AP Syllabus focus:
‘Prokaryotes usually have a single circular chromosome, while eukaryotes have multiple linear DNA chromosomes condensed with histones and associated proteins.’
Chromosomes package an organism’s genetic material so it can fit inside cells and be accurately maintained. Prokaryotes and eukaryotes solve this packaging problem differently, reflecting major differences in cell size, compartmentalization, and DNA-associated proteins.
What a chromosome is (structural focus)
Chromosome: A discrete DNA molecule (with associated proteins in cells) that carries genetic information and is organized for packaging and inheritance.
High-level contrasts required by the syllabus
Prokaryotes: usually one circular chromosome
Eukaryotes: multiple linear DNA chromosomes
Key eukaryotic feature: DNA is condensed with histones and associated proteins
Prokaryotic chromosomes
Overall architecture
Prokaryotic cells (bacteria and archaea) typically have a single, circular double-stranded DNA molecule that contains most essential genes. Because prokaryotic cells lack a nucleus, this chromosome is not enclosed by a nuclear membrane.
Diagram of a typical prokaryotic (bacterial) cell with major structures labeled, including the nucleoid region where the chromosome is concentrated. It helps connect the idea of a “single circular chromosome” to its physical organization in the cell without a surrounding nuclear membrane. Source
Nucleoid: A region of the prokaryotic cell where the circular chromosome is concentrated and organized, without a surrounding membrane.
Packaging and organization
Even without histone-based chromatin like eukaryotes, prokaryotic DNA is still tightly compacted.
Supercoiling: the DNA helix is further twisted to reduce volume
DNA-binding proteins: small proteins help bend, loop, and stabilize compact DNA
High gene density: comparatively less noncoding DNA, so the chromosome is information-dense
Consequences of being circular
Circular chromosomes avoid end structures found in linear DNA (no natural chromosome “ends”), which influences how prokaryotic chromosomes are maintained and organized inside the cell.
Eukaryotic chromosomes
Overall architecture
Eukaryotic cells store most DNA as multiple, linear chromosomes housed in the nucleus. Each chromosome is a long DNA molecule that must be folded extensively to fit and to be partitioned during cell division.
Chromatin: The DNA–protein complex that makes up eukaryotic chromosomes; it enables DNA to be compacted and organized within the nucleus.
Histones and associated proteins (core syllabus emphasis)
A defining feature of eukaryotic chromosomes is that DNA is condensed with histones and associated proteins.
Figure showing DNA wrapped around histone proteins to form nucleosomes (a), alongside an electron micrograph view of the resulting “beads-on-a-string” chromatin (b). This visualizes the foundational packaging step that distinguishes eukaryotic chromosomes: DNA compaction through histone-based chromatin. Source
Histones are positively charged proteins that bind negatively charged DNA
DNA wraps around histone complexes, forming repeating structural units that help compact and regulate accessibility
Additional non-histone proteins contribute to folding, scaffolding, and higher-order organization
Histone: A basic (positively charged) DNA-binding protein in eukaryotes that helps package DNA by promoting tight winding and higher-order folding.
Linear chromosome features
Because eukaryotic chromosomes are linear, they have specialized regions important for stability and organization.
Schematic of a duplicated chromosome with labels pointing to telomeres (chromosome ends) and the centromere (primary constricted region). It clarifies how “ends” and the centromeric region are distinct structural features of linear chromosomes that support stability and accurate segregation. Source
Telomeres: repetitive DNA at chromosome ends that help protect coding DNA near the ends
Centromeres: chromosome regions important for the physical organization of chromosomes during division
These regions are structural hallmarks of linear chromosomes and help explain why eukaryotic chromosomes require extensive protein-based organization.
Chromosome number and sets
Eukaryotes characteristically have multiple chromosomes per nucleus.
In many animals and plants, somatic cells commonly contain pairs of chromosomes (one set from each parent)
Different species have different characteristic chromosome numbers, reflecting genome organization rather than “complexity”
Side-by-side comparison (must-know points)
Shape: prokaryotic circular vs eukaryotic linear
Count: prokaryotes usually single vs eukaryotes multiple
Protein packaging: eukaryotic chromosomes condensed with histones and associated proteins; prokaryotes use other DNA-binding proteins and supercoiling
Location: prokaryotic chromosome in a nucleoid vs eukaryotic chromosomes in a nucleus
FAQ
No. Some bacteria have more than one chromosome, and some species have large secondary chromosomes (“chromids”). The syllabus focus is that prokaryotes usually have a single circular chromosome.
Chemical tags on histone tails can alter how tightly DNA is held.
Tighter packing generally reduces access to DNA
Looser packing generally increases access
This is a structural route to changing DNA accessibility.
Chromosome number is species-specific and shaped by evolutionary events such as chromosome fusions, fissions, and large-scale rearrangements. It does not reliably track organism complexity.
Key strategies include supercoiling and protein-mediated looping/bridging.
Supercoiling reduces overall volume
DNA-binding proteins stabilise bends and loops
Crowding inside the cell further favours compaction
Many archaea have histone-like proteins that can wrap DNA, but they are not identical to eukaryotic histones and do not always form the same chromatin architecture. This supports both shared principles and major structural differences across domains of life.
Practice Questions
State two differences between prokaryotic and eukaryotic chromosomes. (2 marks)
Prokaryotes usually have a single chromosome whereas eukaryotes have multiple chromosomes (1)
Prokaryotic chromosome is circular whereas eukaryotic chromosomes are linear (1)
Eukaryotic chromosomes are condensed with histones and associated proteins (credit as an alternative second difference) (1)
Describe how eukaryotic chromosome structure differs from prokaryotic chromosome structure, including the role of histones and the implications of linear versus circular DNA. (5 marks)
Eukaryotes have multiple chromosomes; prokaryotes usually one (1)
Eukaryotic chromosomes are linear; prokaryotic chromosome is circular (1)
Eukaryotic DNA is packaged with histones (1)
Histones (and associated proteins) enable condensation/compaction of DNA into chromatin (1)
Linear eukaryotic chromosomes have ends (e.g., telomeres) whereas circular prokaryotic chromosomes do not have chromosome ends (1)
