A1.2 Nucleic acids

Explore how nucleotide components, bonding, base pairing and sequence give DNA and RNA their structures, information capacity, shared code and experimental significance.

Learning objectives

A1.2.1DNA as genetic material• DNA is the genetic material of all living organisms• DNA occurs in chromosomes and also in mitochondria and chloroplasts• Some viruses use RNA, but viruses are not considered living organisms A1.2.2Components of a nucleotide• A nucleotide contains a phosphate group, pentose sugar, and nitrogenous base• DNA nucleotides use deoxyribose; RNA nucleotides use ribose• Bases include purines A/G and pyrimidines C/T/U A1.2.3Sugar-phosphate bonding• Condensation reactions link nucleotides by sugar-phosphate bonds• The sugar-phosphate backbone is a continuous covalent chain• Bases project from the backbone and carry sequence information A1.2.4Bases form the basis of a code• Genetic information lies in the order of nitrogenous bases• DNA uses A, T, G, C; RNA uses A, U, G, C• Triplet codons specify amino acids in protein synthesis A1.2.5RNA as a polymer• RNA is a single-stranded polynucleotide formed by condensation• RNA contains ribose and the bases A, U, G, and C• mRNA, tRNA, and rRNA have different roles in protein synthesis A1.2.6DNA as a double helix• DNA has two antiparallel polynucleotide strands in a double helix• Complementary bases pair by hydrogen bonding: A-T and G-C• Draw bases attached to sugars, not phosphates A1.2.7Differences between DNA and RNA• DNA is usually double-stranded; RNA is usually single-stranded• DNA uses deoxyribose and thymine; RNA uses ribose and uracil• RNA molecules are usually much shorter than DNA molecules A1.2.8Complementary base pairing• A pairs with T in DNA and U in RNA; C pairs with G• Complementary base pairing enables accurate DNA replication• It also enables transcription and translation in gene expression A1.2.9Diversity of DNA base sequences• DNA can vary in length and in base sequence• Genome size and gene number vary widely between organisms• Base-sequence diversity gives DNA enormous information-storage capacity A1.2.10Conservation of genetic code• The 64 codons have nearly the same meanings across life• Conserved genes for transcription, translation, and ribosomes support common ancestry• Synonymous mutations can preserve amino acid sequences A1.2.11(HL)—Directionality of RNA and DNA• 3'-5' phosphodiester bonds create 5' and 3' strand ends• DNA strands are antiparallel: one 5' to 3', the other 3' to 5'• RNA is synthesized and translated in the 5' to 3' direction A1.2.12(HL)—Purine-to-pyrimidine bonding and helix stability• Purine-pyrimidine pairing keeps DNA helix width constant• A-T and C-G pairs have equal length and fit the model• Hydrogen bonding between complementary bases stabilizes DNA A1.2.13(HL)—Structure of a nucleosome• DNA wraps nearly twice around an octamer of histone proteins• H1 histone binds linker DNA to the histone core• Nucleosomes package DNA and allow regulated access to genes A1.2.14(HL)—Hershey-Chase experiment• Hershey-Chase used bacteriophages labelled with ³²P in DNA or ³⁵S in protein• ³²P-labelled DNA entered E. coli and appeared in new viruses• Results showed DNA, not protein, carries genetic information A1.2.15(HL)—Chargaff's data• Chargaff found purines equal pyrimidines across DNA samples• A = T and G = C supported complementary base pairing• These data falsified the tetranucleotide hypothesis

In every living organism, DNA is the genetic material. Its base sequence stores information that can be copied before cell division and passed between generations.

In eukaryotic cells, most DNA is organized into chromosomes in the nucleus. Mitochondria and chloroplasts also contain smaller DNA genomes.

Some viruses use RNA as their genetic material. This does not contradict the rule for living organisms because viruses depend on host cells and are not classified as living.

Every nucleotide contains:

a phosphate group
a five-carbon pentose sugar
a nitrogenous base

The sugar is the central connector: the base and phosphate are both bonded to it. DNA nucleotides contain deoxyribose; RNA nucleotides contain ribose. A base alone is not a nucleotide.

Family	Bases	Ring structure
Purines	adenine (A), guanine (G)	two rings
Pyrimidines	cytosine (C), thymine (T), uracil (U)	one ring

A condensation reaction joins the phosphate of one nucleotide to the sugar of the next, releases water and forms a covalent phosphodiester bond. Repetition produces a long polynucleotide.

Alternating sugar and phosphate form a continuous, unvarying backbone. The bases project from the sugars, so the molecule can keep the same structural support while its base sequence changes.

The diagram shows RNA forming through the condensation of nucleotide monomers.

DNA uses: A, T, C and G
RNA uses: A, U, C and G

The sugar–phosphate backbone repeats, so it cannot encode a changing message. The order of bases can vary. When an RNA sequence is read in groups of three, each codon specifies an amino acid or a control signal, connecting nucleotide order to polypeptide sequence.

A nucleotide base sequence is divided into three-base codons and connected to an amino-acid sequence.

Four bases produce 64 possible triplets: 4 × 4 × 4. Different codons can specify the same amino acid, so the code is redundant.

RNA is usually a relatively short, single-stranded polynucleotide made by condensation of ribonucleotides. It contains ribose and the bases A, U, C and G.

A ribosome reads an mRNA codon while a tRNA anticodon pairs with it and carries an amino acid.

RNA	Distinct contribution to protein synthesis
mRNA	carries the codon sequence copied from DNA to a ribosome
tRNA	pairs its anticodon with an mRNA codon and delivers the corresponding amino acid
rRNA	forms the structural and catalytic core of the ribosome

These molecules share the same type of backbone and bases, but differences in sequence, length and folding give them different functions.

DNA contains two polynucleotide strands arranged antiparallel and wound into a double helix. The sugar–phosphate backbones face outward; bases project inward and pair through hydrogen bonds.

Adenine pairs with thymine: A–T
Cytosine pairs with guanine: C–G

A labeled DNA double helix shows complementary antiparallel strands, purine–pyrimidine base pairs, two hydrogen bonds between A and T, three between C and G, and phosphate–sugar backbones.

In a structural diagram, attach every base to a sugar, alternate sugar and phosphate along each backbone, and show the two strands running in opposite directions. The helical twist is not required.

Feature	DNA	RNA
Pentose sugar	deoxyribose	ribose
Distinctive base	thymine (T)	uracil (U)
Usual strand arrangement	two antiparallel strands	one strand
Typical relative length	very long	shorter

Both are polynucleotides with a sugar–phosphate backbone and bases A, C and G. Identify the differences using matched features rather than treating them as unrelated molecules.

DNA is shown as two paired strands using deoxyribose and thymine; RNA is shown as one strand using ribose and uracil.

Because each base has one complementary partner, the sequence of a template strand determines the sequence that is assembled against it. This is the common molecular logic behind copying and expression.

Process	Pairing used	Product specified by the template
DNA replication	A–T and C–G	a new DNA strand
Transcription	A–U and C–G	an RNA strand
Translation	mRNA codon–tRNA anticodon	the order of amino acids

Example: a DNA template written 3′-A C G T-5′ produces RNA 5′-U G C A-3′. The strands are complementary and antiparallel, not identical.

$4^n$

For a sequence of n positions, each position can contain one of four bases, giving 4ⁿ possible sequences. Changing the length or the order changes the information, so long DNA molecules have enormous storage capacity.

A DNA segment built from four possible bases branches into many different triplet sequences.

Genome size is the total amount of DNA, whereas gene number counts genes. Neither value alone is a simple measure of organism complexity.

Across almost all living organisms, the same codons specify the same amino acids. Genes involved in transcription, translation and ribosome function are also highly conserved.

A complex decoding system shared so widely is best explained by inheritance from a common ancestor. Later evolution changed DNA sequences, but retained the core code and molecular machinery.

The code is nearly, not absolutely, universal. Minor exceptions do not erase the much larger conserved pattern. Redundancy also means that some base substitutions are synonymous and do not change the amino acid.

Build and store

Phosphate + pentose sugar + base form a nucleotide.
Condensation creates a covalent sugar–phosphate backbone.
The backbone repeats while base order varies, so the polymer stores information.

Copy and express

Complementary pairing lets one strand specify another. DNA replication preserves information; transcription produces RNA; codon–anticodon pairing helps translate the message into an amino-acid sequence.

Identify from	DNA	RNA
Sugar	deoxyribose	ribose
Distinctive base	T	U
Usual structure	double-stranded	single-stranded

The same structure-to-expression system operates across life, and the nearly universal code is evidence that living organisms inherited it from a common ancestor.

A phosphodiester bond joins the 3′ carbon of one sugar to the 5′ carbon of the next. The unequal ends give every strand a 5′ end and a 3′ end.

The two DNA strands are antiparallel.
New RNA is synthesized 5′→3′ while its DNA template is read 3′→5′.
Ribosomes translate mRNA 5′→3′.

Antiparallel DNA strands are labelled 5′ and 3′ at opposite ends, with A–T and C–G hydrogen-bond counts and an mRNA 5′→3′ arrow.

Direction labels are part of the molecular structure. Reversing them changes the sequence being described and therefore changes how a template is interpreted.

Pairing geometry	Consequence
one purine + one pyrimidine	constant distance between the two backbones
two purines	pair would be too wide
two pyrimidines	pair would be too narrow

Only A–T and C–G place hydrogen-bonding groups in compatible positions. Pairing therefore gives DNA both a nearly constant width and enough reversible attraction to stabilize the double helix.

A nucleosome contains DNA wrapped nearly twice around a histone octamer—eight core histone proteins. Linker DNA joins neighbouring nucleosomes, and histone H1 binds near the linker and core.

DNA is negatively charged, while histones are rich in positively charged amino acids. Electrostatic attraction helps hold DNA around the histone core.

Repeating nucleosomes compact very long DNA molecules into chromosomes. Changes in how tightly DNA is packed also alter how easily transcription machinery can reach particular genes.

DNA wraps nearly twice around a core of eight histone proteins, with linker DNA leaving the core and an additional H1 histone beside the linker.

Hershey–Chase comparison showing 35S-labelled protein remaining outside bacteria while 32P-labelled DNA enters and appears in progeny phage.

Label: ³²P marked DNA because DNA contains phosphorus but no sulfur; ³⁵S marked protein because protein can contain sulfur but DNA does not.

Separate: labelled phages infected E. coli. Blending removed attached coats; centrifugation placed bacteria in the pellet and empty coats in the supernatant.

Infer: ³²P entered the bacteria and appeared in progeny phages, whereas most ³⁵S remained outside. DNA, rather than the protein coat, carried the information needed to make new phages.

Observation across double-stranded DNA samples	What it constrained
A ≈ T	consistent with A–T pairing
G ≈ C	consistent with G–C pairing
A + G ≈ T + C	each pair contains one purine and one pyrimidine
base composition differs among species	DNA is not a fixed repeating A–T–G–C unit

The ratios supported complementary pairing and falsified Levene’s tetranucleotide hypothesis. They constrained a successful structural model, but the ratios alone did not reveal the complete double helix.

Constraint	Structural consequence	Biological significance
3′–5′ phosphodiester bonds	strands have direction and pair antiparallel	controls synthesis and reading direction
purine–pyrimidine pairing	helix width remains nearly constant	supports a stable, repeatable structure
DNA–histone association	nucleosomes compact DNA	packages DNA while regulating access

Evidence	Result	Conclusion supported
Hershey–Chase isotope labels	³²P-DNA entered cells and progeny; ³⁵S-protein mainly did not	DNA carries inherited phage information
Chargaff’s base measurements	A ≈ T and G ≈ C; composition varies among species	complementary pairs fit; fixed tetranucleotide repetition fails

The DNA model succeeds because molecular geometry explains its stable structure, complementarity explains copying, packaging explains chromosome organization, and independent experiments support DNA as the information-bearing molecule.

1 mark

The Human Genome Project completed the sequencing of the human genome by the year 2003. Which could have been a source of the entire genome in humans?

3 marks

Draw a labelled diagram to show the structure of a DNA nucleotide.

2 marks

Outline the bonding between DNA nucleotides.

4 marks

Draw labelled diagrams to show the structure of RNA nucleotides and how they are linked together to form a molecule of RNA.

6 marks

Draw a simple labeled diagram to show the structure of a double stranded DNA molecule, comprising four nucleotides.

3 marks

Distinguish between the structures of DNA and RNA.

1 mark

Deduce the base indicated by X on the diagram.

4 marks

Explain the diversity of possible base sequences in nucleic acids.

1 mark

Some yeast genes can be replaced by human genes that then continue to produce the same human proteins in the yeast cells. Which statement helps to explain this evidence?

1 mark

Identify the terminal indicated by Y on the diagram.

4 marks

Outline the structure and functions of nucleosomes.

3 marks

Explain how this data provides evidence that DNA is the genetic material of cells.

2 marks

Explain the reasons for expecting a thymine percentage of 32.4 %.

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—A2.1 Origins of cellsRead

A1.2 Nucleic acids

Learning objectives

DNA stores the inherited information of living organisms

A nucleotide has three covalently connected parts

Condensation links nucleotides into a strong backbone

The changing base sequence carries the message

One RNA polymer supports three different roles

Complementary pairs connect the two DNA strands

DNA and RNA differ in sugar, base and strand arrangement

Complementarity lets one strand specify another

Four bases generate an immense sequence space

A nearly universal genetic code points to common ancestry

From nucleotide structure to inherited information

Direction controls how nucleic-acid strands are copied and read

Purine–pyrimidine pairing preserves helix geometry

Nucleosomes compact DNA while preserving controlled access

Hershey and Chase traced which phage molecule was inherited

Chargaff’s ratios ruled out a simple repeating DNA sequence

HL synthesis: molecular constraints and evidence converge

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