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B. Biochemistry · Biochemistry

Nucleic Acids and ATP: Nucleotides, DNA and RNA

B3.2 B3.3 B3.5 B2.3 A1.12 A2.2About 65 minutes
Learning goals
  • I can describe the structure of a nucleotide and name its three parts.
  • I can explain how phosphodiester bonds link nucleotides into a strand with a 5′ and a 3′ end.
  • I can describe the double helix (complementary base pairing, hydrogen bonds, antiparallel strands) and compare DNA with RNA.
  • I can explain the functions of DNA, RNA and nucleotides such as ATP and NAD⁺ in cells.

Words to know

nucleotide
The monomer of nucleic acids: a phosphate group, a five-carbon sugar (deoxyribose or ribose) and a nitrogenous base.
nitrogenous base
A ring-shaped molecule containing nitrogen: adenine, guanine, cytosine, thymine (DNA only) or uracil (RNA only).
purine / pyrimidine
Purines (A, G) have two fused rings; pyrimidines (C, T, U) have one ring.
phosphodiester bond
The link between nucleotides: a phosphate joins the 3′ carbon of one sugar to the 5′ carbon of the next. Formed by condensation.
complementary base pairing
In DNA, A pairs with T (2 hydrogen bonds) and G pairs with C (3 hydrogen bonds).
antiparallel
The two strands of DNA run in opposite directions: one 5′→3′, the other 3′→5′.
double helix
The shape of DNA: two strands wound around each other, with sugar-phosphate backbones outside and base pairs inside.
ATP (adenosine triphosphate)
A nucleotide with three phosphate groups. Hydrolysis of its last phosphate releases energy the cell uses to do work.

Four letters, every living thing

The instructions for building a maple tree, a beaver and you are all written with the same four chemical letters: A, T, G and C. They are carried by nucleic acids, the fourth class of biological macromolecules. In this lesson you will learn the structure of these molecules; in Molecular Genetics you will see how cells copy them and read them to make proteins.

Remember from Grade 11

In SBI3U Genetic Processes you learned that DNA is a double helix of nucleotides, that A pairs with T and G with C, and that genes are sections of DNA on chromosomes. Here we add the chemistry: the sugar carbons (1′ to 5′), the phosphodiester bond, the hydrogen bonds in each pair, and why the strands are antiparallel.

Nucleotides: the monomers

Every nucleotide has three parts:

  1. A phosphate group (acidic and negatively charged; this is the "acid" in nucleic acid).
  2. A five-carbon sugar (a pentose): deoxyribose in DNA, ribose in RNA. The sugar's carbons are numbered 1′ to 5′ ("one prime" to "five prime") to tell them apart from the atoms in the base. Deoxyribose has –H on its 2′ carbon where ribose has –OH ("deoxy" = minus an oxygen).
  3. A nitrogenous base attached to the 1′ carbon:
  • Purines (two rings): adenine (A) and guanine (G).
  • Pyrimidines (one ring): cytosine (C), thymine (T) (DNA only) and uracil (U) (RNA only).

The phosphate is attached to the 5′ carbon, and the 3′ carbon carries a free –OH.

sugar(5 C)O (ring)1′2′3′4′5′ CPphosphatebaseA, G, C, T or U3′ –OH–H (DNA) or –OH (RNA)purines: two ringsadenine (A), guanine (G)pyrimidines: one ringcytosine (C), thymine (T),uracil (U, RNA only)
A nucleotide: phosphate on the 5′ carbon, base on the 1′ carbon, and a free –OH on the 3′ carbon. The 2′ carbon has –H in DNA and –OH in RNA. Purines have two rings, pyrimidines one. Simplified (not every atom shown).

Building a strand: phosphodiester bonds

Nucleotides join by condensation: the phosphate on the 5′ carbon of a new nucleotide bonds to the 3′ –OH of the last nucleotide in the chain, releasing water. The link, sugar–O–P–O–sugar, is a phosphodiester bond. The repeating sugar-phosphate chain is the backbone; the bases stick out to the side.

Because of this, every strand has direction: a 5′ end (free phosphate) and a 3′ end (free –OH). Sequences are written 5′→3′ by convention. New nucleotides are always added to the 3′ end, which matters a great deal in DNA replication.

The double helix

In 1953, James Watson and Francis Crick proposed the double-helix model. They relied on X-ray diffraction images made by Rosalind Franklin and Raymond Gosling, on work by Maurice Wilkins, and on Erwin Chargaff's finding that in DNA the amount of A equals T and the amount of G equals C. Watson, Crick and Wilkins received the 1962 Nobel Prize; Franklin had died in 1958 and Nobel Prizes are not awarded after death.

The model:

  • Two strands wind around each other. The sugar-phosphate backbones are on the outside, facing water; the bases are inside, stacked like the rungs of a twisted ladder.
  • Complementary base pairs are held by hydrogen bonds: A=T with 2 and G≡C with 3. A purine always pairs with a pyrimidine, so every rung is the same width.
  • The strands are antiparallel: one runs 5′→3′, the other 3′→5′.
  • Each strand's sequence determines the other's. That is the key to copying DNA.
5′3′3′5′SSATSSGCSSCGSSTASSGC5′→3′5′→3′S = sugar (deoxyribose), circle = phosphate, dashes = hydrogen bonds
Part of a DNA double helix drawn flat. The sugar-phosphate backbones run in opposite directions (antiparallel). A–T pairs have 2 hydrogen bonds and G–C pairs have 3; each pair is one wide purine plus one narrow pyrimidine.
FeatureDNARNA
SugarDeoxyribose (2′ –H)Ribose (2′ –OH)
BasesA, G, C, TA, G, C, U
StrandsUsually double (double helix)Usually single (can fold on itself)
Where (eukaryotes)Nucleus; also mitochondria and chloroplastsMade in the nucleus; works mostly in the cytoplasm
Main jobStores genetic information long-termmRNA carries a gene's message; tRNA brings amino acids; rRNA forms ribosomes
StabilityVery stableLess stable (the 2′ –OH makes it easier to hydrolyze)
Comparing DNA and RNA.

Nucleotides with other jobs

Single nucleotides also do important work:

  • ATP (adenosine triphosphate) = adenine + ribose + three phosphates. The negatively charged phosphates repel each other, and hydrolyzing the last one (ATP + H₂O → ADP + Pᵢ) releases energy that drives muscle contraction, active transport and the building of polymers. Cells regenerate ATP constantly in Metabolic Processes.
  • NAD⁺ and FAD, the electron carriers you met in the redox lesson, are built partly from nucleotides.
  • cAMP (cyclic AMP) carries signals inside cells after a hormone binds the cell surface.
Worked example

Example: Using base-pairing rules

(a) Write the complementary strand to 5′–ATGCGC–3′, labelling its ends, and count the hydrogen bonds holding the two strands together. (b) A sample of DNA is 30% adenine. Find the percentages of T, G and C.

  1. (a) Pair each base: A–T, T–A, G–C, C–G, G–C, C–G. The complementary strand read in the same left-to-right order is 3′–TACGCG–5′.
  2. Written in the standard 5′→3′ direction, it is 5′–GCGCAT–3′.
  3. Hydrogen bonds: 2 A–T type pairs × 2 = 4; 4 G–C type pairs × 3 = 12; total 16.
  4. (b) A = T, so T = 30%. Together A + T = 60%, leaving 40% for G + C.
  5. G = C, so G = 20% and C = 20%.

(a) 5′–GCGCAT–3′ (= 3′–TACGCG–5′ written the other way); 16 hydrogen bonds. (b) T 30%, G 20%, C 20%.

Just for fun

If you could unwind and stretch out all the DNA in one of your cells, it would be about 2 metres long. It fits inside a nucleus only about 6 micrometres across. Talk about good packing.

Hands-on activity

Build a paper DNA model (B2.3)

You need: 2 strips of paper about 30 cm × 3 cm (backbones), 8 rectangles of paper (bases), coloured pencils or markers, tape, a pencil, and scissors (careful).

  1. Cut the 8 rectangles to two lengths: 4 long (5 cm, purines) and 4 short (3 cm, pyrimidines). Label long ones A or G and short ones T or C, and colour each letter a different colour.
  2. On one backbone strip, write 5′ at the top and 3′ at the bottom; on the other, 3′ at the top and 5′ at the bottom (antiparallel). Mark S (sugar) and P (phosphate) alternately down each strip.
  3. Choose a sequence for the first strand, such as 5′–AGCT–3′. Tape the bases to the S marks.
  4. Pair each base with its complement (long with short) on the other strip, so every rung is the same total length (5 + 3 = 8 cm). Draw 2 short lines between A and T and 3 between G and C (hydrogen bonds).
  5. Hold both ends and twist gently to make a helix. Sketch your model with labels: 5′, 3′, sugar, phosphate, base pair, hydrogen bond.

What to look for: every rung is the same length only when a purine pairs with a pyrimidine; trying A with G (long + long) or C with T (short + short) makes rungs that don't fit. Your two backbones should read in opposite directions.

Your turn

1

Name the three parts of a nucleotide.

2

Which bases are purines and which are pyrimidines?

3

Write the complementary DNA strand for 5′–TTAGCA–3′ (in 5′→3′ order).

4

What is the difference between deoxyribose and ribose?

5

Explain what "antiparallel" means for DNA.

6

Why is G–C base pairing stronger than A–T pairing?

More practice: warm-up

1

Which base is found in RNA but not DNA?

2

What type of bond links nucleotides in a strand?

3

What type of bond holds base pairs together?

4

What does ATP stand for?

5

Who made the X-ray images that helped reveal DNA's structure?

More practice: on your own

1

A DNA sample contains 18% guanine. Find the percentages of the other three bases.

2

Why must a purine always pair with a pyrimidine in DNA?

3

Explain why the sugar-phosphate backbone is on the outside of the double helix and the bases are inside.

4

A strand of DNA has 1200 nucleotides. How many phosphodiester bonds does it have, and how many water molecules were released when it was made?

5

Give two differences in structure and one difference in function between DNA and RNA.

Challenge

1

A double-stranded DNA molecule of 100 base pairs is 40% G + C. How many hydrogen bonds hold its strands together?

2

DNA from a heat-loving bacterium has a higher percentage of G and C than DNA from a bacterium that lives at room temperature. Suggest why.

3

Chargaff found that in DNA, A = T and G = C, but A does not equal G. Explain how the double-helix model accounts for both observations.

Check your understanding

Quiz

1.

Which part of a nucleotide differs between DNA and RNA nucleotides containing adenine?

2.

If a DNA sample is 22% thymine, what percentage is guanine?

3.

A phosphodiester bond links:

4.

Which pairing is correct for DNA?

5.

Pyrimidines are:

6.

ATP is best described as:

For parents and teachers

Big idea: This lesson covers B3.2 for nucleic acids (structure and function), the phosphate and hydroxyl groups (B3.3), condensation (B3.5), and building models (B2.3). It also mentions the scientists behind the double helix (A2.2). Replication, protein synthesis and genetic technology come in the Molecular Genetics unit.

How to help: Quiz your teen on writing complementary strands with 5′ and 3′ labels. A common university-level expectation is writing the answer in 5′→3′ order. The paper model is a quick, worthwhile way to see why the strands are antiparallel.

Common difficulties:

  • Forgetting to reverse the complementary strand when writing it 5′→3′.
  • Confusing purines (A, G: two rings) with pyrimidines (C, T, U: one ring). Memory aid: "Pure As Gold" for purines.
  • Thinking base pairs are held by covalent bonds. They are hydrogen bonds; the backbone is covalent.