To understand what a 5' or 3' end is, we need to look at the molecular structure of DNA. DNA is a polymer of nucleotides, where each nucleotide is made up of a sugar deoxyribose , a nitrogenous base, and a phosphate group.
The deoxyribose sugar is a 5 carbon structure, where each carbon can be numbered The base is always connected to Carbon 1 of the sugar and the phosphate group is connected to Carbon 5 of the sugar.
The nucleotides are then connected to one another to form the polymer whereby the phosphate group of one nucleotide on Carbon 5 connects to the next nucleotide sugar via Carbon 3. Therefore when the strand is built, the top nucleotide will have a free phosphate group on the Carbon 5 of the sugar, hence the 5' end, and the last nucleotide of the strand will have a free OH on the Carbon 3 of the sugar.
Since DNA is made up of two antiparallel strands, each strand can have its own directionality. As they are antiparallel, they will run in opposite directions.
Explain what 5' and 3' ends mean in regards to DNA structure? As the chases increased in length, giving DNA more time to replicate, the lagging strand fragments started integrating into longer, heavier, more rapidly sedimenting DNA strands. Today, scientists know that the Okazaki fragments of bacterial DNA are typically between 1, and 2, nucleotides long, whereas in eukaryotic cells, they are only about to nucleotides long.
Bacterial and eukaryotic cells share many of the same basic features of replication; for instance, initiation requires a primer, elongation is always in the 5'-to-3' direction, and replication is always continuous along the leading strand and discontinuous along the lagging strand. But there are also important differences between bacterial and eukaryotic replication, some of which biologists are still actively researching in an effort to better understand the molecular details.
One difference is that eukaryotic replication is characterized by many replication origins often thousands , not just one, and the sequences of the replication origins vary widely among species. On the other hand, while the replication origins for bacteria, oriC, vary in length from about to 1, base pairs and sequence, except among closely related organisms, all bacteria nonetheless have just a single replication origin Mackiewicz et al.
Eukaryotic replication also utilizes a different set of DNA polymerase enzymes e. Scientists are still studying the roles of the 13 eukaryotic polymerases discovered to date. In addition, in eukaryotes, the DNA template is compacted by the way it winds around proteins called histones. This DNA-histone complex, called a nucleosome , poses a unique challenge both for the cell and for scientists investigating the molecular details of eukaryotic replication.
What happens to nucleosomes during DNA replication? Scientists know from electron micrograph studies that nucleosome reassembly happens very quickly after replication the reassembled nucleosomes are visible in the electron micrograph images , but they still do not know how this happens Annunziato, Also, whereas bacterial chromosomes are circular, eukaryotic chromosomes are linear.
During circular DNA replication, the excised primer is readily replaced by nucleotides, leaving no gap in the newly synthesized DNA. In contrast, in linear DNA replication, there is always a small gap left at the very end of the chromosome because of the lack of a 3'-OH group for replacement nucleotides to bind. As mentioned, DNA synthesis can proceed only in the 5'-to-3' direction. If there were no way to fill this gap, the DNA molecule would get shorter and shorter with every generation.
However, the ends of linear chromosomes—the telomeres —have several properties that prevent this. DNA replication occurs during the S phase of cell division. In eukaryotes, the pace is much slower: about 40 nucleotides per second. The coordination of the protein complexes required for the steps of replication and the speed at which replication must occur in order for cells to divide are impressive, especially considering that enzymes are also proofreading , which leaves very few errors behind.
The study of DNA replication started almost as soon as the structure of DNA was elucidated, and it continues to this day. Currently, the stages of initiation, unwinding, primer synthesis, and elongation are understood in the most basic sense, but many questions remain unanswered, particularly when it comes to replication of the eukaryotic genome.
Scientists have devoted decades to the study of replication, and researchers such as Kornberg and Okazaki have made a number of important breakthroughs. Nonetheless, much remains to be learned about replication, including how errors in this process contribute to human disease.
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