2.22 Nitrogenous Bases in the Nucleotide

Introduction

Nitrogenous bases are one of the three essential components of nucleotides, along with pentose sugar and phosphate. They are nitrogen-containing ring structures that store and transmit genetic information. There are two major classes of nitrogenous bases: purines and pyrimidines. The sequence of these bases along a nucleic acid chain encodes the genetic instructions for all living organisms.

Definition

Nitrogenous Bases: Nitrogenous bases are nitrogen-containing ring structures that are attached to the 1' carbon of the pentose sugar in a nucleotide. They are classified into two major classes: purines and pyrimidines.

In simple words: Nitrogenous bases are the "letters" of the genetic code — they carry the information in DNA and RNA.

Core Concept

• Pyrimidines – Single-ring structures
• Purines – Double-ring structures

• Cytosine (C)
• Thymine (T) – only found in DNA
• Uracil (U) – only found in RNA

• Adenine (A)
• Guanine (G)

Detailed Explanation

Pyrimidines

Definition: Pyrimidines are nitrogenous bases that have a single-ring structure.

• Six-membered ring
• Two nitrogen atoms
• Four carbon atoms

Types of Pyrimidines:

• Cytosine (C) is found in both DNA and RNA.
• Thymine (T) is found only in DNA.
• Uracil (U) is found only in RNA.
• Thymine and uracil differ only by a methyl group (-CH₃).
• Thymine has a methyl group.
• Uracil does not have a methyl group.

Purines

Definition: Purines are nitrogenous bases that have a double-ring structure.

• Two fused rings: a six-membered ring fused to a five-membered ring
• Four nitrogen atoms
• Five carbon atoms

Types of Purines:

• Adenine (A) is found in both DNA and RNA.
• Guanine (G) is found in both DNA and RNA.

Comparison of Purines and Pyrimidines

Bases in DNA and RNA

• DNA: A, T, G, C → "AT the GC"
• RNA: A, U, G, C → "AU the GC"

Chargaff's Rule

Definition: In 1951, Erwin Chargaff found that the nitrogenous bases in a DNA show specific ratios.

• The amount of adenine (A) is always equal to the amount of thymine (T).
• The amount of guanine (G) is always equal to the amount of cytosine (C).
• This implies that the total purines and total pyrimidines are in 1:1 ratio in any DNA.

Equations: A = T G = C A + G = T + C Purines = Pyrimidines

In simple words: In DNA, the amount of A equals T, and the amount of G equals C. This is because A pairs with T, and G pairs with C.

Base Pairing

Definition: Base pairing is the specific interaction between a purine and a pyrimidine in DNA.

• Adenine (A) pairs with Thymine (T) – 2 hydrogen bonds
• Guanine (G) pairs with Cytosine (C) – 3 hydrogen bonds

• Adenine (A) pairs with Uracil (U) – 2 hydrogen bonds
• Guanine (G) pairs with Cytosine (C) – 3 hydrogen bonds

• Purines are double-ringed (larger).
• Pyrimidines are single-ringed (smaller).
• A purine + pyrimidine pair maintains a constant width of the DNA double helix.
• If two purines paired, the helix would be too wide.
• If two pyrimidines paired, the helix would be too narrow.

Hydrogen Bonding Between Bases

• G–C pairs are stronger than A–T pairs because they have 3 hydrogen bonds instead of 2.
• This is why DNA with high G–C content has a higher melting temperature.

Nucleosides and Nucleotides

Nucleoside: Base + Sugar Nucleotide: Base + Sugar + Phosphate

Naming of Nucleosides:

Naming of Nucleotides:

Note: The "d" prefix stands for "deoxy."

Table of Nucleosides and Nucleotides (from textbook)

The textbook mentions: "Different terms used for nucleosides and nucleotides are given in the table 2.7."

Biological Importance of Nitrogenous Bases

• Genetic information: The sequence of bases in DNA stores genetic information.
• Protein synthesis: The sequence of bases in mRNA is translated into proteins.
• Base pairing: Complementary base pairing is essential for DNA replication and transcription.
• Structure of DNA: Base pairing maintains the constant width of the DNA double helix.
• Energy currency: ATP (adenine + ribose + 3 phosphates) is the energy currency of the cell.
• Coenzymes: NAD, FAD, and coenzyme A are nucleotide derivatives.
• Signaling molecules: cAMP and cGMP are nucleotide derivatives that act as second messengers.

Intermediate Level

Purines vs Pyrimidines

Base Pairing Rules

• G–C has 3 hydrogen bonds.
• A–T has 2 hydrogen bonds.
• More hydrogen bonds = stronger pairing.

Chargaff's Rule

• **A = T** in DNA
• **G = C** in DNA
• **Purines = Pyrimidines**

• It helped Watson and Crick determine the structure of DNA.
• It showed that A pairs with T and G pairs with C.

Nucleosides and Nucleotides

Naming Conventions

• Nucleoside: Base + Sugar
• Nucleotide: Base + Sugar + Phosphate
• With ribose: Adenosine, Guanosine, Cytidine, Uridine
• With deoxyribose: Deoxyadenosine, Deoxyguanosine, Deoxycytidine, Deoxythymidine
• With one phosphate: AMP, GMP, CMP, TMP, UMP
• With two phosphates: ADP, GDP, CDP, TDP, UDP
• With three phosphates: ATP, GTP, CTP, TTP, UTP

Important Points

• 1. There are two major classes of nitrogenous bases:
• - Pyrimidines – Single-ring
• - Purines – Double-ring
• 2. Pyrimidine bases are of three types:
• - Cytosine (C) – found in both DNA and RNA
• - Thymine (T) – only found in DNA
• - Uracil (U) – only found in RNA
• 3. Purine bases are of two types:
• - Adenine (A) – found in both DNA and RNA
• - Guanine (G) – found in both DNA and RNA
• 4. The nucleotides which take part in the formation of DNA or RNA must contain three phosphates but during their incorporation into DNA or RNA polymer each nucleotide loses its two terminal phosphates.
• 5. Chargaff's rule: The amount of adenine is always equal to the amount of thymine and the amount of guanine is always equal to the amount of cytosine in DNA.
• 6. This implies that the total purines and total pyrimidines are in 1:1 in any DNA.
• 7. Base pairing:
• - A pairs with T (DNA) – 2 hydrogen bonds
• - A pairs with U (RNA) – 2 hydrogen bonds
• - G pairs with C (DNA and RNA) – 3 hydrogen bonds
• 8. Nucleoside: Base + Sugar
• 9. Nucleotide: Base + Sugar + Phosphate
• 10. Different terms used for nucleosides and nucleotides:
• | Base | Nucleoside | Nucleotide |
• | Adenine | Adenosine | Adenosine monophosphate (AMP) |
• | Guanine | Guanosine | Guanosine monophosphate (GMP) |
• | Cytosine | Cytidine | Cytidine monophosphate (CMP) |
• | Thymine | Thymidine | Thymidine monophosphate (TMP) |
• | Uracil | Uridine | Uridine monophosphate (UMP) |

Remember

• - Purines = double ring = A, G
• - Pyrimidines = single ring = C, T, U
• - **DNA bases** = A, T, G, C
• - **RNA bases** = A, U, G, C
• - Base pairing: A–T (DNA), A–U (RNA), G–C (both)
• - **Chargaff's rule:** A = T, G = C
• - **A–T** = 2 hydrogen bonds
• - **G–C** = 3 hydrogen bonds
• - G–C is stronger than A–T
• - Nucleoside = base + sugar
• - Nucleotide = base + sugar + phosphate

Common Mistakes

• 1. Confusing purines and pyrimidines – Purines = double ring (A, G); Pyrimidines = single ring (C, T, U).
• 2. Thinking thymine is in RNA – Thymine is only in DNA; Uracil is in RNA.
• 3. Thinking uracil is in DNA – Uracil is only in RNA; Thymine is in DNA.
• 4. Forgetting Chargaff's rule – A = T and G = C in DNA.
• 5. Confusing the number of hydrogen bonds – A–T = 2; G–C = 3.
• 6. Thinking A pairs with G – A pairs with T (DNA) or U (RNA); G pairs with C.
• 7. Confusing nucleosides and nucleotides – Nucleosides have sugar + base; nucleotides have sugar + base + phosphate.
• 8. Thinking all bases are found in both DNA and RNA – Thymine is only in DNA; Uracil is only in RNA.
• 9. Forgetting that G–C is stronger than A–T – G–C has 3 hydrogen bonds; A–T has 2.
• 10. Confusing the naming of nucleosides and nucleotides – Adenosine is a nucleoside; AMP is a nucleotide.
• 11. Thinking purines pair with purines – Purines pair with pyrimidines to maintain constant width.
• 12. Forgetting the importance of base pairing – Base pairing is essential for DNA replication, transcription, and structure.

Quick Revision

• There are two major classes of nitrogenous bases i.e., single ring pyrimidine and double ring purines.
• Pyrimidine bases are of three types i.e., cytosine (C), thymine (T) and uracil (U).
• Thymine is only found in DNA while the uracil is only found in RNA.
• The purine bases are also of two types i.e., adenine (A) and guanine (G).
• The nucleotides which take part in the formation of DNA or RNA must contain three phosphates but during their incorporation into DNA or RNA polymer each nucleotide losses its two terminal phosphates.
• Different terms used for nucleosides and nucleotides are given in the table 2.7.

• Chargaff's rule: In 1951, Erwin Chargaff found that the nitrogenous bases in a DNA show specific ratios.
• He observed that amount of adenine is always equal to the amount of thymine and amount of guanine is always equal to the amount of cytosine in DNA.
• This implies that the total purines and total pyrimidines are in 1:1 in any DNA.
• This conclusion is known as Chargaff's rule.

60-Second Revision

• Purines = double ring = A, G
• Pyrimidines = single ring = C, T, U
• **DNA bases** = A, T, G, C
• **RNA bases** = A, U, G, C
• Base pairing: A–T (DNA), A–U (RNA), G–C (both)
• **Chargaff's rule:** A = T, G = C
• **A–T** = 2 hydrogen bonds
• **G–C** = 3 hydrogen bonds
• G–C is stronger than A–T
• Nucleoside = base + sugar
• Nucleotide = base + sugar + phosphate
• Adenosine = nucleoside; AMP = nucleotide
• Warning: Thymine is only in DNA; uracil is only in RNA. Purines pair with pyrimidines, not with each other. A–T has 2 hydrogen bonds; G–C has 3. Nucleosides and nucleotides are not the same. Chargaff's rule applies to DNA, not RNA.