7.1 Essential ideas

7.1.1 DNA Structure and replication

  • DNA is arranged in chromosomes in eukaryotes. Each chromosome contains one very long DNA molecule.
  • Packaging of DNA is necessary. For example, in each human cell there is approximately 2m of DNA distributed between 46 chromosomes, yet the average diameter of each cell is only 10–30µm.

Figure 7.1.1a – Packaging of DNA into nucleosomesFigure 7.1.1a – Packaging of DNA into nucleosomes

  • A packaged unit of the chromatin fibre is called a nucleosome, which looks like a bead on a thread.
  • Each nucleosome is composed of:
    • two loops of DNA, approximately 150bp long, wrapped around 8 central histone proteins; central histone proteins have structures that influence how tightly the DNA is packaged
    • another type of histone, called H1, that binds the DNA to the central ‘bead’.
  • There is a short segment of naked DNA between each nucleosome. This is known as linker DNA.

Figure 7.1.1b – Nucleosomes help to supercoil DNAFigure 7.1.1b – Nucleosomes help to supercoil DNA

  • The nucleosomes arrange into coils, and in preparation for nuclear division, the coiled structure coils up again, to form a supercoiled chromosome.
  • Nucleosomes are important for the safe storage of DNA. They also play an important role in the regulation of transcription.

Replication on leading and lagging strands

  • DNA replication begins when helicase unwinds and breaks hydrogen bonds between DNA strands at the origin of replication. This is the first step in creating the replication fork.
  • Both strands of the DNA molecule act as templates for replication – as the replication fork moves along the molecule, the strands are exposed to allow for DNA polymerase to add free nucleotides.
  • DNA polymerases can add free nucleotides in the 5’ to 3’ direction only, but the template strands are anti-parallel, so that only one exposed strand is oriented to allow for continuous replication. This is called the leading strand.
  • Replication on the lagging strand is discontinuous. The lagging strand is replicated in smaller pieces, called Okazaki fragments.

Figure 7.1.1c – Continuous and discontinuous DNA replicationFigure 7.1.1c – Continuous and discontinuous DNA replication

The role of enzymes and proteins in DNA replication

At the replication fork (both strands)

Helicase

Separates two strands of DNA

DNA gyrase

Attaches ahead of the replication fork to release physical strain on the DNA molecule that develops from action of helicase

Single-stranded binding proteins (ssb proteins)

Keep the template strands exposed long enough to allow replication

Replication at the leading strand (continuous)

DNA primase

Adds a single RNA primer at origin of replication

DNA polymerase III

Adds free nucleotides to the 3’ end of growing DNA strand

Replication at the lagging strand (discontinuous)

DNA primase

Adds short RNA primers at intervals as replication fork opens

DNA polymerase III

Adds free nucleotides to the 3’ end of growing DNA strand to form Okazaki fragments

DNA polymerase I

Replaces the RNA primer with correct sequences of DNA

DNA ligase

Joins small fragments of DNA together

Non-coding regions of DNA

  • A gene is generally defined as a region of DNA that codes for one polypeptide. Less than 2% of the base pair sequence of DNA has known protein-coding function.
  • Some regions of DNA do not code for proteins but have other important functions. These include:
    • Introns – sequences that are embedded in coding sequences (exons). Some of these play a role in regulation of gene expression during translation.
    • Centromeres – repetitive sequences that link sister chromatids of a mitotic chromosome.
    • Telomeres – repetitive sequences that are found at the ends of chromosomes. They play a protective role during DNA replication, and are believed to be involved in apoptosis.

Figure 7.1.1d – Telomeres and centromeres are non-coding regions of DNAFigure 7.1.1d – Telomeres and centromeres are non-coding regions of DNA

  • Promoter sequences – sequences located near a gene that act as binding sites for enzymes during transcription, and regulate gene expression.
  • tRNA genes – code for the production of tRNA molecules, which play a role in translation.

The structure of DNA is ideally suited to its function.

Figure 7.1.1e – Replication forksFigure 7.1.1e – Replication forks
Micrograph showing replication forks in a eukaryotic cell

Key questions

  • Explain how DNA is packaged and why DNA packaging is necessary.
  • Distinguish between replication on the leading and lagging strands.
  • Describe non-coding functions of DNA.

Language tools

  • DNA primase is also called RNA primase, because it adds an RNA primer. Sometimes the name is simplified to primase – it is, after all, misleading to call it DNA primase when in fact it is an enzyme that acts on RNA. Do not be confused – all of these names refer to the same enzyme.
  • DNA gyrase is also known as topoisomerase.
  • DNA polymerase I is also known as exonuclease.

Course links

  • Nucleosomes are the ‘spools’ that organise the tangled ‘string’ of DNA 1.1.6.
  • Nucleosomes play an important role in the regulation of transcription 7.1.2.
  • Review the history of the discovery of the structure of DNA in 2.2.6.

Figure 7.1.1f – FranklinFigure 7.1.1f – Franklin
Careful observation in the sciences

Nature of Science

Most people remember the spark of ‘inspiration’ that hit Watson and Crick, but Rosalind Franklin spent many years of careful observation in order to provide crucial evidence for the structure of DNA.