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DNA and RNA: four letters and a rule about pairing
A phosphate, a sugar and a base make one nucleotide. Join a few million of them, run a second strand alongside in the opposite direction, and you have a molecule long enough to hold the instructions for an entire organism and simple enough to copy without losing them.
Before this Condensation and hydrolysis · Hydrogen bonding in water · The nucleus and the nuclear envelope
Before you start
The two strands of a DNA molecule are identical, which is what the word 'double' is telling you, and it is why one strand can serve as a spare copy of the other. The strands really do serve as spares, but identical is the wrong word. They are complementary. Where one strand reads ATGGC the other reads TACCG, and not one base is the same as the base it faces. That is precisely what makes the spare useful: because the pairing rule is fixed, either strand tells you exactly what the other must be. Two identical strands would carry no more information than one, and there would be no rule for rebuilding a lost partner.
What you should be able to do
- Draw a nucleotide and name its three components.
- Explain how the sugar-phosphate backbone is built and what is released as it forms.
- State which bases pair, how many hydrogen bonds hold each pair, and why the pairing cannot be swapped around.
- Say what 5′ and 3′ mean, and why the two strands are called antiparallel.
- Account for four features of DNA structure in terms of the job the molecule does.
- Compare DNA with mRNA, tRNA and rRNA, and give each kind of RNA its role.
Three parts, one nucleotide
A nucleotide is three things joined together: a phosphate group, a pentose sugar with five carbons, and a nitrogen-containing base. The sugar sits in the middle, with the phosphate attached on one side and the base on the other. That arrangement is worth learning by position, because the phosphate and the sugar are what build the backbone while the base is the part that carries meaning.
The sugar is where DNA and RNA part company. DNA uses deoxyribose, which is ribose with one oxygen missing from carbon 2. One atom, and it is enough to change the chemistry: the missing hydroxyl group makes DNA considerably less reactive, and less reactive is exactly what you want in a molecule that has to sit in a nucleus for eighty years without degrading.
- Nucleotide
- A phosphate group, a pentose sugar and a nitrogenous base joined together.
- Polynucleotide
- A chain of nucleotides joined by phosphodiester bonds between the sugar of one and the phosphate of the next.
- Phosphodiester bond
- The covalent bond joining the phosphate group of one nucleotide to the sugar of the next, formed by condensation.
Nucleotides join the way monomers in this subject almost always join. The phosphate of one nucleotide reacts with a hydroxyl group on the sugar of the next, water is released, and a covalent phosphodiester bond forms. Repeat that a few million times and you have a polynucleotide whose backbone is a strict alternation of sugar, phosphate, sugar, phosphate, with the bases sticking out sideways. Hydrolysis runs the reaction backwards, which is what happens to the DNA in a meal before you absorb the nucleotides.
Human chromosome 1 is a single DNA molecule roughly 249 million base pairs long. Stretched out it would be about 8 cm. Every one of those bonds along its backbone was made by the same condensation reaction.
The rungs: which base goes with which
Four bases appear in DNA: adenine, thymine, cytosine and guanine. They are not interchangeable. Adenine only ever pairs with thymine, and guanine only ever pairs with cytosine, and the reason is a matter of shape and of where the hydrogen-bond donors and acceptors sit on each ring system.
Adenine and guanine are purines, built from two fused rings. Thymine and cytosine are pyrimidines, built from one. Because every pair is a purine opposite a pyrimidine, every rung of the ladder is the same width, and the two backbones stay a constant distance apart all the way along. A purine facing a purine would bulge; two pyrimidines would pinch.
The hydrogen-bond counts are worth memorising as numbers rather than as an idea. A–T is two hydrogen bonds. G–C is three. Individually these are weak interactions, easily broken by an enzyme or by heat, which is what allows the strands to be separated whenever the sequence needs reading. Collectively, across millions of pairs, they hold the molecule together very firmly indeed.
Working out the other three bases
A sample of double-stranded DNA is analysed and found to contain 22% adenine. Calculate the percentage of each of the other three bases, and state what result you would expect if the sample had been single-stranded.
Adenine pairs only with thymine, so in a double-stranded molecule every adenine has a thymine opposite it. Thymine is therefore also 22%.
Together A and T account for 44% of the bases, leaving 56% shared between guanine and cytosine. Those two also pair one-for-one, so they split the remainder equally: G = 28% and C = 28%.
For a single-stranded molecule none of this holds. Nothing forces an adenine to have a partner, so the four percentages could be anything at all. A sample in which A does not equal T is a sample that is not double-stranded, and that observation is a real analytical tool.
Two strands, pointing opposite ways
The carbons in the pentose sugar are numbered 1 to 5, and the numbering is why the ends of a strand have names. One end of a polynucleotide finishes with a free phosphate attached to carbon 5 of its last sugar; that is the 5′ end. The other finishes with a free hydroxyl group on carbon 3; that is the 3′ end. A strand therefore has a direction, in the same way a sentence does.
The two strands of a DNA molecule run in opposite directions. Wherever one strand has its 5′ end, the other has its 3′ end. That is what antiparallel means, and it is not a piece of trivia: the enzyme that copies DNA can work in only one direction, so the two strands cannot be copied in the same way. The next lesson is largely about the consequences.
Wind the whole thing into a right-handed spiral and you have the double helix, with roughly ten base pairs per complete turn. The bases are on the inside, shielded from the water around them; the charged sugar-phosphate backbones are on the outside, where being charged is an advantage rather than a problem.
- Antiparallel
- The two strands of a DNA molecule run in opposite directions: the 5′ end of one lies alongside the 3′ end of the other.
- Complementary base pairing
- Adenine pairs with thymine by two hydrogen bonds and guanine pairs with cytosine by three, so the sequence of one strand fixes the sequence of the other.
- Double helix
- Two antiparallel polynucleotide strands wound into a spiral, bases inside and backbones outside.
A structure that fits the job
Questions asking you to relate DNA structure to function come up every year, and they reward specific links rather than general admiration. Four links do most of the work.
It is stable. The backbone is held by covalent phosphodiester bonds, the bases sit tucked inside the helix away from water, and deoxyribose is less reactive than ribose. Genetic information that degraded overnight would be worthless.
It is very long. There is no limit to how many nucleotides can be joined, so an enormous quantity of information fits into one molecule. The human genome runs to about 3.1 billion base pairs.
The base sequence carries the information. The backbone is identical everywhere, so it says nothing; the order of the four bases is free to vary, so it says everything. A stretch of only ten bases can be arranged in 4¹⁰ ways, which is a little over a million.
The strands are complementary. Because the pairing rule is fixed, each strand is a full set of instructions for rebuilding the other. That is what makes accurate copying possible, and it is also why damage to one strand can often be repaired using the other as the reference.
One more feature earns marks when a question mentions packing: in eukaryotes the DNA is wound around histone proteins and coiled repeatedly, which is how 2 metres of DNA fits inside a nucleus about 6 μm across. Prokaryotes have no histones and their DNA is circular and shorter, though it is still supercoiled to fit.
RNA: the same idea, built for a different job
RNA is a polynucleotide too, made the same way, with two changes. The sugar is ribose rather than deoxyribose, and uracil replaces thymine. Uracil pairs with adenine, using the same two hydrogen bonds thymine would have used.
| DNA | RNA | |
|---|---|---|
| Sugar | Deoxyribose | Ribose |
| Bases | A, T, C, G | A, U, C, G |
| Strands | Two, antiparallel, wound into a helix | One, though it often folds back on itself |
| Length | Up to hundreds of millions of nucleotides | Tens to a few thousand nucleotides |
| Stability | Stable enough to last the life of the cell | Broken down quickly; some mRNA lasts minutes |
| Where | Nucleus, mitochondria, chloroplasts | Made in the nucleus, used in the cytoplasm |
| Job | Long-term store of the base sequence | Carrying, reading and assembling |
The short lifetime of RNA is a feature rather than a fault. A cell that has finished making a protein needs the instruction to disappear, otherwise it would keep making it. DNA is the archive; RNA is the working copy that gets thrown away.
- Messenger RNA (mRNA)
- A single-stranded copy of one gene, made in the nucleus and carrying codons to a ribosome in the cytoplasm.
- Transfer RNA (tRNA)
- A small folded RNA of about 80 nucleotides with an anticodon at one end and a binding site for a specific amino acid at the other.
- Ribosomal RNA (rRNA)
- RNA which, with proteins, forms the two subunits of a ribosome and catalyses the formation of peptide bonds.
Each of the three has a shape suited to what it does. mRNA is long and unstructured because it only needs to be read. tRNA folds into a clover leaf held together by hydrogen bonds between complementary stretches of its own sequence, which puts the anticodon at one end and the amino acid at the other. rRNA is not a message at all — it is a structural and catalytic component of the machine.
TRY IT — Reading structure from an experimental result
Two samples of nucleic acid are heated slowly and the temperature at which the strands separate is recorded. Sample X separates at 68 °C and sample Y at 83 °C. Both are double-stranded DNA of the same length. What can you conclude about their base composition, and explain your reasoning.
Check your answer
Sample Y has the higher proportion of guanine and cytosine.
Heating separates the strands by breaking the hydrogen bonds between paired bases. Each G–C pair is held by three hydrogen bonds while each A–T pair is held by only two, so a molecule with more G–C pairs needs more energy, and therefore a higher temperature, before its strands come apart.
Since the two samples are the same length, the difference cannot be a matter of the total number of bonds along the backbone. Note also what you cannot conclude: nothing here tells you the actual sequence, only the proportions.
In the exam
- Two hydrogen bonds for A–T, three for G–C. Questions about heat stability, strand separation and melting temperature all hang on those two numbers.
- 'Complementary' and 'identical' are not synonyms. A strand and its partner carry the same information in mirror form, not the same sequence.
- When a question says antiparallel, it wants opposite directions with 5′ against 3′. Saying the strands are 'the other way round' will not score.
- Structure-and-function questions want links, not lists. Pair each feature with the job it makes possible: covalent backbone with stability, base sequence with information, complementary strands with accurate copying.
- In RNA it is uracil, not thymine. Writing T in an mRNA sequence loses the mark even when everything else in the answer is right.
- Chargaff calculations follow one rule: %A = %T and %G = %C, and the four add to 100. Work out the pair you are given first, then split what is left.
Check yourself
A student writes: 'DNA is a good molecule for storing genetic information because it has a double helix shape.' Rewrite this as an answer that would actually score, referring to at least three features of the molecule.
Answer
The helix by itself explains nothing, because the question is about storing information and a spiral is not a store. Each feature has to be tied to something the molecule has to do.
The backbone is held together by covalent phosphodiester bonds, so the molecule is chemically stable and the information is not lost over time. The bases are also positioned on the inside of the helix, shielded from the water and from reactive molecules in the nucleus.
The sequence of the four bases can vary without limit, and the molecule can be extremely long, so an enormous amount of information can be encoded in one molecule. Ten bases alone allow over a million arrangements.
The two strands are complementary, held by hydrogen bonds that are weak enough to break when the sequence has to be read or copied. Because the pairing rule is fixed, either strand acts as a template for rebuilding the other, which is what makes replication accurate and repair possible.
A good answer names the bond in each case: covalent for the backbone, hydrogen for the pairing. That contrast — strong along, weak across — is the whole design.
Questions
Question 14 marks
Compare the structure of a DNA molecule with the structure of a messenger RNA molecule.
Mark scheme
- B1 DNA contains the pentose sugar deoxyribose, whereas mRNA contains ribose
- B1 DNA contains thymine, whereas mRNA carries uracil in its place
- B1 DNA is two antiparallel strands wound into a helix, whereas mRNA is a single strand
- B1 DNA can be hundreds of millions of nucleotides long, whereas an mRNA molecule is tens to a few thousand nucleotides long
Question 24 marks
A nucleic acid extracted from a virus contains adenine 31%, guanine 19%, cytosine 27% and thymine 23%. Suggest what these figures tell you about the structure of the molecule, and suggest one further measurement that would test your conclusion.
Mark scheme
- B1 in a double-stranded molecule adenine would equal thymine and guanine would equal cytosine, because each base has a fixed partner opposite it
- B1 here adenine at 31% does not equal thymine at 23%, and guanine at 19% does not equal cytosine at 27%
- B1 the molecule cannot therefore be double-stranded; it is single-stranded DNA, since thymine rather than uracil is present
- B1 any one workable further measurement: heat the sample and look for a temperature at which strands separate, since a single-stranded molecule has no paired bases to separate
Question 33 marks
Explain why every base pair in a DNA molecule is the same width, and explain what this means for the shape of the molecule as a whole.
Mark scheme
- B1 adenine and guanine are purines, built from two fused rings, while thymine and cytosine are pyrimidines, built from one
- B1 the pairing rule puts a purine opposite a pyrimidine in every pair, so each rung spans the same distance
- B1 the two sugar-phosphate backbones therefore stay a constant distance apart along the whole molecule, whereas two purines would bulge and two pyrimidines would pinch
Question 43 marks
A sample of double-stranded DNA contains 3200 bases in total, of which 960 are guanine. Calculate the number of adenine bases in the sample.
Mark scheme
- M1 cytosine equals guanine, so there are 960 cytosine bases, giving 1920 bases in the two of them together
- M1 subtracts from the total to leave the adenine and thymine: 3200 − 1920 = 1280
- A1 adenine equals thymine, so 1280 ÷ 2 gives 640 adenine bases
Question 52 marks
Name the three components of a single DNA nucleotide, and name the bond that joins one nucleotide to the next along a strand.
Mark scheme
- B1 a phosphate group, a pentose sugar (deoxyribose) and a nitrogenous base
- B1 a phosphodiester bond, formed by condensation between the phosphate of one nucleotide and the sugar of the next
Worth remembering
- One nucleotide is a phosphate, a pentose sugar and a base.
- The backbone alternates sugar and phosphate, joined by phosphodiester bonds made by condensation.
- A pairs with T through two hydrogen bonds; G pairs with C through three.
- The strands are antiparallel: 5′ on one side lies against 3′ on the other.
- RNA has ribose instead of deoxyribose and uracil instead of thymine, and it is single-stranded.