hello welcome to biology we're going to be talking about chapter 2 The Chemical foundation of life and that is in the open stack biology 2E textbook in this chapter there are three sections so section 2.1 goes over atoms Isotopes ions and molecules so we're going to talk about matter and elements we'll also talk about protons neutrons electrons we're going to talk about how those electrons impact matter and we are going to look at how elements combine to form molecules then they form cells and so on so atoms are the building blocks of all molecules life is composed of matter um matter has mass and it occupies space or takes up space and so elements are atoms and elements are um they each have their own unique property so they each have their own chemical proper properties their own physical properties so take an element of helium um its chemical properties is that it does not react it is a noble gas if you know anything about chemistry it is um happy the way it is and its physical properties is very light and it floats um and so each element or each atom behaves differently elements in the Living World elements cannot be broken down into smaller substances while still behaving um in the in um their specific manner so we can't break down helium and still have it be helium each element is designated by a chemical symbol um one letter would be capitalized two letters would have a capital and a lowercase um the four most common elements for all living organisms are carbon oxygen hydrogen and nitrogen so what if there is a living organism it's going to have those four elements in it and that's a nice way to look and see if you have any living organisms say on like a planet um here is the percentages of those four elements so oxygen in life um living life forms it's about 65% notice the difference in the atmosphere is about 21% in Earth's crust is about 46 so living things have different ratios of these elements than does the atmosphere and um the Earth's crust very different um so atom again is the smallest unit of matter and it retains all the chemical properties of an element U atoms contain two regions there's a center region called the nucleus in an outer region which holds electrons in the nucleus the center region it's little positive it contains protons and neutrons the outermost region is a little more negative and that contains electrons and so these three things together protons neutrons electrons are all called subatomic particles so you may have heard that term before it just refers to those three things that make up an atom here's what it looks like here's the nucleus portion so that Center portion with those positive protons and neutral neutrons and then the outer region out beyond the nucleus is where we can find electrons notice how small they are and they are negative so that outer region is going to be a little more negative okay so here's a quick table that summarizes that information proton has a plus one charge or it's a positive it has a mass of one um AMU means atomic mass units and that's its location Neutron same um Lo same mass no charge electron has a negative charge no Mass because it's so small it's negligible it is very it does have a very small amount of mass but we'll say it's negligible for us and it's in that outer orbital okay so you should be able to fill this information in a should be a uh Neutron let's go over to b b should be electrons over to c c is pointing to the nucleus region and D is referring to those protons so if you need to pause it and fill it in try it yourself um that would be good practice because you'll likely see something like this on an upcoming quiz or test okay so what's the difference between atomic number and atomic mass you've probably heard these before and you probably got them mixed up and that's totally fine because they sound so similar so atoms of each element they have a standard number of protons and a standard number of electrons so that atomic number actually refers to that standard number of protons so for example carbon's atomic number is six so anywhere you see it on a periodic table its atomic number will be six um that means it's going to have a standard number of six protons okay atomic mass is going to talk about the mass of the atom remember if we go back to this table what has mass protons yes but also neutrons so we can talk about the atomic um number of carbon being one and if it has or sorry being six and if it has six protons then that makes up six of its mass well carbon also has neutrons and so those neutrons account for Mass as well and it also has six neutrons so added together six and six is 12 so it has a mass number of 12 and that's for carbon that so again just to summarize atomic mass is equal to protons and neutrons so protons are the amount of positive or or the atomic number is the amount of positive particles or the protons and atomic mass is the positive protons and the neutrons so the total mass what makes up that atom so remember atoms are made up of not just protons but protons neutrons and electrons so we have to account for all of those now we can have different things called Isotopes and Isotopes will differ in the number of neutrons in the nucleus so for carbon we can add another Neutron and it becomes a carbon 13 so mass of 13 we can add two neutrons and it becomes carbon 14 or a mass of 14 so um Isotopes again we don't change the number of protons we're just changing the mass making it heavier or lighter by changing that number of neutrons so here again just a review atomic number is going to be up here in the corner typically the smaller number um for carbon it's six so that's six protons and its mass number is 12 so we know it has six proton we can just subtract 12 - 6 and we know that there's six neutrons pretty simple right okay so answer this question if Xenon has an atomic number of 54 and a mass of 106 how many neutrons does it have um so what are we going to do 106 minus 54 and it's going to leave us with 52 yeah so 52 neutrons and 54 protons make up the mass of xenon which is 106 all right a little bit more about Isotopes so Isotopes again are different forms of an element meaning that there's different numbers of neutrons we can change the number of protons without changing the element but we can change the number of neutrons while still keeping the same element so all of these are forms of hydrogen and they get really special names um so hydrogen um one has no neutrons it's just a proton in the center hydrogen two has a mass of two and so it has a proton and a neutron and hydrogen 3 has that one proton still CU it's still hydrogen and we added another Neutron so we made it heavier okay there is a simulation this one's from the textbook um you follow follow the link in there and that it kind of helps explain what an isotope and atomic mass account for all right the periodic table you've seen this many times I know um the periodic table is arranged by atomic number um and the atomic mass is located at the bottom notice it is a decimal that means it's just the average atomic mass that we could find that element in um round it to the nearest whole number for our purposes um electrons so let's talk about those we already we just talked about protons and neutrons in the nucleus let's talk about electrons out in the orbital so electrons inhabit um very um distinct orbitals if we go by the bore model and they look like this um they have um different Su levels notice they are numbered there and so that's just saying where we're likely to find electrons electrons will normally inhabit the lowest um orbital or the closest orbital to the center of the atom and will fill them going outward okay so electrons fill orbitals closest to the nucleus first then those further away in order so as these orbitals fill up we'll go to the next one one as that orbital fills up we'll go to the next one and so on and so forth and again this is a boore model it is highly simplified for our sake so let's take a look at some atoms here these are some atoms that are pulled from the periodic table um from different groups so group one or column one on the periodic table this is group 14 or column 14 Group 17 group 18 group 18 is the very last column um so each of the red circles are showing you a very important part of every atom um these are the ones that we are concerned with so when when um elements bond to one another they're going to bond by either losing or sharing their electrons and the ones that they lose or share are in you guessed it this outer orbital they're not going to lose or share the ones that they're holding kind of tightly close to themselves they're going to lose or share ones that are you know a little further away that they don't like as much so that's why these are highlighted and that's why they're important so they're they're called the veence shell and they're just the electrons that are kind of left over in that outer shell or outer orbital um really important group 18 um the very last column on the periodic table holds helium neon argon and so forth their outer shell is full and so they aren't going to gain or lose any electrons they are actually happy as is um notice like chlorine here we've got one missing here so it's not happy all of the elements on the periodic table want to be like a noble gas or um an element in group 18 for um instance and so they're going to try to get to that point by gaining or losing or sharing electrons to look like a noble gas everybody wants to be a noble gas uh when the first two outer shells are filled that's called an octet rule and so we reach eight so notice there's 2 4 68 here on that outer orbital so every element wants to try to get to that eight um except for the first two elements hydrogen and helium because they don't have enough electrons to even get to eight and so they're going to go to just two um so just hitting this again four models are incomplete they're highly simplified um electrons don't actually orbit that way but um they do inhabit specific orbits and I'll show you that um if you want to go into Quantum quantum mechanics that helps predict where electrons might be at any given time they are moving very fast and so it's hard to pinpoint where they might be and so that's that's where Quant quantum mechanics comes in so this is actually um representation of how electrons orbit around an atom so notice the first two orbitals are circular but beyond that they start to get this like dumbbell shaped pattern um it's really odd right so um those are specified as SPD andf um we're not going to get into all of the specifics with those but that's just what something I wanted to show you okay so electrons I told you they're important for chemical reactions um electrons are what comes into play when we combine chemicals and so they're going to get rearranged and we're going to redistribute those electrons and that's what helps create new molecules and so the chemical bond that forms between um elements is actually the attrative force between electrons or gaining or losing um so on and so forth so just to recap here what you probably already know what goes into a reaction is called a reactant and what comes out of a reaction is called the product this reaction is showing you hydrogen peroxide breaking down into water and oxygen so we get some bubbles of oxygen out of that um this reaction is called an irreversible reaction it only proceeds in One Direction until all the reactants are used up so as we use up all the hydrogen peroxide we'll just end up with only water and oxygen a reversible reaction has an arrow going both directions and this is going to be um a reaction that reaches equilibrium so we're not going to use up all of the reac or all of the products they're going to re reach a state that um the living thing is happy with or equilibrium Cove valent bonds so during um a chemical reaction we're going to change where electrons are correct chemical um calent bonds is how we share electrons and so coal um bonds can be found in water molecules for instance a hydrogen atom and an oxygen atom are going to share a pair of electrons to reach that octet rule remember that octet rule is eight electrons in that shell that's a full shell for hydrogen it's just two because it you know it doesn't really hold that many so two um but hydrogen has two that it has there oxygen has it's eight and then this other hydrogen is sharing one and that also has two so that's a Cove valent Bond Cove valent bonds are very are pretty strong you can also have a double calent bond you can also have a triple calent bond and that's just talking about the number of pairs that are shared between elements so for instance these oxygen molecules have a double bond because they're sharing two pairs between them ionic bonds are a little different they don't share they kind of just rip it the El from the other one so sodium it has one electron it's a lot easier to give up one than to try to gain seven to reach that eight and so if it gives up one chlorine will happily take it because it needs one to get to eight and so that would be an ionic bond sodium is giving up an electron chlorine is gaining an electron and then this attraction that's created between the positive and negative sodium and chlorine is where that Bond comes from so this is a very strong bond um it's usually between a metal and a non-metal um but yeah that's um ionic bonding okay another type of bond is a polar calent bond and that's an unequal sharing of electrons so yes the electrons are shared like in water but Oxygen's a little bit bigger a little bit more of a bully and so it's going to hold those electrons just a little bit closer to itself than hydrogen so it's sharing but it's not being very nice about the sharing and so it gets a slight negative over here because the electrons are closer this way and a slight positive because the electrons a little further away and so this is called a polar calent bond a non-polar bond is where electrons are shared equally and so they're going to be like halfway between each and every one of those so notice we don't have any partial charges here um and then here's another type of non-polar um no unequal sharing there okay another type of interaction is called a hydrogen bond um you also have a Vander walls interaction both of these are between molecules so they don't actually happen in a molecule but they do happen between adjacent molecules and these are going to be super important like in for for example DNA um DNA in between the two strands there are hydrogen bonds that hold that um DNA ladder together they are super weak bonds but without them life wouldn't proceed as it does so um they're easy to get ripped apart they're easy to get put back together and um that nature of them helps you know live living things Prosper okay so that's 2.1 make sure you know what a matter and element is you can Define both of those make sure you know what a proton neutron electron are um make sure you can compare Co valent and ionic bonds um and hopefully you can talk about how we combine elements what actually is happening so remember those electrons so if you don't know those things go back rewatch um but we're going to continue on here next section is two water we're going to talk about the properties of water um why it's a solvent why it's um super important being in in a solvent as a solvent we'll talk about cohesion and adhesion and acids and bases and buffers um so water makes up 60 70% of the human body is the most critical molecule for life on Earth um Earth has all three states of water present and so that's probably why we have so much um life and why um Earth is such a great planet um it is a polar molecule which means it can dissolve things we'll talk about that in a second and it can also form hydrogen bonds so we just talked about hydrogen bonds they are weak interactions between molecules so in this case we're talking about between water molecules um so again on Earth we have three states of water liquid gas and solid I'm not going to get into those hope you know that um water again has a polar calent bond within it so between the oxygen and hydrogen we have polar calent bonds the oxygen holds those electrons a little bit closer so it's a little negative on that side hydrogen since the electrons are further away it's a little bit more positive on the hydrogen side that positive partial positive partial negative creates attraction between the other water molecules partial positive partial negatives and so that keeps water together so if you ever notice like de um that bubbles up it's going to make a nice like 3d effect right and that's because all of those water molecules are sticking together um and so um hydrogen bonding when we freeze water it makes life um I makes ice less dense than liquid water and that's why it floats um it creates a nice lattice structure and um the molecules are so far apart that it's less dense it's not as heavy and so it's it floats to the surface um other important properties the heat capacity of water it takes a lot of heat to raise the temperature of water and so it can absorb a lot of heat so think about like in the summertime um when you're at the beach um and it's like May or June and it's been hot for you know a few weeks the water is still going to be pretty cold right the ocean water is still going to be pretty cold and that's because water takes a long time to heat up versus say land like concrete okay um it also takes a long time for it to cool down so in the winter time coastal cities aren't going to get that cold as an inland City might and that's because they're controlled by the heat of the water that they're nearby um it also takes a lot of heat to change um water from liquid to gas so evaporation um it's going to take a long time for that to happen as well um so I mentioned earlier that water is a very particular solvent and that's because it's polar and because it has those slight positive slight negatives it can dissolve many many many many many things and so we call it a universal solvent so water is typically going to have minerals dissolved in it um such as sodium and chlorine like the ocean and this is how it looks when if we were to drop some table salt into some water this is exactly what happens so that sodium chloride bond gets broken apart the part partial negative oxygens are attracted to the partial positive or not partial fully positive sodium and the opposite happens over here that chlorine is negative and it attracts the partial positives on those hydrogens and so that actually rips that sodium chlorine apart and um dissolves it yeah just like that so it's a univers so water is a universal solvent other important properties cohesion water can stick um together can stick to um and that's due to um hydrogen bonding cohesion also allows for surface tension so the capacity of a substance to withstand being ruptured so like this needle floating on top of water here that's due to cohesion adhesion is the attraction of water molecules um so cap action or capillary attraction um happens in Plants that's how water moves from the roots to the choots in plants and that's from that pull on water molecules so as one is pulled it pulls the next one and that one pulls the next one and that one pulls the next one it's kind of like a train and it's just pulling right along and that's adhesion um in the real world you can you've probably seen one of these before these are water striders and they stay afloat on top of water because of water's cohesive and adhesive properties because water wants to keep sticking to itself and so it's not going to allow that bug's leg to protrude into the surface okay so answer this question which of the following statements is not true it would be D water makes up 60 70% of Earth atmosphere this should say um the human body okay pH buffers acids bases so pH indicates acidity or alkalinity so acid or base and um a small amount of water molecules as they ionize or dissociate we will get hydrogen ions and hydroxide ions and so hydroxide is going to indicate an acidic solution if we have more of those if we have more hydroxide ions we'll have a more basic solution but if they are in Balance we'll have a completely neutral solution and so a neutral solution is indicated with a pH of seven and that has to do with a logarithmic formula which we won't get into but um a good example of that would be like distilled water um if we have more hydrogen ions in the solution it'll be a iic so that's below a seven so you take a look at all the examples here and then a basic solution would be more hydroxide o molecules and that's above a seven the human body is about a 7.2 7.4 um we're a little bit more than neutral um and you can see sea water is an eight black coffee is a five so you can throw your pH off um by drinking coffee orange juice you'll make it more acidic and so your body has to react to that um by using a buffer system so buffers play a key role in maintaining internal pH um and so this diagram is just showing you the body's buffering of blood pH levels so if it gets too low or Too High um it's going to drive the reaction in a different direction so we talked about this earlier with a double arrow that would be a reversible reaction so it can go go to the right or it can go to the left just based on what the living body needs okay answer this question which of the following statements is true it should be C acids not but not bases can change the pH of a solution so both can right acids and bases can okay and that's section two water so you should be able to talk about the properties of water that are critical U why it's a solvent or why we'd call it an excellent solvent um talk about what cohesion and adhesion are and what an acid and base is and why buffering is important in a living body all right the last section section three which talks about carbon we're going to look at why carbon is important for life and describe what um functional groups are and why they're important in biological molecules which leads us in into our next section so carbon is important if you ever take organic chemistry you're talking about carbon and you're talking about um living things so carbon is a key component of all macromolecules those major four which we'll talk about next week proteins carbohydrates lipids and nucleic acids they all have carbon in them um carbon is awesome because it can form Cove valent bonds with four different atoms so it can make some really large and complex molecules um it allows to be the backbone it has four electrons in the outer shell meaning it can it can form four bonds because it needs to four fill four more um areas to reach that eight and um it allows it to achieve that act rule when we do fill those okay so each carbon atom I just said it it can form bonds with as many as [Music] D4 atoms all right hydrocarbons you may hear this term a lot hydrocarbon refers to a molecule with carbon and hydrogen in it and so this molecule is going to have a lot of bonds bonds store energy when we break those bonds we release energy like the fire in the picture there so this Bond these four bonds here have a lot of energy stored in them so if we burn it methane if you know what it is it's a gas and so it's a um a fuel source and so it releases a lot of energy when we put some fire to it um the energy release Powers our homes cars um it also is in a lot of the food that you eat hydrocarbons are and so they provide your body with a lot of energy hydrocarbons are arranged differently um we're not going to get super deep into this but I just want you to to look at the complexity that you see here so this methane is in like a pyramid format um this ethane so two carbons six hydrogens there very complex structure and then ethine has a double bond so many different ways that we can arrange the hydrocarbons and um they're only showing you up to two here they can get very very long and complex and I'll show you in a little bit so here are some rings aromatic Rings carbons here hydrogen's on the outside so lots of bonds lots of energy being stored in all of those bonds and these are just different ways that they can be arranged um isomers is another term you might hear um they are molecules that have the same chemical formula but their structure is different so if we take a look at butane and isob butane isobutane tells you it's an isomer four carbons in butane four carbons in isobutane but look at the difference so isobutane kind of makes a t shape and butane has this linear shape so they're just a different structure um but the same amount of atoms in each molecule so when up the hydrogens there's 10 there and then there's 10 over here as well but arranged differently um geometric isomers are going to come into play um especially next week where we have an arrangement of molecules around the carbons um and it's a little different so this is Cy and trans trans is like trans fat um and so the little functional group here is on the opposite side so opposites and CIS means same and so that's going to be on the same side and then antimers are left and right oriented so it's kind of like your left and your right hand so you have a thumb and four fingers on your left hand a thumb and four fingers on your right hand but you can't superimpose them right if you put one on top of the other it's just not going to complete completely fit on top the other one you're going to have thumb out to the side right um even if you flip it over it's not the same because you're looking at your palm versus the top of your hand um so that's when an an anomer is a left or right or like a mirror image um here's a look at those CIS and trans so this molecule here these are all carbons that are making up the center um black structure it's not a very good structure but um this is a carbon at each of these little um bumps here or these are hydrogen sorry the carbons are in the center um this is a trans fat so nice and linear this is a Cy fat nice and bent uh Cy fats are better for us trans fats are not because they can compact um notice if we put a bunch of these together they're not going to compact but um this would be a um a good example of of those things and we're going to get more more into that next week when we talk about biomolecules but um this is a long hydrocarbon chain and I just wanted to show you what that looked like in a bigger um setting okay functional groups so functional groups are groups of atoms within a molecule that gives specific properties to the molecule um here's a hydroxy group so o methyl ch3 carbonal carboxy Amino phosphate sulah hydril um each of the four types of macro molecules so carbs proteins nucleic acids lipids um they all have their characteristic uh functional groups so for example proteins they have a lot of amino groups um DNA and nucleic acids have a lot of phosphate groups in them and so you're going to have different ratios based on different macro molecules um functional groups often interact with each other via hydrogen bonding so we're not going to get rid of that term anytime soon we're going to talk about hydrogen bonding throughout the whole semester and it's um super and it's and it's just how important it is um hydrogen bonds again stabilize biological molecules so this is a molecule of DNA on this side there's another molecule of DNA on that side and they're being um held together in the center here by the hydrogen bonds typically hydrogen bonds are showed um by dashed line so that you know that that's not um within a molecule it's between two molecules so remember hydrogen bonds are not in a molecule they're between two separate molecules and so this holds those two strands of DNA together and um keeps it all organized within yourselves and they can be easily broken um separated DNA can get copied they get put back together very easily um and so on okay so you should be able to explain why carbon's important and why or what functional groups are and why uh we talked about functional groups at all really and that is it so hopefully that helps if you need to go back and rewatch parts of the um video please do that um but I hope you have a great week and I'll see you next week