Nucleotides and Base Pairing

Essential Question

How is DNA built, and how is it packaged in different kinds of cells?

A DNA molecule can be millions of units long, yet it is built from only four kinds of building blocks. In this lesson you build DNA from its parts, see why A always pairs with T and G with C, and look at how cells fit very long DNA molecules into very small spaces.

Nucleotides: The Building Blocks

• DNA is a nucleic acid, a polymer made of repeating monomers called nucleotides.
• Each nucleotide has three parts: a phosphate group, a five-carbon sugar called deoxyribose, and a nitrogen base.
• DNA has four bases: adenine (A), thymine (T), guanine (G), and cytosine (C).
• Nucleotides link when the sugar of one joins the phosphate of the next. This forms a sugar-phosphate backbone.
• The order of the bases along the backbone is the sequence. The sequence is the information.

Every DNA nucleotide has the same phosphate and sugar. Only the base differs, so the base is what makes the four nucleotides different.

Base Pairing

• A and G are purines. They have a double-ring structure. T and C are pyrimidines. They have a single ring.
• A always pairs with T, joined by 2 hydrogen bonds. G always pairs with C, joined by 3 hydrogen bonds.
• Each pair is one large base with one small base, so every pair is the same width.
• The two bases in a pair are complementary. The sequence of one strand tells you the sequence of the other.
• Each hydrogen bond is weak, so the strands can be separated when a cell needs to read or copy them.

The pairing rules are the reason A matches T and G matches C in Chargaff’s data.

The Double Helix

• A DNA molecule has two strands that wind around each other in a double helix.
• The sugar-phosphate backbones are on the outside. The base pairs are stacked on the inside, like the rungs of a twisted ladder.
• Each strand has two different ends, called the 5′ end and the 3′ end, so a strand has a direction. The two strands run in opposite directions, so they are called antiparallel. The diagrams in this course leave off the 5′ and 3′ labels.
• Because of base pairing, each strand is a template for the other.

Knowing one strand tells you the other. This is why DNA can be copied and read so reliably.

Packaging DNA in Cells

• A prokaryotic cell has no nucleus. Its DNA is usually one circular chromosome in the cytoplasm.
• A eukaryotic cell keeps its DNA in the nucleus, in several linear chromosomes. Each chromosome is one very long DNA molecule.
• In eukaryotes, DNA is wrapped around proteins called histones. The wrapped DNA coils again to form compact chromosomes.
• Packaging fits a very long molecule into a very small space. A typical human cell has roughly 2 meters of DNA inside a nucleus about 10 micrometers wide.

Prokaryotes and eukaryotes both pack their DNA, but eukaryotes wrap it around histones inside a nucleus.

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Worked Examples

Try each problem on your own first, then open the solution to check your work.

Example 1: Base Percentages From One Base

A sample of double-stranded DNA is 28% adenine. What percent of the sample is thymine, guanine, and cytosine?

Show the solution

1. A pairs with T, so thymine is also 28%.
2. A + T = 28 + 28 = 56%.
3. The rest is G and C: 100 – 56 = 44%.
4. G pairs with C, so they are equal: 44 / 2 = 22% each.
5. Answer: T = 28%, G = 22%, C = 22%.

Example 2: Counting Nucleotides and Hydrogen Bonds

A DNA segment is 40 base pairs long, and 14 of those pairs are G-C pairs. Find (a) the total number of nucleotides, (b) the number of A-T pairs, (c) the number of hydrogen bonds holding the strands together, and (d) the percent of the nucleotides that are guanine.

Show the solution

1. (a) Each base pair has 2 nucleotides: 40 x 2 = 80 nucleotides.
2. (b) A-T pairs = 40 – 14 = 26.
3. (c) A-T pairs have 2 bonds and G-C pairs have 3 bonds: (26 x 2) + (14 x 3) = 52 + 42 = 94 bonds.
4. (d) Each G-C pair has one G, so there are 14 G nucleotides. 14 / 80 x 100 = 17.5%.
5. Answer: (a) 80 nucleotides, (b) 26 A-T pairs, (c) 94 hydrogen bonds, (d) 17.5% guanine.

Example 3: Write the Complementary Strand

One strand of a DNA segment reads TACGGATTCAGC. Write the complementary strand base for base (the strands are drawn side by side). Then count the hydrogen bonds between the two strands.

Show the solution

1. Pair each base: A with T, T with A, G with C, and C with G.
2. TACGGATTCAGC pairs with ATGCCTAAGTCG.
3. Count pairs: 6 A-T pairs and 6 G-C pairs.
4. Hydrogen bonds: (6 x 2) + (6 x 3) = 30.
5. Answer: Complementary strand: ATGCCTAAGTCG, with 30 hydrogen bonds.

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Practice

Use the practice worksheet to label a nucleotide, apply the base pairing rules, count hydrogen bonds, and compare how prokaryotic and eukaryotic cells package DNA.

• Nucleotides and Base Pairing Practice Worksheet (PDF)
• Nucleotides and Base Pairing Practice Answer Key (PDF)

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Lesson Slides

• 9.2 Nucleotides and Base Pairing Slides (PDF)

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Big Ideas

• A nucleotide has a phosphate, the sugar deoxyribose, and one of four bases: A, T, G, or C.
• A pairs with T (2 hydrogen bonds) and G pairs with C (3 hydrogen bonds), so the two strands are complementary.
• DNA is a double helix with sugar-phosphate backbones outside and base pairs inside.
• Prokaryotes usually have one circular chromosome. Eukaryotes have linear chromosomes in a nucleus, with DNA wrapped around histones.
• Each chromosome is one very long DNA molecule, and a gene is a segment of it.

Back to the essential question: DNA is built from nucleotides joined in a sugar-phosphate backbone, with complementary bases pairing across two strands. Prokaryotes keep a circular chromosome in the cytoplasm, and eukaryotes wrap linear chromosomes around histones inside a nucleus.

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