Write the structures of fragments produced on complete hydrolysis of DNA. How are they linked in DNA molecule?

NCERT Exemplar · Q53

Q. Write the structures of fragments produced on complete hydrolysis of DNA. How are they linked in DNA molecule? Draw a diagram to show pairing of nucleotide bases in double helix of DNA.

Uttar Pradesh UpmspLong· 5mImportance★★★★★

78% · 86/110 Questions

🔒 Locked · start free trial →

You're viewing a preview — the full solution, concept, methods & PYQ mapping are locked.

Start your 14-day free trial to unlock the full solution →

Concept understanding — Nucleic Acid Components

Nucleic Acid Components: The Alphabet of Life

Imagine you want to write a book that contains all the instructions for building and running a living organism. You'd need an alphabet — a set of letters that can be combined in endless ways to form words, sentences, and chapters. In living cells, that alphabet is made of nucleic acids (DNA and RNA), and each "letter" is called a nucleotide.

The Big Picture: What Are Nucleic Acids?

Nucleic acids are long, chain-like molecules that store and transmit genetic information. DNA holds the master blueprint; RNA helps execute it. But both are built from the same basic building block: the nucleotide.

Note

Think of a nucleotide as a single Lego brick. DNA and RNA are long chains of these bricks, each brick slightly different from the next.

The Three Parts of a Nucleotide

Every nucleotide has three components, like a three-part key:

A phosphate group — a small, negatively charged group ( $\text{PO}_4^{3-}$ ). It acts like the "handle" that links nucleotides together.
A sugar — either ribose (in RNA) or deoxyribose (in DNA). This is the "body" of the brick.
A nitrogenous base — a ring-shaped molecule containing nitrogen. This is the "colored part" that carries the actual information.

The sugar and base together form a nucleoside. When you add the phosphate, you get a nucleotide.

Nucleoside = Sugar + Base Nucleotide = Sugar + Base + Phosphate

The Two Families of Bases

The bases come in two structural types:

Purines (double-ring structures): Adenine (A) and Guanine (G)
Pyrimidines (single-ring structures): Cytosine (C), Thymine (T) (only in DNA), and Uracil (U) (only in RNA)

Tip

A mnemonic: Purines are Pure as All Gold (A and G). Pyrimidines are CUT (C, U, T).

DNA vs. RNA: The Key Differences

Feature	DNA	RNA
Sugar	Deoxyribose (missing one oxygen)	Ribose (has that oxygen)
Bases	A, G, C, T	A, G, C, U
Structure	Double-stranded helix	Usually single-stranded
Function	Stores genetic information	Carries and executes instructions

Watch out

A common mistake: thinking "nucleoside" and "nucleotide" are the same. Remember: nucleotide has the phosphate; nucleoside does not. ATP (adenosine triphosphate) is a nucleotide — it's the energy currency of the cell.

Why This Matters

The sequence of bases along a DNA strand spells out the genetic code. A change in even one base (a mutation) can alter a protein, sometimes with dramatic consequences — like sickle cell anemia, where a single base change in the hemoglobin gene causes red blood cells to deform. …

Why this formula?

Nucleic Acid Components: Understanding the "Why" Behind the Key Relationships

Let’s start with the big picture: Nucleic acids (DNA and RNA) are polymers made of nucleotides. Each nucleotide has three parts: a nitrogenous base, a pentose sugar, and a phosphate group. The key formulas and relationships in this topic arise from how these parts are linked and how they behave chemically.

1. The Basic Composition Formula

What it says:

A nucleotide = Base + Sugar + Phosphate

Why this holds:

Chemical necessity: The sugar (ribose in RNA, deoxyribose in DNA) has a 5-carbon ring. The base attaches to the 1' carbon (via a glycosidic bond), and the phosphate attaches to the 5' carbon (via an ester bond).
Directionality: This creates a 5' → 3' linkage in the polymer. The phosphate of one nucleotide bonds to the 3' carbon of the next sugar.
Reasoning: Without the phosphate, you have a nucleoside (base + sugar). Adding the phosphate makes it a nucleotide — the monomer that can polymerize.

Key takeaway: The formula isn’t arbitrary — it reflects the specific carbon positions on the sugar that allow for stable, directional chain formation.

2. Chargaff’s Rules (for DNA)

What it says:

In double-stranded DNA:

$[A] = [T]$
$[G] = [C]$
$[A] + [G] = [T] + [C]$

Why this holds:

Base pairing: Adenine (A) forms two hydrogen bonds with Thymine (T). Guanine (G) forms three hydrogen bonds with Cytosine (C).
Structural constraint: The DNA double helix has a constant width (20 Å). A purine (A or G) always pairs with a pyrimidine (T or C) — otherwise the helix would bulge or narrow.
Derivation: If every A on one strand must pair with a T on the opposite strand, then the number of A equals number of T in the whole molecule. Same for G and C.
Consequence: The sum of purines equals sum of pyrimidines ( $A+G = T+C$ ).

Why it’s not just a rule: It’s a geometric and energetic necessity — hydrogen bonding and helix stability force this equality.

3. The Phosphodiester Bond Energy Formula

What it says:

Formation of a phosphodiester bond requires ~30 kJ/mol of energy (from ATP).

Why this holds:

Mechanism: The 3' hydroxyl of one nucleotide attacks the α-phosphate of a nucleotide triphosphate (e.g., ATP). This releases pyrophosphate (PPi).
Energy source: The hydrolysis of PPi to two inorganic phosphates ( $PPi \rightarrow 2P_i$ ) is highly exergonic (ΔG ≈ -30 kJ/mol). This drives the reaction forward.
Reasoning: The bond itself is a covalent ester linkage — strong but not spontaneously formed. The energy comes from breaking a high-energy phosphate bond in the triphosphate.

Key insight: The formula isn’t about the bond’s strength — it’s about the thermodynamic cost of making it in a cell.

4. The Melting Temperature ( $T_m$ ) Formula

What it says:

$T_m$ (in °C) ≈ $4(G+C) + 2(A+T)$ for short oligonucleotides.

Why this holds:

Hydrogen bonds: G-C pairs have 3 H-bonds, A-T pairs have 2 H-bonds. More H-bonds = more energy needed to separate strands.
Stacking interactions: G-C base pairs also have stronger π-stacking (aromatic ring overlap) than A-T.
Derivation: The formula is empirical — it comes from measuring $T_m$ for many sequences. The coefficients (4 and 2) reflect the relative stability contributed by each base pair.
Limitation: For long DNA, this simple formula fails because nearest-neighbor interactions matter more.

Why it works: It’s a linear approximation of the free energy needed to break all base pairs, weighted by H-bond count.

5. The Central Dogma (Information Flow)

What it says:

DNA → RNA → Protein

Why this holds: …

Start your 14-day free trial to unlock the full solution →

The key idea is that DNA is a polynucleotide; complete hydrolysis breaks all phosphodiester and N-glycosidic bonds, yielding three distinct components.

Reasoning:

Hydrolysis of the backbone: The phosphodiester bonds between the $3'$ ‑OH of one sugar and the $5'$ ‑phosphate of the next are broken, releasing free phosphoric acid ( $H_3PO_4$ ) and nucleosides.
Hydrolysis of nucleosides: The N‑glycosidic bond linking the nitrogenous base to the $1'$ ‑carbon of deoxyribose is cleaved, separating the base from the sugar.
Final fragments: The three products are:
- Phosphoric acid ( $H_3PO_4$ )
- Deoxyribose sugar ( $C_5H_{10}O_4$ )
- Nitrogenous bases — Adenine (A), Guanine (G), Cytosine (C), Thymine (T)

Linking in DNA: Nucleotides are linked by $3'$ – $5'$ phosphodiester bonds — the phosphate group bridges the $3'$ ‑OH of one deoxyribose to the $5'$ ‑OH of the next, forming a sugar‑phosphate backbone.

Base pairing in the double helix:

Adenine pairs with Thymine via two hydrogen bonds.
Guanine pairs with Cytosine via three hydrogen bonds.
The strands are antiparallel ( $5' \to 3'$ and $3' \to 5'$ ).

     5'                   3'
      |                   | …

Start your 14-day free trial to unlock the full solution →

Complete hydrolysis of DNA breaks it down into three components: a phosphate group, a deoxyribose sugar, and nitrogenous bases (adenine, guanine, cytosine, thymine). In the DNA molecule, these are linked by phosphodiester bonds between sugars and phosphates, and hydrogen bonds between complementary base pairs (A–T and G–C). The double helix is stabilised by these bonds, with base pairing shown in a diagram.

Concept and Intuition

DNA is a long polymer made of repeating units called nucleotides. Each nucleotide has three parts: a phosphate group, a deoxyribose sugar (with five carbons), and a nitrogenous base. When DNA is completely hydrolysed — meaning all chemical bonds are broken — it falls apart into these individual building blocks. But in the intact DNA molecule, these pieces are linked in a specific way: the sugar of one nucleotide connects to the phosphate of the next via a phosphodiester bond, forming a sugar-phosphate backbone. The bases stick out from this backbone and pair up with bases on the opposite strand through hydrogen bonds, following the rule that adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C). This pairing is what gives the DNA double helix its famous structure.

Watch out

A common mistake is to confuse the products of complete hydrolysis with those of partial hydrolysis. Complete hydrolysis yields individual components (phosphate, sugar, base), not nucleotides or dinucleotides. Partial hydrolysis would give smaller fragments like nucleotides or oligonucleotides.

Step-by-Step Solution

1. Identify the products of complete hydrolysis of DNA

Complete hydrolysis breaks all covalent bonds in the DNA polymer. This means:

The phosphodiester bonds between sugars and phosphates are broken.
The N-glycosidic bonds between sugars and bases are also broken.

So the final fragments are:

Phosphoric acid ( $H_3PO_4$ ) — the phosphate group.
Deoxyribose sugar — a pentose sugar with the formula $C_5H_{10}O_4$ .
Nitrogenous bases — these are of two types:
- Purines: Adenine (A) and Guanine (G).
- Pyrimidines: Cytosine (C) and Thymine (T).

Thus, the complete hydrolysis of DNA yields a mixture of phosphate, deoxyribose, and the four bases (A, G, C, T).

\text{DNA} \xrightarrow{H_2O, H^+} \text{Phosphoric acid} + \text{Deoxyribose} + \text{Adenine} + \text{Guanine} + \text{Cytosine} + \text{Thymine}

2. How are these components linked in the DNA molecule?

In the intact DNA molecule, the linkages are as follows:

Between sugar and phosphate: The phosphate group forms an ester bond with the $5'$ carbon of one deoxyribose sugar and another ester bond with the $3'$ carbon of the next deoxyribose sugar. This creates a phosphodiester bond ( $-O-PO_2-O-$ ) that links nucleotides together in a chain. This forms the sugar-phosphate backbone.
Between sugar and base: The nitrogenous base is attached to the $1'$ carbon of deoxyribose via an N-glycosidic bond (a bond between the anomeric carbon of the sugar and a nitrogen atom of the base).
Between two strands: The two strands of DNA are held together by hydrogen bonds between complementary bases. Adenine (A) pairs with Thymine (T) via two hydrogen bonds, and Guanine (G) pairs with Cytosine (C) via three hydrogen bonds. This is called complementary base pairing.

Tip

Remember the base pairing rule with a mnemonic: Apple Tree (A–T, 2 bonds) and Golf Cart (G–C, 3 bonds). The number of hydrogen bonds is important for stability — G–C pairs are stronger because they have three bonds. …

Start your 14-day free trial to unlock the full solution →

Concept: Structure of DNA and its Hydrolysis Products

DNA (Deoxyribonucleic Acid) is a polymer of nucleotides. Complete hydrolysis breaks all the bonds in the DNA backbone, yielding its simplest building blocks.

Method: Sequential Hydrolysis Analysis

Step 1: Identify the primary structure of DNA

DNA is a polynucleotide chain.
Each nucleotide has three components:
- A nitrogenous base (Adenine, Guanine, Cytosine, Thymine)
- A deoxyribose sugar (a pentose sugar)
- A phosphate group

Step 2: Understand what "complete hydrolysis" means

Complete hydrolysis breaks all covalent bonds between nucleotides.
This yields the monomeric units — not larger fragments.

Step 3: Write the fragments produced

Complete hydrolysis of DNA gives three types of molecules:

Nitrogenous bases:
- Purines: Adenine (A) and Guanine (G)
- Pyrimidines: Cytosine (C) and Thymine (T)
Deoxyribose sugar:
- $\text{C}_5\text{H}_{10}\text{O}_4$ (a pentose sugar)
Phosphoric acid:
- $\text{H}_3\text{PO}_4$

Key result: Complete hydrolysis → Bases + Sugar + Phosphate (no nucleotides remain).

How Are They Linked in the DNA Molecule?

The linkage is through phosphodiester bonds:

A phosphodiester bond forms between the 3' carbon of one deoxyribose sugar and the 5' carbon of the next deoxyribose sugar, via a phosphate group.
This creates a sugar-phosphate backbone with bases projecting inward.

Bonding summary:

N-glycosidic bond: Between base and deoxyribose (C1' of sugar to N1 of pyrimidine or N9 of purine)
Phosphodiester bond: Between adjacent sugars via phosphate

Diagram: Base Pairing in DNA Double Helix

     5'                3'
      |                |
      A = = = = = = = T
      |                |
      G = = = = = = = C
      |                |
      C = = = = = = = G
      |                | …

Start your 14-day free trial to unlock the full solution →

Here are the common mistakes students make on this DNA hydrolysis and structure question, along with how to avoid each.

1. Confusing "Complete Hydrolysis" with "Partial Hydrolysis"

The Mistake:

Students often list nucleotides (sugar + phosphate + base) as the final products.

Complete hydrolysis breaks all chemical bonds in the backbone, yielding three separate components.

How to Avoid:

Remember the hierarchy:

DNA → (complete hydrolysis) → Phosphoric acid + Deoxyribose sugar + Nitrogenous bases (A, T, G, C)
Partial hydrolysis would give nucleotides or nucleosides.

Correct answer:

Fragments = Phosphate group, Deoxyribose sugar, and Nitrogenous bases (Adenine, Thymine, Guanine, Cytosine).

2. Forgetting the Specific Sugar Name

The Mistake:

Writing "ribose" instead of deoxyribose.

This is a classic exam trap — RNA has ribose, DNA has deoxyribose.

How to Avoid:

Link the name to the structure:

Deoxyribose lacks one –OH group at the 2′ carbon (compared to ribose).
Write it explicitly: 2-deoxy-D-ribose.

3. Incorrect Linkage Description (Phosphodiester Bond)

The Mistake:

Saying "phosphate links sugar to base" or "bases are linked by hydrogen bonds" when describing the backbone linkage.

How to Avoid:

Be precise about which atoms are involved:

The linkage is a 3′–5′ phosphodiester bond.
It connects the 3′ carbon of one deoxyribose to the 5′ carbon of the next deoxyribose, via a phosphate group.

Correct phrasing:

"Nucleotides are linked by 3′–5′ phosphodiester bonds between the sugar of one nucleotide and the phosphate of the next."

4. Drawing the Base Pairing Diagram Incorrectly

The Mistake:

Showing A–G or T–C pairs.
Drawing two hydrogen bonds for G–C (it has three).
Forgetting the antiparallel orientation of the two strands.

How to Avoid:

Memorise the Chargaff’s rule pairs:

A = T (2 hydrogen bonds)
G ≡ C (3 hydrogen bonds)

In your diagram:

Draw one strand 5′ → 3′ and the other 3′ → 5′.
Show dashed lines for H-bonds (2 between A–T, 3 between G–C).
Label the sugar-phosphate backbone as two outer ribbons.

Quick diagram (text representation):

5'   3'
|    |
S—P—S—P—S—P
|    |    |
A===T   G≡C
|    |    |
P—S—P—S—P—S
|    |    |
3'   5'

(In your exam, draw a clear, labelled diagram with arrows showing direction.)

5. Omitting the "Antiparallel" Nature

The Mistake: …

Start your 14-day free trial to unlock the full solution →

←Previous questionQ52 — Explain the terms primary and secondary structure of proteins. What is…→Next questionQ54 — Carbohydrates are classified on the basis of their behaviour on hydrol…

Q.Write the structures of fragments produced on complete hydrolysis of DNA. How are they linked in DNA molecule? Draw a diagram to show pairing of nucleotide bases in double helix of DNA.

Concept and Intuition

Step-by-Step Solution

🎓Unlock everything free for 14 days

Unlock everything free for 14 days