A1.2 Nucleic acids

DNA is the genetic material of all living organisms: its base sequence stores information that can be copied and inherited.

DNA occurs in chromosomes and also as smaller genomes in mitochondria and chloroplasts. Copying DNA allows cells and offspring to receive genetic information.

Apply the rule to living organisms, then handle the exception carefully: some viruses use RNA as genetic material, but viruses are not classified as living organisms.

A plant cell contains DNA in its nuclear chromosomes, mitochondria and chloroplasts; all of these DNA molecules carry heritable information.

The existence of RNA viruses does not contradict the statement about all living organisms, because viruses are not regarded as living organisms in this syllabus.

A nucleotide contains three components: a phosphate group, a pentose sugar and a nitrogenous base.

The sugar is the central connector: the base and phosphate are both attached to it. DNA nucleotides contain deoxyribose; RNA nucleotides contain ribose.

For the IB diagram convention, draw the phosphate as a circle, the pentose sugar as a pentagon and the base as a rectangle, with both phosphate and base connected to the sugar.

A DNA nucleotide can be represented as phosphate-circle -> deoxyribose-pentagon -> adenine-rectangle.

A nitrogenous base alone is not a nucleotide; the sugar and phosphate are also required.

Nucleotides join when a phosphate links the sugar of one nucleotide to the sugar of the next, forming a repeating backbone.

The covalent sugar–phosphate links make the strand continuous and give it a direction. Bases project from the backbone, so their order can vary without breaking the structural chain.

When reading a strand, separate:

• the stable sugar–phosphate backbone
• the variable base sequence
• the direction from one end to the other

Joining many nucleotides produces a strand with an alternating sugar–phosphate backbone and a base attached to each sugar.

The bases do not form the backbone; confusing the code with the support structure reverses the roles.

The genetic code is stored in the order of nitrogenous bases, not in the repeating sugar–phosphate backbone. DNA uses A, T, G and C; RNA uses A, U, G and C. Groups of three bases form codons, and the order of codons carries the instructions for the amino-acid sequence of a polypeptide.

RNA is a single-stranded polynucleotide formed by condensation of nucleotide monomers. Its main types have different roles in protein synthesis:

• mRNA carries a transcript of the DNA instructions to the ribosome.
• tRNA carries amino acids to the mRNA sequence.
• rRNA forms part of the ribosome and provides catalytic activity for joining amino acids.

Answer chain: base sequence → genetic instructions; condensation → RNA polymer; mRNA, tRNA and rRNA → different steps in gene expression.

DNA consists of two antiparallel polynucleotide strands whose complementary bases pair inside a double helix.

Hydrogen bonding between paired bases holds the strands together, while the sugar–phosphate backbones face outward. Because each base has a partner, either strand can guide construction of the other during copying. This arrangement combines stability with a built-in template.

The helix depends on three linked features:

• complementary base pairing
• antiparallel strand direction
• an external sugar–phosphate backbone

If one strand reads A–G–C, the opposite strand reads T–C–G at the matching positions.

The two strands are not identical copies in sequence; they are complementary and run in opposite directions.

DNA and RNA differ in sugar, one base and usual strand structure, and those differences fit their different cellular roles.

DNA uses deoxyribose and thymine and is usually double-stranded, making a stable long-term store. RNA uses ribose and uracil and is usually single-stranded, making temporary messages and folded functional molecules practical.

Compare the molecules:

• sugar: deoxyribose / ribose
• base: thymine / uracil
• usual form: double-stranded / single-stranded

A cell can transcribe a DNA sequence into RNA: the RNA copy uses uracil and can leave the nucleus while the DNA template remains protected.

‘RNA is always single-stranded’ is a usual structural description, not a rule that forbids every paired region.

Complementary base pairing means each base has a specific partner, allowing a strand to determine the sequence of its partner.

Hydrogen bonds give the pairs selectivity: adenine pairs with thymine in DNA (uracil in RNA), while cytosine pairs with guanine. This matching is the mechanism behind faithful copying and template reading.

Apply the pairing rule in order:

• A ↔ T (or U in RNA)
• C ↔ G
• preserve the strand positions while switching to the partner base

The DNA sequence A–C–G–T has the complementary sequence T–G–C–A.

Complementary does not mean identical: the partner strand has different letters in the opposite direction.

DNA can vary in both length and base sequence. If a sequence has n positions and each position can contain one of four bases, there are 4ⁿ possible sequences. Even relatively short sequences can therefore store a very large number of different instructions.

Genome size and gene number vary widely between organisms, but neither is a simple measure of organismal complexity. The key idea is that variation in sequence length and order gives DNA an enormous capacity for information storage.

The genetic code is highly conserved across life: the 64 codons have nearly the same meanings in different organisms. Shared codon meanings, together with conserved genes involved in transcription, translation and ribosomes, support the inference that living organisms share a common ancestor.

“Nearly” matters because there are minor exceptions. A synonymous mutation can change a base or codon without changing the amino acid specified, so a change in DNA sequence does not always change the polypeptide sequence.

Nucleic-acid strands have direction because the sugar-phosphate backbone links the 5' carbon of one nucleotide toward the 3' carbon of the next.

During replication and transcription, a new nucleic-acid strand is synthesized 5' to 3' while its template is read 3' to 5'. During translation, the ribosome reads mRNA codons in the 5' to 3' direction.

For any strand, label both ends, keep complementary DNA strands antiparallel, and write the direction before applying base pairing.

A DNA template written 3'-A-G-C-5' directs a new strand written 5'-T-C-G-3'.

Reversing only the 5' and 3' labels changes the sequence interpretation; direction is part of the strand's identity.

In DNA, each base pair combines one two-ring purine with one one-ring pyrimidine, so A-T and C-G pairs have equal length and the helix keeps a consistent width.

Adenine and guanine are purines; cytosine and thymine are pyrimidines. Complementary hydrogen bonding selects A-T and C-G and helps stabilize the two strands.

Classify first, then pair: A or G (purine) must face T or C (pyrimidine); the complementary pairs are A-T and C-G.

Replacing an A-T pair with a C-G pair changes the sequence but not the helix width, because both pairs contain one purine and one pyrimidine.

A purine-purine pair would be too wide and a pyrimidine-pyrimidine pair too narrow; equal pair length does not mean any purine can form the correct hydrogen bonds with any pyrimidine.

A nucleosome consists of DNA wrapped around a core of eight histone proteins, called a histone octamer.

Linker DNA connects neighbouring nucleosomes. An additional histone, H1, attaches to linker DNA and helps hold the packaged structure together.

Identify four parts in a model: wrapped DNA, the eight-protein histone core, linker DNA, and the additional H1 histone.

Repeated nucleosomes give chromatin a beads-on-a-string appearance: each bead is DNA around a histone octamer and each connecting segment is linker DNA.

H1 is additional to the eight core histones; do not count it as one of the histone octamer.

Hershey–Chase experiment (1952)

T2 bacteriophages were prepared with either ³²P-labelled DNA or ³⁵S-labelled protein. After infection of E. coli, the ³²P signal was associated with the bacterial pellet and was found in progeny phages, whereas the ³⁵S protein label remained outside the bacteria.

Observation → conclusion: DNA entered the bacterial cells and was passed to new viruses; protein did not. Therefore DNA, rather than protein, is the genetic material in this system.

Chargaff’s data

Across DNA samples, the amount of purines equalled the amount of pyrimidines, with A = T and G = C. These results supported complementary base pairing and falsified the tetranucleotide hypothesis of a repeating, fixed base pattern.

Evidence rule: state the result first, then explain what it allows us to conclude; do not present the isotope labels as the conclusion itself.