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DNA: the stuff of life. Well, not really, despite the hype. DNA does contain the instructions to make a lot of the stuff of life (proteins), although again, not all the stuff of life. At least not directly. Deoxyribonucleic acid (and its very close cousin ribonucleic acid, or RNA) is a very long chain polymer. You may recall that a polymer is just a really big molecule made by connecting many small similar molecules together). In this polymer, the small (monomer) molecules are known as nucleotides, and are composed of a pentose (5-carbon sugar either deoxyribose or ribose), a nitrogenous base, and a phosphate group.
- 7.1: DNA Structure
- Nucleotides only vary slightly, and only in the nitrogenous base. For DNA, those bases are adenine, guanine, cytosine, and thymine. A and G are classified as purines, while C and T are classified as pyrimidines. As long as we’re naming things, notice “deoxyribose” and “ribose”. As the name implies, deoxyribose is just a ribose without an oxygen. More specifically, where there is a hydroxyl group attached to the 2-carbon of ribose, there is only a hydrogen attached to the 2-carbon of deoxyribose.
- 7.2: Semi-Conservative DNA Replication
- DNA replication is similar to transcription in its most general idea: a polymerase enzyme reads a strand of DNA one nucleotide at a time, it takes a random nucleotide from the nucleoplasm, and if it is complementary to the nucleotide in the DNA, the polymerase adds it to the new strand it is creating. Of course, there are significant differences between replication and transcription too, not the least of which is that both strands of DNA are read simultaneously.
- 7.3: Prokaryotic Replication
- DNA replication begins at an origin of replication. There is only one origin in prokaryotes (in E. coli, oriC) and it is characterized by arrays of repeated sequences. These sequences wrap around a DNA-binding protein, and in doing so, exert pressure on the H-bonds between the strands of DNA, and the chromosome begins to unzip in an AT-rich area wrapped around this protein. Remember that A-T pairs are 33% weaker than G-C pairs due to fewer hydrogen bonds.
- 7.4: Eukaryotic Replication
- Given the crucial nature of chromosomal replication for life to exist, it is not surprising to find that eukaryotic DNA replication is very similar to the prokaryotic process. This section will highlight some of the differences, which are generally elaborations on the prokaryotic version.
- 7.5: DNA Lesions
- The robust nature of DNA due to its complementary double strands has been noted several times already. We now consider in more detail the repair processes that rescue damaged DNA. DNA is not nearly as robust as popular media makes it out to be.
- 7.6: DNA Repair
- DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.
- 7.7: Telomeres
- If there is a mechanism for recognizing loose ends of DNA, what about the ends of every eukaryotic chromosome? They are linear chromosomes, so they have ends, right? What prevents the double-strand-break repair systems from mis-recognizing them all as broken DNA and concatenating all of the chromosomes together? Interestingly, the answer to this question is intimately tied up with the answer to the problem of end- replication, which was very briefly alluded to in our description of replication.
Thumbnail: DNA double helix. (public domain; NIH - Genome Research Institute).