SQA Higher Biology

Nucleotides

DNA (deoxyribonucleic acid) is a polymer of nucleotides. Each nucleotide has three parts joined together: a deoxyribose sugar, a phosphate group and a base. There are four bases, and they fall into two shapes: adenine (A) and guanine (G) are the larger ones, while thymine (T) and cytosine (C) are smaller.

Nucleotides join into a strand through a sugar-phosphate backbone. The phosphate of one nucleotide bonds to the deoxyribose of the next, so the sugars and phosphates alternate along the outside of the strand and the bases project to one side. The order of the bases along a strand is the genetic code, and it is the order and not the backbone that differs from one gene to another.

Base pairing

Two strands lie side by side with their bases facing inwards, and each base pairs with only one partner.

The pairs are held together by hydrogen bonds. Each bond is weak, but a whole chromosome has millions of them, so the two strands stay together until an enzyme pulls them apart. A large base always sits opposite a small one, which keeps the width of the double helix constant along its length.

Because each base has only one partner, one strand predicts the other. This is called complementary base pairing, and it is the reason DNA can be copied accurately. If one strand reads ATTGC, the other must read TAACG opposite it. In a double-stranded molecule the amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine, which is one of the observations that led to the model of the double helix.

Antiparallel strands

Each strand has two different ends, named after the carbon atoms of the deoxyribose sugar. At one end the last nucleotide has a free phosphate group on the 5' carbon, and this is the 5' end. At the other end the last nucleotide has a free hydroxyl group on the 3' carbon, and this is the 3' end, where deoxyribose is exposed.

The two strands of a DNA molecule run in opposite directions. One has its 5' end at the top of the molecule and the other has its 3' end there. This arrangement is antiparallel, and it matters later because DNA polymerase can add nucleotides in one direction only. The two antiparallel strands twist around each other into a double helix.

Reading a double strand

If the top strand is written from its 5' end to its 3' end, the bottom strand is written with its 3' end on the left so that the bases line up:

Every A in the top strand sits opposite a T and every G opposite a C. There are 8 base pairs here. Four of them are G-C pairs with three hydrogen bonds each and four are A-T pairs with two each, so the stretch has $4 \times 3 + 4 \times 2 = 20$ hydrogen bonds between the strands.

How the structure was worked out

The model of the double helix was built from several lines of evidence. Chargaff measured the bases in DNA from many species and found that the amount of adenine always matched the amount of thymine, and guanine matched cytosine, although the ratio of A plus T to G plus C differed between species. Wilkins and Franklin produced X-ray diffraction images of DNA fibres, and Franklin's images showed a pattern that pointed to a helix of a regular, repeating width. Watson and Crick combined these results and built a physical model in which two antiparallel strands are joined by specific base pairs, which explained Chargaff's ratios and fitted the X-ray pattern.

The idea that the base sequence carries the genetic code follows from the structure: the sugar-phosphate backbone is the same along the whole molecule, so the only thing that varies between genes is the order of the bases.

DNA in prokaryotes

Prokaryotes such as bacteria have no nucleus. Their DNA is a single circular chromosome lying free in the cytoplasm. Many bacteria also carry plasmids, which are much smaller circular molecules of DNA separate from the chromosome. Plasmids carry genes that are not needed all the time, for example genes for resistance to an antibiotic, and they can be copied and passed between bacteria. This is what makes plasmids so useful as tools in genetic engineering.

DNA in eukaryotes

Eukaryotes (animals, plants, fungi and protists) keep their DNA in a nucleus, in several linear chromosomes. Each chromosome is one very long DNA molecule that is tightly coiled and packaged with proteins. The packaging proteins are called histones, and the coiling is what allows metres of DNA to fit inside a nucleus only a few micrometres across.

Eukaryotes also have DNA outside the nucleus. Mitochondria and chloroplasts each contain their own circular chromosome, similar in form to a prokaryote's, which is one reason these organelles are thought to have arisen from prokaryotes living inside larger cells.

Yeast is a special case among eukaryotes. It is a single-celled fungus with linear chromosomes in its nucleus, and it also contains plasmids, which most eukaryotes do not. This is part of why yeast is used in genetic engineering.

Where DNA is found