# Nucleotides & Phosphodiester Bonds ## Nucleotides - Nucleotides are the **monomers** from which DNA and RNA **polymers** are built - Think of them like individual LEGO bricks that connect to form long chains

A nucleotide consists of three components: a pentose sugar, a nitrogen-containing organic base, and a phosphate group

- Nucleotide structure includes: - A **pentose sugar** (5-carbon sugar) - A **nitrogen-containing organic base** - A **phosphate group** ## DNA vs RNA Nucleotides ### DNA Nucleotides The components of a DNA nucleotide are: - A **deoxyribose** sugar - A **phosphate group** - One of four nitrogenous bases: - **Adenine (A)** - **Cytosine (C)** - **Guanine (G)** - **Thymine (T)** ### RNA Nucleotides The components of an RNA nucleotide are: - A **ribose** sugar - A **phosphate group** - One of four nitrogenous bases: - **Adenine (A)** - **Cytosine (C)** - **Guanine (G)** - **Uracil (U)**

DNA nucleotides contain deoxyribose sugar and thymine, while RNA nucleotides contain ribose sugar and uracil

## Purines and Pyrimidines The nitrogenous base molecules in DNA and RNA occur in two structural forms: - **Purines** - **Pyrimidines** ### Purines - **Adenine** and **guanine** are purines - They have a **double ring structure** - Think of them as the "larger" bases ### Pyrimidines - **Cytosine**, **thymine** and **uracil** are pyrimidines - They have a **single ring structure** - Think of them as the "smaller" bases ## Deoxyribose and Ribose Sugars - The sugars in nucleotides are **pentose sugars**, meaning that they contain **5 carbon atoms** - The carbons are numbered 1' to 5' (pronounced "one prime" to "five prime") - **Deoxyribose** sugar is found in DNA and **ribose** sugar in RNA - Deoxyribose contains **one fewer oxygen atom** than ribose ### Key Difference - In **ribose**, carbon 2 has an **OH group** (hydroxyl group) - In **deoxyribose**, carbon 2 has an **H group** (just hydrogen) - This is why it's called "deoxy" – it means "without oxygen" ## Nucleotide Structure Comparison Table | **Properties** | **DNA** | **RNA** | |----------------|---------|---------| | **Pentose sugar** | Deoxyribose | Ribose | | **Bases** | Adenine (A)
Thymine (T)
Cytosine (C)
Guanine (G) | Adenine (A)
Uracil (U)
Cytosine (C)
Guanine (G) | | **Number of strands** | Double-stranded
(double helix) | Single-stranded |

Make sure you know the key differences: DNA contains deoxyribose and thymine; RNA contains ribose and uracil. Also be able to identify which bases are purines and which are pyrimidines

## Phosphodiester Bonds - DNA and RNA are **polymers** (polynucleotides), meaning that they are made up of many nucleotides joined together in long chains - Separate nucleotides are **joined together via condensation reactions** - These condensation reactions occur between the **phosphate group** of one nucleotide and the **pentose sugar** of the next nucleotide

A phosphodiester bond is formed between two nucleotides and consists of a phosphate group and two ester bonds

### How Phosphodiester Bonds Form - A condensation reaction between two nucleotides forms a **phosphodiester bond** - It is called a phosphodiester bond because it consists of: - A **phosphate group** - **Two ester bonds** (one on each side of the phosphate) ### The Sugar-Phosphate Backbone - The chain of alternating phosphate groups and pentose sugars produced as a result of many phosphodiester bonds is known as the **sugar-phosphate backbone** (of the DNA or RNA molecule) - This backbone forms the structural framework of nucleic acid molecules - Imagine it like the sides of a ladder, with the bases pointing inward ### Synthesis vs Breakdown - The **synthesis** of polynucleotides requires the **formation** of phosphodiester bonds - Condensation reactions join nucleotides together - The **breakdown** of polynucleotides requires the **breakage** of phosphodiester bonds - Hydrolysis reactions break nucleotides apart

In condensation reactions, a molecule of water is released. In hydrolysis reactions, a molecule of water is added

### Key Points About Phosphodiester Bonds - They are **covalent bonds** (strong bonds) - They link the **5-carbon** of one deoxyribose sugar molecule to the **phosphate group** from the same nucleotide - The phosphate group is then linked by another phosphodiester bond to the **3-carbon** of the deoxyribose sugar molecule of the next nucleotide in the strand - This creates a directional structure with distinct **3' end** and **5' end**