carbon for example its atomic number is six that means it always has six protons if i add a proton to that i no longer have carbon i now have seven protons therefore i have nitrogen all right the atomic number the number of protons in the nucleus is going to determine what element you have every element has a different atomic number and it is always specific it is always the same carbon will always have six protons nitrogen will always have seven a mass number on the other hand is actually the sum of protons and neutrons in the nucleus so the sum of the protons plus neutrons found in the nucleus so if we were to look at that atom we just looked at on the previous slide i'm going to skip back for a second the mass number for this is going to be 1 2 protons plus one two two neutrons my mass number would be four the actual atomic mass is going to be close to what the mass number is you'll probably remember that protons and neutrons have about the same mass and daltons and that electrons really don't have very much mass at all so to determine atomic mass we are mostly looking at mass number we're approximating it using the mass number so here's an example titanium has an atomic number of 22. how many protons neutrons and electrons are there in an isotope of titanium with mass number of 48 so let's see we have an atomic number of 22. atomic number means number of protons so let's see i want to make sure i get one with an atomic number of 22. okay so that knocks these three choices out completely this is a great tactic when you're looking at questions on an exam that you're not sure of the answer of you can eliminate some choices that you know are incorrect immediately and then focus on the ones that are a possibility so let's look at the second part of the question how many protons neutrons and electrons are in one with mass number of 48 so i'm just going to use mass number like this mass number we hopefully remember is number of protons plus number of neutrons so how could i solve for that 48 equals 22 protons plus the number of neutrons 48 minus 22 is 26 is my number of neutrons so which answer is that oh this one's eliminated must be the correct answer up here 22 protons 26 neutrons pause for a second why 22 electrons this is a question of charge so hopefully you'll remember protons have a positive charge electrons have a negative charge we didn't talk about charge anywhere up here right so if there's zero charge the amount of protons and electrons must be equal check our answer we were exactly right 22 protons 26 neutrons and 22 electrons there's a word on that previous screen that we hadn't yet introduced and that word was isotope so when we're talking about isotopes we're talking about changing one of those three numbers we're either changing the number of protons neutrons or electrons well we hopefully remember that all atoms and of an element have the same number of protons i can't change the number of protons without changing an element so therefore i can't change the number of protons in an isotope rather isotopes are two atoms of an element that differ in number of neutrons these are neutral in charge so isotopes do not have different charges what they will have is different masses so different masses in an isotope so say for example basic carbon carbon has an atomic number of six has a mass number generally of 12. this is also what's known as carbon 12. another isotope of carbon might be atomic number of six remember this is protons i can't change it mass number of 13. so carbon 13 has one more neutron than carbon 12. carbon 13 is an isotope of carbon now some isotopes are radioactive and what that means is they decay spontaneously they break down spontaneously and some of them do give off different particles and energy you'll see that a lot in iodine which i'll talk to you about in a second so radioactive isotopes are ones that decay spontaneously and here's a great example so looking in the throat here we're actually seeing cancerous throat tissue we're looking particularly at thyroid tissue at the moment and the thyroid is very very heavy in iodine iodine is necessary to create something called thyroid hormone or thyroxine and so what we can do is introduce iodine into this person's system a radioactive isotope of iodine and actually use this as a radioactive tracer so we're looking for where that radioactivity is where the particles are being given off in order to determine where that cancer is so this is one way for us to trace atoms through the body is by using a radioactive isotope something else that we can do with isotopes is something called radiometric dating so the parent isotope is going to begin to decay into its different daughter isotopes and it does this is at excuse me at a fixed rate and that fixed rate is something known as the half-life all right and so half-lives we're talking about how long it takes until half of the original matter has broken down so what some scientists can do is called something called radiometric dating and what scientists will do is measure the ratio of those different isotopes and they're going to calculate how many of those half-lives is passed since that fossil was formed so depending on what isotope we're looking at it's going to give it a different half-life and so we can tell how old something is based on about how many half-lives have passed based on how much of the original quantity of the isotope has broken down now it's time to talk about something i tend to have way too much of energy so what is energy energy is the capacity to cause change and energy comes in a diff a couple different types one of these is what is known as potential energy and potential energy is energy that matter has because of its location or because of its structure so different electrons in an atom are going to differ in the amount of potential energy it has and so those states of potential energy are their energy levels or their electron shells so we're going to be looking at the different electron shells in an atom and determining about how much energy each of those electrons have so one example that we can actually use in terms of potential energy is seeing how a ball bounces down the stairs so there's higher potential energy more capacity for change when it's all the way at the top of the stairs and at the bottom but just like the electrons in an atom you'll notice that this ball can only stop on each one of the steps it can't stop in between the electrons in an atom have a similar situation so i have several different energy levels those closest to the nucleus have the lowest energy levels those further away from the nucleus have higher and higher energy levels so each of these electrons cannot stop between levels but can bounce just like the ball on the stairs boing boing boing from one energy level to the next whether the energy is being absorbed or whether the energy is being lost so those electrons on the outermost shells of each atom are going to have the most potential energy they're going to be at the highest energy level so let's take a quick look at some examples here so just like i showed you before the atomic number is up here on the top this is helium h e this atomic number tells me how many protons my atom has down here is my atomic mass this tells me about how many protons plus neutrons okay you look at me going mrs k that's not even yeah i know because atomic mass is actually an average of all known isotopes so while the most common isotope of helium is helium-4 there are ones like helium-5 that exist that might have an extra neutron but it's very uncommon so we're taking the average of all of those masses together within helium i have two protons and two electrons here are my two electrons both of these electrons are sitting in the first electron shell or first energy level each of these shells the first shell can only hold at most two electrons each shell after that can hold up to eight electrons at a time so you'll see for example i'm going to take the two in the front here one two lithium is going to have three the third one goes into the next energy level it goes into the next electron shell the example i always give students is going to a concert where do you want to sit when you go to a concert are you going to if you get your choice of sitting anywhere sit all the way in the back probably not you're going to want to sit in the seats closest to the stage so you're going to fill all of those seats those closest to the nucleus those at lower energy levels before i start filling higher and higher and higher energy levels so let's take a look great in other examples are buddy carbon i have two in the first shell six total i have one two three four more left four plus two that's six total neon great example i have two in the first shell 10 total so the rest of the eight one two three four five six seven eight are in the second shell this shell is now full so what happens to any electrons after that like in sodium my first shell is full with two i have eight more that brings me to ten but i need eleven total that last one goes in a new energy level so we're going to fill from the shells closest to the nucleus and work our way out going to higher and higher energy levels as the atoms accumulate more and more and more electrons so electrons that we're going to be most concerned about when we're talking about a lot of the things today are going to be those called valence electrons so valence electrons are those in the highest energy level those in the valence shell in the outermost shell and that's what's going to determine the chemical behavior of a lot of these different elements so we're going to be looking and seeing how they bond how they react this is happening because of how many electrons are in the valence shell so those who have a full valence shell those that are stable and full are actually what's known as chemically inert but you've probably heard them referred to as the noble gases so these are chemically inert a great example of some chemically inert atoms are those that are the noble gases and let's take a look at y again so the noble gases sit out here i don't have any more electrons i can add on to this without adding a new shell that's probably not going to be a great idea same thing here same thing here in neon and argon so because these shells are full they tend not to want to add additional electrons they tend not to want to give away electrons all right these are going to be chemically inert these are going to tend not to react and they are what are called noble gases so we're using those rings to give you a basic idea of where the electrons are going to be found but truthfully that's not really what the structure of an atom looks like electrons are actually found in something called orbitals and orbitals themselves are three-dimensional spaces where they're found so within the cloud they are found in these particular orbitals and each of the electron shells consists of a specific number of orbitals so in the first shell i only have one orbital okay and this is what's known as the 1s orbital excuse me s orbitals are round they're spherical like this and this orbital can hold two electrons so somewhere within that orbital i'll find the two electrons of the first shell the second shell has up to eight electrons so it has two of the electrons in one of the two s orbital but the other electrons are found in each of the two three p two three two p orbitals excuse me i can't talk today so i have one two s orbital and then i have three 2p orbitals so the orbitals look kind of like a figure eight so here p orbital looks kind of like this and i have three of them that all get attached each of these orbitals will have a max of two electrons so that's two four six in the p orbitals they're the other two for eight and what actually happens to these orbitals is they get something called hybridized so here's my hybridized 1s 2s and 2p orbitals so you can get an idea of where those electrons could actually sit within those orbitals okay so this is what the structure of those circles really looks like it's more of a predictive model as to where the electrons can be found why do i care so much about electrons about knowing where electrons are and finding electrons well when you have an incomplete valence shell when you're not chemically inert an atom may decide that it wants to share those electrons that it can find and adam may decide that it wants to transfer electrons between specific atoms so depending on how many electrons there are i may decide that i want to share to get to a state of stability i might decide that i want to transfer electrons to get to a state of stability and so these interactions caused by sharing electrons or transferring electrons are what you probably have heard of as different types of chemical bonds bond chemical bond right sorry i couldn't resist the double o seven joke so these interactions are going to let the atoms stay close together those atoms will be held by an attraction called a chemical bond and these chemical bonds are caused by sharing of electrons or transferring of electrons okay hopefully you remember that except in the first shell which can only have two all other shells will have a maximum of eight eight is that point where stability is reached so i'm ideally going to want to share electrons or transfer electrons to get my valence shell to be completely empty or completely full okay i want that valence shell to be full with as many electrons as possible so say for example i have two eight and one in my valence shell right well maybe i want to transfer this one to another atom so now my outermost shell the one with eight is full maybe i have two in my first eight in the second and seven in my valence shell okay well maybe i want to pick up one from another atom that's a possibility maybe i have two and i have four oh it'd be tough for me to lose these four it'd be tough for me to get four from somebody else so maybe i want to share with someone else who has four with another atom that has four okay so this is the way that atoms might share or transfer depending on what their valence shell looks like to get themselves to that full inert state so one type of bond that you can make is what's called a covalent bond and a covalent bond is sharing sharing is caring so we're talking about sharing a pair of valence electrons between two atoms it's an e so sharing a pair of valence electrons between two atoms so those valence electrons that are being shared are going to count as both atoms valence shell okay they're going to count for everybody so here's a great example looking at hydrogen hydrogen has one proton so it will have one electron in each of its valence shells those two hydrogen atoms will be drawn close together by an attraction to create a hydrogen molecule so let me actually do this with a dot diagram okay so i'm going to use a lewis dot diagram to show you guys this so here's my hydrogen there's my proton i have one electron and one electron those two electrons are being drawn close together so now both hydrogens are going to share these electrons until the two atoms of hydrogen bond in terms of a covalent bond if you see a line like that in a diagram that's talking about a bond all right so those bonds that have now been created mean that those two electrons that you can see in the second picture i drew are now being shared by both atoms both atoms of hydrogen count as having two electrons in their valence shell right now so a molecule like the one we just saw of hydrogen gas is going to consist of two or more atoms that are being held together by covalent bonds i originally showed you a single covalent bond or single bond which is expressed with one line much like this this is the sharing of one pair of valence electrons but what if i have a situation like carbon monoxide carbon has four valence electrons oxygen has six okay if i want carbon to have enough and i want oxygen to have enough they're going to share both of these pairs okay so if i'm sharing two pairs that means that i am going to have oops sorry about that a double covalent bond or a double bond i am going to be sharing two pairs of valence electrons at the same time two pairs of valence electrons means a double bond expressed with two lines much like you see here so i just showed you again a structural formula remember that this line right here is representing a single bond you may also see the notation of two lines which is a double bond and then rarely you may actually see three lines a triple bond okay i can also abbreviate this h bonded to h is h2 two atoms of hydrogen alright so this is hydrogen gas as a molecular formula here are some other cool examples i showed you before here's hydrogen with the lewis dot structure like we drew before and the structural formula this is oxygen gas see in the middle here there are two pairs of valence electrons being shared so we're seeing a double bond in oxygen gas here's water all right oxygen had six valence electrons one two three four five six and it shares with two hydrogen atoms here and here so two bonds h2 one two o there's water you'll see this space filling model a lot in your book they love this notation the colors will also stay the same white will be hydrogen in all space filling models red will be oxygen and black will always be carbon so this dark black grayish color will always be carbon carbon is neat because carbon can share with up to four atoms at a time it has four valence electrons so right now carbon is sharing with one two three four hydrogens four single bonds my formula is c one carbon h4 one two three four hydrogens and this is methane gas so these are all examples of different covalent formulas that you may see covalent means that they are sharing so when you're talking about which atoms are more likely to bond with others we need to start talking about valence just like we said before what kind of valence does a certain atom have well some atoms can bond more than others can you just saw that a second ago carbon can have up to four bonds at a time oxygen already has six valence electrons it only wants to share two oxygen can only make two bonds at a time all right and what you're also going to see is that different bonds form between atoms of the same element but they can also bond to different elements so again some compounds that you might see a great example of a compound was water that we saw before methane and another example that we've given in the past is glucose c6h12o6 a larger compound so two or more different elements is a compound now we don't always share at least you don't always share equally remind me to tell you this story in live class but one of the things that happens when you have siblings is siblings don't always share fairly so if i have say one piece of cake for example right much like the one you see here i'll draw you a piece of cake there's the icing okay sorry about that there's my icing and you ask my sister to cut it so that she and i can share odds are good that she'll cut it right there that'll be my piece that'll be her piece she will get a lot more than i will right she's still sharing with me she gave me some but she did not share equally atoms do the same thing and the degree to which an atom is attracted to electrons is called electro negativity so an atom's attraction for the electrons in a covalent bond is what is known as electronegativity so the more electronegative an atom is the more strongly it begins to pull electrons toward itself so it will begin to pull electrons toward itself so how do i know which atoms are more likely to be more electronegative when you are looking at the periodic table which you see here atoms that are more electronegative will be found more near the top and more to the right with the most electronegative element being fluorine others that are very electronegative include nitrogen oxygen and chlorine okay so those that are more electronegative have greater affinity for electrons they pull more on the electrons they get the bigger piece of cake they are more electronegative why does this matter well because covalent bonds come in two types you either have polar covalent bonds or nonpolar covalent bonds in a polar covalent bond the electrons are not shared equally excuse me i keep hitting that button so in a polar covalent bond the electrons are not being shared equally and what you'll see in a polar covalent bond is that one atom will be more negative so if you see this delta negative that means it has a partial negative charge and the other part of the bond will be partial positive delta positive partial positive water is a great example of polar covalent bonding as you saw on the periodic table a minute ago oxygen is extremely electronegative meaning it tends to pull the electrons toward itself and it tends to gain a partial negative charge so that partial negative charge is more common for electronegative atoms like oxygen nitrogen will be another great example because the electrons are being pulled more strongly to oxygen so is the negative charge gets a partial negative charge the other end of that bond is hydrogen down here the electrons are being pulled away from it leaving a partial positive charge in a nonpolar covalent bond the electrons are shared equally so no atom is more electronegative than the other they are shared equally so most of the ones we looked at before were polar covalent excuse me nonpolar covalent in which they were being shared equally the two had the same equal charge like an oxygen gas however water is a great example of a molecule with a polar covalent bond meaning the electrons are not shared equally and this is happening because oxygen is so much more electronegative than hydrogen is so oxygen is pulling on those electrons really hard giving it a partial negative charge and because that negative charge has been pulled away from hydrogen hydrogen is no longer neutral it's now partially positive okay water is a great example of a polar covalent bond so real quick and this is a bit of review for you i hope isotopes and ions so isotopes meant that we had different numbers of neutrons ions ions are charged atoms and charged atoms had different numbers of electrons okay so if i'm looking at each one of these this one immediately this charge here is telling me that this is an ion this is a negative charge okay so i have a negative charge on this sulfur atom all right over here this is my isotope because i have a different number of neutrons my mass number is different than both of the other two that you see here so each of these has 16 protons 16 and 16 is 32 so i have 16 neutrons and 16 electrons in my second one i have 16 protons top number i have 17 neutrons remember that neutrons was mass number minus protons and i have 16 electrons because the number of protons and electrons are equal in my ion over here i had 16 protons because otherwise it wouldn't be sulfur anymore 16 and 16 is 32 i have 16 neutrons what about electrons if i have two extra negatives negative two that means i would have 18 electrons in total if i had a positive charge i'd have fewer electrons than you'd expect so these are some examples of how to look at isotopes and ions and to calculate protons neutrons and electrons we needed to talk about ions charged atoms charged molecules because ions are important in what's called ionic bonding and in ionic bonding atoms are not sharing electrons rather they are taking or giving up so we are transferring electrons from one atom to the next a great example is the transfer of the electron from sodium to chlorine so in ions these are molecules or atoms that have a charge for example you might see sodium plus chlorine minus magnesium two plus oxygen two minus right each of these are ions ions are going to have a charge so how did that get the charge well electrons got transferred somehow if i gained an electron i became more negative i would be a negative ion if i lost an electron i become more positive so here you'll see a sodium atom and a chlorine atom sodium has one valence electron here in red whereas chlorine has seven ideally sodium wants to give up this one electron so that its outermost shell its next valence shell is full and chlorine only needs one more to make up its next valence shell so instead of sharing electrons sodium will give up that and now be full on the outside have a full valence shell but because it lost an electron it now becomes positive chlorine on the other hand gains that electron from sodium now full but because it gained an electron it also gains a negative charge and becomes what is known as cl minus or an anion there is a short video here if you would like to watch the process of ionic bonding between sodium and chlorine so go back and take a look at this when you download the powerpoint later there were two words that you saw before one was a cation and a cation is a positively charged ion two ways for you to remember this one is that cations are positive meow right like cats have paws so cat ions are positive but you can also remember that the t in cation looks like a plus negatively charged ions are what are known as anions so anions are negatively charged i had a student once tell me that the way they remembered anions anions were negative they didn't like onions it sounded like onion to them and they said i don't like onions onions are bad onions are negative and that's how they remembered it okay please remember that a cat ion a positively charged ion has lost electrons and become more positive and that an anion has become more negative because it gains electrons that is a misconception that i see with students all the time so please be very very careful with that as you're continuing to go through this so an ionic bond is going to be an attraction excuse me between a cation and an anion so we're attracting between a cat on a cation excuse me and an anion this is because opposite charges attract so a positive and a negative are likely to be drawn together two positives would be pushed away from one another so here is that crystalline structure of sodium and chlorine this makes sodium chloride or table salt so all of my sodium plus is that a cation or an anion sodium is positive it's a cation chlorine is my negative anion and all of these have linked together to form this crystalline structure of table salt so ionic compounds like salts do often crystallize much like the one you see here the next type of bonding that we want to quickly talk about are what are called hydrogen bonds so when you're looking at weak interactions like hydrogen bonds this is for x forming when a hydrogen atom that's covalently bonded to one electronegative atom is attracted to another electronegative atom oh that's weird it's going to be easier once you see it in an image okay i'll show you in a second the electronegative partners in living cells are usually oxygen or nitrogen so hydrogen bonds often form between hydrogen and either oxygen or nitrogen because those are the most common electronegative partners at least in living systems so what does a hydrogen bond look like we are showing this with a dotted line and i'm forming right now one between water and ammonia nh3 so here's my hydrogen bond it's that partial positive charge being attracted to the partial negative charge of the electronegative atom so this interaction is not particularly strong okay hydrogen bonds are actually very weak interactions they are easily broken apart we are going to see both in biological macromolecules like proteins and also in the chemistry of water why the excuse me the easy breaking and forming of hydrogen bonds is important to the structures of both of these classes of molecules right it gives it special properties because they can break very easily another type of weak interaction is something called the van der waals interaction so these are interactions between molecules that are close together so i get a whole lot of electrons that are unevenly distributed accumulating in one part of a molecule and so each one of those interactions is very weak by itself but when i have a lot of interactions like that they're very very strong a great example of how many van der waals interactions at once can be strong are the interactions in a gecko's toe hairs and a wall surface so one interaction would not allow the gecko to hang onto the wall but many of these interactions allows that gecko to climb the wall so very very weak separately but when combined can be very very strong so these were two types of weaker interactions please remember and i'm going to go back for a second that we drew this knot as a solid line like a covalent bond we drew the hydrogen bond as a dotted line because these interactions are much weaker they are much easier to break but that is a positive and we're going to see how the easy breaking of these hydrogen bonds will become important later on so size and shape you are going to see this a lot all right a lot a lot a lot in the phrase you'll hear me say a lot is form defines function so the size and shape of a molecule are always going to help determine what sorts of functions it can have so we kind of alluded to this idea before of s and p orbitals hybridizing and creating different shapes to an atom so up here i have my orbitals which have been hybridized the three p orbitals so these were the three two p orbitals and here's my 2s orbital here as well all of these have hybridized so now i'm going to get a shape determined by all of these interacting which will be a tetrahedral shape all right and so this shape of where these electrons are is going to be pushing the electron pairs away from one another so you'll actually see that because i'm trying to push away from these unbonded pairs naturally that these arms on this water kind of bend downward all right and this gives different functionality because the molecules are bent in a certain way here's another example and this is actually a bit more specific example of how form can define function why does morphine work for pain so morphine actually shares a similar structure and you can see that actually in the piece that's been boxed out here and here two natural endorphins so endorphins are those chemicals you get say for example from a runner's high people who love to run will often talk about gaining natural endorphins and those endorphins are going to give you positive feelings so we have receptors for those endorphins in your brain morphine tricks the brain because it's same shape as endorphin into thinking that endorphins are bonding so when you're given morphine it's going to trigger those exact same endorphin receptors and set them off giving positive feelings this is actually how a lot of different drugs work because they are able to bind to receptors for other things your body already makes remind me i'll talk to you about one of my professors who actually researches something called endocannabinoids and those are actually why things like cbd can work in your brain as it bonds to these cannabinoid receptors within your brain it bonds to receptors for chemicals your brain already makes so this is an example of how the form of the molecule the shape of the molecule can determine what its functions are within the brain all right last little bit of this chunk is going to be talking about chemical reactions so chemical reactions are making and breaking of bonds so in a chemical reaction i'm either going to be making bonds or breaking bonds creating new molecules breaking those molecules apart the starting molecules in a chemical reaction are always called reactants the things that are doing the reacting and the things that i am making are called products so reactants and products hopefully you'll remember that the reactants go on the left-hand side of your chemical equation this arrow here is talking about what reaction is taking place um you'll often hear that this arrow is read as yields so combining this reactant and this reactant yields this product right reactants on the left products on the right you may see some equations that look like this and that i have the reactants and the products what this double arrow would mean is that this reaction is reversible meaning that this reaction can be run in both directions these reactants can form this product and the breakdown of this product can form the reactants so i can run the reaction in either direction a great example of this is photosynthesis so the reactants in photosynthesis are carbon dioxide and water and when those reactants are combined it forms the products glucose and oxygen gas but this reaction is also reversible i can take glucose and oxygen gas to make carbon dioxide and water let me quickly put the balancing back in so this reaction is reversible it can be run in both directions we are going to see this reaction again in a couple of weeks this is actually a way that we can show that the reaction is taking place so as photosynthesis is happening i'm using carbon dioxide and water to form sugar and oxygen gas so the leaf in the sunlight which is powering the reaction is forming the production of oxygen gas and i can see the oxygen bubbles forming another example of a reversible reaction all right is the one that you see here so i'm taking hydrogen and nitrogen all right to create nh3 i can break nh3 back down here's those two headed arrows back into nitrogen and hydrogen gas now if i have reversible reactions like the ones you've seen here you may actually reach something called chemical equilibrium so chemical equilibrium gets reached when your forward and reverse reactions go at the same rate all right so neither of the reactions is going faster than the other one so the concentrations of reactants and products do not change they just continue to power each other the whole way through they both continue to react so that's chemical equilibrium i hope that a lot of this material sounded familiar to you this is mostly things you should have learned in chemistry but it will be foundational to the next couple of chapters if you are having problems with this chemistry please feel free to contact me and i hope you have a great rest of your day thanks bye