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The structure of DNA

DNA structure

DNA (deoxyribonucleic acid) is a large molecule which carries the genetic information, or blueprint, of all life on Earth. Mutations arising in the DNA code account for the diversity upon which evolution by natural selection can work. Therefore, it is not far-fetched to say that DNA is one of the central, most important molecules in living organisms.

For such an important molecule, it sure looks beautiful:

DNA is a double helix i.e. two individual strands running along each other in an anti-parallel way, connected to one another by relatively weak hydrogen bonds. DNA’s structure can be learned easily by thinking about the strands and the “stuff in-between” separately.

What are the strands made of?

The strands are made of repeating units consisting of a deoxyribose (sugar) molecule with a phosphate molecule attached to it; hence, it is called a sugar-phosphate backbone.

Phosphodiester bonds between nucleotides (above) create the backbone:

DNA is made of 2 of these strands running in an anti-parallel structure. Because the strands have a specific orientation, they are termed differently. It happens that at the end of each strand, the nucleotide with the unattached phosphate group is found at one end, while the deoxyribose sugar is found at the opposite end, with its phosphate group linked to the above nucleotide via the phosphodiester bond.

The end with the free phosphate group is called the 5′ (five prime) end because the group is attached to its nucleotide by the fifth carbon in the ring, while the opposite end is called the 3′ (three prime) end because the (hydroxyl) group is attached to the third carbon in the ring. The 5′ to 3′ direction is also the direction DNA is synthesised in living things.

What is the centre made of?

Attached to the sugar molecules in the backbone are a different type of molecule called nitrogenous base. There are 4 bases in DNA: adenine, thymine, cytosine and guanine. These are abbreviated by their initials: A, T, C and G.

The hydrogen bonds are formed between these bases. Due to their complementary shapes, A always pairs with T, and C always pairs with G. A-T is linked by 2 H bonds, while C-G is linked by 3.

Here is a diagram of this arrangement:

And another:

The bases can be sorted into two categories: purines and pyrimidines depending on their ring structure:

As you can see, adenine and guanine are bigger and have two rings, while thymine and cytosine only have one ring. Uracil is similar to thymine and also pairs with adenine. The presence of uracil instead of thymine occurs in RNA rather than DNA.

It is the sequence of these bases that encodes genes and the sum of an organism’s genetic material, termed genotype.

DNA is a very stable molecule, as its purpose of carrying genetic information is very important. Features of this are:

1. DNA is very temperature-resistant, and the H bonds only break at temperatures of about 92 degrees Celsius
2. The sugar-phosphate backbone acts as a shield to the bases, preventing interference from outside chemical reactions
3. The double helix gives stability
4. Many H bonds contribute to the stability
5. The structure of the sugar-phosphate backbone itself confers strength.

DNA organisation

DNA and chromosomes may seem like completely separate things. Well, they’re not. In fact, all chromosomes are individual DNA molecules coiled and twisted around, because DNA is huge. At least in eukaryotes it is. That’s one of the first differences between eukaryotes and prokaryotes in their DNA – prokaryotes have less DNA.

Eukaryotic DNA is stored within the nucleus of each cell (apart from cells without one, e.g. red blood cells). Because of its sheer size, it must be organised well. Proteins called histones help do just that:

This is the second difference: eukaryotes have histones around which the DNA coils, while prokaryotes don’t. So what does prokaryotic DNA look like?

The DNA above is stored as a small loop (the bacterial chromosome), and as a plasmid. A plasmid is even smaller, and may be copied and transferred to another bacterium of the same or different species by a process called conjugation (or, more colloquially, bacteria sex).

Eukaryotic DNA is linear, rather than circular. That means the DNA, despite being coiled numerous times, has a distinguishable start point and end point, while prokaryotic DNA is a continuous circle (see above picture).

An exception to this is the DNA of yeast which are also eukaryotic but whose genetic material is instead a circular plasmid. Circular chromosomes are also found in eukaryotic cell organelles like mitochondria and chloroplasts. These organelles have functions in energy production through cellular respiration and photosynthesis. Their different DNA can be explained by the ancestry of these organelles. They used to be standalone prokaryotic cells, and underwent phagocytosis events where they were engulfed by bigger cells.

The Differences between Eukaryotic and Prokaryotic DNA

Size large small
Shape linear circular
Histones present absent





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