Nucleic acids – DNA and RNA structure
In this video we will study about nucleic acids. Nucleic acids are basically biopolymers, which are made of monomeric units known as nuclotides. We have two important functions for nucleic acids, that is, they hold our genetic information and they perform a variety of other functions that we will discuss later. We have two important types of nucleic acids in our body, the DNA and the RNA. Let’s first try to understand the definition of nucleic acids. So, nucleic acids are biopolymers. “Bio” means that they are synthesized inside biological systems, and they are not synthetically synthesized. They are polymers, which means they are made of repeated units called monomers, which in this case are nucleotides. Now take this example. We have many different types of biopolymers in our body; one of them are the proteins. And most of you know that the proteins are made up of repeated units called amino acids. Similarly, nucleic acids are also important biopolymers in our body. Which are made up of repeated units which are known as nucleotides. The next important thing is to understand the basic structure of a nucleotide, which will help us understand the structure of nucleic acids in detail. Now, this is a simple diagram explaining the structure of a nucleotide. As you can see, the single nucleotide is made up of three important groups: The phosphate, the sugar, and the nitrogenous base, and these groups are attached to one another by bonds, which we will discuss later. To understand the complete structure of a nucleotide, let’s try to understand the structure of these groups one by one. The first is the sugar. The sugar present inside the nucleic acids are five carbon sugars. Now most of you know the sixth carbon sugar present inside the body, and most important of them is the glucose. In chemical nomenclature, all six carbon sugars are called hexoses, the word “hex” meaning “six.” There are different types of hexoses in our body other than glucose like the mannose and galactose Similarly, five carbon sugars are called pentoses, the word “pent” meaning “five.” There are different types of pentoses in our body, but the two important types of pentoses that are present in the nucleic acids are the ribose, and the deoxyribose. but this is a simplified structure of the sugar present inside the nucleotide. Now is you compare this structure with the chemical structure of the ribose and deoxyribose on the right, you can see the structure clearly. We have carbon atoms on each of these corners. Note that the last carbon atom is located outside the ring. We have an oxygen atom at the center topmost position. You can also see in this chemical structure that the carbon atoms are named from one to five in a clockwise direction. So the carbon atom next to the right of the oxygen is called C1, so C2, C3, C4 and C5 C5 is located outside the ring. You can also see in this chemical structure we have different types of functional groups attached to these carbon atoms like the hydroxyl group and the hydrogen atom. The most important of these functional groups, which determine whether the sugar is ribose or deoxyribose are present at the carbon number 2 and the carbon number 3. In the sugar ribose, we have a hydroxyl group that is attached to the carbon number 2. This is the chemical structure of ribose Now, if you compare this structure with the structure of deoxyribose, the only major difference is at carbon number 2 the carbon number 2 contains only a hydrogen atom, and not the hydroxyl group so the resulting sugar is called a deoxyribose. Here, you can see the carbon number 2 in deoxyribose contains only a hydrogen atom, whereas in ribose the carbon number 2 contains a hydroxyl group. You can also tell this by the difference in their names, that the deoxyribose has a prefix “deoxy,” which means the removal of oxygen. The resulting sugar, the deoxyribose, is more stable as compared to ribose because of one less functional group. The deoxyribose is present in DNA and ribose is present in RNA. You can also remember by the starting of DNA which starts with D, so the “deoxyribose” and the RNA which starts with R, so the sugar is the ribose. The next important group we’re studying for the structure of nucleotides is the phosphate group which is this little detail here. The phosphare group consists of a phosphorus atom in the center, to which four oxygen atoms are attached, which are negatively charged. The phosphate group is the same phosphate group which is present in the adenosine triphosphate, the energy-carrying molecule of the body. However, in ATP we have three molecules of phosphate, which are attached to one another by high-energy phospho-ester bonds. The phosphate group is a polar molecule due to the presence of highly ionized oxygen atoms, which impart negative charge to the phosphate group. Now, the third important structure present in the structure of a nucleotide is the nitrogenous base. Nitrogenous bases are basically molecules that contain nitrogen in varying amounts, and they act as a base. Most of you know that the human body contains organic chemicals, which have carbon, hydrogen and oxygen in varying amounts. In nitrogenous bases, nitrogen combines with all of these atoms to form ring-like structures. These molecules are called bases since they can donate electrons to other molecules and form new molecules in this process. The nitrogen combines with all of these other atoms to form ring structures. Now, we can have two different types of ring structures. One where there are single rings, and second, where there are double rings. The single rings are called pyramidines. And the double rings are called purines. We have three different types of pyramidines: the thymine, cytosine, and the uricil. And we have two different types of purines, called adenine, and guanine. In the center you can see the chemical structure of each of these bases. As you can see, the purines, which are the double-ring structures, adenine and guanine. Due to the presence of double rings, these purines are larger as compared to the pyramidines. The thymine, cytosine and uracil all are single-ring structures, and they are smaller as compared to the purines. The difference in the size of these bases is very important, as it helps to bear these bases in the structure of DNA properly, which we’ll study later. So now you know the individual structures which are present in a single nucleotide. Next we will look at how these individual structures bond to each other to form a single nucleotide, and then we will look at how many nucleotides bind to each other to form a chain of nucleotides, which is called a polynucleotide, which can be either DNA or RNA. So, if we take a sugar and name just the important carbons here, which will be carbon number 1 and carbon number 5 and of course you can see that at the carbon number 2 there is only a single hydrogen atom so this sugar will be a deoxyribose. To pair this deoxyribose sugar with this pyramidine ring, the bond formed will be between the N1 of the pyramidine ring and the C1 of the sugar. If you want to go into the details about how these nitrogens are named, you can check the link in the description below for IUPAC nomenclature for the aromatic compounds. Now this bond will be an example of a glycosidic bond, which is a covalent bond which links carbohydrates with other structures. If we have to pair a purine ring at a similar position, the bond formed will be between the N9 of the purine ring. Next, let’s attach the phosphate. The phosphate group attaches with the carbon number 5 of the sugar, and the bond formed is the example of the ester bond which is also a strong covalent bond. So now you know how the three structures in a single nucleotide bind to each other to form one nucleotide. Next, we look at how many nucleotides bind to each other to form a chain of nucleotides called a polynucleotide. You can see basically what happens is that the phosphate group that attaches to the carbon number 5 of the sugar below also forms a bond with the carbon number 3 of the sugar above, and this pattern is repeated again and again. So you can see that the phosphate groups form bonds both above and below the chain of these nucleotides. As a result, a long chain of nucleotides is formed which consists of a sugar-phosphate backbone and in the center we have all these nitrogenous bases, which project from the sugar-phosphate backbone. Now this can be an example of RNA if the sugar present in this example will be a ribose sugar. But if you take a similar strand of polynucleotides and run it in opposite direction then this strand binds with the original strand through hydrogen bonds. Now here comes the rule of complementary base pairing. What complimentary base pairing says is that only adenine forms a hydrogen bond with thymine, and only guanine forms a hydrogen bond with cytosine. This is a universal rule that is applied in the structure of DNA. Here you can see adenine forms a hydrogen bond with thymine, and similarly thymine forms a hydrogen bond with only adenine. In similar case, guanine forms a hydrogen bond with cytosine and vice versa. This is the basic structure of DNA and you can compare this with a step ladder structure of DNA. You can see that the supports of the ladder in red are basically representing the sugar-phosphate backbone and the rungs of the ladder represent the nitrogenous bases that are forming hydrogen bonds with each other. Of course, the original structure of DNA is that of a double helix, so you you can compare the structure with a double helix, where the helices of the structure represent the sugar-phosphate backbone, and in the center you can see the red lines which represent the different nitrogenous bases that are forming bonds with each other. So this was an introductory video explaining the structure of nucleic acids. In subsequent videos, we will study in detail the structure of DNA, the structure of RNA, DNA replication, transcription, translation, and many other topics. 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