DNA Structure in Prokaryotes and Eukaryotes — AQA A-level Biology

SPEC 3.4.1 - GENETIC INFORMATION

DNA, Genes & Chromosomes

Genome, locus, triplet code, introns & exons — the molecular language of life

What Is DNA?

DNA (deoxyribonucleic acid) carries genetic information in all living organisms. It is a polymer of nucleotides — each nucleotide contains deoxyribose, a phosphate group and one of four bases: A, T, C or G.

Genome

The complete set of genes (all the DNA) in a cell.

Gene

A sequence of DNA bases that codes for a specific polypeptide or functional RNA molecule.

Note: functional RNA includes rRNA and tRNA — not all genes code for protein.

Key Fact

All nucleated cells in an organism contain the same genome, but different genes are expressed in different cell types. This is how a liver cell differs from a nerve cell despite identical DNA.

DNA Location: Prokaryotes vs Eukaryotes

Where and how DNA is packaged differs fundamentally between cell types — a regular source of exam marks.

FeatureProkaryoteEukaryote (nucleus)Mitochondria / Chloroplasts

ShapeCircularLinearCircular

Histones?NoYesNo

LengthShortVery longShort

LocationFree in cytoplasmWithin nuclear envelopeWithin organelle

Exam Tip

Mitochondria and chloroplasts contain short, circular DNA not associated with histones — just like prokaryotes. This is evidence for the endosymbiotic theory and may appear in synoptic questions.

Chromosome Structure

In eukaryotic nuclei, each DNA molecule is associated with histone proteins. DNA wraps around histone proteins to form nucleosomes, which coil and compact to form chromosomes.

Definition

A chromosome = a DNA molecule + its associated histone proteins. In eukaryotes: long and linear. In prokaryotes and organelles: short and circular, no histones.

Locus, Alleles & Homologous Chromosomes

Locus

The fixed position of a gene on a particular chromosome.

Allele

An alternative version of a gene, occupying the same locus on homologous chromosomes.

Homologous chromosomes carry genes for the same characteristics at the same loci, but may carry different alleles. Human body cells: 23 pairs (46 total).

Diploid (2n) — see Lesson 4.04

Two copies of each chromosome. Human body cells: 2n = 46

Haploid (n) — see Lesson 4.04

One copy of each chromosome. Human gametes: n = 23

Examiner Alert

Locus ≠ Gene. The locus is the position; the gene is the base sequence at that position. Different alleles occupy the same locus in different individuals.

The Triplet Code

Genetic information is encoded in triplets — sequences of three consecutive DNA bases. Each triplet codes for a specific amino acid (or a start/stop signal).

Triplet Code

A sequence of three DNA bases that codes for a specific amino acid.

Why Triplets?

With 4 bases and 3 positions: 4³ = 64 possible codons for only 20 amino acids — giving useful redundancy.

PropertyMeaningConsequence

Triplet3 bases code for 1 amino acid64 codons for 20 amino acids

DegenerateMost amino acids coded by >1 tripletMany substitutions don't change amino acid

Non-overlappingEach base belongs to only one tripletDeletion shifts ALL downstream codons

UniversalSame triplets = same amino acids in virtually all organismsEvidence for common ancestry

Degenerate & Universal Code

Degenerate Code

Most amino acids are coded for by 2–6 different triplets. Example: leucine is coded by 6 different triplets (CTT, CTC, CTA, CTG, TTA, TTG). A change at the 3rd base often produces the same amino acid — a silent (synonymous) mutation.

Why it matters: Buffers against point mutations — not all base changes alter the protein.

Universal Code

The same codons specify the same amino acids in virtually all known organisms. This is strong evidence that all life shares a common ancestor and the code evolved once, very early in evolution.

Application: This is why bacteria can produce human proteins — when human cDNA is inserted into a bacterial plasmid, bacterial ribosomes correctly read the codons because the code is identical.

Synoptic Link — Topic 8

The universality of the genetic code underpins recombinant DNA technology. Note: cDNA (made from mRNA, introns removed) must be used — bacteria cannot splice out introns.

Introns & Exons

In eukaryotes, much nuclear DNA does not code for polypeptides. Within genes, coding and non-coding sequences are interspersed.

Exon

A coding sequence within a gene that is retained after RNA processing and is translated into protein.

Intron

A non-coding sequence within a gene that is transcribed into pre-mRNA but spliced out before translation.

Non-Coding DNA

In eukaryotes, a large proportion of nuclear DNA does not code for polypeptides. Two main types:

Two Types of Non-Coding DNA

Introns — within genes; transcribed into pre-mRNA, then spliced out before translation

Non-coding repeats — between genes; multiple repeats of base sequences; may play roles in chromosome structure and gene regulation

Examiner Alert

Never write "junk DNA" in an AQA answer — this term is not acceptable. Some non-coding sequences have regulatory functions. Always write "non-coding DNA."

Contrast with Prokaryotes

Prokaryotic DNA has much less non-coding DNA and typically no introns. This is a key difference between pro- and eukaryotic cells tested regularly at A Level.

Genome vs Proteome

Proteome

The full range of proteins that a cell is able to produce.

The proteome is always larger than the number of genes in the genome. The AQA spec explanation is:

Alternative Splicing

Different combinations of exons can be joined to produce different mature mRNAs from the same gene. One gene can therefore code for multiple different polypeptides, depending on which exons are included.

Spec Boundary

AQA spec 3.4.1 requires only alternative splicing as the explanation for proteome diversity. In exam answers for this spec point, cite alternative splicing as your explanation.

Reading Frame & Frameshift Mutations

Because the code is non-overlapping, the ribosome reads mRNA in consecutive groups of three (codons). The diagram uses DNA base notation — on mRNA, T is replaced by U.

A single base deletion shifts every subsequent triplet — a frameshift that usually destroys protein function.

DEEP Framework: The Triplet Code

Use this structure for 4–6 mark questions on the properties and significance of the genetic code.

DEEP CHAIN — "Explain the significance of the degenerate and non-overlapping nature of the genetic code"

D

Define The genetic code is degenerate — most amino acids are coded for by more than one triplet of DNA bases. It is non-overlapping — each base is part of only one triplet.

E

Explain Mechanism Because the code is degenerate, a base substitution at the 3rd position of a triplet often produces a synonymous codon — one that codes for the same amino acid. The polypeptide sequence is therefore unchanged and the protein retains its function.

E

Evidence / Example Leucine is coded by 6 different DNA triplets (e.g. CTT, CTC, CTA, CTG, TTA, TTG). A mutation from CTT → CTC does not alter the amino acid — a silent mutation. In contrast, a single base deletion causes a frameshift: every triplet after the deletion shifts, changing every subsequent amino acid and typically producing a non-functional protein.

P

Practical / Quantitative With 4 bases and a 3-base code: 4³ = 64 possible codons for only 20 amino acids. This excess of codons (64 vs 20) is what makes degeneracy possible. Using a codon table, students can determine whether a given base change is synonymous (silent) or non-synonymous (missense).

Common Exam Errors

Error 1 — Triplet vs Codon (Anticodon in Lesson 4.02)

Students confuse the DNA triplet with the mRNA codon. These are different sequences:

DNA triplet — on the template (antisense) strand, e.g. TAC

mRNA codon — complementary to the DNA template strand, e.g. AUG. RNA uses uracil (U) not thymine (T)

The mRNA codon has the same sequence as the coding (sense) strand — except T is replaced by U

tRNA anticodons are covered in Lesson 4.02.

Error 2 — Introns in Prokaryotes

Prokaryotes generally do not have introns. This is why, in genetic engineering, cDNA (made from mature mRNA, introns already removed) must be used to insert human genes into bacteria — bacterial cells cannot splice out introns.

Error 3 — "Non-coding = no function"

Non-coding DNA is NOT functionless. Non-coding sequences may have regulatory roles. Never write "junk DNA" — AQA mark schemes do not accept this term.

Practice Question

A section of a gene has the following base sequence on the template (antisense) strand of DNA:

3' — TAC — GCA — ATT — CGG — ACT — 5'

(a) How many amino acids would this sequence code for? [1 mark]

(b) Explain what is meant by the genetic code being degenerate and state one consequence of this property. [3 marks]

(c) A single base deletion occurs at position 4 (first base of the second triplet). Explain the likely effect on the polypeptide produced. [3 marks]

a)

5 amino acids — 5 triplets; the code is non-overlapping so each triplet codes for one amino acid.

D:

Degenerate means most amino acids are coded for by more than one triplet of DNA bases.

E:

A base substitution at the 3rd position of a triplet often produces a synonymous codon, coding for the same amino acid.

E:

Consequence: not all point mutations change the amino acid sequence — many mutations have no effect on protein structure or function.

c)

The deletion causes a frameshift mutation. Every triplet downstream is altered, changing every amino acid from position 2 onwards. The polypeptide is likely non-functional as its tertiary structure (active/binding site) is changed.

Synoptic Links

Topic 4.01 connects to many other spec areas — tested in Paper 3 synoptic questions and essays.

Topic 1.06 — DNA Structure

The double helix, antiparallel strands, base pairing rules, and nucleotide structure are prerequisite knowledge for this lesson.

Topic 4.02 — Protein Synthesis

The triplet code on DNA becomes codons on mRNA during transcription and anticodons on tRNA during translation. The reading frame established here is central to 4.02.

Topic 4.03 — Mutations

Frameshifts (from deletions/insertions) and silent mutations (substitutions) arise directly from the non-overlapping and degenerate properties of the code.

Topic 8.04 — Recombinant DNA

The universal code explains why human genes function in bacteria. cDNA is used because bacteria lack spliceosomes to remove introns.

Summary

Key Definitions — Learn These Exactly

TermMark-Scheme Definition

GeneA sequence of DNA bases that codes for a specific polypeptide or functional RNA molecule

GenomeThe complete set of genes (all the DNA) in a cell

LocusThe fixed position of a gene on a particular chromosome

AlleleAn alternative version of a gene occupying the same locus on homologous chromosomes

ExonA coding sequence within a gene retained after RNA processing and translated into protein

IntronA non-coding sequence within a gene transcribed into pre-mRNA then spliced out before translation

ProteomeThe full range of proteins that a cell is able to produce

4 Properties of the Genetic Code

Triplet — 3 bases = 1 amino acid

Degenerate — multiple codons per amino acid

Non-overlapping — each base in only one triplet

Universal — same codons in all organisms

DNA Location Summary

Prokaryotes: short, circular, no histones

Eukaryote nucleus: long, linear, with histones

Mitochondria/Chloroplasts: short, circular, no histones

Exam Tip

For a base deletion question: (1) frameshift, (2) all triplets downstream altered, (3) different amino acid sequence, (4) protein likely non-functional — tertiary structure changed. Four points = 4 marks.