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IB Biology · Theme A · A1.2

Nucleic acids

How life stores and copies information
Guiding questions

How does the structure of nucleic acids allow hereditary information to be stored?

How does the structure of DNA facilitate accurate replication?

Part one

Building blocks

A1.2.1 – A1.2.5
A1.2.1

The universal genetic material

DNA (deoxyribonucleic acid) is the molecule that stores genetic information and passes it from one generation to the next.
  • Every living organism — bacteria, archaea, fungi, plants, animals — uses DNA to store the instructions for building proteins and passing them on.
  • Nucleic acids have two jobs: storing genetic information, and carrying the code that tells the cell which proteins to build.
The exceptionSome viruses (influenza, SARS-CoV-2) carry RNA instead of DNA — this doesn't break the rule, because viruses aren't classified as living organisms: they have no cells and can't metabolise or reproduce on their own.
Silhouettes of a bacterium, tree, fish, and bird each containing a glowing DNA double helix
A nucleotide in data-booklet notation: a blue circle (phosphate) joined through carbon 5 prime to the left corner of a yellow pentagon (pentose sugar), whose ring oxygen is at the top and carbons 1 prime to 4 prime are numbered. A rectangle (base: A, C, G or T) joins carbon 1 prime on the right, and an OH group sits on carbon 3 prime at the lower left, where the next nucleotide joins
A1.2.2

The nucleotide

A nucleotide is the monomer of a nucleic acid — one phosphate group, one pentose (5-carbon) sugar, and one nitrogenous base.
  • The sugar's five carbons are numbered 1′ to 5′ — the prime symbol keeps them separate from the carbons inside the base.
  • Position matters: the base attaches to carbon 1′, the phosphate attaches to carbon 5′, and carbon 3′ carries a free —OH group — exactly where the next nucleotide in the chain will join.
IB conventionDiagrams draw the three parts as simple shapes: a circle for phosphate, a pentagon for the sugar, a rectangle for the base — the same notation used throughout this deck.
A1.2.3

The sugar-phosphate backbone

The backbone is the alternating chain of sugars and phosphates, joined by covalent bonds, running the length of a strand.
  • Nucleotides join by a condensation reaction — two molecules bond and a water molecule is released.
  • The new bond, a phosphodiester bond (a strong covalent bond), forms between the —OH on carbon 3′ of the nucleotide already in the chain and the phosphate on carbon 5′ of the nucleotide being added.
Why it mattersSo a strand has two different ends: a free phosphate at the 5′ end and a free —OH at the 3′ end. The backbone never changes, so the information is in the order of the bases.
Two nucleotides drawn as circle, pentagon and rectangle, one above the other. A coral phosphodiester bond joins carbon 3 prime of the upper sugar to the phosphate of the lower nucleotide. The free phosphate at the top is the 5 prime end and the free OH at the bottom is the 3 prime end. A panel shows the condensation reaction: 3 prime OH plus phosphate gives a phosphodiester bond plus water
A long DNA molecule with one section highlighted as one gene. A zoom shows the gene as two strands of coloured base boxes, ATGGCATCAGTA paired with TACCGTAGTCAT. The order of the four bases along one strand carries the instructions for one product, usually a polypeptide
A1.2.4

The bases are the code

  • DNA has four bases: adenine (A), thymine (T), cytosine (C) and guanine (G).
  • All four are nitrogen-containing rings joined to carbon 1′ of the sugar, so any base can sit at any position.
  • Each has a different shape and hydrogen-bonding pattern, so each has only one partner it can pair with.
A gene is a length of DNA whose base sequence codes for one specific product, usually a polypeptide, and so influences a characteristic.
Why it mattersThe order of the bases is the information, like letters in a word: ATGCAT means something different from TACGTA.
A single RNA strand of four nucleotides, A, U, G and C, drawn as circles, pentagons and rectangles. Coral phosphodiester bonds join carbon 3 prime of each ribose to the next phosphate. Each ribose has an OH on carbon 2 prime. The 5 prime end is a free phosphate and the 3 prime end a free OH; uracil replaces thymine
A1.2.5

RNA is built the same way

  • RNA is a polymer too, formed by condensation of RNA nucleotide monomers — the same reaction, releasing the same water, joined by the same phosphodiester bonds into a sugar-phosphate backbone.
Only two differencesThe sugar is ribose instead of deoxyribose, and uracil appears instead of thymine. The way the chain is put together is otherwise identical — and RNA is normally single-stranded, one chain instead of two.

Key vocabulary — building blocks

Worth being able to define in a single sentence each

Nucleotide
phosphate + sugar + base — the monomer of a nucleic acid.
Phosphodiester bond
the covalent bond joining one sugar's 3′ to the next nucleotide's 5′ phosphate.
Condensation reaction
a reaction that joins two molecules and releases water.
Backbone
the alternating chain of sugars and phosphates running the length of a strand.
Gene
a DNA sequence whose base order codes for one specific product.
5′ end / 3′ end
the two different ends of a strand — free phosphate vs free —OH.
Quick check

A student draws a nucleotide with the base attached to the sugar's 3′ carbon, and the phosphate attached to the 1′ carbon. What's wrong?

Nothing — that's correct
The base should attach to carbon 1′, and the phosphate to carbon 5′
Phosphates never attach directly to a sugar
The sugar should be drawn as a rectangle, not a pentagon
Correct answer: the positions are swapped. The base attaches to carbon 1′; the phosphate attaches to carbon 5′; carbon 3′ carries the free —OH where the next nucleotide joins.
Part two

The double helix and its jobs

A1.2.6 – A1.2.10
A1.2.6

The double helix

  • DNA is two strands wound around each other.
  • Complementary base pairing fixes A with T and C with G — the shapes and hydrogen-bonding atoms of the bases allow no other combination.
  • Hydrogen bonds hold the pairs together: 2 bonds between A and T, 3 bonds between C and G — weak alone, but millions together hold the molecule firmly while still allowing it to be "unzipped" by enzymes.
AntiparallelThe two strands run in opposite directions — where one has its 5′ end, the other has its 3′ end. This arrangement lines up the bases facing each other so hydrogen bonds can form.
Four base pairs between two antiparallel backbones of phosphates and sugars: A with T, T with A, G with C and C with G. Two dashed hydrogen bonds join each A–T pair and three join each G–C pair. Arrows show the left strand running 5 prime to 3 prime downwards and the right strand 5 prime to 3 prime upwards
A1.2.3 · A1.2.6

One DNA molecule, part by part

Two antiparallel strands of nucleotides, held together by hydrogen bonds between complementary bases.
  • Along each strand, a phosphodiester bond joins every sugar to the next phosphate, making the sugar–phosphate backbone.
  • The bases point inward from the two backbones: A pairs with T and C pairs with G.
  • The strands run in opposite directions, so the 5′ end of one lies beside the 3′ end of the other.
Draw itSketch two antiparallel strands with A–T and C–G pairs. The helical twist is not required.
A labelled DNA duplex of six base pairs drawn flat as a ladder. The top strand, an arrow running from its 5′ end on the left to its 3′ end on the right, is a chain of blue phosphate circles and yellow deoxyribose pentagons joined by coral phosphodiester bonds; the bases G, A, T, C, A, C hang down from the sugars. The bottom strand is drawn the same way running the opposite direction, 5′ end on the right and 3′ end on the left, with the bases C, T, A, G, T, G pointing up. Each base faces its complement, joined by dashed hydrogen bonds: three between G and C, two between A and T, two between T and A, three between C and G, two between A and T, three between C and G. One nucleotide (a phosphate, a sugar and a base) is boxed. Labels name the phosphate, deoxyribose sugar, base, hydrogen bonds, phosphodiester bond and sugar–phosphate backbone. A panel on the right lists the two backbones, complementary bases and antiparallel strands.
Ribose and deoxyribose drawn as pentagons with the ring oxygen at the top and carbons 1 prime to 4 prime numbered, with CH2OH on carbon 4 prime, OH on carbons 1 prime and 3 prime. On carbon 2 prime, ribose has OH and deoxyribose has H, one oxygen fewer
A1.2.7

DNA compared with RNA

DNA
  • Sugar: deoxyribose
  • Two strands (double helix)
  • Very long, stable, long-lived
  • Eukaryotes: in the nucleus (also mitochondria and chloroplasts); prokaryotes: in the cytoplasm
RNA
  • Sugar: ribose; base U not T
  • One strand
  • Shorter, often broken down after use
  • Made in the nucleus, works in the cytoplasm
A useful way to hold itDNA is the master copy kept in the archive; RNA is the photocopy you take to the workshop.
A1.2.8

Job one: replication

  • Replication (copying): hydrogen bonds break and the two strands separate; each old strand acts as a template, so free nucleotides pair up according to the rule.
  • Because each base has only one possible partner, the new strand can only be an exact complement — producing two identical DNA molecules, each made of one old strand and one new one.
Why it mattersThis “semi-conservative” copying — each new molecule keeps one original strand — is how genetic information passes accurately from a cell to its daughter cells.
A parent DNA molecule of six base pairs with two blue (old) strands. The strands separate and free nucleotides pair with the exposed bases, A with T and C with G, forming orange new strands. The result is two identical DNA molecules, each with one blue old strand and one orange new strand
A 3D render of RNA polymerase sitting on a DNA double helix. Inside the enzyme the two DNA strands are separated into a transcription bubble, and a new RNA strand grows out of the enzyme. Labels name RNA polymerase, the new RNA strand, the non-template (coding) strand, the DNA template strand and the transcription bubble
A1.2.8

Job two: transcription

  • Transcription (expression): one DNA strand acts as a template for a new mRNA strand, built by the same base-pairing rule — except A on the DNA pairs with U on the RNA, since RNA has no thymine.
  • Unlike replication, only a short stretch of DNA — one gene — is transcribed at a time, and only one of the two strands is used as the template.
Why it mattersThe finished mRNA carries a faithful copy of the gene’s message out to the ribosome, where it directs protein synthesis — this is how the code stored in DNA gets expressed as a working protein.
Left, a grid of all 16 possible sequences two bases long, from AA to TT. Right, a table: 1 base gives 4 sequences, 2 bases 16, 3 bases 64, 10 bases 1 048 576, and 1 000 bases about 10 to the power 602, far more than the atoms in the observable universe
A1.2.9

Vast storage

  • Any of the four bases can sit at any position — no chemical rule restricts the order.
  • A strand n bases long has 4ⁿ possible sequences, and the number explodes fast: 10 bases gives about a million sequences; a modest 1,000-base gene gives 4¹⁰⁰⁰, a number far larger than the atoms in the observable universe.
Why it mattersA human genome — about 3 billion base pairs — has vastly more possible sequences than there have ever been organisms, which is why every species, and every individual, can have its own unique sequence.
A1.2.10

One shared genetic code

The genetic code is the set of rules by which a sequence of bases is read in triplets and translated into amino acids.
  • The code is universal — the same triplet stands for the same amino acid in bacteria, a mushroom, an oak tree, and you.
  • There's nothing chemically necessary about these assignments — no reason the triplet GGC has to mean glycine.
  • If life began independently more than once, we'd expect different codes.
A practical consequenceBecause the code is shared, a human gene put into a bacterium is read the same way, so bacteria can make human insulin. The code is almost universal: a few minor variations exist, for example in mitochondria.
A single glowing DNA helix branching outward into silhouettes of different life forms
Higher Level

Extension

A1.2.11 – A1.2.15 · not on the SL course
A1.2.11 · HL

Directionality: 5′ and 3′

  • A strand is not symmetrical.
  • New nucleotides are added only to the free —OH at the 3′ end, so a strand is always built 5′ → 3′.
In replicationDNA polymerase only works 5′ → 3′. Because the two templates are antiparallel, only one new strand — the leading strand — is made continuously toward the replication fork; the other, the lagging strand, is made in short pieces.
In transcription & translationRNA polymerase also works 5′ → 3′, reading the DNA template 3′ → 5′. The ribosome then moves along the finished mRNA from its 5′ end toward its 3′ end, reading codon by codon.
A strand of four nucleotides running down the page, with the free phosphate at the top labelled the 5 prime end and a free OH on carbon 3 prime of the bottom sugar labelled the 3 prime end. A new nucleotide approaches and its phosphate bonds to that OH. An arrow shows that strands are always built 5 prime to 3 prime
Two base pairs between two backbones: adenine (two fused rings) with thymine (one ring), and guanine (two rings) with cytosine (one ring), joined by two and three dashed hydrogen bonds. Each pair spans the same distance between the backbones. A panel shows that two purines would be too wide and two pyrimidines too narrow
A1.2.12 · HL

Purines, pyrimidines, and helix stability

  • The four bases fall into two structural groups:
    • Purines (adenine, guanine) — two fused rings, larger
    • Pyrimidines (cytosine, thymine, and uracil in RNA) — single ring, smaller
  • In DNA, a purine always bonds to a pyrimidine.
Why it mattersEvery base pair is the same width, so the two backbones stay a constant distance apart along the whole molecule — the helix has a uniform diameter that doesn't bulge or pinch, which keeps the hydrogen-bonding atoms exactly the right distance apart to bond.
A1.2.13 · HL

The nucleosome

A nucleosome is a DNA molecule wound about twice around a core of eight histone proteins, held by an additional H1 histone.
  • A human cell holds about 2 metres of DNA inside a nucleus a few micrometres across.
  • During interphase, DNA exists as chromatin — DNA plus histones, arranged as a repeating "beads on a string" of nucleosomes, connected by stretches of linker DNA.
  • Explore one in molecular visualization software (Protein Data Bank entry 1AOI).
How it's held onThe backbone is negatively charged (phosphates) and histones are positively charged, so they attract whatever the base sequence. How tightly DNA is packed also affects whether a gene can be transcribed.
A 3D render of DNA wound around a row of purple histone cores like beads on a string. Labels: histone core, eight histone proteins; DNA, wound about twice round the core; linker DNA, joining one nucleosome to the next. Notes: an extra H1 histone, not shown, holds the DNA in place, and the negative phosphates of DNA are attracted to the positive histones
The Hershey–Chase experiment in two rows. Top: phages with radioactive sulfur-35 in their protein coats infect bacteria, are blended to shake off the coats and centrifuged; the radioactivity is in the liquid, so the protein stayed outside. Bottom: phages with radioactive phosphorus-32 in their DNA; the radioactivity is in the pellet of bacteria, so the DNA entered the cells
A1.2.14 · HL

The Hershey-Chase experiment

  • The question: a bacteriophage is only protein (coat) and DNA (inside) — which one is the genetic material it injects into a bacterium?
  • The tool: radioisotopes, a new research technology that made the experiment possible. Protein contains sulfur but no phosphorus and DNA contains phosphorus but no sulfur, so ³⁵S labelled the protein and ³²P the DNA.
  • After infection the mixture was blended to shake off the empty coats, then centrifuged: bacteria formed a pellet and the coats stayed in the liquid.
Result³⁵S was mainly in the supernatant (protein stayed outside) and ³²P mainly in the pellet (DNA entered the cells), so DNA is the genetic material. The separation wasn't perfect, but the clear difference between the batches made the case.
A1.2.15 · HL

Chargaff's data

  • In the 1940s-50s, Erwin Chargaff measured base percentages across many species.
  • Within any one species, A ≈ T and G ≈ C — a purine-to-pyrimidine ratio of about 1:1.
  • But the proportions weren't the same between species — humans have far more A and T than G and C, while E. coli has roughly equal amounts of all four.
FalsifiabilityThe tetranucleotide hypothesis predicted 25% of each base in every species. Chargaff's data falsified it. No number of confirming cases can prove a general claim (the problem of induction), but one reliable contradiction can disprove it. The 1:1 ratios also hinted that the bases are paired.
A bar chart of the percentage of A, T, G and C in the DNA of humans (30.9, 29.4, 19.9, 19.8), wheat (27.3, 27.1, 22.7, 22.8), E. coli (24.7, 23.6, 26.0, 25.7) and yeast (31.3, 32.9, 18.7, 17.1). Within each species A is about equal to T and G about equal to C, but the proportions differ between species
Quick check · HL

DNA polymerase can only add a new nucleotide to a strand's free 3′ —OH. In which direction is a new strand always built?

3′ → 5′
5′ → 3′
It depends on which strand is being copied
Both directions at once
Correct answer: 5′ → 3′, always. Because the new phosphodiester bond forms with the free —OH on carbon 3′, growth can only happen at that end — which is also why the lagging strand has to be built in short, separate pieces during replication.

Key vocabulary — HL extension

Worth being able to define in a single sentence each

Purine
a base with two fused rings: adenine or guanine.
Pyrimidine
a base with a single ring: cytosine, thymine, or uracil.
Chromatin
DNA together with its histones, as it exists during interphase.
Histone
a positively charged protein that DNA winds around.
Nucleosome
DNA wound around a histone octamer, held by an H1 histone.
Radioisotope
a detectable form of an element that behaves normally in reactions.

Where this shows up again

D1.1 · DNA replication
How is the base sequence copied when DNA replicates before cell division?
D1.2 · Protein synthesis
How is the information in a DNA base sequence used to build a specific protein?
D1.3 · Mutation
How do mutations change the base sequence, and what can be the consequences?
A2.3 · Viruses
How do some viruses use RNA instead of DNA as their genetic material?

A1.2 Nucleic acids — one-page recap

Screenshot this slide to revise from

The nucleotide
  • Phosphate + sugar + base
  • Base on 1′, phosphate on 5′, —OH on 3′
Backbone & code
  • Phosphodiester bonds via condensation
  • Base order is the information
DNA vs RNA
  • Deoxyribose/ribose; T vs U
  • Double- vs single-stranded
The double helix
  • A-T (2 H-bonds), C-G (3 H-bonds)
  • Antiparallel strands
Replication & code
  • Each strand templates its complement
  • Genetic code ≈ universal → common ancestry
HL · Structure & evidence
  • Strands build 5′→3′ only
  • Purine+pyrimidine = constant width
  • Nucleosome: DNA + 8 histones
Next step

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Four letters. Vast information.

That's the whole code of life.
A1.2 Nucleic acids · BioCentral IB
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