Nucleic Acids: DNA and RNA Structure

Master DNA and RNA structure, base pairing, double helix, and genetic information storage for JEE Chemistry

11 min read

The Hook: The Blueprint of Life

Connect: Real Life → Chemistry

Every cell in your body contains the same DNA - the instruction manual for making YOU! DNA paternity tests, COVID-19 PCR tests, genetic engineering, CRISPR gene editing - all depend on understanding nucleic acid chemistry. Your eye color, height, even susceptibility to diseases are encoded in DNA sequences.

Here’s the JEE question: Why does adenine always pair with thymine and guanine with cytosine? Why is DNA more stable than RNA? And how can a molecule just 2 nm wide store information for an entire organism?

The Core Concept

What are Nucleic Acids?

Nucleic acids = Polymers of nucleotides that store and transmit genetic information

Two types:

  1. DNA: Deoxyribonucleic acid (genetic blueprint)
  2. RNA: Ribonucleic acid (protein synthesis)

Functions:

  • Storage of genetic information (DNA)
  • Transfer of genetic information (mRNA)
  • Protein synthesis (tRNA, rRNA)
JEE Weightage
Nucleic Acids: 2-3 questions in JEE Main, 1-2 in JEE Advanced Focus areas: Structure of nucleotides, base pairing rules, DNA vs RNA, double helix

Building Blocks: Nucleotides

Structure of Nucleotides

Nucleotide = Sugar + Base + Phosphate

Three components:

1. Pentose Sugar:

  • Ribose (in RNA)
  • 2-Deoxyribose (in DNA)

2. Nitrogenous Base:

  • Purines: Adenine (A), Guanine (G)
  • Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

3. Phosphate Group:

  • -PO₄³⁻ (phosphoric acid)

Ribose vs Deoxyribose

Ribose (RNA):

     OH
      |
  5 CH₂—O  1 Base
      |  \  /
   4 H—C  C—H
      |    |
   3 H—C—C—H 2
      |    |
     OH   OH ← OH at C2

2-Deoxyribose (DNA):

      5 CH₂—O  1 Base
      |  \  /
   4 H—C  C—H
      |    |
   3 H—C—C—H 2
      |    |
     OH    H ← No OH at C2 (deoxy)

Key difference: DNA lacks OH at C2 position

JEE Concept: Why DNA is More Stable

DNA is more stable than RNA because:

Missing 2’-OH in DNA:

  • Less reactive (no OH at C2)
  • Cannot undergo base-catalyzed hydrolysis
  • More chemically stable
  • Better for long-term storage

RNA with 2’-OH:

  • More reactive
  • Can be hydrolyzed in alkaline conditions
  • Less stable
  • Suitable for temporary messages

This is why DNA stores genes, RNA is temporary messenger!

JEE Tip: “DNA is Durable (no OH at C2), RNA is Reactive (has OH)”

Nitrogenous Bases

Purines (Double ring)

Adenine (A):

        NH₂
         |
    N—C  C—N
   ||   ||   |
    C   C—N  CH
     \  /
      N

Guanine (G):

       O
       ||
    N—C  C—NH₂
   ||   ||    |
    C   C—N   CH
     \  /
      N

Pyrimidines (Single ring)

Cytosine (C):

        NH₂
         |
    N—C  C=O
   ||   ||
    C—C—NH

Thymine (T) - DNA only:

       O
       ||
    N—C  C—CH₃
   ||   ||
    C—C—NH
       ||
       O

Uracil (U) - RNA only:

       O
       ||
    N—C  C—H
   ||   ||
    C—C—NH
       ||
       O
Memory Trick: Bases

Purines: “PURe As Gold”

  • PURines: Adenine, Guanine
  • Larger (double ring)

Pyrimidines: “CUT the PY”

  • PYrimidines: Cytosine, Uracil, Thymine
  • Smaller (single ring)

DNA: “Thymine is in DNA (T looks like D)” RNA: “Uracil is Unique to RNA”

JEE Tip: DNA has T, RNA has U (instead of T)

Nucleoside vs Nucleotide

Nucleoside = Sugar + Base

  • No phosphate group
  • Examples: Adenosine, Guanosine, Cytidine

Nucleotide = Sugar + Base + Phosphate

  • Complete building block
  • Examples: Adenosine monophosphate (AMP), Guanosine monophosphate (GMP)

DNA Structure

Primary Structure

Phosphodiester linkage between nucleotides:

    Base₁
     |
5' —O—P—O—CH₂—O
     ||       \
     O         \
              3'-OH
                |
    Base₂      5'-CH₂—O
     |              \
    O—P—O            \
     ||            3'-OH
     O

Backbone:

  • Sugar-phosphate forms the backbone
  • Bases project inward
  • 5’ to 3’ direction (phosphate at 5’, OH at 3')

Secondary Structure: The Double Helix

Discovered by: James Watson and Francis Crick (1953)

Key features:

1. Two antiparallel strands:

  • One strand: 5’ → 3'
  • Other strand: 3’ → 5'

2. Right-handed double helix:

  • Diameter: 2 nm
  • One complete turn: 3.4 nm (10 base pairs)

3. Base pairing:

  • Adenine pairs with Thymine (A=T)
  • Guanine pairs with Cytosine (G≡C)

4. Complementary strands:

  • If one strand is A-G-C-T
  • Other strand is T-C-G-A

Chargaff’s Rules

Base pairing rules:

$$\boxed{[\text{A}] = [\text{T}]}$$ $$\boxed{[\text{G}] = [\text{C}]}$$

Purines = Pyrimidines:

$$[\text{A}] + [\text{G}] = [\text{T}] + [\text{C}]$$

Consequence:

  • %A = %T
  • %G = %C
  • %Purines = %Pyrimidines

Base Pairing: Watson-Crick Model

A-T pair (2 hydrogen bonds):

Adenine (A)          Thymine (T)

    N—H···O
    |     ||
    C     C—CH₃
    ||    |
    N···H—N

G-C pair (3 hydrogen bonds):

Guanine (G)          Cytosine (C)

    O···H—N
    ||    |
    C     C
    |     ||
    N—H···O
    |
    N—H···N
JEE Concept: Why Specific Pairing?

A always pairs with T, G always pairs with C because:

1. Geometry/Size:

  • Purine + Pyrimidine = constant width (2 nm)
  • Purine + Purine = too wide (distorts helix)
  • Pyrimidine + Pyrimidine = too narrow (unstable)

2. Hydrogen bonding:

  • A-T: 2 H-bonds (specific donor-acceptor match)
  • G-C: 3 H-bonds (specific donor-acceptor match)
  • Other combinations: wrong H-bond pattern

3. Thermodynamic stability:

  • G-C more stable (3 H-bonds vs 2)
  • Higher %GC → higher melting temperature

Consequences:

  • If 30% A, then 30% T (Chargaff’s rule)
  • Remaining 40% must be 20% G + 20% C

JEE Tip: G-C is stronger (3 bonds) than A-T (2 bonds)!

Forces Stabilizing DNA

1. Hydrogen bonds:

  • Between complementary bases
  • A=T (2 bonds), G≡C (3 bonds)

2. Base stacking:

  • Van der Waals forces between stacked bases
  • Hydrophobic interactions
  • Major source of stability

3. Ionic interactions:

  • Between phosphate groups and cations (Na⁺, Mg²⁺)

Interactive Demo: Visualize DNA Double Helix

Explore the 3D structure of DNA and see how base pairs stack together.

RNA Structure

Types of RNA

1. Messenger RNA (mRNA):

  • Carries genetic information from DNA to ribosomes
  • Template for protein synthesis
  • 5-10% of total RNA

2. Transfer RNA (tRNA):

  • Brings amino acids to ribosomes
  • Cloverleaf structure
  • 15% of total RNA

3. Ribosomal RNA (rRNA):

  • Structural and catalytic component of ribosomes
  • 80% of total RNA

RNA vs DNA

FeatureDNARNA
Sugar2-DeoxyriboseRibose
BasesA, G, C, TA, G, C, U
StrandsDouble helixUsually single strand
StabilityMore stable (no 2’-OH)Less stable
LocationNucleus (mainly)Nucleus and cytoplasm
FunctionStores genetic infoTransfers info, makes proteins
AmountConstant in cellVaries with activity
JEE Question: DNA vs RNA

Q: Give three structural differences between DNA and RNA.

Solution:

1. Sugar:

  • DNA: 2-Deoxyribose (no OH at C2)
  • RNA: Ribose (has OH at C2)

2. Bases:

  • DNA: Adenine, Guanine, Cytosine, Thymine
  • RNA: Adenine, Guanine, Cytosine, Uracil

3. Structure:

  • DNA: Double-stranded helix (two antiparallel strands)
  • RNA: Usually single-stranded (can fold into complex structures)

Additional differences:

  • Stability: DNA more stable (no 2’-OH)
  • Function: DNA stores info, RNA transfers/translates
  • Location: DNA in nucleus, RNA in nucleus + cytoplasm

JEE Tip: Remember “DNA is Durable and Double, RNA is Reactive and has Ribose”

Central Dogma of Molecular Biology

Information flow in cells:

$$\boxed{\text{DNA} \xrightarrow{\text{Replication}} \text{DNA}}$$ $$\boxed{\text{DNA} \xrightarrow{\text{Transcription}} \text{RNA}}$$ $$\boxed{\text{RNA} \xrightarrow{\text{Translation}} \text{Protein}}$$

Replication:

  • DNA → DNA
  • Self-copying
  • Before cell division

Transcription:

  • DNA → RNA
  • Gene → mRNA
  • In nucleus

Translation:

  • RNA → Protein
  • mRNA → Polypeptide
  • At ribosomes

Genetic Code

Codons

Codon = 3 nucleotides (triplet) coding for 1 amino acid

Properties:

  1. Triplet code: 3 bases = 1 amino acid
  2. 64 possible codons (4³ = 64)
  3. 20 amino acids → code is degenerate (multiple codons for same amino acid)
  4. Universal: Same code in all organisms

Special codons:

  • Start: AUG (codes for methionine)
  • Stop: UAA, UAG, UGA (no amino acid)

Common Mistakes to Avoid

Mistake #1: Confusing T and U

Wrong: “DNA has uracil” or “RNA has thymine”

Correct:

  • DNA has Thymine
  • RNA has Uracil

Memory: “T for DNA (T looks like upside-down D)”

Mistake #2: Wrong Base Pairing

Wrong: “A pairs with C” or “G pairs with T”

Correct:

  • A = T (or A = U in RNA)
  • G ≡ C

Memory: “AT the GC (A-T and G-C)”

Mistake #3: Nucleoside = Nucleotide

Wrong: Using terms interchangeably

Correct:

  • Nucleoside: Sugar + Base (no phosphate)
  • Nucleotide: Sugar + Base + Phosphate

Memory: “NucleoTIDE has Phosphate (P for Tide)”

Practice Problems

Level 1: Foundation (NCERT)

Problem 1: Components

Q: What are the three components of a nucleotide?

Solution:

Three components:

  1. Pentose sugar:

    • Ribose (in RNA)
    • 2-Deoxyribose (in DNA)

  2. Nitrogenous base:

    • Purines: Adenine (A), Guanine (G)
    • Pyrimidines: Cytosine (C), Thymine (T), Uracil (U)

  3. Phosphate group:

    • Phosphoric acid (H₃PO₄)
    • Links nucleotides together

Structure: Sugar-Base-Phosphate

Problem 2: Base Pairing

Q: State the base pairing rules in DNA.

Solution:

Watson-Crick base pairing:

1. Adenine pairs with Thymine (A=T):

  • 2 hydrogen bonds
  • Purine + Pyrimidine

2. Guanine pairs with Cytosine (G≡C):

  • 3 hydrogen bonds
  • Purine + Pyrimidine

Chargaff’s Rules:

  • %A = %T
  • %G = %C
  • %Purines = %Pyrimidines

In RNA: A pairs with U (instead of T)

Level 2: JEE Main

Problem 3: Chargaff's Rule Application

Q: If a DNA sample contains 30% adenine, what are the percentages of the other bases?

Solution:

Given: %A = 30%

Using Chargaff’s rules:

Step 1: %A = %T

  • %T = 30%

Step 2: Total purines + pyrimidines = 100%

  • %A + %T + %G + %C = 100%
  • 30% + 30% + %G + %C = 100%
  • %G + %C = 40%

Step 3: %G = %C

  • %G = 20%
  • %C = 20%

Answer:

  • Adenine: 30%
  • Thymine: 30%
  • Guanine: 20%
  • Cytosine: 20%

Check: 30 + 30 + 20 + 20 = 100% ✓

Problem 4: Complementary Strand

Q: If one strand of DNA has sequence 5’-ATGC-3’, what is the sequence of the complementary strand?

Solution:

Given strand: 5’-ATGC-3'

Step 1: Apply base pairing rules

  • A pairs with T
  • T pairs with A
  • G pairs with C
  • C pairs with G

Step 2: Write complementary bases

  • A → T
  • T → A
  • G → C
  • C → G

Step 3: Remember antiparallel orientation

  • Given: 5’-A-T-G-C-3'
  • Complement: 3’-T-A-C-G-5'

Answer: 3’-TACG-5’

(Or written in standard 5’→3’ direction: 5’-GCAT-3')

JEE Tip: Strands are antiparallel - one 5’→3’, other 3’→5'!

Level 3: JEE Advanced

Problem 5: Stability Comparison

Q: Explain why DNA is more stable than RNA.

Solution:

DNA is more stable than RNA due to:

1. Chemical structure:

  • DNA: 2-Deoxyribose (no OH at C2')

    • Less reactive
    • Cannot undergo base-catalyzed hydrolysis

  • RNA: Ribose (has OH at C2')

    • More reactive
    • 2’-OH can attack phosphodiester bond
    • Susceptible to alkaline hydrolysis

2. Double helix structure (DNA):

  • Two complementary strands protect bases

  • Base stacking provides stability

  • H-bonds stabilize structure

  • RNA: Usually single-stranded

    • Bases more exposed
    • Less protected

3. Thymine vs Uracil:

  • Thymine (DNA): Has methyl group (-CH₃)

    • Extra stability
    • Protects from UV damage

  • Uracil (RNA): No methyl group

    • Less stable

Consequence:

  • DNA suitable for long-term storage (genes)
  • RNA suitable for temporary messages (mRNA)

This is why genetic information is stored in DNA, not RNA!

Problem 6: Melting Temperature

Q: Two DNA samples have the following composition: Sample A: 20% G, 20% C, 30% A, 30% T Sample B: 30% G, 30% C, 20% A, 20% T

Which has higher melting temperature? Why?

Solution:

Answer: Sample B has higher melting temperature

Reason:

G-C content:

  • Sample A: %G + %C = 20% + 20% = 40%
  • Sample B: %G + %C = 30% + 30% = 60%

G-C base pairs:

  • Have 3 hydrogen bonds (stronger)
  • More energy required to break
  • Higher melting temperature

A-T base pairs:

  • Have 2 hydrogen bonds (weaker)
  • Less energy required to break
  • Lower melting temperature

Relationship:

$$\text{Tm (melting temp)} \propto \%\text{GC content}$$

Conclusion:

  • Sample B (60% GC) > Sample A (40% GC)
  • Sample B requires more heat to denature
  • Higher Tm for Sample B

JEE Application: This principle is used in PCR and DNA analysis!

Quick Revision Box

TopicKey PointsJEE Fact
NucleotideSugar + Base + PhosphateBuilding block of DNA/RNA
SugarRibose (RNA), Deoxyribose (DNA)DNA lacks OH at C2
Bases (DNA)A, G, C, TT only in DNA
Bases (RNA)A, G, C, UU only in RNA
PurinesA, G (double ring)Larger bases
PyrimidinesC, T, U (single ring)Smaller bases
Base PairingA=T (2 H-bonds), G≡C (3 H-bonds)Chargaff’s rules
DNA StructureDouble helix, antiparallelWatson-Crick model
RNA StructureUsually single-strandedmRNA, tRNA, rRNA
StabilityDNA > RNANo 2’-OH in DNA

Connection to Other Topics

Prerequisites:

Related Topics:

Applications:

Teacher’s Summary

Key Takeaways

1. Nucleotide Structure:

  • Components: Sugar + Base + Phosphate
  • DNA sugar: 2-Deoxyribose (no OH at C2')
  • RNA sugar: Ribose (has OH at C2')

2. Nitrogenous Bases:

  • Purines: A, G (double ring) - larger
  • Pyrimidines: C, T, U (single ring) - smaller
  • DNA: A, G, C, T
  • RNA: A, G, C, U (U instead of T)

3. Base Pairing (Watson-Crick):

  • A = T (or A = U in RNA) - 2 H-bonds
  • G ≡ C - 3 H-bonds
  • Chargaff’s rules: %A = %T, %G = %C

4. DNA Double Helix:

  • Two antiparallel strands (5’→3’ and 3’→5')
  • Right-handed helix (2 nm diameter)
  • Complementary base pairing
  • Sugar-phosphate backbone (outside), bases inside

5. DNA vs RNA (HIGH-YIELD):

FeatureDNARNA
SugarDeoxyriboseRibose
BasesA, G, C, TA, G, C, U
StrandsDoubleSingle
StabilityMore stableLess stable

6. Stability:

  • DNA > RNA because:
    • No 2’-OH (less reactive)
    • Double helix (protected bases)
    • Thymine vs Uracil (methyl group)

7. Central Dogma:

  • DNA → DNA (Replication)
  • DNA → RNA (Transcription)
  • RNA → Protein (Translation)

“DNA is the blueprint, RNA is the messenger, proteins do the work!”

Next: Study Vitamins to learn about essential micronutrients and deficiency diseases!