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The DNA molecules found in bacteria and archaea are circular; they have no free ends.[291] Eukaryotic cells can contain more than 1000 times the DNA found in a typical bacterial cell. Instead of circles, they contain multiple linear molecules that form the structural basis of their chromosomes (more soon). The free ends of chromosomes are known as telomeres. The linearity of eukaryotic chromosomes creates problems replicating DNA ends. Left alone, more and more of the lagging strand end of the chromosome would go unreplicated and, after removal of the primer, would be single-stranded and unstable. The result? the end of the chromosome would begin to disappear with each DNA replication cycle. To address this “design limitation” eukaryotes use another RNA-protein complex, telomerase.[292]
The ends for linear DNA molecules are known as telomeres. In humans, they are composed of repeated copies of the sequence TTAGGG-3’ (→). Telomerase is composed of a polypeptide, encoded by the TERT gene, and an RNA, encoded by the TERC gene.[293] The TERC RNA does not encode a polypeptide; it contains a sequence complementary to the telomere DNA sequence and serves as the template for the synthesis of GGTTAG from the 3’ end of the telomere’s lagging strand - this process can occur multiple times, after which primase and DNA-dependent, DNA polymerase can fill in the telomere end. For more details, look to an advanced molecular biology course or follow the footnote for a further discussion of telomeres and telomerase.[294]
Topoisomerases
The circular nature of prokaryotic chromosomes creates its own issues based on molecular topology. After replication, the two double-stranded DNA circles are linked together. In eukaryotic cells extremely long linear DNA molecules can become entangled and the unwinding of DNA during replication leads to DNA supercoiling. Left unresolved, supercoiling will inhibit DNA strand DNA synthesis, perhaps you can suggest why.[295] These topological issues are resolved by enzymes known as topoisomerases; they can interconvert topologically distinct versions of a molecule. There are two generic types of DNA topoisomerases: type I topoisomerases (→) bind to the DNA, catalyze the breaking of a single bond in one sugar-phosphate-sugar backbone; the molecule "relaxes" with release of overwinding through rotation the tension is released around the bonds in the intact chain. The enzyme then catalyzes the reformation of the broken bond. Both bond breaking and formation are coupled to ATP hydrolysis. Type II topoisomerases (↓) are
involved in “unknotting” and untangling DNA molecules. These enzymes bind to the DNA, catalyze the hydrolysis of both backbone chains, but hold on to the now free ends. This allows another double-stranded molecule to “pass through” the broken strand. The enzyme also catalyzes the reverse reaction, reforming the bonds originally broken.
Replication fork collisions
In addition to having typically much more DNA, the eukaryotic DNA replication enzyme complex is slower, about 1/20th as fast as the prokaryotic system. A bacterial cell can replicate its circular ~3 x 106 base pair chromosome in ~1500 seconds using a single replication origin. Eukaryotes use many origins of replication, scattered along the length of each chromosome. So what happens when replication forks collide with one another? In the case of a circular DNA molecule, with its single origin of replication, the replication forks resolve in a specific DNA region known as the terminator. At this point type II topoisomerases allow the two circular DNA molecules to disengage from one another, the cell division machinery forms between the two DNA molecules and they move to opposite ends of the cell. The system in eukaryotes, with their multiple linear chromosomes, is much more complex, although topoisomerases are still involved in separating replicated chromosomes (considered in greater detail in chapter 12).
Questions to answer
- During DNA/RNA synthesis what is the average ratio of productive to unproductive interactions between an incoming nucleotide and the polymerase?
- Why do you need to denature (melt) the DNA double-helix to copy it? How would DNA replication change if H-bonds were as strong as covalent bonds?
- Explain how DNA polymerase might recognize a mistake associated with a mismatched base pair.
Questions to ponder:
- How would evolution be impacted if DNA were totally stable and DNA replication was error-free?
- What would be the effect if a mutation inactivated the the proof-reading function of the DNA polymerase complex?
- How might mutations in the genes encoding the clamp/clamp-loader system influence DNA replication?
References
[291] The mitochondria and chloroplasts of eukaryotic cells also contain circular DNA molecules, another homology with their ancestral bacterial parents. ,
[292] http://en.wikipedia.org/wiki/Telomerase
[293] You can explore the known genetic diseases by using the On-line Mendelian Inheritance in Man (OMIM) database:
[294] more on telomerase: http://blogs.scientificamerican.com/...as-too-little/
[295] see this video on DNA supercoiling and topoisomerases: http://youtu.be/EYGrElVyHnU
This page titled 7.10: Further replication complexities was last modified on Thu, 08 Jan 2026 23:37:07 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Michael W. Klymkowsky and Melanie M. Cooper.
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