Source: Based on Klug and Cummings (1997).
Source: Based on Klug and Cummings (1997).
DNA code is transformed into those proteins are summarized below. Several of these processes have environmental significance. Others are of interest simply because they explain the working of the machine of life, or for the utilitarian reason that scientists are learning to manipulate (i.e., "engineer") the processes to our own purposes, and we will have to make societal and individual choices about their use. We are interested primarily in three processes (Figure 6.3), which we discuss in turn.
Replication is the production of two DNA molecules from one. As described in Section 4.6, this occurs during the interphase of mitosis as the cell prepares to divide. The basic mechanism is similar for prokaryotes and eukaryotes. The DNA of eukaryotes exists in the nucleus wrapped around a complex of special proteins called histones. The complex must be dissociated for replication to occur. Furthermore, eukaryotes typically have on the order of 10,000 times as much DNA as prokaryotes, and it is present in a number of linear DNA molecules rather than a single ring as in prokaryotes. It would be worthwhile at this point to review the description of nucleic acids in Section 3.6.4.
The replication process starts with an uncoiling of the DNA double helix. Then the double strands are separated at a special origin, forming a replication bubble (see Figure 6.4). Replication then proceeds along the DNA molecule, expanding the bubble
in one direction only. The point where the DNA separates at the end of the replication bubble in the direction of synthesis is called the replication fork. Prokaryotes have only one replication fork, whereas eukaryotic DNA has tens of thousands. Thus, eukar-yotic DNA replication can occur simultaneously at numerous points on the molecule, increasing the overall speed of the process.
A short piece of RNA known as a primer is attached to the DNA at the origin. This provides a free nucleotide end for the DNA chain to start building on. Free nucleotides diffuse into the replication fork and pair up with the exposed nucleotides on the single strands of DNA. Recall, as shown in Figure 3.14, that the two strands of the DNA run in opposite directions, and the two ends can be designated by the terminal bonding carbon number on the base: namely, either 3 or 5. DNA synthesis can proceed only in a direction toward the 5' end of the molecule. Since the two strands run in opposite directions, the "wrong" strand has to add new primers repeatedly as the fork moves along, and synthesis proceeds backward in short segments. The primers are removed periodically and the gaps filled.
The final step is the formation of the ester bonds between the phosphate groups and the sugars, linking the adjacent nucleotides together. This is accomplished by a group of enzymes known as DNA polymerase. A DNA polymerase molecule moves along the pair of separated DNA strands just behind the replication fork. The replication fork and the DNA polymerase travel along the DNA strand, leaving two complete double helix strands in their wake. Each cell has several types of DNA polymerase. Because prokar-yotes have only a single DNA molecule with a single origin of replication, they have few molecules of the main form of DNA polymerase (15, in the case of Escherichia coli). Eukaryotes, on the other hand, have about 50,000, so as to be able to copy the large genome rapidly. As we shall see, DNA polymerase is also an important tool in genetic engineering.
Not infrequently, the wrong nucleotide will have moved into position for polymerization. DNA polymerase can detect these mistakes, back up, remove the offending nucleotide, and then continue forward again. This is called proofreading, and it greatly increases the accuracy of the replication. The overall error rate is about 10~9. Thus, a human egg or sperm with its 3.2 billion base pairs will have an average of three errors each. Some of these errors will have minor effects; others will render the zygote nonvi-able, resulting in a spontaneous abortion. Some errors may result in hereditable defects, and a very few may actually produce hereditable advantages to offspring. Advantageous errors contribute to the natural variation that drives evolution.
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