Chemical Constitution of Nucleic Acids

Transcript

0:00Introduction

Hello everyone! Let us start with a small puzzle. The DNA in your cells carries heredity, and RNA helps to make proteins. Both are very long chains. But break either one down completely, and you get only three kinds of simple pieces: a sugar, phosphoric acid, and a few bases. And the sugars of the two differ by just one oxygen atom. So how do such simple pieces build such long chains, and which oxygen is missing? By the end, you will answer both. Nucleic acids are a part of JEE chemistry, so let's begin.

0:37Nucleic acids are polynucleotides

So, look at the figure. On its left is one nucleotide: the circle marked P is a phosphate group, the pentagon is a sugar, and the box is a base. The small numbers with a dash, like five prime, number the carbons of the sugar, and we will come to them soon. Nucleic acids are long-chain polymers of nucleotides, like the chain on the right of the figure. That is why the heading calls them polynucleotides. Okay? Now let me ask you this. If we hydrolyse this chain completely, what simple pieces come out? The figure gives you a big hint. Yes, exactly, the parts of each nucleotide. Complete hydrolysis gives a pentose sugar, which means a sugar with five carbon atoms. Right? It also gives phosphoric acid, from the phosphate groups, and the bases, which contain nitrogen. These are the three pieces from our puzzle. With me?

1:31The sugar: ribose or 2-deoxyribose

Now, the sugar. In RNA, it is beta D ribose. Beta, the Greek letter on screen, and the capital D describe the exact form of this sugar. Its formula is C five H ten O five, where the small numbers are subscripts. Clear? In DNA, the sugar has a longer name, two deoxyribose. Deoxy means without an oxygen. So tell me, what is this sugar missing? It is missing one oxygen atom, that is correct. DNA has beta D two deoxyribose, C five H ten O four: the same formula as ribose, with one oxygen fewer. Right? And where is it missing? Look at C two prime, carbon two prime of the sugar. Ribose has an O H group on carbon two prime, but deoxyribose has just a hydrogen in its place, and that is the missing oxygen from our puzzle! And both sugars are in the furanose form, which the brackets tell you is a five-membered ring. Got it?

2:29The bases: nitrogen-containing heterocycles

Next, the bases. As the heading says, they are heterocycles: their rings contain nitrogen atoms as well as carbon. And they come in two families. The purines have two fused rings, two rings sharing one side. There are two of them, adenine and guanine, and the capital letter in brackets is the short name of each. Okay? The pyrimidines have just one ring: cytosine, thymine and uracil. Here is a trick to keep them apart. Purine is the shorter name, but the bigger base, with two rings. And the three pyrimidines, C, T and U, rearrange to spell the word cut. With me? Now, there are five bases, but each nucleic acid uses only four of them. So which base is found in DNA, but not in RNA? The answer is thymine, very good. DNA has adenine, guanine, cytosine and thymine, while RNA has adenine, guanine, cytosine and uracil. So in the bases, the only difference is that DNA has thymine where RNA has uracil. Clear? And thymine is very close to uracil. It is five methyluracil, which means uracil with a methyl group on carbon five. Notice that there is no prime here, because this carbon five belongs to the base, not to the sugar. Right?

3:51Nucleoside and nucleotide

Now, back to the figure, to the single unit on its left. The base joined to the sugar is called a nucleoside, and the shorter curly brace under them marks it. So, nucleoside equals base plus sugar. Got it? Where do they join? From carbon one prime of the sugar, the one prime label in the figure, to a nitrogen atom in the ring of the base. Because the bond goes to a nitrogen, it is called an N-glycosidic bond. With me? Now add the phosphate group, the circle marked P, to this nucleoside. Is the whole unit still a nucleoside, or something else? It is a nucleotide, and the longer brace covers all three parts. Nucleotide equals nucleoside plus phosphate, with the phosphate on carbon five prime. Students often swap these two words, but the nucleotide is the one carrying the phosphate. Okay?

4:43Phosphodiester linkages make the chain

So how do nucleotides join into a chain? Look at the right side of the figure. Each phosphate in the middle links two sugars, from carbon three prime of one sugar to carbon five prime of the next. This is called a phosphodiester linkage, as the heading says. Right? Now think. When two nucleotides join like this, what small molecule is given off? Yes, it is water, exactly. One water molecule is lost at each linkage, and remember this, because example two needs it. Clear? Now see the two ends of the chain in the figure, the five prime end at the top and the three prime end at the bottom. Reading from the five prime end, the bases here are adenine, guanine and cytosine. This order of bases along the chain is called the primary structure. Got it?

5:33DNA versus RNA: strands, place and job

Now the remaining differences, in strands, place and job. DNA is a double helix, found mainly in the nucleus. It carries heredity, and it can replicate, that is, make copies of itself. Okay? RNA is a single strand, found mainly in the cytoplasm, and its job is protein synthesis. So two strands against one, and nucleus against cytoplasm. Clear?

5:57Example 1: the three products of complete hydrolysis of DNA

Time for example one, an easy one. What are the three products of complete hydrolysis of DNA? Pause the video and try it first. Done? Okay, let's check. It is DNA, so the sugar is two deoxyribose, and not ribose; that is the first trap. The second product is phosphoric acid. Right? And the third is the bases: adenine, guanine, cytosine and thymine. If you wrote uracil, be careful, because uracil belongs to RNA, and DNA has thymine instead. Got it?

6:34Example 2: linkages and water in a 100-nucleotide strand

Now a harder one. How many phosphodiester linkages are there in a single strand of one hundred nucleotides? And how many molecules of water are needed to hydrolyse it to nucleotides? Pause the video and try it first. Done? Okay, let's check. One hundred nucleotides, so one hundred linkages, right? Wait, that is exactly the trap, so let us try small cases first. Two nucleotides need only one linkage between them, and three nucleotides need two linkages. Okay? So the linkages are always one fewer than the nucleotides. One hundred minus one gives ninety nine phosphodiester linkages. Right? And for the water, remember that one water molecule was lost at each linkage. So hydrolysis needs one molecule of water, H two O, to break each linkage, and that is ninety nine water molecules. So the answers are ninety nine and ninety nine. See how the small cases saved us?

7:37Quick revision: nucleoside, nucleotide, DNA vs RNA, linkage

So, quick revision. Nucleoside is base plus sugar, joined at carbon one prime, and a nucleotide adds the phosphate at carbon five prime. DNA has two deoxyribose with adenine, guanine, cytosine and thymine, while RNA has ribose with adenine, guanine, cytosine and uracil. And phosphodiester linkages join carbon three prime to carbon five prime, with one water lost at each. Now go and try the practice problems on this page. All the best!