TRANSCRIPTION - FROM DNA TO RNAThis page takes a simple look at the structure of RNA and howthe information in DNA is used to make messenger RNA. It isdesigned for 16 - 18 year old chemistry students, and if you aredoing biology or biochemistry, you will probably need more detailthan this page gives.Note: If you have come straight to this page from a searchengine), you should be aware that this is the third page in asequence of pages about DNA. These pages are written tobe read one after the other, so unless you already understandthe structure of DNA, follow this link to start from thebeginning.The structure of RNAThe function of messenger RNA in the cellYou will probably know that the sequence of bases in DNAcarries the genetic code. Scattered along the DNA molecule areparticularly important sequences of bases known as genes.Each gene is a coded description for making a particular protein.Note: It would be more accurate to say that each genecoded for a particular polypeptide, because some proteinsare made of more than one polypeptide chain. For simplicity,I'm going to refer from now on to the synthesis of a protein,rather than a polypeptide - it sounds less scary!To be really accurate, some genes code for other sorts ofmolecule apart from proteins, but we are only going to belooking at the genes involved in protein synthesis.Getting from the code in DNA to the final protein is a verycomplicated process.The code is first transcribed ("copied", although with oneimportant difference - see later) to messenger RNA. That thentravels out of the nucleus of the cell (where the DNA is found)into the cytoplasm of the cell. The cytoplasm contains essentiallyeverything else in the cell apart from the nucleus. Here the codeis read and the protein is synthesised with the help of two otherforms of RNA - ribosomal RNA and transfer RNA. We'll talk a lotmore about those in a later page.I'm going to take this complicated process very gently - a bit at atime!How does messenger RNA differ from DNA?There are several important differences.LengthRNA is much shorter than DNA. DNA contains the code formaking lots and lots of different proteins. Messenger RNAcontains the information to make just one single polypeptidechain - in other words for just one protein, or even just a part ofa protein if it is made up of more than one polypeptide chain.Overall structureDNA has two strands arranged in a double helix. RNA consistsof a single strand.The sugar present in the backbone of the chainDNA (deoxyribonucleic acid) has a backbone of alternatingdeoxyribose and phosphate groups. In RNA (ribonucleic acid),the sugar ribose replaces deoxyribose.If you have read this sequence of pages from the beginning, youwill already have come across the difference between these twosugars. But to remind you . . .The only difference is the presence of an -OH group on the 2'carbon atom in ribose.Note: If you don't understand what 2' means, you obviouslyhaven't read the first page in this sequence of pages. It's abad idea trying to take short cuts with this!RNA uses the base uracil (U) rather than thymine (T)The structure of uracil is very similar to that of thymine.The nitrogen shown in blue in the uracil is the one whichattaches to the 1' carbon in the ribose. In the process, thehydrogen shown in blue is lost together with the -OH group onthe 1' carbon in the ribose.The only difference between the two molecules is the presenceor absence of the CH3 group.Uracil can form exactly the same hydrogen bonds with adenineas thymine can - the shape of the two molecules is exactly thesame where it matters.Compare the hydrogen bonding between adenine (A) andthymine (T):. . . with that between adenine (A) and uracil (U):In DNA the hydrogen bonding between A and T helps to tie thetwo strands together into the double helix. That isn't relevant inRNA because it is only a single strand. However, you will findseveral examples in what follows on this and further pageswhere the ability of adenine (A) to attract and bond with uracil(U) is central to the processes going on.The base pairing of guanine (G) and cytosine (C) is just thesame in DNA and RNA.So in RNA the important base pairs are:adenine (A) pairs with uracil (U);guanine (G) pairs with cytosine (C).TranscriptionTranscription is the name given to the process where theinformation in a gene in a DNA strand is transferred to an RNAmolecule.The coding strand and the template strand of DNAThe important thing to realise is that the genetic information iscarried on only one of the two strands of the DNA. This is knownas the coding strand.The other strand is known as the template strand, for reasonswhich will become obvious is a moment.Note: These two strands are often given other names aswell, sometimes in a very confusing way (at least to a non-biochemist!). The two terms coding and template arecommonly used, and seem to me to best describe thefunction of the two chains.The coding strandThe information in a gene on the coding strand is read in thedirection from the 5' end to the 3' end.Remember that the 5' end is the end which has the phosphategroup attached to the 5' carbon atom. The 3' end is the endwhere the phosphate is attached to a 3' carbon atom - or if it isat the very end of the DNA chain has a free -OH group on the 3'carbon.You may remember this diagram of a tiny part of a DNA chainfrom the first page in this sequence:If the left-hand chain was the coding chain, the genetic codewould be read from the top end (the 5' end) downwards. Thecode in this very small fragment of a gene would be read as ". . .A T T G C . . .".The template strandThe template strand is complementary to the coding strand.That means that every A on the coding strand is matched by a Ton the template strand (and vice versa). Every G on the codingstrand is matched by a C on the template strand (and again viceversa).If you took the template strand and built a new DNA strand on it(as happens in DNA replication), you would get an exact copy ofthe original DNA coding strand formed.Almost exactly the same thing happens when you make RNA. Ifyou build an RNA strand on the template strand, you will get acopy of the information on the DNA coding strand - but with oneimportant difference.In RNA, uracil (U) is used instead of thymine (T). So if theoriginal DNA coding strand had the sequence A T T G C T, thiswould end up in the RNA as A U U G C U - everything is exactlythe same except that every T had been replaced by U.The