VCE Biology

Nucleic acids

Nucleic acids are polymers made of monomers called nucleotides. They carry the instructions that cells use to build proteins, so a sequence of nucleotides in DNA is, in effect, a stored set of directions for making a particular polypeptide. The two kinds are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Every nucleotide has three parts: a five-carbon (pentose) sugar, a phosphate group and a nitrogenous base. The sugar is joined to the base at its 1' carbon and to the phosphate at its 5' carbon. The carbons of the sugar are numbered 1' to 5' (said "one prime") to tell them apart from the carbons in the base.

The structure of DNA

Nucleotides in DNA

The sugar in DNA is deoxyribose, which has a hydrogen atom rather than a hydroxyl group on its 2' carbon. There are four bases, in two groups:

The polynucleotide strand

Nucleotides join by a condensation reaction between the phosphate on one nucleotide and the 3' hydroxyl of the sugar on the next. The bond is a phosphodiester bond, and a repeating chain of sugar and phosphate, the sugar-phosphate backbone, runs along the length of the strand with the bases pointing away from it. The strand therefore has direction: one end has a free phosphate on a 5' carbon (the 5' end) and the other has a free hydroxyl on a 3' carbon (the 3' end). New nucleotides are always added at the 3' end.

The double helix

DNA is a double helix of two polynucleotide strands wound around each other. The strands run in opposite directions, so that the 5' end of one lies beside the 3' end of the other, and they are described as antiparallel. The bases in the middle of the helix pair by hydrogen bonds:

• adenine pairs with thymine, with two hydrogen bonds
• cytosine pairs with guanine, with three hydrogen bonds

Each pair is one purine and one pyrimidine, which keeps the width of the helix constant. This complementary base pairing means that the sequence of one strand fixes the sequence of the other, and it is the reason DNA can be copied accurately and read by enzymes. In any double-stranded DNA the amount of A equals the amount of T and the amount of C equals the amount of G, so a sample that is 30% adenine is also 30% thymine, and the remaining 40% is split evenly, with 20% cytosine and 20% guanine.

The hydrogen bonds are individually weak but there are very many of them, so the helix is stable, and they can still be broken by enzymes or heat in order to separate the strands for copying or reading. The phosphodiester bonds of the backbone are covalent and much stronger, which protects the order of the bases. The negatively charged phosphate groups on the outside of the helix are also what makes DNA move towards the positive electrode in gel electrophoresis.

Eukaryotic DNA is linear and sits in the nucleus wrapped around histone proteins; it is also found in mitochondria and chloroplasts. Prokaryotic DNA is a single circular chromosome in the cytoplasm, often with small circular plasmids as well.

RNA

RNA differs from DNA in three ways. Its sugar is ribose, which keeps a hydroxyl group on the 2' carbon. It uses uracil (U) in place of thymine, and uracil pairs with adenine. And it is usually a single strand, although a single strand can fold back on itself so that some of its bases pair and form a three-dimensional shape.

Three main forms of RNA take part in gene expression.

Messenger RNA (mRNA)

mRNA is a copy of one gene, made in transcription. It is a linear strand whose sequence is read in groups of three bases called codons. It carries the code from the DNA, which stays in the nucleus in eukaryotes, to the ribosome in the cytoplasm, where it is used as the template for building a polypeptide. mRNA molecules are short-lived, which lets the cell change which proteins it makes.

Transfer RNA (tRNA)

tRNA is a single strand of roughly 75 to 90 nucleotides that folds, through base pairing within the strand, into a compact cloverleaf shape. Two regions matter. At one end there is an attachment site for a specific amino acid, and on one of the loops there is a triplet of bases called the anticodon, which pairs with a complementary codon on the mRNA. Each tRNA carries the one amino acid that matches its anticodon, so tRNA is the molecule that translates the language of nucleotides into the language of amino acids.

Ribosomal RNA (rRNA)

rRNA combines with proteins to make the two subunits of a ribosome, the structure where translation happens. Ribosomal RNA makes up most of the ribosome's mass, and it is the rRNA that holds mRNA and tRNAs in position and catalyses the formation of peptide bonds between amino acids. rRNA is the most abundant kind of RNA in a cell.

Comparing DNA and the three forms of RNA

Worked example

A double-stranded DNA sample contains 1,200 nucleotides in total, and 18% of them are guanine. Because G pairs with C, cytosine is also 18%, so G and C together are 36%, which leaves 64% for A and T. Adenine and thymine are then 32% each. Adenine therefore makes up $0.32 \times 1\,200 = 384$ nucleotides. The number of hydrogen bonds is found from the pairs: there are 600 base pairs, of which $0.36 \times 600 = 216$ are G-C pairs with 3 bonds and the other 384 are A-T pairs with 2 bonds, giving $216 \times 3 + 384 \times 2 = 648 + 768 = 1\,416$ hydrogen bonds.

Finding the structure

The double helix was worked out in 1953 by James Watson and Francis Crick, using X-ray diffraction images made by Rosalind Franklin and Raymond Gosling and data from Maurice Wilkins, together with Erwin Chargaff's finding that the amounts of A and T, and of C and G, are equal in any sample of DNA. The model is a standard example of a scientific model built from several lines of evidence from different researchers and then tested against further data.