Nucleic acids

Nucleotides: the building blocks

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids: polymers made of monomers called nucleotides. Each nucleotide has three parts:

• A five-carbon sugar: deoxyribose in DNA, ribose in RNA.
• A phosphate group.
• A nitrogenous base: a ring-shaped molecule containing nitrogen.

The sugar's carbons are numbered 1′ to 5′ (said "one-prime" to "five-prime"; the prime mark separates them from the atoms of the base). The base is attached to the 1′ carbon and the phosphate to the 5′ carbon. The 3′ carbon carries an –OH group, which is where the next nucleotide will join.

Five bases in two shapes

There are five bases. Adenine (A) and guanine (G) are purines, with two fused rings. Cytosine (C), thymine (T) and uracil (U) are pyrimidines, with a single ring. DNA uses A, G, C and T. RNA uses A, G, C and U: uracil takes the place of thymine.

A handy memory trick: "CUT the Py". Cytosine, uracil and thymine are the pyrimidines, the smaller single-ring bases.

The backbone and its direction

Nucleotides are linked by phosphodiester bonds. The phosphate on the 5′ carbon of one nucleotide bonds to the 3′ –OH of the previous one. Repeat this and you get a chain with alternating sugar and phosphate units, the sugar–phosphate backbone, with a base hanging off every sugar.

Because every link joins a 3′ carbon to a 5′ carbon, the chain has a direction. One end has a free phosphate on a 5′ carbon (the 5′ end), and the other has a free –OH on a 3′ carbon (the 3′ end). By convention, sequences are written from 5′ to 3′. New nucleotides are always added to the 3′ end, so nucleic acids grow in the 5′→3′ direction.

Each phosphate in the backbone carries a negative charge. That makes DNA and RNA strongly negative overall, which is why DNA moves toward the positive end in gel electrophoresis.

The double helix

DNA is usually two strands wound around each other in a double helix. The sugar–phosphate backbones run along the outside, and the bases point inward, meeting in the middle like the rungs of a twisted ladder.

The bases pair by complementary base pairing: A always pairs with T, and G always pairs with C. Each pair is one purine with one pyrimidine, so every rung is the same width and the helix stays even. A–T pairs are held by two hydrogen bonds and G–C pairs by three.

The two strands are antiparallel: they run in opposite directions. If one strand runs 5′→3′ from top to bottom, its partner runs 3′→5′. This matters a lot later. Because DNA can only be built 5′→3′, copying the two antiparallel strands has to happen in two different ways, which gives replication its leading and lagging strands.

Complementary pairing explains Chargaff's rules: in double-stranded DNA, the amount of A equals the amount of T, and G equals C. Chargaff's own figures for human DNA were close to this: about 29% A, 30% T, 21% G and 20% C.

RNA: DNA's versatile relative

RNA differs from DNA in three main ways. Its sugar is ribose, which has an extra –OH group on the 2′ carbon. It uses uracil instead of thymine, and U pairs with A. And it's usually single-stranded, although a single strand can fold back and base-pair with itself to form hairpins and complex 3-D shapes.

That flexibility lets RNA do many jobs. Messenger RNA (mRNA) carries a copy of a gene to the ribosome. Transfer RNA (tRNA) brings amino acids. Ribosomal RNA (rRNA) forms the core of the ribosome, and microRNAs help control which genes are used.

The 2′ –OH also makes RNA less stable. It can attack the neighbouring phosphodiester bond and cut the chain, so RNA breaks down much more easily than DNA. That suits the jobs: DNA is a long-term archive that must last a lifetime, while most RNA messages are temporary and are meant to be cleared away.

Key terms

Nucleotide

The monomer of nucleic acids: a five-carbon sugar, a phosphate group and a nitrogenous base.

Purine / pyrimidine

A double-ring base (A, G) / a single-ring base (C, T, U).

Phosphodiester bond

The link between the 3′ carbon of one nucleotide's sugar and the 5′ phosphate of the next.

Sugar–phosphate backbone

The alternating chain of sugars and phosphates that forms the outside of a nucleic acid strand.

5′ and 3′ ends

The two ends of a strand: one with a free 5′ phosphate, the other with a free 3′ –OH.

Complementary base pairing

A pairs with T (or U in RNA), and G pairs with C.

Antiparallel

Running in opposite directions, as the two strands of DNA do.

Chargaff's rules

In double-stranded DNA, the amount of A equals T, and G equals C.

Base stacking

Attraction between flat bases stacked on top of each other; the main source of the helix's stability.

Check yourself

Try answering in your head before you open each answer.

• 1.A sample of nucleic acid contains 22% A, 30% G, 26% C and 22% U. Is it DNA or RNA, and is it double- or single-stranded? Explain.Show answerHide

  RNA, because it contains uracil and no thymine. It's probably single-stranded, because G (30%) doesn't equal C (26%). In a fully double-stranded molecule, complementary pairing would force G = C and A = U.

• 2.Two DNA fragments are the same length. Fragment X is 60% G + C; fragment Y is 35% G + C. Which needs a higher temperature to separate its strands, and why?Show answerHide

  Fragment X. GC-rich DNA stacks more strongly, and G–C pairs have three hydrogen bonds rather than two, so more energy is needed to pull the strands apart.

• 3.An enzyme can only add nucleotides to a free 3′ –OH. Explain why the two strands of a DNA molecule can't both be copied continuously in the same direction as the replication fork opens.Show answerHide

  The strands are antiparallel. As the fork opens, one template lets the new strand grow 5′→3′ continuously toward the fork, but on the other template growing 5′→3′ means moving away from the fork. That strand has to be built in short pieces, which is the lagging strand.