# Structure of DNA and RNA

> CIE A-Level Biology · 9700
> Source: https://www.owlsprep.com/study/cie-9700-u6-structure-of-dna-and-rna/

This subtopic covers the structure of nucleotides, how they polymerize to form polynucleotide chains, and compares the overall structure of DNA and RNA. It is the foundational base for all molecular biology topics in this unit.

**Prerequisites:** [Basic biological molecules](https://www.owlsprep.com/study/cie-9700-u2-biological-molecules/)

## Learning objectives

- Describe the structure of nucleotides and differences between DNA and RNA nucleotides
- Outline how nucleotides join to form polynucleotide chains
- Compare the structure of DNA and different types of RNA
- Explain complementary base pairing and its significance

## Nucleotide Structure

**Nucleotide** — The monomer subunit of nucleic acids (DNA and RNA), consisting of three covalently bonded components: a pentose sugar, a nitrogenous base, and one or more phosphate groups.

*Example:* A deoxyribose nucleotide is the monomer that makes up DNA

All nucleotides share a common core structure. The pentose sugar is a 5-carbon sugar: DNA uses *deoxyribose*, while RNA uses *ribose*. Deoxyribose lacks an oxygen atom on carbon 2 compared to ribose.

Nitrogenous bases are divided into two groups:

- **Purines**: Double-ring structures: adenine (A) and guanine (G)
- **Pyrimidines**: Single-ring structures: cytosine (C), thymine (T) (DNA only) and uracil (U) (RNA only)

**Worked example:** A student draws an RNA nucleotide with thymine attached to ribose. Identify two mistakes and explain why they are incorrect.

1. First mistake: Thymine is not found in RNA
2. RNA uses uracil instead of thymine. Thymine is only present in DNA nucleotides.
3. Second mistake (common alternative): The phosphate group is not attached to the correct carbon
4. Phosphate groups always attach to carbon 5 of the pentose sugar, and the base attaches to carbon 1.
5. A corrected RNA nucleotide would be: ribose sugar + uracil base + phosphate group.

## Polynucleotide Formation

Individual nucleotides are joined by condensation reactions to form a polynucleotide chain, which has a sugar-phosphate backbone with nitrogenous bases projecting sideways out from the backbone.

**Phosphodiester bond** — The covalent bond formed between the 5' phosphate group of one nucleotide and the 3' hydroxyl (-OH) group of the next nucleotide in a chain, formed during a condensation reaction that releases one water molecule.

All polynucleotide chains have directionality: one end has a free 5' phosphate group (the 5' end) and the other has a free 3' hydroxyl group (the 3' end).

**Worked example:** Explain how three adjacent nucleotides join to form a short polynucleotide chain.

1. 1. Each nucleotide has a phosphate on carbon 5 of its pentose, and a hydroxyl group on carbon 3.
2. 2. A condensation reaction occurs between the 5' phosphate of the second nucleotide and the 3' hydroxyl of the first nucleotide.
3. 3. A water molecule is removed, forming a phosphodiester bond between the two nucleotides.
4. 4. A second condensation reaction occurs between the 5' phosphate of the third nucleotide and the 3' hydroxyl of the second nucleotide, forming a second phosphodiester bond.
5. The resulting chain has a free 5' end and a free 3' end, with an uninterrupted sugar-phosphate backbone.

## DNA Double Helix Structure

DNA is made of two polynucleotide strands twisted around each other to form a stable double helix. The two strands run in opposite 5' to 3' directions, so they are described as antiparallel.

Bases on opposite strands pair specifically via hydrogen bonds: adenine (A) always pairs with thymine (T), and guanine (G) always pairs with cytosine (C). This is called complementary base pairing.

> **tip**
>
> A-T forms 2 hydrogen bonds, G-C forms 3 hydrogen bonds. You will be expected to recall this number for CIE exam questions.

**Worked example:** A double-stranded DNA molecule has 18% adenine bases. Calculate the percentage of guanine bases.

1. Final answer: Guanine makes up 32% of the DNA molecule.

*Conclusion:* Since G = C, guanine = 64% / 2 = 32%

## RNA Structure and Types

RNA is usually a single-stranded polynucleotide. Key differences from DNA: it has ribose instead of deoxyribose, and uracil instead of thymine. There are three main types of RNA involved in protein synthesis, each with a unique structure suited to its function:

| RNA Type | Structure | Main Function |
| --- | --- | --- |
| mRNA (messenger) | Linear single chain | Carries genetic code from DNA to ribosomes |
| tRNA (transfer) | Folded clover shape, held by hydrogen bonds between bases | Carries specific amino acids to ribosomes during translation |
| rRNA (ribosomal) | Folded globular structure | Forms the structural core of ribosomes |

**Worked example:** List three structural differences between DNA and messenger RNA (mRNA).

1. Three valid differences (any three are accepted in exams):
2. 1. DNA contains deoxyribose sugar, mRNA contains ribose sugar
3. 2. DNA contains thymine, mRNA contains uracil instead of thymine
4. 3. DNA is double-stranded double helix, mRNA is single-stranded linear
5. Other valid differences: DNA is much longer than mRNA, DNA has two antiparallel strands while mRNA is a single strand

## Common pitfalls

- **Wrong:** Attaching the phosphate group to the nitrogenous base instead of the pentose sugar in a nucleotide drawing
  - Why it fails: All three components of a nucleotide bond to the pentose sugar, not to each other
  - Correct: Phosphate bonds to C5 of pentose, base bonds to C1 of pentose
- **Wrong:** Claiming phosphodiester bonds hold complementary base pairs together
  - Why it fails: Phosphodiester bonds link adjacent nucleotides in the same strand, not bases on opposite strands
  - Correct: Phosphodiester bonds form the sugar-phosphate backbone; hydrogen bonds link complementary base pairs
- **Wrong:** Stating RNA is always double-stranded or DNA is always single-stranded
  - Why it fails: Cellular DNA is double-stranded, cellular RNA is typically single-stranded; viral exceptions are not expected for this syllabus
  - Correct: For CIE 9700, state DNA is double-stranded and RNA is usually single-stranded
- **Wrong:** Calculating base percentages incorrectly for double-stranded DNA
  - Why it fails: Forgetting that complementary bases have equal percentages
  - Correct: Double the given base percentage to get the total for its pair, subtract from 100, divide by 2 to get the percentage of the other base pair
- **Wrong:** Calling deoxyribose a 6-carbon sugar
  - Why it fails: The sugar in nucleotides is always a 5-carbon pentose sugar
  - Correct: Both deoxyribose and ribose are 5-carbon (pentose) sugars

## Cheatsheet

| Feature | DNA | RNA |
| --- | --- | --- |
| Pentose sugar | Deoxyribose | Ribose |
| Nitrogenous bases | A, T, C, G | A, U, C, G |
| Number of strands | 2 (antiparallel double helix) | Usually 1 |
| Relative size | Very long | Much shorter than DNA |
| Bond between nucleotides | Phosphodiester | Phosphodiester |
| Base pairing bonds | A-T (2 H bonds), G-C (3 H bonds) | Only in folded regions (e.g. tRNA) |

## What's next

The rules of nucleotide structure and complementary base pairing you learned here are the foundation for every topic in the nucleic acids unit. Complementary base pairing enables accurate semi-conservative DNA replication, the process that copies genetic information before cell division. Structural differences between DNA and RNA explain their distinct roles in protein synthesis: DNA stores genetic information long-term, while RNA carries short-lived copies of genes for translation. Mastering this subtopic makes understanding replication, transcription and translation much more straightforward, as all these processes rely on the core principles of base pairing and polynucleotide structure you have covered here.

- [DNA Replication](https://www.owlsprep.com/study/cie-9700-u6-dna-replication/)
- [Transcription](https://www.owlsprep.com/study/cie-9700-u6-transcription/)
- [The genetic code](https://www.owlsprep.com/study/cie-9700-u6-the-genetic-code/)

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