A1.2 Nucleic acids

DNA is the molecule that stores the base sequence inherited by cells and organisms.

The sequence of bases carries information because different triplets can specify different amino acids or regulatory signals. Copying the sequence lets daughter cells receive the same genetic instructions, while a changed sequence can alter a gene product.

Use the sequence itself as the information-bearing feature:

• the sugar–phosphate backbone provides a stable chain
• the bases provide the variable code
• copying preserves order from one generation of cells to the next

A mutation that changes one DNA base can change a codon; if that codon encodes a different amino acid, the resulting protein may change.

DNA stores information in base order, not in the phosphate or sugar names alone.

A nucleotide is made from a phosphate group, a pentose sugar and a nitrogenous base.

The sugar is the central connector: the phosphate attaches to one carbon of the sugar and the base attaches to another. Nucleotides can then join into a nucleic-acid strand through sugar–phosphate links, so the same three-part unit can be repeated many times.

Identify the three components:

• phosphate group
• pentose sugar (ribose or deoxyribose)
• nitrogenous base

In a DNA nucleotide, deoxyribose plus phosphate plus one base such as adenine forms one repeating unit of the DNA strand.

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

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: one end is 5′ and the other is 3′, and polymerases extend a new strand at its 3′ end.

The labels refer to carbon positions in the sugar. Because the two DNA strands are antiparallel, a template is read in the opposite direction from the strand being synthesized.

For any strand diagram, check:

• which end is 5′ and which is 3′
• whether the template is read 3′→5′
• whether the new strand grows 5′→3′

A template written 3′–A–G–C–5′ produces a complementary strand written 5′–T–C–G–3′.

DNA or RNA is not read equally well in both directions; reversing the labels changes the sequence interpretation.

DNA pairs a two-ring purine with a one-ring pyrimidine, keeping the double helix at a nearly constant width.

A purine–purine pair would be too wide and a pyrimidine–pyrimidine pair too narrow. The A–T and C–G pairings also provide the hydrogen-bond pattern needed for stable, selective matching.

Classify before pairing:

• purines: adenine and guanine
• pyrimidines: cytosine and thymine
• valid DNA pairs: A–T and C–G

Replacing an A–T pair with a G–T pair would put two pyrimidines together and disrupt the normal geometry and pairing pattern.

Base-pair stability is not just the number of hydrogen bonds; fitting the helix and stacking interactions also matter.

A nucleosome is a segment of DNA wrapped around a core of histone proteins, compacting DNA while leaving it accessible for regulated use.

Positive histone proteins attract negatively charged DNA. Linker DNA connects neighbouring nucleosomes, and chemical changes to histones or DNA can alter how tightly the region is packed and therefore how readily genes are transcribed.

Identify the structure:

• histone core
• DNA wrapped around the core
• linker DNA between nucleosomes

Wrapping a long DNA molecule around many histone cores lets it fit in the nucleus; loosening a selected region can make its genes easier for transcription machinery to reach.

Nucleosomes package DNA but do not erase its base sequence; accessibility changes how the information is used.

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.