Nucleic acids

📚The biology

DNA as the genetic material

Every living organism — bacterium, fungus, plant, animal — stores its genetic information as DNA (deoxyribonucleic acid). Some viruses use RNA (ribonucleic acid) as their genetic material instead, but viruses are not considered living (A2.3), so the statement “all living things use DNA” still holds.

Nucleotides

DNA and RNA are polymers whose monomers are nucleotides. Every nucleotide has three parts:

In a diagram the phosphate and the base are both attached to the sugar, on opposite sides of it: the phosphate joins carbon 5 of the pentose and the base joins carbon 1.

The sugar–phosphate backbone

Nucleotides are joined by condensation reactions: the phosphate of one nucleotide bonds covalently to the sugar of the next, and a molecule of water is released. Repeating this produces a continuous chain of alternating sugar and phosphate — the sugar–phosphate backbone — with a base sticking out from every sugar.

Because every link in the backbone is a covalent bond, the strand is strong and stable. The information is carried by the sequence of bases along it, and that sequence is not disturbed when the two strands of DNA separate, because separation breaks only the weak hydrogen bonds between bases, not the backbone.

The bases and the code

There are four bases in each nucleic acid:

The order of bases along a strand is a code. Genes are sequences of bases, read three at a time during protein synthesis (D1.2), and the sequence determines the amino acid sequence of the polypeptide made.

RNA as a polymer

RNA is normally a single strand of nucleotides linked by condensation reactions into a sugar–phosphate backbone. To draw it, draw several nucleotides in a column, each phosphate (circle) linked to the sugar (pentagon) of the nucleotide above or below, with the bases (rectangles) all projecting to one side.

The DNA double helix

DNA is made of two strands of nucleotides wound into a double helix. Three features define it:

• The strands are antiparallel — they run in opposite directions. In a diagram, draw one strand with its sugars the right way up and the other upside down.
• Bases pair across the middle, joined by hydrogen bonds, with the backbones on the outside.
• Pairing is complementary: adenine always pairs with thymine, and guanine always pairs with cytosine.

You do not need to draw the helical twist, memorize which bases are larger, or learn how many hydrogen bonds hold each pair together.

DNA and RNA compared

The two sugars differ at a single carbon. Ribose has an –OH group on carbon 2; deoxyribose (“de-oxy”, one oxygen fewer) has only –H there. To sketch them, draw the same five-membered ring (four carbons and an oxygen) with carbon 5 sticking up outside the ring, and change only the group on carbon 2.

Examples of nucleic acids worth knowing by name: the DNA of chromosomes; messenger RNA (mRNA), which carries a copy of a gene to ribosomes; transfer RNA (tRNA), which brings amino acids; and ribosomal RNA (rRNA), part of the structure of ribosomes.

Why complementary pairing matters

Because A pairs only with T (or U) and G pairs only with C, the base sequence of one strand determines the sequence of the other. That one rule does two jobs.

• Replication. The two strands separate and each acts as a template: new nucleotides are added by complementary pairing, so the two new molecules have the same sequence as the original (D1.1).
• Expression. In transcription, an RNA copy of a gene is made by pairing RNA nucleotides with one DNA strand; in translation, tRNA anticodons pair with mRNA codons (D1.2).

In each case, the specificity comes from hydrogen bonding: only the correct base pair has hydrogen-bonding groups in the right positions to fit.

The capacity of DNA to store information

Any base can follow any other base, and a DNA molecule can be any length. So the number of possible sequences is enormous: with four bases, a sequence \( n \) bases long can be arranged in \( 4^{n} \) ways. A sequence just 10 bases long already has over a million possibilities; the human genome has about 3 billion base pairs.

DNA is also extraordinarily compact: the entire genome of a human cell, about two metres of DNA, fits inside a nucleus a few micrometres across. No human-made storage medium holds so much information in so little space.

A universal code and common ancestry

With very few, minor exceptions, every organism uses the same genetic code: the same three-base codon specifies the same amino acid in bacteria, plants and humans. There is no functional reason why one particular set of codon meanings should be the only one that works. The simplest explanation for all life sharing it is that all life inherited it from a single common ancestor. This is why a human gene inserted into a bacterium can be translated into the correct human protein.

Directionality AHL

The carbons of the pentose sugar are numbered 1′ to 5′. In the backbone, each phosphate links the 5′ carbon of one sugar to the 3′ carbon of the next. As a result every strand has two different ends: a 5′ end with a free phosphate on carbon 5′, and a 3′ end with a free –OH on carbon 3′. A strand therefore has a direction, written 5′ → 3′.

In double-stranded DNA, “antiparallel” means exactly this: one strand runs 5′ to 3′ and its partner runs 3′ to 5′ alongside it. Directionality matters because the enzymes that work on nucleic acids can only work in one direction:

• Replication: DNA polymerase only adds nucleotides to the 3′ end of a growing strand, which is why the two strands are copied differently (D1.1).
• Transcription: RNA is also built 5′ → 3′.
• Translation: ribosomes read mRNA from its 5′ end towards its 3′ end.

Purine–pyrimidine pairing AHL

Adenine and guanine are purines, with a double-ring structure. Thymine, cytosine and uracil are pyrimidines, with a single ring. Every base pair in DNA is one purine with one pyrimidine (A–T, G–C), so every base pair is the same length. The two backbones are therefore always the same distance apart, and the double helix has the same regular three-dimensional shape whatever the base sequence. That regularity is part of what makes the helix stable, and it means enzymes can bind DNA in the same way anywhere along its length.

Nucleosomes AHL

In eukaryotes, DNA is wound around proteins called histones. A nucleosome is a length of DNA wrapped around a core of eight histone proteins, with a further histone protein attached to the linker DNA that runs between nucleosomes, holding the arrangement together. A string of nucleosomes looks like beads on a thread, and it can be coiled further to condense chromosomes for division (D2.1).

DNA is negatively charged (its phosphates), and histones are rich in positively charged amino acids, so the two are held together by attraction between opposite charges. Molecular visualization software (for example the RCSB Protein Data Bank viewer) lets you rotate a nucleosome and see the DNA wrapped around its histone core.

Hershey and Chase: DNA, not protein AHL

By the 1950s it was known that chromosomes contain both protein and DNA, and many scientists expected protein, which is far more varied, to be the genetic material. Alfred Hershey and Martha Chase settled the question using bacteriophages, viruses that consist only of a protein coat and DNA and that inject their genetic material into bacteria.

• One batch of viruses was grown with radioactive sulfur-35. Sulfur is in protein but not DNA, so this labelled the protein coats.
• Another batch was grown with radioactive phosphorus-32. Phosphorus is in DNA but hardly at all in protein, so this labelled the DNA.
• Each batch infected bacteria. The mixture was agitated in a blender to knock the virus coats off the bacteria, then centrifuged: the heavier bacteria formed a pellet and the lighter virus coats stayed in the liquid.

Result: the radioactive sulfur was mostly in the liquid, with the empty coats; the radioactive phosphorus was mostly in the pellet, inside the bacteria, which went on to produce new viruses. So the material entering the cell and directing the production of new viruses was DNA.

The experiment was only possible because radioisotopes had become available as research tools — a good example of new technology opening up a new kind of experiment.

Chargaff’s data AHL

An early idea, the tetranucleotide hypothesis, proposed that DNA was a simple repeating sequence of the four bases in equal amounts — too dull a molecule to carry genetic information. Erwin Chargaff measured the proportions of the bases in DNA from many different organisms and found two patterns:

• the proportions of bases differ between species, so the four bases are not present in equal amounts;
• but within any species, the amount of A equals T and the amount of G equals C, so purines = pyrimidines.

The first pattern falsified the tetranucleotide hypothesis. This is a point about how science works: however many observations agree with a hypothesis, they cannot prove it true (the “problem of induction”), but one reliable set of contradicting observations can prove it false. The second pattern was a clue that Watson and Crick later explained with complementary base pairing.