DNA Structure and Replication

DNA Structure and Replication

DNA (Deoxyribonucleic Acid) is the genetic material in most organisms. It stores, replicates and transmits hereditary information from one generation to the next.

DNA को hereditary material इसलिए कहा जाता है क्योंकि इसमें organism के genetic information का storage होता है और यह information cell division के दौरान नई cells तक पहुँचती है।

Discovery of DNA as Genetic Material

The identification of DNA as the genetic material was established through a series of important experiments.

Scientist(s)	Important Contribution
Frederick Griffith	Demonstrated the phenomenon of transformation in bacteria.
Avery, MacLeod and McCarty	Showed that DNA was the transforming principle.
Hershey and Chase	Provided strong evidence that DNA is the genetic material using bacteriophages.
Watson and Crick	Proposed the double-helical structure of DNA in 1953.

Structure of DNA

DNA is a polymer made up of repeating units called nucleotides. Each nucleotide consists of three components:

1. Nitrogenous base
2. Pentose sugar
3. Phosphate group

Nucleotide and Nucleoside

Term	Components
Nucleoside	Nitrogenous base + sugar
Nucleotide	Nitrogenous base + sugar + phosphate group

Remember: Nucleoside = Sugar + Base, whereas Nucleotide = Sugar + Base + Phosphate.

Nitrogenous Bases of DNA

DNA contains four nitrogenous bases:

Base	Type	Abbreviation
Adenine	Purine	A
Guanine	Purine	G
Cytosine	Pyrimidine	C
Thymine	Pyrimidine	T

Watson and Crick Model of DNA

In 1953, James Watson and Francis Crick proposed the three-dimensional double-helical structure of DNA using available experimental evidence, including the work of Rosalind Franklin and Maurice Wilkins.

Important Features of DNA Double Helix

• DNA consists of two polynucleotide chains.
• The two strands are arranged in a double helix.
• The two strands are antiparallel.
• One strand runs in the 5′ → 3′ direction and the other in the 3′ → 5′ direction.
• The sugar-phosphate backbone lies on the outside.
• Nitrogenous bases project towards the interior.
• Adenine pairs with thymine.
• Guanine pairs with cytosine.
• A and T are joined by two hydrogen bonds.
• G and C are joined by three hydrogen bonds.
• The distance between two consecutive base pairs is approximately 0.34 nm.
• One complete turn of the DNA helix contains approximately 10 base pairs.
• The pitch of the helix is approximately 3.4 nm.

Complementary Base Pairing

DNA strands are complementary (पूरक) because a particular base on one strand pairs with a specific base on the other strand.

Base	Complementary Base	Hydrogen Bonds
Adenine (A)	Thymine (T)	2
Guanine (G)	Cytosine (C)	3

A = T     and     G ≡ C

Chargaff's Rule

Chargaff's rule states that in double-stranded DNA, the amount of adenine is equal to thymine and the amount of guanine is equal to cytosine.

Therefore:

A = T    and    G = C

Hence, the total amount of purines is equal to the total amount of pyrimidines.

Example

If a double-stranded DNA molecule contains 30% adenine, then thymine will also be 30%.

The remaining 40% consists of G and C. Since G = C:

G = 20%, C = 20%

Why DNA is More Stable Than RNA

DNA is generally more stable than RNA because of several structural features.

• DNA contains deoxyribose sugar, whereas RNA contains ribose.
• DNA contains thymine, whereas RNA contains uracil.
• DNA is usually double-stranded, providing greater stability.

DNA का double-stranded structure complementary base pairing के कारण genetic information को अधिक securely maintain करता है।

Packaging of DNA

DNA Packaging in Prokaryotes

In prokaryotes such as bacteria, DNA is generally present as a circular molecule in the nucleoid region. It is associated with some positively charged proteins.

DNA Packaging in Eukaryotes

Eukaryotic DNA is associated with positively charged proteins called histones.

A histone octamer consists of two copies each of H2A, H2B, H3 and H4.

The negatively charged DNA molecule wraps around the histone octamer to form a structure called a nucleosome.

Approximately 146 base pairs of DNA are wrapped around a histone octamer in a nucleosome.

DNA Replication

DNA replication is the process by which a DNA molecule produces an identical copy of itself.

Replication usually occurs before cell division so that each daughter cell receives a copy of the genetic information.

Semi-Conservative Replication

DNA replication is semi-conservative.

This means that each daughter DNA molecule contains:

• one parental strand
• one newly synthesised strand

अर्थात् replication के बाद दोनों daughter DNA molecules में एक पुरानी strand और एक नई strand होती है।

Meselson and Stahl Experiment

Matthew Meselson and Franklin Stahl experimentally demonstrated the semi-conservative nature of DNA replication in Escherichia coli.

They used nitrogen isotopes ¹⁵N and ¹⁴N to distinguish old and newly synthesised DNA.

Basic Experimental Logic

1. E. coli was grown in a medium containing ¹⁵N.
2. The DNA became heavy because ¹⁵N was incorporated.
3. The bacteria were transferred to a medium containing ¹⁴N.
4. After one generation, DNA showed an intermediate density.
5. After two generations, both intermediate and light DNA molecules were observed.

Mechanism of DNA Replication

DNA replication is a complex enzymatic process involving several enzymes and proteins.

Step 1: Unwinding of DNA

The double-stranded DNA must first be separated into two individual strands.

The enzyme helicase helps unwind the DNA double helix by breaking the hydrogen bonds between complementary bases.

Step 2: Formation of Replication Fork

The region where the two DNA strands separate is called the replication fork.

Replication may proceed from a specific origin of replication.

Step 3: Primer Formation

DNA polymerase cannot start DNA synthesis from nothing. A short RNA primer provides a free 3′-OH group from which DNA synthesis can begin.

The enzyme primase synthesises the RNA primer.

Step 4: DNA Synthesis

DNA polymerase adds nucleotides to the growing DNA strand.

DNA synthesis always occurs in the 5′ → 3′ direction.

Leading and Lagging Strands

Because the two DNA strands are antiparallel and DNA polymerase can synthesise DNA only in the 5′ → 3′ direction, replication occurs differently on the two templates.

Feature	Leading Strand	Lagging Strand
Synthesis	Continuous	Discontinuous
Fragments	Generally absent	Okazaki fragments formed
Direction of new DNA synthesis	5′ → 3′	5′ → 3′

Okazaki Fragments

Okazaki fragments are short DNA fragments synthesised discontinuously on the lagging strand during DNA replication.

These fragments are later joined together by the enzyme DNA ligase.

Important Enzymes in DNA Replication

Enzyme / Protein	Function
Helicase	Unwinds the DNA double helix.
Primase	Synthesises RNA primer.
DNA polymerase	Synthesises new DNA strand.
DNA ligase	Joins Okazaki fragments.
Topoisomerase	Helps relieve torsional strain during DNA unwinding.

Direction of DNA Replication

DNA strands are antiparallel:

5′ → 3′

3′ ← 5′

Since DNA polymerase synthesises DNA only in the 5′ → 3′ direction, one strand is synthesised continuously while the other is synthesised discontinuously.

DNA Replication: Complete Sequence

1. DNA double helix opens.
2. Helicase separates the two strands.
3. Replication fork is formed.
4. Primase forms RNA primer.
5. DNA polymerase adds complementary nucleotides.
6. Leading strand is synthesised continuously.
7. Lagging strand is synthesised discontinuously.
8. Okazaki fragments are formed.
9. RNA primers are removed/replaced as appropriate.
10. DNA ligase joins the DNA fragments.
11. Two daughter DNA molecules are produced.

Important Differences

DNA vs RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Purine bases	Adenine, Guanine	Adenine, Guanine
Pyrimidine bases	Cytosine, Thymine	Cytosine, Uracil
Strands	Usually double-stranded	Usually single-stranded
Main role	Storage of genetic information	Gene expression and protein synthesis

Important Terms

Term	Meaning
Nucleotide	Base + sugar + phosphate
Nucleoside	Base + sugar
Antiparallel	Two DNA strands run in opposite directions.
Complementary base pairing	A pairs with T and G pairs with C.
Replication fork	Region where DNA strands separate during replication.
Okazaki fragments	Short DNA fragments formed on the lagging strand.
Semi-conservative replication	Each daughter DNA has one parental and one new strand.
Nucleosome	DNA wrapped around a histone octamer.

Board Important Questions

Very Short Answer Questions

1. What is DNA?
2. Who proposed the double-helical model of DNA?
3. What are the three components of a nucleotide?
4. What is a nucleoside?
5. Name the purine bases of DNA.
6. Name the pyrimidine bases of DNA.
7. How many hydrogen bonds are present between A and T?
8. How many hydrogen bonds are present between G and C?
9. What is meant by antiparallel DNA strands?
10. What is semi-conservative replication?
11. Name the enzyme that unwinds DNA.
12. What is the function of DNA ligase?
13. What are Okazaki fragments?
14. Which enzyme synthesises the RNA primer?

Short Answer Questions

1. Describe the structure of a nucleotide.
2. Explain the Watson-Crick model of DNA.
3. What is Chargaff's rule?
4. Why are the two strands of DNA called complementary?
5. Explain semi-conservative replication of DNA.
6. Describe the role of helicase, primase, DNA polymerase and DNA ligase in DNA replication.
7. Differentiate between leading and lagging strands.
8. What are Okazaki fragments and why are they formed?

Long Answer Questions

1. Describe the Watson-Crick model of DNA with all important structural features.
2. Explain the mechanism of DNA replication.
3. Describe the Meselson and Stahl experiment and explain how it established semi-conservative replication.
4. Explain DNA packaging in eukaryotes.

Multiple Choice Questions

1. DNA stands for:
   (A) Deoxyribonucleic Acid
   (B) Deoxyribose Nitrogen Acid
   (C) Dinitro Ribonucleic Acid
   (D) Double Ribonucleic Acid
   Answer: (A) Deoxyribonucleic Acid
2. The double-helical structure of DNA was proposed by:
   (A) Mendel
   (B) Watson and Crick
   (C) Meselson and Stahl
   (D) Griffith
   Answer: (B) Watson and Crick
3. Which of the following is a purine?
   (A) Cytosine
   (B) Thymine
   (C) Adenine
   (D) Uracil
   Answer: (C) Adenine
4. In DNA, adenine pairs with:
   (A) Guanine
   (B) Cytosine
   (C) Uracil
   (D) Thymine
   Answer: (D) Thymine
5. Guanine and cytosine are joined by:
   (A) One hydrogen bond
   (B) Two hydrogen bonds
   (C) Three hydrogen bonds
   (D) Four hydrogen bonds
   Answer: (C) Three hydrogen bonds
6. The two DNA strands are:
   (A) Parallel
   (B) Antiparallel
   (C) Identical in sequence
   (D) Unrelated
   Answer: (B) Antiparallel
7. DNA replication is:
   (A) Conservative
   (B) Semi-conservative
   (C) Dispersive only
   (D) Random
   Answer: (B) Semi-conservative
8. The enzyme responsible for unwinding DNA is:
   (A) Ligase
   (B) Primase
   (C) Helicase
   (D) Polymerase
   Answer: (C) Helicase
9. Okazaki fragments are formed on the:
   (A) Leading strand
   (B) Lagging strand
   (C) RNA strand
   (D) Template-free strand
   Answer: (B) Lagging strand
10. DNA synthesis takes place in:
    (A) 3′ → 5′ direction
    (B) 5′ → 3′ direction
    (C) Both directions on the same strand
    (D) Random direction
    Answer: (B) 5′ → 3′ direction
11. The enzyme that joins Okazaki fragments is:
    (A) Helicase
    (B) Primase
    (C) DNA ligase
    (D) RNA polymerase
    Answer: (C) DNA ligase
12. A nucleotide consists of:
    (A) Sugar + base
    (B) Sugar + phosphate
    (C) Sugar + base + phosphate
    (D) Base + phosphate only
    Answer: (C) Sugar + base + phosphate
13. A nucleosome contains DNA wrapped around:
    (A) Ribosome
    (B) Histone octamer
    (C) RNA polymerase
    (D) Cellulose
    Answer: (B) Histone octamer
14. If adenine constitutes 25% of a double-stranded DNA molecule, guanine constitutes:
    (A) 25%
    (B) 50%
    (C) 75%
    (D) 12.5%
    Answer: (D) 25%
15. Meselson and Stahl used which isotope of nitrogen to label DNA?
    (A) ¹²N
    (B) ¹³N
    (C) ¹⁴N
    (D) ¹⁵N
    Answer: (D) ¹⁵N

Fill in the Blanks

1. DNA contains the sugar ______.
2. The two DNA strands are ______ to each other.
3. Adenine pairs with ______.
4. Guanine pairs with ______.
5. A-T pair contains ______ hydrogen bonds.
6. G-C pair contains ______ hydrogen bonds.
7. DNA replication is ______-conservative.
8. The enzyme that unwinds DNA is ______.
9. Okazaki fragments are formed on the ______ strand.
10. Okazaki fragments are joined by ______.

Match the Following

Column A	Column B
1. Helicase	a. Joins DNA fragments
2. Primase	b. Unwinds DNA
3. DNA polymerase	c. Synthesises RNA primer
4. DNA ligase	d. Synthesises new DNA

Answers: 1-b, 2-c, 3-d, 4-a

Quick Revision

DNA stores genetic information, replicates semi-conservatively, and passes hereditary information from one generation to the next.