Nucleic Acids and DNA Replication

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Senior 5 · Biology

Nucleic Acids and DNA Replication

5 lessons

Lesson 2 of 5

The structure of DNA and RNA: the Watson–Crick model

25 min

A model built from other people's numbers

In the spring of 1953, James Watson and Francis Crick in Cambridge built a model of DNA out of metal plates and wire. They did no experiments on DNA themselves. They fitted together evidence from others: the base ratios measured by Erwin Chargaff, and X-ray diffraction photographs of DNA fibres made at King's College London by Rosalind Franklin, her student Raymond Gosling and Maurice Wilkins. Their one-page paper in Nature on 25 April 1953 explained at once how DNA could carry information and how it could be copied. This lesson takes the model apart piece by piece, together with its single-stranded relative, RNA.

The evidence

Evidence	Who	What it showed
Base ratios in DNA from many species	Erwin Chargaff (1950)	The amount of A equals T, and G equals C, in every species; but the A + T to G + C ratio differs between species
X-ray diffraction of DNA fibres	Rosalind Franklin and Raymond Gosling; Maurice Wilkins (1950–1953)	DNA is a helix of constant width, about 2 nm, with a repeat every 3.4 nm; the phosphate groups are on the outside
Chemistry of nucleotides	Many chemists	Nucleotides are joined by sugar–phosphate bonds into long chains

Franklin's sharpest photograph, known as "Photo 51", showed a clear X-shaped pattern that indicated a helix. Wilkins showed it to Watson without her knowledge, and Crick later saw a report that included her measurements. Franklin died in 1958, aged 37. In 1962 Watson, Crick and Wilkins shared the Nobel Prize in Physiology or Medicine, which is never awarded after death. Historians still debate how fairly her contribution was treated.

Definition

Double helix: the shape of DNA: two polynucleotide strands wound around each other in a right-handed spiral.

Antiparallel: running in opposite directions; one strand runs 5′ to 3′ and its partner runs 3′ to 5′.

Complementary base pairing: the pairing of a specific purine with a specific pyrimidine by hydrogen bonds: adenine with thymine (2 hydrogen bonds) and guanine with cytosine (3 hydrogen bonds). In RNA, adenine pairs with uracil.

The Watson–Crick model

Two strands, each a polynucleotide with a sugar–phosphate backbone.
The strands are antiparallel.
The backbones are on the outside; the bases point inwards and pair across the middle.
Pairing is complementary: A–T with 2 hydrogen bonds, G–C with 3. A purine always pairs with a pyrimidine, so every rung is the same length and the helix keeps a constant width of 2 nm. This also explains Chargaff's rule.
The strands are twisted into a right-handed double helix with 10 base pairs per turn: one turn is 3.4 nm long, so the pairs are 0.34 nm apart.

Each hydrogen bond is weak, but a gene has thousands of them, and the flat bases stack on each other, so the molecule is very stable. Yet the two strands can be "unzipped" by enzymes when DNA is copied or read, because hydrogen bonds break far more easily than the covalent bonds of the backbone. Since the sequence of one strand fixes the sequence of the other, each strand can act as a template for a new partner: as Watson and Crick wrote, the pairing "immediately suggests a possible copying mechanism for the genetic material".

Worked example 1: using Chargaff's rule

A sample of double-stranded DNA contains 21 % adenine. Calculate the percentages of thymine, guanine and cytosine.

A pairs with T, so T = A = 21 %.
A + T = 42 %, so G + C = 100 − 42 = 58 %.
G pairs with C, so G = C = $\frac{58}{2} = 29\,\%$ .

Check: purines = A + G = 21 + 29 = 50 %, and pyrimidines = T + C = 21 + 29 = 50 %, as the model requires.

Worked example 2: a gene in numbers

A gene is 1 500 base pairs long, and 40 % of its base pairs are G–C. Calculate (a) its length, (b) the number of turns of the helix, and (c) the number of hydrogen bonds between its strands.

(a) $1\,500 \times 0.34\,\mathrm{nm} = 510\,\mathrm{nm}$ .
(b) $\frac{1\,500}{10} = 150$ turns.
(c) G–C pairs: $0.40 \times 1\,500 = 600$ , with 3 bonds each: 1 800. A–T pairs: 900, with 2 bonds each: 1 800. Total = 3 600 hydrogen bonds.

Use: DNA rich in G–C needs more energy (a higher temperature) to separate its strands, a fact used in the laboratory technique PCR.

RNA

RNA (ribonucleic acid) is usually a single polynucleotide strand. Its nucleotides contain ribose, and the base uracil replaces thymine. Parts of one RNA strand can fold back and pair with itself (A with U, G with C), giving each type of RNA its own shape. Cells make three main types, all copied from DNA:

Messenger RNA (mRNA): a copy of a gene that carries its code from the nucleus to the ribosomes.
Transfer RNA (tRNA): short molecules, about 75 to 90 nucleotides long, folded into a cloverleaf; each carries one kind of amino acid and has an anticodon that pairs with mRNA.
Ribosomal RNA (rRNA): with proteins, forms the ribosomes, where proteins are made.

Feature	DNA	RNA
Number of strands	Two, in a double helix	Usually one
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Length	Very long: millions of nucleotides	Short: tens to thousands of nucleotides
Where found in a eukaryotic cell	Nucleus (and mitochondria, chloroplasts)	Nucleus, cytoplasm and ribosomes
Stability	Very stable; lasts the life of the cell	Less stable; mRNA is broken down within minutes to hours
Function	Stores genetic information	Carries and uses it to make proteins

TED-Ed: "Rosalind Franklin: DNA's unsung hero" by Cláudio L. Guerra. Watch for how X-ray diffraction revealed the helix, and for the evidence Watson and Crick used to build their model.

Warning

Common mistakes

Applying Chargaff's rule to RNA or to single-stranded DNA. A = T and G = C only in double-stranded DNA, because of base pairing.
Writing that A–T is held by three hydrogen bonds. A–T has two; G–C has three.
Saying that the bases are joined by covalent bonds across the helix. The bonds between the strands are hydrogen bonds; the covalent bonds are within each strand.

Tip

Chargaff shortcut: in double-stranded DNA, %A = %T, %G = %C, and %A + %G = 50 %. Given any one base, you can find the other three.

✦

Practice: DNA and RNA structure

State what Chargaff's rule says and explain it using the Watson–Crick model.
Explain why a purine always pairs with a pyrimidine.
Explain the meaning of "antiparallel".
Double-stranded DNA from a plant contains 32 % guanine. Find the percentages of the other three bases.
A DNA molecule has 4 000 base pairs, 35 % of them A–T. Calculate the number of hydrogen bonds between the strands.
How long, in nm, is a stretch of DNA that makes 25 complete turns?
Give four differences between DNA and RNA.
A virus contains nucleic acid with 24 % A, 18 % G, 32 % C and 26 % U. What can you conclude about its genetic material? Explain.

Show answersHide answers

In double-stranded DNA the amount of A equals T and G equals C. In the model A always pairs with T and G with C, so every A on one strand is matched by a T on the other.
A purine has two rings and a pyrimidine one; a purine–pyrimidine pair is the right length to fit between the backbones and keeps the helix 2 nm wide; two purines would be too wide and two pyrimidines too narrow. Only these pairs also form the correct hydrogen bonds.
The two strands run in opposite directions: one 5′ to 3′, the other 3′ to 5′.
C = 32 %; G + C = 64 %; A = T = $\frac{36}{2} = 18\,\%$ .
A–T pairs: 1 400 × 2 = 2 800; G–C pairs: 2 600 × 3 = 7 800; total 10 600 hydrogen bonds.
$25 \times 3.4 = 85\,\mathrm{nm}$ .
Any four: DNA is double-stranded, RNA usually single; deoxyribose versus ribose; thymine versus uracil; DNA is much longer; DNA is more stable; DNA stores information while RNA uses it.
It contains uracil, so it is RNA; A ≠ U and G ≠ C, so it is single-stranded RNA.

Key points

Watson–Crick model (1953): two antiparallel strands in a right-handed double helix, backbones outside, bases inside.
A–T (2 hydrogen bonds), G–C (3); purine with pyrimidine keeps the width 2 nm.
One turn = 3.4 nm = 10 base pairs; 0.34 nm per pair.
RNA: usually single-stranded, ribose, uracil; mRNA, tRNA and rRNA.

Sources and credits

Written by Ganzaa. The quotation is from J. D. Watson and F. H. C. Crick, "Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid", Nature 171 (1953), 737–738.
Drawing: Rosalind Franklin, Rori!, CC BY-SA 4.0, via Wikimedia Commons.
Video: Rosalind Franklin: DNA's unsung hero, TED-Ed, embedded from YouTube.

Figures 1 and 2, the tables, the worked examples and the practice questions are written by Ganzaa.

1A model built from other people's numbers

2The evidence

3The Watson–Crick model

4RNA

A model built from other people's numbers

The evidence

The Watson–Crick model

RNA