What is the difference between a nucleoside and a nucleotide?

A nucleoside is a nitrogenous base joined to a pentose sugar through an N-glycosidic linkage — examples are adenosine, guanosine, cytidine and deoxythymidine. A nucleotide is a nucleoside that additionally carries a phosphate group esterified to the 5' carbon of the sugar through a phosphoester linkage. In short, nucleotide = nucleoside + phosphate. DNA and RNA are polymers of nucleotides, not nucleosides.

Why are the two strands of DNA called antiparallel?

The two polynucleotide chains of DNA run in opposite directions: if one strand has the polarity 5'→3', the partner strand has the polarity 3'→5'. This opposite orientation is called antiparallel polarity. It is a salient feature of the Watson-Crick model and is essential because base pairing geometry — and later, the 5'→3' action of DNA polymerase during replication — depends on the strands lying head-to-tail rather than side-by-side.

Why does adenine always pair with thymine and guanine with cytosine?

Base pairing follows the rule that a purine always pairs with a pyrimidine. Adenine forms two hydrogen bonds with thymine, and guanine forms three hydrogen bonds with cytosine. A purine-pyrimidine pair is exactly the right width to bridge the two sugar-phosphate backbones, so the distance between the strands stays approximately uniform. A purine-purine pair would be too wide and a pyrimidine-pyrimidine pair too narrow.

What are the key dimensions of B-form DNA?

In the B-form double helix described by Watson and Crick, the helix diameter is about 2 nm, the pitch (length of one complete turn) is 3.4 nm, there are roughly 10 base pairs per turn, and the rise — the distance between two adjacent base pairs — is approximately 0.34 nm. The two chains are coiled in a right-handed fashion.

What is Chargaff's rule and how does it support the double helix?

Erwin Chargaff observed that in any double-stranded DNA the ratio of adenine to thymine and the ratio of guanine to cytosine are both constant and equal to one — that is, A = T and G = C. This equivalence is exactly what complementary base pairing predicts: every A on one strand is matched by a T on the other, and every G by a C. Chargaff's data was one of the observations that guided Watson and Crick toward the base-paired model.

What forms the backbone of a polynucleotide chain?

The backbone of a polynucleotide chain is built from alternating sugar and phosphate units, joined by 3'-5' phosphodiester linkages. The nitrogenous bases are attached to the sugar and project inward from this backbone. One end of the chain carries a free phosphate on the 5' carbon (the 5' end) and the other carries a free hydroxyl on the 3' carbon (the 3' end).

The DNA — Structure — NEET Notes

NCERT grounding

NCERT Class 12 Biology, Chapter 5 (Molecular Basis of Inheritance), opens with Section 5.1, The DNA. It defines DNA as "a long polymer of deoxyribonucleotides" and notes that its length is measured as the number of nucleotides — or base pairs — present in it. Section 5.1.1, Structure of Polynucleotide Chain, then recapitulates the chemistry: a nucleotide has three components, and the chain is held together by 3'-5' phosphodiester linkages. The chapter culminates in the salient features of the Double-helix structure proposed by James Watson and Francis Crick in 1953, based on the X-ray diffraction data of Maurice Wilkins and Rosalind Franklin and on Erwin Chargaff's equivalence rule.

The NIOS Biology supplement (Chapter 23) reinforces the same model and adds the B-DNA diameter explicitly: "The diameter of the double helical DNA molecule is 2.0 nm." This page treats DNA structure as its own deep-dive — the single concept from which replication and transcription later follow.

"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."
— Watson and Crick, 1953 (quoted in NCERT)

From nucleotide to double helix

The DNA molecule is best understood by building it up in stages: first the monomer unit, then the single strand, and finally the paired, helical double strand. Each stage adds a layer of structure, and NEET questions are scattered across all three.

The nucleotide — the monomer unit

Nucleic acids are polymers, and their repeating monomer is the nucleotide. A nucleotide has exactly three components: a nitrogenous base, a pentose sugar, and a phosphate group. In DNA the pentose sugar is deoxyribose; in RNA it is ribose, which carries an additional –OH group at the 2' position. That single chemical difference makes RNA more reactive and less stable than DNA.

The nitrogenous bases fall into two chemical families. Purines have a double-ring structure and comprise adenine (A) and guanine (G). Pyrimidines have a single-ring structure and comprise cytosine (C), thymine (T) and uracil. Cytosine is common to both DNA and RNA; thymine is found in DNA, while uracil replaces it in RNA. Thymine is chemically 5-methyl uracil.

Mnemonic anchor: Purines are "Pure As Gold" — Adenine and Guanine. Everything else (Cytosine, Thymine, Uracil) is a pyrimidine. Purines are larger (two rings); pyrimidines are smaller (one ring).

Purines

A & G

Adenine, Guanine

Double-ring (fused six- and five-membered rings).

Larger bases — found in both DNA and RNA.

Pyrimidines

C, T & U

Cytosine, Thymine, Uracil

Single-ring (one six-membered ring).

Smaller bases — T in DNA, U in RNA, C in both.

Two assembly steps build the nucleotide. First, a nitrogenous base links to the –OH of the 1' carbon of the pentose sugar through an N-glycosidic linkage, producing a nucleoside — for example adenosine, guanosine, cytidine or, in the deoxy series, deoxyadenosine and deoxythymidine. Second, a phosphate group links to the –OH of the 5' carbon of the nucleoside through a phosphoester linkage, producing the nucleotide. The distinction is a perennial NEET favourite: nucleoside = base + sugar; nucleotide = base + sugar + phosphate.

The polynucleotide chain — backbone and polarity

When two nucleotides join, the phosphate at the 5' carbon of one nucleotide bonds to the 3' carbon of the next, forming a 3'-5' phosphodiester linkage and yielding a dinucleotide. Repeating this linkage produces a long polynucleotide chain. The alternating sugar and phosphate units form the sugar-phosphate backbone; the nitrogenous bases, attached to the sugars, project away from this backbone.

A polynucleotide chain is not symmetrical end-to-end — it has direction, or polarity. One end carries a free phosphate group on the 5' carbon of its terminal sugar; this is the 5' end. The other end carries a free hydroxyl (–OH) on the 3' carbon; this is the 3' end. By convention, sequences are written 5'→3' from left to right. This polarity is not a cosmetic detail: it dictates how the two strands are arranged in the helix and, later, the direction in which polymerases can build new strands.

Figure 1

Figure 1. A single polynucleotide chain. Alternating sugar (pentagons) and phosphate (orange circles) form the backbone; bases project sideways. The chain runs from a free 5'-phosphate end to a free 3'-OH end, the two joined by 3'-5' phosphodiester linkages.

The Watson-Crick double helix

In 1953, Watson and Crick proposed that DNA is not a single chain but a double helix of two polynucleotide chains. The model rested on two external observations: the X-ray diffraction data of Wilkins and Franklin, which indicated a helical, regular structure, and Chargaff's equivalence rule, which stated that in any double-stranded DNA the amount of adenine equals that of thymine and the amount of guanine equals that of cytosine — the ratios A/T and G/C both being constant and equal to one.

The salient features of the double helix, as listed in NCERT, are precise and examinable. The molecule is made of two polynucleotide chains whose backbones are constituted by sugar-phosphate, with the bases projecting inside. The two chains are coiled around a common axis in a right-handed fashion. And critically, the two chains have antiparallel polarity.

5' —A—T—G—C—A—T—G—C— 3'
   |  |  |  |  |  |  |  |
3' —T—A—C—G—T—A—C—G— 5'

Antiparallel orientation — going deep

Antiparallel polarity means the two strands run in opposite directions. If one chain has the polarity 5'→3' (reading left to right), its partner has the polarity 3'→5'. Place the two strands side by side and the 5' end of one lies next to the 3' end of the other — they are arranged head-to-tail, not head-to-head. This is one of the most heavily tested single facts in the chapter, and it is worth understanding why the molecule is built this way rather than merely memorising it.

The geometry of a base pair forces it. When adenine pairs with thymine, the two bases do not align symmetrically with respect to the strand direction; each base is attached to its sugar at a fixed angle. For the two glycosidic bonds — one from each base to its own backbone — to point toward their respective backbones at the correct geometry, the two backbones must run in opposite senses. If the strands were parallel, the bases could not form a stable, flat, hydrogen-bonded pair, and the regular helix would not close up.

Antiparallel orientation also has consequences that surface later in the chapter. DNA polymerase can add nucleotides only in the 5'→3' direction; because the two template strands run oppositely, replication proceeds continuously on one strand and discontinuously on the other. None of that would arise if the strands were parallel. For the structure subtopic, the examinable point is simply this: 5'→3' on one strand always implies 3'→5' on the other.

Antiparallel strands — the two ends compared

Strand 1

5' → 3'

left end is 5', right end is 3'

Terminal 5' carbon carries a free phosphate
Terminal 3' carbon carries a free –OH
Read in the conventional left-to-right direction

Strand 2 (partner)

3' → 5'

left end is 3', right end is 5'

Lies head-to-tail against strand 1
Its 5' end faces strand 1's 3' end
Sequence is complementary, not identical

Complementary base pairing and helix geometry

The two strands are held together by hydrogen bonds between bases on opposite chains. The pairing is strict: adenine pairs only with thymine through two hydrogen bonds, and guanine pairs only with cytosine through three hydrogen bonds. Because A and G are purines while T and C are pyrimidines, every base pair couples one purine with one pyrimidine.

A=T | G≡C

Hydrogen-bond count

A–T is held by two hydrogen bonds; G–C by three. A higher proportion of G–C pairs therefore makes a DNA segment more thermally stable.

This purine-pyrimidine rule is the structural reason behind the helix's most striking feature: a uniform width. A purine paired with a pyrimidine spans a fixed distance — wide enough to bridge the two backbones, but no wider. A purine-purine pair would be too bulky and bow the backbones outward; a pyrimidine-pyrimidine pair would be too narrow and pinch them inward. By always matching a large base with a small one, the molecule keeps an approximately uniform distance between the two strands along its entire length. NCERT explicitly poses this as a question — "why the distance between two polynucleotide chains in DNA remains almost constant?" — and the answer is exactly this geometry.

Complementary pairing also makes the two strands complementary, not identical. Knowing the sequence of one strand allows the other to be predicted completely: every A is matched by T, every G by C. This single property is what makes DNA copyable, and it is the structural basis of semi-conservative replication.

Figure 2

Figure 2. Complementary base pairing. Each pair joins one purine to one pyrimidine: A–T by two hydrogen bonds, G–C by three. Because every pair has the same purine-plus-pyrimidine width, the two backbones stay an approximately uniform distance apart.

B-DNA geometry — the numbers to memorise

The double helix described by Watson and Crick is the B-form of DNA, the form found under typical cellular conditions. Its dimensions are fixed numbers that NEET asks directly, both as recall and as inputs to length calculations.

B-DNA — the four key dimensions

Right-handed helix

Diameter
~2 nm

Width of the helix; constant because every base pair is purine + pyrimidine.
Pitch
3.4 nm

Length of one complete turn of the helix.
bp per turn
~10 bp

Roughly ten base pairs are stacked within each turn.
Rise per bp
0.34 nm

Distance between two adjacent base pairs (pitch ÷ 10).

These four numbers are internally consistent. The pitch of 3.4 nm divided by roughly 10 base pairs per turn gives a rise of 0.34 nm per base pair. The rise is the figure used to calculate the physical length of a DNA molecule: total length equals the number of base pairs multiplied by 0.34 nm. Using this, NCERT calculates that the DNA of a typical diploid human cell — about 6.6 × 10⁹ base pairs — is roughly 2.2 metres long, far larger than the nucleus that contains it.

The flatness and regular stacking of the base pairs add a final stabilising feature. The plane of one base pair stacks over the plane of the next, and this base stacking, together with the hydrogen bonds, confers stability on the helical structure. Hydrogen bonds hold the strands across the helix; stacking interactions hold the pairs along it.

A purine always comes opposite a pyrimidine — and that one rule keeps the helix exactly 2 nm wide along its whole length.

The geometry of B-DNA

Worked examples

Worked example 1

A double-stranded DNA molecule contains 22% adenine. Calculate the percentage of guanine in the molecule.

By Chargaff's rule, A = T, so thymine is also 22%. Together A + T = 44%. The remaining 56% is shared equally by G and C, since G = C. Therefore guanine = 56% ÷ 2 = 28% (and cytosine is likewise 28%).

Worked example 2

One strand of a DNA segment reads 5'-ATGCGT-3'. Write its complementary strand in the 5'→3' direction.

First pair each base: A↔T, T↔A, G↔C, C↔G, G↔C, T↔A gives the partner 3'-TACGCA-5'. The partner is antiparallel, so its 5' end is at the right. Rewriting it in the conventional 5'→3' direction reverses the order: 5'-ACGCAT-3'.

Worked example 3

A B-DNA molecule has 6.6 × 10⁹ base pairs. If the distance between two consecutive base pairs is 0.34 nm, what is its approximate length?

Length = number of base pairs × rise per base pair = 6.6 × 10⁹ × 0.34 × 10⁻⁹ m = 2.244 m, i.e. approximately 2.2 metres. This is the standard NCERT figure for the DNA of a typical mammalian (diploid human) cell.

Worked example 4

Classify each of the following: adenine, deoxyadenosine, adenylic acid (adenosine monophosphate).

Adenine is a nitrogenous base — specifically a purine. Deoxyadenosine is a nucleoside: a base joined to deoxyribose sugar through an N-glycosidic linkage. Adenylic acid is a nucleotide: a nucleoside with a phosphate group esterified to the 5' carbon of the sugar. The ladder is base → nucleoside → nucleotide.

Common confusion & NEET traps

DNA structure is conceptually clean but riddled with near-identical terms. The errors that cost marks cluster around four distinctions: nucleoside versus nucleotide, the hydrogen-bond counts, what antiparallel really means, and the helix dimensions.

The DNA — Structure