welcome back to our last video for chapter 3 material and we're going to be wrapping up chapter 3 by looking at nucleic acids so nucleic acids are our final type of biological macromolecule we've gone over carbohydrates lipids proteins and again this one is our last one nucleic acids so why are nucleic acids important this is because they make up the genetic material of all living organisms and we've got two types deoxyribonucleic acid or DNA or ribonucleic acid which is RNA these are found in the nucleus of eukaryotic cells we find them in mitochondria and chloroplasts of eukaryotic cells as well prokaryotic cells do not have a nucleus so we will just see them in the cytoplasm in the center or in the middle of the cell somewhere all of the DNA in your cell is known as the Genome of your cell and DNA is very long and it's like a string like substance it reminds me of like the back of my TV or where our computers are where there are a bunch of different chords charger cords computer chords Etc imagine you have all the string and you need to organize it DNA in our cells are organized by wrapping the DNA around proteins called histone proteins and this is true and again eukaryotic organisms like us prokaryotes don't have histone proteins but they do have similar similar proteins that they use to organize their DNA DNA complex with histone proteins together is known as chromatin and chromatin is further condensed to pack it tightly within the cell or the nucleus into structures we call chromosomes now there are thousands of genes in our DNA and genes are what contain the instructions for building proteins or other types of molecules like RNA in our cell the DNA really controls all of the activities inside of the cell and it does so by turning genes on and off RNA on the other hand is mainly involved in the synthesis of proteins and there are three types of RNA that are involved in the synthesis of proteins the first one is messenger RNA also known as mRNA and this is really like an intermediate nucleic acid I say intermediate because we start with DNA DNA will go through a process called transcription in order to produce mRNA and mRNA usually leaves the nucleus in eukaryotes in order to go through further changes to produce our eventual polypeptide and protein Transfer RNA or TRNA is also involved in this process of translation which serves as a bridge between nucleotides and the final amino acid chain and then finally ribosomal RNA is involved in protein synthesis as it is going to be part of a structure involved in translation so looking back when we were talking about carbohydrates monosaccharides or the monomers of carbs proteins were made of amino acids and now looking at nucleic acids the monomers of DNA and RNA are nucleotides and nucleotides are made of three different parts here's one nucleotide over here the first part is the nitrogenous base then we have our pentose sugar and we have one or more phosphate groups attached to the sugar looking more closely at the nitrogenous base which is an organic molecule with Chon remember carbon hydrogen oxygen and nitrogen we can divide these into two groups one group is known as the pyrimidines and these are shown up here these are single ring bases that include cytosine thymine and uracil which differ in their functional groups and then the other are two ring bases known as purines these include adenine and guanine and one of my former instructors taught me this a long time ago that to remember these two groups we could remember pyrimidines kind of sounds like pyramids like a pyramid shown here pyramids are kind of sharp at the edges or the points I should say so you can think pyramids cut cytosine uracil and thymine purines they taught us pure silver the atomic symbol for silver is a g so you can remember that as pure pure silver and then when I'm looking at the sugars the purple part here the type of sugar you have in your nucleotide really depends on if you're looking at DNA or RNA so DNA you'll have deoxyribose as your pentose sugar and RNA you'll have ribose as your pentose sugar and just as I asked you to be able to draw a generic amino acid when we were talking about proteins you should also be able to sketch a generic nucleotide for something like one of our tests so if I wanted to start drawing one I almost always start by drawing my pentose sugar and I'm going to make it generic I'm not going to label anything these are supposed to be straight lines sorry shaky hands so that's my pentose sugar I know I have a base a nitrogenous base I'm just going to write base that's my nitrogenous base and I know that can be a c t or G or even U if I'm looking at RNA and then I know that I have a phosphate group attached to the sugar for the sugar I know from chemistry that the points at the edges over here these represent carbon atoms and this is carbon number one this is number two three four and five and we actually say one prime that little apostrophe stands for prime one prime two prime three prime four Prime carbon five Prime to differentiate it from the carbons that are found in the nitrogenous bases so there there we have a generic structure of the nucleotide all right so what are some differences between DNA and RNA besides that ribose sugar usually DNA is double stranded and we'll see something called a double helix and usually RNA is single stranded although there are exceptions in viruses and there are some viruses that have single stranded DNA and double-stranded RNA there are also some exceptions in our own cells where the RNA structure is not double stranded but parts of it will fold up on itself and hydrogen bond with itself all right we said there were differences in the Pento sugar DNA has deoxyribose whereas RNA had ribose what's the difference in the sugar if I look at these two it really lies in carbon number two so if I look at what's attached to carbon number two in DNA it's a hydrogen atom whereas an RNA it's a hydroxyl group and this actually makes RNA less stable because hydroxyl groups are more reactive more reactive meaning less stable compared to DNA if I look at the nitrogenous bases there are also differences here in DNA we have adenine thymine guanine and cytosine whereas in RNA there is no thymine instead we'll find uracil last note here it's not really a difference but whenever you're building a polynucleotide using these nucleotide monomers you're going to be adding nucleotides to the growing Chain by adding on to the three prime end of the pentose sugar over here so if I wanted to add another nucleotide and build I would add here and then add another one and add another one always continuing the growth at the three prime end you cannot add to the five Prime carbon because it's already attached to a phosphate group you're not going to knock that off to add something so again we're only going to add to the three prime end so let's say we have our typical structure of DNA which is in its double stranded or double helix structure usually what this looks like is a twisted ladder if I have a ladder here with the rungs over here if you could twist it if I could make this an animation and I twisted it I would see the double helix the backbone are the sides of the ladder and I'll make them dark red here that's known as the backbone and I see them here in greenish blue that zigzag over here and then also an orangish red color and the backbone is comprised of the sugar and phosphate components of the nucleotide the nitrogenous bases on the other hand are in the middle they represent the rungs of the ladder so this is where you see the atg and C of DNA it's also interesting to note that the backbone when we're looking at the strands of DNA the double strands they are anti-parallel they run in opposite directions so what this means is one strand will run from five Prime to three prime whereas the other strand will face the opposite direction 5 Prime to three prime so you can see these are opposites they're not facing in the same direction and again that's called anti-parallel and the reason that DNA can can be double-stranded is because the nitrogenous bases that form the rungs of the ladder here are going to be hydrogen bonding to the base on the opposite side or the opposite strand and here's another look at that base pairing of these nitrogenous bases so if I'm looking at a partial segment of double-stranded DNA here the sides are the backbone the sides of the ladder that we just saw earlier and I can see it's made of phosphate and that sugar phosphate pentose sugar phosphate pentose sugar Etc and here are my bases thymine adenine guanine cytosine and I can see that the base pairing is through the formation hydrogen bonds here our our labels are found five Prime to three prime three prime to five Prime so I can see that they're running anti-parallel to each other for the two strands and if I look carefully at what bases pair with each other a always pairs with t and G always pairs with C or you could say it the other way you could say t pairs with A and C pairs with G the number of hydrogen bonds is also indicated in this picture and also I try to do that in the parentheses here there are always three hydrogen bonds between G's and C's and two hydrogen bonds between A's and T's and because of this if you have DNA and it has a greater percentage of G's and C's compared to A's and T's that would actually make it a little bit more stable because of the greater number of hydrogen bonds so if we understand the base pairing rules in DNA if we have only one strand of DNA such as the one given here we can create the second strand we'll know what the other side is going to be and earlier I mentioned we always grow build DNA build polynucleotides by adding to the three prime n so I'm actually going to start on the right side I'm going to start with a fry Prime end where the phosphate group is and I'm going to build from there so I know C always pairs with G so that's going to be a g here that's going to be c c g a always pairs with t this is going to be a a and t and this will be my three prime end additionally if you understand the base pairing rules that can give you a heads up as to the composition of DNA if you're given the percentage of one nucleotide type so if I know a double-stranded DNA molecule is comprised of or composed of 30 cytosine bases then I know C always pairs with G so G must also be 30 percent and that adds up to 60 percent I know there's 40 percent left and I know the percentages A's of A's and T's has to be the same so that must be 20 percent and that must also be 20 percent there are actually four types of RNA and earlier we talked about the first three messenger RNA ribosomal RNA and transfer RNA and their involvement in protein synthesis there's actually one more type called micro RNA which we'll talk about more later on in the course these are the smallest RNA molecules and they're going to be involved in the control of gene expression whether DNA is allowed to be read and eventually produce proteins or not so how do we get from DNA to protein the first part is or I should say the first step is transcription you read DNA and you make messenger RNA just like the double-stranded DNA that we saw earlier where if you're given one strand you can figure out the sequence of the second strand the same is true in your synthesizing messenger RNA except remember in RNA instead of thymine we have uracil so if you read a and you would otherwise pair it with T through base pairing rules instead of thymine you would put down a uracil so what do I mean by this let's say I want to go through the process of transcription right here and I'm given my DNA sequence one strand of my DNA how do I figure out what my mRNA molecule is going to be and sometimes we call it a transcript which is your product of transcription so just like before we can only build from adding nucleotides to the three prime end so I'm going to start with a five print end here and this is my messenger RNA so if I read cytosine I know it's going to pair with guanine and vice versa here's guanine G pairs with C T pairs with a T pairs with a a pairs with t but wait I'm looking at RNA so a here I'm going to put U uracil instead of thymine and then my three prime end here so what happens after we make our messenger RNA The Next Step involves the process of translation and we're going to see it's a multi-step process and I'm going to show you a picture that summarizes the phrases here so we have our messenger RNA and the next thing we want to do is start building our polypeptide chain made of amino acid monomers how do we do that a large protein structure called a ribosome is going to come into play and ribosomes actually have two subunits a larger subunit and a smaller subunit and both pieces are made of ribosomal RNA plus proteins so what will happen is our messenger RNA sits between the two subunits of the ribosome and we're going to have our again this is our messenger RNA we're going to have tRNA molecules come in and tRNA molecules are going to recognize three bases on the messenger RNA that are clustered together into something known as a codon so three letters on the MRNA such as ccg or Aug when they come together these are called codons and each of these is equivalent to something called or it's going to be equivalent to or encode an amino acid and they each encode usually unique amino acids the TRNA is able to bind to the three-letter codon on messenger RNA because it's going to have a complementary set of nucleotides on one end of the TRNA molecule on the other side of the TRNA molecule the transfer RNA molecule you'll see the amino acid that corresponds to the codon and we're going to see this in a lot more detail in a future future lecture our book provides us a nice little table to summarize some of the key differences between DNA and RNA so we know DNA carries our genetic information it contains the instructions to produce all of the proteins and some of the other molecules like RNA in our body or in cells whereas RNA is primarily involved in protein synthesis where do we find these DNA is in the nucleus of eukaryotes it's going to be in the cytoplasm of prokaryotes and RNA is able to leave the nucleus in eukaryotes DNA is usually double-stranded in that form of the double helix RNA is usually single stranded although we said there are some exceptions in viruses the sugar in DNA is deoxyribose and RNA it's ribose they're pyrimidines we see are cytosine and thymine and DNA whereas we have uracil and RNA and the purines are the same in both and I just wanted to make a note that even though RNA is usually single stranded with exceptions that I mentioned earlier in viruses there are many RNA molecules that actually will form three-dimensional structures even are in our own cells and this is formed by hydrogen bonding with itself folding up upon itself to form some kind of three-dimensional structure that is critical to their function inside of our cells looking at DNA and RNA and we briefly talked about how these are involved in protein synthesis this picture shown here the process of going from DNA to RNA through transcription and going from RNA to protein through translation is known as the central dogma of molecular biology or sometimes the central dogma of life DNA can make copies of itself as well through a process of replication but this part how we produce proteins is really the central dogma and it was first stated or articulated by Francis Crick there are some developments in biology you could say discoveries in biology over the last four decades that has China slightly changed our our view of this so we used to think that it's not possible to go backwards right but now we know that there are some viruses such as human immunodeficiency virus HIV the virus that causes AIDS that are in a group called retro viruses interestingly these retroviruses contain an enzyme called reverse reverse transcript ASE reverse transcriptase all abbreviated RT for short it does what it sounds like the reverse of transcription so these viruses they have this enzyme and they can take RNA and go backwards turn RNA into DNA and that's actually what HIV does if it infects human cells it injects its RNA uses its own reverse transcriptase to read RNA and convert it into DNA and that DNA will insert itself into our own DNA and hide itself there we can also use reverse transcriptase in the lab on purpose when we want to clone or copy DNA and we'll see how to do this at the end of the semester as well all right that takes us to the end of the fifth and last video for chapter three next time we'll start chapter 4 which looks at the cell the smallest unit of life and this will include both prokaryotic and eukaryotic cells all right thanks so much for listening and I'll see you next time