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Written by Tim Sheppard MBBS BSc. Last updated 9/11/10

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What is DNA?

You've probably heard a thousand times, 'amino acids are the building blocks of life', and you might have heard that genes code for proteins. But how does it all fit in? You might have picked up from the amino acids section that amino acids join together to form proteins, and that the order of the amino acids affects the structure and properties of that protein. This obviously means that the order that you put them together is really important. Cells (and for the purposes of most of this, we'll consider cells in the human body) generally have to make their own proteins from amino acids that are floating around. The food that we eat contains proteins, and we break up the proteins into amino acids so that we can reuse the amino acids for making new proteins. If that weren't confusing enough, trying to make sure that all the amino acids fit together in the right order is a nightmare; but someone has designed an incredible system for making sure it all works out.

DNA stands for Deoxyribonucleic Acid, which shows that it contains the sugar 'deoxyribose', and that it is made up of nucleotides. It falls under a category of chemicals called 'nucleic acids'. However, this doesn't really help to show what DNA is.

A better way to think of DNA is like a code, which communicates the order that amino acids are supposed to go in. Each cell has machinery set up to read the code and translate it, and make sure that the proteins produced are the desired ones. The code is made up of a series of nucleotides, and it is the order of these nucleotides which determines the order of the amino acids.

That would be simple enough, but there are only four different types of nucleotides in DNA - given the letters A, C, G and T (which stand for adenine, cytosine, guanine and thymine respectively, since these are the nitrogenous organic bases present on the respective nucleotides). This means that DNA comes up with a slightly more complicated code, where a particular sequence of three bases will code for one amino acid. For instance, if nucleotides G, C and A (guanine, cytosine and adenine) appear one after the other, it will be translated as 'Alanine'; that is, if the DNA code shows GCA, we know that the next amino acid needs to be alanine.

Each set of three letters is called a codon. Since there are only these four letters, there are a total of 64 different possible codons. There are only 20 amino acids, and so many of the amino acids are coded for by more than one codon (e.g. GCA and GCC both code for the amino acid alanine); the code is therefore called degenerate.

How does DNA fit together?

DNA is made up of two strands of nucleotides. Each strand is made by binding the phosphate group from one nucleotide to the third carbon of the next nucleotide, which gives rise to what is sometimes called a 'backbone' of phosphate-sugar-phosphate-sugar etc. As shown in the diagram, arising from each of the sugars is an organic base. These organic bases form hydrogen bonds with a complimentary base to form a base pair . Since every nucleotide has an organic base, each base on one strand will pair up with a base on another strand. This is how the two strands bond with each other.

Because hydrogen bonds are not as strong as, say, covalent bonds, the two strands of nucleotides can come apart. However, collectively, the hydrogen bonds are strong, because there are so many of them. This means that a DNA molecule will happily float around without randomly just falling apart!

The two DNA strands are said to be antiparallel. This is because, though parallel, they run in opposite directions. As seen in the diagram, where one strand goes from the 5' end to the 3' end , the other goes from the 3' end to the 5' end.

Perhaps the other main detail about DNA structure is that when it has formed hydrogen bonds between two strands, it coils into a right-handed helix . However, it's not too important to understand what this means, as most of the time when we're looking at DNA, we're looking at what it does when it is unwound.

How does DNA replicate?

When you grow, you produce more cells, and in each cell you need DNA in order for that cell to produce proteins. If a cell divides, it's going to split the DNA between the two cells. If you don't copy the DNA, then some of the code will go to one cell, and some will go to the other. DNA replication is the process whereby DNA copies itself, to produce two identical copies.

Firstly the DNA unwinds. It starts off in its right-handed helix, and then straightens out and splits up. This means that the individually weak hydrogen bonds break, and the nitrogenous bases of each nucleotide are left exposed. Any nucleotides floating about could come along and form hydrogen bonds with the exposed base.

This is exactly what happens. There are loads of free-floating nucleotides, and so when the bases of the DNA are exposed, a complimentary DNA nucleotide (e.g. if adenine was exposed, a nucleotide containing thymine would come along) will bind with the exposed base.

This is build up in the 5' to 3' direction - in other words, new nucleotides are added on to the third-carbon-in-the-sugar end. Both strands have exposed bases because they have split apart, but they run in opposite directions (they are antiparallel), so the 5' to 3' direction for one strand is opposite to the 5' to 3' direction for the other. This means that when DNA replicates, the replication goes on in both directions.

So, first of all the DNA strands split. The area where they start splitting is called the replication origin sequence - the sequence from where the replication originates. There are several of these sequences, and so 'bubbles' form along the molecule where the two strands have split. The fork-shaped area where a double-stranded section of DNA splits is called a replication fork.

Free nucleotides around the molecule take the opportunity to come in and bond specifically with the exposed bases, building up a complimentary strand in the 5' to 3' direction. From each of these 'bubbles', the split grows in both directions so that replication can continue to occur on both strands in the 5' to 3' direction. Eventually two 'bubbles' will meet and join up. The complimentary strand growing in one 'bubble' will meet the beginning of the strand in the next 'bubble', and join up. When all of the 'bubbles' along a molecule have joined up and reached the ends of the molecule, the two original strands will be completely separated.

Since free nucleotides have been coming in and joining with the exposed bases all the while, each separated strand will already have started to form its own double-strand. Because of the specific way that bases pair up (A only bonds with T in DNA, C only bonds with G), when an adenine splits up from its original thymine, the only free nucleotide it will pair up with is a thymine one. Similarly, if a guanine splits from its original cytosine, it's only going to pair up with a free cytosine.

Imagine the original strands were Strand A and Strand B. Strand A is complimentary to Strand B, because all of the bases pair up. When Strand A splits off, the new strand which forms from all the free nucleotides pairing with Strand A will have to be complimentary to Strand A, which means it will have to be the same as Strand B. The equivalent is true for Strand B - its new strand must be the same as Strand A. This means that although the original double-helix has split up, the two products are exactly the same as the original. The DNA has cloned itself.

What is RNA?

RNA is basically very similar to DNA. It stands for Ribonucleic Acid, so it's obviously a nucleic acid again. However, instead of having deoxyribose as the sugar in its nucleotides, it has ribose. The other main difference is that instead of having adenine, cytosine, guanine and thymine as its organic bases, it has adenine, cytosine, guanine and uracil.

RNA tends to be just in a single strand, so it won't form a double-helix like DNA. The main thing to remember about DNA and RNA, though, is the difference in their function. DNA is like the blueprint - the original code, the basis, the all important genuine article. It is from DNA that the amino acid sequence is determined. RNA has lots of other purposes, depending on what type of RNA it is.

Messenger RNA, or mRNA, is the type of RNA that copies the original code from the DNA and takes it from where the DNA is to where the translating machinery is, so that the original code can be translated into an amino acid sequence.

Ribosomal RNA, or rRNA, is the RNA that goes into the translating machinery. The main part of the equipment that translates the DNA code is the ribosome, and it contains RNA that has unoriginally been named ribosomal RNA!

Transfer RNA, or tRNA, is the RNA which carries amino acids to the ribosomes so that they can be put in the right order - it transfers the amino acids to the place where the code is read.

More information is available in the Types of RNA section.

What is transcription?

When DNA wants to do its stuff, it starts off almost exactly the same as in DNA replication. Somewhere in the DNA molecule there will be the desired gene. This gene will code for, say, 'protein X', the protein we want to make. At this point, the DNA will unwind, and the two strands will split apart, exposing the bases that make up the code for the protein.

This time, however, instead of DNA nucleotides coming in, RNA nucleotides come in and pair up with the DNA nucleotides. A cytosine from the DNA will pair up with guanine from the RNA, guanine from the DNA will pair up with cytosine from the RNA, thymine from the DNA will pair up with adenine from the RNA, but adenine from the DNA will pair up with uracil from the RNA, as there is no thymine. The RNA nucleotides will join up and eventually form one long complimentary strand - much like in DNA replication, only this time is is a strand of RNA instead of DNA.

Because it's made of RNA, the new strand won't want to stick to the DNA for long, and it will break free, allowing the DNA to coil up again with its original strands. This section of RNA that has been produced, however, will contain all of the nucleotides needed to code for a new protein - it contains all of the information from one gene. This is messenger RNA, mRNA, which carries the message to where it can be translated.

The process of forming mRNA from an original DNA template is known as transcription.

What are 5' (5 prime) and 3' (3 prime)?

When the nucleotides of a DNA or RNA molecule are joined together in a strand, it is helpful to have some way of describing a particular end of the chain. It is for this reason that the 5' (five prime) and 3' (three prime) terms have arisen, refering to carbons on the sugar of the nucleotide.

The 5 prime end of a DNA or RNA strand is the end closest to the fifth carbon in the sugar, as shown in the diagram. This means that if all the nucleotides were joined together, at the 5' end, the fifth carbon will not be joined to another nucleotide. The fifth carbon is, in a way, 'sticking out'.

The 3 prime end is the end closest to the third carbon in the sugar, as shown in the diagram. This means that if all the nucleotides were joined together, at the 3' end, the third carbon will not be joined to another nucleotide. The third carbon is, in a way, 'sticking out'.

What is a right-handed helix?

A helix is a vertical spiral, much like on a corkscrew. In biology, a molecule with hydrogen bonds between two strands (e.g. a protein, DNA) will often form a helix. However, the two strands can spiral around each other in two different ways. The easiest way to describe this is through hands.

For a right-handed helix, take your right hand so that the forefinger is pointing up, the thumb is pointing out, and the palm is facing towards you. Now push your hand up, rotating it as you go (as in the diagram) so that your thumb points to the left and the forefinger is still pointing upwards. The routes that the tip of your forefinger and thumb drew in the air are the routes that the two strands would make around each other. The same can be done with your left hand to show a left-handed helix.

Another way of seeing it is that in a right-handed helix, the right strand will pass in front of the left strand when they cross over; the left strand will cross over the right strand when they cross over in a left-handed helix.

Further Reading