this is the lecture for biochemistry for general biology at laramie county community college looking at biochemistry for biology we're going to go through four groups of biological molecules and these are really the building blocks for cells and therefore for organisms all across the living world we're going to look at lipids which are basically fats things that aren't soluble in water carbohydrates like starches and sugars nucleic acids the main one we'll talk about dna and then proteins which are the components that really make you up run all of the reactions in your body assemble all the parts of who you are we'll also make the connection between dna and protein in terms of seeing how protein synthesis works and being able to work through that on our own so connecting with what we've already learned in chemistry um we can look at the makeup at an elemental level of life and then also you know in comparison with where those elements are being pulled from and so for life about 25 of the elements from the periodic table are required and it's about because it's not the same for every organism there are a few elements on the periodic table that are required by some organisms but not others for example humans require selenium but plants do not and there are some plants that require silica whereas humans do not so you can see in life we actually have four elements that make up 96 of the living matter and that is nitrogen hydrogen carbon and oxygen with the majority of course being oxygen whereas in the earth's crust itself we do have a high proportion of oxygen but our second most common element is silicon which is sand also that is made into glass and then you can see we don't actually get to our first required element until we get down here to iron and you can't even see iron in here because the amount we require is so small and then in comparison when we look at the universe overall it's really helium and hydrogen so these much much smaller elements and so you can get a feel for when scientists are looking out in the universe for other forms of life one of the ways that they can try to make predictions about that is by which elements they're finding when they're looking at in these different environments and so of course it's good to know what elements compose us but the elements themselves they're not they're not freestanding right you're not just like a big bag of hydrogen okay so things have to be built into the structures that make up what we are both in terms of like physically what we see but also all of the different compounds in your body that do things for you right like shuttle different types of molecules from your digestive system to your nervous system or be able to alter the way an electrical signal is sent so that you can contract your muscle and actually move your arm and so for the majority of this lecture we're going to actually start looking at these larger molecules that are many many sometimes even hundreds of elements assembled together and for all of them the core component is carbon and so carbon has an atomic number of six and so just a reminder looking at what that looks like from a bonding perspective our carbon molecule has two electrons in the middle and then it actually has four electrons in its shell which means it's going to bond with four things so that it can share four electrons um and therefore have a full outer shell some of the time so if we just use a different color to show which ones he's sharing you can tell the carbon here is sharing with hydrogen and the carbons letting the hydrogen use its electrons some of the time and each of the four hydrogens that are bonded here are letting the carbon share their electrons some of the time so now everyone has a full outer valence shell and everybody's happy so a good way to look at this and think about it is this idea of carbon is always going to have four hands out there to hold on to things and generally we're not talking about any type of ionic bonds here typically of four covalent bonds almost the sorry kind of tilty there um four covalent bonds that almost give us like a scaffold set up right so everything gets connected and then you can build on to it and add the different complexity around the edges which is really what we see happening in in the chemistry that makes up life one other piece on this is the study of carbon-based chemistry is called organic chemistry and so as you go on in biology you typically have to take general chemistry and then you also take organic chemistry after that which is the study of those carbon based things which are typically again as i mentioned earlier much much larger so you do a little bit more synthesis you do a little bit more identifying and so any carbon-based chemistry is what we consider to be organic and of course that is what life then is for us so just an example of carbon and why it's so such a great kind of building block for us to use for life so this picture here this is showing graphite which is what we find in our pencils and so this is a 2d carbon molecule with lots of carbons hooked to each other and as you drag your pencil across the paper it leaves those sheets of graphite which are basically non-reactive and so they sit there on your paper until you use an eraser to lift them off and then then it's no longer present or if you've ever been stabbed with a pencil in the arm when you were a kid and you still have a gray spot there that's because of the stability of the graphite and of course if we get 3d with our bonding and you have bonds from the carbon in all directions then that is what gives us diamonds which are one of the hardest molecules that exists in nature okay so as we start talking about these much larger molecules we have to have different ways to describe them based on what information it is that we want to know about them and so one of the ways we can do that is just say which actual elements are in there and so in this case c4h10o tells us that we have four carbons 10 hydrogens and one oxygen so sometimes that level of information is enough depending on what it is we're trying to accomplish other times we need to know the physical layout of that molecule so in that case we may need to actually draw it out and show what's connected to what and so all of these and there's actually even more options than just these three are representing c4h10o and so in this case you can see the o is here towards the end here you can see it's on a middle branch um here you can see the carbons are branched and so if the structure is important then we may need to have a different way to articulate that so the reason i want to show you this slide is that all of these things represent the same thing and so for one given question you may see a structure like this which is telling you how the carbons are connected to hydrogens and then to an oxygen over on this end where that oxygen is located and because carbon is so prominent in organic chemistry we can also use a shorthand version of it where basically every single corner or end is representative of a carbon with all of its possible bonding sites filled with hydrogen and so basically you just use the line to show the carbons and then you write out any additional pieces and so when we're looking at these these two one two are the same thing being represented one is just shorthand and one is fully drawn out okay and there may be other times where all that matters is we want to know how many carbons there are per hydrogen then we may just use the numbers as well and so the point of this slide again is just to show you the different ways we can represent these different compounds and you can always come back to this slide if you're if you see something on a later slide and don't remember exactly it is what it is that i was talking about so as we look at these large molecules it is unlikely that the entire large molecule is going to be reactive and we see this just across the board in organic chemistry because some of these molecules may be hundreds of carbons and hydrogens and and just really really large and so what happens is we end up having these pieces so let's just draw a sample here so let's pretend this is like our giant molecule here and it's all a bunch of carbon and what we find is that there's these little groups that are attached to the edges that are actually where the reactions occur so how this molecule bonds to something else how this molecule interacts with something else where energy is contained in this molecule is typically on these kind of fringe areas and what has been discovered is that there are really particular groups that we find over and over again on the outside of an organic molecule and what those groups do from a chemistry perspective is predictable and so we take this pile of reactionary groups and we call them functional groups so they're basically the areas of this large molecule where the reactions occur okay and as you can see the same functional group will undergo the same chemical reaction regardless of which molecule it's attached to and so we can look at a large molecule identify the functional groups and then make some predictions about how we expect that molecule to work and so that may be important thinking about like how a drug is going to interact with a cell after it's been administered or maybe it's important to know how a protein is going to react with something else in the body or even how a gene is going to result in a protein and so all of these different pieces are things we can kind of look at the structure of the molecule and get a feel for what's happening so in terms of this class i do want you to know what a functional group is but i'm not necessarily going to have you memorize all of the different functional groups i will tell you they will be helpful as you go on in biology or in chemistry um but we're just going to look at a subset of them here and so i would encourage you to to learn these guys so you can identify them but again i'm not going to be testing you on them so here's just a small sample of some of those functional groups and these ones are really common ones that we're going to see throughout this class so our first one is a hydroxyl group that's an o h and that is what makes a molecule into an alcohol the carbonyl group is a o double bonded to a carbon and the carboxyl will actually see a lot which is a combination of these two and so here you can see the double bond o and then here is the alcohol group okay so those are kind of the carbon oxygen ones then we also have the amino group which is a nitrogen bound to two hydrogens and we'll see this guy in our amino acids that make up proteins and then the sulfhydryl group is a sulfur connected with a hydrogen we will also see this guy in proteins it's probably the one we'll talk about the least there's just one good example of him and then the last one the phosphate group here's our phosphorus in the middle surrounded by oxygens right and just a reminder that those oxygens are super electronegative okay which means they can take electrons from almost anything else and so to have so much electronegativity in one area means this guy is going to take a lot of energy to hold this together and sure enough we're going to see this phosphate group showing up over and over again as we look at how energy transfer occurs in cells and then ultimately in organisms so now we've talked about the main elements that we see that build up things that we see in biological systems and then we've also talked about the functional groups which is where a lot of the reactivity occurs so let's go ahead and focus in now on our actual four biological molecule groups and so just a reminder those are the lipids which are fats the carbohydrates the nucleic acids and proteins okay so of these three of them these three here actually are what we refer to as polymers and so they are long chains of like a repeating molecule that's hooked together and those repeating molecules we call monomers the analogy that i like to use for this is like a train where you have a train that's made up of a variety of cars all hooked together and sometimes the trains are longer or shorter and sometimes it's a mix of different cars but for each of these three of our biological molecules they are smaller compounds that are then connected to make this larger functioning compound lipids are an exception to this they're not quite the same and we'll talk about them specifically but you are going to hear me use these terms polymer versus monomer and that's really talking about is it the big compound made up of lots of little parts so is it the whole train or is it the individual components like the cars that make up the train and so we want to get familiar with those terms as well so that we're all on the same page as we go forward talking about these different groups all right so again here's the four groups we're going to go through we're going to start with lipids because they are the oddball they are assembled a little bit differently than the other three and they also have quite different properties and so we'll focus on those guys first and then we'll move on to the remaining three of carbohydrates nucleic acids and proteins so lipids as i mentioned these are the fats and so they are made mostly of carbon and hydrogen we don't call them polymers as i mentioned because they don't follow the whole train made up of many cars pattern instead they are called oligomers because they're more like instead of a train so like this which would be like a polymer we just keep connecting things they're more like take one thing and connect two pieces to it and now we're good to go okay and so an oligomer is made up of few parts instead of a polymer which is made up of many parts and so lipids are are finite in size you just attach the pieces together and then you're done in addition to being structurally different our lipids also have a unique property in that they are hydrophobic and so when we look at this term hydrophobic means water hydro phobic or phobia is fearing these are water fearing which means they do not dissolve in water and you've seen this before when you look at say for example salad dressing and you can see the oil portion separate out from the water portion and that's actually super critical remember that we talked about in chemistry that the ability of water to be a really good solvent is key for life right most of the things that your body requires are able to dissolve in water and therefore be transported around the cell or in your blood or you know whatever organism we're talking about for lipids to not be able to dissolve in water means that the body has to deal with them in a different way and so we're going to come back and talk about this some more as to how we use lipids and how they get moved around through the body because they can't use the regular path that everything else uses which is just traveling in water and speaking of that everything else all those other things are hydrophilic and philic is loving and so that's everything that can dissolve in water so salts and sugars and proteins and almost all of the rest of the compounds all right so there are many many lipids out there in existence i'm just going to talk through three of them with you um that are that we're gonna continue looking at as we go forward in the class and so our first one is the most simple component of any given lipid and those are called the fatty acids and so these fatty acids are long chains of carbon and hydrogen and you can see this just whole chain of carbon here in the middle and all of the spots have hydrogen in them this piece that's that carboxyl functional group and so that is where the lipid is able to attach to something else so that's not necessarily part of the lipid itself like not the part that has the properties that are hydrophobic it's really this area down here this pile of carbon and hydrogen that have those hydrophobic properties so an interesting thing about fatty acids is that they can have full saturation and therefore be a saturated fat which you may be familiar with that term from a nutritional perspective and what that means is saturated with hydrogen and so the picture being shown here is a saturated fat if it was an unsaturated fat then that means at least one carbon instead of having all hydrogens in all of the bonding spots has a double bond between two carbons instead so we do a double bond there and that's going to kick off two of these hydrogens okay so that would be an example of an unsaturated fat and you can have multiple unsaturations so maybe we have another double bond here we kick off some more hydrogens so then we have two unsaturated spots in this case and so when we get to the test and we're looking at these different compounds you would want to be comfortable with being able to see this picture and know that it is a lipid because it's just carbon and hydrogen but also be able to tell me if it is saturated meaning all the spots are filled with hydrogen or if it's unsaturated meaning there are some spots where hydrogens are kicked off and there's carbon double bonds instead so that's our most basic building block in lipids and we're going to see the fatty acids used in the other two we're going to talk about so the next one is the triglyceride and the triglyceride is a glycerol which is this guy and you'll notice this is an alcohol right it has three of those oh functional groups on it and so it's that one glycerol attached to three fatty acids so one two three and that's why we get the triglyceride name and this is the most common way that lipids do travel in your blood and they actually use the glycerol here which is hydrophilic and can dissolve into water and then the lipids because they're covalently hooked to them here can be dragged along and taken to where they need to be so keep in mind if you just had this free floating fatty acid in your blood it would just sit on top and it would be really hard to get it to where you want it and then our last lipid the one we definitely will talk about the most is the phospholipid and so again we have a glycerol here's our glycerol and now we have two fatty acid chains and that third bonding spot on the glycerol actually gets this phosphate functional group and so reminder that guy is the phosphorus surrounded by four oxygens so this guy is super hydrophilic okay so really dissolves into water with all those charges and on those oxygens interacting with water whereas the fatty acid tails which are mostly just carbon and hydrogen um do not and so a phospholipid is a really cool molecule because it basically has these tails that are hydrophobic right so they won't dissolve in water and then it has this head that is hydrophilic and does dissolve in water and these are so critical for biology because they are actually the structure that makes up cell membranes and so here you can see lots of phospholipids all lined up together with this being the outside of the cell and this being the inside of the cell and you can see that the hydrophilic heads are dissolved in the water here and these hydrophilic heads are dissolved in the water here and then we have this fatty hydrophobic layer here in the middle that actually creates a barrier that stuff that is dissolved in water can't get past and so this is how the inside and outside of a cell is separated it's actually using that hydrophobic chemistry to create the barrier and we'll talk more about these in the next unit when we get to our lecture on membranes so one other piece just thinking about the saturated versus unsaturated this is a great slide for you to be able to really visualize what that looks like chemically so here's our saturated fat again this is a functional group so we kind of just set that aside and this is the piece we're talking about for the lipid we have every single carbon has a hydrogen in each possible bonding spot okay whereas this fatty acid again not counting our functional group on the end you can see here there's a lot of hydrogens that have been kicked off and we have all of these double bonds between the carbons instead and so this one is saturated this one is unsaturated and in addition to what we can see differently with the chemistry layout they also have different properties because of that so saturated fats are solid at room temperature most of these fats in our diet come from warm blooded animals so like cows you can see all the different dairy products there whereas unsaturated fats are liquid at room temperature and so these are typically the oils so the different plant-based oils and fish oil they they function differently um you know they have different properties at the same temperature which we're going to come back to in membranes it's actually super critical for different organisms that survive in different environmental parameters to still have a functioning membrane and the saturation component is going to play a role in that so our first group of actual polymers are the carbohydrates and so looking at the name here it already gives you a hint in terms of what carbohydrates are made of structurally so carbo of course is carbon and then hydrate is water so if we have c h and o carbon hydrogen and oxygen that is what's going to give us carbohydrates so you'll notice the difference here the lipids that we just looked at are just carbon and hydrogen when we add in oxygen that is our difference between a lipid and a carbohydrate which is like a sugar and so looking at our image here you can see clean up my slide a little bit you can see at first glance this looks a lot like a lipid right there's this chain of carbon in the middle there's some hydrogens there but the key piece that you're looking at to determine if it's a lipid or a carbohydrate is those oxygens and so you'll notice instead of hydrogens everywhere we have hydroxyl groups showing up okay and so that's what tells us this particular guy is a sugar instead of a lipid okay so as i mentioned this is our first group of polymers that we're actually talking about and so reminder that is a lot of smaller compounds all hooked together in a chain to make something much bigger okay so monomer this is the monomer this whole thing would be the polymer okay so for carbohydrates there's actually lots of different monomers that make them up um generally we call them monosaccharides which is just monomer sugars but for the purposes of this class we're just going to learn one monomer which is glucose and then we're going to look at three different polymers of glucose so you can see glucose here a lot of times we just kind of simplify it by drawing it as a six-sided compound because it often will fold up like this and so again this is a great example of glucose is c6h12o6 so six carbons 12 hydrogens six oxygens and it can be linear and everybody's represented there or it can be circular and everyone is present there as well and so most of the time in biological systems we are going to see glucose in its circular form okay one other piece i want to mention while we're on this slide is that as we go throughout the class we're actually going to see several examples of the ending of a name giving us a hint about what it is that we're talking about and so this is our first one when you come across something that ends in oaths so glucose fructose amylose cellulose all sorts of different names they all end in oaths that tells us it is a carbohydrate okay so it's going to be our first hint but of course like almost everything in biology there's always an exception so there are some carbohydrates whose names do not end in oaths and so you can't use that to exclude things from carbohydrates but you can use it to include them in carbohydrates so of glucose we are going to look as i mentioned at three different polymers so glucose is the monomer and then the polymers are the first one is amylose which is commonly known as starch the second one is cellulose which is the compound that makes up wood and paper and fiber in your diet and the last one is glycogen which is the main type of energy source found in animals and so you'll notice already right there glycogen doesn't end in oaths even though it is a carbohydrate always an exception right so we're going to just talk through each one of these guys so starch is the food storage molecule that's made mostly by plants and then consumed by animals and also by plants of course they eat their own food that they make but starch is a chain of glucose and interestingly the thing that defines starch is the type of bond between those individual glucose molecules okay and so you'll notice when we're looking at the glucose here we're going to kind of zoom in just a little bit so this is one glucose right here and you'll notice it has carbon carbon carbon carbon carbon so one two three four five and then here is our sixth one up here okay so even though it's a six-sided ring each one of those six points in that hexagon isn't carbon we do have one that kind of sticks up and i always think of it as like this little flag so we have our glucose molecule and it has this little flag carbon that sticks up like this okay and that's important because the distinction between the different polymers that we're talking about here actually have to do with the bond between the glucose molecules because it changes the positioning of that glucose so here for starch all of the glucose molecules are facing the same direction and so you'll notice carbon facing up carbon facing up and that actually makes it so that we're able to have enzymes that are able to grab hold of it and break it down and so that's what makes this such a great food storage molecule is that because all of the glucose molecules are facing the same way we have enzymes that can access it and use it to extract the energy from in contrast cellulose actually has alternating bonds and so you'll notice here we have actually an alpha bond like we saw on the last page and then we have a beta bond and so now you'll notice here on this glucose molecule the carbon is facing up and then on this next glucose molecule the carbon is facing down so because the glucose molecules alternate one up one down one up one down we start getting interaction between one chain of glucose you know so one polymer there with another chain and we get these hydrogen bonds forming between them and because of that we get chain linked with chain linked to a chain linked to a chain and you end up having the difference between starch which we can access because enzymes can get in there and cellulose which we cannot access because all of these chains are stuck together with hydrogen bonds it's kind of crazy to think about just this little change in position so having one glucose facing up and then one glucose facing down is the difference between potato chips good source of energy maybe not super healthy but good source of energy and wood which is not a good source of energy for biological systems of course there's still tons of energy in there the energy's still present right and we use wood like for example in a campfire and all of that heat is released that is energy but we can't access it as biological organisms because we can't get in here with an enzyme to try to separate those monomers and so just that little change in the positioning of if the glucose is facing all the same direction or not is the difference between starch and cellulose and then our last polymer glycogen is just like starch so you'll notice carbon facing up carbon facing up right and so we still have that alpha bond in between which keeps both of those in the same direction the difference between glycogen and starch though is glycogen is highly branched whereas starch is more linear okay but even though it is highly branched it is still easy to get in there because we don't have all those hydrogen bonds and so the picture shown here is actually liver cells where glycogen has been stained red and so you can see there's a lot of glycogen stored in your liver typically about 24 hours worth of energy supplies for you just in case you don't eat this is why we can go and have three meals a day instead of eating constantly all the time to provide energy for our bodies so we eat starch you know you eat potato chips goes into your body gets broken down into glucose and then that glucose gets taken to your liver and reassembled into glycogen so this is the storage molecule the energy storage molecule we find most commonly in animals um and actually also in fungi so we before we go on to our next polymer group which is the nucleic acids i want to take a little side jaunt here to just do a couple slides on how we actually assemble polymers from those monomers because we're going to see the same kind of chemistry happen for our carbohydrates our nucleic acids and for our proteins so i'm going to just play this little video first and then we'll talk through it a little bit more on the next slide [Music] many important biological molecules are made of repeating subunits called monomers when many monomers join the result is a polymer for example amino acid monomers join to form a protein polymer and glucose monomers combine to form a complex carbohydrate polymer biological polymers formed by dehydration synthesis reactions as you can see here each of the monomers in this reaction has a hydrogen or h and a hydroxyl or oh group in the course of the reaction the hydrogen is removed from one monomer and the hydroxyl group from the other the hydrogen and hydroxyl group combine to form water and a bond links the two monomers hydrolysis is the opposite of a dehydration synthesis reaction during a hydrolysis reaction a polymer is reduced to its monomer subunits by the addition of water in fact the word hydrolysis literally means to break water the hydroxyl group from a water molecule attaches to one monomer and the remaining hydrogen attaches to the other monomer in other words water is used to break the bond holding monomers together let's do a quick recap during dehydration synthesis monomers join to form polymers and water is released the opposite happens during hydrolysis where water is added to the reaction to break a polymer into monomers all right so that's a nice little overview of that so sometimes this kind of trips me up in in my head in terms of remembering these terms correctly and so i always learn the assembly of the polymer as dehydration synthesis and so i'll just kind of add that on there right so dehydration synthesis when we pull the water out it is what is actually then combining the two monomers together with a covalent bond to work on building the polymer so that's what we can kind of see here right we're going to take out an h off of one side and an o h off of the other side that gets pulled out to make h2o and then the remaining bonding sites that were there get connected for the polymer and then same thing for taking it apart we're going to take that h2o and split it into an h let's see down here an h on one side and an o h on the other side to actually break that bond and keep in mind like almost everything that we see in biology this does not happen spontaneously we want the molecules to be able to be controlled by the cell so they're assembled when they're needed and they're disassembled when they're not needed and not just reacting on their own kind of willy-nilly everything that we see going on in the cell for the most part is very highly controlled so that the cell can kind of allocate its energy and resources as needed because keep in mind the cells make up the organism and the organism is surviving and reproducing um to to do its best in terms of living for the next generation and so we see very little spontaneous chemical activity at the cellular level because it is too much of a risk to be that inefficient okay so just another picture kind of showing that so here's zooming in on looking at an actual carbohydrate in this case and you can see the oh on one monomer and the h off of another monomer both being pulled off to form water right that's our dehydration synthesis and that remaining bonding spot is open to then connect those two monomers okay and we do see the same process occur in proteins and nucleic acids as well so that brings us to our next polymer which are nucleic acids and nucleic acid polymers the two examples we're going to look at dna is a polymer and rna is a polymer both of them are built from monomers so put a little m on here the monomer is the nucleotide and a nucleotide has a specific structure it has a phosphate functional group just a reminder that's that phosphorus surrounded by oxygens okay it has a sugar and which sugar it uses actually is slightly different depending on which molecule we're talking about and then it also has a nitrogen containing base up here and so these are also variable depending on which nucleotide we're talking about so each nucleotide has the same basic structure where there's a nitrogen base a sugar and a phosphate but which sugar in which base can be slightly altered and i do just want to point out that there's actually a whole bunch of nucleotides that we're going to talk about in this class and not all of them make polymers and so for this part of this lecture we're going to focus solely on the nucleotides that are used to assemble the polymers dna and rna so as i mentioned one of the areas where we can have differences in the nucleotides is the sugar and this is actually one of the differences we see between the dna and the rna polymers and so the nucleotides in dna only use deoxyribose whereas the nucleotides in rna use ribose as their sugar okay and if we look at the names that's actually what that means so dna is an abbreviation for deoxyribonucleic acid and so that d is telling us which sugar is being used here whereas rna is ribonucleic acid so same thing and you'll notice down here on the ribose there's an o h and there's an o h and in the deoxyribo so d oxy we've actually taken off one of the oxygens so we still have an o h here but here we just have an h because the oxygen has been removed hence the name deoxyribose and the other place where we can have variability is in the nitrogen base and so just a reminder we're only talking about the nucleotides that are actually assembled into polymers at this point in the class we will get back to those other nucleotides a little bit later but in terms of the ones that are able to be built into polymers these are our five nitrogen bases that we find so adenine we abbreviate a guanine we abbreviate g cytosine we abbreviate c thymine abbreviate t and last one uracil we abbreviate u and so we actually find a g c and t are all part of the dna polymer and then when we switch to rna we actually swap out t and substitute it with u so for rna we have a g c and u as the four nitrogen bases present so zooming in on the structure of the polymer you can see that each one of those nucleotides so here's our phosphate sugar and nitrogen base that we know makes up an individual nucleotide and we can actually see that they are covalently bonded to each other between the sugar of one and the phosphate of a next and so they make that chain just like we saw with the dehydration synthesis so in addition to the polymer itself there's also some interesting components that we see in dna and rna based on the function of that polymer so with carbohydrates we talked about that the main function is energy but in the case of nucleic acids it's actually a chemical message that is the instructions of how to build you and so we'll talk about that in the next section of the biochemistry lecture where we're going to look at how do we get the message out of the nucleic acids and into the proteins which actually assembles you and so looking at what we can see here this is a picture of dna of course and we already know that just by seeing that we have a t g and c right so we have t instead of u so we know this is dna and you'll notice that in the dna double helix where two strands interact with each other they actually form these hydrogen bonds in between the nitrogen bases and this is part of how we conserve that message and make sure that it's maintained within the dna so that you're built correctly each time and you'll notice a only binds with t or swaps out with u in rna and g only binds with c and part of the reason why we have that specificity is you'll notice between a and t there are two hydrogen bonds and between g and c there are three hydrogen bonds and so this again kind of comes back to the idea of like you have to line up with the right puzzle piece and so our message doesn't get messed up because a can't accidentally bind with g it has to line up with something that has two hydrogen bonds which is either going to be t in dna or swap out for u in rna and as mentioned that message is critical right this is how to provide the instructions to ultimately make the proteins that create your body overall carry out your reactions make up your structure is how you look et cetera et cetera and so the last piece that's critical in terms of the polymer for both dna and rna is they are directional okay so you have to read it in the correct direction and so we are going to use these numbers and we're not going to spend a lot of time on this but i do want to have it in here as kind of an fyi so we have these numbers which we call 5 prime and 3 prime so that you know which direction it is that we're talking about and so if you're reading the message here make eyes or make brown eyes right if you read it this way it tells you to do that correctly if you read it this way it says say in warb eek am right like that's not gonna give us brown eyes right and so the direction matters and in addition for dna they're actually what we call anti-parallel meaning that if you read the top strand this way it says make brown eyes and if you read the bottom strand this way it says the exact same thing and so yes direction matters but also we have two copies that are in there that are able to provide the information needed and so this is really important when you start doing things in molecular biology is that you have to make sure you're doing it in the correct direction to make sure ultimately you get the correct message conveyed and therefore the correct protein so one other piece because of this bonding so the fact that a always equals t and g always equals c is we can actually make some predictions on the distribution of the these nucleotides within for example dna in this case and so if we have 20 percent c the question is how much a would we have so if we have 20 percent c then we also have to have 20 percent g because we know every single c is perfectly bound to a g okay and so if in the end we want to get 100 percent then we look at how much we've used so far so this is 40 which means we have a remainder of 60 percent and we're going to have to split it perfectly equally between a and t so we take our 60 and we divide it in half and that's going to give 30 for a and 30 for t and so by knowing just one of these concentrations of a nucleotide we're actually able to calculate out all of the rest because again of the idea that a only bonds with t and dna and g only binds with c you will want to make sure you practice this just a little bit because you might see a question like this on the exam so in addition to the differences that we already mentioned including that the sugar used in dna is deoxyribose and the sugar in rna is ribose and then of course a binds to t in dna whereas a binds to u and rna one other difference that we see is that dna is double stranded so you can see it here and rna is actually single stranded and so it is just a temporary copy of the information out of the dna so the dna is long term and of course stored in your nucleus but when we need to get that information out into the cell to be used to build protein we're going to copy that information into a temporary strand of rna which can then leave the nucleus and be used for that purpose so a little bit historical side jaunt here for a few minutes so the structure of dna itself this idea of the double helix and that a binds with t and g binds with c was actually first elucidated by james watson and francis crick in the 50s um they didn't do any of the experimentation themselves but they actually were looking at a whole variety of other types of information and so they knew some things about how things are inherited had some hypotheses about how things were copied um they also knew from someone else's research that a equals t and that g equals c and so they started kind of playing with it chemically well how would a phosphate interact how would these sugars interact how could we get all of these pieces to play a role where it satisfies what we know about the chemistry as well as satisfying what we know about the biology and they were the ones who proposed what we now know as the correct structure for dna and you'll notice they were awarded the nobel prize in 1962 not even 10 years later than they first published their work and so that really speaks to how critical knowing this chemical structure of dna was to the ability of biology to move forward so again here's some of those pieces of information that they used knowing that the bonding is very specific and then also they had access to an image that shows that the dna is symmetrical that it is 3d and symmetrical symmetry and so let's talk about that piece for a minute because it has some historical importance so the x-ray crystallograph which is actually this picture right here um and this type of technique was actually done quite a bit during the mid-1900s this was we were getting a lot of information about the chemical structure of a variety of molecules and so basically what you do is you take a purified version of the whatever the molecule is you're interested in and you hydrate it and then dehydrate it over and over and over again until you get a crystal and if as a kid you ever did one of those crystal growing sets this is kind of the same idea just much more difficult because you have to keep your particular thing that you're interested in pure and so you make the crystal and then you can shine x-rays through it which then give you some type of specific pattern that is reflective of the bonding in that molecule and so the work on dna for this was actually done by rosalind franklin and female scientists in the 1950s would have been a pretty pretty tough road to hoe there so she actually did this work and then it was taken by her supervisor and given to watson and crick without her permission or her knowledge and so like super bad example of sexism um and not giving appropriate credit where credit is due and so there are people in in the scientific community that think that rosalind would have come to the conclusions on her own because she had such a key piece of the the clues that ultimately led to the the idea of dna structure and unfortunately she actually died from ovarian cancer just a few years later super young and nobel prizes are not awarded to people after they have died and so she was not included as a nobel laureate and i think this is just a good reminder of scientists are human too both good and bad right so even though watson and crick are credited with doing these fantastic um you know deductions to come up with a structure of dna which then ushered in the new generation of molecular biology which we have done amazing things with in terms of medicine and our understanding of things like cancer they still did it on not the most ethical terms and in the way that they used someone else's information and were okay with that without giving credit where credit was due and so there's still issues with you know racism and sexism and other types of pieces where not everyone's contributions are considered equally and it's something we have to continue to strive to work for because ultimately our goal is for all ideas to be equally valued at the table so that we can get to full understanding right like the goal is having the correct evidence to draw conclusions accurate conclusions and if we're only using part of the scientific workforce then we may be missing pieces and that harms all of us okay so the last piece that you can see in watson and crick's publication is that they suggested a way that dna could be replicated and it was ultimately found to be correct and that's that it's semi-conservative so what that means is the original dna double helix splits into the two sides and then those two sides are used as templates for the new dna to be matched up with it and again this is a way that the message is able to be conserved okay so just kind of showing that picture again if this was our original template right this was our original dna you can see this enzyme here dna polymerase he's building the polymer he's going to be able to take in those nucleotides and say hey well this next one is a g therefore i have to put in a c up here to bond with that and then this one's an a which means this one has to be a t to bond with that right so again the idea of being able to use that pre-existing template is going to make it less likely that inaccuracies in the message would be put in there so just some fun facts thinking about overall what we're talking about in terms of volume for nucleic acids so e coli has about 46 million base pairs e coli is a common bacteria and a base pair is where one nucleotide is bound to the other one on the other strand right and so we're not counting both strands separately we kind of count them as one humans have 46 chromosomes that translates to about 6 billion base pairs so you can see we have significantly more information to build us which is obvious when you look at our biology right we have a much different level of complexity than an e coli bacteria does and thinking about the information contained in our dna if you typed it out like a textbook it would fill 1200 books and then it gets even crazier because your body can actually copy that in just a few hours with almost no errors so like i can't even type a text without having errors in it let alone textbook upon textbook then just a couple other pieces the amount of information required in dna to code for one protein is about 10 000 base pairs so pretty big instructions for a single protein and then we end up with some of those errors do get through which we call mutations so when the letters get changed in your dna then your instructions are slightly different and overall we end up with about 33 new mutations per generation so that takes us to our last polymer group which is proteins and protein is the polymer and the monomer is the amino acid and so we talked about earlier with the functional group the amino group which you can see here is actually what this compound is named for and so every single amino acid has the amino group it has this central carbon here and then it also has this carboxyl group over here and so those two key functional groups are there and they're actually how the amino acids get attached to each other again using the dehydration synthesis like we already talked about but the piece that actually gives us distinctive amino acids and there are about 20 of them is this variable group so it's this fourth thing connected to that central carbon and sometimes it's called the r group or the variable group it kind of depends on which textbook you're looking at and so we'll use both of those terms and this is just showing the different amino acids so again there's 20 um and i i should say about 20 because again just like we talked about with elements there is a little bit of variation when we look across life as a whole but there are ones that have things that make them easy to dissolve in water there are some that have specific charges on them either positive or negative charges and then there are also some that are actually more hydrophobic and we can see that here right when you have this whole pile of carbon and hydrogen that kind of reminds us of a lipid and so it actually behaves similar to a lipid and is slightly hydrophobic so just like the other polymers we've seen we're going to assemble those monomers using dehydration synthesis and so we're going to take out the h and the o-h forming water leaving what was a previously bonded site now as open for them to be able to connect the amino acids together and i do want you to notice that variable group is not involved in this part right so this is the amino group of one bonding to the carboxyl group of the next and all of those variable groups continue to stick out from the sides and that's going to become very important as we look at how the chemistry of a protein influences its function so before we go into the actual shape of the protein which i just mentioned is key in terms of its ability to function i want to play this video for you which is a really good overview it's going to walk you through kind of the distinctions of the amino acids as well as how they get assembled and how the folding happens this is just one of those things that the terms that describe it aren't usually very easy to understand and so being able to visualize it i think really helps so let's go ahead and do this video and then we will continue on with our protein polymers proteins play countless roles throughout the biological world some transport nutrients throughout the body some help chemical reactions to happen at faster rates others build the structures that make up living things despite this wide range of functions all proteins are made out of the same 21 building blocks called amino acids amino acids are made of carbon oxygen nitrogen and hydrogen atoms and some contain sulfur atoms selenocystine is the only standard amino acid that contains a selenium atom these atoms form an amino group a carboxyl group and a side chain all attached to a central carbon atom the side chain determines an amino acids properties and is the only part that varies from amino acid to amino acid hydrophobic amino acids have carbon rich side chains which don't interact well with water hydrophilic or polar amino acids interact well with water charged amino acids interact with oppositely charged amino acids or with other molecules primary structure the primary structure of a protein is the linear sequence of amino acids as included by dna the amino acids in a protein are joined by peptide bonds which link the amino group of one amino acid to the carboxyl group of another a water molecule is released each time a peptide bond is formed this linked series of carbon nitrogen and oxygen atoms is the protein backbone protein chains often fold into two types of secondary structures alpha helices and beta sheets an alpha helix is a right-handed coil stabilized by hydrogen bonds between the amine and carboxyl groups of nearby amino acids beta sheets are formed when hydrogen bonds stabilize two or more adjacent strands of amino acids the tertiary structure of a protein is the three-dimensional shape of the protein chain this shape is determined by the characteristics of the amino acids making up the chain many proteins form globular shapes with hydrophobic side chains sheltered on the inside away from surrounding water molecules membrane-bound proteins have hydrophobic amino acids clustered together on their exteriors so that hydrophobic side chains can interact with the lipids in the membrane charged amino acids allow proteins to interact with molecules that have complementary charges the functions of many proteins rely upon their three-dimensional shapes for example hemoglobin forms a pocket to hold heme a small molecule with an iron atom in the center that binds to oxygen quaternary structure two or more polypeptide chains can come together to form one functional molecule with several subunits the four subunits of hemoglobin cooperate so the complex can more easily pick up oxygen in the lungs and release it in the body different visual representations of proteins can give us visual clues about protein structure and function this space filling diagram shows all of the atoms that make up this protein this representation called a ribbon or cartoon diagram shows the organization of the protein backbone and highlights alpha helices this surface representation shows the areas of the protein that are accessible to water molecules most proteins are smaller than the wavelength of light for example the hemoglobin molecule is about 6.5 nanometers in size hemoglobin is found in high concentration in red blood cells a typical red blood cell contains about 280 million hemoglobin molecules the three-dimensional shapes of proteins determine their function the flexible arms of antibodies protect us from disease by recognizing and binding to pathogens and targeting them for destruction by the immune system the hormone insulin is a small stable protein that can easily maintain its shape while traveling through the blood to regulate blood glucose levels alpha amylase is an enzyme that begins digestion of starches in our saliva the calcium pump is aided by magnesium and powered by atp to move calcium ions back to the sarcoplasmic reticulum after each muscle contraction ferritin is a spherical protein with channels that allow iron atoms to enter and exit depending upon an organism the needs on the inside ferritin forms a hollow space with iron atoms attached to the inner wall ferritin stores iron in a non-toxic form collagen forms a strong triple helix that is used throughout the body for structural support collagen molecules can form elongated fibrils which aggregate to form collagen fibers this type of collagen is abundant in skin and tendons learn more about the functions and 3d structures of proteins and other molecular machines at the rcsb protein databank okay so that gives us a good overview of the different levels of structure i apologize for the white noise you can see my computer was struggling with recording a video of a video um of an embedded video so it's running its fan and trying to do its thing but i think you can still get the gist of it there so as discussed in the video protein shape equals function and we will talk about this over and over in this class so just map this into your head shape equals function when we're talking about proteins and so again as was mentioned there the primary shape is just that chain of amino acids we can get some secondary shape from hydrogen bonding but the tertiary shape is really where we get that unique folding that occurs with each different protein that translates to its individual function so now looking at that visually we can see here is our tertiary i'm sorry our primary structure there's our chain of amino acids here's our secondary structure where we see the beta sheets and alpha helices and then here is that tertiary structure where we have that very unique folding where it's going to create the appropriate shape to do what it needs to do and this particular image that i'm showing you here is hemoglobin like they talked about several times in the video and it does have quaternary structure because it has four subunits that all come together to ultimately be functional not all proteins have that some of them will stop at the tertiary structure piece and so this is just kind of zooming in showing some of those interactions that we see with the tertiary structure so even though we do have hydrogen bonds in the secondary we can also have them in the tertiary so you could have something you know over here on one side say amino acid number 10 interacting with amino acid 31 over here and their side chains have a hydrogen bond or those side chains can have hydrophobic interactions especially when they are all carbon and hydrogen just like lipids that we've talked about before we can also have ionic bonds where we have two different charges being attracted to each other and then here's that one spot where we see that sulfhydryl functional group um the two sh's actually kick off both of you know we had an h here and had an h here and they're going to kick off both of those and bond with each other and this is actually the only covalent interaction that we see in terms of protein folding so it plays a really critical role and of course if we lose that shape then we can also lose function and so this is interesting to think about because if you unfold so this was our nice 3d you know has its tertiary structure therefore has its function and if it gets unwound into just having primary structure all of the amino acids are still there but it's kind of like having a car that you've taken apart into all its individual pieces you still have a car but it no longer works because it's not assembled correctly and so really anything that could interfere with how those side chains are interacting with each other so especially changes in ph which are going to provide different ions so those can mess with bonds same with salt and then temperature which is just an addition of energy can also mess with bonds so anything that's going to be breaking those bonds between those r groups has the potential to unwind the protein and when it gets unwound and loses its shape we call that denaturation or a protein becoming denatured and so we actually do this intentionally in our food so we take eggs in the morning for breakfast right and we have our egg and it has all of the chicken proteins in it you know to be able to build the chicken but we don't need those proteins to work right we don't need to build a chicken inside of us and so we actually apply a temperature we heat up that egg and it goes from being liquid to being solid because each of those little individual proteins is going to denature and when they denature the side chains are still there they just no longer have the correct shape individually so they start sticking to each other and so we end up getting instead of all these little individual proteins floating around in liquid we get this gigantic lump of protein because all of those individual proteins are now stuck together but again this is fine for us as humans because we don't need those proteins to be functional we're now going to eat that egg chop this whole thing up into in individual amino acids via digestion and then reassemble them into human proteins so they can do human jobs for us so not good for the chicken but perfectly fine for us but we don't want something like say for example heat stroke to denature our own proteins then we could have some damage okay so overall as i've mentioned a couple times proteins do almost all the jobs in our body just like we saw in the video as well and so the instructions are in our nucleic acids to build the proteins to do the jobs to make us be able to function and survive in our environment so we're going to actually end part one of biochemistry here and then there will be a separate lecture for you to watch to actually work your way through protein synthesis where we're going to look at how we use the information in dna to actually get the protein built so i will talk to you in that one